Update

pyproject.toml

@@ -5,22 +5,21 @@ description = "trackastra tracking"
 readme = "README.md"
 license = {file = "LICENSE"}
 authors = [
-  {name = "Martin Weigert"},
-  {email = "[email protected]"},
+  {name = "Martin Weigert, Benjamin Gallusser"},
+  {email = "[email protected], [email protected]"},
 ]
 classifiers = [
-    "Development Status :: 2 - Pre-Alpha",
+    "Development Status :: 3 - Alpha",
     "Framework :: napari",
     "Intended Audience :: Developers",
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
-    "Programming Language :: Python",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "napari",
     "numpy",
@@ -87,6 +86,7 @@ lint.select = [
     "SIM", # flake8-simplify
 ]
 lint.ignore = [
+    "F401",
     "E501", # line too long. let black handle this
     "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
     "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9

src/napari_trackastra/__init__.py

@@ -1,4 +1,2 @@
 __version__ = "0.0.1"
 from ._widget import Tracker
-
-

src/napari_trackastra/_sample_data.py

@@ -6,19 +6,24 @@
 
 Replace code below according to your needs.
 """
+
 from __future__ import annotations
 
-from pathlib import Path
 import numpy
-import tifffile
 from trackastra import data
 
 
-def test_data_bacteria() -> list[tuple[numpy.ndarray, dict, str]]:
-    imgs, masks = data.example_data_bacteria() 
-    return [(imgs, dict(name='img'), 'image'), (masks, dict(name='mask'), 'labels')]
+def example_data_bacteria() -> list[tuple[numpy.ndarray, dict, str]]:
+    imgs, masks = data.example_data_bacteria()
+    return [
+        (imgs, {"name": "img"}, "image"),
+        (masks, {"name": "mask"}, "labels"),
+    ]
 
 
-def test_data_hela() -> list[tuple[numpy.ndarray, dict, str]]:
-    imgs, masks = data.example_data_hela() 
-    return [(imgs, dict(name='img'), 'image'), (masks, dict(name='mask'), 'labels')]
+def example_data_hela() -> list[tuple[numpy.ndarray, dict, str]]:
+    imgs, masks = data.example_data_hela()
+    return [
+        (imgs, {"name": "img"}, "image"),
+        (masks, {"name": "mask"}, "labels"),
+    ]

src/napari_trackastra/_tests/test_widget.py

@@ -1,20 +1,19 @@
-import numpy as np
 import napari
+from trackastra.data import example_data_bacteria
+
 from napari_trackastra._widget import Tracker
-from trackastra.data import test_data_bacteria
 
 
 def test_widget():
     viewer = napari.Viewer()
-    img, mask = test_data_bacteria()
+    img, mask = example_data_bacteria()
     viewer.add_image(img)
     viewer.add_labels(mask)
 
     viewer.window.add_dock_widget(Tracker(viewer))
-    
+
 
 if __name__ == "__main__":
     test_widget()
 
     napari.run()
-

src/napari_trackastra/_widget.py

@@ -1,67 +1,85 @@
-
-import torch 
-import numpy as np
-
-
 import napari
-from magicgui import magic_factory, magicgui
-from magicgui.widgets import CheckBox, Container, create_widget, PushButton, FileEdit, ComboBox, RadioButtons
-from pathlib import Path
-from typing import List, OrderedDict
-from napari.utils import progress
+import numpy as np
+import torch
 import trackastra
-from trackastra.utils import normalize
+from magicgui.widgets import (
+    ComboBox,
+    Container,
+    FileEdit,
+    PushButton,
+    RadioButtons,
+    create_widget,
+)
+from napari.utils import progress
 from trackastra.model import Trackastra
 from trackastra.tracking import graph_to_ctc, graph_to_napari_tracks
-
-device = "cuda" if torch.cuda.is_available() else "cpu"
+from trackastra.utils import normalize
 
+device = "cuda" if torch.cuda.is_available() else "cpu"
 
 
 # logo = Path(__file__).parent/"resources"/"trackastra_logo_small.png"
-# logo_html = f"""<div style="display: flex; 
+# logo_html = f"""<div style="display: flex;
 # align-items: center;">
-# <img src="{logo}" alt="Logo" style="margin-right: 50px; width: 30px; height: 30px;"> 
+# <img src="{logo}" alt="Logo" style="margin-right: 50px; width: 30px; height: 30px;">
 # <span style="line-height: 50px;">
 # Trackastra
 # </div>"""
 
 
-
-def _track_function(model, imgs, masks, mode="greedy", **kwargs):    
+def _track_function(model, imgs, masks, mode="greedy", **kwargs):
     print("Normalizing...")
     imgs = np.stack([normalize(x) for x in imgs])
     print(f"Tracking with mode {mode}...")
-    track_graph = model.track(imgs, masks, mode=mode, 
-                                max_distance=128,
-                                progbar_class=progress,
-                                **kwargs)  # or mode="ilp"
+    track_graph = model.track(
+        imgs,
+        masks,
+        mode=mode,
+        max_distance=128,
+        progbar_class=progress,
+        **kwargs,
+    )  # or mode="ilp"
     # Visualise in napari
-    df, masks_tracked = graph_to_ctc(track_graph,masks,outdir=None)
+    df, masks_tracked = graph_to_ctc(track_graph, masks, outdir=None)
     napari_tracks, napari_tracks_graph, _ = graph_to_napari_tracks(track_graph)
     return track_graph, masks_tracked, napari_tracks
 
