Ultrack_indices (#35)

* add all indices

* reader v3

* test: fixed tset

Signed-off-by: Sricharan Reddy Varra <[email protected]>

---------

Signed-off-by: Sricharan Reddy Varra <[email protected]>
Co-authored-by: Sricharan Reddy Varra <[email protected]>

Author: edyoshikun

pyproject.toml

@@ -11,7 +11,7 @@ license = { file = "LICENSE" }
 authors = [
   { name = "CZ Biohub SF and napari-iohub contributors", email = "[email protected]" },
 ]
-dependencies = ["iohub>=0.1.0", "magicgui", "qtpy"]
+dependencies = ["iohub>=0.1.0", "dask>=2024.12.0", "magicgui", "qtpy"]
 dynamic = ["version"]
 classifiers = [
   "Development Status :: 2 - Pre-Alpha",

src/napari_iohub/_cell_state_annotator.py

@@ -41,7 +41,17 @@
 _logger = logging.getLogger(__name__)
 
 # Index columns for ultrack-compatible CSV output
-INDEX_COLUMNS = ["fov_name", "track_id", "t", "z", "y", "x"]
+ULTRACK_INDEX_COLUMNS = [
+    "fov_name",
+    "track_id",
+    "t",
+    "id",
+    "parent_track_id",
+    "parent_id",
+    "z",
+    "y",
+    "x",
+]
 
 # Annotation layer definitions
 ANNOTATION_LAYERS = [
@@ -748,7 +758,9 @@ def _save_annotations(self) -> None:
             )
 
             # Reorder columns
-            index_cols = [col for col in INDEX_COLUMNS if col in merged_df.columns]
+            index_cols = [
+                col for col in ULTRACK_INDEX_COLUMNS if col in merged_df.columns
+            ]
             annotation_cols = [
                 "cell_division_state",
                 "infection_state",

src/napari_iohub/_reader.py

@@ -72,9 +72,7 @@ def _get_node(path: StrOrBytesPath):
         zgroup.store.close()
         node = open_ome_zarr(store_path=path, mode="r")
     else:
-        raise KeyError(
-            f"NGFF plate or well metadata not found under '{zgroup.name}'"
-        )
+        raise KeyError(f"NGFF plate or well metadata not found under '{zgroup.name}'")
     return node
 
 
@@ -121,9 +119,7 @@ def _get_multiscales(pos: Position):
         try:
             multiscales.append(pos[im].dask_array())
         except Exception as e:
-            logging.warning(
-                f"Skipped array '{im}' at position {pos.zgroup.name}: {e}"
-            )
+            logging.warning(f"Skipped array '{im}' at position {pos.zgroup.name}: {e}")
     return len(multiscales), multiscales
 
 
@@ -144,13 +140,8 @@ def _ome_to_napari_by_channel(
 ):
     if metadata.omero is None:
         if num_channels is None:
-            raise ValueError(
-                "num_channels must be set when omero is not present"
-            )
-        return [
-            {"name": f"{i}", "blending": "additive"}
-            for i in range(num_channels)
-        ]
+            raise ValueError("num_channels must be set when omero is not present")
+        return [{"name": f"{i}", "blending": "additive"} for i in range(num_channels)]
     omero: OMEROMeta = metadata.omero
     layers_kwargs = []
     for channel in omero.channels:
@@ -221,13 +212,9 @@ def fov_to_layers(fov: Position, layer_type: str = "image"):
     )
 
 
-def well_to_layers(
-    well: Well, mode: Literal["stitch", "stack"], layer_type: str
-):
+def well_to_layers(well: Well, mode: Literal["stitch", "stack"], layer_type: str):
     if mode == "stitch":
-        layers_kwargs, ch_axis, arrays = stitch_well_by_channel(
-            well, row_wrap=4
-        )
+        layers_kwargs, ch_axis, arrays = stitch_well_by_channel(well, row_wrap=4)
     elif mode == "stack":
         layers_kwargs, ch_axis, arrays = stack_well_by_position(well)
     return layers_from_arrays(
@@ -258,9 +245,7 @@ def make_bbox(bbox_extents):
     maxr = bbox_extents[2]
     maxc = bbox_extents[3]
 
-    bbox_rect = np.array(
-        [[minr, minc], [maxr, minc], [maxr, maxc], [minr, maxc]]
-    )
+    bbox_rect = np.array([[minr, minc], [maxr, minc], [maxr, maxc], [minr, maxc]])
     bbox_rect = np.moveaxis(bbox_rect, 2, 0)
 
     return bbox_rect
@@ -300,9 +285,7 @@ def plate_to_layers(
                 ]
                 for k in range(len(boxes)):
                     boxes[k].append(box_extents[k] - 0.5)
-                properties["fov"].append(
-                    well_path + "/" + next(well.positions())[0]
-                )
+                properties["fov"].append(well_path + "/" + next(well.positions())[0])
             else:
                 row_arrays.append(None)
         plate_arrays.append(row_arrays)

src/napari_iohub/_tests/test_cell_state_annotator.py

@@ -5,7 +5,7 @@
 
 from napari_iohub._cell_state_annotator import (
     ANNOTATION_LAYERS,
-    INDEX_COLUMNS,
+    ULTRACK_INDEX_COLUMNS,
     CellStateAnnotatorWidget,
 )
 
@@ -30,8 +30,8 @@ def test_annotation_layers_constant():
 
 def test_index_columns_constant():
     """Test that index columns match ultrack expectations."""
-    expected = ["fov_name", "track_id", "t", "z", "y", "x"]
-    assert INDEX_COLUMNS == expected
+    expected = ["fov_name", "track_id", "t", "id", "parent_track_id", "parent_id", "z", "y", "x"]
+    assert ULTRACK_INDEX_COLUMNS == expected
 
 
 def test_state_expansion_logic():