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fix: reopen declared native output checkpoints through original inventory - #399

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fix/persisted-result-reopen-20261001
Oct 1, 2026
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trissim merged 5 commits into
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fix/persisted-result-reopen-20261001

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@trissim trissim commented Oct 1, 2026 •

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Status: DONE for reader/inventory/bounded-sample/ordinary saved-image reopen. Merged e3765e3 at2026-10-01T21:45:10Z; production remains reviewed6cea76331. Installed stream qualification is precisely paired with Lorentz397229dea725dd0cc82c4fae06835617ac19c5d7722, not the earlier unpaired stream. Closes #398 image scope; broad graph reopening #134 / shared writer #394 is separate and unfinished.

Parent actual private installed PUBLIC MCP acceptance: all9 inventory records; candidate_mask and unrooted_residual resolution0 samples at exact origin180,745/shape40x45/integer channel2/calibration1.3556. Fresh ordinary saved candidate stream, native readback and render-complete capture PASS. Native payload1024x1024 uint8, Site1/Ch2/Z1/T1/A01, calibration1.3556; summary9815 nonzero binary0..1. Parent personally opened both default black capture (display0..255) and revealed binary capture after original MCP intensity control0..1/gamma1. No biological pipeline pass: candidate1b remains REJECTED.

Original evidence under paired397-388-installed-20261001: reopen399-installed-read-native-channel/ACCEPTANCE.json, reopen399-installed-viewer-projected/transport-and-capture.json, reopen399-projected-binary-review/REVIEW.json. Capture receipts retain original5000ms deadline/2.5s observation bound and completed native frames. The original wrong string-channel harness failure and original aggregate-domain stream007 failure remain preserved; acceptance follows the separately owned producer fix, not replay or evidence rewriting.

Owner architecture: existing OpenHCSMetadataHandler reuses its conflict-checked no-main native output projection and original document loader; duplicate JSON reader deleted. Generic inventory, sampler and streaming consumers have no399 edits; no new registry/receipt fabrication/guard weakening. Independent extra declaration passes unchanged consumers. Source18 PASS /45 explicit unrelated deselections, original pinned R0 PASS with class excess183 to168 and other deltas zero. Full-context NRA512MiB OOM remains incomplete, not waived or claimed globally clean.

Canonical receiving receipt docs/validation/persisted-result-reopen-398.rst is updated in docs-only follow-up #403 at5d38ecad7. Diataxis reference treatment keeps engineering acceptance separate from biological judgement. Original byte-exact source failures/archive retained; prior owned scratch4.3MiB already released. No new scratch, source implementation, installation, tests, native startup or runtime interaction for this docs update. Exact parent viewer2339091/create1790890853.17 DISPLAY91/5992 remains parent/Dalton handover-owned; no authority to edit its frozen environment. Singer retains coordinated394 graph-sidecar seam, not historical unbound graph recovery.

@trissim trissim changed the title fix: reopen declared native persisted result images fix: reopen declared native output checkpoints through original inventory Oct 1, 2026
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trissim commented Oct 1, 2026

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Singer: Lorentz owns parent-assigned PR397 follow-up for the terminal installed selected-checkpoint image stream failure paired with399 at8d0480ef. I am tracing producer pixel-axis declarations through ordinary persisted TIFF/manual image streaming, including a plain-TIFF regression. Strict NapariAggregateAxisBindingAuthority stays unchanged; no historical metadata/source receipt rewrite or native replay. I will avoid your microscopes/openhcs.py surface unless the trace requires an explicit shared-owner change; source-only tested checkpoint remains in397. Please flag any overlap you are already implementing.

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Receiving acceptance update: installed PUBLIC MCP inventory9 and resolution0 candidate/unrooted samples PASS (exact origin180,745/40x45/int channel2/calibration1.3556); original string-versus-int harness failure retained separately. Subsequent ordinary saved candidate stream007 FAILED, not timed out, at native exact plane_component_values guard. Parent owns live viewer2263287/create1790888684.96 and closure, no replay. Existing saved pixels retain one source_binding axis; ordinary producer item_fields omits the singleton exact domain. Parent-authorized Lorentz397 owns that declaration-producer repair; detailed source boundary/required original receiver fixture posted at comment5940614032. No397 or399 production edits, native/runtime/package operations or guard weakening. Updated receiving RST retains original request/response hashes and fixture coverage limitation;399 installed stream/capture remains FAILED/pending repair, not accepted.

