Merge branch 'main' into public/main

MANIFEST.in

@@ -1,3 +1,3 @@
 include README.md
 include LICENSE
-include ultrack/widgets/ultrackwidget/resources/*.json
+recursive-include ultrack/widgets/ultrackwidget/resources *.json

examples/api/environment_gpu.yml

@@ -7,7 +7,7 @@ channels:
 dependencies:
   - coin-or-cbc
   - cucim
-  - cupy!=13.0.*
+  - cupy!=13.*
   - gurobi
   - jupyter
   - pip

examples/flow_field_3d/environment_gpu.yml

@@ -9,7 +9,7 @@ channels:
 dependencies:
   - coin-or-cbc
   - cucim
-  - cupy!=13.0.*
+  - cupy!=13.*
   - gurobi
   - jupyter
   - napari

examples/micro_sam/environment_gpu.yml

@@ -9,7 +9,7 @@ channels:
 dependencies:
   - coin-or-cbc
   - cucim
-  - cupy!=13.0.*
+  - cupy!=13.*
   - gurobi
   - jupyter
   - pip

examples/multi_color_ensemble/environment_gpu.yml

@@ -8,7 +8,7 @@ dependencies:
   - cellpose
   - coin-or-cbc
   - cucim
-  - cupy!=13.0.*
+  - cupy!=13.*
   - gurobi
   - jupyter
   - pip

examples/neuromast_plantseg/environment_gpu.yml

@@ -9,7 +9,7 @@ channels:
 dependencies:
   - coin-or-cbc
   - cucim
-  - cupy!=13.0.*
+  - cupy!=13.*
   - gurobi
   - jupyter
   - pyqt

examples/stardist_2d/environment_gpu.yml

@@ -10,7 +10,7 @@ dependencies:
   - conda-forge::cudatoolkit=11.2
   - conda-forge::cudnn=8.4.1
   - conda-forge::tensorflow-gpu=2.11.0
-  - conda-forge::cupy!=13.0.*
+  - conda-forge::cupy!=13.*
   - coin-or-cbc
   - gurobi
   - jupyter

examples/zebrahub/environment_gpu.yml

@@ -7,7 +7,7 @@ channels:
 dependencies:
   - coin-or-cbc
   - cucim
-  - cupy!=13.0.*
+  - cupy!=13.*
   - gurobi
   - jupyter
   - pip

setup.cfg

@@ -44,6 +44,7 @@ install_requires =
     httpx >= 0.26.0
     websockets >= 12.0
     qtawesome >= 1.3.1
+    pydot >= 2.0.0
 
 [options.extras_require]
 testing =
@@ -71,4 +72,6 @@ napari.manifest =
     ultrack = ultrack:napari.yaml
 
 [options.package_data]
-ultrack = napari.yaml
+ultrack =
+    napari.yaml
+    widgets/ultrackwidget/resources/*.json

ultrack/__init__.py

@@ -16,9 +16,11 @@
 
 from ultrack.config.config import MainConfig, load_config
 from ultrack.core.export.ctc import to_ctc
+from ultrack.core.export.exporter import export_tracks_by_extension
 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.interactive import add_new_node
 from ultrack.core.linking.processing import link
 from ultrack.core.main import track
 from ultrack.core.segmentation.processing import segment

ultrack/api/__init__.py

@@ -1,3 +1,2 @@
+from ultrack.api.database import Experiment, ExperimentStatus
 from ultrack.api.main import start_server
-from ultrack.api.database import Experiment
-from ultrack.api.database import ExperimentStatus

ultrack/api/database.py

@@ -7,7 +7,7 @@
 
 import sqlalchemy as sqla
 from pydantic import BaseModel, Json, validator
-from sqlalchemy import JSON, Column, DateTime, Enum, Integer, String, Text
+from sqlalchemy import JSON, Column, Enum, Integer, String, Text
 from sqlalchemy.orm import declarative_base, sessionmaker
 
 from ultrack import MainConfig
@@ -262,8 +262,6 @@ def update_experiment(experiment: Experiment) -> None:
     session.close()
 
