From 509bc5c316f88c2e845953416f23375cfc768674 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Thu, 1 Oct 2026 02:54:01 -0400 Subject: [PATCH 1/8] Materialize aligned images through shared full-stack payload owner (#342) --- docs/refactor/cp-aligned-full-stack-342.rst | 74 +++++++++++ openhcs/core/aligned_image_payload.py | 116 ++++++++++++++---- openhcs/core/runtime_slice_projection.py | 20 +++ .../runtime/function_contract_execution.py | 4 +- ...cellprofiler_full_stack_materialization.py | 38 ++++++ 5 files changed, 224 insertions(+), 28 deletions(-) create mode 100644 docs/refactor/cp-aligned-full-stack-342.rst create mode 100644 tests/unit/test_cellprofiler_full_stack_materialization.py diff --git a/docs/refactor/cp-aligned-full-stack-342.rst b/docs/refactor/cp-aligned-full-stack-342.rst new file mode 100644 index 0000000000..f64b58f468 --- /dev/null +++ b/docs/refactor/cp-aligned-full-stack-342.rst @@ -0,0 +1,74 @@ +CellProfiler aligned full-stack boundary (#342) +============================================== + +Owner: H003g runtime repair worker, under parent integration. +Audited base: OpenHCS main 0c0563e6538af313345391f2dc314270a86933a0. +H003g remains a frozen FAILED development repeat. No scientific retry or +native/MCP/viewer startup is authorized by this repair. + +Diagnosis +--------- + +``CellProfilerModuleExecutor._image_request`` composes source/artifact image +values through ``compose_aligned_image_payload``. Multiple runtime-aligned +inputs produce an ``AlignedImageStack`` with one composed image bundle per +runtime slice. ``_invocation_request`` then applies the callable-owned +``runtime_image_execution_mode``. A FULL_STACK declaration supersedes the +composition's ALIGNED_MULTI_IMAGE_STACK mode without materializing its payload. +``CellProfilerFunctionContractExecutor.execute_pure_3d`` passes this alignment +carrier straight to the raw callable, whose numeric array contract is violated. + +The retained candidate SHA256 is +7b69ce1f4256e2a64b32ecb1fefd6d22adef7ba3a1d98f5e2a3fc0125eab96b3; +the retained native log identifier is 1790835483807054701. The first failing +call is rescale_intensity, at RescaleIntensityContext.from_settings, +``source_data.astype(np.float32, copy=False)``: float(AlignedImageStack). + +The synthetic two-runtime-plane/two-input composition reproduces this exact +stack. It does not read the trial images or scientific outputs. The executor's +unchanged contract suite passed 32 cases while this added case failed. +The raw full-stack pass-through exists in 9110b10479 (June 2026); PR326 changes +neither this executor nor aligned_image_payload. This is an existing uncovered +boundary, not demonstrated to be a PR326 regression. Historical #204 is the +separate selector/input-scope surface and does not supply a fix here. + +Ownership and migration +----------------------- + +BOUND-2 and IMPL-12/13: the existing pixel stacking, mask composition and typed +provenance authorities are reused, not copied into the CellProfiler executor. +``ImagePayloadStackComposition`` is the actual owning ABC/template algorithm. +The existing same-slice ``ImagePayloadBundleContext`` inherits it through the +explicit dense-stack context, retaining its channel/spatial-mask hooks. +``AlignedImageStack`` inherits the same algorithm with runtime-slice inputs and +contributor provenance hooks. ``ImageOutputBundle`` remains a distinct named +source-binding axis; it is not treated as anonymous runtime alignment. + +The existing AutoRegisterMeta/MRO-owned RuntimeSliceProjectionStrategy family +supplies the full-stack projection hook. The aligned image leaf calls the +payload owner; every other nominal family retains its own value. The executor +uses this authority for the primary image and kwargs before the raw call. +Object labels, measurement rows, graphs and RuntimeSliceAlignedValues are not +flattened into guessed arrays. The existing PURE_3D rejection of slice-aligned +non-image kwargs remains active. No callable-name branch, second registry, +numeric wrapper, alternate executor or installation change is introduced. + +Initial working gate +-------------------- + +33 source cases passed, 2.35 seconds pytest / 3.08 seconds wall, +305672 KiB RSS. One CPU and a 512 MiB cgroup with no swap, 60-second timeout. +The isolated installed interpreter supplies existing dependencies; the source +runner resolves this worktree's Python code and only the unchanged installed +``_tabular_native.abi3.so`` artifact. No download/build/install is performed. + +The first complete-package NRA attempt rejected a misdeclared context root. +The corrected whole-package plus recorded external dependency scan timed out +at 60 seconds with 511664 KiB RSS. No complete global semantic/proof certificate +is claimed. Manual ownership evidence and source behavior tests are distinct. +The initial slotted-dataclass zero-argument super failure is retained and fixed +with explicit cooperative super(AlignedImageStack, self), not suppressed. + +Remaining gate: broaden family/metadata/mask/projection controls and regression +consumers, then parent integration and scheduled fresh installed acceptance. +This working source checkpoint is not live readiness or biological success. diff --git a/openhcs/core/aligned_image_payload.py b/openhcs/core/aligned_image_payload.py index bf9e42710b..d8939de65e 100644 --- a/openhcs/core/aligned_image_payload.py +++ b/openhcs/core/aligned_image_payload.py @@ -396,8 +396,6 @@ def resolve_source_spatial_value(self, value: Any) -> Any: return adapter.value_in_payload_domain(reference) - - def stack_image_payload_context( image_payloads: Sequence[Any], stack: RuntimeArrayData, @@ -413,6 +411,68 @@ def stack_image_payload_context( return metadata.payload_with(stack, _stack_image_payload_mask(payloads, stack)) +class ImagePayloadStackComposition(ABC): + """Compose pixels, masks and provenance on one declared leading axis.""" + + @property + @abstractmethod + def composition_payloads(self) -> tuple[Any, ...]: ... + + @property + @abstractmethod + def composition_metadata_mode(self) -> ImagePayloadMetadataCompositionMode: ... + + def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: + return tuple( + image_payload_metadata(payload) for payload in self.composition_payloads + ) + + def compose(self) -> Any: + payloads = self.composition_payloads + composed = self.compose_unmasked( + tuple(image_payload_data(payload) for payload in payloads) + ) + metadata = ImagePayloadMetadata.compose( + payloads, + mode=self.composition_metadata_mode, + source_metadata=self.composition_source_metadata(), + ) + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) + + def compose_unmasked( + self, payloads: tuple[RuntimeArrayData, ...] + ) -> RuntimeArrayData: + memory_type = detect_memory_type(payloads[0]) + return stack_runtime_slices( + payloads, memory_type, MemoryType(memory_type).device_id_of(payloads[0]) + ) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask(self.composition_payloads, composed) + + +@dataclass(slots=True) +class ImagePayloadStackContext(ImagePayloadStackComposition): + """Explicit dense stack inputs; the ancestor owns composition.""" + + payloads: Sequence[RuntimeArrayData] + metadata_mode: ImagePayloadMetadataCompositionMode + + def __post_init__(self) -> None: + self.payloads = tuple(self.payloads) + if not self.payloads: + raise ValueError("Cannot stack an empty image payload sequence.") + + @property + def composition_payloads(self) -> tuple[Any, ...]: + return tuple(self.payloads) + + @property + def composition_metadata_mode(self) -> ImagePayloadMetadataCompositionMode: + return self.metadata_mode + + def stack_image_payloads( image_payloads: Sequence[Any], *, @@ -420,16 +480,7 @@ def stack_image_payloads( ) -> Any: """Stack image payloads in their declared memory domain with full context.""" - payloads = tuple(image_payloads) - if not payloads: - raise ValueError("Cannot stack an empty image payload sequence.") - arrays = tuple(image_payload_data(payload) for payload in payloads) - memory_type = detect_memory_type(arrays[0]) - return stack_image_payload_context( - payloads, - stack_runtime_slices(arrays, memory_type, 0), - metadata_mode=metadata_mode, - ) + return ImagePayloadStackContext(image_payloads, metadata_mode).compose() def stack_image_payload_context_from_metadata( @@ -692,10 +743,9 @@ def preserved_plane_projection( @dataclass(slots=True) -class ImagePayloadBundleContext: +class ImagePayloadBundleContext(ImagePayloadStackContext): """Compose same-slice image bundle data, masks, and metadata together.""" - payloads: Sequence[RuntimeArrayData] metadata_mode: ImagePayloadMetadataCompositionMode = ( ImagePayloadMetadataCompositionMode.BUNDLE ) @@ -754,17 +804,6 @@ def from_payloads( metadata_mode=metadata_mode, ) - def compose(self) -> Any: - composed = self.compose_unmasked(self.data_payloads) - metadata = ImagePayloadMetadata.compose( - self.payloads, - mode=self.metadata_mode, - ) - return metadata.payload_with( - composed, - self.compose_mask(composed, metadata), - ) - def compose_mask( self, composed: Any, @@ -1064,12 +1103,29 @@ def __post_init__(self) -> None: @dataclass(slots=True) -class AlignedImageStack: +class AlignedImageStack(ImagePayloadStackComposition): """Per-slice multi-image bundles aligned to one OpenHCS stack.""" slices: tuple[Any, ...] slice_contexts: tuple[AlignedImageSliceContext, ...] = () + @property + def composition_payloads(self) -> tuple[Any, ...]: + return self.slices + + @property + def composition_metadata_mode(self) -> ImagePayloadMetadataCompositionMode: + return ImagePayloadMetadataCompositionMode.STACK + + def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: + """Inner image bundles contribute provenance, not an outer slice axis.""" + return tuple( + metadata.with_source_provenance( + metadata.source_provenance.with_runtime_planes_as_contributors() + ) + for metadata in super(AlignedImageStack, self).composition_source_metadata() + ) + def __post_init__(self) -> None: self.slices = tuple(self.slices) self.slice_contexts = tuple(self.slice_contexts) @@ -1144,6 +1200,14 @@ def output_payload( class ImageOutputBundle(AlignedImageStack): """Named main-flow image outputs sharing one invocation context.""" + @property + def composition_metadata_mode(self) -> ImagePayloadMetadataCompositionMode: + return ImagePayloadMetadataCompositionMode.BUNDLE + + def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: + """Named output surfaces remain source-binding planes, not runtime slices.""" + return ImagePayloadStackComposition.composition_source_metadata(self) + def __post_init__(self) -> None: AlignedImageStack.__post_init__(self) if not self.slice_contexts or any( diff --git a/openhcs/core/runtime_slice_projection.py b/openhcs/core/runtime_slice_projection.py index dbc82ace20..0e40ab2b4b 100644 --- a/openhcs/core/runtime_slice_projection.py +++ b/openhcs/core/runtime_slice_projection.py @@ -421,6 +421,10 @@ def identity_projected_value( del context return value + def full_stack_value(self, value: RuntimeProjectionData) -> RuntimeProjectionData: + """Preserve values already in their callable's whole-stack domain.""" + return value + def slice_count_for_value( self, value: RuntimeProjectionData, @@ -506,6 +510,9 @@ class AlignedImageStackRuntimeSliceProjectionStrategy(RuntimeSliceProjectionStra value_type = AlignedImageStack + def full_stack_value(self, value: RuntimeProjectionData) -> RuntimeProjectionData: + return cast(AlignedImageStack, value).compose() + def value_for_slice( self, value: RuntimeProjectionData, @@ -881,6 +888,19 @@ def slice_count_for_value( class RuntimeSliceProjection: """SSOT for runtime-slice count and value projection.""" + @classmethod + def full_stack_value(cls, value: RuntimeProjectionData) -> RuntimeProjectionData: + """Materialize nominal image alignment without changing other domains.""" + return RuntimeSliceProjectionStrategy.strategy_for_value( + value + ).full_stack_value(value) + + @classmethod + def full_stack_kwargs( + cls, kwargs: Mapping[str, RuntimeProjectionData] + ) -> dict[str, RuntimeProjectionData]: + return {name: cls.full_stack_value(value) for name, value in kwargs.items()} + @classmethod def preserved_context_for_value( cls, diff --git a/openhcs/interop/cellprofiler/runtime/function_contract_execution.py b/openhcs/interop/cellprofiler/runtime/function_contract_execution.py index d6667d5f76..c1279ed9cd 100644 --- a/openhcs/interop/cellprofiler/runtime/function_contract_execution.py +++ b/openhcs/interop/cellprofiler/runtime/function_contract_execution.py @@ -305,8 +305,8 @@ def execute_pure_3d( ) -> RuntimeCallableArgument: function_name = callable_contract.function_name projection_started_at = time.perf_counter() - projected_image = image - projected_kwargs = dict(kwargs) + projected_image = RuntimeSliceProjection.full_stack_value(image) + projected_kwargs = RuntimeSliceProjection.full_stack_kwargs(kwargs) if callable_contract.processing_contract is ProcessingContract.PURE_3D: _validate_pure_3d_kwargs_do_not_carry_runtime_slice_alignment( callable_contract, diff --git a/tests/unit/test_cellprofiler_full_stack_materialization.py b/tests/unit/test_cellprofiler_full_stack_materialization.py new file mode 100644 index 0000000000..007855ab1c --- /dev/null +++ b/tests/unit/test_cellprofiler_full_stack_materialization.py @@ -0,0 +1,38 @@ +"""Dense full-stack ABI must consume aligned source/artifact values correctly.""" + +import numpy as np +import pytest + +from openhcs.core.aligned_image_payload import ( + AlignedImageStack, + ImagePayloadExecutionMode, + compose_aligned_image_payload, +) +from openhcs.core.callable_contract import CallableContract +from openhcs.core.runtime_image_values import ImagePayloadMetadata, image_payload_data +from openhcs.core.runtime_plane_projection import RuntimePlaneAxis +from openhcs.interop.cellprofiler.runtime.function_contract_execution import ( + CellProfilerFunctionContractExecutor, +) +from openhcs.processing.backends.cellprofiler.intensity import rescale_intensity + + +def test_real_rescale_full_stack_materializes_composed_runtime_sources(): + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + source = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE + ).payload_with(data, None) + composition = compose_aligned_image_payload( + "synthetic source inputs", (source, source) + ) + assert isinstance(composition.payload, AlignedImageStack) + contract = CallableContract.from_callable(rescale_intensity) + result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + expected = np.stack((data, data), axis=1) / 23.0 + np.testing.assert_allclose(image_payload_data(result), expected) From 63ad7c65296c109e51700ab6213a40d617fe469b Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Thu, 1 Oct 2026 03:10:13 -0400 Subject: [PATCH 2/8] Cover aligned full-stack masks, provenance and cooperative family hooks --- .../complete-owned-families-corrected.log | 42 + .../complete-owned-families-corrected.xml | 1 + diagnostics/complete-owned-families.log | 1030 +++++++++++++++++ diagnostics/complete-owned-families.xml | 934 +++++++++++++++ diagnostics/family-controls-corrected.log | 128 ++ diagnostics/family-controls-corrected.xml | 81 ++ diagnostics/family-controls.log | 93 ++ diagnostics/family-controls.xml | 42 + diagnostics/final-owned-families.log | 42 + diagnostics/final-owned-families.xml | 1 + diagnostics/first-repair.log | 92 ++ diagnostics/first-repair.xml | 45 + diagnostics/frozen-executor-reproducer.log | 110 ++ diagnostics/frozen-executor-reproducer.xml | 62 + diagnostics/nra-before-corrected.json | 14 + diagnostics/nra-before-corrected.stderr | 25 + diagnostics/nra-before.json | 0 diagnostics/nra-before.stderr | 63 + diagnostics/projection-regressions.log | 41 + diagnostics/projection-regressions.xml | 1 + .../provenance-contract-regressions.log | 119 ++ .../provenance-contract-regressions.xml | 72 ++ diagnostics/run_source_tests.py | 37 + diagnostics/unchanged-main-abi-fixture.log | 114 ++ diagnostics/unchanged-main-abi-fixture.xml | 72 ++ diagnostics/working-checkpoint.log | 41 + diagnostics/working-checkpoint.xml | 1 + docs/refactor/cp-aligned-full-stack-342.rst | 61 +- openhcs/core/aligned_image_payload.py | 64 +- openhcs/core/runtime_slice_projection.py | 4 +- ...cellprofiler_full_stack_materialization.py | 202 +++- 31 files changed, 3608 insertions(+), 26 deletions(-) create mode 100644 diagnostics/complete-owned-families-corrected.log create mode 100644 diagnostics/complete-owned-families-corrected.xml create mode 100644 diagnostics/complete-owned-families.log create mode 100644 diagnostics/complete-owned-families.xml create mode 100644 diagnostics/family-controls-corrected.log create mode 100644 diagnostics/family-controls-corrected.xml create mode 100644 diagnostics/family-controls.log create mode 100644 diagnostics/family-controls.xml create mode 100644 diagnostics/final-owned-families.log create mode 100644 diagnostics/final-owned-families.xml create mode 100644 diagnostics/first-repair.log create mode 100644 diagnostics/first-repair.xml create mode 100644 diagnostics/frozen-executor-reproducer.log create mode 100644 diagnostics/frozen-executor-reproducer.xml create mode 100644 diagnostics/nra-before-corrected.json create mode 100644 diagnostics/nra-before-corrected.stderr create mode 100644 diagnostics/nra-before.json create mode 100644 diagnostics/nra-before.stderr create mode 100644 diagnostics/projection-regressions.log create mode 100644 diagnostics/projection-regressions.xml create mode 100644 diagnostics/provenance-contract-regressions.log create mode 100644 diagnostics/provenance-contract-regressions.xml create mode 100644 diagnostics/run_source_tests.py create mode 100644 diagnostics/unchanged-main-abi-fixture.log create mode 100644 diagnostics/unchanged-main-abi-fixture.xml create mode 100644 diagnostics/working-checkpoint.log create mode 100644 diagnostics/working-checkpoint.xml diff --git a/diagnostics/complete-owned-families-corrected.log b/diagnostics/complete-owned-families-corrected.log new file mode 100644 index 0000000000..674064bef5 --- /dev/null +++ b/diagnostics/complete-owned-families-corrected.log @@ -0,0 +1,42 @@ +Running as unit: run-p826825-i13396276.scope; invocation ID: 1667839ab3e345e585c7eb0f48d91350 +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +........................................................................ 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[100%] +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/complete-owned-families-corrected.xml - +110 passed, 2 warnings in 6.96s + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/complete-owned-families-corrected.xml" + User time (seconds): 4.06 + System time (seconds): 0.29 + Percent of CPU this job got: 47% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:09.09 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 322484 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 52185 + Voluntary context switches: 2 + Involuntary context switches: 1822 + Swaps: 0 + File system inputs: 0 + File system outputs: 256 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/diagnostics/complete-owned-families-corrected.xml b/diagnostics/complete-owned-families-corrected.xml new file mode 100644 index 0000000000..e0e72df4ef --- /dev/null +++ b/diagnostics/complete-owned-families-corrected.xml @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/diagnostics/complete-owned-families.log b/diagnostics/complete-owned-families.log new file mode 100644 index 0000000000..557abe5971 --- /dev/null +++ b/diagnostics/complete-owned-families.log @@ -0,0 +1,1030 @@ +Running as unit: run-p825374-i13435855.scope; invocation ID: 37d59bea3a5241e2afd366827a52bf6a +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +FFFFFFFFFFF.FF.......................................................... [ 65%] +...................................... [100%] +=================================== FAILURES =================================== +______ test_real_rescale_full_stack_materializes_composed_runtime_sources ______ + + def test_real_rescale_full_stack_materializes_composed_runtime_sources(): + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + source = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE + ).payload_with(data, None) + composition = compose_aligned_image_payload( + "synthetic source inputs", (source, source) + ) + assert isinstance(composition.payload, AlignedImageStack) + contract = CallableContract.from_callable(rescale_intensity) +> result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:47: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + ...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) +composed = array([[[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + [ 8., 9., 10., 11.]], + + [[ 0., 1., 2.... 23.]], + + [[12., 13., 14., 15.], + [16., 17., 18., 19.], + [20., 21., 22., 23.]]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_3D] _ + +processing_contract = +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): +> CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:89: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_2D] _ + +processing_contract = +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.FLEXIBLE] _ + +processing_contract = +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.VOLUMETRIC_TO_SLICE] _ + +processing_contract = +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_3D] _ + +processing_contract = +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): +> CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:89: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_2D] _ + +processing_contract = +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.FLEXIBLE] _ + +processing_contract = +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.VOLUMETRIC_TO_SLICE] _ + +processing_contract = +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_aligned_materialization_retains_masks_calibration_and_exact_contributors _ + + def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + sources = [] + expected_paths = [] + for channel, alias in ((1, "DNA"), (2, "actin")): + paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) + expected_paths.extend(paths) + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=paths, + component_metadata=tuple( + {"well": "A01", "site": str(site), "channel": str(channel)} + for site in (1, 2) + ), + ), + source_voxel_spacing=spacing, + source_dtype="uint8", + intensity_scale=255.0, + source_spatial_domain=SourceSpatialDomain( + source_shape_yx=(3, 4), origin_yx=(0, 0) + ), + ) + pixels = np.full((2, 3, 4), channel, dtype=np.float32) + mask = np.ones_like(pixels, dtype=bool) + mask[0, 0, 0] = False + sources.append(metadata.payload_with(pixels, mask)) + composed = compose_aligned_image_payload( + "matched synthetic inputs", tuple(sources) + ).payload +> dense = RuntimeSliceProjection.full_stack_value(composed) + +tests/unit/test_cellprofiler_full_stack_materialization.py:142: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(MaskedImagePayload(data=array([[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1.,...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) +composed = array([[[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], + + [[2., 2., 2., 2.], + ... [1., 1., 1., 1.]], + + [[2., 2., 2., 2.], + [2., 2., 2., 2.], + [2., 2., 2., 2.]]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +______ test_named_output_bundle_materializes_its_own_source_binding_axis _______ + + def test_named_output_bundle_materializes_its_own_source_binding_axis(): + planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) + bundle = ImageOutputBundle( + planes, + tuple( + AlignedImageSliceContext.main_flow(name, artifact_kind="image") + for name in ("red", "green") + ), + ) +> dense = RuntimeSliceProjection.full_stack_value(bundle) + +tests/unit/test_cellprofiler_full_stack_materialization.py:193: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = ImageOutputBundle(slices=(array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32), ...age'), AlignedImageSliceContext(output_kind='main', output_key='green', projection_key='main', artifact_kind='image'))) +composed = array([[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], + + [[2., 2., 2., 2.], + [2., 2., 2., 2.], + [2., 2., 2., 2.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_independent_composition_capabilities_cooperate_in_both_mro_orders[False] _ + +reverse = False + + @pytest.mark.parametrize("reverse", (False, True)) + def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): + calls = [] + + class PixelCapability: + def compose_unmasked(self, payloads): + calls.append("pixels") + return super().compose_unmasked(payloads) + 1 + + class MaskCapability: + def compose_mask(self, composed, metadata): + calls.append("mask") + return super().compose_mask(composed, metadata) + + bases = ( + (MaskCapability, PixelCapability) + if reverse + else (PixelCapability, MaskCapability) + ) + probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) + probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) + assert isinstance(probe, ImagePayloadStackComposition) +> dense = RuntimeSliceProjection.full_stack_value(probe) + +tests/unit/test_cellprofiler_full_stack_materialization.py:230: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask + return super().compose_mask(composed, metadata) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], + [0., 0., 0.]]), array([[1., 1., 1.], + [1., 1., 1.]])), slice_contexts=()) +composed = array([[[1., 1., 1.], + [1., 1., 1.]], + + [[2., 2., 2.], + [2., 2., 2.]]]) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +_ test_independent_composition_capabilities_cooperate_in_both_mro_orders[True] _ + +reverse = True + + @pytest.mark.parametrize("reverse", (False, True)) + def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): + calls = [] + + class PixelCapability: + def compose_unmasked(self, payloads): + calls.append("pixels") + return super().compose_unmasked(payloads) + 1 + + class MaskCapability: + def compose_mask(self, composed, metadata): + calls.append("mask") + return super().compose_mask(composed, metadata) + + bases = ( + (MaskCapability, PixelCapability) + if reverse + else (PixelCapability, MaskCapability) + ) + probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) + probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) + assert isinstance(probe, ImagePayloadStackComposition) +> dense = RuntimeSliceProjection.full_stack_value(probe) + +tests/unit/test_cellprofiler_full_stack_materialization.py:230: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask + return super().compose_mask(composed, metadata) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], + [0., 0., 0.]]), array([[1., 1., 1.], + [1., 1., 1.]])), slice_contexts=()) +composed = array([[[1., 1., 1.], + [1., 1., 1.]], + + [[2., 2., 2.], + [2., 2., 2.]]]) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/complete-owned-families.xml - +=========================== short test summary info ============================ +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_real_rescale_full_stack_materializes_composed_runtime_sources +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_3D] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_2D] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.FLEXIBLE] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.VOLUMETRIC_TO_SLICE] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_3D] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_2D] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.FLEXIBLE] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.VOLUMETRIC_TO_SLICE] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_aligned_materialization_retains_masks_calibration_and_exact_contributors +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_named_output_bundle_materializes_its_own_source_binding_axis +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_independent_composition_capabilities_cooperate_in_both_mro_orders[False] +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_independent_composition_capabilities_cooperate_in_both_mro_orders[True] +13 failed, 97 passed, 2 warnings in 4.35s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/complete-owned-families.xml" + User time (seconds): 4.79 + System time (seconds): 0.30 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.15 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 325096 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 17 + Minor (reclaiming a frame) page faults: 52978 + Voluntary context switches: 27 + Involuntary context switches: 28 + Swaps: 0 + File system inputs: 944 + File system outputs: 496 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/complete-owned-families.xml b/diagnostics/complete-owned-families.xml new file mode 100644 index 0000000000..fdddaeb5df --- /dev/null +++ b/diagnostics/complete-owned-families.xml @@ -0,0 +1,934 @@ +def test_real_rescale_full_stack_materializes_composed_runtime_sources(): + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + source = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE + ).payload_with(data, None) + composition = compose_aligned_image_payload( + "synthetic source inputs", (source, source) + ) + assert isinstance(composition.payload, AlignedImageStack) + contract = CallableContract.from_callable(rescale_intensity) +> result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:47: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + ...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) +composed = array([[[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + [ 8., 9., 10., 11.]], + + [[ 0., 1., 2.... 23.]], + + [[12., 13., 14., 15.], + [16., 17., 18., 19.], + [20., 21., 22., 23.]]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_3D: 'Pure3DProcessingContract'> +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): +> CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:89: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_2D: 'Pure2DProcessingContract'> +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.FLEXIBLE: 'FlexibleProcessingContract'> +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.VOLUMETRIC_TO_SLICE: 'VolumetricToSliceProcessingContract'> +slice_count = 1 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_3D: 'Pure3DProcessingContract'> +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): +> CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:89: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_2D: 'Pure2DProcessingContract'> +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.FLEXIBLE: 'FlexibleProcessingContract'> +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.VOLUMETRIC_TO_SLICE: 'VolumetricToSliceProcessingContract'> +slice_count = 2 + + @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) + @pytest.mark.parametrize("slice_count", (1, 2)) + def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count + ): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None +> result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:99: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) +composed = array([[[0., 0., 0., 0.], + [0., 0., 0., 0.], + [0., 0., 0., 0.]], + + [[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrordef test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + sources = [] + expected_paths = [] + for channel, alias in ((1, "DNA"), (2, "actin")): + paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) + expected_paths.extend(paths) + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=paths, + component_metadata=tuple( + {"well": "A01", "site": str(site), "channel": str(channel)} + for site in (1, 2) + ), + ), + source_voxel_spacing=spacing, + source_dtype="uint8", + intensity_scale=255.0, + source_spatial_domain=SourceSpatialDomain( + source_shape_yx=(3, 4), origin_yx=(0, 0) + ), + ) + pixels = np.full((2, 3, 4), channel, dtype=np.float32) + mask = np.ones_like(pixels, dtype=bool) + mask[0, 0, 0] = False + sources.append(metadata.payload_with(pixels, mask)) + composed = compose_aligned_image_payload( + "matched synthetic inputs", tuple(sources) + ).payload +> dense = RuntimeSliceProjection.full_stack_value(composed) + +tests/unit/test_cellprofiler_full_stack_materialization.py:142: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(MaskedImagePayload(data=array([[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1.,...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) +composed = array([[[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], + + [[2., 2., 2., 2.], + ... [1., 1., 1., 1.]], + + [[2., 2., 2., 2.], + [2., 2., 2., 2.], + [2., 2., 2., 2.]]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrordef test_named_output_bundle_materializes_its_own_source_binding_axis(): + planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) + bundle = ImageOutputBundle( + planes, + tuple( + AlignedImageSliceContext.main_flow(name, artifact_kind="image") + for name in ("red", "green") + ), + ) +> dense = RuntimeSliceProjection.full_stack_value(bundle) + +tests/unit/test_cellprofiler_full_stack_materialization.py:193: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = ImageOutputBundle(slices=(array([[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], dtype=float32), ...age'), AlignedImageSliceContext(output_kind='main', output_key='green', projection_key='main', artifact_kind='image'))) +composed = array([[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], + + [[2., 2., 2., 2.], + [2., 2., 2., 2.], + [2., 2., 2., 2.]]], dtype=float32) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorreverse = False + + @pytest.mark.parametrize("reverse", (False, True)) + def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): + calls = [] + + class PixelCapability: + def compose_unmasked(self, payloads): + calls.append("pixels") + return super().compose_unmasked(payloads) + 1 + + class MaskCapability: + def compose_mask(self, composed, metadata): + calls.append("mask") + return super().compose_mask(composed, metadata) + + bases = ( + (MaskCapability, PixelCapability) + if reverse + else (PixelCapability, MaskCapability) + ) + probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) + probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) + assert isinstance(probe, ImagePayloadStackComposition) +> dense = RuntimeSliceProjection.full_stack_value(probe) + +tests/unit/test_cellprofiler_full_stack_materialization.py:230: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask + return super().compose_mask(composed, metadata) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], + [0., 0., 0.]]), array([[1., 1., 1.], + [1., 1., 1.]])), slice_contexts=()) +composed = array([[[1., 1., 1.], + [1., 1., 1.]], + + [[2., 2., 2.], + [2., 2., 2.]]]) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorreverse = True + + @pytest.mark.parametrize("reverse", (False, True)) + def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): + calls = [] + + class PixelCapability: + def compose_unmasked(self, payloads): + calls.append("pixels") + return super().compose_unmasked(payloads) + 1 + + class MaskCapability: + def compose_mask(self, composed, metadata): + calls.append("mask") + return super().compose_mask(composed, metadata) + + bases = ( + (MaskCapability, PixelCapability) + if reverse + else (PixelCapability, MaskCapability) + ) + probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) + probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) + assert isinstance(probe, ImagePayloadStackComposition) +> dense = RuntimeSliceProjection.full_stack_value(probe) + +tests/unit/test_cellprofiler_full_stack_materialization.py:230: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:441: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask + return super().compose_mask(composed, metadata) +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], + [0., 0., 0.]]), array([[1., 1., 1.], + [1., 1., 1.]])), slice_contexts=()) +composed = array([[[1., 1., 1.], + [1., 1., 1.]], + + [[2., 2., 2.], + [2., 2., 2.]]]) + + def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: + del metadata + return _stack_image_payload_mask( + self.composition_payloads, + composed, +> output_mask_domain=metadata.mask_domain(composed), + ) +E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value + +openhcs/core/aligned_image_payload.py:456: UnboundLocalError \ No newline at end of file diff --git a/diagnostics/family-controls-corrected.log b/diagnostics/family-controls-corrected.log new file mode 100644 index 0000000000..89aeab476e --- /dev/null +++ b/diagnostics/family-controls-corrected.log @@ -0,0 +1,128 @@ +Running as unit: run-p820746-i13427978.scope; invocation ID: 09e0b7d729e04b9c9302d3cccd0c4bb3 +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +.........F.................................... [100%] +=================================== FAILURES =================================== +_ test_aligned_materialization_retains_masks_calibration_and_exact_contributors _ + + def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + sources = [] + expected_paths = [] + for channel, alias in ((1, "DNA"), (2, "actin")): + paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) + expected_paths.extend(paths) + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=paths, + component_metadata=tuple( + {"well": "A01", "site": str(site), "channel": str(channel)} + for site in (1, 2) + ), + ), + source_voxel_spacing=spacing, + source_dtype="uint8", + intensity_scale=255.0, + source_spatial_domain=SourceSpatialDomain( + source_shape_yx=(3, 4), origin_yx=(0, 0) + ), + ) + pixels = np.full((2, 3, 4), channel, dtype=np.float32) + mask = np.ones_like(pixels, dtype=bool) + mask[0, 0, 0] = False + sources.append(metadata.payload_with(pixels, mask)) + composed = compose_aligned_image_payload( + "matched synthetic inputs", tuple(sources) + ).payload +> dense = RuntimeSliceProjection.full_stack_value(composed) + +tests/unit/test_cellprofiler_full_stack_materialization.py:142: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:440: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +openhcs/core/runtime_image_values.py:785: in payload_with + return MaskedImagePayload(data=data, mask=mask, metadata=self) +:6: in __init__ + ??? +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = MaskedImagePayload(data=array([[[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], + + [[2...one, mask_defines_border=None, source_channel_axis=None, plane_axis=)) + + def __post_init__(self) -> None: + data_geometry = ArrayGeometry.require_from_value( + self.data, + value_name="MaskedImagePayload.data", + ) + if data_geometry.ndim == 0: + raise TypeError( + "MaskedImagePayload.data requires array-like image data, " + f"got {type(self.data).