Merge branch 'main' into 322-rendering-of-contour-labels-in-3d

Author: AnniekStok

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
         exclude: ^\.napari-hub/.*
       - id: check-yaml # checks for correct yaml syntax for github actions ex.
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.11
+    rev: v0.14.13
     hooks:
       - id: ruff
         args: [--fix, -v]

README.md

@@ -3,9 +3,10 @@
 [![tests](https://github.com/funkelab/motile_tracker/workflows/tests/badge.svg)](https://github.com/funkelab/motile_tracker/actions)
 [![codecov](https://codecov.io/gh/funkelab/motile_tracker/branch/main/graph/badge.svg)](https://codecov.io/gh/funkelab/motile_tracker)
 
+
+An application for interactive tracking with [motile](https://github.com/funkelab/motile).
 The full documentation of the plugin can be found [here](https://funkelab.github.io/motile_tracker/).
 
-An application for interactive tracking with [motile](https://github.com/funkelab/motile)
 Motile is a library that makes it easy to solve tracking problems using optimization
 by framing the task as an Integer Linear Program (ILP).
 See the motile [documentation](https://funkelab.github.io/motile)
@@ -60,6 +61,8 @@ track objects in napari Labels or Points layers. For details, please read the
 
 ![motile_tracker_quick_demo](https://github.com/user-attachments/assets/07a4a954-3d2d-4d67-8f75-aec11ee14697)
 
+If you are new to using motile-tracker, you can follow this [tutorial](./assets/motile-tracker_tutorial.pdf) to learn the basics.
+
 ## Package the application into an executable and create the installer
 
 Tagging any branch will automatically trigger the deploy.yml workflow,

assets/motile-tracker_tutorial.md

@@ -82,10 +82,19 @@ def add_napari_layers(self) -> None:
 
         if self.tracks_layer is not None:
             self.viewer.add_layer(self.tracks_layer)
-        if self.seg_layer is not None:
-            self.viewer.add_layer(self.seg_layer)
         if self.points_layer is not None:
             self.viewer.add_layer(self.points_layer)
+        if self.seg_layer is not None:
+            self.viewer.add_layer(self.seg_layer)
+            # silly fix for loading zarr on Windows: load labels only at the end and then
+            # swap layer order here to avoid error "access violation reading..."
+            self.viewer.layers.move(-1, -2)
+
+            # This is just to ensure that the layer selection makes sense, because after
+            # moving a layer, the layer tools are not updated correctly.
+            self.viewer.layers.selection.clear()
+            self.viewer.layers.selection.add(self.viewer.layers[-1])
+
         # self.link_experimental_clipping_planes()
 
     def link_experimental_clipping_planes(self):

assets/motile-tracker_tutorial.pdf

@@ -120,7 +120,6 @@ def _update_field_map_and_scale(self, checked: bool | None = None) -> None:
         self.seg = (
             self.segmentation_widget.include_seg() if checked is None else not checked
         )
-        self.scale_widget.setVisible(self.seg)
 
         if self.import_type == "csv":
             self.incl_z = self.dimension_widget.incl_z
@@ -161,6 +160,8 @@ def _update_field_map_and_scale(self, checked: bool | None = None) -> None:
             self.prop_map_widget.mapping_labels["seg_id"].setVisible(self.seg)
 
         self._update_finish_button()
+        self.scale_widget.setVisible(self.seg)
+
         self._resize_dialog()
 
     def infer_dims_from_segmentation(self) -> None:
@@ -198,10 +199,9 @@ def infer_dims_from_segmentation(self) -> None:
     def _update_segmentation_widget(self) -> None:
         """Refresh the geff segmentation widget based on the geff root group."""
 
+        self.segmentation_widget.setVisible(False)
         if self.import_widget.root is not None:
             self.segmentation_widget.update_root(self.import_widget.root)
-        else:
-            self.segmentation_widget.setVisible(False)
         self._update_finish_button()
         self._resize_dialog()
 

src/motile_tracker/data_views/views/layers/tracks_layer_group.py

@@ -163,7 +163,7 @@ def extract_geff_property_fields(
         self.seg = seg
         self.incl_z = incl_z
 
-        self.setVisible(True)
+        self.setVisible(False)
         self.node_attrs = list(root["nodes"]["props"].group_keys())
         self.metadata = dict(root.attrs.get("geff", {}))
 
@@ -192,6 +192,7 @@ def extract_geff_property_fields(
                 self.standard_fields.insert(1, "z")
 
         self.update_mapping(seg)
+        self.setVisible(True)
 
     def _update_props_left(self) -> None:
         """Update the list of columns that have not been mapped yet"""
@@ -412,6 +413,7 @@ def update_mapping(self, seg: bool = False) -> None:
             seg (bool = False): whether a segmentation is associated with this data
         """
 
+        self.setVisible(False)
         self.mapping_labels = {}
         self.mapping_widgets = {}
         clear_layout(self.mapping_layout)  # clear layout first
@@ -458,6 +460,8 @@ def update_mapping(self, seg: bool = False) -> None:
         self.optional_mapping_layout.addWidget(header_assign, 0, 1)
         self.optional_mapping_layout.addWidget(header_recompute, 0, 2)
         self._update_props_left()
+
+        self.setVisible(True)
         self.setMinimumHeight(350)
 
     def get_name_map(self) -> dict[str, str]:

src/motile_tracker/import_export/menus/import_dialog.py

@@ -61,7 +61,6 @@ def update(self, metadata: dict | None = None, incl_z: bool = False) -> None:
             ndim = 4 if incl_z else 3
             self.scale = list([1.0] * ndim)
 
-        self.setVisible(True)
         clear_layout(self.scale_layout)
         self.scale_form_layout = QFormLayout()
 
@@ -78,6 +77,7 @@ def update(self, metadata: dict | None = None, incl_z: bool = False) -> None:
         self.scale_form_layout.addRow(QLabel("x"), self.x_spin_box)
 
         self.scale_layout.addLayout(self.scale_form_layout)
+        self.setVisible(True)
 
     def _scale_spin_box(self, value: float) -> QDoubleSpinBox:
         """Return a QDoubleSpinBox for scaling values"""

src/motile_tracker/import_export/menus/prop_map_widget.py

@@ -331,11 +331,11 @@ def update_root(self, root: zarr.Group | None) -> None:
         Args:
             root (zarr.Group | None): The root group of the geff zarr store.
         """
+        self.setVisible(False)
         self.root = root
         clear_layout(self.related_objects_layout)
         self.related_object_radio_buttons = {}
         if self.root is not None:
-            self.setVisible(True)
             metadata = dict(self.root.attrs)
             related_objects = metadata.get("geff", {}).get("related_objects", None)
             if related_objects:
@@ -346,8 +346,7 @@ def update_root(self, root: zarr.Group | None) -> None:
                         self.button_group.addButton(radio)
                         self.related_object_radio_buttons[obj.get("path", None)] = radio
                         self.related_objects_layout.addWidget(radio)
-        else:
-            self.setVisible(False)
+            self.setVisible(True)
 
     def _toggle_segmentation(self, checked: bool) -> None:
         """Toggle visibility of the segmentation widget based on the radio button