Merge pull request #240 from funkelab/213-improve-user-experience-for-making-a-new-track-id-when-labeling-with-segs

213 improve user experience for making a new track id when labeling with segs

Author: cmalinmayor

pyproject.toml

@@ -44,7 +44,7 @@ dependencies =[
     "dask[array]>=2021.10.0",
     "fonticon-fontawesome6>=6,<7",
     "pyqtgraph>=0.13,<1",
-    "napari-orthogonal-views @ git+https://github.com/AnniekStok/napari-orthogonal-views.git@v0.0.4",
+    "napari-orthogonal-views==0.0.6",
     "lxml_html_clean>=0.4,<1",
     "zarr>=2.10,<3",
 ]

src/motile_tracker/application_menus/editing_menu.py

@@ -1,6 +1,8 @@
 import napari
 from qtpy.QtWidgets import (
     QGroupBox,
+    QHBoxLayout,
+    QLabel,
     QPushButton,
     QVBoxLayout,
     QWidget,
@@ -17,6 +19,15 @@ def __init__(self, viewer: napari.Viewer):
         self.tracks_viewer.selected_nodes.list_updated.connect(self.update_buttons)
         layout = QVBoxLayout()
 
+        self.label = QLabel(f"Current Track ID: {self.tracks_viewer.selected_track}")
+        self.tracks_viewer.update_track_id.connect(self.update_track_id_color)
+        new_track_btn = QPushButton("Start new")
+        new_track_btn.clicked.connect(self.tracks_viewer.request_new_track)
+        track_layout = QHBoxLayout()
+        track_layout.addWidget(self.label)
+        track_layout.addWidget(new_track_btn)
+        layout.addLayout(track_layout)
+
         node_box = QGroupBox("Edit Node(s)")
         node_box.setMaximumHeight(60)
         node_box_layout = QVBoxLayout()
@@ -69,7 +80,22 @@ def __init__(self, viewer: napari.Viewer):
         layout.addWidget(self.redo_btn)
 
         self.setLayout(layout)
-        self.setMaximumHeight(300)
+        self.setMaximumHeight(400)
+
+    def update_track_id_color(self):
+        """Display track ID value and color"""
+
+        color = self.tracks_viewer.track_id_color
+        r, g, b, a = [int(c * 255) if i < 3 else c for i, c in enumerate(color)]
+        css_color = f"rgba({r}, {g}, {b}, {a})"
+        self.label.setText(f"Current Track ID: {self.tracks_viewer.selected_track}")
+        self.label.setStyleSheet(
+            f"""
+            color: white;
+            border: 2px solid {css_color};
+            padding: 5px;
+            """
+        )
 
     def update_buttons(self):
         """Set the buttons to enabled/disabled depending on the selected nodes"""

src/motile_tracker/data_views/_tests/conftest.py

@@ -0,0 +1,73 @@
+import networkx as nx
+import numpy as np
+import pytest
+from funtracks.data_model import NodeAttr
+
+from motile_tracker.data_views.views_coordinator.tracks_viewer import TracksViewer
+
+
+@pytest.fixture(autouse=True)
+def reset_tracks_viewer():
+    # clear the singleton before test
+    if hasattr(TracksViewer, "_instance"):
+        del TracksViewer._instance
+
+    # after test, close all viewers and clear again
+    yield
+    if hasattr(TracksViewer, "_instance"):
+        del TracksViewer._instance
+
+
+@pytest.fixture
+def graph_3d():
+    graph = nx.DiGraph()
+    nodes = [
+        (
+            1,
+            {
+                NodeAttr.POS.value: [50, 50, 50],
+                NodeAttr.TIME.value: 0,
+                NodeAttr.AREA.value: 1000,
+            },
+        ),
+        (
+            2,
+            {
+                NodeAttr.POS.value: [20, 50, 80],
+                NodeAttr.TIME.value: 1,
+                NodeAttr.AREA.value: 1000,
+            },
+        ),
+        (
+            3,
+            {
+                NodeAttr.POS.value: [60, 50, 45],
+                NodeAttr.TIME.value: 2,
+                NodeAttr.AREA.value: 1000,
+            },
+        ),
+        (
+            4,
+            {
+                NodeAttr.POS.value: [40, 70, 60],
+                NodeAttr.TIME.value: 2,
+                NodeAttr.AREA.value: 1000,
+            },
+        ),
+    ]
+    edges = [(1, 2), (2, 3), (2, 4)]
+    graph.add_nodes_from(nodes)
+    graph.add_edges_from(edges)
+    return graph
+
+
+@pytest.fixture
+def segmentation_3d():
+    frame_shape = (100, 100, 100)
+    total_shape = (5, *frame_shape)
+    segmentation = np.zeros(total_shape, dtype="int32")
+    segmentation[0, 45:55, 45:55, 45:55] = 1
+    segmentation[1, 15:25, 45:55, 75:85] = 2
+    segmentation[2, 55:65, 45:55, 40:50] = 3
+    segmentation[2, 35:45, 65:75, 55:65] = 4
+    return segmentation

src/motile_tracker/data_views/_tests/test_ortho_views.py

@@ -1,7 +1,5 @@
-import networkx as nx
 import numpy as np
-import pytest
-from funtracks.data_model import NodeAttr, SolutionTracks
+from funtracks.data_model import SolutionTracks
 from napari.layers import Labels, Points
 from napari_orthogonal_views.ortho_view_widget import OrthoViewWidget
 
@@ -13,52 +11,6 @@
 from motile_tracker.data_views.views_coordinator.tracks_viewer import TracksViewer
 
 
-@pytest.fixture
-def graph_3d():
-    graph = nx.DiGraph()
-    nodes = [
-        (
-            1,
-            {
-                NodeAttr.POS.value: [50, 50, 50],
-                NodeAttr.TIME.value: 0,
-            },
-        ),
-        (
-            2,
-            {
-                NodeAttr.POS.value: [20, 50, 80],
-                NodeAttr.TIME.value: 1,
-            },
-        ),
-        (
-            3,
-            {
-                NodeAttr.POS.value: [60, 50, 45],
-                NodeAttr.TIME.value: 1,
-            },
-        ),
-    ]
-    edges = [
-        (1, 2),
-        (1, 3),
-    ]
-    graph.add_nodes_from(nodes)
-    graph.add_edges_from(edges)
-    return graph
-
-
-@pytest.fixture
-def segmentation_3d():
-    frame_shape = (100, 100, 100)
-    total_shape = (5, *frame_shape)
-    segmentation = np.zeros(total_shape, dtype="int32")
-    segmentation[0, 45:55, 45:55, 45:55] = 1
-    segmentation[1, 15:25, 45:55, 75:85] = 2
-    segmentation[1, 55:65, 45:55, 40:50] = 3
-    return segmentation
-
-
 class MockEvent:
     def __init__(self, value):
         self.value = value
@@ -71,52 +23,74 @@ def test_ortho_views(make_napari_viewer, qtbot, graph_3d, segmentation_3d):
     viewer = make_napari_viewer()
     m = initialize_ortho_views(viewer)
 
-    m.show()
-    qtbot.waitUntil(lambda: m.is_shown(), timeout=1000)
-    assert isinstance(m.right_widget, OrthoViewWidget)
-
     # Create example tracks
     tracks = SolutionTracks(graph=graph_3d, segmentation=segmentation_3d, ndim=4)
     tracks_viewer = TracksViewer.get_instance(viewer)
     tracks_viewer.update_tracks(tracks=tracks, name="test")
 
     assert isinstance(viewer.layers[-1], TrackPoints)
     assert isinstance(viewer.layers[-2], TrackLabels)
+
+    # change attributes on the TrackLabels layer to check that they are correctly copied
+    viewer.layers[-2].contour = 1
+    viewer.layers[-2].mode = "erase"
+
+    # show orthogonal views and check attributes
+    m.show()
+    qtbot.waitUntil(lambda: m.is_shown(), timeout=1000)
+    assert isinstance(m.right_widget, OrthoViewWidget)
     assert isinstance(m.right_widget.vm_container.viewer_model.layers[-1], Points)
     assert isinstance(m.bottom_widget.vm_container.viewer_model.layers[-1], Points)
     assert isinstance(m.right_widget.vm_container.viewer_model.layers[-2], Labels)
     assert isinstance(m.bottom_widget.vm_container.viewer_model.layers[-2], Labels)
+    assert (
+        m.right_widget.vm_container.viewer_model.layers[-2].contour
+        == viewer.layers[-2].contour
+    )
+    assert (
+        m.right_widget.vm_container.viewer_model.layers[-2].mode
+        == viewer.layers[-2].mode
+    )
+
+    # set to paint mode and test syncing
+    viewer.layers[-2].mode = "paint"
+    assert (
+        viewer.layers[-2].mode
+        == m.right_widget.vm_container.viewer_model.layers[-2].mode
+        == m.bottom_widget.vm_container.viewer_model.layers[-2].mode
+    )
 
     # Test paint event on main viewer (indices, orig value, target_value)
     event_val = [
         (
             (np.array([1]), np.array([15]), np.array([45]), np.array([75])),
             np.array([2], dtype=np.uint16),
-            np.uint16(4),
+            np.uint16(5),
         )
     ]
     event = MockEvent(event_val)
+    step = list(viewer.dims.current_step)
+    step[0] = 1
+    viewer.dims.current_step = step
     viewer.layers[-2]._on_paint(event)
 
-    assert viewer.layers[-2].data[1, 15, 45, 75] == 4
+    assert viewer.layers[-2].data[1, 15, 45, 75] == 5
     assert np.array_equal(
         viewer.layers[-2].data, m.right_widget.vm_container.viewer_model.layers[-2].data
     )
 
-    # test paint even on one of the ortho views and see if a new node is added
+    # test paint event on one of the ortho views and see if a new node is added
+    assert len(tracks_viewer.tracks.graph.nodes) == 5
+    step = list(viewer.dims.current_step)
+    step[0] = 2
+    viewer.dims.current_step = step
     m.right_widget.vm_container.viewer_model.layers[-2].paint(
-        coord=(2, 63, 20, 30), new_label=5, refresh=True
+        coord=(2, 63, 20, 30), new_label=6, refresh=True
     )
-    assert len(tracks_viewer.tracks.graph.nodes) == 5
+    assert len(tracks_viewer.tracks.graph.nodes) == 6
 
     # test syncing of properties
-    viewer.layers[-2].mode = "paint"
-    assert (
-        viewer.layers[-2].mode
-        == m.right_widget.vm_container.viewer_model.layers[-2].mode
-        == m.bottom_widget.vm_container.viewer_model.layers[-2].mode
-    )
-    viewer.layers[-2].selected_label = 6
+    viewer.layers[-2].selected_label = 7  # forward sync only
     assert (
         viewer.layers[-2].selected_label
         == m.right_widget.vm_container.viewer_model.layers[-2].selected_label