__name__}." + ) + mask_shape = ArrayGeometry.require_from_value( + self.mask, + value_name="MaskedImagePayload.mask", + ).shape + if not mask_shape: + raise TypeError( + "MaskedImagePayload.mask requires array-like mask data, " + f"got {type(self.mask).__name__}." + ) + data_shape = data_geometry.shape + if not self.metadata.mask_domain(self.data).accepts(mask_shape): +> raise ValueError( + "MaskedImagePayload.mask shape must match the image spatial " + f"domain; got mask {mask_shape!r} for image {data_shape!r}." + ) +E ValueError: MaskedImagePayload.mask shape must match the image spatial domain; got mask (2, 3, 4) for image (2, 2, 3, 4). + +openhcs/core/runtime_image_values.py:1246: ValueError +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/family-controls-corrected.xml - +=========================== short test summary info ============================ +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_aligned_materialization_retains_masks_calibration_and_exact_contributors +1 failed, 45 passed, 2 warnings in 2.68s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/family-controls-corrected.xml" + User time (seconds): 3.16 + System time (seconds): 0.29 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.48 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 309204 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 1 + Minor (reclaiming a frame) page faults: 50492 + Voluntary context switches: 3 + Involuntary context switches: 26 + Swaps: 0 + File system inputs: 8 + File system outputs: 408 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/family-controls-corrected.xml b/diagnostics/family-controls-corrected.xml new file mode 100644 index 0000000000..62510bd04f --- /dev/null +++ b/diagnostics/family-controls-corrected.xml @@ -0,0 +1,81 @@ +def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + sources = [] + expected_paths = [] + for channel, alias in ((1, "DNA"), (2, "actin")): + paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) + expected_paths.extend(paths) + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=paths, + component_metadata=tuple( + {"well": "A01", "site": str(site), "channel": str(channel)} + for site in (1, 2) + ), + ), + source_voxel_spacing=spacing, + source_dtype="uint8", + intensity_scale=255.0, + source_spatial_domain=SourceSpatialDomain( + source_shape_yx=(3, 4), origin_yx=(0, 0) + ), + ) + pixels = np.full((2, 3, 4), channel, dtype=np.float32) + mask = np.ones_like(pixels, dtype=bool) + mask[0, 0, 0] = False + sources.append(metadata.payload_with(pixels, mask)) + composed = compose_aligned_image_payload( + "matched synthetic inputs", tuple(sources) + ).payload +> dense = RuntimeSliceProjection.full_stack_value(composed) + +tests/unit/test_cellprofiler_full_stack_materialization.py:142: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/core/runtime_slice_projection.py:898: in full_stack_value + ).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:440: in compose + return metadata.payload_with(composed, self.compose_mask(composed, metadata)) +openhcs/core/runtime_image_values.py:785: in payload_with + return MaskedImagePayload(data=data, mask=mask, metadata=self) +<string>:6: in __init__ + ??? +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = MaskedImagePayload(data=array([[[[1., 1., 1., 1.], + [1., 1., 1., 1.], + [1., 1., 1., 1.]], + + [[2...one, mask_defines_border=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.RUNTIME_SLICE: 'runtime_slice'>)) + + def __post_init__(self) -> None: + data_geometry = ArrayGeometry.require_from_value( + self.data, + value_name="MaskedImagePayload.data", + ) + if data_geometry.ndim == 0: + raise TypeError( + "MaskedImagePayload.data requires array-like image data, " + f"got {type(self.data).__name__}." + ) + mask_shape = ArrayGeometry.require_from_value( + self.mask, + value_name="MaskedImagePayload.mask", + ).shape + if not mask_shape: + raise TypeError( + "MaskedImagePayload.mask requires array-like mask data, " + f"got {type(self.mask).__name__}." + ) + data_shape = data_geometry.shape + if not self.metadata.mask_domain(self.data).accepts(mask_shape): +> raise ValueError( + "MaskedImagePayload.mask shape must match the image spatial " + f"domain; got mask {mask_shape!r} for image {data_shape!r}." + ) +E ValueError: MaskedImagePayload.mask shape must match the image spatial domain; got mask (2, 3, 4) for image (2, 2, 3, 4). + +openhcs/core/runtime_image_values.py:1246: ValueError \ No newline at end of file diff --git a/diagnostics/family-controls.log b/diagnostics/family-controls.log new file mode 100644 index 0000000000..032e5b8b7e --- /dev/null +++ b/diagnostics/family-controls.log @@ -0,0 +1,93 @@ +Running as unit: run-p818047-i13391681.scope; invocation ID: e7368d61945f49c0a3b4aa711e587423 +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +.........FF................................... [100%] +=================================== FAILURES =================================== +_ test_aligned_materialization_retains_masks_calibration_and_exact_contributors _ + + def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + sources = [] + expected_paths = [] + for channel, alias in ((1, "DNA"), (2, "actin")): + paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) + expected_paths.extend(paths) +> metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=paths, + component_metadata=tuple( + {"well": "A01", "site": str(site), "channel": str(channel)} + for site in (1, 2) + ), + ), + source_voxel_spacing=spacing, + source_dtype="uint8", + intensity_scale=255.0, + source_spatial_shape_yx=(3, 4), + spatial_origin_yx=(0, 0), + ) +E TypeError: ImagePayloadMetadata.__init__() got an unexpected keyword argument 'source_spatial_shape_yx' + +tests/unit/test_cellprofiler_full_stack_materialization.py:117: TypeError +______ test_named_output_bundle_materializes_its_own_source_binding_axis _______ + + def test_named_output_bundle_materializes_its_own_source_binding_axis(): + planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) + bundle = ImageOutputBundle( + planes, + tuple( + AlignedImageSliceContext.main_flow(name, artifact_kind="image") + for name in ("red", "green") + ), + ) + dense = RuntimeSliceProjection.full_stack_value(bundle) +> assert image_payload_metadata(dense).plane_axis is RuntimePlaneAxis.SOURCE_BINDING +E AssertionError: assert None is +E + where None = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit= = RuntimePlaneAxis.SOURCE_BINDING + +tests/unit/test_cellprofiler_full_stack_materialization.py:187: AssertionError +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/family-controls.xml - +=========================== short test summary info ============================ +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_aligned_materialization_retains_masks_calibration_and_exact_contributors +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_named_output_bundle_materializes_its_own_source_binding_axis +2 failed, 44 passed, 2 warnings in 3.57s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/family-controls.xml" + User time (seconds): 3.27 + System time (seconds): 0.27 + Percent of CPU this job got: 77% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.59 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 306600 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 2 + Minor (reclaiming a frame) page faults: 48322 + Voluntary context switches: 5 + Involuntary context switches: 407 + Swaps: 0 + File system inputs: 56 + File system outputs: 128 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/family-controls.xml b/diagnostics/family-controls.xml new file mode 100644 index 0000000000..64c61e5290 --- /dev/null +++ b/diagnostics/family-controls.xml @@ -0,0 +1,42 @@ +def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + sources = [] + expected_paths = [] + for channel, alias in ((1, "DNA"), (2, "actin")): + paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) + expected_paths.extend(paths) +> metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=paths, + component_metadata=tuple( + {"well": "A01", "site": str(site), "channel": str(channel)} + for site in (1, 2) + ), + ), + source_voxel_spacing=spacing, + source_dtype="uint8", + intensity_scale=255.0, + source_spatial_shape_yx=(3, 4), + spatial_origin_yx=(0, 0), + ) +E TypeError: ImagePayloadMetadata.__init__() got an unexpected keyword argument 'source_spatial_shape_yx' + +tests/unit/test_cellprofiler_full_stack_materialization.py:117: TypeErrordef test_named_output_bundle_materializes_its_own_source_binding_axis(): + planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) + bundle = ImageOutputBundle( + planes, + tuple( + AlignedImageSliceContext.main_flow(name, artifact_kind="image") + for name in ("red", "green") + ), + ) + dense = RuntimeSliceProjection.full_stack_value(bundle) +> assert image_payload_metadata(dense).plane_axis is RuntimePlaneAxis.SOURCE_BINDING +E AssertionError: assert None is <RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'> +E + where None = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit=<SourceVoxelSpacingUnit.MICROMETERS: ...ce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=None, plane_axis=None).plane_axis +E + where ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit=<SourceVoxelSpacingUnit.MICROMETERS: ...ce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=None, plane_axis=None) = image_payload_metadata(ImageOutputBundle(slices=(array([[1., 1., 1., 1.],\n [1., 1., 1., 1.],\n [1., 1., 1., 1.]], dtype=float32), ...age'), AlignedImageSliceContext(output_kind='main', output_key='green', projection_key='main', artifact_kind='image')))) +E + and <RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'> = RuntimePlaneAxis.SOURCE_BINDING + +tests/unit/test_cellprofiler_full_stack_materialization.py:187: AssertionError \ No newline at end of file diff --git a/diagnostics/final-owned-families.log b/diagnostics/final-owned-families.log new file mode 100644 index 0000000000..ff3ee40c69 --- /dev/null +++ b/diagnostics/final-owned-families.log @@ -0,0 +1,42 @@ +Running as unit: run-p838608-i13388825.scope; invocation ID: a3cf34b0738f4facbc377db3be07d38e +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +........................................................................ [ 65%] +...................................... [100%] +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/final-owned-families.xml - +110 passed, 2 warnings in 3.38s + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/final-owned-families.xml" + User time (seconds): 3.81 + System time (seconds): 0.28 + Percent of CPU this job got: 97% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.19 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 322736 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 111 + Minor (reclaiming a frame) page faults: 52085 + Voluntary context switches: 203 + Involuntary context switches: 24 + Swaps: 0 + File system inputs: 5952 + File system outputs: 248 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/diagnostics/final-owned-families.xml b/diagnostics/final-owned-families.xml new file mode 100644 index 0000000000..6539aa7bd3 --- /dev/null +++ b/diagnostics/final-owned-families.xml @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/diagnostics/first-repair.log b/diagnostics/first-repair.log new file mode 100644 index 0000000000..aa0667118c --- /dev/null +++ b/diagnostics/first-repair.log @@ -0,0 +1,92 @@ +Running as unit: run-p804421-i13390833.scope; invocation ID: 4407f7635b2d4259b50ccbc37953c19d +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +F................................ [100%] +=================================== FAILURES =================================== +______ test_real_rescale_full_stack_materializes_composed_runtime_sources ______ + + def test_real_rescale_full_stack_materializes_composed_runtime_sources(): + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + source = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE + ).payload_with(data, None) + composition = compose_aligned_image_payload("synthetic source inputs", (source, source)) + assert isinstance(composition.payload, AlignedImageStack) + contract = CallableContract.from_callable(rescale_intensity) +> result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:28: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:894: in full_stack_value + return RuntimeSliceProjectionStrategy.strategy_for_value(value).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:436: in compose + source_metadata=self.composition_source_metadata(), +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + ...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) + + def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: + """Inner image bundles contribute provenance, not an outer slice axis.""" + return tuple( + metadata.with_source_provenance( + metadata.source_provenance.with_runtime_planes_as_contributors() + ) +> for metadata in super().composition_source_metadata() + ) +E TypeError: super(type, obj): obj must be an instance or subtype of type + +openhcs/core/aligned_image_payload.py:1120: TypeError +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/first-repair.xml - +=========================== short test summary info ============================ +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_real_rescale_full_stack_materializes_composed_runtime_sources +1 failed, 32 passed, 2 warnings in 2.90s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/first-repair.xml" + User time (seconds): 3.07 + System time (seconds): 0.28 + Percent of CPU this job got: 87% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.82 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 308204 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 1 + Minor (reclaiming a frame) page faults: 49335 + Voluntary context switches: 4 + Involuntary context switches: 201 + Swaps: 0 + File system inputs: 8 + File system outputs: 224 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/first-repair.xml b/diagnostics/first-repair.xml new file mode 100644 index 0000000000..1f20183a9b --- /dev/null +++ b/diagnostics/first-repair.xml @@ -0,0 +1,45 @@ +def test_real_rescale_full_stack_materializes_composed_runtime_sources(): + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + source = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE + ).payload_with(data, None) + composition = compose_aligned_image_payload("synthetic source inputs", (source, source)) + assert isinstance(composition.payload, AlignedImageStack) + contract = CallableContract.from_callable(rescale_intensity) +> result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:28: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute + result = executor.execute_pure_3d( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d + projected_image = RuntimeSliceProjection.full_stack_value(image) +openhcs/core/runtime_slice_projection.py:894: in full_stack_value + return RuntimeSliceProjectionStrategy.strategy_for_value(value).full_stack_value(value) +openhcs/core/runtime_slice_projection.py:514: in full_stack_value + return cast(AlignedImageStack, value).compose() +openhcs/core/aligned_image_payload.py:436: in compose + source_metadata=self.composition_source_metadata(), +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + ...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) + + def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: + """Inner image bundles contribute provenance, not an outer slice axis.""" + return tuple( + metadata.with_source_provenance( + metadata.source_provenance.with_runtime_planes_as_contributors() + ) +> for metadata in super().composition_source_metadata() + ) +E TypeError: super(type, obj): obj must be an instance or subtype of type + +openhcs/core/aligned_image_payload.py:1120: TypeError \ No newline at end of file diff --git a/diagnostics/frozen-executor-reproducer.log b/diagnostics/frozen-executor-reproducer.log new file mode 100644 index 0000000000..4323af0c9e --- /dev/null +++ b/diagnostics/frozen-executor-reproducer.log @@ -0,0 +1,110 @@ +Running as unit: run-p821979-i13439347.scope; invocation ID: 74faa71f68444ca39ef75065ca49c1ed +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +baseline executor ref: 20ca4f825 +F [100%] +=================================== FAILURES =================================== +______ test_real_rescale_full_stack_materializes_composed_runtime_sources ______ + + def test_real_rescale_full_stack_materializes_composed_runtime_sources(): + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + source = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE + ).payload_with(data, None) + composition = compose_aligned_image_payload( + "synthetic source inputs", (source, source) + ) + assert isinstance(composition.payload, AlignedImageStack) + contract = CallableContract.from_callable(rescale_intensity) +> result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:47: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +git:20ca4f825:function_contract_execution.py:148: in execute + ??? +git:20ca4f825:function_contract_execution.py:330: in execute_pure_3d + ??? +openhcs/processing/backends/lib_registry/unified_registry.py:263: in call + return target( +openhcs/processing/backends/cellprofiler/intensity.py:1877: in rescale_intensity + context = RescaleIntensityContext.from_settings( +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +cls = +image = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + ...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) + + @classmethod + def from_settings( + cls, + image: np.ndarray, + *, + automatic_low: AutomaticLow, + automatic_high: AutomaticHigh, + source_low: float, + source_high: float, + dest_low: float, + dest_high: float, + divisor_value: float, + ) -> "RescaleIntensityContext": + source_data = np.asarray(image_payload_data(image)) + return cls( +> data=source_data.astype(np.float32, copy=False), + automatic_low=coerce_cellprofiler_enum(AutomaticLow, automatic_low), + automatic_high=coerce_cellprofiler_enum(AutomaticHigh, automatic_high), + source_low=source_low, + source_high=source_high, + dest_low=dest_low, + dest_high=dest_high, + divisor_value=divisor_value, + ) +E TypeError: float() argument must be a string or a real number, not 'AlignedImageStack' + +openhcs/processing/backends/cellprofiler/intensity.py:1712: TypeError +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/frozen-executor-reproducer.xml - +=========================== short test summary info ============================ +FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_real_rescale_full_stack_materializes_composed_runtime_sources +1 failed, 13 deselected, 2 warnings in 0.73s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py -k real_rescale --junitxml=diagnostics/frozen-executor-reproducer.xml" + User time (seconds): 2.45 + System time (seconds): 0.21 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.68 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 285564 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 41894 + Voluntary context switches: 10 + Involuntary context switches: 25 + Swaps: 0 + File system inputs: 0 + File system outputs: 64 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/frozen-executor-reproducer.xml b/diagnostics/frozen-executor-reproducer.xml new file mode 100644 index 0000000000..b4756bf2a3 --- /dev/null +++ b/diagnostics/frozen-executor-reproducer.xml @@ -0,0 +1,62 @@ +def test_real_rescale_full_stack_materializes_composed_runtime_sources(): + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + source = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE + ).payload_with(data, None) + composition = compose_aligned_image_payload( + "synthetic source inputs", (source, source) + ) + assert isinstance(composition.payload, AlignedImageStack) + contract = CallableContract.from_callable(rescale_intensity) +> result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + +tests/unit/test_cellprofiler_full_stack_materialization.py:47: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ +git:20ca4f825:function_contract_execution.py:148: in execute + ??? +git:20ca4f825:function_contract_execution.py:330: in execute_pure_3d + ??? +openhcs/processing/backends/lib_registry/unified_registry.py:263: in call + return target( +openhcs/processing/backends/cellprofiler/intensity.py:1877: in rescale_intensity + context = RescaleIntensityContext.from_settings( +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +cls = <class 'openhcs.processing.backends.cellprofiler.intensity.RescaleIntensityContext'> +image = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], + [ 4., 5., 6., 7.], + ...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) + + @classmethod + def from_settings( + cls, + image: np.ndarray, + *, + automatic_low: AutomaticLow, + automatic_high: AutomaticHigh, + source_low: float, + source_high: float, + dest_low: float, + dest_high: float, + divisor_value: float, + ) -> "RescaleIntensityContext": + source_data = np.asarray(image_payload_data(image)) + return cls( +> data=source_data.astype(np.float32, copy=False), + automatic_low=coerce_cellprofiler_enum(AutomaticLow, automatic_low), + automatic_high=coerce_cellprofiler_enum(AutomaticHigh, automatic_high), + source_low=source_low, + source_high=source_high, + dest_low=dest_low, + dest_high=dest_high, + divisor_value=divisor_value, + ) +E TypeError: float() argument must be a string or a real number, not 'AlignedImageStack' + +openhcs/processing/backends/cellprofiler/intensity.py:1712: TypeError \ No newline at end of file diff --git a/diagnostics/nra-before-corrected.json b/diagnostics/nra-before-corrected.json new file mode 100644 index 0000000000..9ded6e5b8a --- /dev/null +++ b/diagnostics/nra-before-corrected.json @@ -0,0 +1,14 @@ +{ + "findings": [], + "plans": [], + "finding_payload_mode": "deadline_incomplete", + "finding_count": null, + "finding_counts": null, + "scan_status": { + "complete": false, + "deadline_exceeded": true, + "stage": "parse_python_module", + "budget_seconds": 20.0, + "elapsed_seconds": 20.0 + } +} diff --git a/diagnostics/nra-before-corrected.stderr b/diagnostics/nra-before-corrected.stderr new file mode 100644 index 0000000000..b6fdba5c32 --- /dev/null +++ b/diagnostics/nra-before-corrected.stderr @@ -0,0 +1,25 @@ +Running as unit: run-p794985-i13374683.scope; invocation ID: 08466ebbae644e88a01df4ae29b65c99 +Command exited with non-zero status 124 + Command being timed: "/home/ts/code/projects/nominal-refactor-advisor/.venv/bin/python -m nominal_refactor_advisor openhcs --context-root openhcs --context-root /home/ts/wt/openhcs-s1-installed-parent-20261001/external --json --raw-findings --json-payload full --parse-workers 1 --analysis-workers 1 --no-cache" + User time (seconds): 20.20 + System time (seconds): 0.50 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:20.89 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 511664 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 174621 + Voluntary context switches: 152 + Involuntary context switches: 147 + Swaps: 0 + File system inputs: 9896 + File system outputs: 8 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 124 diff --git a/diagnostics/nra-before.json b/diagnostics/nra-before.json new file mode 100644 index 0000000000..e69de29bb2 diff --git a/diagnostics/nra-before.stderr b/diagnostics/nra-before.stderr new file mode 100644 index 0000000000..44e390c0e3 --- /dev/null +++ b/diagnostics/nra-before.stderr @@ -0,0 +1,63 @@ +Running as unit: run-p792461-i13332203.scope; invocation ID: 4284e2fc31094171b2b323910bad8990 +Traceback (most recent call last): + File "", line 198, in _run_module_as_main + File "", line 88, in _run_code + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/__main__.py", line 4, in + raise SystemExit(process_main()) + ^^^^^^^^^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cli.py", line 4270, in process_main + return main(hard_exit_on_deadline=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/.local/share/uv/python/cpython-3.11-linux-x86_64-gnu/lib/python3.11/contextlib.py", line 81, in inner + return func(*args, **kwds) + ^^^^^^^^^^^^^^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cli.py", line 4259, in main + return _main_without_deadline(invocation) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cli.py", line 3974, in _main_without_deadline + analysis_result = analyze_modules_with_cache( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/.local/share/uv/python/cpython-3.11-linux-x86_64-gnu/lib/python3.11/contextlib.py", line 81, in inner + return func(*args, **kwds) + ^^^^^^^^^^^^^^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/analysis.py", line 3650, in analyze_modules_with_cache + focused_cache_identity = AnalysisCacheIdentity.from_modules( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/analysis_cache.py", line 875, in from_modules + report_filter_roots=tuple( + ^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/analysis_cache.py", line 876, in + checkout_relative_path(report_root, roots) + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cache_checkout.py", line 115, in checkout_relative_path + return _admitted_checkout_path(lexical_path, observed_roots) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/scan_cache.py", line 45, in invoke + return implementation(*args, **kwargs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cache_checkout.py", line 49, in _admitted_checkout_path + raise CacheCheckoutPathError(f"{candidate} {reason}") +nominal_refactor_advisor.cache_checkout.CacheCheckoutPathError: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/openhcs outside every admitted root +Command exited with non-zero status 1 + Command being timed: "/home/ts/code/projects/nominal-refactor-advisor/.venv/bin/python -m nominal_refactor_advisor openhcs --context-root /home/ts/wt/basicpy-live-candidate-20260930/external --json --raw-findings --json-payload full --parse-workers 1 --analysis-workers 1 --no-cache" + User time (seconds): 0.88 + System time (seconds): 0.05 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.95 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 60700 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 13017 + Voluntary context switches: 15 + Involuntary context switches: 5 + Swaps: 0 + File system inputs: 712 + File system outputs: 0 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/projection-regressions.log b/diagnostics/projection-regressions.log new file mode 100644 index 0000000000..4de8a91f29 --- /dev/null +++ b/diagnostics/projection-regressions.log @@ -0,0 +1,41 @@ +Running as unit: run-p819450-i13391801.scope; invocation ID: 859dae61a656455aa2257a2a2ffa55eb +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +................................................................ [100%] +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/projection-regressions.xml - +64 passed, 2 warnings in 2.41s + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/projection-regressions.xml" + User time (seconds): 2.81 + System time (seconds): 0.21 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.04 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 188736 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 3 + Minor (reclaiming a frame) page faults: 36351 + Voluntary context switches: 5 + Involuntary context switches: 22 + Swaps: 0 + File system inputs: 416 + File system outputs: 840 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/diagnostics/projection-regressions.xml b/diagnostics/projection-regressions.xml new file mode 100644 index 0000000000..6a19a910cd --- /dev/null +++ b/diagnostics/projection-regressions.xml @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/diagnostics/provenance-contract-regressions.log b/diagnostics/provenance-contract-regressions.log new file mode 100644 index 0000000000..fc04e26f5a --- /dev/null +++ b/diagnostics/provenance-contract-regressions.log @@ -0,0 +1,119 @@ +Running as unit: run-p822498-i13407678.scope; invocation ID: 8d17818f726c465ca717574fa79a0469 +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +.................................F........... [100%] +=================================== FAILURES =================================== +________ test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots _________ + + def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: + source = ArtifactSpec.input("Input", ImageArtifactType) + measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) + labels = ArtifactSpec.output( + "Objects", + ObjectLabelsArtifactType, + relations=(GroupLineageSourceRelation(source=source.ref()),), + ) + + for func in (identify_primary_objects, watershed_cellprofiler4): + contract = _contract(func, (source,)) + contract = replace( + contract, + metadata=replace( + contract.metadata, + artifact_outputs=(measurements, labels), + ), + ) + +> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) + +tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +cls = +func = +contract = CallableContract(func=, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) + + @classmethod + def validate_callable_artifact_abi( + cls, + func: "Callable[..., RuntimeFunctionOutput]", + contract: CallableContract, + ) -> None: + """Validate one raw callable ABI against its callable artifact declarations.""" + + from openhcs.core.aligned_image_payload import AlignedImageStack + + module_name = contract.module_name + if not isinstance(module_name, str) or not module_name: + raise ValueError("CellProfiler callable contract requires a module name.") + declared_outputs = contract.artifact_outputs + invalid_source_context_outputs = tuple( + (spec.ref(), sources) + for spec in declared_outputs + for sources in (spec.source_context_sources(),) + if spec.artifact_type.carries_source_image_context and len(sources) != 1 + ) + if invalid_source_context_outputs: + raise ValueError( + f"CellProfiler module {module_name!r} image/object outputs " + "must declare exactly one runtime-context source: " + f"{invalid_source_context_outputs!r}." + ) + return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) + return_variants = _callable_return_slot_variants(return_annotation) + canonical_outputs = contract.canonical_return_output_specs + trailing_outputs = contract.trailing_return_output_specs + expected_slot_count = len(trailing_outputs) + 1 + matching_variants = tuple( + slots for slots in return_variants if len(slots) == expected_slot_count + ) + if not matching_variants: +> raise ValueError( + f"callable {func.__name__!r} return annotation " + f"{return_annotation!r} does not declare the canonical return " + f"followed by exactly {len(trailing_outputs)} trailing " + "artifact-output slot(s)." + ) +E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). + +openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/provenance-contract-regressions.xml - +=========================== short test summary info ============================ +FAILED tests/unit/test_cellprofiler_runtime_input_binding_contract.py::test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots +1 failed, 44 passed, 2 warnings in 4.71s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_source_image_provenance.py tests/unit/test_source_image_provenance_hotpath.py tests/unit/test_derived_runtime_image_provenance.py tests/unit/test_cellprofiler_runtime_input_binding_contract.py tests/unit/test_cellprofiler_artifact_activation_identity.py --junitxml=diagnostics/provenance-contract-regressions.xml" + User time (seconds): 5.63 + System time (seconds): 0.36 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.05 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 380652 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 8 + Minor (reclaiming a frame) page faults: 60960 + Voluntary context switches: 22 + Involuntary context switches: 36 + Swaps: 0 + File system inputs: 408 + File system outputs: 6080 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/provenance-contract-regressions.xml b/diagnostics/provenance-contract-regressions.xml new file mode 100644 index 0000000000..221abefabe --- /dev/null +++ b/diagnostics/provenance-contract-regressions.xml @@ -0,0 +1,72 @@ +def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: + source = ArtifactSpec.input("Input", ImageArtifactType) + measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) + labels = ArtifactSpec.output( + "Objects", + ObjectLabelsArtifactType, + relations=(GroupLineageSourceRelation(source=source.ref()),), + ) + + for func in (identify_primary_objects, watershed_cellprofiler4): + contract = _contract(func, (source,)) + contract = replace( + contract, + metadata=replace( + contract.metadata, + artifact_outputs=(measurements, labels), + ), + ) + +> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) + +tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +cls = <class 'openhcs.interop.cellprofiler.module_callable_abi.CellProfilerModuleCallableABI'> +func = <function identify_primary_objects at 0x7f8f189c6ca0> +contract = CallableContract(func=<function identify_primary_objects at 0x7f8f189c6ca0>, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) + + @classmethod + def validate_callable_artifact_abi( + cls, + func: "Callable[..., RuntimeFunctionOutput]", + contract: CallableContract, + ) -> None: + """Validate one raw callable ABI against its callable artifact declarations.""" + + from openhcs.core.aligned_image_payload import AlignedImageStack + + module_name = contract.module_name + if not isinstance(module_name, str) or not module_name: + raise ValueError("CellProfiler callable contract requires a module name.") + declared_outputs = contract.artifact_outputs + invalid_source_context_outputs = tuple( + (spec.ref(), sources) + for spec in declared_outputs + for sources in (spec.source_context_sources(),) + if spec.artifact_type.carries_source_image_context and len(sources) != 1 + ) + if invalid_source_context_outputs: + raise ValueError( + f"CellProfiler module {module_name!r} image/object outputs " + "must declare exactly one runtime-context source: " + f"{invalid_source_context_outputs!r}." + ) + return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) + return_variants = _callable_return_slot_variants(return_annotation) + canonical_outputs = contract.canonical_return_output_specs + trailing_outputs = contract.trailing_return_output_specs + expected_slot_count = len(trailing_outputs) + 1 + matching_variants = tuple( + slots for slots in return_variants if len(slots) == expected_slot_count + ) + if not matching_variants: +> raise ValueError( + f"callable {func.__name__!r} return annotation " + f"{return_annotation!r} does not declare the canonical return " + f"followed by exactly {len(trailing_outputs)} trailing " + "artifact-output slot(s)." + ) +E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). + +openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError \ No newline at end of file diff --git a/diagnostics/run_source_tests.py b/diagnostics/run_source_tests.py new file mode 100644 index 0000000000..4f7a443623 --- /dev/null +++ b/diagnostics/run_source_tests.py @@ -0,0 +1,37 @@ +"""Run owned source checks using only the unchanged installed native artifact.""" + +import os +import subprocess +import sys +from pathlib import Path + +root = Path(__file__).resolve().parents[1] +root = Path(os.environ.get("SOURCE_BASELINE_ROOT", str(root))).resolve() +sys.path.insert(0, str(root)) +import openhcs.core + +artifact_root = Path( + "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core" +) +openhcs.core.