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trissim commented Oct 1, 2026

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Installed saved-image reopening checkpoint

Parent integration source 8d0480e
combines main402, existing388/397, and Singer3997b38. This is a private
integration installation, not canonical main or a changed global package.
Offline wheel bce59f7b8724b2d5c9c380892b3933ab7d58efb383381a75ac63975fc797a99e
built in12.77s/227MiB and installed in4.13s/86.23MiB without dependency
downloads. Installed native metadata handler matches reviewed source:
0ee1d23324f21963f913d14136da2563f6c899a1a70b88785520a6c1be27dd69.

Actual public MCP health/contexts/discovery precede every journey. Ordinary
tool observation remains10s; the original declared dev-client decoder and
PublicJourney journal are reused unchanged. No scientific job is replayed.

Working installed path

reopen399-installed-read-native-channel/ retains the fresh installed public
inventory and resolution0 samples from the original candidate1b metadata-owning
input_openhcs root. Nine image records, zero errors/warnings/truncation.
candidate_mask and unrooted_residual retain exact physical references,
channel2/FITC, source calibration1.3556um/pixel, native source shape[1,1024,1024].
Both exact samples originate at(180,745), shape[1,40,45], with all1800 values
included. No result_directory, historical viewer receipt, synthetic metadata,
new decoder or direct TIFF read was used. Acquisition/candidate bytes unchanged.

The initial harness expected channel='2', but the real declared checkpoint
metadata stores integer2. Its failed assertion and successful inventory remain
in reopen399-installed-read/. The harness expectation was corrected to the
observed native contract, not the product or original receipt.

Remaining actual viewer defect

reopen399-installed-viewer/007 retains the single original public saved-image
stream request and terminal plate_file_stream_failed result. The viewer started
on DISPLAY=:91 as PID2263287/create_time1790888684.96. Its actual stack reaches
NapariAggregateAxisBindingAuthority.bindings and refuses the absent exact
plane_component_values declaration. This is a producer-declaration defect,
not an observation deadline, absent file, or no-main metadata failure.

Lorentz owns397 and this declaration producer correction; Singer399 coordinates
that crossing. No viewer guard weakening, rank-based axis inference, old
metadata rewrite, restart, or original stream replay is authorized as a repair.
Full installed viewer reopening is not accepted yet;399 remains open.

Exact parent-owned failed viewer was observed and closed through MCP.
reopen399-failed-viewer-disposition/CLOSED.json proves process_exited=true;
independent ps and listener checks confirm2263287/resource tracker gone and
5992/6992/5993/6993 clear. Desktop0 and H00290/5690 were not changed.

Earlier original native2153942 was also positively closed via exact owned
runtime MCP. Its registration009 remains originally failed/uncertain despite
positive read-only persisted-source/catalog reconciliation. Public020 failed
before compilation/execution at enum kwargs; Dewey388 owns that ingress repair.
Do not adopt the old handles as live or replay old jobs/registration.

closed-native-and-reopen399-viewer-logs.tar.gz retains the exact native log,
startup JSONL and failed viewer log. SHA256
d98703af89d86491f9d4b94576088000e52bcded3de73b1628266720b1173e76.
tar comparison against all originals passed. Owned compilation/cache contents
remain available for reuse; the archive is persistent, not a volatile handoff.

Scientific continuation

Dalton resumed in the same assisted2 context for original site001. Canonical
saved-stage MCP reads now work; independent stage diagnosis and preparation of
one discriminating repair can continue while397 repairs viewer transport.
No counts/parameters/answer coaching was supplied by the parent. Original
rejected candidate and frozen383 remain preserved. Eight reserve-site pixels
and reference answers stay sealed. Current evidence is development/engineering,
not a new accepted autonomous biological analysis.

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trissim commented Oct 1, 2026

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Trace: original saved image_metadata explicitly declares SOURCE_BINDING with exactly one runtime provenance plane; plain2D projections have no leading axis. Manual ImageStreamingRequest currently validates native windows but forwards the retained singleton to strict binding with no varying component domain. Proposed397 source-only extension: existing ImageStreamingRequest owns display-plane projection derived from declared plane_axis + provenance count, delegated to original RuntimeSliceProjection (validates exact shape and preserves masks/calibration); StreamingService invokes that nominal request method after existing window admission. FullWindowImageStreamingRequest retains cooperative full-window validation before display projection. No edits to your metadata handler, PR394 runtime projection owners, viewer guard, or historical files.

