motile-tracker 3.1.3.dev0__tar.gz → 3.1.4.dev0__tar.gz

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: motile-tracker
-Version: 3.1.3.dev0
+Version: 3.1.4.dev0
 Summary: Application for interactive tracking with global optimization
 Author-email: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>
 License: BSD 3-Clause License

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev0}/src/motile_tracker/application_menus/menu_widget.py

@@ -13,24 +13,31 @@ class MenuWidget(QScrollArea):
     def __init__(self, viewer: napari.Viewer):
         super().__init__()
 
+        self.viewer = viewer
         tracks_viewer = TracksViewer.get_instance(viewer)
 
         motile_widget = MotileWidget(viewer)
         editing_widget = EditingMenu(viewer)
         view3D_widget = View3D(viewer)
+        view3D_widget.update_tab.connect(self.update_3D_tab)
 
-        tabwidget = QTabWidget()
+        self.tabwidget = QTabWidget()
 
-        tabwidget.addTab(view3D_widget, "3D viewing")
-        tabwidget.addTab(motile_widget, "Track with Motile")
-        tabwidget.addTab(editing_widget, "Edit Tracks")
-        tabwidget.addTab(tracks_viewer.tracks_list, "Results List")
-        tabwidget.addTab(tracks_viewer.collection_widget, "Collections")
+        self.tabwidget.addTab(view3D_widget, "3D viewing")
+        self.tabwidget.addTab(motile_widget, "Track with Motile")
+        self.tabwidget.addTab(editing_widget, "Edit Tracks")
+        self.tabwidget.addTab(tracks_viewer.tracks_list, "Results List")
+        self.tabwidget.addTab(tracks_viewer.collection_widget, "Collections")
 
         layout = QVBoxLayout()
-        layout.addWidget(tabwidget)
+        layout.addWidget(self.tabwidget)
 
-        self.setWidget(tabwidget)
+        self.setWidget(self.tabwidget)
         self.setWidgetResizable(True)
 
         self.setLayout(layout)
+
+    def update_3D_tab(self):
+        if self.tabwidget.currentIndex() == 0:
+            self.tabwidget.setCurrentIndex(1)
+            self.tabwidget.setCurrentIndex(0)

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev0}/src/motile_tracker/data_model/solution_tracks.py

@@ -1,8 +1,10 @@
 from __future__ import annotations
 
+import json
 from typing import TYPE_CHECKING
 
 import networkx as nx
+import pandas as pd
 from motile_toolbox.candidate_graph.graph_attributes import NodeAttr
 
 from .tracks import Tracks
@@ -177,31 +179,35 @@ class SolutionTracks(Tracks):
         }
         header = header + list(additional_attrs)
 
-        with open(outfile, "w") as f:
-            f.write(",".join(header))
-            for node_id in self.graph.nodes():
-                parents = list(self.graph.predecessors(node_id))
-                parent_id = "" if len(parents) == 0 else parents[0]
-                track_id = self.get_track_id(node_id)
-                time = self.get_time(node_id)
-                position = self.get_position(node_id)
-                lineage_id = self.get_lineage_id(node_id)
-                color = colormap.map(track_id)[:3] * 255
-                attrs = [
-                    self._get_node_attr(node_id, attr) for attr in additional_attrs
-                ]
-                row = [
-                    time,
-                    *position,
-                    node_id,
-                    parent_id,
-                    track_id,
-                    lineage_id,
-                    color,
-                    *attrs,
-                ]
-                f.write("\n")
-                f.write(",".join(map(str, row)))
+        data = []
+        for node_id in self.graph.nodes():
+            parents = list(self.graph.predecessors(node_id))
+            parent_id = "" if len(parents) == 0 else parents[0]
+            track_id = self.get_track_id(node_id)
+            time = self.get_time(node_id)
+            position = self.get_position(node_id)
+            lineage_id = self.get_lineage_id(node_id)
+            color = colormap.map(track_id)[:3] * 255
+            attrs = [
+                self._get_node_attr(node_id, attr)
+                if attr != "group"
+                else json.dumps(self._get_node_attr(node_id, attr))
+                for attr in additional_attrs
+            ]
+            row = [
+                time,
+                *position,
+                node_id,
+                parent_id,
+                track_id,
+                lineage_id,
+                color,
+                *attrs,
+            ]
+            data.append(row)
+
+        df = pd.DataFrame(data, columns=header)
+        df.to_csv(outfile, index=False)
 
     def add_nodes(
         self,

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev0}/src/motile_tracker/data_views/views/layers/contour_labels.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import functools
 from typing import Optional
 
 import napari
@@ -47,9 +46,7 @@ def get_contours(
 
     # instead of filling with background label, fill the group label with their normal color
     if group_labels is not None and len(group_labels) > 0:
-        group_mask = functools.reduce(
-            np.logical_or, (labels == val for val in group_labels)
-        )
+        group_mask = np.isin(labels, group_labels)
         combined_mask = not_boundaries & group_mask
         contours = np.where(combined_mask, labels, contours)
 
@@ -100,6 +97,7 @@ class ContourLabels(napari.layers.Labels):
             Returns None if the contour parameter is less than 1,
             or if the label array has more than 2 dimensions.
         """
+
         if self.contour < 1:
             return None
         if labels.ndim > 2:

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev0}/src/motile_tracker/data_views/views/layers/track_labels.py

@@ -45,7 +45,7 @@ def _new_label(layer: TrackLabels, new_track_id=True):
     """
 
     if isinstance(layer.data, np.ndarray):
-        new_selected_label = np.max(layer.data) + 1
+        new_selected_label = int(np.max(layer.data) + 1)
         if layer.selected_label == new_selected_label:
             show_info(
                 trans._(
@@ -362,7 +362,7 @@ class TrackLabels(ContourLabels):
             else:
                 if self.viewer.dims.ndisplay == 2:
                     self.contour = 1
-                    self.group_labels = visible
+                    self.group_labels = visible + highlighted._list
                     self.update_group_labels.emit(self.group_labels)
                 else:
                     self.colormap.color_dict = {

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev0}/src/motile_tracker/data_views/views/view_3d/view3D.py

@@ -1,4 +1,5 @@
 import napari
+from psygnal import Signal
 from qtpy.QtWidgets import QLabel, QVBoxLayout, QWidget
 
 from .clipping_plane_sliders import PlaneSliderWidget
@@ -30,6 +31,8 @@ class OrthogonalViews(QWidget):
 class View3D(QWidget):
     """Widget to combine multiple views and cross widget together."""
 
+    update_tab = Signal()
+
     def __init__(
         self,
         viewer: napari.Viewer,
@@ -59,7 +62,7 @@ class View3D(QWidget):
         self.plane_widget.hide()
         self.widget_2d.hide()
 
-        # Show the correct widget initially
+        # Show the correct widget
         self.display_changed()
 
     def display_changed(self, event=None):
@@ -75,5 +78,7 @@ class View3D(QWidget):
                 self.plane_widget.show()
             elif self.viewer.dims.ndisplay == 2:
                 self.orth_views.show()
+                self.orth_views.update()
+                self.update_tab.emit()
         else:
             self.widget_2d.show()

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev0}/src/motile_tracker.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: motile-tracker
-Version: 3.1.3.dev0
+Version: 3.1.4.dev0
 Summary: Application for interactive tracking with global optimization
 Author-email: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>
 License: BSD 3-Clause License