Fix geometry handling in BaseDataPanel to use unified format and update tests for consistency

Author: PierreRaybaut

datalab/adapters_plotpy/objects/base.py

@@ -25,6 +25,7 @@
     TypeObj,
 )
 
+from datalab.adapters_metadata import GeometryAdapter
 from datalab.adapters_plotpy.base import (
     config_annotated_shape,
     items_to_json,
@@ -134,9 +135,7 @@ def iterate_shape_items(self, editable: bool = False):
                         self.obj, fmt=fmt, lbl=lbl, editable=False
                     )
             # Process geometry results from metadata (using GeometryAdapter)
-            elif key.startswith("Geometry_") and key.endswith("_array"):
-                # pylint: disable=import-outside-toplevel
-                from datalab.adapters_metadata import GeometryAdapter
+            elif GeometryAdapter.match(key, _value):
                 from datalab.adapters_plotpy.objects.scalar import GeometryPlotPyAdapter
 
                 try:

datalab/adapters_plotpy/objects/scalar.py

@@ -187,7 +187,7 @@ def iterate_plot_items(
         Yields:
             Plot item
         """
-        for coords in self.result_adapter.raw_data:
+        for coords in self.result_adapter.result.coords:
             yield self.create_shape_item(coords, fmt, lbl, option)
 
     def create_shape_item(

datalab/gui/panel/base.py

@@ -745,85 +745,65 @@ def _rename_results_in_clipboard(self, prefix: str) -> None:
         Args:
             prefix: Prefix to add to result titles
         """
-        # Handle geometry results
+        # Handle geometry results (new unified format)
         geometry_keys = [
             k
-            for k in self.__metadata_clipboard.keys()
-            if k.startswith("Geometry_") and k.endswith("_array")
+            for k, v in self.__metadata_clipboard.items()
+            if GeometryAdapter.match(k, v)
         ]
 
-        for array_key in geometry_keys:
+        for dict_key in geometry_keys:
             try:
-                # Extract title from key: "Geometry_title_array" -> "title"
-                title = array_key[9:-6]  # Remove "Geometry_" and "_array"
+                # Get the geometry data
+                geometry_data = self.__metadata_clipboard[dict_key]
+
+                # Update the title in the geometry data
+                if isinstance(geometry_data, dict) and "title" in geometry_data:
+                    new_title = prefix + geometry_data["title"]
+                    geometry_data = geometry_data.copy()  # Don't modify original
+                    geometry_data["title"] = new_title
+
+                    # Create new key with updated title
+                    new_dict_key = (
+                        f"{GeometryAdapter.META_PREFIX}{new_title}"
+                        f"{GeometryAdapter.SUFFIX}"
+                    )
 
-                # Find all related keys for this geometry result
-                title_key = f"Geometry_{title}_title"
-                shape_key = f"Geometry_{title}_shape"
+                    # Remove old entry and add new one
+                    del self.__metadata_clipboard[dict_key]
+                    self.__metadata_clipboard[new_dict_key] = geometry_data
 
-                if (
-                    title_key in self.__metadata_clipboard
-                    and shape_key in self.__metadata_clipboard
-                ):
-                    # Get the values
-                    array_val = self.__metadata_clipboard[array_key]
-                    title_val = self.__metadata_clipboard[title_key]
-                    shape_val = self.__metadata_clipboard[shape_key]
-
-                    # Create new keys with prefix
-                    new_title = prefix + title_val
-                    new_array_key = f"Geometry_{new_title}_array"
-                    new_title_key = f"Geometry_{new_title}_title"
-                    new_shape_key = f"Geometry_{new_title}_shape"
-
-                    # Remove old entries
-                    del self.__metadata_clipboard[array_key]
-                    del self.__metadata_clipboard[title_key]
-                    del self.__metadata_clipboard[shape_key]
-
-                    # Add new entries
-                    self.__metadata_clipboard[new_array_key] = array_val
-                    self.__metadata_clipboard[new_title_key] = new_title
-                    self.__metadata_clipboard[new_shape_key] = shape_val
-
-            except (KeyError, ValueError, IndexError):
+            except (KeyError, ValueError, IndexError, TypeError):
                 # If we can't process this geometry result, leave it as is
                 continue
+                continue
 
-        # Handle table results (similar logic)
+        # Handle table results (new unified format)
         table_keys = [
-            k
-            for k in self.__metadata_clipboard.keys()
-            if k.startswith("Table_") and k.endswith("_array")
+            k for k, v in self.__metadata_clipboard.items() if TableAdapter.match(k, v)
         ]
 
-        for array_key in table_keys:
+        for data_key in table_keys:
             try:
-                # Extract title from key: "Table_title_array" -> "title"
-                title = array_key[6:-6]  # Remove "Table_" and "_array"
-
-                # Find all related keys for this table result
-                title_key = f"Table_{title}_title"
-
-                if title_key in self.__metadata_clipboard:
-                    # Get the values
-                    array_val = self.__metadata_clipboard[array_key]
-                    title_val = self.__metadata_clipboard[title_key]
-
-                    # Create new keys with prefix
-                    new_title = prefix + title_val
-                    new_array_key = f"Table_{new_title}_array"
-                    new_title_key = f"Table_{new_title}_title"
-
-                    # Remove old entries
-                    del self.__metadata_clipboard[array_key]
-                    del self.__metadata_clipboard[title_key]
+                # Get the table data
+                table_data = self.__metadata_clipboard[data_key]
+
+                # Update the title in the table data
+                if isinstance(table_data, dict) and "title" in table_data:
+                    new_title = prefix + table_data["title"]
+                    table_data = table_data.copy()  # Don't modify original
+                    table_data["title"] = new_title
+
+                    # Create new key with updated title
+                    new_data_key = (
+                        f"{TableAdapter.META_PREFIX}{new_title}{TableAdapter.SUFFIX}"
+                    )
 