__path__.append(str(artifact_root)) +print("source root:", root, flush=True) +print("native artifact:", artifact_root / "_tabular_native.abi3.so", flush=True) +baseline_ref = os.environ.get("BASELINE_EXECUTOR_REF") +if baseline_ref: + import openhcs.interop.cellprofiler.runtime.function_contract_execution as executor_module + + source = subprocess.check_output( + [ + "git", "show", + f"{baseline_ref}:openhcs/interop/cellprofiler/runtime/function_contract_execution.py", + ], + cwd=root, + ) + print("baseline executor ref:", baseline_ref, flush=True) + exec( + compile(source, f"git:{baseline_ref}:function_contract_execution.py", "exec"), + executor_module.__dict__, + ) +import pytest + +raise SystemExit(pytest.main(sys.argv[1:])) diff --git a/diagnostics/unchanged-main-abi-fixture.log b/diagnostics/unchanged-main-abi-fixture.log new file mode 100644 index 0000000000..bd3159ab95 --- /dev/null +++ b/diagnostics/unchanged-main-abi-fixture.log @@ -0,0 +1,114 @@ +Running as unit: run-p826798-i13431838.scope; invocation ID: 30883a82c95d448b9b09644ea8306b6d +source root: /home/ts/.cache/agent-scratch/h003g-runtime-repair-baseline-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +F [100%] +=================================== FAILURES =================================== +________ test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots _________ + + def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: + source = ArtifactSpec.input("Input", ImageArtifactType) + measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) + labels = ArtifactSpec.output( + "Objects", + ObjectLabelsArtifactType, + relations=(GroupLineageSourceRelation(source=source.ref()),), + ) + + for func in (identify_primary_objects, watershed_cellprofiler4): + contract = _contract(func, (source,)) + contract = replace( + contract, + metadata=replace( + contract.metadata, + artifact_outputs=(measurements, labels), + ), + ) + +> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) + +../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +cls = +func = +contract = CallableContract(func=, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) + + @classmethod + def validate_callable_artifact_abi( + cls, + func: "Callable[..., RuntimeFunctionOutput]", + contract: CallableContract, + ) -> None: + """Validate one raw callable ABI against its callable artifact declarations.""" + + from openhcs.core.aligned_image_payload import AlignedImageStack + + module_name = contract.module_name + if not isinstance(module_name, str) or not module_name: + raise ValueError("CellProfiler callable contract requires a module name.") + declared_outputs = contract.artifact_outputs + invalid_source_context_outputs = tuple( + (spec.ref(), sources) + for spec in declared_outputs + for sources in (spec.source_context_sources(),) + if spec.artifact_type.carries_source_image_context and len(sources) != 1 + ) + if invalid_source_context_outputs: + raise ValueError( + f"CellProfiler module {module_name!r} image/object outputs " + "must declare exactly one runtime-context source: " + f"{invalid_source_context_outputs!r}." + ) + return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) + return_variants = _callable_return_slot_variants(return_annotation) + canonical_outputs = contract.canonical_return_output_specs + trailing_outputs = contract.trailing_return_output_specs + expected_slot_count = len(trailing_outputs) + 1 + matching_variants = tuple( + slots for slots in return_variants if len(slots) == expected_slot_count + ) + if not matching_variants: +> raise ValueError( + f"callable {func.__name__!r} return annotation " + f"{return_annotation!r} does not declare the canonical return " + f"followed by exactly {len(trailing_outputs)} trailing " + "artifact-output slot(s)." + ) +E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). + +../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError +=============================== warnings summary =============================== +../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/processing/backends/numpy_runtime.py:7 +../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/processing/backends/numpy_runtime.py:7 + /home/ts/.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/processing/backends/numpy_runtime.py:7: DeprecationWarning: numpy.core is deprecated and has been renamed to numpy._core. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core._multiarray_umath. + from numpy.core import _multiarray_umath + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/unchanged-main-abi-fixture.xml - +=========================== short test summary info ============================ +FAILED ../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py::test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots +1 failed, 11 deselected, 2 warnings in 9.61s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q /home/ts/.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py -k callable_abi_keeps --junitxml=diagnostics/unchanged-main-abi-fixture.xml" + User time (seconds): 5.98 + System time (seconds): 0.37 + Percent of CPU this job got: 55% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:11.39 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 381476 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 9 + Minor (reclaiming a frame) page faults: 62873 + Voluntary context switches: 11 + Involuntary context switches: 1930 + Swaps: 0 + File system inputs: 248 + File system outputs: 20968 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/unchanged-main-abi-fixture.xml b/diagnostics/unchanged-main-abi-fixture.xml new file mode 100644 index 0000000000..d4baf63bfb --- /dev/null +++ b/diagnostics/unchanged-main-abi-fixture.xml @@ -0,0 +1,72 @@ +def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: + source = ArtifactSpec.input("Input", ImageArtifactType) + measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) + labels = ArtifactSpec.output( + "Objects", + ObjectLabelsArtifactType, + relations=(GroupLineageSourceRelation(source=source.ref()),), + ) + + for func in (identify_primary_objects, watershed_cellprofiler4): + contract = _contract(func, (source,)) + contract = replace( + contract, + metadata=replace( + contract.metadata, + artifact_outputs=(measurements, labels), + ), + ) + +> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) + +../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +cls = <class 'openhcs.interop.cellprofiler.module_callable_abi.CellProfilerModuleCallableABI'> +func = <function identify_primary_objects at 0x7f8de0a260c0> +contract = CallableContract(func=<function identify_primary_objects at 0x7f8de0a260c0>, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) + + @classmethod + def validate_callable_artifact_abi( + cls, + func: "Callable[..., RuntimeFunctionOutput]", + contract: CallableContract, + ) -> None: + """Validate one raw callable ABI against its callable artifact declarations.""" + + from openhcs.core.aligned_image_payload import AlignedImageStack + + module_name = contract.module_name + if not isinstance(module_name, str) or not module_name: + raise ValueError("CellProfiler callable contract requires a module name.") + declared_outputs = contract.artifact_outputs + invalid_source_context_outputs = tuple( + (spec.ref(), sources) + for spec in declared_outputs + for sources in (spec.source_context_sources(),) + if spec.artifact_type.carries_source_image_context and len(sources) != 1 + ) + if invalid_source_context_outputs: + raise ValueError( + f"CellProfiler module {module_name!r} image/object outputs " + "must declare exactly one runtime-context source: " + f"{invalid_source_context_outputs!r}." + ) + return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) + return_variants = _callable_return_slot_variants(return_annotation) + canonical_outputs = contract.canonical_return_output_specs + trailing_outputs = contract.trailing_return_output_specs + expected_slot_count = len(trailing_outputs) + 1 + matching_variants = tuple( + slots for slots in return_variants if len(slots) == expected_slot_count + ) + if not matching_variants: +> raise ValueError( + f"callable {func.__name__!r} return annotation " + f"{return_annotation!r} does not declare the canonical return " + f"followed by exactly {len(trailing_outputs)} trailing " + "artifact-output slot(s)." + ) +E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). + +../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError \ No newline at end of file diff --git a/diagnostics/working-checkpoint.log b/diagnostics/working-checkpoint.log new file mode 100644 index 0000000000..ae0b3c936b --- /dev/null +++ b/diagnostics/working-checkpoint.log @@ -0,0 +1,41 @@ +Running as unit: run-p805711-i13394976.scope; invocation ID: b8f7aae1cfb94e84886989021e81dbf8 +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +................................. [100%] +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/working-checkpoint.xml - +33 passed, 2 warnings in 2.35s + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/working-checkpoint.xml" + User time (seconds): 2.81 + System time (seconds): 0.24 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.08 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 305672 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 1 + Minor (reclaiming a frame) page faults: 48253 + Voluntary context switches: 3 + Involuntary context switches: 20 + Swaps: 0 + File system inputs: 8 + File system outputs: 312 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/diagnostics/working-checkpoint.xml b/diagnostics/working-checkpoint.xml new file mode 100644 index 0000000000..0e9f5b00b8 --- /dev/null +++ b/diagnostics/working-checkpoint.xml @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/docs/refactor/cp-aligned-full-stack-342.rst b/docs/refactor/cp-aligned-full-stack-342.rst index f64b58f468..dc8c63b930 100644 --- a/docs/refactor/cp-aligned-full-stack-342.rst +++ b/docs/refactor/cp-aligned-full-stack-342.rst @@ -25,7 +25,10 @@ call is rescale_intensity, at RescaleIntensityContext.from_settings, ``source_data.astype(np.float32, copy=False)``: float(AlignedImageStack). The synthetic two-runtime-plane/two-input composition reproduces this exact -stack. It does not read the trial images or scientific outputs. The executor's +stack with EMPTY kwargs: the primary image is the immediate root, not an +auxiliary binding. It does not read trial images or scientific outputs. Aligned +image kwargs have the same unmaterialized boundary and are covered separately. +The executor's unchanged contract suite passed 32 cases while this added case failed. The raw full-stack pass-through exists in 9110b10479 (June 2026); PR326 changes neither this executor nor aligned_image_payload. This is an existing uncovered @@ -53,8 +56,8 @@ flattened into guessed arrays. The existing PURE_3D rejection of slice-aligned non-image kwargs remains active. No callable-name branch, second registry, numeric wrapper, alternate executor or installation change is introduced. -Initial working gate --------------------- +Source checkpoints +------------------ 33 source cases passed, 2.35 seconds pytest / 3.08 seconds wall, 305672 KiB RSS. One CPU and a 512 MiB cgroup with no swap, 60-second timeout. @@ -69,6 +72,52 @@ is claimed. Manual ownership evidence and source behavior tests are distinct. The initial slotted-dataclass zero-argument super failure is retained and fixed with explicit cooperative super(AlignedImageStack, self), not suppressed. -Remaining gate: broaden family/metadata/mask/projection controls and regression -consumers, then parent integration and scheduled fresh installed acceptance. -This working source checkpoint is not live readiness or biological success. +Expanded checkpoint: 110 cases PASS, 3.38 seconds pytest / 4.19 seconds wall, +322736 KiB RSS, under the same one CPU / 512 MiB / no swap / 60-second bound. +The 14 new cases cover the real rescale callable, all four ProcessingContract +families with singleton and two-slice image/auxiliary inputs, exact contributor +identities and slice projections, voxel calibration, masked source-binding +planes composed into a runtime stack, named output bundles, ragged-input +rejection before dispatch, and independent pixel/mask capabilities composed in +both cooperative MRO orders. The other 96 are unchanged executor and nominal +projection/alignment/device/registry controls. The named bundle strategy now +inherits the aligned-image strategy's full-stack hook; its own source-binding +projection/count behavior stays separate. Shared input validation uses +cooperative super; metadata composition stays in the ABC with a small +per-input provenance hook, not a direct jump around an ancestor algorithm. + +The masked 4D control found that stacking shared 2D masks produces a 3D mask +outside the outer runtime axis's domain. The existing mask owner now consults +the composed ImageMaskDomain and uses its declared broadcast authority only +when required. Pixel values and exact masks are checked; no relaxed domain +check or ndarray coercion is used. Intermediate failed attempts remain in +diagnostics alongside the working logs and JUnit receipts. + +A broader metadata/artifact-consumer shard had 44 PASS / 1 FAIL. The failure, +test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots, declares only +two outputs although identify_primary_objects now has seven diagnostic image +slots in addition to the canonical slots. The exact same test fails on a +complete unchanged production source snapshot of main 0c0563e65, not merely +an executor substitution. No production ABI assertion or fixture was weakened. +This pre-existing fixture mismatch is separately recorded under parent +integration; the shard is not claimed fully passing. + +Affected nominal owners: aligned runtime image stacks and their named-output +bundle subtype require materialization; already-dense image metadata/masked +payloads and arrays keep their own domains. Object labels, aligned non-image +values, measurement tables/columnar rows, relationships, sparse labels, +projectable identities and spatial graphs retain their registered strategies. +PURE_3D's prohibition on non-image slice-aligned kwargs is preserved. FULL_STACK +is shared by all processing contracts; ordinary slice modes are unchanged. +This is source evidence, not a claim that every backend/input combination was +executed or that GPU/device coverage is complete. + +Disposable baseline source snapshot: owner H003g runtime repair worker, +/home/ts/.cache/agent-scratch/h003g-runtime-repair-baseline-20261001, 31 MiB, +purpose unchanged-main fixture control. It contains no scientific data and is +recoverable from Git; logs are retained here before removing that owned scratch. + +Remaining gate: original structural/R1 guard disposition, parent integration +and scheduled fresh installed entrypoint acceptance with synthetic inputs. +This source checkpoint is not live readiness or biological success. H003g +stays FAILED and is not a validation dataset for this repair. diff --git a/openhcs/core/aligned_image_payload.py b/openhcs/core/aligned_image_payload.py index d8939de65e..23e33482c5 100644 --- a/openhcs/core/aligned_image_payload.py +++ b/openhcs/core/aligned_image_payload.py @@ -32,6 +32,7 @@ ImagePayloadSliceProjector, ImagePayloadMetadataCarrier, ImagePayloadMetadataCompositionMode, + ImageMaskDomain, image_payload_data, image_payload_mask, image_payload_metadata, @@ -424,9 +425,16 @@ def composition_metadata_mode(self) -> ImagePayloadMetadataCompositionMode: ... def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: return tuple( - image_payload_metadata(payload) for payload in self.composition_payloads + self.composition_payload_metadata(image_payload_metadata(payload)) + for payload in self.composition_payloads ) + def composition_payload_metadata( + self, metadata: ImagePayloadMetadata + ) -> ImagePayloadMetadata: + """Preserve each input's declared provenance unless the axis owner projects it.""" + return metadata + def compose(self) -> Any: payloads = self.composition_payloads composed = self.compose_unmasked( @@ -448,8 +456,11 @@ def compose_unmasked( ) def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask(self.composition_payloads, composed) + return _stack_image_payload_mask( + self.composition_payloads, + composed, + output_mask_domain=metadata.mask_domain(composed), + ) @dataclass(slots=True) @@ -503,6 +514,8 @@ def stack_image_payload_context_from_metadata( def _stack_image_payload_mask( image_payloads: Sequence[Any], stack: RuntimeArrayData, + *, + output_mask_domain: ImageMaskDomain | None = None, ) -> RuntimeArrayData | None: masks = tuple(image_payload_mask(payload) for payload in image_payloads) if not any(mask is not None for mask in masks): @@ -526,6 +539,18 @@ def _stack_image_payload_mask( strict=True, ) ) + stacked_mask_shape = (len(payloads), *tuple(np.shape(resolved_masks[0]))) + if output_mask_domain is not None and not output_mask_domain.accepts( + stacked_mask_shape + ): + resolved_masks = tuple( + image_payload_metadata(payload) + .mask_domain(slice_domain) + .broadcast_to_data(mask) + for payload, slice_domain, mask in zip( + payloads, output_slice_domains, resolved_masks, strict=True + ) + ) return stack_runtime_slices( resolved_masks, detect_memory_type(stack), @@ -751,9 +776,7 @@ class ImagePayloadBundleContext(ImagePayloadStackContext): ) def __post_init__(self) -> None: - self.payloads = tuple(self.payloads) - if not self.payloads: - raise ValueError("ImagePayloadBundleContext.payloads cannot be empty.") + super(ImagePayloadBundleContext, self).__post_init__() declared_axes = tuple( ( index, @@ -774,7 +797,7 @@ def __post_init__(self) -> None: @property def source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: - return tuple(image_payload_metadata(payload) for payload in self.payloads) + return self.composition_source_metadata() @property def data_payloads(self) -> tuple[RuntimeArrayData, ...]: @@ -1117,13 +1140,13 @@ def composition_payloads(self) -> tuple[Any, ...]: def composition_metadata_mode(self) -> ImagePayloadMetadataCompositionMode: return ImagePayloadMetadataCompositionMode.STACK - def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: + def composition_payload_metadata( + self, metadata: ImagePayloadMetadata + ) -> ImagePayloadMetadata: """Inner image bundles contribute provenance, not an outer slice axis.""" - return tuple( - metadata.with_source_provenance( - metadata.source_provenance.with_runtime_planes_as_contributors() - ) - for metadata in super(AlignedImageStack, self).composition_source_metadata() + metadata = super(AlignedImageStack, self).composition_payload_metadata(metadata) + return metadata.with_source_provenance( + metadata.source_provenance.with_runtime_planes_as_contributors() ) def __post_init__(self) -> None: @@ -1200,16 +1223,25 @@ def output_payload( class ImageOutputBundle(AlignedImageStack): """Named main-flow image outputs sharing one invocation context.""" + @property + def composition_payloads(self) -> tuple[Any, ...]: + return tuple( + context.contextualize_image_payload(payload) + for payload, context in zip(self.slices, self.slice_contexts, strict=True) + ) + @property def composition_metadata_mode(self) -> ImagePayloadMetadataCompositionMode: return ImagePayloadMetadataCompositionMode.BUNDLE - def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: + def composition_payload_metadata( + self, metadata: ImagePayloadMetadata + ) -> ImagePayloadMetadata: """Named output surfaces remain source-binding planes, not runtime slices.""" - return ImagePayloadStackComposition.composition_source_metadata(self) + return metadata def __post_init__(self) -> None: - AlignedImageStack.__post_init__(self) + super(ImageOutputBundle, self).__post_init__() if not self.slice_contexts or any( context.is_anonymous_main_flow for context in self.slice_contexts ): diff --git a/openhcs/core/runtime_slice_projection.py b/openhcs/core/runtime_slice_projection.py index 0e40ab2b4b..02d2f2203b 100644 --- a/openhcs/core/runtime_slice_projection.py +++ b/openhcs/core/runtime_slice_projection.py @@ -546,7 +546,9 @@ def slice_count_for_value( return len(cast(AlignedImageStack, value).slices) -class ImageOutputBundleRuntimeSliceProjectionStrategy(RuntimeSliceProjectionStrategy): +class ImageOutputBundleRuntimeSliceProjectionStrategy( + AlignedImageStackRuntimeSliceProjectionStrategy +): """Project each named output through its shared declared runtime axis.""" value_type = ImageOutputBundle diff --git a/tests/unit/test_cellprofiler_full_stack_materialization.py b/tests/unit/test_cellprofiler_full_stack_materialization.py index 007855ab1c..5da0fd37d5 100644 --- a/tests/unit/test_cellprofiler_full_stack_materialization.py +++ b/tests/unit/test_cellprofiler_full_stack_materialization.py @@ -4,17 +4,34 @@ import pytest from openhcs.core.aligned_image_payload import ( + AlignedImageSliceContext, AlignedImageStack, + ImageOutputBundle, ImagePayloadExecutionMode, + ImagePayloadStackComposition, compose_aligned_image_payload, ) -from openhcs.core.callable_contract import CallableContract -from openhcs.core.runtime_image_values import ImagePayloadMetadata, image_payload_data -from openhcs.core.runtime_plane_projection import RuntimePlaneAxis +from openhcs.core.callable_contract import CallableContract, CallableMetadata +from openhcs.core.runtime_image_values import ( + ImagePayloadMetadata, + image_payload_data, + image_payload_mask, + image_payload_metadata, +) +from openhcs.core.runtime_plane_projection import ( + RuntimePlaneAxis, + RuntimePlaneAxisValueProjection, +) +from openhcs.core.runtime_slice_alignment import RuntimeSliceAlignedValues +from openhcs.core.runtime_slice_projection import RuntimeSliceProjection +from openhcs.core.source_image_provenance import SourceImageProvenancePlanes +from openhcs.core.source_metadata import SourceVoxelSpacing, SourceVoxelSpacingUnit +from openhcs.core.source_spatial_domain import SourceSpatialDomain from openhcs.interop.cellprofiler.runtime.function_contract_execution import ( CellProfilerFunctionContractExecutor, ) from openhcs.processing.backends.cellprofiler.intensity import rescale_intensity +from openhcs.processing.backends.lib_registry.unified_registry import ProcessingContract def test_real_rescale_full_stack_materializes_composed_runtime_sources(): @@ -36,3 +53,182 @@ def test_real_rescale_full_stack_materializes_composed_runtime_sources(): ) expected = np.stack((data, data), axis=1) / 23.0 np.testing.assert_allclose(image_payload_data(result), expected) + + +@pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) +@pytest.mark.parametrize("slice_count", (1, 2)) +def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( + processing_contract, slice_count +): + planes = tuple( + np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) + ) + aligned = AlignedImageStack(planes) + opaque = RuntimeSliceAlignedValues(("not an image",)) + calls = [] + + def dense_callable(image, *, reference, token): + calls.append((image, reference, token)) + assert not isinstance(image, AlignedImageStack) + assert not isinstance(reference, AlignedImageStack) + assert token is opaque + np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) + np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) + return image + + contract = CallableContract( + func=dense_callable, + function_name="dense_callable", + module_name="DenseProbeModule", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + kwargs = {"reference": aligned, "token": opaque} + # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. + if processing_contract is ProcessingContract.PURE_3D: + with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): + CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [] + kwargs["token"] = None + opaque = None + result = CellProfilerFunctionContractExecutor().execute( + contract, + dense_callable, + aligned, + kwargs, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert len(calls) == 1 + np.testing.assert_array_equal(image_payload_data(result), np.stack(planes)) + assert kwargs["reference"] is aligned + + +def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + sources = [] + expected_paths = [] + for channel, alias in ((1, "DNA"), (2, "actin")): + paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) + expected_paths.extend(paths) + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=paths, + component_metadata=tuple( + {"well": "A01", "site": str(site), "channel": str(channel)} + for site in (1, 2) + ), + ), + source_voxel_spacing=spacing, + source_dtype="uint8", + intensity_scale=255.0, + source_spatial_domain=SourceSpatialDomain( + source_shape_yx=(3, 4), origin_yx=(0, 0) + ), + ) + pixels = np.full((2, 3, 4), channel, dtype=np.float32) + mask = np.ones_like(pixels, dtype=bool) + mask[0, 0, 0] = False + sources.append(metadata.payload_with(pixels, mask)) + composed = compose_aligned_image_payload( + "matched synthetic inputs", tuple(sources) + ).payload + dense = RuntimeSliceProjection.full_stack_value(composed) + assert dense.shape == (2, 2, 3, 4) + metadata = image_payload_metadata(dense) + assert metadata.plane_axis is RuntimePlaneAxis.RUNTIME_SLICE + assert metadata.source_voxel_spacing == spacing + assert metadata.source_spatial_shape_yx == (3, 4) + assert set(metadata.source_provenance.represented_source_image_names) == { + "DNA", + "actin", + } + assert { + identity.path + for identity in metadata.source_provenance.represented_source_identities + } == set(expected_paths) + np.testing.assert_array_equal( + image_payload_mask(dense), + np.stack( + [ + np.broadcast_to(image_payload_mask(plane), (2, 3, 4)) + for plane in composed.slices + ] + ), + ) + for index in range(2): + projected = RuntimeSliceProjection.value_for_slice( + dense, + RuntimePlaneAxisValueProjection.from_selected_plane( + axis=RuntimePlaneAxis.RUNTIME_SLICE, plane_index=index, axis_size=2 + ), + ) + np.testing.assert_array_equal( + image_payload_data(projected), image_payload_data(composed.slices[index]) + ) + expected = {f"/synthetic/A01_s{index + 1}_w{channel}.tif" for channel in (1, 2)} + assert { + identity.path + for identity in image_payload_metadata( + projected + ).source_provenance.represented_source_identities + } == expected + + +def test_named_output_bundle_materializes_its_own_source_binding_axis(): + planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) + bundle = ImageOutputBundle( + planes, + tuple( + AlignedImageSliceContext.main_flow(name, artifact_kind="image") + for name in ("red", "green") + ), + ) + dense = RuntimeSliceProjection.full_stack_value(bundle) + assert image_payload_metadata(dense).plane_axis is RuntimePlaneAxis.SOURCE_BINDING + assert image_payload_metadata( + dense + ).source_provenance.represented_source_image_names == ("red", "green") + np.testing.assert_array_equal(image_payload_data(dense), np.stack(planes)) + assert bundle.slices == planes + + +def test_ragged_aligned_images_fail_before_dense_callable(): + aligned = AlignedImageStack((np.zeros((2, 3)), np.zeros((3, 3)))) + with pytest.raises(ValueError, match="one exact shape"): + RuntimeSliceProjection.full_stack_value(aligned) + + +@pytest.mark.parametrize("reverse", (False, True)) +def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): + calls = [] + + class PixelCapability: + def compose_unmasked(self, payloads): + calls.append("pixels") + return super().compose_unmasked(payloads) + 1 + + class MaskCapability: + def compose_mask(self, composed, metadata): + calls.append("mask") + return super().compose_mask(composed, metadata) + + bases = ( + (MaskCapability, PixelCapability) + if reverse + else (PixelCapability, MaskCapability) + ) + probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) + probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) + assert isinstance(probe, ImagePayloadStackComposition) + dense = RuntimeSliceProjection.full_stack_value(probe) + assert calls == ["pixels", "mask"] + np.testing.assert_array_equal( + image_payload_data(dense), np.stack((np.ones((2, 3)), np.full((2, 3), 2))) + ) From ede0c4331d70cf5e256aa19249281d85ab937bbd Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Thu, 1 Oct 2026 03:15:48 -0400 Subject: [PATCH 3/8] Record original guard disposition and align diagnostic ABI fixture --- .../final-consumer-regressions-corrected.log | 41 + .../final-consumer-regressions-corrected.xml | 1 + diagnostics/final-consumer-regressions.log | 44 + diagnostics/final-consumer-regressions.xml | 1 + diagnostics/r0-original-openhcs-corrected.log | 46 + diagnostics/r0-original-openhcs-python314.log | 15526 ++++++++++++++++ diagnostics/r0-original-openhcs.log | 42 + diagnostics/r1-original.log | 31 + docs/refactor/cp-aligned-full-stack-342.rst | 33 +- ...cellprofiler_full_stack_materialization.py | 9 +- ...profiler_runtime_input_binding_contract.py | 17 +- 11 files changed, 15783 insertions(+), 8 deletions(-) create mode 100644 diagnostics/final-consumer-regressions-corrected.log create mode 100644 diagnostics/final-consumer-regressions-corrected.xml create mode 100644 diagnostics/final-consumer-regressions.log create mode 100644 diagnostics/final-consumer-regressions.xml create mode 100644 diagnostics/r0-original-openhcs-corrected.log create mode 100644 diagnostics/r0-original-openhcs-python314.log create mode 100644 diagnostics/r0-original-openhcs.log create mode 100644 diagnostics/r1-original.log diff --git a/diagnostics/final-consumer-regressions-corrected.log b/diagnostics/final-consumer-regressions-corrected.log new file mode 100644 index 0000000000..9e0bf5e613 --- /dev/null +++ b/diagnostics/final-consumer-regressions-corrected.log @@ -0,0 +1,41 @@ +Running as unit: run-p851644-i13389581.scope; invocation ID: 25c0c584cd6f43e3b74de0fac8d05ea8 +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +............................................. [100%] +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/final-consumer-regressions-corrected.xml - +45 passed, 2 warnings in 4.11s + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_source_image_provenance.py tests/unit/test_source_image_provenance_hotpath.py tests/unit/test_derived_runtime_image_provenance.py tests/unit/test_cellprofiler_runtime_input_binding_contract.py tests/unit/test_cellprofiler_artifact_activation_identity.py --junitxml=diagnostics/final-consumer-regressions-corrected.xml" + User time (seconds): 5.00 + System time (seconds): 0.28 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.35 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 372804 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 55 + Minor (reclaiming a frame) page faults: 59106 + Voluntary context switches: 89 + Involuntary context switches: 33 + Swaps: 0 + File system inputs: 2336 + File system outputs: 144 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/diagnostics/final-consumer-regressions-corrected.xml b/diagnostics/final-consumer-regressions-corrected.xml new file mode 100644 index 0000000000..b98deb05c8 --- /dev/null +++ b/diagnostics/final-consumer-regressions-corrected.xml @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/diagnostics/final-consumer-regressions.log b/diagnostics/final-consumer-regressions.log new file mode 100644 index 0000000000..378661503a --- /dev/null +++ b/diagnostics/final-consumer-regressions.log @@ -0,0 +1,44 @@ +Running as unit: run-p850385-i13417204.scope; invocation ID: 097751a8a19b4c83bd854375c69b1cfa +source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 +native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so +ERROR: file or directory not found: tests/unit/test_image_payload_metadata_composition.py + + +=============================== warnings summary =============================== +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 + /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode + + self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") + +-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/final-consumer-regressions.xml - +2 warnings in 0.00s +Command exited with non-zero status 4 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_runtime_input_binding_contract.py tests/unit/test_image_payload_metadata_composition.py tests/unit/test_image_payload_provenance.py tests/unit/test_callable_artifact_inputs.py tests/unit/test_cellprofiler_callable_contracts.py --junitxml=diagnostics/final-consumer-regressions.xml" + User time (seconds): 0.35 + System time (seconds): 0.03 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.39 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 38912 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 6759 + Voluntary context switches: 1 + Involuntary context switches: 4 + Swaps: 0 + File system inputs: 0 + File system outputs: 64 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 4 diff --git a/diagnostics/final-consumer-regressions.xml b/diagnostics/final-consumer-regressions.xml new file mode 100644 index 0000000000..8565e6dd58 --- /dev/null +++ b/diagnostics/final-consumer-regressions.xml @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/diagnostics/r0-original-openhcs-corrected.log b/diagnostics/r0-original-openhcs-corrected.log new file mode 100644 index 0000000000..db078eb908 --- /dev/null +++ b/diagnostics/r0-original-openhcs-corrected.log @@ -0,0 +1,46 @@ +Running as unit: run-p843977-i13393447.scope; invocation ID: 26cbfff711a7439688ae2c34822627f3 +Traceback (most recent call last): + File "", line 189, in _run_module_as_main + File "", line 112, in _get_module_details + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/__init__.py", line 5, in + from .exporting import ( + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/exporting.py", line 25, in + from .registration import Registration + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/registration.py", line 15, in + from .native_input_owner import RegistryOwner + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/native_input_owner.py", line 19, in + from .native_admission_rules import ( + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/native_admission_rules.py", line 11, in + from .reservation_rules import ReservationRule, RuleCheck + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/reservation_rules.py", line 12, in + from .selected_source import SelectedAdmissionSource, SelectedSource, SessionRevision + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/selected_source.py", line 20, in + class SelectedSource(DeclaredFamily, affix="Source"): + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/selected_source.py", line 36, in SelectedSource + def original_has_started(self, inputs: InputDocument) -> bool: + ^^^^^^^^^^^^^ +NameError: name 'InputDocument' is not defined +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python -m agent_comms.debt_ratchet --root openhcs --base 0c0563e6538af313345391f2dc314270a86933a0 --head 63ad7c652" + User time (seconds): 0.45 + System time (seconds): 0.04 + Percent of CPU this job got: 94% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.52 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 32640 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 6 + Minor (reclaiming a frame) page faults: 5634 + Voluntary context switches: 78 + Involuntary context switches: 6 + Swaps: 0 + File system inputs: 1520 + File system outputs: 2096 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/r0-original-openhcs-python314.log b/diagnostics/r0-original-openhcs-python314.log new file mode 100644 index 0000000000..33c0f6ab59 --- /dev/null +++ b/diagnostics/r0-original-openhcs-python314.log @@ -0,0 +1,15526 @@ +Running as unit: run-p845111-i13413035.scope; invocation ID: ade2bc6f9ef4420b86725990f6944c9d +{ + "root": "openhcs/", + "base_revision": "0c0563e6538af313345391f2dc314270a86933a0", + "head_revision": "63ad7c65296c109e51700ab6213a40d617fe469b", + "paths": [ + "openhcs/core/aligned_image_payload.py", + "openhcs/core/runtime_slice_projection.py", + 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"CodecSubclass:openhcs/interop/cellprofiler/runtime/function_contract_execution.py": 0, + "StringSubscript": 0 + } +} + Command being timed: "/usr/bin/python3.14 -m agent_comms.debt_ratchet --root openhcs --base 0c0563e6538af313345391f2dc314270a86933a0 --head 63ad7c652" + User time (seconds): 12.71 + System time (seconds): 3.14 + Percent of CPU this job got: 84% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:18.75 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 89428 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 3 + Minor (reclaiming a frame) page faults: 558101 + Voluntary context switches: 13148 + Involuntary context switches: 10654 + Swaps: 0 + File system inputs: 2064 + File system outputs: 8624 