 
-
 class Tracker(Container):
     def __init__(self, viewer: "napari.viewer.Viewer"):
         super().__init__()
         self._viewer = viewer
-        self._label = create_widget(widget_type="Label", label="<h2>Trackastra</h2>")
-        self._image_layer = create_widget(label="Images", annotation="napari.layers.Image")
-
-
-        self._mask_layer = create_widget(label="Masks", annotation="napari.layers.Labels")
-        self._model_type = RadioButtons(label="Model Type", choices=["Pretrained", "Custom"], orientation="horizontal", value="Pretrained")
-        self._model_pretrained = ComboBox(label="Pretrained Model", 
-                                          choices=tuple(trackastra.model.pretrained._MODELS.keys()), value="general_2d")
+        self._label = create_widget(
+            widget_type="Label", label="<h2>Trackastra</h2>"
+        )
+        self._image_layer = create_widget(
+            label="Images", annotation="napari.layers.Image"
+        )
+
+        self._mask_layer = create_widget(
+            label="Masks", annotation="napari.layers.Labels"
+        )
+        self._model_type = RadioButtons(
+            label="Model Type",
+            choices=["Pretrained", "Custom"],
+            orientation="horizontal",
+            value="Pretrained",
+        )
+        self._model_pretrained = ComboBox(
+            label="Pretrained Model",
+            choices=tuple(trackastra.model.pretrained._MODELS.keys()),
+            value="general_2d",
+        )
         self._model_path = FileEdit(label="Model Path", mode="d")
         self._model_path.hide()
         self._run_button = PushButton(label="Track")
-
-        self._linking_mode = ComboBox(label="Linking", 
-                            choices=("greedy_nodiv","greedy", "ilp"), value="greedy")
-
+
+        self._linking_mode = ComboBox(
+            label="Linking",
+            choices=("greedy_nodiv", "greedy", "ilp"),
+            value="greedy",
+        )
+
         self._out_mask, self._out_tracks = None, None
 
         self._model_type.changed.connect(self._model_type_changed)
@@ -93,40 +111,47 @@ def _model_type_changed(self, event):
 
     def _update_model(self, event=None):
         if self._model_type.value == "Pretrained":
-            self.model = Trackastra.from_pretrained(self._model_pretrained.value, device=device)
+            self.model = Trackastra.from_pretrained(
+                self._model_pretrained.value, device=device
+            )
         else:
-            self.model = Trackastra.from_folder(self._model_path.value, device=device)
-
+            self.model = Trackastra.from_folder(
+                self._model_path.value, device=device
+            )
 
     def _show_activity_dock(self, state=True):
         # show/hide activity dock if there is actual progress to see
         self._viewer.window._status_bar._toggle_activity_dock(state)
 
-
     def _run(self, event=None):
         self._update_model()
-        
+
         if self.model is None:
             raise ValueError("Model not loaded")
-        
+
         imgs = np.asarray(self._image_layer.value.data)
         masks = np.asarray(self._mask_layer.value.data)
 
         self._show_activity_dock(True)
-        track_graph, masks_tracked, napari_tracks = _track_function(self.model, imgs, masks, mode=self._linking_mode.value)
-
+        track_graph, masks_tracked, napari_tracks = _track_function(
+            self.model, imgs, masks, mode=self._linking_mode.value
+        )
+
         self._mask_layer.value.visible = False
         self._show_activity_dock(False)
 
-        lays = tuple(lay for lay in self._viewer.layers if lay.name=="masks_tracked")
+        lays = tuple(
+            lay for lay in self._viewer.layers if lay.name == "masks_tracked"
+        )
         if len(lays) > 0:
             lays[0].data = masks_tracked
         else:
             self._viewer.add_labels(masks_tracked, name="masks_tracked")
-
-        lays = tuple(lay for lay in self._viewer.layers if lay.name=="tracks")
+
+        lays = tuple(
+            lay for lay in self._viewer.layers if lay.name == "tracks"
+        )
         if len(lays) > 0:
             lays[0].data = napari_tracks
         else:
             self._viewer.add_tracks(napari_tracks, name="tracks")
-

src/napari_trackastra/napari.yaml

@@ -5,20 +5,20 @@ visibility: public
 categories: ["Segmentation"]
 contributions:
   commands:
-    - id: napari-trackastra.test_data_bacteria
-      python_name: napari_trackastra._sample_data:test_data_bacteria
+    - id: napari-trackastra.example_data_bacteria
+      python_name: napari_trackastra._sample_data:example_data_bacteria
       title: Sample bacteria images and masks
-    - id: napari-trackastra.test_data_hela
-      python_name: napari_trackastra._sample_data:test_data_hela
+    - id: napari-trackastra.example_data_hela
+      python_name: napari_trackastra._sample_data:example_data_hela
       title: Sample bacteria images and masks
     - id: napari-trackastra.track
       python_name: napari_trackastra:Tracker
       title: Create Plugin
   sample_data:
-    - command: napari-trackastra.test_data_bacteria
+    - command: napari-trackastra.example_data_bacteria
       display_name: bacteria
       key: unique_id.1
-    - command: napari-trackastra.test_data_hela
+    - command: napari-trackastra.example_data_hela
       display_name: hela
       key: unique_id.2
   widgets: