Merge pull request #44 from funkelab/v0.2.1-patch

V0.2.1 patch

Author: cmalinmayor

finn/track_import_export/load_tracks.py

@@ -225,7 +225,7 @@ def tracks_from_df(
         attrs.update(row_dict)
 
         if "track_id" in df.columns:
-            attrs[NodeAttr.TRACK_ID.value] = row["track_id"]
+            attrs[NodeAttr.TRACK_ID.value] = int(row["track_id"])
 
         # add the node to the graph
         graph.add_node(_id, **attrs)

finn_builtins/_tests/test_example_data.py

@@ -39,5 +39,5 @@ def test_Fluo_N2DL_Hela(ds_function, img_shape, point_shape):
     assert raw_data.shape == img_shape
     assert seg_data.shape == img_shape
     assert raw_data.dtype == np.uint16
-    assert seg_data.dtype == np.uint16
+    assert seg_data.dtype == np.uint64
     assert points.shape == point_shape

finn_builtins/example_data.py

@@ -280,15 +280,14 @@ def _convert_tiff_stack_to_zarr(
     files = sorted(tiff_path.glob("*.tif"))
     logger.info("%s time points found.", len(files))
     example_image = tifffile.imread(files[0])
+    dtype = np.uint64 if relabel else example_image.dtype
     data_shape = (len(files), *example_image.shape)
     # prepare zarr
-    zarr_array = _create_zarr(
-        zarr_path, zarr_group, shape=data_shape, dtype=example_image.dtype
-    )
+    zarr_array = _create_zarr(zarr_path, zarr_group, shape=data_shape, dtype=dtype)
     # load and save data in zarr
     max_label = 0
     for t, file in enumerate(files):
-        frame = tifffile.imread(file)
+        frame = tifffile.imread(file).astype(dtype)
         if relabel:
             frame[frame != 0] += max_label
             max_label = int(np.max(frame))

pyproject.toml

@@ -301,6 +301,9 @@ ignore = [
 ]
 
 [tool.ruff.lint.per-file-ignores]
+"scripts/*" = [
+    "INP001", # implicit namespace
+]
 # ignoring a lot of napari debt so that we can continue to check in new code
 "finn/_app_model/*" = [
     "E501", # line too long