 
-
-
 def get_experiment(id: int) -> Experiment:
     """Get an experiment from the database.
 

ultrack/api/main.py

@@ -1,29 +1,30 @@
 import os
 from multiprocessing import Process
 from pathlib import Path
-from threading import Thread
 from typing import Union
 
 import uvicorn
 
+from ultrack import MainConfig
 from ultrack.api import app
-from ultrack.config import DataConfig
 
 
 def _in_notebook():
     try:
         from IPython import get_ipython
-        if 'IPKernelApp' not in get_ipython().config:  # pragma: no cover
+
+        if "IPKernelApp" not in get_ipython().config:  # pragma: no cover
             return False
     except ImportError:
         return False
     except AttributeError:
         return False
     return True
 
+
 def start_server(
     api_results_path: Union[Path, str, None] = None,
-    ultrack_data_config: Union[DataConfig, None] = None,
+    ultrack_data_config: Union[MainConfig, None] = None,
     host: str = "0.0.0.0",
     port: int = 8000,
 ):
@@ -41,8 +42,10 @@ def start_server(
         os.environ["ULTRACK_DATA_CONFIG"] = ultrack_data_config.json()
 
     if _in_notebook():
+
         def start_in_notebook():
             uvicorn.run(app.app, host=host, port=port)
+
         Process(target=start_in_notebook).start()
     else:
         uvicorn.run(app.app, host=host, port=port)

ultrack/cli/_test/test_cli.py

@@ -13,6 +13,9 @@
 from ultrack.utils.data import make_config_content
 
 
+def _run_server(instance_config_path: str):
+    _run_command(["server", "--port", "54123", "-cfg", instance_config_path])
+
 def _run_command(command_and_args: List[str]) -> None:
     try:
         main(command_and_args)
@@ -161,6 +164,25 @@ def test_clear_database(self, instance_config_path: str, mode: str) -> None:
             ]
         )
 
+    def test_server(self, instance_config_path: str) -> None:
+        # Start server in a background thread
+        process = Process(target=_run_server, args=(instance_config_path,))
+        process.start()
+
+        # Wait for server to start
+        import time
+
+        time.sleep(10)
+
+        response = requests.get("http://127.0.0.1:54123")
+        print(response.content)
+
+        assert process.is_alive()
+        assert response.status_code == 200
+
+        process.terminate()
+        process.join()
+
 
 def test_create_config(tmp_path: Path) -> None:
     _run_command(["create_config", str(tmp_path / "config.toml")])
@@ -178,28 +200,3 @@ def test_labels_to_contours(zarr_dataset_paths: List[str], tmp_path: Path) -> No
 
 def test_check_gurobi() -> None:
     _run_command(["check_gurobi"])
-
-
-def _run_server():
-    _run_command(["server", "--port", "54123"])
-
-
-def test_server() -> None:
-
-    # Start server in a background thread
-    process = Process(target=_run_server)
-    process.start()
-
-    # Wait for server to start
-    import time
-
-    time.sleep(10)
-
-    response = requests.get("http://127.0.0.1:54123")
-    print(response.content)
-
-    assert process.is_alive()
-    assert response.status_code == 200
-
-    process.terminate()
-    process.join()

ultrack/cli/server.py

@@ -1,9 +1,12 @@
-import os
+from typing import Optional
 
 import click
-import uvicorn
+import toml
 
-from ultrack.api.app import app
+from ultrack import MainConfig
+from ultrack.api import start_server
+from ultrack.cli.utils import config_option
+from ultrack.config import DataConfig
 