@trissim

trissim commented Oct 1, 2026

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Installed ordinary saved-image reopening and viewer acceptance

Parent integration source8fa891db7707006a3ae8a7d65558ee846f0bf0e1 contains
PR3998388921e5 inventory reader, PR397229dea725 image-request projection and
PR388629f7a361 canonical enum annotation deduplication. Private OpenHCS0.8.7
wheel SHA256f310110b94344ec018bee75b0fcf427dfacb297f4c36c094b19ea2c44cb6b8ff.
No global/shared package, backing dependency or acquisition file was changed.
Offline build6.88s/230.23MiB and install5.41s/69.85MiB; no downloads.

Original enum-fixed engineering execution remains complete but its full-label
oracle FAILED. Public original final saved/main viewer pixels both contain
4096 calibration values1.3556, float64. This is not evidence of an int/float
decoder defect. Original fixture declares the calibration image first; public
measurement-only contract main-flow preservation is being reconciled by Dewey.
The original fixture, driver, failed oracle and execution evidence are unchanged.
Exact engineering viewer2311563/create1790889915.51 and native2301210/create
1790889748.97 closed through MCP; independent process/listener checks passed.
Evidence: public388-original-main-diagnosis-and-close/DIAGNOSIS.json and CLOSED.json.

Fresh ordinary saved-candidate submission after installation used the original
public inventory/image stream route, not a custom viewer loader or pixel decoder.
reopen399-installed-viewer-projected retains every request/response, source
inventory, actual native state and render-complete bitmap. Source original
reopen399-installed-viewer/007 failure stays retained; it was not retried.
One new post-fix submission completed successfully with exact declared source.

The actual packet readback is uint8[1024,1024], source channel2/site1/Z1/T1/A01,
pixel scale1.3556um, spatial origin(0,0), native domain(1024,1024), binary min0/max1,
9815 nonzero pixels. The leading declared singleton plane is projected by the
existing RuntimeSliceProjection through ImageStreamingRequest; no receiver
guard or metadata declaration was weakened and no historical file was rewritten.

Parent personally opened the original default0..255 capture and found that
window unsuitable for a binary0/1 mask. Existing MCP native-intensity control
applied0..1/gamma1; readback verified it. Parent personally opened the resulting
1440x944 widget bitmap and confirmed visible sparse binary foreground plus
exact channel2 source labels. This is transport/source/presentation acceptance,
not full-field biological recall or acceptance of the rejected candidate1b.
The default camera does not display the full1024 square in its shorter canvas.

Second evidence: reopen399-projected-binary-review/REVIEW.json, original payload,
after-state and render-complete capture. Capture SHA256 and exact path are in
the original response. No microscope pixel reader outside MCP was used.

Current viewer2339091/create1790890853.17 remains alive on display91/5992.
Parent transfers that exact isolated viewer to Dalton for the retained assisted
one-site context. Native5993/6993 are absent. The retained author must use a new
journal/output identity, existing launch/status mechanisms and unchanged sealed
reserves; no private install is authorized while its MCP/native/viewer is alive.
All future biological claims still require distributed matched raw/result/combined
QA and native measurement/geometry reconciliation. Assistance is not autonomy.

Original source R0 for397 is pending owner publication;399 original inventory
reader guard and native sampling are source/installed-qualified. PR388 all248
source controls and original R0 pass, but new correctly scoped live label/main
journey remains distinct from the preserved failing original oracle.

@trissim
trissim marked this pull request as ready for review October 1, 2026 21:45
Copilot AI balanced review requested due to automatic review settings October 1, 2026 21:45
@trissim
trissim merged commit e3765e3 into main Oct 1, 2026
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@trissim

trissim commented Oct 1, 2026

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Receiving receipt now marks DONE reader/reopen with precise paired397229 installed stream qualification; canonical RST update is visible docs-only #403 head5d38ecad7. Original failures remain chronological and archived. Graph134/394 separate; candidate1b REJECTED; no biological pass. No installed/runtime/source implementation or test changes.

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Reopen native persisted image checkpoints without a historical viewer-state receipt

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