-                    # Add new entries
-                    self.__metadata_clipboard[new_array_key] = array_val
-                    self.__metadata_clipboard[new_title_key] = new_title
+                    # Remove old entry and add new one
+                    del self.__metadata_clipboard[data_key]
+                    self.__metadata_clipboard[new_data_key] = table_data
 
-            except (KeyError, ValueError, IndexError):
+            except (KeyError, ValueError, IndexError, TypeError):
                 # If we can't process this table result, leave it as is
                 continue
 
@@ -845,17 +825,17 @@ def paste_metadata(self, param: PasteMetadataParam | None = None) -> None:
             metadata[ROI_KEY] = self.__metadata_clipboard[ROI_KEY]
         if param.keep_geometry:
             for key, value in self.__metadata_clipboard.items():
-                if key.startswith("Geometry_"):
+                if GeometryAdapter.match(key, value):
                     metadata[key] = value
         if param.keep_tables:
             for key, value in self.__metadata_clipboard.items():
-                if key.startswith("Table_"):
+                if TableAdapter.match(key, value):
                     metadata[key] = value
         if param.keep_other:
             for key, value in self.__metadata_clipboard.items():
                 if (
-                    not key.startswith("Geometry_")
-                    and not key.startswith("Table_")
+                    not GeometryAdapter.match(key, value)
+                    and not TableAdapter.match(key, value)
                     and key not in (ROI_KEY,)
                 ):
                     metadata[key] = value

datalab/tests/features/common/metadata_app_test.py

@@ -17,6 +17,7 @@
 import sigima.proc.signal as sigima_signal
 from sigima.tests.data import create_paracetamol_signal
 
+from datalab.adapters_metadata.geometry_adapter import GeometryAdapter
 from datalab.env import execenv
 from datalab.gui.panel.base import BaseDataPanel, PasteMetadataParam
 from datalab.gui.panel.image import ImagePanel
@@ -57,7 +58,9 @@ def __test_metadata_features(panel: BaseDataPanel):
     source_metadata = source_obj.metadata.copy()
 
     # Verify source object has geometry results
-    geometry_keys = [k for k in source_metadata.keys() if k.startswith("Geometry_")]
+    geometry_keys = [
+        k for k, v in source_metadata.items() if GeometryAdapter.match(k, v)
+    ]
     execenv.print(f"  Source object has {len(geometry_keys)} geometry metadata keys")
     assert len(geometry_keys) > 0, "Source object should have geometry results"
 
@@ -70,7 +73,7 @@ def __test_metadata_features(panel: BaseDataPanel):
 
     # Verify target has no geometry metadata before paste
     target_geo_keys_before = [
-        k for k in target_obj.metadata.keys() if k.startswith("Geometry_")
+        k for k, v in target_obj.metadata.items() if GeometryAdapter.match(k, v)
     ]
     execenv.print(
         f"  Target object has {len(target_geo_keys_before)} geometry keys before paste"
@@ -87,7 +90,7 @@ def __test_metadata_features(panel: BaseDataPanel):
     # Verify the paste worked
     target_metadata_after = target_obj.metadata.copy()
     target_geo_keys_after = [
-        k for k in target_metadata_after.keys() if k.startswith("Geometry_")
+        k for k, v in target_metadata_after.items() if GeometryAdapter.match(k, v)
     ]
     execenv.print(
         f"  Target object has {len(target_geo_keys_after)} geometry keys after paste"
@@ -98,16 +101,14 @@ def __test_metadata_features(panel: BaseDataPanel):
         "Target object should have geometry results after paste"
     )
 
-    # Verify that all geometry metadata types are present (array, title, shape)
+    # Verify that all geometry metadata uses the new unified format (_dict)
     for key in target_geo_keys_after:
-        if key.endswith("_array"):
-            base_key = key[:-6]  # Remove "_array"
-            title_key = base_key + "_title"
-            shape_key = base_key + "_shape"
-
-            assert title_key in target_metadata_after, f"Missing title key: {title_key}"
-            assert shape_key in target_metadata_after, f"Missing shape key: {shape_key}"
-            execenv.print(f"  ✓ Complete geometry entry: {base_key}")
+        # Verify the geometry data is valid
+        geometry_data = target_metadata_after[key]
+        assert isinstance(geometry_data, dict), f"Geometry data should be dict: {key}"
+        assert "title" in geometry_data, f"Missing title in geometry data: {key}"
+        assert "coords" in geometry_data, f"Missing coords in geometry data: {key}"
+        execenv.print(f"  ✓ Valid geometry entry: {key}")
 
     execenv.print("  ✓ Metadata copy/paste verification passed")
 

datalab/tests/features/image/blobs_app_test.py

@@ -31,6 +31,8 @@ def test_blobs():
             (sigima.params.BlobOpenCVParam, "blob_opencv", "BlobOpenCV"),
         ):
             param = paramclass()
+            param.min_sigma = 10.0
+            param.max_sigma = 30.0
             image = create_image(name, data)
             create_adapter_from_object(image).add_label_with_title()
             panel.add_object(image)