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/diagnostics/r0-original-openhcs.log b/diagnostics/r0-original-openhcs.log new file mode 100644 index 0000000000..71c5f84749 --- /dev/null +++ b/diagnostics/r0-original-openhcs.log @@ -0,0 +1,42 @@ +Running as unit: run-p842680-i13393374.scope; invocation ID: 5131522ed8314e50b3c859baabb28a67 +Traceback (most recent call last): + File "", line 189, in _run_module_as_main + File "", line 112, in _get_module_details + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/__init__.py", line 5, in + from .exporting import ( + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/exporting.py", line 20, in + from .catalog_store import ChannelCatalog + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/catalog_store.py", line 11, in + from .catalog_document import CatalogDocument + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/catalog_document.py", line 10, in + from .channels import Channel, SavedView, ViewPredicate + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/channels.py", line 11, in + from .declared_family import DeclaredFamily + File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/declared_family.py", line 9, in + from metaclass_registry import AutoRegisterMeta, RegistryConfig # type: ignore[import-untyped] + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +ModuleNotFoundError: No module named 'metaclass_registry' +Command exited with non-zero status 1 + Command being timed: "/home/ts/.agent-comms/.venv/bin/python -m agent_comms.debt_ratchet --root openhcs --base 0c0563e6538af313345391f2dc314270a86933a0 --head 63ad7c652" + User time (seconds): 0.04 + System time (seconds): 0.01 + Percent of CPU this job got: 90% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.06 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 21796 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 2829 + Voluntary context switches: 17 + Involuntary context switches: 0 + Swaps: 0 + File system inputs: 432 + File system outputs: 248 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/diagnostics/r1-original.log b/diagnostics/r1-original.log new file mode 100644 index 0000000000..3d52d157b0 --- /dev/null +++ b/diagnostics/r1-original.log @@ -0,0 +1,31 @@ +Running as unit: run-p845313-i13401382.scope; invocation ID: 9876ef16563241b4bd80f95bc95374fd +Traceback (most recent call last): + File "", line 198, in _run_module_as_main + File "", line 88, in _run_code + File "/home/ts/wt/openhcs-cp-aligned-materialization-20261001/scripts/check_refactor_r1.py", line 27, in + from nominal_refactor_advisor.detectors import ( +ImportError: cannot import name 'RedundantTypeCheckDetector' from 'nominal_refactor_advisor.detectors' (/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/detectors/__init__.py) +Command exited with non-zero status 1 + Command being timed: "/home/ts/code/projects/nominal-refactor-advisor/.venv/bin/python -m scripts.check_refactor_r1 --base 0c0563e6538af313345391f2dc314270a86933a0 --head 63ad7c652 --scratch-root /home/ts/.cache/agent-scratch/h003g-runtime-repair-r1-20261001 --budget-seconds 60" + User time (seconds): 1.10 + System time (seconds): 0.06 + Percent of CPU this job got: 48% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.37 + Average shared text size (kbytes): 0 + Average unshared data size (kbytes): 0 + Average stack size (kbytes): 0 + Average total size (kbytes): 0 + Maximum resident set size (kbytes): 61004 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 13061 + Voluntary context switches: 100 + Involuntary context switches: 428 + Swaps: 0 + File system inputs: 2000 + File system outputs: 40 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/docs/refactor/cp-aligned-full-stack-342.rst b/docs/refactor/cp-aligned-full-stack-342.rst index dc8c63b930..71a00281ba 100644 --- a/docs/refactor/cp-aligned-full-stack-342.rst +++ b/docs/refactor/cp-aligned-full-stack-342.rst @@ -66,8 +66,11 @@ runner resolves this worktree's Python code and only the unchanged installed ``_tabular_native.abi3.so`` artifact. No download/build/install is performed. The first complete-package NRA attempt rejected a misdeclared context root. -The corrected whole-package plus recorded external dependency scan timed out -at 60 seconds with 511664 KiB RSS. No complete global semantic/proof certificate +The corrected whole-package scan admitted the installed candidate's external +directory, but that candidate's submodules are uninitialized; this is not +complete dependency context. The CLI's own 20-second deadline expired while +parsing (outer shard bound 60 seconds), with 511664 KiB RSS. +No complete global semantic/proof certificate is claimed. Manual ownership evidence and source behavior tests are distinct. The initial slotted-dataclass zero-argument super failure is retained and fixed with explicit cooperative super(AlignedImageStack, self), not suppressed. @@ -99,8 +102,13 @@ two outputs although identify_primary_objects now has seven diagnostic image slots in addition to the canonical slots. The exact same test fails on a complete unchanged production source snapshot of main 0c0563e65, not merely an executor substitution. No production ABI assertion or fixture was weakened. -This pre-existing fixture mismatch is separately recorded under parent -integration; the shard is not claimed fully passing. +This pre-existing fixture mismatch is owned by the runtime repair worker under +parent integration. Its fixture is now aligned by deriving diagnostic artifact +specs from PrimaryObjectDiagnosticPlanes.artifact_specs, the same authority +used by the production module declaration. No new role/name inventory or +production relaxation is introduced. The original failure receipts stay +retained, including the unrelated failed shard invocation with nonexistent +test paths; corrected consumer checks are reported separately. Affected nominal owners: aligned runtime image stacks and their named-output bundle subtype require materialization; already-dense image metadata/masked @@ -121,3 +129,20 @@ Remaining gate: original structural/R1 guard disposition, parent integration and scheduled fresh installed entrypoint acceptance with synthetic inputs. This source checkpoint is not live readiness or biological success. H003g stays FAILED and is not a validation dataset for this repair. + +Guard disposition at source checkpoint 63ad7c652: original CI-pinned R0 +debt_ratchet.py (agent-comms 3b03785f45df2ef5dc62ba6aed99294192ecbb01, +SHA256 e323c94d49c2b72d9524a5169f123e64b4a6e46a41035ca9fb4497e49b6ca562) +and its direct owner dependencies are byte-identical in the existing cached +package. It ran with the CI's Python 3.14 using existing local dependencies: +production openhcs root PASS, 18.75 seconds wall / 89428 KiB RSS, one CPU, +512 MiB / no swap / 60 seconds. Earlier interpreter/dependency import failures +remain retained. Changed-source counts have no positive structural deltas. + +The original scripts.check_refactor_r1 is NOT passing: the existing current +NRA environment fails to import RedundantTypeCheckDetector from the detector +package before scanning. The worktree's recorded dependency gitlinks are also +uninitialized, so full-context source materialization is not yet qualified. +No detector substitution, narrowed context, script modification, download or +dependency installation has been used to manufacture a passing result. Parent +integration must disposition/qualify the original R1 environment separately. diff --git a/tests/unit/test_cellprofiler_full_stack_materialization.py b/tests/unit/test_cellprofiler_full_stack_materialization.py index 5da0fd37d5..c9d5128fca 100644 --- a/tests/unit/test_cellprofiler_full_stack_materialization.py +++ b/tests/unit/test_cellprofiler_full_stack_materialization.py @@ -217,7 +217,11 @@ def compose_unmasked(self, payloads): class MaskCapability: def compose_mask(self, composed, metadata): calls.append("mask") - return super().compose_mask(composed, metadata) + mask = super().compose_mask(composed, metadata) + if mask is None: + mask = np.ones_like(composed, dtype=bool) + mask[:, 0, 0] = False + return mask bases = ( (MaskCapability, PixelCapability) @@ -232,3 +236,6 @@ def compose_mask(self, composed, metadata): np.testing.assert_array_equal( image_payload_data(dense), np.stack((np.ones((2, 3)), np.full((2, 3), 2))) ) + expected_mask = np.ones((2, 2, 3), dtype=bool) + expected_mask[:, 0, 0] = False + np.testing.assert_array_equal(image_payload_mask(dense), expected_mask) diff --git a/tests/unit/test_cellprofiler_runtime_input_binding_contract.py b/tests/unit/test_cellprofiler_runtime_input_binding_contract.py index 4902047a6f..12b438abf9 100644 --- a/tests/unit/test_cellprofiler_runtime_input_binding_contract.py +++ b/tests/unit/test_cellprofiler_runtime_input_binding_contract.py @@ -40,6 +40,9 @@ RuntimeInputBindingRequest, ) from openhcs.processing.backends.cellprofiler import identify_primary_objects +from openhcs.processing.backends.cellprofiler.primary_object_diagnostics import ( + PrimaryObjectDiagnosticPlanes, +) from openhcs.processing.backends.cellprofiler.watershed import watershed_cellprofiler4 from tests.unit.cellprofiler_runtime_test_support import ( @@ -653,7 +656,7 @@ def process(image: np.ndarray) -> np.ndarray: CellProfilerModuleCallableABI.validate_callable_artifact_abi(process, contract) -def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: +def test_callable_abi_keeps_main_flow_artifacts_in_declared_slots() -> None: source = ArtifactSpec.input("Input", ImageArtifactType) measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) labels = ArtifactSpec.output( @@ -662,13 +665,21 @@ def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: relations=(GroupLineageSourceRelation(source=source.ref()),), ) - for func in (identify_primary_objects, watershed_cellprofiler4): + for func, diagnostics in ( + ( + identify_primary_objects, + PrimaryObjectDiagnosticPlanes.artifact_specs( + source_image=source, objects=labels + ), + ), + (watershed_cellprofiler4, ()), + ): contract = _contract(func, (source,)) contract = replace( contract, metadata=replace( contract.metadata, - artifact_outputs=(measurements, labels), + artifact_outputs=(measurements, labels, *diagnostics), ), ) From 34203beb15a49da522b8719f08020e6fc9f2e9b9 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Thu, 1 Oct 2026 03:22:41 -0400 Subject: [PATCH 4/8] Publish merged-main source gates and compact byte-preserved runtime receipts --- diagnostics/.gitignore | 5 + diagnostics/README.rst | 97 + diagnostics/SHA256SUMS | 51 + .../complete-owned-families-corrected.log | 42 - .../complete-owned-families-corrected.xml | 1 - diagnostics/complete-owned-families.log | 1030 - diagnostics/complete-owned-families.xml | 934 - diagnostics/family-controls-corrected.log | 128 - diagnostics/family-controls-corrected.xml | 81 - diagnostics/family-controls.log | 93 - diagnostics/family-controls.xml | 42 - .../final-consumer-regressions-corrected.log | 41 - .../final-consumer-regressions-corrected.xml | 1 - diagnostics/final-consumer-regressions.log | 44 - diagnostics/final-consumer-regressions.xml | 1 - diagnostics/final-owned-families.log | 42 - diagnostics/final-owned-families.xml | 1 - diagnostics/first-repair.log | 92 - diagnostics/first-repair.xml | 45 - diagnostics/frozen-executor-reproducer.log | 110 - diagnostics/frozen-executor-reproducer.xml | 62 - diagnostics/nra-before-corrected.json | 14 - diagnostics/nra-before-corrected.stderr | 25 - diagnostics/nra-before.json | 0 diagnostics/nra-before.stderr | 63 - diagnostics/projection-regressions.log | 41 - diagnostics/projection-regressions.xml | 1 - .../provenance-contract-regressions.log | 119 - .../provenance-contract-regressions.xml | 72 - diagnostics/r0-original-openhcs-corrected.log | 46 - diagnostics/r0-original-openhcs-python314.log | 15526 ---------------- diagnostics/r0-original-openhcs.log | 42 - diagnostics/r1-original.log | 31 - diagnostics/unchanged-main-abi-fixture.log | 114 - diagnostics/unchanged-main-abi-fixture.xml | 72 - diagnostics/working-checkpoint.log | 41 - diagnostics/working-checkpoint.xml | 1 - docs/refactor/cp-aligned-full-stack-342.rst | 45 +- .../cp-aligned-full-stack-342-20261001.tar.gz | Bin 0 -> 334305 bytes ...cellprofiler_full_stack_materialization.py | 47 + 40 files changed, 244 insertions(+), 18999 deletions(-) create mode 100644 diagnostics/.gitignore create mode 100644 diagnostics/README.rst create mode 100644 diagnostics/SHA256SUMS delete mode 100644 diagnostics/complete-owned-families-corrected.log delete mode 100644 diagnostics/complete-owned-families-corrected.xml delete mode 100644 diagnostics/complete-owned-families.log delete mode 100644 diagnostics/complete-owned-families.xml delete mode 100644 diagnostics/family-controls-corrected.log delete mode 100644 diagnostics/family-controls-corrected.xml delete mode 100644 diagnostics/family-controls.log delete mode 100644 diagnostics/family-controls.xml delete mode 100644 diagnostics/final-consumer-regressions-corrected.log delete mode 100644 diagnostics/final-consumer-regressions-corrected.xml delete mode 100644 diagnostics/final-consumer-regressions.log delete mode 100644 diagnostics/final-consumer-regressions.xml delete mode 100644 diagnostics/final-owned-families.log delete mode 100644 diagnostics/final-owned-families.xml delete mode 100644 diagnostics/first-repair.log delete mode 100644 diagnostics/first-repair.xml delete mode 100644 diagnostics/frozen-executor-reproducer.log delete mode 100644 diagnostics/frozen-executor-reproducer.xml delete mode 100644 diagnostics/nra-before-corrected.json delete mode 100644 diagnostics/nra-before-corrected.stderr delete mode 100644 diagnostics/nra-before.json delete mode 100644 diagnostics/nra-before.stderr delete mode 100644 diagnostics/projection-regressions.log delete mode 100644 diagnostics/projection-regressions.xml delete mode 100644 diagnostics/provenance-contract-regressions.log delete mode 100644 diagnostics/provenance-contract-regressions.xml delete mode 100644 diagnostics/r0-original-openhcs-corrected.log delete mode 100644 diagnostics/r0-original-openhcs-python314.log delete mode 100644 diagnostics/r0-original-openhcs.log delete mode 100644 diagnostics/r1-original.log delete mode 100644 diagnostics/unchanged-main-abi-fixture.log delete mode 100644 diagnostics/unchanged-main-abi-fixture.xml delete mode 100644 diagnostics/working-checkpoint.log delete mode 100644 diagnostics/working-checkpoint.xml create mode 100644 docs/refactor/receipts/cp-aligned-full-stack-342-20261001.tar.gz diff --git a/diagnostics/.gitignore b/diagnostics/.gitignore new file mode 100644 index 0000000000..42bcb8627f --- /dev/null +++ b/diagnostics/.gitignore @@ -0,0 +1,5 @@ +# Raw receipts are preserved in the reviewed tar.gz, byte-for-byte. +*.log +*.xml +*.json +*.stderr diff --git a/diagnostics/README.rst b/diagnostics/README.rst new file mode 100644 index 0000000000..eba3184f40 --- /dev/null +++ b/diagnostics/README.rst @@ -0,0 +1,97 @@ +Runtime repair #342 source receipts +================================== + +Owner: H003g runtime repair worker under parent integration; draft PR #344. +H003g is permanently FAILED. These are synthetic source checks, not a trial +retry, installed acceptance, result QA or biological success evidence. + +Runner: run_source_tests.py. It prepends this worktree's Python source and +uses only the unchanged installed _tabular_native.abi3.so from +/home/ts/wt/openhcs-s1-installed-parent-20261001. Existing dependency packages +are reused without any download, build, install or configuration change. +All execution shards use CPU affinity 0, one CPU quota, 512 MiB MemoryMax, +zero swap, 60-second timeout, OPENHCS_CPU_ONLY=true, numerical threads 1, +and PYTEST_DISABLE_PLUGIN_AUTOLOAD=1. Two unknown asyncio configuration +warnings are expected because optional pytest plugins are disabled. + +Final receipt interpretation +---------------------------- + +merged-main-final-family-controls: 111 PASS, including 15 added full-stack +tests plus 96 existing executor/projection/alignment/device/registry controls. +merged-main-consumer-regressions: 45 PASS, including the unchanged-main ABI +fixture corrected using the real diagnostic declaration owner. +r0-merged-main-openhcs/scripts/benchmark: all PASS. Base main 7b0ec3f5, +head b7702664, exact three changed production paths. Subsequent edits affect +only tests/documentation/receipt packaging, not production sources. + +r1-original: import failure BEFORE scanning. The existing current NRA +environment does not export RedundantTypeCheckDetector at the original +guard's import site. Worktree external gitlinks are uninitialized as well. +No passing R1 certificate or complete dependency-context audit is claimed. +nra-before-corrected: deadline_incomplete structured report with null counts, +20-second CLI deadline, parsing unfinished. Its admitted candidate external +directory is uninitialized. This is NOT a successful no-findings report. + +Unsuccessful receipts remain in the archive: first-repair slotted-dataclass +super error; family-controls fixture argument and named bundle failure; +family-controls-corrected mask-domain failure; complete-owned-families +temporary metadata deletion error; frozen-executor-reproducer expected exact +float(AlignedImageStack) failure using original executor 20ca4f825 with empty +kwargs; provenance-contract-regressions stale diagnostic ABI fixture; +unchanged-main-abi-fixture confirms that failure on full unchanged main +0c0563e65; final-consumer-regressions nonexistent test paths/zero tests; +r0-original interpreter/dependency import failures; and nra-before incorrectly +admitted root. Earlier passing checkpoints are retained, not substituted for +the merged-main receipts. Logs contain exact original argv and time/RSS/exit +status, and JUnit files contain test identities and timestamps. + +Materialization scope +--------------------- + +The actual shared ABC algorithm owns pixels, masks and typed provenance. +Dense stacks, same-slice bundles, aligned runtime stacks and named output +bundles inherit it, with small axis/domain hooks. Existing nominal registry +dispatch adds full-stack projection for primary images and image kwargs; +other declared runtime families keep their own domains. No name switch, +np.asarray fix, mirrored registry/store or copied executor is shipped. + +The MRO cases use two independent test-only capabilities over the actual +composition owner: pixel offset and validity-mask creation. Both cooperative +super orders verify exact pixel and mask effects. They are not a claim of +production MI implementation or whole-package semantic equivalence. + +Artifact authority / bounded source replay +------------------------------------------ + +SHA256SUMS in this receipt archive covers all raw receipt files, the runner, +the five final changed Python files and the architectural source receipt. +Verify it after extracting into the reviewed source worktree. No science +input or trial output is included. Archived original stdout is byte-preserved; +whitespace within tracebacks is not normalized. + +Use the original runner and final log argv under the bounds above. To obtain +the expected pre-repair executor failure, set BASELINE_EXECUTOR_REF=20ca4f825 +and select only test_real_rescale_full_stack_materializes_composed_runtime_sources. +For a full unchanged-main baseline, git archive the recorded production and +fixture paths and set SOURCE_BASELINE_ROOT to the owned extracted directory. +No MCP/native/viewer startup is part of either source replay. + +R0 package: existing cached agent-comms package corresponding to original +CI pin 3b03785f45df2ef5dc62ba6aed99294192ecbb01. debt_ratchet.py SHA256 +e323c94d49c2b72d9524a5169f123e64b4a6e46a41035ca9fb4497e49b6ca562; +direct DeclaredFamily/FieldCodec/MroDispatch sources compare byte-identical. +The successful entrypoint uses /usr/bin/python3.14 and existing local +metaclass-registry source, matching the workflow interpreter, without install. +Original R1 source/script is unchanged; its environment failure is retained. + +Disposable scratch ownership +---------------------------- + +Only owned scratch h003g-runtime-repair-baseline-20261001 under +/home/ts/.cache/agent-scratch was used: 31 MiB unchanged-main source archive, +recoverable from Git. Its process completed and its failure logs are preserved +before cleanup. The attempted r1 scratch path was never created (import failed). +No native/viewer/MCP process, lifecycle lock or shared slot was acquired. +Parent owns installation/integration and actual synthetic installed acceptance +after #338. Held-out/reference data and frozen H003g remain sealed/unmodified. diff --git a/diagnostics/SHA256SUMS b/diagnostics/SHA256SUMS new file mode 100644 index 0000000000..c7c0c347ad --- /dev/null +++ b/diagnostics/SHA256SUMS @@ -0,0 +1,51 @@ +bd6a2291768984da8620e4ad12b2e15eb5017de95f5c5e74c175d2d35dbc6e87 diagnostics/complete-owned-families-corrected.log +bb22b22168aa5f1b93331d39f4bbdea068e8546a87accfd4412a47e97bd90b4e diagnostics/complete-owned-families.log +dec6e1ce77ce33abd98924a0263266415ee128bde87143797f7f7d19e1efb380 diagnostics/family-controls-corrected.log +bfff89adb6b1353253efa2e8238b01b598e098960ab8efc20401ca862cf5e26b diagnostics/family-controls.log +585c48a3e033ff3bb72ad30bc3414ee503c39983ea8449d82db31871303f1506 diagnostics/final-consumer-regressions-corrected.log +f6339b1ac8389a5db2849d540a7fc4f79a569ffe0b05acc4a1d834274f352f4f diagnostics/final-consumer-regressions.log +35da4640556585d845b3194a662d29e8e515976d1e9f8ed2dcaf87683e0bf389 diagnostics/final-owned-families.log 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b/diagnostics/complete-owned-families-corrected.log deleted file mode 100644 index 674064bef5..0000000000 --- a/diagnostics/complete-owned-families-corrected.log +++ /dev/null @@ -1,42 +0,0 @@ -Running as unit: run-p826825-i13396276.scope; invocation ID: 1667839ab3e345e585c7eb0f48d91350 -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -........................................................................ 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[100%] -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/complete-owned-families-corrected.xml - -110 passed, 2 warnings in 6.96s - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/complete-owned-families-corrected.xml" - User time (seconds): 4.06 - System time (seconds): 0.29 - Percent of CPU this job got: 47% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:09.09 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 322484 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 52185 - Voluntary context switches: 2 - Involuntary context switches: 1822 - Swaps: 0 - File system inputs: 0 - File system outputs: 256 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/diagnostics/complete-owned-families-corrected.xml b/diagnostics/complete-owned-families-corrected.xml deleted file mode 100644 index e0e72df4ef..0000000000 --- a/diagnostics/complete-owned-families-corrected.xml +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/diagnostics/complete-owned-families.log b/diagnostics/complete-owned-families.log deleted file mode 100644 index 557abe5971..0000000000 --- a/diagnostics/complete-owned-families.log +++ /dev/null @@ -1,1030 +0,0 @@ -Running as unit: run-p825374-i13435855.scope; invocation ID: 37d59bea3a5241e2afd366827a52bf6a -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -FFFFFFFFFFF.FF.......................................................... 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[100%] -=================================== FAILURES =================================== -______ test_real_rescale_full_stack_materializes_composed_runtime_sources ______ - - def test_real_rescale_full_stack_materializes_composed_runtime_sources(): - data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) - source = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE - ).payload_with(data, None) - composition = compose_aligned_image_payload( - "synthetic source inputs", (source, source) - ) - assert isinstance(composition.payload, AlignedImageStack) - contract = CallableContract.from_callable(rescale_intensity) -> result = CellProfilerFunctionContractExecutor().execute( - contract, - contract.resolve_canonical_raw_callable(), - composition.payload, - {}, - execution_mode=contract.runtime_image_execution_mode, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:47: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - ...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) -composed = array([[[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - [ 8., 9., 10., 11.]], - - [[ 0., 1., 2.... 23.]], - - [[12., 13., 14., 15.], - [16., 17., 18., 19.], - [20., 21., 22., 23.]]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_3D] _ - -processing_contract = -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): -> CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:89: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_2D] _ - -processing_contract = -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.FLEXIBLE] _ - -processing_contract = -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.VOLUMETRIC_TO_SLICE] _ - -processing_contract = -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_3D] _ - -processing_contract = -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): -> CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:89: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_2D] _ - -processing_contract = -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.FLEXIBLE] _ - -processing_contract = -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.VOLUMETRIC_TO_SLICE] _ - -processing_contract = -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_aligned_materialization_retains_masks_calibration_and_exact_contributors _ - - def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): - spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) - sources = [] - expected_paths = [] - for channel, alias in ((1, "DNA"), (2, "actin")): - paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) - expected_paths.extend(paths) - metadata = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, - source_image_names=(alias,), - source_image_provenance_planes=SourceImageProvenancePlanes.from_components( - paths=paths, - component_metadata=tuple( - {"well": "A01", "site": str(site), "channel": str(channel)} - for site in (1, 2) - ), - ), - source_voxel_spacing=spacing, - source_dtype="uint8", - intensity_scale=255.0, - source_spatial_domain=SourceSpatialDomain( - source_shape_yx=(3, 4), origin_yx=(0, 0) - ), - ) - pixels = np.full((2, 3, 4), channel, dtype=np.float32) - mask = np.ones_like(pixels, dtype=bool) - mask[0, 0, 0] = False - sources.append(metadata.payload_with(pixels, mask)) - composed = compose_aligned_image_payload( - "matched synthetic inputs", tuple(sources) - ).payload -> dense = RuntimeSliceProjection.full_stack_value(composed) - -tests/unit/test_cellprofiler_full_stack_materialization.py:142: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(MaskedImagePayload(data=array([[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1.,...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) -composed = array([[[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], - - [[2., 2., 2., 2.], - ... [1., 1., 1., 1.]], - - [[2., 2., 2., 2.], - [2., 2., 2., 2.], - [2., 2., 2., 2.]]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -______ test_named_output_bundle_materializes_its_own_source_binding_axis _______ - - def test_named_output_bundle_materializes_its_own_source_binding_axis(): - planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) - bundle = ImageOutputBundle( - planes, - tuple( - AlignedImageSliceContext.main_flow(name, artifact_kind="image") - for name in ("red", "green") - ), - ) -> dense = RuntimeSliceProjection.full_stack_value(bundle) - -tests/unit/test_cellprofiler_full_stack_materialization.py:193: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = ImageOutputBundle(slices=(array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32), ...age'), AlignedImageSliceContext(output_kind='main', output_key='green', projection_key='main', artifact_kind='image'))) -composed = array([[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], - - [[2., 2., 2., 2.], - [2., 2., 2., 2.], - [2., 2., 2., 2.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_independent_composition_capabilities_cooperate_in_both_mro_orders[False] _ - -reverse = False - - @pytest.mark.parametrize("reverse", (False, True)) - def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): - calls = [] - - class PixelCapability: - def compose_unmasked(self, payloads): - calls.append("pixels") - return super().compose_unmasked(payloads) + 1 - - class MaskCapability: - def compose_mask(self, composed, metadata): - calls.append("mask") - return super().compose_mask(composed, metadata) - - bases = ( - (MaskCapability, PixelCapability) - if reverse - else (PixelCapability, MaskCapability) - ) - probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) - probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) - assert isinstance(probe, ImagePayloadStackComposition) -> dense = RuntimeSliceProjection.full_stack_value(probe) - -tests/unit/test_cellprofiler_full_stack_materialization.py:230: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask - return super().compose_mask(composed, metadata) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], - [0., 0., 0.]]), array([[1., 1., 1.], - [1., 1., 1.]])), slice_contexts=()) -composed = array([[[1., 1., 1.], - [1., 1., 1.]], - - [[2., 2., 2.], - [2., 2., 2.]]]) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -_ test_independent_composition_capabilities_cooperate_in_both_mro_orders[True] _ - -reverse = True - - @pytest.mark.parametrize("reverse", (False, True)) - def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): - calls = [] - - class PixelCapability: - def compose_unmasked(self, payloads): - calls.append("pixels") - return super().compose_unmasked(payloads) + 1 - - class MaskCapability: - def compose_mask(self, composed, metadata): - calls.append("mask") - return super().compose_mask(composed, metadata) - - bases = ( - (MaskCapability, PixelCapability) - if reverse - else (PixelCapability, MaskCapability) - ) - probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) - probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) - assert isinstance(probe, ImagePayloadStackComposition) -> dense = RuntimeSliceProjection.full_stack_value(probe) - -tests/unit/test_cellprofiler_full_stack_materialization.py:230: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask - return super().compose_mask(composed, metadata) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], - [0., 0., 0.]]), array([[1., 1., 1.], - [1., 1., 1.]])), slice_contexts=()) -composed = array([[[1., 1., 1.], - [1., 1., 1.]], - - [[2., 2., 2.], - [2., 2., 2.]]]) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/complete-owned-families.xml - -=========================== short test summary info ============================ -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_real_rescale_full_stack_materializes_composed_runtime_sources -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_3D] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.PURE_2D] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.FLEXIBLE] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[1-ProcessingContract.VOLUMETRIC_TO_SLICE] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_3D] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.PURE_2D] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.FLEXIBLE] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_every_full_stack_processing_family_materializes_image_and_image_kwargs[2-ProcessingContract.VOLUMETRIC_TO_SLICE] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_aligned_materialization_retains_masks_calibration_and_exact_contributors -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_named_output_bundle_materializes_its_own_source_binding_axis -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_independent_composition_capabilities_cooperate_in_both_mro_orders[False] -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_independent_composition_capabilities_cooperate_in_both_mro_orders[True] -13 failed, 97 passed, 2 warnings in 4.35s -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/complete-owned-families.xml" - User time (seconds): 4.79 - System time (seconds): 0.30 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.15 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 325096 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 17 - Minor (reclaiming a frame) page faults: 52978 - Voluntary context switches: 27 - Involuntary context switches: 28 - Swaps: 0 - File system inputs: 944 - File system outputs: 496 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/complete-owned-families.xml b/diagnostics/complete-owned-families.xml deleted file mode 100644 index fdddaeb5df..0000000000 --- a/diagnostics/complete-owned-families.xml +++ /dev/null @@ -1,934 +0,0 @@ -def test_real_rescale_full_stack_materializes_composed_runtime_sources(): - data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) - source = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE - ).payload_with(data, None) - composition = compose_aligned_image_payload( - "synthetic source inputs", (source, source) - ) - assert isinstance(composition.payload, AlignedImageStack) - contract = CallableContract.from_callable(rescale_intensity) -> result = CellProfilerFunctionContractExecutor().execute( - contract, - contract.resolve_canonical_raw_callable(), - composition.payload, - {}, - execution_mode=contract.runtime_image_execution_mode, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:47: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - ...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) -composed = array([[[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - [ 8., 9., 10., 11.]], - - [[ 0., 1., 2.... 23.]], - - [[12., 13., 14., 15.], - [16., 17., 18., 19.], - [20., 21., 22., 23.]]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_3D: 'Pure3DProcessingContract'> -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): -> CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:89: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_2D: 'Pure2DProcessingContract'> -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.FLEXIBLE: 'FlexibleProcessingContract'> -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.VOLUMETRIC_TO_SLICE: 'VolumetricToSliceProcessingContract'> -slice_count = 1 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32),), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_3D: 'Pure3DProcessingContract'> -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): -> CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:89: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.PURE_2D: 'Pure2DProcessingContract'> -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.FLEXIBLE: 'FlexibleProcessingContract'> -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorprocessing_contract = <ProcessingContract.VOLUMETRIC_TO_SLICE: 'VolumetricToSliceProcessingContract'> -slice_count = 2 - - @pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) - @pytest.mark.parametrize("slice_count", (1, 2)) - def test_every_full_stack_processing_family_materializes_image_and_image_kwargs( - processing_contract, slice_count - ): - planes = tuple( - np.full((3, 4), index, dtype=np.float32) for index in range(slice_count) - ) - aligned = AlignedImageStack(planes) - opaque = RuntimeSliceAlignedValues(("not an image",)) - calls = [] - - def dense_callable(image, *, reference, token): - calls.append((image, reference, token)) - assert not isinstance(image, AlignedImageStack) - assert not isinstance(reference, AlignedImageStack) - assert token is opaque - np.testing.assert_array_equal(image_payload_data(image), np.stack(planes)) - np.testing.assert_array_equal(image_payload_data(reference), np.stack(planes)) - return image - - contract = CallableContract( - func=dense_callable, - function_name="dense_callable", - module_name="DenseProbeModule", - metadata=CallableMetadata(processing_contract=processing_contract), - ) - kwargs = {"reference": aligned, "token": opaque} - # Retain the PURE_3D prohibition on slice-aligned non-image kwargs. - if processing_contract is ProcessingContract.PURE_3D: - with pytest.raises(ValueError, match="runtime-slice-aligned kwargs.