Add export to trackmate format (#45)

NOTES

@@ -0,0 +1,35 @@
+# REFACTOR:
+    - merge multiple solver classes methods into constructor to make a single deeper function
+
+# TODO:
+    - IMPORTANT: free nodes after each hierarchy insertation to database and measure performance.
+    - IMPORTANT: refactor widget to use a tab per option (segment, link, track)
+    - add warning when DB already contains data.
+    - create homepage/docs.
+        - document config
+        - document database
+    - option to lock segmentations from hypothesis viz widget
+
+# NOTES:
+    - heuristic optimizer:
+        - add monte-carlo (probabilist) moves into local search function
+        - local search by removing a node and trying to add its overlapping nodes
+
+    - slurm:
+        - segment: 1hr 30min, 790 jobs
+        - link: 30min, 789 jobs
+        - track 1st: 2hr 30min, 8 jobs of 100 time points + overlap
+        - track 2nd: 2hr, 8 jobs of 100 time points + overlap
+        - export: 20min
+        - total: about 7 hours
+        - NOTES:
+            - fix window overlap sql solution update by adding parents only when it already exists on solution
+            - segment step memory usage must be improved, with Daxi dataset it's using about 100GB per frame
+            - tracks should be divided into smaller chunks
+            - reduce tracking model build time with vector variables
+
+# ARTICLE:
+    - experiments comparing tracking results from essemble of connected components, watershed, cellpose, stardist vs their accuracy alone;
+    - experiments comparing results from binary contour (their own algorithm post processing) vs contour obtained from network output directly;
+    - cell-tracking challenge benchmark;
+    - qualitative results our dataset and jan funke datasets;

pyproject.toml

@@ -36,6 +36,7 @@ pre-commit = "^3.2.2"
 pytest-qt = "^4.2.0"
 asv = "^0.5.1"
 "testing.postgresql" = "^1.3.0"
+pytrackmate = {git = "https://github.com/hadim/pytrackmate.git"}
 
 [tool.poetry.extras]
 flow = [

tox.ini

@@ -34,6 +34,7 @@ deps =
     pyqt5
     poetry
     testing.postgresql
+    git+https://github.com/hadim/pytrackmate.git
 commands =
     pytest -v --color=yes --cov=ultrack --cov-report=xml --durations=15 --ignore=ultrack/widgets
 

ultrack/__init__.py

@@ -12,6 +12,7 @@
 
 from ultrack.config.config import MainConfig, load_config
 from ultrack.core.export.ctc import to_ctc
+from ultrack.core.export.trackmate import to_trackmate
 from ultrack.core.export.tracks_layer import to_tracks_layer
 from ultrack.core.export.zarr import tracks_to_zarr
 from ultrack.core.linking.processing import link

ultrack/analysis/utils.py

@@ -156,6 +156,7 @@ def get_subgraph(
         compressed_df["track_id"].to_numpy(dtype=int),
         compressed_df["parent_track_id"].to_numpy(dtype=int),
     )
+    roots = np.asarray(roots, dtype=int)
 
     subforest = []
     for root in roots:

ultrack/cli/_test/test_cli.py

@@ -15,7 +15,7 @@ def _run_command(command_and_args: List[str]) -> None:
     try:
         main(command_and_args)
     except SystemExit as exit:
-        assert exit.code == 0
+        assert exit.code == 0, f"{command_and_args} failed with exit code {exit.code}"
 
 
 @pytest.mark.usefixtures("zarr_dataset_paths")
@@ -105,6 +105,18 @@ def test_ctc_export(self, instance_config_path: str, tmp_path: Path) -> None:
             ]
         )
 
+    def test_trackmate_export(self, instance_config_path: str, tmp_path: Path) -> None:
+        _run_command(
+            [
+                "export",
+                "trackmate",
+                "-cfg",
+                instance_config_path,
+                "-o",
+                str(tmp_path / "tracks.xml"),
+            ]
+        )
+
     def test_zarr_napari_export(
         self,
         instance_config_path: str,

ultrack/cli/export.py

@@ -14,7 +14,7 @@
     tuple_callback,
 )
 from ultrack.config import MainConfig
-from ultrack.core.export import to_ctc, to_tracks_layer, tracks_to_zarr
+from ultrack.core.export import to_ctc, to_trackmate, to_tracks_layer, tracks_to_zarr
 from ultrack.core.export.utils import maybe_overwrite_path
 from ultrack.imgproc.measure import tracks_properties
 
@@ -162,10 +162,33 @@ def zarr_napari_cli(
         tracks_w_measures.to_csv(tracks_path, index=False)
 
 
+@click.command("trackmate")
+@click.option(
+    "--output-path",
+    "-o",
+    required=True,
+    type=click.Path(path_type=Path),
+    show_default=True,
+    help="TrackMate XML output path.",
+)
+@config_option()
+@overwrite_option()
+def trackmate_cli(
+    config: MainConfig,
+    output_path: Path,
+    overwrite: bool,
+) -> None:
+    """
+    Exports tracking results to TrackMate XML format.
+    """
+    to_trackmate(config, output_path, overwrite)
+
+
 @click.group("export")
 def export_cli() -> None:
     """Exports tracking and segmentation results to selected format."""
 
 
 export_cli.add_command(ctc_cli)
+export_cli.add_command(trackmate_cli)
 export_cli.add_command(zarr_napari_cli)

ultrack/core/export/__init__.py

@@ -1,3 +1,4 @@
 from ultrack.core.export.ctc import to_ctc
+from ultrack.core.export.trackmate import to_trackmate
 from ultrack.core.export.tracks_layer import to_tracks_layer
 from ultrack.core.export.zarr import tracks_to_zarr

ultrack/core/export/_test/test_trackmate.py

@@ -0,0 +1,37 @@
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+from pytrackmate import trackmate_peak_import
+
+from ultrack.core.database import NO_PARENT
+from ultrack.core.export.trackmate import tracks_layer_to_trackmate
+
+
+def test_trackmate_writer(tmp_path: Path) -> None:
+    tracks_outpath = tmp_path / "tracks.xml"
+
+    tracks_df = pd.DataFrame(
+        {
+            "id": [1, 2, 3, 4],
+            "parent_id": [NO_PARENT, 1, 2, 2],
+            "track_id": [1, 1, 2, 3],
+            "t": [0, 1, 2, 2],
+            "z": [0, 0, 0, 0],
+            "y": [10, 20, 30, 10],
+            "x": [1, 2, 3, 1],
+        }
+    )
+
+    xml_str = tracks_layer_to_trackmate(tracks_df)
+    with open(tracks_outpath, "w") as f:
+        f.write(xml_str)
+
+    trackmate_df = trackmate_peak_import(tracks_outpath)
+    print(trackmate_df)
+
+    assert trackmate_df.shape[0] == tracks_df.shape[0]
+
+    np.testing.assert_allclose(
+        tracks_df[["t", "z", "y", "x"]], trackmate_df[["t_stamp", "z", "y", "x"]]
+    )