Merge branch 'main' into public-main

Author: JoOkuma

Diff for: ultrack/cli/main.py

@@ -12,6 +12,7 @@
 from ultrack.cli.segment import segmentation_cli
 from ultrack.cli.server import server_cli
 from ultrack.cli.solve import solve_cli
+from ultrack.cli.view import view_cli
 
 
 @click.group()
@@ -31,3 +32,4 @@ def main():
 main.add_command(segmentation_cli)
 main.add_command(solve_cli)
 main.add_command(server_cli)
+main.add_command(view_cli)

Diff for: ultrack/cli/view.py

@@ -0,0 +1,21 @@
+import click
+import napari
+
+from ultrack.cli.utils import config_option
+from ultrack.config import MainConfig
+from ultrack.widgets.hierarchy_viz_widget import HierarchyVizWidget
+
+
+@click.group("view")
+def view_cli() -> None:
+    """View data in napari."""
+
+
+@view_cli.command("hierarchy")
+@config_option()
+def view_hierarchy_cli(config: MainConfig) -> None:
+    """Opens napari viewer with hierarchy visualization widget."""
+    viewer = napari.Viewer()
+    widget = HierarchyVizWidget(viewer, config)
+    viewer.window.add_dock_widget(widget)
+    napari.run()

Diff for: ultrack/config/config.py

@@ -80,3 +80,9 @@ def load_config(path: Union[str, Path]) -> MainConfig:
         data = toml.load(f)
         LOG.info(data)
         return MainConfig.model_validate(data)
+
+
+def save_config(config, path: Union[str, Path]):
+    """Saved MainConfig to TOML file."""
+    with open(path, mode="w") as f:
+        toml.dump(config.model_dump(by_alias=True), f)

Diff for: ultrack/napari.yaml

@@ -17,6 +17,10 @@ contributions:
       python_name: ultrack.widgets:UltrackWidget
       title: Ultrack
 
+    - id: ultrack.hierarchy_viz_widget
+      python_name: ultrack.widgets:HierarchyVizWidget
+      title: Hierarchy visualization
+
 ###### DEPRECATED & WIP WIDGETS  #####
 #     - id: ultrack.labels_to_edges_widget
 #       python_name: ultrack.widgets:LabelsToContoursWidget
@@ -67,5 +71,8 @@ contributions:
     # - command: ultrack.division_annotation_widget
     #   display_name: Division annotation
 
+    - command: ultrack.hierarchy_viz_widget
+      display_name: Hierarchy visualization
+
     # - command: ultrack.track_inspection
     #   display_name: Track inspection

Diff for: ultrack/utils/_test/test_utils_array.py

@@ -1,7 +1,11 @@
+from typing import Tuple
+
 import numpy as np
 import pytest
 
+from ultrack.config import MainConfig
 from ultrack.utils.array import array_apply
+from ultrack.utils.ultrack_array import UltrackArray
 
 
 @pytest.mark.parametrize("axis", [0, 1])
@@ -17,3 +21,34 @@ def sample_func(arr_1, arr_2):
     array_apply(in_data, in_data, out_array=out_data, func=sample_func, axis=axis)
     other_axes_length = in_data.shape[1 - axis]
     assert np.array_equal(out_data, 2 * in_data + other_axes_length)
+
+
+@pytest.mark.parametrize(
+    "key,timelapse_mock_data",
+    [
+        (1, {"n_dim": 3}),
+        (1, {"n_dim": 2}),
+        ((slice(None), 1), {"n_dim": 3}),
+        ((slice(None), 1), {"n_dim": 2}),
+        ((0, [1, 2]), {"n_dim": 3}),
+        ((0, [1, 2]), {"n_dim": 2}),
+        # ((-1, np.asarray([0, 3])),{'n_dim':3}),       #does testing negative time make sense?
+        # ((-1, np.asarray([0, 3])),{'n_dim':2}),
+        ((slice(1), -2), {"n_dim": 3}),
+        ((slice(1), -2), {"n_dim": 2}),
+        ((np.asarray(0),), {"n_dim": 3}),
+        ((np.asarray(0),), {"n_dim": 2}),
+        ((0, 0, slice(32)), {"n_dim": 3}),
+        ((0, 0, slice(32)), {"n_dim": 2}),
+    ],
+    indirect=[
+        "timelapse_mock_data",
+    ],
+)
+def test_ultrack_array(
+    segmentation_database_mock_data: MainConfig,
+    key: Tuple,
+):
+    ua = UltrackArray(segmentation_database_mock_data)
+    ua_numpy = ua[slice(None)]
+    np.testing.assert_equal(ua_numpy[key], ua[key])

Diff for: ultrack/utils/segmentation.py

@@ -266,6 +266,6 @@ def copy_segments(
         )  # not sure why this is necessary in large datasets
     else:
         for t in tqdm(range(segments.shape[0]), "Copying segments"):
-            out_segments[t] = segments[t]
+            out_segments[t] = np.asarray(segments[t])
 
     return out_segments