*token"): - CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - assert calls == [] - kwargs["token"] = None - opaque = None -> result = CellProfilerFunctionContractExecutor().execute( - contract, - dense_callable, - aligned, - kwargs, - execution_mode=ImagePayloadExecutionMode.FULL_STACK, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:99: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(array([[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], dtype=float32), array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32)), slice_contexts=()) -composed = array([[[0., 0., 0., 0.], - [0., 0., 0., 0.], - [0., 0., 0., 0.]], - - [[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrordef test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): - spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) - sources = [] - expected_paths = [] - for channel, alias in ((1, "DNA"), (2, "actin")): - paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) - expected_paths.extend(paths) - metadata = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, - source_image_names=(alias,), - source_image_provenance_planes=SourceImageProvenancePlanes.from_components( - paths=paths, - component_metadata=tuple( - {"well": "A01", "site": str(site), "channel": str(channel)} - for site in (1, 2) - ), - ), - source_voxel_spacing=spacing, - source_dtype="uint8", - intensity_scale=255.0, - source_spatial_domain=SourceSpatialDomain( - source_shape_yx=(3, 4), origin_yx=(0, 0) - ), - ) - pixels = np.full((2, 3, 4), channel, dtype=np.float32) - mask = np.ones_like(pixels, dtype=bool) - mask[0, 0, 0] = False - sources.append(metadata.payload_with(pixels, mask)) - composed = compose_aligned_image_payload( - "matched synthetic inputs", tuple(sources) - ).payload -> dense = RuntimeSliceProjection.full_stack_value(composed) - -tests/unit/test_cellprofiler_full_stack_materialization.py:142: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(MaskedImagePayload(data=array([[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1.,...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) -composed = array([[[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], - - [[2., 2., 2., 2.], - ... [1., 1., 1., 1.]], - - [[2., 2., 2., 2.], - [2., 2., 2., 2.], - [2., 2., 2., 2.]]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrordef test_named_output_bundle_materializes_its_own_source_binding_axis(): - planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) - bundle = ImageOutputBundle( - planes, - tuple( - AlignedImageSliceContext.main_flow(name, artifact_kind="image") - for name in ("red", "green") - ), - ) -> dense = RuntimeSliceProjection.full_stack_value(bundle) - -tests/unit/test_cellprofiler_full_stack_materialization.py:193: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = ImageOutputBundle(slices=(array([[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], dtype=float32), ...age'), AlignedImageSliceContext(output_kind='main', output_key='green', projection_key='main', artifact_kind='image'))) -composed = array([[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], - - [[2., 2., 2., 2.], - [2., 2., 2., 2.], - [2., 2., 2., 2.]]], dtype=float32) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorreverse = False - - @pytest.mark.parametrize("reverse", (False, True)) - def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): - calls = [] - - class PixelCapability: - def compose_unmasked(self, payloads): - calls.append("pixels") - return super().compose_unmasked(payloads) + 1 - - class MaskCapability: - def compose_mask(self, composed, metadata): - calls.append("mask") - return super().compose_mask(composed, metadata) - - bases = ( - (MaskCapability, PixelCapability) - if reverse - else (PixelCapability, MaskCapability) - ) - probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) - probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) - assert isinstance(probe, ImagePayloadStackComposition) -> dense = RuntimeSliceProjection.full_stack_value(probe) - -tests/unit/test_cellprofiler_full_stack_materialization.py:230: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask - return super().compose_mask(composed, metadata) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], - [0., 0., 0.]]), array([[1., 1., 1.], - [1., 1., 1.]])), slice_contexts=()) -composed = array([[[1., 1., 1.], - [1., 1., 1.]], - - [[2., 2., 2.], - [2., 2., 2.]]]) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalErrorreverse = True - - @pytest.mark.parametrize("reverse", (False, True)) - def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): - calls = [] - - class PixelCapability: - def compose_unmasked(self, payloads): - calls.append("pixels") - return super().compose_unmasked(payloads) + 1 - - class MaskCapability: - def compose_mask(self, composed, metadata): - calls.append("mask") - return super().compose_mask(composed, metadata) - - bases = ( - (MaskCapability, PixelCapability) - if reverse - else (PixelCapability, MaskCapability) - ) - probe_type = type("IndependentCompositionProbe", (*bases, AlignedImageStack), {}) - probe = probe_type((np.zeros((2, 3)), np.ones((2, 3)))) - assert isinstance(probe, ImagePayloadStackComposition) -> dense = RuntimeSliceProjection.full_stack_value(probe) - -tests/unit/test_cellprofiler_full_stack_materialization.py:230: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:441: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -tests/unit/test_cellprofiler_full_stack_materialization.py:220: in compose_mask - return super().compose_mask(composed, metadata) -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = IndependentCompositionProbe(slices=(array([[0., 0., 0.], - [0., 0., 0.]]), array([[1., 1., 1.], - [1., 1., 1.]])), slice_contexts=()) -composed = array([[[1., 1., 1.], - [1., 1., 1.]], - - [[2., 2., 2.], - [2., 2., 2.]]]) - - def compose_mask(self, composed: Any, metadata: ImagePayloadMetadata) -> Any | None: - del metadata - return _stack_image_payload_mask( - self.composition_payloads, - composed, -> output_mask_domain=metadata.mask_domain(composed), - ) -E UnboundLocalError: cannot access local variable 'metadata' where it is not associated with a value - -openhcs/core/aligned_image_payload.py:456: UnboundLocalError \ No newline at end of file diff --git a/diagnostics/family-controls-corrected.log b/diagnostics/family-controls-corrected.log deleted file mode 100644 index 89aeab476e..0000000000 --- a/diagnostics/family-controls-corrected.log +++ /dev/null @@ -1,128 +0,0 @@ -Running as unit: run-p820746-i13427978.scope; invocation ID: 09e0b7d729e04b9c9302d3cccd0c4bb3 -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -.........F.................................... [100%] -=================================== FAILURES =================================== -_ test_aligned_materialization_retains_masks_calibration_and_exact_contributors _ - - def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): - spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) - sources = [] - expected_paths = [] - for channel, alias in ((1, "DNA"), (2, "actin")): - paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) - expected_paths.extend(paths) - metadata = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, - source_image_names=(alias,), - source_image_provenance_planes=SourceImageProvenancePlanes.from_components( - paths=paths, - component_metadata=tuple( - {"well": "A01", "site": str(site), "channel": str(channel)} - for site in (1, 2) - ), - ), - source_voxel_spacing=spacing, - source_dtype="uint8", - intensity_scale=255.0, - source_spatial_domain=SourceSpatialDomain( - source_shape_yx=(3, 4), origin_yx=(0, 0) - ), - ) - pixels = np.full((2, 3, 4), channel, dtype=np.float32) - mask = np.ones_like(pixels, dtype=bool) - mask[0, 0, 0] = False - sources.append(metadata.payload_with(pixels, mask)) - composed = compose_aligned_image_payload( - "matched synthetic inputs", tuple(sources) - ).payload -> dense = RuntimeSliceProjection.full_stack_value(composed) - -tests/unit/test_cellprofiler_full_stack_materialization.py:142: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:440: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -openhcs/core/runtime_image_values.py:785: in payload_with - return MaskedImagePayload(data=data, mask=mask, metadata=self) -:6: in __init__ - ??? -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = MaskedImagePayload(data=array([[[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], - - [[2...one, mask_defines_border=None, source_channel_axis=None, plane_axis=)) - - def __post_init__(self) -> None: - data_geometry = ArrayGeometry.require_from_value( - self.data, - value_name="MaskedImagePayload.data", - ) - if data_geometry.ndim == 0: - raise TypeError( - "MaskedImagePayload.data requires array-like image data, " - f"got {type(self.data).__name__}." - ) - mask_shape = ArrayGeometry.require_from_value( - self.mask, - value_name="MaskedImagePayload.mask", - ).shape - if not mask_shape: - raise TypeError( - "MaskedImagePayload.mask requires array-like mask data, " - f"got {type(self.mask).__name__}." - ) - data_shape = data_geometry.shape - if not self.metadata.mask_domain(self.data).accepts(mask_shape): -> raise ValueError( - "MaskedImagePayload.mask shape must match the image spatial " - f"domain; got mask {mask_shape!r} for image {data_shape!r}." - ) -E ValueError: MaskedImagePayload.mask shape must match the image spatial domain; got mask (2, 3, 4) for image (2, 2, 3, 4). - -openhcs/core/runtime_image_values.py:1246: ValueError -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/family-controls-corrected.xml - -=========================== short test summary info ============================ -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_aligned_materialization_retains_masks_calibration_and_exact_contributors -1 failed, 45 passed, 2 warnings in 2.68s -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/family-controls-corrected.xml" - User time (seconds): 3.16 - System time (seconds): 0.29 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.48 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 309204 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 1 - Minor (reclaiming a frame) page faults: 50492 - Voluntary context switches: 3 - Involuntary context switches: 26 - Swaps: 0 - File system inputs: 8 - File system outputs: 408 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/family-controls-corrected.xml b/diagnostics/family-controls-corrected.xml deleted file mode 100644 index 62510bd04f..0000000000 --- a/diagnostics/family-controls-corrected.xml +++ /dev/null @@ -1,81 +0,0 @@ -def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): - spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) - sources = [] - expected_paths = [] - for channel, alias in ((1, "DNA"), (2, "actin")): - paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) - expected_paths.extend(paths) - metadata = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, - source_image_names=(alias,), - source_image_provenance_planes=SourceImageProvenancePlanes.from_components( - paths=paths, - component_metadata=tuple( - {"well": "A01", "site": str(site), "channel": str(channel)} - for site in (1, 2) - ), - ), - source_voxel_spacing=spacing, - source_dtype="uint8", - intensity_scale=255.0, - source_spatial_domain=SourceSpatialDomain( - source_shape_yx=(3, 4), origin_yx=(0, 0) - ), - ) - pixels = np.full((2, 3, 4), channel, dtype=np.float32) - mask = np.ones_like(pixels, dtype=bool) - mask[0, 0, 0] = False - sources.append(metadata.payload_with(pixels, mask)) - composed = compose_aligned_image_payload( - "matched synthetic inputs", tuple(sources) - ).payload -> dense = RuntimeSliceProjection.full_stack_value(composed) - -tests/unit/test_cellprofiler_full_stack_materialization.py:142: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/core/runtime_slice_projection.py:898: in full_stack_value - ).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:440: in compose - return metadata.payload_with(composed, self.compose_mask(composed, metadata)) -openhcs/core/runtime_image_values.py:785: in payload_with - return MaskedImagePayload(data=data, mask=mask, metadata=self) -<string>:6: in __init__ - ??? -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = MaskedImagePayload(data=array([[[[1., 1., 1., 1.], - [1., 1., 1., 1.], - [1., 1., 1., 1.]], - - [[2...one, mask_defines_border=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.RUNTIME_SLICE: 'runtime_slice'>)) - - def __post_init__(self) -> None: - data_geometry = ArrayGeometry.require_from_value( - self.data, - value_name="MaskedImagePayload.data", - ) - if data_geometry.ndim == 0: - raise TypeError( - "MaskedImagePayload.data requires array-like image data, " - f"got {type(self.data).__name__}." - ) - mask_shape = ArrayGeometry.require_from_value( - self.mask, - value_name="MaskedImagePayload.mask", - ).shape - if not mask_shape: - raise TypeError( - "MaskedImagePayload.mask requires array-like mask data, " - f"got {type(self.mask).__name__}." - ) - data_shape = data_geometry.shape - if not self.metadata.mask_domain(self.data).accepts(mask_shape): -> raise ValueError( - "MaskedImagePayload.mask shape must match the image spatial " - f"domain; got mask {mask_shape!r} for image {data_shape!r}." - ) -E ValueError: MaskedImagePayload.mask shape must match the image spatial domain; got mask (2, 3, 4) for image (2, 2, 3, 4). - -openhcs/core/runtime_image_values.py:1246: ValueError \ No newline at end of file diff --git a/diagnostics/family-controls.log b/diagnostics/family-controls.log deleted file mode 100644 index 032e5b8b7e..0000000000 --- a/diagnostics/family-controls.log +++ /dev/null @@ -1,93 +0,0 @@ -Running as unit: run-p818047-i13391681.scope; invocation ID: e7368d61945f49c0a3b4aa711e587423 -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -.........FF................................... [100%] -=================================== FAILURES =================================== -_ test_aligned_materialization_retains_masks_calibration_and_exact_contributors _ - - def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): - spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) - sources = [] - expected_paths = [] - for channel, alias in ((1, "DNA"), (2, "actin")): - paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) - expected_paths.extend(paths) -> metadata = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, - source_image_names=(alias,), - source_image_provenance_planes=SourceImageProvenancePlanes.from_components( - paths=paths, - component_metadata=tuple( - {"well": "A01", "site": str(site), "channel": str(channel)} - for site in (1, 2) - ), - ), - source_voxel_spacing=spacing, - source_dtype="uint8", - intensity_scale=255.0, - source_spatial_shape_yx=(3, 4), - spatial_origin_yx=(0, 0), - ) -E TypeError: ImagePayloadMetadata.__init__() got an unexpected keyword argument 'source_spatial_shape_yx' - -tests/unit/test_cellprofiler_full_stack_materialization.py:117: TypeError -______ test_named_output_bundle_materializes_its_own_source_binding_axis _______ - - def test_named_output_bundle_materializes_its_own_source_binding_axis(): - planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) - bundle = ImageOutputBundle( - planes, - tuple( - AlignedImageSliceContext.main_flow(name, artifact_kind="image") - for name in ("red", "green") - ), - ) - dense = RuntimeSliceProjection.full_stack_value(bundle) -> assert image_payload_metadata(dense).plane_axis is RuntimePlaneAxis.SOURCE_BINDING -E AssertionError: assert None is -E + where None = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit= = RuntimePlaneAxis.SOURCE_BINDING - -tests/unit/test_cellprofiler_full_stack_materialization.py:187: AssertionError -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/family-controls.xml - -=========================== short test summary info ============================ -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_aligned_materialization_retains_masks_calibration_and_exact_contributors -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_named_output_bundle_materializes_its_own_source_binding_axis -2 failed, 44 passed, 2 warnings in 3.57s -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/family-controls.xml" - User time (seconds): 3.27 - System time (seconds): 0.27 - Percent of CPU this job got: 77% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.59 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 306600 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 2 - Minor (reclaiming a frame) page faults: 48322 - Voluntary context switches: 5 - Involuntary context switches: 407 - Swaps: 0 - File system inputs: 56 - File system outputs: 128 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/family-controls.xml b/diagnostics/family-controls.xml deleted file mode 100644 index 64c61e5290..0000000000 --- a/diagnostics/family-controls.xml +++ /dev/null @@ -1,42 +0,0 @@ -def test_aligned_materialization_retains_masks_calibration_and_exact_contributors(): - spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) - sources = [] - expected_paths = [] - for channel, alias in ((1, "DNA"), (2, "actin")): - paths = tuple(f"/synthetic/A01_s{site}_w{channel}.tif" for site in (1, 2)) - expected_paths.extend(paths) -> metadata = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, - source_image_names=(alias,), - source_image_provenance_planes=SourceImageProvenancePlanes.from_components( - paths=paths, - component_metadata=tuple( - {"well": "A01", "site": str(site), "channel": str(channel)} - for site in (1, 2) - ), - ), - source_voxel_spacing=spacing, - source_dtype="uint8", - intensity_scale=255.0, - source_spatial_shape_yx=(3, 4), - spatial_origin_yx=(0, 0), - ) -E TypeError: ImagePayloadMetadata.__init__() got an unexpected keyword argument 'source_spatial_shape_yx' - -tests/unit/test_cellprofiler_full_stack_materialization.py:117: TypeErrordef test_named_output_bundle_materializes_its_own_source_binding_axis(): - planes = tuple(np.full((3, 4), index, dtype=np.float32) for index in (1, 2)) - bundle = ImageOutputBundle( - planes, - tuple( - AlignedImageSliceContext.main_flow(name, artifact_kind="image") - for name in ("red", "green") - ), - ) - dense = RuntimeSliceProjection.full_stack_value(bundle) -> assert image_payload_metadata(dense).plane_axis is RuntimePlaneAxis.SOURCE_BINDING -E AssertionError: assert None is <RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'> -E + where None = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit=<SourceVoxelSpacingUnit.MICROMETERS: ...ce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=None, plane_axis=None).plane_axis -E + where ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit=<SourceVoxelSpacingUnit.MICROMETERS: ...ce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=None, plane_axis=None) = image_payload_metadata(ImageOutputBundle(slices=(array([[1., 1., 1., 1.],\n [1., 1., 1., 1.],\n [1., 1., 1., 1.]], dtype=float32), ...age'), AlignedImageSliceContext(output_kind='main', output_key='green', projection_key='main', artifact_kind='image')))) -E + and <RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'> = RuntimePlaneAxis.SOURCE_BINDING - -tests/unit/test_cellprofiler_full_stack_materialization.py:187: AssertionError \ No newline at end of file diff --git a/diagnostics/final-consumer-regressions-corrected.log b/diagnostics/final-consumer-regressions-corrected.log deleted file mode 100644 index 9e0bf5e613..0000000000 --- a/diagnostics/final-consumer-regressions-corrected.log +++ /dev/null @@ -1,41 +0,0 @@ -Running as unit: run-p851644-i13389581.scope; invocation ID: 25c0c584cd6f43e3b74de0fac8d05ea8 -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -............................................. [100%] -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/final-consumer-regressions-corrected.xml - -45 passed, 2 warnings in 4.11s - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_source_image_provenance.py tests/unit/test_source_image_provenance_hotpath.py tests/unit/test_derived_runtime_image_provenance.py tests/unit/test_cellprofiler_runtime_input_binding_contract.py tests/unit/test_cellprofiler_artifact_activation_identity.py --junitxml=diagnostics/final-consumer-regressions-corrected.xml" - User time (seconds): 5.00 - System time (seconds): 0.28 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.35 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 372804 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 55 - Minor (reclaiming a frame) page faults: 59106 - Voluntary context switches: 89 - Involuntary context switches: 33 - Swaps: 0 - File system inputs: 2336 - File system outputs: 144 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/diagnostics/final-consumer-regressions-corrected.xml b/diagnostics/final-consumer-regressions-corrected.xml deleted file mode 100644 index b98deb05c8..0000000000 --- a/diagnostics/final-consumer-regressions-corrected.xml +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/diagnostics/final-consumer-regressions.log b/diagnostics/final-consumer-regressions.log deleted file mode 100644 index 378661503a..0000000000 --- a/diagnostics/final-consumer-regressions.log +++ /dev/null @@ -1,44 +0,0 @@ -Running as unit: run-p850385-i13417204.scope; invocation ID: 097751a8a19b4c83bd854375c69b1cfa -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -ERROR: file or directory not found: tests/unit/test_image_payload_metadata_composition.py - - -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/final-consumer-regressions.xml - -2 warnings in 0.00s -Command exited with non-zero status 4 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_runtime_input_binding_contract.py tests/unit/test_image_payload_metadata_composition.py tests/unit/test_image_payload_provenance.py tests/unit/test_callable_artifact_inputs.py tests/unit/test_cellprofiler_callable_contracts.py --junitxml=diagnostics/final-consumer-regressions.xml" - User time (seconds): 0.35 - System time (seconds): 0.03 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.39 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 38912 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 6759 - Voluntary context switches: 1 - Involuntary context switches: 4 - Swaps: 0 - File system inputs: 0 - File system outputs: 64 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 4 diff --git a/diagnostics/final-consumer-regressions.xml b/diagnostics/final-consumer-regressions.xml deleted file mode 100644 index 8565e6dd58..0000000000 --- a/diagnostics/final-consumer-regressions.xml +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/diagnostics/final-owned-families.log b/diagnostics/final-owned-families.log deleted file mode 100644 index ff3ee40c69..0000000000 --- a/diagnostics/final-owned-families.log +++ /dev/null @@ -1,42 +0,0 @@ -Running as unit: run-p838608-i13388825.scope; invocation ID: a3cf34b0738f4facbc377db3be07d38e -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -........................................................................ [ 65%] -...................................... [100%] -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/final-owned-families.xml - -110 passed, 2 warnings in 3.38s - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/final-owned-families.xml" - User time (seconds): 3.81 - System time (seconds): 0.28 - Percent of CPU this job got: 97% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.19 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 322736 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 111 - Minor (reclaiming a frame) page faults: 52085 - Voluntary context switches: 203 - Involuntary context switches: 24 - Swaps: 0 - File system inputs: 5952 - File system outputs: 248 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/diagnostics/final-owned-families.xml b/diagnostics/final-owned-families.xml deleted file mode 100644 index 6539aa7bd3..0000000000 --- a/diagnostics/final-owned-families.xml +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/diagnostics/first-repair.log b/diagnostics/first-repair.log deleted file mode 100644 index aa0667118c..0000000000 --- a/diagnostics/first-repair.log +++ /dev/null @@ -1,92 +0,0 @@ -Running as unit: run-p804421-i13390833.scope; invocation ID: 4407f7635b2d4259b50ccbc37953c19d -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -F................................ [100%] -=================================== FAILURES =================================== -______ test_real_rescale_full_stack_materializes_composed_runtime_sources ______ - - def test_real_rescale_full_stack_materializes_composed_runtime_sources(): - data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) - source = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE - ).payload_with(data, None) - composition = compose_aligned_image_payload("synthetic source inputs", (source, source)) - assert isinstance(composition.payload, AlignedImageStack) - contract = CallableContract.from_callable(rescale_intensity) -> result = CellProfilerFunctionContractExecutor().execute( - contract, - contract.resolve_canonical_raw_callable(), - composition.payload, - {}, - execution_mode=contract.runtime_image_execution_mode, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:28: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:894: in full_stack_value - return RuntimeSliceProjectionStrategy.strategy_for_value(value).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:436: in compose - source_metadata=self.composition_source_metadata(), -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - ...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) - - def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: - """Inner image bundles contribute provenance, not an outer slice axis.""" - return tuple( - metadata.with_source_provenance( - metadata.source_provenance.with_runtime_planes_as_contributors() - ) -> for metadata in super().composition_source_metadata() - ) -E TypeError: super(type, obj): obj must be an instance or subtype of type - -openhcs/core/aligned_image_payload.py:1120: TypeError -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/first-repair.xml - -=========================== short test summary info ============================ -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_real_rescale_full_stack_materializes_composed_runtime_sources -1 failed, 32 passed, 2 warnings in 2.90s -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/first-repair.xml" - User time (seconds): 3.07 - System time (seconds): 0.28 - Percent of CPU this job got: 87% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.82 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 308204 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 1 - Minor (reclaiming a frame) page faults: 49335 - Voluntary context switches: 4 - Involuntary context switches: 201 - Swaps: 0 - File system inputs: 8 - File system outputs: 224 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/first-repair.xml b/diagnostics/first-repair.xml deleted file mode 100644 index 1f20183a9b..0000000000 --- a/diagnostics/first-repair.xml +++ /dev/null @@ -1,45 +0,0 @@ -def test_real_rescale_full_stack_materializes_composed_runtime_sources(): - data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) - source = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE - ).payload_with(data, None) - composition = compose_aligned_image_payload("synthetic source inputs", (source, source)) - assert isinstance(composition.payload, AlignedImageStack) - contract = CallableContract.from_callable(rescale_intensity) -> result = CellProfilerFunctionContractExecutor().execute( - contract, - contract.resolve_canonical_raw_callable(), - composition.payload, - {}, - execution_mode=contract.runtime_image_execution_mode, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:28: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:148: in execute - result = executor.execute_pure_3d( -openhcs/interop/cellprofiler/runtime/function_contract_execution.py:308: in execute_pure_3d - projected_image = RuntimeSliceProjection.full_stack_value(image) -openhcs/core/runtime_slice_projection.py:894: in full_stack_value - return RuntimeSliceProjectionStrategy.strategy_for_value(value).full_stack_value(value) -openhcs/core/runtime_slice_projection.py:514: in full_stack_value - return cast(AlignedImageStack, value).compose() -openhcs/core/aligned_image_payload.py:436: in compose - source_metadata=self.composition_source_metadata(), -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -self = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - ...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) - - def composition_source_metadata(self) -> tuple[ImagePayloadMetadata, ...]: - """Inner image bundles contribute provenance, not an outer slice axis.""" - return tuple( - metadata.with_source_provenance( - metadata.source_provenance.with_runtime_planes_as_contributors() - ) -> for metadata in super().composition_source_metadata() - ) -E TypeError: super(type, obj): obj must be an instance or subtype of type - -openhcs/core/aligned_image_payload.py:1120: TypeError \ No newline at end of file diff --git a/diagnostics/frozen-executor-reproducer.log b/diagnostics/frozen-executor-reproducer.log deleted file mode 100644 index 4323af0c9e..0000000000 --- a/diagnostics/frozen-executor-reproducer.log +++ /dev/null @@ -1,110 +0,0 @@ -Running as unit: run-p821979-i13439347.scope; invocation ID: 74faa71f68444ca39ef75065ca49c1ed -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -baseline executor ref: 20ca4f825 -F [100%] -=================================== FAILURES =================================== -______ test_real_rescale_full_stack_materializes_composed_runtime_sources ______ - - def test_real_rescale_full_stack_materializes_composed_runtime_sources(): - data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) - source = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE - ).payload_with(data, None) - composition = compose_aligned_image_payload( - "synthetic source inputs", (source, source) - ) - assert isinstance(composition.payload, AlignedImageStack) - contract = CallableContract.from_callable(rescale_intensity) -> result = CellProfilerFunctionContractExecutor().execute( - contract, - contract.resolve_canonical_raw_callable(), - composition.payload, - {}, - execution_mode=contract.runtime_image_execution_mode, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:47: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -git:20ca4f825:function_contract_execution.py:148: in execute - ??? -git:20ca4f825:function_contract_execution.py:330: in execute_pure_3d - ??? -openhcs/processing/backends/lib_registry/unified_registry.py:263: in call - return target( -openhcs/processing/backends/cellprofiler/intensity.py:1877: in rescale_intensity - context = RescaleIntensityContext.from_settings( -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -cls = -image = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - ...r=None, source_channel_axis=None, plane_axis=))), slice_contexts=()) - - @classmethod - def from_settings( - cls, - image: np.ndarray, - *, - automatic_low: AutomaticLow, - automatic_high: AutomaticHigh, - source_low: float, - source_high: float, - dest_low: float, - dest_high: float, - divisor_value: float, - ) -> "RescaleIntensityContext": - source_data = np.asarray(image_payload_data(image)) - return cls( -> data=source_data.astype(np.float32, copy=False), - automatic_low=coerce_cellprofiler_enum(AutomaticLow, automatic_low), - automatic_high=coerce_cellprofiler_enum(AutomaticHigh, automatic_high), - source_low=source_low, - source_high=source_high, - dest_low=dest_low, - dest_high=dest_high, - divisor_value=divisor_value, - ) -E TypeError: float() argument must be a string or a real number, not 'AlignedImageStack' - -openhcs/processing/backends/cellprofiler/intensity.py:1712: TypeError -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/frozen-executor-reproducer.xml - -=========================== short test summary info ============================ -FAILED tests/unit/test_cellprofiler_full_stack_materialization.py::test_real_rescale_full_stack_materializes_composed_runtime_sources -1 failed, 13 deselected, 2 warnings in 0.73s -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py -k real_rescale --junitxml=diagnostics/frozen-executor-reproducer.xml" - User time (seconds): 2.45 - System time (seconds): 0.21 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.68 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 285564 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 41894 - Voluntary context switches: 10 - Involuntary context switches: 25 - Swaps: 0 - File system inputs: 0 - File system outputs: 64 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/frozen-executor-reproducer.xml b/diagnostics/frozen-executor-reproducer.xml deleted file mode 100644 index b4756bf2a3..0000000000 --- a/diagnostics/frozen-executor-reproducer.xml +++ /dev/null @@ -1,62 +0,0 @@ -def test_real_rescale_full_stack_materializes_composed_runtime_sources(): - data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) - source = ImagePayloadMetadata( - plane_axis=RuntimePlaneAxis.RUNTIME_SLICE - ).payload_with(data, None) - composition = compose_aligned_image_payload( - "synthetic source inputs", (source, source) - ) - assert isinstance(composition.payload, AlignedImageStack) - contract = CallableContract.from_callable(rescale_intensity) -> result = CellProfilerFunctionContractExecutor().execute( - contract, - contract.resolve_canonical_raw_callable(), - composition.payload, - {}, - execution_mode=contract.runtime_image_execution_mode, - ) - -tests/unit/test_cellprofiler_full_stack_materialization.py:47: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -git:20ca4f825:function_contract_execution.py:148: in execute - ??? -git:20ca4f825:function_contract_execution.py:330: in execute_pure_3d - ??? -openhcs/processing/backends/lib_registry/unified_registry.py:263: in call - return target( -openhcs/processing/backends/cellprofiler/intensity.py:1877: in rescale_intensity - context = RescaleIntensityContext.from_settings( -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -cls = <class 'openhcs.processing.backends.cellprofiler.intensity.RescaleIntensityContext'> -image = AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1., 2., 3.], - [ 4., 5., 6., 7.], - ...r=None, source_channel_axis=None, plane_axis=<RuntimePlaneAxis.SOURCE_BINDING: 'source_binding'>))), slice_contexts=()) - - @classmethod - def from_settings( - cls, - image: np.ndarray, - *, - automatic_low: AutomaticLow, - automatic_high: AutomaticHigh, - source_low: float, - source_high: float, - dest_low: float, - dest_high: float, - divisor_value: float, - ) -> "RescaleIntensityContext": - source_data = np.asarray(image_payload_data(image)) - return cls( -> data=source_data.astype(np.float32, copy=False), - automatic_low=coerce_cellprofiler_enum(AutomaticLow, automatic_low), - automatic_high=coerce_cellprofiler_enum(AutomaticHigh, automatic_high), - source_low=source_low, - source_high=source_high, - dest_low=dest_low, - dest_high=dest_high, - divisor_value=divisor_value, - ) -E TypeError: float() argument must be a string or a real number, not 'AlignedImageStack' - -openhcs/processing/backends/cellprofiler/intensity.py:1712: TypeError \ No newline at end of file diff --git a/diagnostics/nra-before-corrected.json b/diagnostics/nra-before-corrected.json deleted file mode 100644 index 9ded6e5b8a..0000000000 --- a/diagnostics/nra-before-corrected.