 
 @click.command("server")
@@ -22,9 +25,9 @@
     default=None,
     show_default=True,
 )
-def server_cli(host: str, port: int, api_results_path: str) -> None:
+@config_option()
+def server_cli(
+    host: str, port: int, api_results_path: Optional[str], config: MainConfig
+) -> None:
     """Start the websockets ultrack API."""
-    if api_results_path is not None:
-        os.environ["API_RESULTS_PATH"] = str(api_results_path)
-
-    uvicorn.run(app, host=host, port=port)
+    start_server(api_results_path, ultrack_data_config=config, host=host, port=port)

ultrack/core/_test/test_interactive.py

@@ -0,0 +1,57 @@
+from typing import Tuple
+
+import numpy as np
+import pytest
+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+
+from ultrack import MainConfig, add_new_node
+from ultrack.core.database import LinkDB, NodeDB, OverlapDB
+
+
+def _get_table_sizes(session: Session) -> Tuple[int, int, int]:
+    return (
+        session.query(NodeDB).count(),
+        session.query(LinkDB).count(),
+        session.query(OverlapDB).count(),
+    )
+
+
+@pytest.mark.parametrize(
+    "config_content",
+    [
+        {
+            "data.database": "sqlite",
+            "segmentation.n_workers": 4,
+            "linking.n_workers": 4,
+            "linking.max_distance": 500,  # too big and ignored
+        },
+    ],
+    indirect=True,
+)
+def test_clear_solution(
+    linked_database_mock_data: MainConfig,
+) -> None:
+
+    mask = np.ones((7, 12, 12), dtype=bool)
+    bbox = np.array([15, 24, 24, 22, 36, 36], dtype=int)
+
+    engine = create_engine(linked_database_mock_data.data_config.database_path)
+    with Session(engine) as session:
+        n_nodes, n_links, n_overlaps = _get_table_sizes(session)
+
+        add_new_node(
+            linked_database_mock_data,
+            0,
+            mask,
+            bbox,
+        )
+
+        new_n_nodes, new_n_links, new_n_overlaps = _get_table_sizes(session)
+
+    assert new_n_nodes == n_nodes + 1
+    assert new_n_overlaps > n_overlaps
+    # could smaller than max neighbors because of radius
+    assert (
+        new_n_links == n_links + linked_database_mock_data.linking_config.max_neighbors
+    )

ultrack/core/export/_test/test_exporter.py

@@ -0,0 +1,42 @@
+from pathlib import Path
+
+from ultrack import MainConfig, export_tracks_by_extension
+
+
+def test_exporter(tracked_database_mock_data: MainConfig, tmp_path: Path) -> None:
+    file_ext_list = [".xml", ".csv", ".zarr", ".dot", ".json"]
+    last_modified_time = {}
+    for file_ext in file_ext_list:
+        tmp_file = tmp_path / f"tracks{file_ext}"
+        export_tracks_by_extension(tracked_database_mock_data, tmp_file)
+
+        # assert file exists
+        assert (tmp_path / f"tracks{file_ext}").exists()
+        # assert file size is not zero
+        assert (tmp_path / f"tracks{file_ext}").stat().st_size > 0
+
+        # store last modified time
+        last_modified_time[str(tmp_file)] = tmp_file.stat().st_mtime
+
+    # loop again testing overwrite=False
+    for file_ext in file_ext_list:
+        tmp_file = tmp_path / f"tracks{file_ext}"
+        try:
+            export_tracks_by_extension(
+                tracked_database_mock_data, tmp_file, overwrite=False
+            )
+            assert False, "FileExistsError should be raised"
+        except FileExistsError:
+            pass
+
+    # loop again testing overwrite=True
+    for file_ext in file_ext_list:
+        tmp_file = tmp_path / f"tracks{file_ext}"
+        export_tracks_by_extension(tracked_database_mock_data, tmp_file, overwrite=True)
+
+        # assert file exists
+        assert (tmp_path / f"tracks{file_ext}").exists()
+        # assert file size is not zero
+        assert (tmp_path / f"tracks{file_ext}").stat().st_size > 0
+
+        assert last_modified_time[str(tmp_file)] != tmp_file.stat().st_mtime