Fix synthetic Opera identity, source refs and calibration (#172, #335)

openhcs/core/components/parser_metaprogramming.py

@@ -202,6 +202,22 @@ def construct_filename(self, components: FilenameParseResult) -> str:
         """Construct a filename from one nominal component result."""
         pass
 
+    def construct_acquisition_filename(
+        self,
+        components: FilenameParseResult,
+        *,
+        include_all_components: bool = False,
+        plate_name: str | None = None,
+        include_site: bool = True,
+        include_channel: bool = True,
+    ) -> str:
+        """Spell a physical acquisition name; semantic identity stays complete.
+
+        Formats with folder-encoded axes or acquisition-specific spelling own
+        those conventions in their existing parser, not in the producer.
+        """
+        return self.construct_filename(components)
+
     def get_component_names(self) -> tuple[str, ...]:
         """Get all component names for this parser."""
         return AllComponents.ordered_names()

openhcs/microscopes/imagexpress.py

@@ -416,6 +416,10 @@ def construct_filename(
         site_padding: int = 3,
         z_padding: int = 3,
         timepoint_padding: int = 3,
+        *,
+        plate_name: str | None = None,
+        include_site: bool = True,
+        include_channel: bool = True,
     ) -> str:
         """Construct an ImageXpress filename from nominal component values."""
 
@@ -425,13 +429,13 @@ def construct_filename(
         z_index = components.value_for(AllComponents.Z_INDEX)
         timepoint = components.value_for(AllComponents.TIMEPOINT)
 
-        parts = [well]
+        parts = [f"{plate_name}_{well}" if plate_name is not None else well]
 
-        # Always add site
-        parts.append(f"_s{format_filename_component(site, site_padding)}")
+        if include_site:
+            parts.append(f"_s{format_filename_component(site, site_padding)}")
 
-        # Always add channel
-        parts.append(f"_w{format_filename_component(channel)}")
+        if include_channel:
+            parts.append(f"_w{format_filename_component(channel)}")
 
         if z_index is not None:
             parts.append(f"_z{format_filename_component(z_index, z_padding)}")
@@ -442,6 +446,28 @@ def construct_filename(
         base_name = "".join(parts)
         return f"{base_name}{components.extension}"
 
+    def construct_acquisition_filename(
+        self,
+        components: FilenameParseResult,
+        *,
+        include_all_components: bool = False,
+        plate_name: str | None = None,
+        include_site: bool = True,
+        include_channel: bool = True,
+    ) -> str:
+        """Own MetaXpress acquisition spelling, including folder-only Z axes."""
+        if not include_all_components or plate_name is not None:
+            components = components.with_values(
+                ((AllComponents.Z_INDEX, None), (AllComponents.TIMEPOINT, None))
+            )
+        return self.construct_filename(
+            components,
+            site_padding=0 if plate_name is not None else 3,
+            plate_name=plate_name,
+            include_site=include_site if plate_name is not None else True,
+            include_channel=include_channel if plate_name is not None else True,
+        )
+
 
 class ImageXpressMetadataHandler(DiskImageFileListingMetadataHandler):
     """

openhcs/microscopes/opera_phenix.py

@@ -522,15 +522,9 @@ def construct_filename(
         z_index = components.required_value(AllComponents.Z_INDEX)
         timepoint = components.required_value(AllComponents.TIMEPOINT)
 
-        # Extract row and column from well name
-        # Check if well is in Opera Phenix format (e.g., 'R01C03')
-        match = self._well_pattern.match(well)
-        if match:
-            # Extract row and column from Opera Phenix format
-            row = int(match.group(1))
-            col = int(match.group(2))
-        else:
-            raise ValueError(f"Invalid well format: {well}. Expected format: 'R01C03'")
+        row_name, column_name = self.extract_component_coordinates(well)
+        row = ord(row_name) - ord("A") + 1
+        col = int(column_name)
 
         # Construct filename in Opera Phenix format
         site_part = f"f{format_filename_component(site, site_padding)}"
@@ -542,6 +536,18 @@ def construct_filename(
             f"-ch{format_filename_component(channel)}{sk_part}fk1fl1{components.extension}"
         )
 
+    def construct_acquisition_filename(
+        self,
+        components: FilenameParseResult,
+        *,
+        include_all_components: bool = False,
+        plate_name: str | None = None,
+        include_site: bool = True,
+        include_channel: bool = True,
+    ) -> str:
+        """Keep Harmony's physical field/plane spelling on the format owner."""
+        return self.construct_filename(components, site_padding=0, z_padding=2)
+
     def remap_field_in_filename(
         self, filename: str, xml_parser: Optional[OperaPhenixXmlParser] = None
     ) -> str:

tests/integration/helpers/fixture_utils.py

@@ -355,7 +355,7 @@ def create_synthetic_plate_data(
             else:  # OperaPhenix
                 sub_dir = "Images"
 
-            generator.generate_openhcs_metadata(sub_dir=sub_dir, pixel_size=0.65)
+            generator.generate_openhcs_metadata(sub_dir=sub_dir)
 
     # Return the plate directory
     return plate_dir