Merge pull request #15 from lowe-lab-ucl/initial-tracking-widget

napari_btrack/__init__.py

@@ -2,8 +2,3 @@
     from ._version import version as __version__
 except ImportError:
     __version__ = "unknown"
-
-
-
-from ._dock_widget import napari_experimental_provide_dock_widget
-

napari_btrack/_tests/test_dock_widget.py

@@ -1,19 +1,9 @@
-from napari_btrack import napari_experimental_provide_dock_widget
 import pytest
+from ..track import track
 
-"""
-# this is your plugin name declared in your napari.plugins entry point
-MY_PLUGIN_NAME = "napari-btrack"
-# the name of your widget(s)
-MY_WIDGET_NAMES = ["Example Q Widget", "example_magic_widget"]
 
-
-@pytest.mark.parametrize("widget_name", MY_WIDGET_NAMES)
-def test_something_with_viewer(widget_name, make_napari_viewer):
+def test_add_widget(make_napari_viewer):
     viewer = make_napari_viewer()
-    num_dw = len(viewer.window._dock_widgets)
-    viewer.window.add_plugin_dock_widget(
-        plugin_name=MY_PLUGIN_NAME, widget_name=widget_name
-    )
-    assert len(viewer.window._dock_widgets) == num_dw + 1
-"""
+    num_dw = len(list(viewer.window._dock_widgets))
+    viewer.window.add_function_widget(function=track)
+    assert len(list(viewer.window._dock_widgets)) == num_dw + 1

napari_btrack/napari.yaml

@@ -0,0 +1,10 @@
+name: napari-btrack
+schema_version: 0.1.0
+contributions:
+  commands:
+  - id: napari-btrack.track
+    title: Create Track
+    python_name: napari_btrack.track:track
+  widgets:
+  - command: napari-btrack.track
+    display_name: Track

napari_btrack/track.py

@@ -0,0 +1,53 @@
+import btrack
+import napari
+
+from btrack.utils import segmentation_to_objects
+from magicgui import magicgui
+from magicgui.widgets import FunctionGui
+from pathlib import Path
+from typing import Optional
+
+
+def run_tracker(objects, config_file_path):
+    with btrack.BayesianTracker() as tracker:
+        # configure the tracker using a config file
+        tracker.configure_from_file(config_file_path)
+        tracker.max_search_radius = 50
+
+        # append the objects to be tracked
+        tracker.append(objects)
+
+        # set the volume
+        tracker.volume = ((0, 1600), (0, 1200), (-1e5, 64.0))
+
+        # track them (in interactive mode)
+        tracker.track_interactive(step_size=100)
+
+        # generate hypotheses and run the global optimizer
+        tracker.optimize()
+
+        # get the tracks in a format for napari visualization
+        data, properties, graph = tracker.to_napari(ndim=2)
+        return data, properties, graph
+
+
+def track() -> FunctionGui:
+    @magicgui(
+        call_button=True,
+        persist=True,
+        config_file_path=dict(value=Path.home()),
+        reset_button=dict(widget_type="PushButton", text="Reset defaults"),
+    )
+    def widget(
+        viewer: napari.Viewer,
+        segmentation: napari.layers.Image,
+        config_file_path: Optional[Path],
+        reset_button,
+    ):
+        segmented_objects = segmentation_to_objects(segmentation.data[:100, ...])
+        data, properties, graph = run_tracker(segmented_objects, config_file_path)
+        viewer.add_tracks(
+            data=data, properties=properties, graph=graph, name=f"{segmentation}_btrack"
+        )
+
+    return widget

setup.cfg

@@ -7,7 +7,7 @@ url = https://github.com/quantumjot/napari-btrack
 description = A plugin to use btrack from napari
 long_description = file: README.md
 long_description_content_type = text/markdown
-classifiers =
+classifiers = 
     Development Status :: 2 - Pre-Alpha
     Intended Audience :: Developers
     Framework :: napari
@@ -30,7 +30,10 @@ install_requires =
     numpy
     btrack>=0.4.1
 
-
 [options.entry_points]
-napari.plugin =
-    napari-btrack = napari_btrack
+napari.manifest =
+    napari-btrack = napari_btrack:napari.yaml
+
+[options.package_data]
+napari_btrack = napari.yaml
+

setup.py

@@ -2,7 +2,6 @@
 # -*- coding: utf-8 -*-
 from setuptools import setup
 
-
 # https://github.com/pypa/setuptools_scm
 use_scm = {"write_to": "napari_btrack/_version.py"}