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "findings": [], - "plans": [], - "finding_payload_mode": "deadline_incomplete", - "finding_count": null, - "finding_counts": null, - "scan_status": { - "complete": false, - "deadline_exceeded": true, - "stage": "parse_python_module", - "budget_seconds": 20.0, - "elapsed_seconds": 20.0 - } -} diff --git a/diagnostics/nra-before-corrected.stderr b/diagnostics/nra-before-corrected.stderr deleted file mode 100644 index b6fdba5c32..0000000000 --- a/diagnostics/nra-before-corrected.stderr +++ /dev/null @@ -1,25 +0,0 @@ -Running as unit: run-p794985-i13374683.scope; invocation ID: 08466ebbae644e88a01df4ae29b65c99 -Command exited with non-zero status 124 - Command being timed: "/home/ts/code/projects/nominal-refactor-advisor/.venv/bin/python -m nominal_refactor_advisor openhcs --context-root openhcs --context-root /home/ts/wt/openhcs-s1-installed-parent-20261001/external --json --raw-findings --json-payload full --parse-workers 1 --analysis-workers 1 --no-cache" - User time (seconds): 20.20 - System time (seconds): 0.50 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:20.89 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 511664 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 174621 - Voluntary context switches: 152 - Involuntary context switches: 147 - Swaps: 0 - File system inputs: 9896 - File system outputs: 8 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 124 diff --git a/diagnostics/nra-before.json b/diagnostics/nra-before.json deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/diagnostics/nra-before.stderr b/diagnostics/nra-before.stderr deleted file mode 100644 index 44e390c0e3..0000000000 --- a/diagnostics/nra-before.stderr +++ /dev/null @@ -1,63 +0,0 @@ -Running as unit: run-p792461-i13332203.scope; invocation ID: 4284e2fc31094171b2b323910bad8990 -Traceback (most recent call last): - File "", line 198, in _run_module_as_main - File "", line 88, in _run_code - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/__main__.py", line 4, in - raise SystemExit(process_main()) - ^^^^^^^^^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cli.py", line 4270, in process_main - return main(hard_exit_on_deadline=True) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/ts/.local/share/uv/python/cpython-3.11-linux-x86_64-gnu/lib/python3.11/contextlib.py", line 81, in inner - return func(*args, **kwds) - ^^^^^^^^^^^^^^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cli.py", line 4259, in main - return _main_without_deadline(invocation) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cli.py", line 3974, in _main_without_deadline - analysis_result = analyze_modules_with_cache( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/ts/.local/share/uv/python/cpython-3.11-linux-x86_64-gnu/lib/python3.11/contextlib.py", line 81, in inner - return func(*args, **kwds) - ^^^^^^^^^^^^^^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/analysis.py", line 3650, in analyze_modules_with_cache - focused_cache_identity = AnalysisCacheIdentity.from_modules( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/analysis_cache.py", line 875, in from_modules - report_filter_roots=tuple( - ^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/analysis_cache.py", line 876, in - checkout_relative_path(report_root, roots) - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cache_checkout.py", line 115, in checkout_relative_path - return _admitted_checkout_path(lexical_path, observed_roots) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/scan_cache.py", line 45, in invoke - return implementation(*args, **kwargs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/cache_checkout.py", line 49, in _admitted_checkout_path - raise CacheCheckoutPathError(f"{candidate} {reason}") -nominal_refactor_advisor.cache_checkout.CacheCheckoutPathError: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/openhcs outside every admitted root -Command exited with non-zero status 1 - Command being timed: "/home/ts/code/projects/nominal-refactor-advisor/.venv/bin/python -m nominal_refactor_advisor openhcs --context-root /home/ts/wt/basicpy-live-candidate-20260930/external --json --raw-findings --json-payload full --parse-workers 1 --analysis-workers 1 --no-cache" - User time (seconds): 0.88 - System time (seconds): 0.05 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.95 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 60700 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 13017 - Voluntary context switches: 15 - Involuntary context switches: 5 - Swaps: 0 - File system inputs: 712 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/projection-regressions.log b/diagnostics/projection-regressions.log deleted file mode 100644 index 4de8a91f29..0000000000 --- a/diagnostics/projection-regressions.log +++ /dev/null @@ -1,41 +0,0 @@ -Running as unit: run-p819450-i13391801.scope; invocation ID: 859dae61a656455aa2257a2a2ffa55eb -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -................................................................ [100%] -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/projection-regressions.xml - -64 passed, 2 warnings in 2.41s - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_runtime_slice_projection.py tests/unit/test_runtime_image_singleton_alignment.py tests/unit/test_aligned_main_flow_projection.py tests/unit/test_aligned_output_projection.py tests/unit/test_aligned_image_payload_device.py tests/unit/test_aligned_image_payload_registry.py --junitxml=diagnostics/projection-regressions.xml" - User time (seconds): 2.81 - System time (seconds): 0.21 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.04 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 188736 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 3 - Minor (reclaiming a frame) page faults: 36351 - Voluntary context switches: 5 - Involuntary context switches: 22 - Swaps: 0 - File system inputs: 416 - File system outputs: 840 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/diagnostics/projection-regressions.xml b/diagnostics/projection-regressions.xml deleted file mode 100644 index 6a19a910cd..0000000000 --- a/diagnostics/projection-regressions.xml +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/diagnostics/provenance-contract-regressions.log b/diagnostics/provenance-contract-regressions.log deleted file mode 100644 index fc04e26f5a..0000000000 --- a/diagnostics/provenance-contract-regressions.log +++ /dev/null @@ -1,119 +0,0 @@ -Running as unit: run-p822498-i13407678.scope; invocation ID: 8d17818f726c465ca717574fa79a0469 -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -.................................F........... [100%] -=================================== FAILURES =================================== -________ test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots _________ - - def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: - source = ArtifactSpec.input("Input", ImageArtifactType) - measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) - labels = ArtifactSpec.output( - "Objects", - ObjectLabelsArtifactType, - relations=(GroupLineageSourceRelation(source=source.ref()),), - ) - - for func in (identify_primary_objects, watershed_cellprofiler4): - contract = _contract(func, (source,)) - contract = replace( - contract, - metadata=replace( - contract.metadata, - artifact_outputs=(measurements, labels), - ), - ) - -> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) - -tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -cls = -func = -contract = CallableContract(func=, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) - - @classmethod - def validate_callable_artifact_abi( - cls, - func: "Callable[..., RuntimeFunctionOutput]", - contract: CallableContract, - ) -> None: - """Validate one raw callable ABI against its callable artifact declarations.""" - - from openhcs.core.aligned_image_payload import AlignedImageStack - - module_name = contract.module_name - if not isinstance(module_name, str) or not module_name: - raise ValueError("CellProfiler callable contract requires a module name.") - declared_outputs = contract.artifact_outputs - invalid_source_context_outputs = tuple( - (spec.ref(), sources) - for spec in declared_outputs - for sources in (spec.source_context_sources(),) - if spec.artifact_type.carries_source_image_context and len(sources) != 1 - ) - if invalid_source_context_outputs: - raise ValueError( - f"CellProfiler module {module_name!r} image/object outputs " - "must declare exactly one runtime-context source: " - f"{invalid_source_context_outputs!r}." - ) - return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) - return_variants = _callable_return_slot_variants(return_annotation) - canonical_outputs = contract.canonical_return_output_specs - trailing_outputs = contract.trailing_return_output_specs - expected_slot_count = len(trailing_outputs) + 1 - matching_variants = tuple( - slots for slots in return_variants if len(slots) == expected_slot_count - ) - if not matching_variants: -> raise ValueError( - f"callable {func.__name__!r} return annotation " - f"{return_annotation!r} does not declare the canonical return " - f"followed by exactly {len(trailing_outputs)} trailing " - "artifact-output slot(s)." - ) -E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). - -openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/provenance-contract-regressions.xml - -=========================== short test summary info ============================ -FAILED tests/unit/test_cellprofiler_runtime_input_binding_contract.py::test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots -1 failed, 44 passed, 2 warnings in 4.71s -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_source_image_provenance.py tests/unit/test_source_image_provenance_hotpath.py tests/unit/test_derived_runtime_image_provenance.py tests/unit/test_cellprofiler_runtime_input_binding_contract.py tests/unit/test_cellprofiler_artifact_activation_identity.py --junitxml=diagnostics/provenance-contract-regressions.xml" - User time (seconds): 5.63 - System time (seconds): 0.36 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.05 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 380652 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 8 - Minor (reclaiming a frame) page faults: 60960 - Voluntary context switches: 22 - Involuntary context switches: 36 - Swaps: 0 - File system inputs: 408 - File system outputs: 6080 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/provenance-contract-regressions.xml b/diagnostics/provenance-contract-regressions.xml deleted file mode 100644 index 221abefabe..0000000000 --- a/diagnostics/provenance-contract-regressions.xml +++ /dev/null @@ -1,72 +0,0 @@ -def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: - source = ArtifactSpec.input("Input", ImageArtifactType) - measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) - labels = ArtifactSpec.output( - "Objects", - ObjectLabelsArtifactType, - relations=(GroupLineageSourceRelation(source=source.ref()),), - ) - - for func in (identify_primary_objects, watershed_cellprofiler4): - contract = _contract(func, (source,)) - contract = replace( - contract, - metadata=replace( - contract.metadata, - artifact_outputs=(measurements, labels), - ), - ) - -> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) - -tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -cls = <class 'openhcs.interop.cellprofiler.module_callable_abi.CellProfilerModuleCallableABI'> -func = <function identify_primary_objects at 0x7f8f189c6ca0> -contract = CallableContract(func=<function identify_primary_objects at 0x7f8f189c6ca0>, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) - - @classmethod - def validate_callable_artifact_abi( - cls, - func: "Callable[..., RuntimeFunctionOutput]", - contract: CallableContract, - ) -> None: - """Validate one raw callable ABI against its callable artifact declarations.""" - - from openhcs.core.aligned_image_payload import AlignedImageStack - - module_name = contract.module_name - if not isinstance(module_name, str) or not module_name: - raise ValueError("CellProfiler callable contract requires a module name.") - declared_outputs = contract.artifact_outputs - invalid_source_context_outputs = tuple( - (spec.ref(), sources) - for spec in declared_outputs - for sources in (spec.source_context_sources(),) - if spec.artifact_type.carries_source_image_context and len(sources) != 1 - ) - if invalid_source_context_outputs: - raise ValueError( - f"CellProfiler module {module_name!r} image/object outputs " - "must declare exactly one runtime-context source: " - f"{invalid_source_context_outputs!r}." - ) - return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) - return_variants = _callable_return_slot_variants(return_annotation) - canonical_outputs = contract.canonical_return_output_specs - trailing_outputs = contract.trailing_return_output_specs - expected_slot_count = len(trailing_outputs) + 1 - matching_variants = tuple( - slots for slots in return_variants if len(slots) == expected_slot_count - ) - if not matching_variants: -> raise ValueError( - f"callable {func.__name__!r} return annotation " - f"{return_annotation!r} does not declare the canonical return " - f"followed by exactly {len(trailing_outputs)} trailing " - "artifact-output slot(s)." - ) -E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). - -openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError \ No newline at end of file diff --git a/diagnostics/r0-original-openhcs-corrected.log b/diagnostics/r0-original-openhcs-corrected.log deleted file mode 100644 index db078eb908..0000000000 --- a/diagnostics/r0-original-openhcs-corrected.log +++ /dev/null @@ -1,46 +0,0 @@ -Running as unit: run-p843977-i13393447.scope; invocation ID: 26cbfff711a7439688ae2c34822627f3 -Traceback (most recent call last): - File "", line 189, in _run_module_as_main - File "", line 112, in _get_module_details - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/__init__.py", line 5, in - from .exporting import ( - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/exporting.py", line 25, in - from .registration import Registration - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/registration.py", line 15, in - from .native_input_owner import RegistryOwner - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/native_input_owner.py", line 19, in - from .native_admission_rules import ( - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/native_admission_rules.py", line 11, in - from .reservation_rules import ReservationRule, RuleCheck - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/reservation_rules.py", line 12, in - from .selected_source import SelectedAdmissionSource, SelectedSource, SessionRevision - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/selected_source.py", line 20, in - class SelectedSource(DeclaredFamily, affix="Source"): - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/selected_source.py", line 36, in SelectedSource - def original_has_started(self, inputs: InputDocument) -> bool: - ^^^^^^^^^^^^^ -NameError: name 'InputDocument' is not defined -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python -m agent_comms.debt_ratchet --root openhcs --base 0c0563e6538af313345391f2dc314270a86933a0 --head 63ad7c652" - User time (seconds): 0.45 - System time (seconds): 0.04 - Percent of CPU this job got: 94% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.52 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 32640 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 6 - Minor (reclaiming a frame) page faults: 5634 - Voluntary context switches: 78 - Involuntary context switches: 6 - Swaps: 0 - File system inputs: 1520 - File system outputs: 2096 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/r0-original-openhcs-python314.log b/diagnostics/r0-original-openhcs-python314.log deleted file mode 100644 index 33c0f6ab59..0000000000 --- a/diagnostics/r0-original-openhcs-python314.log +++ /dev/null @@ -1,15526 +0,0 @@ -Running as unit: run-p845111-i13413035.scope; invocation ID: ade2bc6f9ef4420b86725990f6944c9d -{ - "root": "openhcs/", - "base_revision": "0c0563e6538af313345391f2dc314270a86933a0", - "head_revision": "63ad7c65296c109e51700ab6213a40d617fe469b", - "paths": [ - "openhcs/core/aligned_image_payload.py", - "openhcs/core/runtime_slice_projection.py", - "openhcs/interop/cellprofiler/runtime/function_contract_execution.py" - ], - "base": { - "StringDispatch:openhcs/core/aligned_image_payload.py": 0, - "StringDispatch:openhcs/core/runtime_slice_projection.py": 0, - "StringDispatch:openhcs/interop/cellprofiler/runtime/function_contract_execution.py": 0, - "TypeSwitch:openhcs/core/aligned_image_payload.py": 1, - "TypeSwitch:openhcs/core/runtime_slice_projection.py": 0, - "TypeSwitch:openhcs/interop/cellprofiler/runtime/function_contract_execution.py": 0, - "StringDispatchArms:openhcs/core/aligned_image_payload.py": 0, - "StringDispatchArms:openhcs/core/runtime_slice_projection.py": 0, - "StringDispatchArms:openhcs/interop/cellprofiler/runtime/function_contract_execution.py": 0, - "TypeSwitchArms:openhcs/core/aligned_image_payload.py": 4, - "TypeSwitchArms:openhcs/core/runtime_slice_projection.py": 0, - "TypeSwitchArms:openhcs/interop/cellprofiler/runtime/function_contract_execution.py": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::AuthoringContextRoute": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::AuthoringContextDeclaration": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::PipelineSystemModelContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::CellProfilerTranslationContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::RuntimeUiCoordinationContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::StateCodeRoundtripContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::CustomFunctionRuntimeContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::SourceBindingWorkflowContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::ExampleCorpusContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::PipelineAuthoringRulesContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::ImageAnalysisWorkflowContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::CustomFunctionAuthoringRulesContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::FirstUseWorkflowContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::FolderOnboardingContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::DomainExpertAssistedSetupContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::UiVisibleWorkflowContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::HeadlessExecutionContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::DebuggingWorkflowContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::ViewerReviewContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::ObjectStateEditingContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::FirstUseAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::UiVisibleWorkflowAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::DomainExpertAssistedSetupAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::FolderOnboardingAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::PipelineAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::ImageAnalysisWorkflowAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::CustomFunctionAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::HeadlessExecutionAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::DebuggingAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::ViewerReviewAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::ObjectStateEditingAuthoringContext": 0, - "GodClassExcess:openhcs/agent/authoring_contexts.py::CellProfilerTranslationAuthoringContext": 0, - "GodClassExcess:openhcs/agent/blind_recipe_audit.py::ReviewDecision": 0, - 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Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/diagnostics/r0-original-openhcs.log b/diagnostics/r0-original-openhcs.log deleted file mode 100644 index 71c5f84749..0000000000 --- a/diagnostics/r0-original-openhcs.log +++ /dev/null @@ -1,42 +0,0 @@ -Running as unit: run-p842680-i13393374.scope; invocation ID: 5131522ed8314e50b3c859baabb28a67 -Traceback (most recent call last): - File "", line 189, in _run_module_as_main - File "", line 112, in _get_module_details - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/__init__.py", line 5, in - from .exporting import ( - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/exporting.py", line 20, in - from .catalog_store import ChannelCatalog - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/catalog_store.py", line 11, in - from .catalog_document import CatalogDocument - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/catalog_document.py", line 10, in - from .channels import Channel, SavedView, ViewPredicate - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/channels.py", line 11, in - from .declared_family import DeclaredFamily - File "/home/ts/.cache/uv/archive-v0/E-EBIFdHrL_Wo3vh/agent_comms/declared_family.py", line 9, in - from metaclass_registry import AutoRegisterMeta, RegistryConfig # type: ignore[import-untyped] - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -ModuleNotFoundError: No module named 'metaclass_registry' -Command exited with non-zero status 1 - Command being timed: "/home/ts/.agent-comms/.venv/bin/python -m agent_comms.debt_ratchet --root openhcs --base 0c0563e6538af313345391f2dc314270a86933a0 --head 63ad7c652" - User time (seconds): 0.04 - System time (seconds): 0.01 - Percent of CPU this job got: 90% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.06 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 21796 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 2829 - Voluntary context switches: 17 - Involuntary context switches: 0 - Swaps: 0 - File system inputs: 432 - File system outputs: 248 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/r1-original.log b/diagnostics/r1-original.log deleted file mode 100644 index 3d52d157b0..0000000000 --- a/diagnostics/r1-original.log +++ /dev/null @@ -1,31 +0,0 @@ -Running as unit: run-p845313-i13401382.scope; invocation ID: 9876ef16563241b4bd80f95bc95374fd -Traceback (most recent call last): - File "", line 198, in _run_module_as_main - File "", line 88, in _run_code - File "/home/ts/wt/openhcs-cp-aligned-materialization-20261001/scripts/check_refactor_r1.py", line 27, in - from nominal_refactor_advisor.detectors import ( -ImportError: cannot import name 'RedundantTypeCheckDetector' from 'nominal_refactor_advisor.detectors' (/home/ts/code/projects/nominal-refactor-advisor/nominal_refactor_advisor/detectors/__init__.py) -Command exited with non-zero status 1 - Command being timed: "/home/ts/code/projects/nominal-refactor-advisor/.venv/bin/python -m scripts.check_refactor_r1 --base 0c0563e6538af313345391f2dc314270a86933a0 --head 63ad7c652 --scratch-root /home/ts/.cache/agent-scratch/h003g-runtime-repair-r1-20261001 --budget-seconds 60" - User time (seconds): 1.10 - System time (seconds): 0.06 - Percent of CPU this job got: 48% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.37 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 61004 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 13061 - Voluntary context switches: 100 - Involuntary context switches: 428 - Swaps: 0 - File system inputs: 2000 - File system outputs: 40 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/unchanged-main-abi-fixture.log b/diagnostics/unchanged-main-abi-fixture.log deleted file mode 100644 index bd3159ab95..0000000000 --- a/diagnostics/unchanged-main-abi-fixture.log +++ /dev/null @@ -1,114 +0,0 @@ -Running as unit: run-p826798-i13431838.scope; invocation ID: 30883a82c95d448b9b09644ea8306b6d -source root: /home/ts/.cache/agent-scratch/h003g-runtime-repair-baseline-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -F [100%] -=================================== FAILURES =================================== -________ test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots _________ - - def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: - source = ArtifactSpec.input("Input", ImageArtifactType) - measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) - labels = ArtifactSpec.output( - "Objects", - ObjectLabelsArtifactType, - relations=(GroupLineageSourceRelation(source=source.ref()),), - ) - - for func in (identify_primary_objects, watershed_cellprofiler4): - contract = _contract(func, (source,)) - contract = replace( - contract, - metadata=replace( - contract.metadata, - artifact_outputs=(measurements, labels), - ), - ) - -> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) - -../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -cls = -func = -contract = CallableContract(func=, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) - - @classmethod - def validate_callable_artifact_abi( - cls, - func: "Callable[..., RuntimeFunctionOutput]", - contract: CallableContract, - ) -> None: - """Validate one raw callable ABI against its callable artifact declarations.""" - - from openhcs.core.aligned_image_payload import AlignedImageStack - - module_name = contract.module_name - if not isinstance(module_name, str) or not module_name: - raise ValueError("CellProfiler callable contract requires a module name.") - declared_outputs = contract.artifact_outputs - invalid_source_context_outputs = tuple( - (spec.ref(), sources) - for spec in declared_outputs - for sources in (spec.source_context_sources(),) - if spec.artifact_type.carries_source_image_context and len(sources) != 1 - ) - if invalid_source_context_outputs: - raise ValueError( - f"CellProfiler module {module_name!r} image/object outputs " - "must declare exactly one runtime-context source: " - f"{invalid_source_context_outputs!r}." - ) - return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) - return_variants = _callable_return_slot_variants(return_annotation) - canonical_outputs = contract.canonical_return_output_specs - trailing_outputs = contract.trailing_return_output_specs - expected_slot_count = len(trailing_outputs) + 1 - matching_variants = tuple( - slots for slots in return_variants if len(slots) == expected_slot_count - ) - if not matching_variants: -> raise ValueError( - f"callable {func.__name__!r} return annotation " - f"{return_annotation!r} does not declare the canonical return " - f"followed by exactly {len(trailing_outputs)} trailing " - "artifact-output slot(s)." - ) -E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). - -../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError -=============================== warnings summary =============================== -../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/processing/backends/numpy_runtime.py:7 -../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/processing/backends/numpy_runtime.py:7 - /home/ts/.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/processing/backends/numpy_runtime.py:7: DeprecationWarning: numpy.core is deprecated and has been renamed to numpy._core. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core._multiarray_umath. - from numpy.core import _multiarray_umath - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/unchanged-main-abi-fixture.xml - -=========================== short test summary info ============================ -FAILED ../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py::test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots -1 failed, 11 deselected, 2 warnings in 9.61s -Command exited with non-zero status 1 - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q /home/ts/.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py -k callable_abi_keeps --junitxml=diagnostics/unchanged-main-abi-fixture.xml" - User time (seconds): 5.98 - System time (seconds): 0.37 - Percent of CPU this job got: 55% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:11.39 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 381476 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 9 - Minor (reclaiming a frame) page faults: 62873 - Voluntary context switches: 11 - Involuntary context switches: 1930 - Swaps: 0 - File system inputs: 248 - File system outputs: 20968 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 1 diff --git a/diagnostics/unchanged-main-abi-fixture.xml b/diagnostics/unchanged-main-abi-fixture.xml deleted file mode 100644 index d4baf63bfb..0000000000 --- a/diagnostics/unchanged-main-abi-fixture.xml +++ /dev/null @@ -1,72 +0,0 @@ -def test_callable_abi_keeps_main_flow_artifacts_in_trailing_slots() -> None: - source = ArtifactSpec.input("Input", ImageArtifactType) - measurements = ArtifactSpec.output("Measurements", MeasurementsArtifactType) - labels = ArtifactSpec.output( - "Objects", - ObjectLabelsArtifactType, - relations=(GroupLineageSourceRelation(source=source.ref()),), - ) - - for func in (identify_primary_objects, watershed_cellprofiler4): - contract = _contract(func, (source,)) - contract = replace( - contract, - metadata=replace( - contract.metadata, - artifact_outputs=(measurements, labels), - ), - ) - -> CellProfilerModuleCallableABI.validate_callable_artifact_abi(func, contract) - -../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/tests/unit/test_cellprofiler_runtime_input_binding_contract.py:675: -_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - -cls = <class 'openhcs.interop.cellprofiler.module_callable_abi.CellProfilerModuleCallableABI'> -func = <function identify_primary_objects at 0x7f8de0a260c0> -contract = CallableContract(func=<function identify_primary_objects at 0x7f8de0a260c0>, function_name='identify_primary_objects',...imary_image_carrier_requirement=None, primary_image_carrier_transition=None), runtime_batch_executors=mappingproxy({})) - - @classmethod - def validate_callable_artifact_abi( - cls, - func: "Callable[..., RuntimeFunctionOutput]", - contract: CallableContract, - ) -> None: - """Validate one raw callable ABI against its callable artifact declarations.""" - - from openhcs.core.aligned_image_payload import AlignedImageStack - - module_name = contract.module_name - if not isinstance(module_name, str) or not module_name: - raise ValueError("CellProfiler callable contract requires a module name.") - declared_outputs = contract.artifact_outputs - invalid_source_context_outputs = tuple( - (spec.ref(), sources) - for spec in declared_outputs - for sources in (spec.source_context_sources(),) - if spec.artifact_type.carries_source_image_context and len(sources) != 1 - ) - if invalid_source_context_outputs: - raise ValueError( - f"CellProfiler module {module_name!r} image/object outputs " - "must declare exactly one runtime-context source: " - f"{invalid_source_context_outputs!r}." - ) - return_annotation = get_type_hints(func).get("return", inspect.Signature.empty) - return_variants = _callable_return_slot_variants(return_annotation) - canonical_outputs = contract.canonical_return_output_specs - trailing_outputs = contract.trailing_return_output_specs - expected_slot_count = len(trailing_outputs) + 1 - matching_variants = tuple( - slots for slots in return_variants if len(slots) == expected_slot_count - ) - if not matching_variants: -> raise ValueError( - f"callable {func.__name__!r} return annotation " - f"{return_annotation!r} does not declare the canonical return " - f"followed by exactly {len(trailing_outputs)} trailing " - "artifact-output slot(s)." - ) -E ValueError: callable 'identify_primary_objects' return annotation typing.Tuple[numpy.ndarray, openhcs.core.measurement_row_materialization.DataclassMeasurementColumnarRows, openhcs.core.runtime_object_labels.ObjectLabelPayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload, openhcs.core.runtime_image_values.MaskedImagePayload] does not declare the canonical return followed by exactly 2 trailing artifact-output slot(s). - -../../.cache/agent-scratch/h003g-runtime-repair-baseline-20261001/openhcs/interop/cellprofiler/module_callable_abi.py:300: ValueError \ No newline at end of file diff --git a/diagnostics/working-checkpoint.log b/diagnostics/working-checkpoint.log deleted file mode 100644 index ae0b3c936b..0000000000 --- a/diagnostics/working-checkpoint.log +++ /dev/null @@ -1,41 +0,0 @@ -Running as unit: run-p805711-i13394976.scope; invocation ID: b8f7aae1cfb94e84886989021e81dbf8 -source root: /home/ts/wt/openhcs-cp-aligned-materialization-20261001 -native artifact: /home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/_tabular_native.abi3.so -................................. [100%] -=============================== warnings summary =============================== -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - -../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441 - /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode - - self._warn_or_fail_if_strict(f"Unknown config option: {key}\n") - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -- generated xml file: /home/ts/wt/openhcs-cp-aligned-materialization-20261001/diagnostics/working-checkpoint.xml - -33 passed, 2 warnings in 2.35s - Command being timed: "/home/ts/wt/openhcs-s1-installed-parent-20261001/.venv/bin/python diagnostics/run_source_tests.py -q tests/unit/test_cellprofiler_full_stack_materialization.py tests/unit/test_cellprofiler_function_contract_execution.py --junitxml=diagnostics/working-checkpoint.xml" - User time (seconds): 2.81 - System time (seconds): 0.24 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.08 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 305672 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 1 - Minor (reclaiming a frame) page faults: 48253 - Voluntary context switches: 3 - Involuntary context switches: 20 - Swaps: 0 - File system inputs: 8 - File system outputs: 312 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/diagnostics/working-checkpoint.xml b/diagnostics/working-checkpoint.xml deleted file mode 100644 index 0e9f5b00b8..0000000000 --- a/diagnostics/working-checkpoint.xml +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/docs/refactor/cp-aligned-full-stack-342.rst b/docs/refactor/cp-aligned-full-stack-342.rst index 71a00281ba..0b88b01ace 100644 --- a/docs/refactor/cp-aligned-full-stack-342.rst +++ b/docs/refactor/cp-aligned-full-stack-342.rst @@ -125,7 +125,7 @@ Disposable baseline source snapshot: owner H003g runtime repair worker, purpose unchanged-main fixture control. It contains no scientific data and is recoverable from Git; logs are retained here before removing that owned scratch. -Remaining gate: original structural/R1 guard disposition, parent integration +Remaining gate: original R1 environment disposition, parent integration and scheduled fresh installed entrypoint acceptance with synthetic inputs. This source checkpoint is not live readiness or biological success. H003g stays FAILED and is not a validation dataset for this repair. @@ -146,3 +146,46 @@ uninitialized, so full-context source materialization is not yet qualified. No detector substitution, narrowed context, script modification, download or dependency installation has been used to manufacture a passing result. Parent integration must disposition/qualify the original R1 environment separately. + +Merged-main source gate (2026-10-01) +----------------------------------- + +Main 7b0ec3f5ab5a35a586d77c480fb7d5d6b1c85ba0 was merged normally, without +rebase, force push, runtime install or frozen trial modification. Merge commit +b770266428c5faac96069011c636fe93a1712acc is the original R0 head; the only +subsequent source changes add source tests (no production changes). + +Original R0 compared exactly against main 7b0ec3f5: openhcs, scripts and +benchmark roots all PASS, respectively 17.65 / 2.52 / 3.37 seconds wall and +88244 / 59028 / 57892 KiB RSS. No detector or threshold was modified. All +shards retained one CPU, 512 MiB / no swap and a 60-second bound. + +111 family controls PASS after this merge (3.33 seconds pytest / 4.10 seconds +wall, 322492 KiB RSS), including a direct full-stack identity test for object +labels, measurement tables/columnar rows, spatial graphs, aligned non-image +tokens and already-dense image/array carriers. 45 consumer controls PASS +(4.01 seconds pytest / 5.27 seconds wall, 372736 KiB RSS), including the +declaration-derived diagnostic ABI fixture correction. These 156 source cases +supersede the initial 33-case checkpoint, but are not fresh installed numeric +or native acceptance. + +The two MRO cases contain real independent TEST capabilities: one changes +pixels, the other adds validity masks. Both use cooperative super through the +actual AlignedImageStack composition owner, and both orderings check exact +pixels AND masks. This proves that extension seam, not a new production MI +family or a complete NRA equivalence certificate. + +Raw receipts, unsuccessful attempts and source/artifact SHA256 manifests are +retained in docs/refactor/receipts/cp-aligned-full-stack-342-20261001.tar.gz; +diagnostics/README.rst indexes their interpretation and replay commands. +The worker's 31 MiB disposable unchanged-main source snapshot was removed +after its processes completed and failure receipts were retained; it can be +recreated from the recorded Git commit. No H003g scratch, source, environment, +input, harness, logs or sealed data was changed. + +Next acceptance belongs to the parent after #338: reviewed source must be +installed into a separately isolated candidate, then the actual installed +user entrypoint must execute matched synthetic aligned primary and auxiliary +images, retain exact typed outputs/masks/provenance and satisfy the raw +callable's dense ABI. Neither source tests nor old frozen H003g are substitutes +for that gate. 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zx?iWi6I=7b(SNqf&P?a`x=b6*P3q!W`ulqxE9+a@zd3rxwQfh>*djf*bdUScUUO@S zyIIz(jZyAuJ9$~lSa_Zxor}u}zUA_xv43IWPHJ?~P&>hA@45M}^NFaj8o3h2wT;=J znI7Do+V2b6rRj`l!`YB!uG-xH1gt1v8a#HT&lZZ89nEpw zKed~^5&mqauBW(gnkCC2?y_n74P}CRR7Fe8E5ATWS&~svieh?fj;oK`v`ee=8qny9 zUNR^CB)!IG70Dme93ZgcR&1Ts?>`bBx-|t)+N317@AMyZk@pA%OLU6O_)(m%E4Dnu z+u&bF6y7Np50ahMvsbtDgJv`}gi923-`7_hVH!6jD{PPM)aUkSk*T#2S_A2@ZKI^g z7O^-wRYzriE2TuI9HyG6wArh zNj7YGVLAf3dl#S}cqUtY)c;QkLPB-Re|4?l31%LcJZH^w3h-SYy^L)iU6M+yb>K)B zil<6~0-lu4F2LHY84s{?e1&<~m7J$#JFzS(P;4O8Pjcp9490!h9qHQ;}$1@NHaU zgK4f6-G=Qi^JPfbv2QF!oYtTW2ML7t0)oA-Oz9+DxwZGeJjE1B$;86}oF%Ra>uO)6 z5?O|@uPQp+_fddM^?Y*>OkNAlf1~jm6yXOZ7heCcw$BbpKOW*^Uj@4UcAA2a^A&5>w#*|bwlXRgFC}sGp2@o2<7@9@k;g~;t;sG_V zs!}q6Rn@)H&@lotp4o;h`N;pQ^yoy$5u;0Yt#a+Ki-eN{jKY9=9f z9yX_w)}70IF+s%~R84GT*sOQs_`|yE5=sB?H|NFP$>BXErU59L=?4yqA*5mk)HIS$#p;l^3K+;iNxRNN_{i~y{(sKcvn7tL?OX5Htn-N4&U(tLQ;>+M*k 0 + ) + aligned_tokens = RuntimeSliceAlignedValues((labels, table)) + kwargs = { + "rows": rows, + "table": table, + "labels": labels, + "graph": graph, + "tokens": aligned_tokens, + "array": array, + "image": image, + } + materialized = RuntimeSliceProjection.full_stack_kwargs(kwargs) + assert materialized is not kwargs + for name, value in kwargs.items(): + assert materialized[name] is value + + @pytest.mark.parametrize("reverse", (False, True)) def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): calls = [] From a14d471e3f2a92148f88a60b6c972e1a49f67db0 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Thu, 1 Oct 2026 03:40:20 -0400 Subject: [PATCH 5/8] Preserve opaque full-stack kwargs and prove nominal extension contracts --- docs/refactor/cp-aligned-full-stack-342.rst | 35 ++++++ openhcs/core/runtime_slice_projection.py | 7 +- ...cellprofiler_full_stack_materialization.py | 111 ++++++++++++++++++ 3 files changed, 149 insertions(+), 4 deletions(-) diff --git a/docs/refactor/cp-aligned-full-stack-342.rst b/docs/refactor/cp-aligned-full-stack-342.rst index 0b88b01ace..f0aacbf692 100644 --- a/docs/refactor/cp-aligned-full-stack-342.rst +++ b/docs/refactor/cp-aligned-full-stack-342.rst @@ -189,3 +189,38 @@ user entrypoint must execute matched synthetic aligned primary and auxiliary images, retain exact typed outputs/masks/provenance and satisfy the raw callable's dense ABI. Neither source tests nor old frozen H003g are substitutes for that gate. Original R1 remains explicitly unqualified as described above. + +Binding nominal review / opaque-kwarg correction +------------------------------------------------ + +The current NRA skill and authoritative refactor-audit ZIP main, pattern +README, implementation, membership, boundaries and surface-receipt references +were reread personally. IMPL-12/13 and BOUND-2 still identify the actual shared +composition/projection owners; no new copied procedure or mirror is needed. + +The review tightened two witnesses. A new CalibratedAlignedImageStack supplies +only a cooperative per-input calibration hook; the existing registered MRO +projection and real rescale executor consume it with no dispatcher/executor +edit. Exact pixels, runtime axis, spacing and original source identities pass. +A named bundle now includes real inner runtime-plane provenance and asserts +the exact outer SOURCE_BINDING aliases and contributor paths after selection. +The bundle's identity metadata hook is an alternative axis policy: it must not +clear the named outer alias by applying the runtime-stack contributor promotion. +Both use the ancestor's actual compose algorithm, not a leaf copy or direct +ancestor jump. The older bare-array bundle test alone did not prove this. + +Full-stack projection must not impose the slice-mode registration requirement +on opaque kwargs. The facade now asks the existing nominal registry's optional +for_nominal_value resolver and preserves an unregistered whole-stack value +unchanged. Registered image owners still materialize through their hooks; +slice-mode strategy_for_value remains strict. Four added actual executor +controls prove opaque kwarg identity for every ProcessingContract, alongside +the typed non-image/image identity control. This fixes a regression risk in +published 34203beb1, not a new scientific input requirement or fallback reader. + +Local corrected source: 117 family cases PASS, 3.36 seconds pytest / 4.15 +seconds wall, 322644 KiB RSS, under the existing one CPU / 512 MiB / no swap / +60-second shard. The original 34203beb1 source/installed receipts are retained +and are not relabelled as acceptance of this correction. Parent explicitly +dispositioned that prepared predecessor before publication/rebuild. Original +R1 remains unqualified; updated exact-production R0 is recorded separately. diff --git a/openhcs/core/runtime_slice_projection.py b/openhcs/core/runtime_slice_projection.py index 02d2f2203b..283b9a9e84 100644 --- a/openhcs/core/runtime_slice_projection.py +++ b/openhcs/core/runtime_slice_projection.py @@ -892,10 +892,9 @@ class RuntimeSliceProjection: @classmethod def full_stack_value(cls, value: RuntimeProjectionData) -> RuntimeProjectionData: - """Materialize nominal image alignment without changing other domains.""" - return RuntimeSliceProjectionStrategy.strategy_for_value( - value - ).full_stack_value(value) + """Materialize declared alignment; preserve opaque whole-stack arguments.""" + strategy = RuntimeSliceProjectionStrategy.for_nominal_value(value) + return value if strategy is None else strategy.full_stack_value(value) @classmethod def full_stack_kwargs( diff --git a/tests/unit/test_cellprofiler_full_stack_materialization.py b/tests/unit/test_cellprofiler_full_stack_materialization.py index cbfa0975c1..d4fd62b96b 100644 --- a/tests/unit/test_cellprofiler_full_stack_materialization.py +++ b/tests/unit/test_cellprofiler_full_stack_materialization.py @@ -208,6 +208,87 @@ def test_named_output_bundle_materializes_its_own_source_binding_axis(): assert bundle.slices == planes +def test_named_bundle_preserves_outer_aliases_with_real_inner_plane_provenance(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + payloads = [] + for channel, alias in enumerate(("red", "green"), start=1): + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=(alias,), + source_voxel_spacing=spacing, + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=tuple(f"/synthetic/{alias}_s{site}.tif" for site in (1, 2)), + component_metadata=tuple( + {"site": str(site), "channel": str(channel)} for site in (1, 2) + ), + ), + ) + payloads.append(metadata.payload_with(np.full((2, 3, 4), channel), None)) + bundle = ImageOutputBundle( + tuple(payloads), + tuple(AlignedImageSliceContext.main_flow(alias) for alias in ("red", "green")), + ) + dense = RuntimeSliceProjection.full_stack_value(bundle) + metadata = image_payload_metadata(dense) + assert metadata.plane_axis is RuntimePlaneAxis.SOURCE_BINDING + assert metadata.source_image_names == ("red", "green") + assert metadata.source_provenance.source_plane_count == 2 + assert metadata.source_voxel_spacing == spacing + for index, alias in enumerate(("red", "green")): + selected = RuntimeSliceProjection.value_for_slice( + dense, + RuntimePlaneAxisValueProjection.from_selected_plane( + axis=RuntimePlaneAxis.SOURCE_BINDING, plane_index=index, axis_size=2 + ), + ) + np.testing.assert_array_equal( + image_payload_data(selected), image_payload_data(payloads[index]) + ) + selected_metadata = image_payload_metadata(selected) + assert selected_metadata.source_image_names == (alias,) + assert { + identity.path + for identity in selected_metadata.source_provenance.represented_source_identities + } == {f"/synthetic/{alias}_s{site}.tif" for site in (1, 2)} + + +def test_new_calibrated_nominal_stack_reaches_real_callable_without_dispatch_edits(): + spacing = SourceVoxelSpacing((1.25, 2.5, 3.0), SourceVoxelSpacingUnit.MICROMETERS) + + class CalibratedAlignedImageStack(AlignedImageStack): + """A generated acquisition grid owns one additional metadata fact.""" + + def composition_payload_metadata(self, metadata): + return super().composition_payload_metadata(metadata).replace_fields( + source_voxel_spacing=spacing + ) + + data = np.arange(24, dtype=np.float32).reshape(2, 3, 4) + payloads = tuple( + ImagePayloadMetadata(source_path=f"/synthetic/site_{index}.tif").payload_with( + plane, None + ) + for index, plane in enumerate(data) + ) + aligned = CalibratedAlignedImageStack(payloads) + contract = CallableContract.from_callable(rescale_intensity) + result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + aligned, + {}, + execution_mode=contract.runtime_image_execution_mode, + ) + np.testing.assert_allclose(image_payload_data(result), data / 23.0) + metadata = image_payload_metadata(result) + assert metadata.plane_axis is RuntimePlaneAxis.RUNTIME_SLICE + assert metadata.source_voxel_spacing == spacing + assert { + identity.path + for identity in metadata.source_provenance.represented_source_identities + } == {"/synthetic/site_0.tif", "/synthetic/site_1.tif"} + + def test_ragged_aligned_images_fail_before_dense_callable(): aligned = AlignedImageStack((np.zeros((2, 3)), np.zeros((3, 3)))) with pytest.raises(ValueError, match="one exact shape"): @@ -237,6 +318,7 @@ def test_full_stack_preserves_nonimage_identity_domains_and_dense_images(): array, array > 0 ) aligned_tokens = RuntimeSliceAlignedValues((labels, table)) + opaque = object() kwargs = { "rows": rows, "table": table, @@ -245,6 +327,7 @@ def test_full_stack_preserves_nonimage_identity_domains_and_dense_images(): "tokens": aligned_tokens, "array": array, "image": image, + "opaque": opaque, } materialized = RuntimeSliceProjection.full_stack_kwargs(kwargs) assert materialized is not kwargs @@ -252,6 +335,34 @@ def test_full_stack_preserves_nonimage_identity_domains_and_dense_images(): assert materialized[name] is value +@pytest.mark.parametrize("processing_contract", tuple(ProcessingContract)) +def test_full_stack_raw_callable_keeps_opaque_nonimage_kwargs(processing_contract): + opaque = object() + image = np.ones((2, 3, 4), dtype=np.float32) + calls = [] + + def consume(image, *, options): + calls.append(options) + assert options is opaque + return image + + contract = CallableContract( + func=consume, + function_name="consume", + module_name="OpaqueFullStackProbe", + metadata=CallableMetadata(processing_contract=processing_contract), + ) + result = CellProfilerFunctionContractExecutor().execute( + contract, + consume, + image, + {"options": opaque}, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + ) + assert calls == [opaque] + assert image_payload_data(result) is image + + @pytest.mark.parametrize("reverse", (False, True)) def test_independent_composition_capabilities_cooperate_in_both_mro_orders(reverse): calls = [] From 327cec9f6bc87d0eb8afb7c46ca0b67b814e01d9 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Thu, 1 Oct 2026 03:54:32 -0400 Subject: [PATCH 6/8] Publish aligned RescaleIntensity engineering document and a14 source receipts --- diagnostics/NOMINAL_REVIEW_SHA256SUMS | 25 ++++ diagnostics/README.rst | 38 ++++- diagnostics/test_344_engineering_document.py | 60 ++++++++ docs/refactor/344-engineering-acceptance.rst | 140 ++++++++++++++++++ .../344-aligned-rescale-engineering.py | 81 ++++++++++ ...igned-full-stack-342-a14-supplement.tar.gz | Bin 0 -> 199562 bytes 6 files changed, 341 insertions(+), 3 deletions(-) create mode 100644 diagnostics/NOMINAL_REVIEW_SHA256SUMS create mode 100644 diagnostics/test_344_engineering_document.py create mode 100644 docs/refactor/344-engineering-acceptance.rst create mode 100644 docs/refactor/examples/344-aligned-rescale-engineering.py create mode 100644 docs/refactor/receipts/cp-aligned-full-stack-342-a14-supplement.tar.gz diff --git a/diagnostics/NOMINAL_REVIEW_SHA256SUMS b/diagnostics/NOMINAL_REVIEW_SHA256SUMS new file mode 100644 index 0000000000..a3e8fb5e5a --- /dev/null +++ b/diagnostics/NOMINAL_REVIEW_SHA256SUMS @@ -0,0 +1,25 @@ +3514ad8f2346e5b5e82aaf4410610afc2fc8616eaf4596d5af1eaa387a85efe5 openhcs/core/aligned_image_payload.py +cd6c7553efba0838205f153e96b15570c285894e304827d8c3f3d0c38de664bd openhcs/core/runtime_slice_projection.py +51fa66703e1d789c199ba485f80ec71152bb1f64a3864ed2414d167660ffc2f8 openhcs/interop/cellprofiler/runtime/function_contract_execution.py +ffc6bfe96a431e72611da4e287d496065af9d4bed71984881a29c3f7a902a1ec tests/unit/test_cellprofiler_full_stack_materialization.py +ae1313ed11505caf35ef1d3e183b811a0d8968a187ff45f73cba1e30a572a63b diagnostics/README.rst +2dd04e5005b9cde8b1b9b86f0d17e3b9c45120795e9be0ed9b556787b33ffdf2 diagnostics/run_source_tests.py +9599cb9152d642e834b4056d820856c3dba9593647ea7554c36f0589c72b3798 diagnostics/test_344_engineering_document.py +b7493d7e12dafec853e02498f6f65979859c5c041010716bd4cf9f4669318fd4 docs/refactor/cp-aligned-full-stack-342.rst +7183385aa0e0a5b79ec9fb343f596c79de29668d608154fdb48c7c0560e26d0b docs/refactor/344-engineering-acceptance.rst +5e0e39229fcfeb34548565dafeb6b04a4dbaa4b40c03603ef65d4f924d6608e2 docs/refactor/examples/344-aligned-rescale-engineering.py +d9a74653eda0f076d505bd42471d09b24c66057ac91d8e5678fe74720bc06526 diagnostics/nominal-review-family-controls.log +6611a228f092fc75374580b61f710f454bf24f6ac61617815d3bc34cc500fe28 diagnostics/nominal-review-family-controls.xml +93bdd1a80cdd48b9ff3ff5c28a0d8ea449f934d9ec212a5c0ddf3f5796225ec0 diagnostics/nominal-review-opaque-controls.log +bdcf8c04e606ffcb6e963283860d24048e6e2ce2a23fd7737a4ebe8058cf7c87 diagnostics/nominal-review-opaque-controls.xml +1c9d31d078d8391c46fd9ff15e2b7a2c52d293be78b22ac4c0a1e28382f9bb21 diagnostics/a14-consumer-controls.log +e79acaefe8b1e66a5b0f95b20c21e5c8040116d7939e178713582396962da39d diagnostics/a14-consumer-controls.xml +c9ac3b4f586accb4d7993b7b20c70f9035a53d195195b7532f61941091609ca9 diagnostics/a14-r0-openhcs.log +96331d5fe50a4bd165a433b503caedbef0c2b4a2cf10689aeb5314f343c7e3ad diagnostics/a14-r0-scripts.log +c1d63a1befd427c68ecb3f5ea30f7e60ce72a361dbb979e36aef74cb46f74307 diagnostics/a14-r0-benchmark.log +5938b383ffbd7bd3899cf642f956e0c12019b9549b4f0f68acaa675beb41ee8e diagnostics/engineering-document-source.log +b9213321e2975c2ec76550c6cfd02592a4b63ad63592061e13021468efe7a1c0 diagnostics/engineering-document-source.xml +0621f1642170818f6c73edf6477a9052f71a1d61163296d2dbb7c3612796892c diagnostics/engineering-document-source-corrected.log +e88365a2b02946daebd1952f360047f6a5de4e76aaa0adaff3ab1d98262b9947 diagnostics/engineering-document-source-corrected.xml +3f823fd0246416a730e68aed4eb63ef1cd4113d2d1d3319b1db74091a7f9e444 diagnostics/engineering-document-separate-planes.log +2a0fd5014902bd62a8ba5638a0de37111d185db93ae27b40d315d6516e66a3ed diagnostics/engineering-document-separate-planes.xml diff --git a/diagnostics/README.rst b/diagnostics/README.rst index eba3184f40..29fb259ac9 100644 --- a/diagnostics/README.rst +++ b/diagnostics/README.rst @@ -14,8 +14,8 @@ zero swap, 60-second timeout, OPENHCS_CPU_ONLY=true, numerical threads 1, and PYTEST_DISABLE_PLUGIN_AUTOLOAD=1. Two unknown asyncio configuration warnings are expected because optional pytest plugins are disabled. -Final receipt interpretation ----------------------------- +Predecessor receipt interpretation (public 34203beb1) +--------------------------------------------------- merged-main-final-family-controls: 111 PASS, including 15 added full-stack tests plus 96 existing executor/projection/alignment/device/registry controls. @@ -23,7 +23,7 @@ merged-main-consumer-regressions: 45 PASS, including the unchanged-main ABI fixture corrected using the real diagnostic declaration owner. r0-merged-main-openhcs/scripts/benchmark: all PASS. Base main 7b0ec3f5, head b7702664, exact three changed production paths. Subsequent edits affect -only tests/documentation/receipt packaging, not production sources. +only tests/documentation/receipt packaging until the subsequent a14 correction. r1-original: import failure BEFORE scanning. The existing current NRA environment does not export RedundantTypeCheckDetector at the original @@ -33,6 +33,38 @@ nra-before-corrected: deadline_incomplete structured report with null counts, 20-second CLI deadline, parsing unfinished. Its admitted candidate external directory is uninitialized. This is NOT a successful no-findings report. +Current source correction (a14d471e3) +------------------------------------ + +nominal-review-opaque-controls: 117 PASS (21 full-stack cases plus 96 existing +family controls), 3.36 seconds pytest, 322644 KiB RSS. New calibrated subtype, +real runtime-plane named bundle and opaque kwargs across all four contracts. +a14-consumer-controls: 45 PASS, 3.96 seconds pytest, 372732 KiB RSS. +a14-r0-openhcs/scripts/benchmark: exact original CI-pinned packaged ratchet, +base main 7b0ec3f5, head a14d471e3, all PASS. Root wall times 16.93/1.88/2.45 +seconds, RSS 88124/59020/57732 KiB. Optional-neutral nominal resolution is +the only additional production change after 34203beb1; opaque values keep +identity at FULL_STACK while slice-mode registration remains strict. + +engineering-document-separate-planes: 1 PASS, source authoring only, 1.95 +seconds pytest / 2.55 seconds wall / 277676 KiB RSS. The initial +decorator-wrapper object-identity failure and corrected +nominal/raw-callable identity receipt remain in the supplemental archive. +No compile, fixture pixels, MCP/native/viewer or installed check was run here. +The complete document and identity/path/metadata acceptance gates are under +docs/refactor/344-engineering-acceptance.rst and examples/. + +Parent independently retains the original installed opaque-kwargs failure; +those predecessor receipts are not relabelled. Parent owns the normal main +integration, paired rebuilt wheel and fresh installed/native numeric gate. +Original R1 remains unqualified for the previously recorded environment and +dependency-context limits; no new R1 completeness claim is made. + +Supplement: docs/refactor/receipts/cp-aligned-full-stack-342-a14-supplement.tar.gz. +NOMINAL_REVIEW_SHA256SUMS authenticates the current three production files, +test/document sources and new byte-preserved raw receipts. The original +cp-aligned-full-stack-342-20261001.tar.gz and SHA256SUMS are unchanged. + Unsuccessful receipts remain in the archive: first-repair slotted-dataclass super error; family-controls fixture argument and named bundle failure; family-controls-corrected mask-domain failure; complete-owned-families diff --git a/diagnostics/test_344_engineering_document.py b/diagnostics/test_344_engineering_document.py new file mode 100644 index 0000000000..554e5c5ecc --- /dev/null +++ b/diagnostics/test_344_engineering_document.py @@ -0,0 +1,60 @@ +"""Source-authoring checks only: no data loading, compile, execution or processes.""" + +from pathlib import Path + +from openhcs.constants import AllComponents, GroupBy, Microscope, VariableComponents +from openhcs.core.aligned_image_payload import ImagePayloadExecutionMode +from openhcs.core.artifacts import ArtifactInputPlan, ArtifactOutputPlan, ImageArtifactType +from openhcs.core.callable_contract import CallableContract +from openhcs.core.pipeline_document import PipelineDocumentAuthority +from openhcs.interop.cellprofiler.module_declarations import CellProfilerModule +from openhcs.processing.backends.cellprofiler.intensity import ( + RescaleIntensityModule, + rescale_intensity, +) +from openhcs.processing.backends.lib_registry.unified_registry import ProcessingContract + + +def test_complete_engineering_document_uses_declared_primary_sources(): + source = ( + Path(__file__).resolve().parents[1] + / "docs/refactor/examples/344-aligned-rescale-engineering.py" + ).read_text() + document = PipelineDocumentAuthority.from_source(source) + assert document.original_source == source + assert document.pipeline_config.microscope is Microscope.IMAGEXPRESS + plan = document.pipeline_config.source_bindings_config + # Each fixture file is 2-D. Z varies across files, not inside each TIFF. + assert plan.source_stack_components == () + assert plan.source_voxel_spacing.values_zyx == (4.0, 0.5, 0.5) + assert tuple(binding.alias for binding in plan.bindings) == ( + "EngineeringCH1", "EngineeringCH2", + ) + assert tuple(binding.selector.components[0].value for binding in plan.bindings) == ( + "1", "2", + ) + (step,) = document.pipeline_steps + assert step.processing_config.variable_components == [VariableComponents.Z_INDEX] + assert step.processing_config.group_by is GroupBy.NONE + assert step.source_bindings.enabled + func, kwargs = step.func + # The document authority canonicalizes decorator callables via RegistryService. + contract = CallableContract.from_callable(func) + assert CellProfilerModule.require_callable_contract_owner(contract) is RescaleIntensityModule + assert contract.resolve_canonical_raw_callable() is ( + CallableContract.from_callable(rescale_intensity).resolve_canonical_raw_callable() + ) + bindings = RescaleIntensityModule.declared_artifact_bindings( + plan_type=ArtifactInputPlan, artifact_type=ImageArtifactType, + ) + assert len(bindings) == 2 + assert all(binding.runtime_parameter_name is None for binding in bindings) + assert tuple(kwargs[binding.require_parameter_name()] for binding in bindings) == ( + "EngineeringCH1", "EngineeringCH2", + ) + (output,) = RescaleIntensityModule.declared_artifact_bindings( + plan_type=ArtifactOutputPlan, artifact_type=ImageArtifactType, + ) + assert kwargs[output.require_parameter_name()] == "EngineeringRescaled" + assert contract.runtime_image_execution_mode is ImagePayloadExecutionMode.FULL_STACK + assert contract.metadata.processing_contract is ProcessingContract.PURE_2D diff --git a/docs/refactor/344-engineering-acceptance.rst b/docs/refactor/344-engineering-acceptance.rst new file mode 100644 index 0000000000..46fed46020 --- /dev/null +++ b/docs/refactor/344-engineering-acceptance.rst @@ -0,0 +1,140 @@ +PR344 engineering document handoff +================================= + +Runtime source checkpoint: a14d471e3f2a92148f88a60b6c972e1a49f67db0. +Parent owns installed integration with main 05c3cf288 and the sole native +5993 slot. This child has not loaded fixture pixels, compiled the document, +started MCP/native/viewer, or executed a pipeline. This is not H003g, a +scientific retry, biological validation, or an installed acceptance receipt. + +Complete source +--------------- + +``examples/344-aligned-rescale-engineering.py`` is one complete public Python +PipelineDocument: pipeline_config plus one ordered FunctionStep. Submit the +entire file through the ordinary MCP document authoring/validation/compile +route. Do not call a custom function, construct runtime arrays or invoke the +contract executor as a substitute for that route. Imports are explicit in +the source; input/output keyword keys come from +RescaleIntensityModule.declared_artifact_bindings().require_parameter_name(). + +Fixture request for the parent +----------------------------- + +Use the existing synthetic ImageXpress fixture infrastructure, not any frozen +H003g input or artifact. Proposed separate root:: + + /home/ts/wt/openhcs-344-engineering-20261001/raw/EngineeringPlate/ + TimePoint_1/ZStep_1/plate_A01_s1_w1.tif + TimePoint_1/ZStep_1/plate_A01_s1_w2.tif + TimePoint_1/ZStep_2/plate_A01_s1_w1.tif + TimePoint_1/ZStep_2/plate_A01_s1_w2.tif + +Each file: one 32x32 uint16 plane, one site, one timepoint; distinct channels +and Z planes. One deterministic nonconstant engineering pattern is +``1000*(channel-1) + 100*(z-1) + 32*y + x`` with channel/z in {1,2} and +x/y in [0,31]. Record actual fixture creation, input hashes and inventory in +the parent's receipt; no fixture files were created by this child. + +Two typed aliases explicitly select channel 1 and channel 2. Step variable +components select Z_INDEX, group_by is NONE, and both aliases are enabled. +There are no embedded stack axes in a 2-D file: source_stack_components +deliberately remains empty. The existing source-bound artifact resolver loads +each alias's members and calls stack_image_payloads in RUNTIME_SLICE mode +(core/runtime_adapters.py). Two declared primary image inputs then pass +through CellProfilerModuleExecutor._image_request and +compose_aligned_image_payload: an AlignedImageStack with a two-channel bundle +per Z slice. The callable's FULL_STACK mode overrides slice execution. +This is the original primary carrier failure path, not an auxiliary kwarg +or the ordinary single dense two-channel input path. + +Compile identity gates, before execution +--------------------------------------- + +Require the actual inventory to contain A01/site 1/timepoint 1, channel 1/2, +Z 1/2. Main 05c3cf288 includes the parent's raw ImageXpress ZStep fix. +Reject a flattened singleton-Z inventory rather than accepting a different +test. Require the registered declaration owner RescaleIntensityModule, +function_name rescale_intensity, ProcessingContract.PURE_2D and +ImagePayloadExecutionMode.FULL_STACK. The public document authority +canonicalizes decorator callables through RegistryService: callable object +identity before/after normalization is NOT the identity gate. Its canonical +raw callable and module declaration owner are the gates. + +Require exactly two ImageArtifactType input occurrences, in declared order: +EngineeringCH1 and EngineeringCH2. Both declaration bindings have +runtime_parameter_name None; compiled artifact input parameter_name is None. +No auxiliary runtime keyword image is injected. Each alias's source payload +must retain two exact Z members in RUNTIME_SLICE order. The composed primary +must be aligned before the full-stack contract materializes it, and its dense +callable input should be (2 Z, 2 bindings, 32 Y, 32 X). These are acceptance +requirements inferred from inspected production authorities, NOT a claimed +compile or native observation. Preserve the observed typed plan and logs; +if the entrypoint does not expose carrier evidence, do not invent it from a +successful run or from file/channel count alone. + +Require one output ImageArtifactType named EngineeringRescaled. Its declared +SourceStackLineageSourceRelation is anchored to EngineeringCH1 by +RescaleIntensityModule.artifact_output_relations. Output contextualization +and materialization remain owned by the existing output policies. This +declaration does not promise a new four-source output identity contract. + +Addresses, pixels and metadata gates +----------------------------------- + +Configured output plate root:: + + /home/ts/wt/openhcs-344-engineering-20261001/output/EngineeringPlate_openhcs + +For axis A01, step 0 and no grouping key, PathPlannerPaths.artifact_path +derives this canonical runtime artifact address:: + + results/A01_EngineeringRescaled_step0.pkl + +This is an artifact-store address, NOT a claim that a durable pickle exists. +ImageArtifactType projects disk exports under ``images/EngineeringRescaled`` +when its writer uses plane projection, or uses its declared source-identity +filename policy for scalar exports. Retain exact compiled output/materialization +plans and returned artifact descriptors before asserting TIFF suffixes or +export filenames; this child has not compiled or observed those paths. + +For the proposed integer pattern, the dense default stretch expectation is +``(input - 0) / 2123`` across both Z planes and both source bindings. Confirm +the actual callable normalization/dtype policy and compare every output +plane against the recorded fixture, not just extrema or a run-success flag. +The original failing full-stack path would raise float(AlignedImageStack) +before emitting the image. Preserve a real original failure if available; +do not reinstall/replay an old candidate merely to manufacture that receipt. + +Configuration declares synthetic physical calibration (4.0, 0.5, 0.5) +micrometers in Z/Y/X order, and both source aliases retain their exact source +paths, channel/Z coordinates and native 32x32 spatial domain. Inspect typed +metadata at input composition and output contextualization separately. +The input composition must retain all four source contributors and both +aliases; output source scope follows the actual first-source lineage relation. +Do not silently equate a virtual workspace path with its physical raw path: +resolve provenance through the recorded source projection before comparing. +Calibration metadata preservation is not a physical measurement validation. + +Ordinary raw TIFFs carry no validity mask: require mask None to remain None. +``load_as_mask`` converts pixel values to booleans; it does NOT manufacture +a validity mask. Nontrivial MaskedImagePayload preservation and independent +mask capability MRO cases are covered by the source family controls. A live +nontrivial-mask claim would require a separate parent-approved typed masked +fixture/path; this minimal document does not claim that coverage. + +Source-only checks +------------------ + +diagnostics/test_344_engineering_document.py executes only the Python +configuration document through PipelineDocumentAuthority.from_source and +checks declared source selectors, calibrated config, step axis and canonical +registered identity. It does not load data, compile or execute a pipeline. +The initial object-identity assertion failed because canonical normalization +replaces the decorator wrapper; that receipt is retained. The corrected test +uses the owning module and canonical raw callable identity instead. + +No biological guide/validated assay recipe was retrieved or claimed. The +use-openhcs skill's complete-document rule applies, but the parent's explicit +source-only/no-MCP instruction defers its live catalog/schema/compile gates +to the installed acceptance owner. Do not label this source check MCP validated. diff --git a/docs/refactor/examples/344-aligned-rescale-engineering.py b/docs/refactor/examples/344-aligned-rescale-engineering.py new file mode 100644 index 0000000000..0b1b7a92b6 --- /dev/null +++ b/docs/refactor/examples/344-aligned-rescale-engineering.py @@ -0,0 +1,81 @@ +# OpenHCS pipeline +# Synthetic engineering fixture only. Parent owns fixture creation and MCP execution. +from pathlib import Path + +from openhcs.constants import AllComponents, GroupBy, Microscope, VariableComponents +from openhcs.constants.input_source import InputSource +from openhcs.core.artifacts import ArtifactInputPlan, ArtifactOutputPlan, ImageArtifactType +from openhcs.core.config import ( + LazyPathPlanningConfig, + LazyProcessingConfig, + LazyVFSConfig, + MaterializationBackend, + PipelineConfig, +) +from openhcs.core.source_bindings import ( + ComponentSelector, + LazySourceBindingsConfig, + LazyStepSourceBindingsConfig, + NamedSourceBinding, + SourceSelector, +) +from openhcs.core.source_metadata import SourceVoxelSpacing, SourceVoxelSpacingUnit +from openhcs.core.steps.function_step import FunctionStep +from openhcs.processing.backends.cellprofiler.intensity import ( + RescaleIntensityModule, + rescale_intensity, +) + +primary_binding, reference_binding = RescaleIntensityModule.declared_artifact_bindings( + plan_type=ArtifactInputPlan, artifact_type=ImageArtifactType, +) +(output_binding,) = RescaleIntensityModule.declared_artifact_bindings( + plan_type=ArtifactOutputPlan, artifact_type=ImageArtifactType, +) + +pipeline_config = PipelineConfig( + num_workers=1, + use_threading=False, + microscope=Microscope.IMAGEXPRESS, + materialization_results_path=Path("results"), + path_planning_config=LazyPathPlanningConfig( + global_output_folder=Path("/home/ts/wt/openhcs-344-engineering-20261001/output"), + output_dir_suffix="_openhcs", + ), + vfs_config=LazyVFSConfig(materialization_backend=MaterializationBackend.DISK), + source_bindings_config=LazySourceBindingsConfig( + source_voxel_spacing=SourceVoxelSpacing( + (4.0, 0.5, 0.5), SourceVoxelSpacingUnit.MICROMETERS, + ), + bindings=( + NamedSourceBinding( + alias="EngineeringCH1", + selector=SourceSelector( + components=(ComponentSelector(AllComponents.CHANNEL, "1"),), + ), + ), + NamedSourceBinding( + alias="EngineeringCH2", + selector=SourceSelector( + components=(ComponentSelector(AllComponents.CHANNEL, "2"),), + ), + ), + ), + ), +) +pipeline_steps = [ + FunctionStep( + name="Engineering aligned full-stack RescaleIntensity", + func=(rescale_intensity, { + primary_binding.require_parameter_name(): "EngineeringCH1", + reference_binding.require_parameter_name(): "EngineeringCH2", + output_binding.require_parameter_name(): "EngineeringRescaled", + }), + processing_config=LazyProcessingConfig( + input_source=InputSource.PIPELINE_START, + variable_components=[VariableComponents.Z_INDEX], + group_by=GroupBy.NONE, + ), + source_bindings=LazyStepSourceBindingsConfig(enabled=True), + ), +] diff --git a/docs/refactor/receipts/cp-aligned-full-stack-342-a14-supplement.tar.gz b/docs/refactor/receipts/cp-aligned-full-stack-342-a14-supplement.tar.gz new file mode 100644 index 0000000000000000000000000000000000000000..337f1936320dded032c77103c33f672d210b89c7 GIT binary patch literal 199562 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| 135 +++++++++ docs/refactor/344-engineering-acceptance.rst | 276 +++++++++--------- .../344-aligned-rescale-engineering.py | 66 ++--- ...-aligned-full-stack-342-acquisition.tar.gz | Bin 0 -> 35719 bytes 6 files changed, 339 insertions(+), 180 deletions(-) create mode 100644 diagnostics/ACQUISITION_SHA256SUMS create mode 100644 diagnostics/test_344_source_binding_ingress.py create mode 100644 docs/refactor/receipts/cp-aligned-full-stack-342-acquisition.tar.gz diff --git a/diagnostics/ACQUISITION_SHA256SUMS b/diagnostics/ACQUISITION_SHA256SUMS new file mode 100644 index 0000000000..edb5f600a2 --- /dev/null +++ b/diagnostics/ACQUISITION_SHA256SUMS @@ -0,0 +1,15 @@ +3514ad8f2346e5b5e82aaf4410610afc2fc8616eaf4596d5af1eaa387a85efe5 openhcs/core/aligned_image_payload.py +cd6c7553efba0838205f153e96b15570c285894e304827d8c3f3d0c38de664bd openhcs/core/runtime_slice_projection.py +51fa66703e1d789c199ba485f80ec71152bb1f64a3864ed2414d167660ffc2f8 openhcs/interop/cellprofiler/runtime/function_contract_execution.py +939b5cfa8c32eb2db38cee2606ffa755be3eaf96fbe3640674f038ced125f5fc diagnostics/README.rst +2dd04e5005b9cde8b1b9b86f0d17e3b9c45120795e9be0ed9b556787b33ffdf2 diagnostics/run_source_tests.py +9599cb9152d642e834b4056d820856c3dba9593647ea7554c36f0589c72b3798 diagnostics/test_344_engineering_document.py +f398b5db2435208a1317f0e97bf347e7e837e4b64f91ac0887e2e571d6da913c diagnostics/test_344_source_binding_ingress.py +0df290b3cb92862b5aba67a27f45558d0d6f10cd53504f9fffab6f6378a9c296 docs/refactor/344-engineering-acceptance.rst +323ab83b8462a9a8f4e8cc873e446eab1de15a114a3f3a07740ea8b682b7666f docs/refactor/examples/344-aligned-rescale-engineering.py +4679d9be9612f31adb1dd42dad7efae887484466edf7fad6afe7e7937bccf095 diagnostics/engineering-source-bindings-ingress.log +54f76ba7e2240dacadaaf95dedee73620a46dcd5650b79a9bedfec1b6c6a0391 diagnostics/engineering-source-bindings-ingress.xml +0f9b93720ac0fe0c7c3b9ebc78c2dfeb6fa710173b071659e0d1f9072606c459 diagnostics/engineering-source-bindings-identity-controls.log +79b7422ea0f90d73a7de03e2042e20c47af77cdbd9c51f643a76688dc1b57173 diagnostics/engineering-source-bindings-identity-controls.xml +ef0531fa77aa73b5a47cbf40210d516cca94b8dc72330b1de0ab6d9c7ff4397a diagnostics/engineering-acquisition-final-source.log +5381057c14505fa925ff9e070ff3c2ed7ab839d85e7d98b74fb4979503a52994 diagnostics/engineering-acquisition-final-source.xml diff --git a/diagnostics/README.rst b/diagnostics/README.rst index 29fb259ac9..e019344787 100644 --- a/diagnostics/README.rst +++ b/diagnostics/README.rst @@ -1,6 +1,33 @@ Runtime repair #342 source receipts ================================== +Latest engineering authoring disposition +--------------------------------------- + +The public example is corrected to the parent's admitted acquisition contracts: +IS_TIF filter; exact FILE_NAME acquisition metadata; METADATA pairing on +well/site/z_index/timepoint; per-alias CHANNEL component_identity. The failed +minimal example at 327cec9f6 remains in Git and the original a14 archive. +No production code changes after a14d471e3. The existing native handler does +not promise named source projection; do not infer ingestion owner from a +requested microscope enum or input occurrences from storage-plan rendering. + +engineering-acquisition-final-source: 6 PASS, 2.78s pytest / 3.50s wall / +334736 KiB RSS. Document parsing and synthetic path/declaration checks only; +no pixel load, initialization, compile, scientific execution or native startup. +engineering-source-bindings-ingress: initial 3 PASS / 1 FAIL, incorrect expected +exception class for an existing metadata conflict; original receipt retained. +engineering-source-bindings-identity-controls: 5 PASS, before final adoption +of the parent's precise complete authoring recipe. Source receipts remain +separate from the parent's installed21 and continuous installed MCP/native gate. +Parent reports compile/run complete, 8192 comparisons with maximum error +1.23e-7, exact declared calibration/first-source scope; no direct carrier/mask +inspection and no biology or R1 acceptance. See 344-engineering-acceptance.rst. + +New authoring receipts: docs/refactor/receipts/cp-aligned-full-stack-342-acquisition.tar.gz +and diagnostics/ACQUISITION_SHA256SUMS. Prior archives/manifests are unchanged; +their source hashes authenticate their recorded snapshots, not this revised example. + Owner: H003g runtime repair worker under parent integration; draft PR #344. H003g is permanently FAILED. These are synthetic source checks, not a trial retry, installed acceptance, result QA or biological success evidence. diff --git a/diagnostics/test_344_source_binding_ingress.py b/diagnostics/test_344_source_binding_ingress.py new file mode 100644 index 0000000000..489c1c5297 --- /dev/null +++ b/diagnostics/test_344_source_binding_ingress.py @@ -0,0 +1,135 @@ +"""Pure path/declaration reproducer: no pixels, workspace writes or native calls.""" + +from dataclasses import replace +from pathlib import Path + +import pytest +from polystore.base import _create_storage_registry +from polystore.filemanager import FileManager + +from openhcs.constants import AllComponents, Backend, Microscope +from openhcs.core.pipeline_document import PipelineDocumentAuthority +from openhcs.core.source_binding_workspace import SourceBindingWorkspaceProjector, SourceSetAssembler +from openhcs.core.source_bindings import ( + MetadataExtractionRule, MetadataSource, source_bindings_defaults_to_base, +) +from openhcs.core.source_projection import OpenHCSPlaneAddress, SourceProjectionSet +from openhcs.microscopes.microscope_base import create_microscope_handler +from openhcs.microscopes.source_bindings_handler import SourceBindingsHandler + + +EXAMPLE = ( + Path(__file__).resolve().parents[1] + / "docs/refactor/examples/344-aligned-rescale-engineering.py" +) +ROOT = Path("/synthetic/engineering-fixture") +PATHS = tuple( + ROOT / f"TimePoint_1/ZStep_{z}/A01_s{site:03}_w{channel}_z{z:03}_t001.tif" + for z in (1, 2) for site in (1, 2) for channel in (1, 2) +) + + +def _config(): + document = PipelineDocumentAuthority.from_source(EXAMPLE.read_text()) + assert document.pipeline_config.microscope is Microscope.IMAGEXPRESS + return source_bindings_defaults_to_base(document.pipeline_config.source_bindings_config) + + +def test_explicit_imagexpress_with_bindings_is_routed_to_generic_ingestion(): + # Factory construction only. No initialize_workspace, I/O or compile. + handler = create_microscope_handler( + microscope_type=Microscope.IMAGEXPRESS.value, + filemanager=FileManager(_create_storage_registry()), + source_bindings_config=_config(), + ) + assert isinstance(handler, SourceBindingsHandler) + + +def test_metadata_empty_candidates_reproduce_exact_order_guard(): + config = replace(_config(), metadata_rules=(), match_plan=None) + projector = SourceBindingWorkspaceProjector(config) + candidates = projector.source_candidates(ROOT, PATHS, source_backend=Backend.DISK) + selected = projector._candidates_by_alias(ROOT, candidates, filemanager=None) + refs = tuple(tuple(item.source_ref for item in values) for values in selected.values()) + assert len(refs) == 2 and refs[0] == refs[1] and len(refs[0]) == 8 + with pytest.raises(ValueError, match="ORDER source bindings must distinguish aliases"): + SourceSetAssembler.for_config(config).source_sets(None, selected, ()) + + +def test_declared_acquisition_metadata_distinguishes_channels_site_and_z(): + config = _config() + projector = SourceBindingWorkspaceProjector(config) + candidates = projector.source_candidates(ROOT, PATHS, source_backend=Backend.DISK) + assert len(candidates) == 8 + selected = projector._candidates_by_alias(ROOT, candidates, filemanager=None) + assert tuple(selected) == ("EngineeringCH1", "EngineeringCH2") + assert tuple(len(values) for values in selected.values()) == (2, 2) + for channel, alias in enumerate(selected, start=1): + members = selected[alias] + assert tuple(member.metadata["z_index"] for member in members) == ("1", "2") + assert all(member.metadata["well"] == "A01" for member in members) + assert all(member.metadata["site"] == "1" for member in members) + assert all(member.metadata["timepoint"] == "1" for member in members) + assert all(member.metadata["channel"] == str(channel) for member in members) + assert tuple(member.source_ref.backend_address for member in members) == tuple( + f"TimePoint_1/ZStep_{z}/A01_s001_w{channel}_z{z:03}_t001.tif" for z in (1, 2) + ) + sets = SourceSetAssembler.for_config(config).source_sets(config.match_plan, selected, ()) + assert len(sets) == 2 + for source_set in sets: + members = tuple(source_set.candidates_by_alias.values()) + assert members[0].source_ref != members[1].source_ref + assert members[0].metadata["z_index"] == members[1].metadata["z_index"] + + +def test_declared_folder_and_filename_z_conflicts_remain_rejected(): + config = _config() + # The shipped recipe declares filename identity; this extra rule is a conflict + # control of the existing extractor, not an extra required fixture declaration. + config = replace(config, metadata_rules=(*config.metadata_rules, MetadataExtractionRule( + MetadataSource.FOLDER_NAME, + r"(?:^|/)ZStep_0*(?P[1-9][0-9]*)$", + ))) + projector = SourceBindingWorkspaceProjector(config) + mismatched = ROOT / "TimePoint_1/ZStep_2/A01_s001_w1_z001_t001.tif" + with pytest.raises(RuntimeError, match="Conflicting metadata field 'z_index'"): + projector.source_candidates(ROOT, (mismatched,), source_backend=Backend.DISK) + + +def test_store_singleton_addresses_need_declared_component_identity(): + config = _config() + projector = SourceBindingWorkspaceProjector(config) + candidates = projector.source_candidates(ROOT, PATHS, source_backend=Backend.DISK) + # This reproduces the parent's stated store-plane boundary without reading TIFFs. + singleton = OpenHCSPlaneAddress.from_values( + well="A01", site="1", channel="1", z_index="1", timepoint="1", + ) + candidates = tuple(replace(item, declared_address=singleton) for item in candidates) + metadata_only = replace(config, bindings=tuple( + replace(binding, component_identity=()) for binding in config.bindings + )) + old_projector = SourceBindingWorkspaceProjector(metadata_only) + old_selected = old_projector._candidates_by_alias(ROOT, candidates, filemanager=None) + old_sets = SourceSetAssembler.for_config(metadata_only).source_sets( + metadata_only.match_plan, old_selected, (), + ) + with pytest.raises(ValueError, match="Duplicate source projection address"): + SourceProjectionSet(old_projector._source_set_projections(metadata_only.bindings, old_sets)) + + selected = projector._candidates_by_alias(ROOT, candidates, filemanager=None) + sets = SourceSetAssembler.for_config(config).source_sets(config.match_plan, selected, ()) + projections = SourceProjectionSet(projector._source_set_projections(config.bindings, sets)) + assert len(projections.projections) == 4 + assert tuple(( + projection.address.value_for(AllComponents.WELL), + projection.address.value_for(AllComponents.SITE), + projection.address.value_for(AllComponents.CHANNEL), + projection.address.value_for(AllComponents.Z_INDEX), + projection.address.value_for(AllComponents.TIMEPOINT), + ) for projection in projections.projections) == ( + ("A01", "1", "1", "1", "1"), ("A01", "1", "2", "1", "1"), + ("A01", "1", "1", "2", "1"), ("A01", "1", "2", "2", "1"), + ) + assert {projection.ref for projection in projections.projections} == { + item.source_ref for members in selected.values() for item in members + } diff --git a/docs/refactor/344-engineering-acceptance.rst b/docs/refactor/344-engineering-acceptance.rst index 46fed46020..2556bd77e9 100644 --- a/docs/refactor/344-engineering-acceptance.rst +++ b/docs/refactor/344-engineering-acceptance.rst @@ -1,140 +1,146 @@ -PR344 engineering document handoff -================================= +PR344 engineering document and acceptance disposition +==================================================== Runtime source checkpoint: a14d471e3f2a92148f88a60b6c972e1a49f67db0. -Parent owns installed integration with main 05c3cf288 and the sole native -5993 slot. This child has not loaded fixture pixels, compiled the document, -started MCP/native/viewer, or executed a pipeline. This is not H003g, a -scientific retry, biological validation, or an installed acceptance receipt. - -Complete source ---------------- - -``examples/344-aligned-rescale-engineering.py`` is one complete public Python -PipelineDocument: pipeline_config plus one ordered FunctionStep. Submit the -entire file through the ordinary MCP document authoring/validation/compile -route. Do not call a custom function, construct runtime arrays or invoke the -contract executor as a substitute for that route. Imports are explicit in -the source; input/output keyword keys come from -RescaleIntensityModule.declared_artifact_bindings().require_parameter_name(). - -Fixture request for the parent ------------------------------ - -Use the existing synthetic ImageXpress fixture infrastructure, not any frozen -H003g input or artifact. Proposed separate root:: - - /home/ts/wt/openhcs-344-engineering-20261001/raw/EngineeringPlate/ - TimePoint_1/ZStep_1/plate_A01_s1_w1.tif - TimePoint_1/ZStep_1/plate_A01_s1_w2.tif - TimePoint_1/ZStep_2/plate_A01_s1_w1.tif - TimePoint_1/ZStep_2/plate_A01_s1_w2.tif - -Each file: one 32x32 uint16 plane, one site, one timepoint; distinct channels -and Z planes. One deterministic nonconstant engineering pattern is -``1000*(channel-1) + 100*(z-1) + 32*y + x`` with channel/z in {1,2} and -x/y in [0,31]. Record actual fixture creation, input hashes and inventory in -the parent's receipt; no fixture files were created by this child. - -Two typed aliases explicitly select channel 1 and channel 2. Step variable -components select Z_INDEX, group_by is NONE, and both aliases are enabled. -There are no embedded stack axes in a 2-D file: source_stack_components -deliberately remains empty. The existing source-bound artifact resolver loads -each alias's members and calls stack_image_payloads in RUNTIME_SLICE mode -(core/runtime_adapters.py). Two declared primary image inputs then pass -through CellProfilerModuleExecutor._image_request and -compose_aligned_image_payload: an AlignedImageStack with a two-channel bundle -per Z slice. The callable's FULL_STACK mode overrides slice execution. -This is the original primary carrier failure path, not an auxiliary kwarg -or the ordinary single dense two-channel input path. - -Compile identity gates, before execution ---------------------------------------- - -Require the actual inventory to contain A01/site 1/timepoint 1, channel 1/2, -Z 1/2. Main 05c3cf288 includes the parent's raw ImageXpress ZStep fix. -Reject a flattened singleton-Z inventory rather than accepting a different -test. Require the registered declaration owner RescaleIntensityModule, -function_name rescale_intensity, ProcessingContract.PURE_2D and -ImagePayloadExecutionMode.FULL_STACK. The public document authority -canonicalizes decorator callables through RegistryService: callable object -identity before/after normalization is NOT the identity gate. Its canonical -raw callable and module declaration owner are the gates. - -Require exactly two ImageArtifactType input occurrences, in declared order: -EngineeringCH1 and EngineeringCH2. Both declaration bindings have -runtime_parameter_name None; compiled artifact input parameter_name is None. -No auxiliary runtime keyword image is injected. Each alias's source payload -must retain two exact Z members in RUNTIME_SLICE order. The composed primary -must be aligned before the full-stack contract materializes it, and its dense -callable input should be (2 Z, 2 bindings, 32 Y, 32 X). These are acceptance -requirements inferred from inspected production authorities, NOT a claimed -compile or native observation. Preserve the observed typed plan and logs; -if the entrypoint does not expose carrier evidence, do not invent it from a -successful run or from file/channel count alone. - -Require one output ImageArtifactType named EngineeringRescaled. Its declared -SourceStackLineageSourceRelation is anchored to EngineeringCH1 by -RescaleIntensityModule.artifact_output_relations. Output contextualization -and materialization remain owned by the existing output policies. This -declaration does not promise a new four-source output identity contract. - -Addresses, pixels and metadata gates ------------------------------------ - -Configured output plate root:: - - /home/ts/wt/openhcs-344-engineering-20261001/output/EngineeringPlate_openhcs - -For axis A01, step 0 and no grouping key, PathPlannerPaths.artifact_path -derives this canonical runtime artifact address:: +Parent integrated current main and owns installed/native acceptance. Later +child checkpoints change only authoring examples, diagnostic checks and receipts. +H003g remains permanently FAILED and untouched. This is engineering, not biology. + +Corrected complete source +------------------------- + +examples/344-aligned-rescale-engineering.py is one complete PipelineDocument +with pipeline_config and one ordinary registered RescaleIntensity FunctionStep. +Its imports and declaration-derived input/output keyword names are explicit. +It contains no custom callable, executor wrapper, arrays or pixel-file operations. + +The current recipe adopts the parent's successfully admitted private engineering +document's acquisition declarations, with only this example's output root/header +different. Submit the entire source via normal MCP authoring/compile/run. +Never strip its pipeline source bindings or substitute another config argument. + +Separate fixture: the parent's cp-stack-installed-20261001/fixture contains +eight 2-D TIFFs, sites 1/2, channels 1/2, Z 1/2, timepoint 1. Representative +physical spelling:: + + TimePoint_1/ZStep_1/A01_s001_w1_z001_t001.tif + TimePoint_1/ZStep_2/A01_s001_w2_z002_t001.tif + +Required existing declarations: + +* source_filters EXTENSION / IS_TIF excludes HTD and other sidecars. +* FILE_NAME MetadataExtractionRule extracts well/site/channel/z_index/timepoint + from the actual verified filename grammar. Zero padding is excluded from the + numeric capture, so s001 resolves site "1", not a new site "001". +* METADATA SourceBindingMatchPlan explicitly pairs both aliases by + well/site/z_index/timepoint. Channel distinguishes aliases, not the pair key. +* Both typed selectors restrict SITE "1" and their respective CHANNEL. +* Each NamedSourceBinding.component_identity explicitly declares CHANNEL "1" + or "2", selecting the documented semantic coordinate projection. +* Calibration is (4.0, 0.5, 0.5) micrometers Z/Y/X. There are no embedded stack + axes in a 2-D file, so source_stack_components remains empty. The step declares + variable Z_INDEX, GroupBy.NONE and enabled inherited source bindings. + +Source diagnosis and ownership +------------------------------- + +Inspected source: public 327cec9f6 and parent candidate c7ed2acc4. Their +source_binding_workspace.py is byte-identical. SourceBindingWorkspaceProjector +source_candidates (line 886) builds file candidates from declared extraction +rules, not an injected native filename parser. _component_is_compatible permits +absent coordinates (line 997); _candidate_with_binding_components then assigns +selector coordinates. Without acquisition metadata, both aliases therefore +select the same physical universe; the ORDER ambiguity guard correctly rejects it. + +ImageXpress inherits MicroscopeHandler.projects_declared_source_bindings False. +The current create_microscope_handler factory selects SourceBindingsHandler for +nonempty bindings when the requested owner does not project them. Raw inspection +without bindings can retain ImageXpress and parse its native coordinates. Thus +IMAGEXPRESS in pipeline source alone does not certify the resolved ingestion owner. +The child construction-only test verifies the factory route, not the parent's +live handler class; preserve actual handler identity in the parent receipt. + +For store-emitted candidates, _source_set_projections (line 1157) retains +declared_address unless component_identity is explicitly declared. Metadata +extraction alone does not override a store's singleton address. NamedSourceBinding +documents component_identity as authoritative over inferred store coordinates +(source_bindings.py line 867). Explicit channel identity invokes the existing +coordinate projection; matched metadata supplies well/site/Z/time. + +Disposition: the minimal public recipe omitted required acquisition declarations. +It was not a compiled valid native-alias recipe. Its inference of native alias +projection was wrong. The existing native handler does not promise that capability; +automatic propagation is a product/ingestion limitation, not a proven regression +of a promised alias-projection contract. No production intake, selector, guard, +dispatcher or executor changes are made. NRA BOUND-2 guidance keeps identity with +the existing metadata/binding/coordinate owners rather than adding a second parser. + +Predecessors are not relabelled as passes. Parent reports four original admission +attempts retained, including same-ref ORDER rejection, duplicate projection address, +and HTD lacking well identity. Public predecessor source survives at 327cec9f6 +and inside the original a14 supplemental archive. The promoted example now carries +the complete admitted acquisition declarations rather than the invalid minimal form. + +Plans, occurrence evidence and output scope +------------------------------------------- + +Expected projected source inventory: A01/site1/time1, four virtual files +CH1/2 x Z1/2, with exact physical refs and calibration. Both RescaleIntensity +declaration inputs are primary ImageArtifactType occurrences with no runtime +parameter injection. Callable mode is FULL_STACK, contract PURE_2D. + +The public artifact-plan artifact_inputs list is not the complete input-occurrence +surface: _bounded_step_summaries renders step_plan.artifact_inputs storage plans. +PathPlanner skips a storage input plan when an exact source binding satisfies it +(path_planner.py line 1817). Exact invocation occurrences instead live in +CompiledFunctionInvocation.artifact_input_edges and contract.artifact_inputs. +RuntimeInputBindingRequest selects those declarations through RuntimeAdapterRequest, +then resolves a source-satisfied edge via source_binding_plan/source_artifact_payload. + +For direct carrier proof, inspect those exact selected occurrences, their two +source bindings, runtime source payload axes and composed primary value before +the FULL_STACK projection. An empty storage-plan list does not prove missing +bindings, and a successful multi-plane output does not prove the carrier's type. +The actual MCP surface did not expose carrier or validity-mask inspection. + +EngineeringRescaled declares SourceStackLineageSourceRelation to EngineeringCH1. +Output source identity must follow that first-source lineage, not a fabricated +four-source output contract. Output plate root for this published example:: + + /home/ts/wt/openhcs-344-engineering-20261001/output/fixture_openhcs + +For plate name fixture, well A01, step0, no grouping key, the canonical runtime +artifact-store address is:: results/A01_EngineeringRescaled_step0.pkl -This is an artifact-store address, NOT a claim that a durable pickle exists. -ImageArtifactType projects disk exports under ``images/EngineeringRescaled`` -when its writer uses plane projection, or uses its declared source-identity -filename policy for scalar exports. Retain exact compiled output/materialization -plans and returned artifact descriptors before asserting TIFF suffixes or -export filenames; this child has not compiled or observed those paths. - -For the proposed integer pattern, the dense default stretch expectation is -``(input - 0) / 2123`` across both Z planes and both source bindings. Confirm -the actual callable normalization/dtype policy and compare every output -plane against the recorded fixture, not just extrema or a run-success flag. -The original failing full-stack path would raise float(AlignedImageStack) -before emitting the image. Preserve a real original failure if available; -do not reinstall/replay an old candidate merely to manufacture that receipt. - -Configuration declares synthetic physical calibration (4.0, 0.5, 0.5) -micrometers in Z/Y/X order, and both source aliases retain their exact source -paths, channel/Z coordinates and native 32x32 spatial domain. Inspect typed -metadata at input composition and output contextualization separately. -The input composition must retain all four source contributors and both -aliases; output source scope follows the actual first-source lineage relation. -Do not silently equate a virtual workspace path with its physical raw path: -resolve provenance through the recorded source projection before comparing. -Calibration metadata preservation is not a physical measurement validation. - -Ordinary raw TIFFs carry no validity mask: require mask None to remain None. -``load_as_mask`` converts pixel values to booleans; it does NOT manufacture -a validity mask. Nontrivial MaskedImagePayload preservation and independent -mask capability MRO cases are covered by the source family controls. A live -nontrivial-mask claim would require a separate parent-approved typed masked -fixture/path; this minimal document does not claim that coverage. - -Source-only checks ------------------- - -diagnostics/test_344_engineering_document.py executes only the Python -configuration document through PipelineDocumentAuthority.from_source and -checks declared source selectors, calibrated config, step axis and canonical -registered identity. It does not load data, compile or execute a pipeline. -The initial object-identity assertion failed because canonical normalization -replaces the decorator wrapper; that receipt is retained. The corrected test -uses the owning module and canonical raw callable identity instead. - -No biological guide/validated assay recipe was retrieved or claimed. The -use-openhcs skill's complete-document rule applies, but the parent's explicit -source-only/no-MCP instruction defers its live catalog/schema/compile gates -to the installed acceptance owner. Do not label this source check MCP validated. +This is not a promised durable pickle. Compile/materialization plans own actual +TIFF destinations; retain the descriptors rather than guessing filenames. +The earlier EngineeringPlate example root changes if that is the input basename. + +Bounded source checks and parent acceptance +------------------------------------------- + +Child source-only checks parse the complete document and verify registered owner/ +canonical raw callable identity. Pure synthetic path/declaration checks reproduce +the ambiguity and singleton-address failures, then prove four unique coordinates +with the same physical SourcePixelRefs. No TIFF pixels are loaded, no workspace is +initialized, and no pipeline is compiled/executed by this child. A first conflict +test used the wrong exception class; its 3-pass/1-fail receipt is retained, and the +corrected assertion preserves the actual existing RuntimeError contract. + +Parent's reported installed/native gate (2026-10-01): same owned native5993, +ordinary MCP compile job1 COMPLETE in 1.823s; execution job2 COMPLETE in 0.745s. +Main-flow and EngineeringRescaled each yielded two Z TIFFs, each (2,32,32) float32. +MCP samples were compared against all four raw planes with global stretch +min90/max8405: 8192 pixel comparisons across both destinations, maximum error +1.23e-7 and zero errors over 1e-6. Parent reports exact declared calibration and +first-source CH1/Z scope, and retains the actual native observation export. +These are parent observations, not independently rerun child measurements. + +This clears the reported installed dense ABI continuity gate, not direct carrier/ +mask inspection or biology. Raw TIFF validity masks are None; source MaskedImagePayload +and capability-MRO controls are separate evidence. Child source117+45 and parent's +revised installed21 cases remain distinct from this continuous MCP/native gate. +R1 remains unqualified. Parent alone closes/verifies owned processes, archives live +receipts and integrates the public PR. No frozen H003g retry or held-out access occurs. diff --git a/docs/refactor/examples/344-aligned-rescale-engineering.py b/docs/refactor/examples/344-aligned-rescale-engineering.py index 0b1b7a92b6..b0a2c41066 100644 --- a/docs/refactor/examples/344-aligned-rescale-engineering.py +++ b/docs/refactor/examples/344-aligned-rescale-engineering.py @@ -1,37 +1,17 @@ # OpenHCS pipeline -# Synthetic engineering fixture only. Parent owns fixture creation and MCP execution. +# Corrected engineering recipe; predecessor failure remains in Git/receipts. from pathlib import Path - from openhcs.constants import AllComponents, GroupBy, Microscope, VariableComponents from openhcs.constants.input_source import InputSource from openhcs.core.artifacts import ArtifactInputPlan, ArtifactOutputPlan, ImageArtifactType -from openhcs.core.config import ( - LazyPathPlanningConfig, - LazyProcessingConfig, - LazyVFSConfig, - MaterializationBackend, - PipelineConfig, -) -from openhcs.core.source_bindings import ( - ComponentSelector, - LazySourceBindingsConfig, - LazyStepSourceBindingsConfig, - NamedSourceBinding, - SourceSelector, -) +from openhcs.core.config import LazyPathPlanningConfig, LazyProcessingConfig, LazyVFSConfig, MaterializationBackend, PipelineConfig +from openhcs.core.source_bindings import ComponentSelector, LazySourceBindingsConfig, LazyStepSourceBindingsConfig, MetadataExtractionRule, MetadataSource, NamedSourceBinding, SourceBindingMatchDimension, SourceBindingMatchField, SourceBindingMatchMethod, SourceBindingMatchPlan, SourceFilterClause, SourceFilterMatchType, SourceFilterSubject, SourceSelector from openhcs.core.source_metadata import SourceVoxelSpacing, SourceVoxelSpacingUnit from openhcs.core.steps.function_step import FunctionStep -from openhcs.processing.backends.cellprofiler.intensity import ( - RescaleIntensityModule, - rescale_intensity, -) +from openhcs.processing.backends.cellprofiler.intensity import RescaleIntensityModule, rescale_intensity -primary_binding, reference_binding = RescaleIntensityModule.declared_artifact_bindings( - plan_type=ArtifactInputPlan, artifact_type=ImageArtifactType, -) -(output_binding,) = RescaleIntensityModule.declared_artifact_bindings( - plan_type=ArtifactOutputPlan, artifact_type=ImageArtifactType, -) +primary_binding, reference_binding = RescaleIntensityModule.declared_artifact_bindings(plan_type=ArtifactInputPlan, artifact_type=ImageArtifactType) +(output_binding,) = RescaleIntensityModule.declared_artifact_bindings(plan_type=ArtifactOutputPlan, artifact_type=ImageArtifactType) pipeline_config = PipelineConfig( num_workers=1, @@ -44,22 +24,22 @@ ), vfs_config=LazyVFSConfig(materialization_backend=MaterializationBackend.DISK), source_bindings_config=LazySourceBindingsConfig( - source_voxel_spacing=SourceVoxelSpacing( - (4.0, 0.5, 0.5), SourceVoxelSpacingUnit.MICROMETERS, + source_filters=(SourceFilterClause(SourceFilterSubject.EXTENSION, SourceFilterMatchType.IS_TIF),), + metadata_rules=(MetadataExtractionRule( + MetadataSource.FILE_NAME, + r"(?PA01)_s0*(?P[1-9][0-9]*)_w(?P[1-9][0-9]*)_z0*(?P[1-9][0-9]*)_t0*(?P[1-9][0-9]*)\.tif$", + ),), + match_plan=SourceBindingMatchPlan( + method=SourceBindingMatchMethod.METADATA, + dimensions=tuple(SourceBindingMatchDimension(fields=tuple( + SourceBindingMatchField(alias=alias, metadata_field=field) + for alias in ("EngineeringCH1", "EngineeringCH2") + )) for field in ("well", "site", "z_index", "timepoint")), ), + source_voxel_spacing=SourceVoxelSpacing((4.0, 0.5, 0.5), SourceVoxelSpacingUnit.MICROMETERS), bindings=( - NamedSourceBinding( - alias="EngineeringCH1", - selector=SourceSelector( - components=(ComponentSelector(AllComponents.CHANNEL, "1"),), - ), - ), - NamedSourceBinding( - alias="EngineeringCH2", - selector=SourceSelector( - components=(ComponentSelector(AllComponents.CHANNEL, "2"),), - ), - ), + NamedSourceBinding(alias="EngineeringCH1", selector=SourceSelector(components=(ComponentSelector(AllComponents.CHANNEL, "1"), ComponentSelector(AllComponents.SITE, "1"))), component_identity=(ComponentSelector(AllComponents.CHANNEL, "1"),)), + NamedSourceBinding(alias="EngineeringCH2", selector=SourceSelector(components=(ComponentSelector(AllComponents.CHANNEL, "2"), ComponentSelector(AllComponents.SITE, "1"))), component_identity=(ComponentSelector(AllComponents.CHANNEL, "2"),)), ), ), ) @@ -71,11 +51,7 @@ reference_binding.require_parameter_name(): "EngineeringCH2", output_binding.require_parameter_name(): "EngineeringRescaled", }), - processing_config=LazyProcessingConfig( - input_source=InputSource.PIPELINE_START, - variable_components=[VariableComponents.Z_INDEX], - group_by=GroupBy.NONE, - ), + processing_config=LazyProcessingConfig(input_source=InputSource.PIPELINE_START, variable_components=[VariableComponents.Z_INDEX], group_by=GroupBy.NONE), source_bindings=LazyStepSourceBindingsConfig(enabled=True), ), ] diff --git a/docs/refactor/receipts/cp-aligned-full-stack-342-acquisition.tar.gz b/docs/refactor/receipts/cp-aligned-full-stack-342-acquisition.tar.gz new file mode 100644 index 0000000000000000000000000000000000000000..ceb9fd61e3f44b32816b3dcf954f8e15ccb3df84 GIT binary patch literal 35719 zcmV(#K;*w4iwFP!000001MEF(bKAyt`K(`o@Jq=%6ax|jK&pZ#&+6D*hH-+Ab}>c8aUEyDR%bARE7%lTrt2)}aY 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00:00:00 2001 From: Tristan Simas Date: Thu, 1 Oct 2026 04:13:33 -0400 Subject: [PATCH 8/8] Record installed MCP native acceptance for aligned full-stack rescaling --- .../344-installed-native-acceptance.rst | 123 ++++++++++++++++++ ...stack-installed-native-344-20261001.tar.gz | Bin 0 -> 199971 bytes 2 files changed, 123 insertions(+) create mode 100644 docs/refactor/344-installed-native-acceptance.rst create mode 100644 docs/refactor/receipts/cp-stack-installed-native-344-20261001.tar.gz diff --git a/docs/refactor/344-installed-native-acceptance.rst b/docs/refactor/344-installed-native-acceptance.rst new file mode 100644 index 0000000000..af0c7516cd --- /dev/null +++ b/docs/refactor/344-installed-native-acceptance.rst @@ -0,0 +1,123 @@ +PR344 installed native engineering acceptance +============================================ + +Integration owner: parent. Source owner: Darwin. Runtime source a14d471e3; +paired private integration c7ed2acc4 includes main 05c3cf288. Documentation-only +327cec9f6 was normally merged afterward at 29e08a1c9. All three changed +production files are byte-identical to the installed wheel and a14 source. +No worker worktree, frozen trial, user desktop or global package was modified. +The example correction a422c4f08 changes only authoring/diagnostics/receipts, +not the installed production code. + +BOUND-2 / IMPL-12 / IMPL-13: existing ImagePayloadStackComposition owns the +shared pixel/mask/provenance algorithm; nominal projection hooks materialize +aligned primary and auxiliary images. Cooperative capability MRO checks are +source/installed tests, not a new production mixin-family claim. The original +R0 source guard passes; full NRA/R1 remains unqualified for the reasons in +cp-aligned-full-stack-342.rst. This gate does not clear that missing audit. + +Installed candidate +------------------- + +Private interpreter: /home/ts/wt/openhcs-cp-stack-installed-parent-20261001/.venv. +Revised wheel SHA256: +5e4fc51f8d6c28ed73ae9dc1a3ac68126eee37cf0ddb7e37e797694ca29a8f0e. +Build: PASS, 7.32 seconds, 249.61 MiB combined RSS, one CPU/512 MiB/60 seconds. +Actual installed numeric controls: 21 PASS, 2.81 seconds wall, 269.38 MiB RSS. +These include opaque kwargs, calibrated subtype, exact pixels/masks/provenance, +named source bundles and independent capability composition in both MRO orders. + +Original installed predecessor and failures remain separately retained: its +15 numeric cases passed, but the additional opaque-kwarg check failed with +RuntimeSliceProjectionDeclarationError. The first pytest invocation failed +before collection because of a repository plugin; the isolated invocation +disables repo-only configuration without weakening tests. No failed receipt +was overwritten or relabelled as revised acceptance. + +Continuous installed MCP/native journey +-------------------------------------- + +Engineering root: +/home/ts/wt/openhcs-issue-batch-20260929/cp-stack-installed-20261001. +Actual installed dev-client shell used ordinary 10-second observation limits. +Health was current, packaged resources ready, no source drift. CPU-only owned +TCP 127.0.0.1:5993 native process 918063/create_time 1790840817.41 was started +ONCE through MCP, observed by its complete handle and retained through cold +capability preparation until READY. Function catalogue preparation then reported +READY on that same incarnation. No retry/restart on observation expiration. + +MCP generated a fresh ImageXpress fixture: eight 32x32 uint16 files, two sites, +two channels, two Z planes, one A01/timepoint. The complete PipelineDocument +selects site 1 only, two named primary sources, Z_INDEX, GroupBy.NONE and the +ordinary registered CellProfiler RescaleIntensity callable. No direct array +executor, custom wrapper, H003g data or scientific parameter reuse was involved. + +The initial engineering document was incomplete at acquisition ingress. Three +failed artifact-plan admissions are retained in order: identical ORDER source +references, duplicate projection address, then unfiltered HTD missing well +metadata. Correct authoring uses existing typed authorities: TIFF source filter; +explicit filename metadata extraction; METADATA pairing by well/site/Z/time; +explicit channel component_identity. The ambiguity guard was never bypassed. +These source declarations distinguish selection, acquisition identity and source +pairing; they are not processing-function filename parsing or library patches. +The requested IMAGEXPRESS enum is not proof of the effective alias-ingestion +owner. Its handler does not project declared bindings; the existing factory +selects SourceBindingsHandler for this document. Native execution here means +the real installed execution server, not a claimed native-vendor alias handler. +The original minimal recipe was incomplete; no promised ingestion regression +was demonstrated and no production source-selection fix was introduced. + +The final artifact plan has exactly four distinct physical planes and aliases +EngineeringCH1/EngineeringCH2 across Z1/Z2, all at site1/A01/timepoint1. Source +metadata retains exact physical paths and explicitly declared synthetic physical +spacing (4,0.5,0.5) micrometers. This override is an engineering metadata check, +not a measured physical calibration of the generated assay. + +Headless session session-1: compile job-1 / aa473313-f45c-478c-bac1-103d42acd9d9 +COMPLETE in 1.823 seconds; execution job-2 / +3a9bf8c4-dec9-4960-b25c-db5fcae07499 COMPLETE in 0.745 seconds. Execution also +recompiled through the ordinary route; no compile-cache speed claim. Runtime +observation was exported through MCP and retained without an external image +decoder. Native step compute was 0.035 seconds. No UI/viewer was launched. + +Output verification and limits +------------------------------ + +MCP inspected/query/sampled the actual output plate. Both main-flow and named +EngineeringRescaled destinations contain two Z-position TIFFs; each is a +float32 (2,32,32) source-binding bundle. Exact full-resolution MCP samples of +the four raw planes and all four output files compare every output pixel to +(input-90)/(8405-90). Across 8192 comparisons the maximum absolute error is +1.2279345340537873e-7; zero exceed 1e-6. Both bindings and both Z positions are +numerically exercised, not merely nonzero/extrema checked. + +Output metadata correctly follows the declared FIRST-source lineage: CH1 alias, +Z1/Z2, original source paths and declared spacing survive. This is not a new +all-contributor output-provenance contract. Input plan inspection has four +source-workspace entries but artifact_inputs is empty for bound sources; the +surface does not directly expose the composed invocation carrier. Accordingly +this receipt does not claim direct native carrier or nontrivial validity-mask +inspection. Those nominal/mask witnesses are separate source/installed controls. +Output inspection reports its missing grid_dimensions warning; it is retained, +not hidden by successful pixel comparisons. No biological completeness, counts, +held-out generalization or segmentation QA is inferred. + +Same-handle MCP force close acknowledged, endpoint terminated, process_exited +true. Parent confirmed MCP/client/native PIDs absent and 5993/6993 listeners +gone; the shell's exit status1 is retained, not reported as a clean CLI exit. +No foreign endpoint or user's isolated H002 viewer was touched. + +verify_mcp_acceptance.py replays only recorded JSON payloads: PASS, 0.15 seconds, +15.48 MiB RSS. It asserts all three original admission failures, final source +identity/calibration, exact job scope, all pixel values and exact owned close. +Archive includes raw transcript/input/timing, fixture/output, complete document, +runtime observation, installed JUnit/build/failure logs and verifier. Wheel files +remain local and are identified by hash; no redundant binary wheel is in Git. +Archive: receipts/cp-stack-installed-native-344-20261001.tar.gz (199971 bytes), +SHA256 d6d53528b2a8508f4004a6d1d6b7adfc411a7dea9a1ed1844bb19736731faad5. +Fresh extraction reran the recorded-payload verifier successfully and compared +the extracted transcript byte-for-byte to its original. + +Remaining: full NRA/R1 disposition, wider S1/ZIP closure, updated paired install +and a NEW bounded context-isolated blind run with distributed matched visual QA. +Frozen H003g remains FAILED; this is neither its replay nor biological acceptance. diff --git a/docs/refactor/receipts/cp-stack-installed-native-344-20261001.tar.gz b/docs/refactor/receipts/cp-stack-installed-native-344-20261001.tar.gz new file mode 100644 index 0000000000000000000000000000000000000000..483b0fb9226ba407eb3ba1bd4ed1f22a1ea96699 GIT binary patch literal 199971 zcmV)DK*7HsiwFP!000001MFP=bJ|9??$7!w_VRY7b_aw6*x2Oq-XS)rd20hTq-k#6 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