Multi canvas labeler (#50)

* slow version working

* add multi labeler

* guard against validated labels not set

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: trailing-whitespace
         exclude: ^.napari-hub/*
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         args: ["--profile", "black"]

src/morphometrics/_gui/_qt/multiple_viewer_widget.py

@@ -210,10 +210,16 @@ def _order_update(self):
             return
 
         order[-3:] = order[-2], order[-3], order[-1]
-        self.ortho_viewer_models[0].dims.order = order
+        self.ortho_viewer_models[1].dims.order = order
         order = list(self.viewer.dims.order)
         order[-3:] = order[-1], order[-2], order[-3]
-        self.ortho_viewer_models[1].dims.order = order
+        self.ortho_viewer_models[0].dims.order = order
+
+        # order[-3:] = order[-2], order[-3], order[-1]
+        # self.ortho_viewer_models[0].dims.order = order
+        # order = list(self.viewer.dims.order)
+        # order[-3:] = order[-1], order[-2], order[-3]
+        # self.ortho_viewer_models[1].dims.order = order
 
     def _layer_added(self, event):
         """add layer to additional viewers and connect all required events.

src/morphometrics/_gui/label_curator/label_cleaning.py

@@ -1,7 +1,8 @@
-from typing import TYPE_CHECKING, List
+from typing import TYPE_CHECKING, Dict, List
 
 import napari
 import numpy as np
+from napari.utils.colormaps import color_dict_to_colormap
 from napari.utils.events import EmitterGroup, Event, EventedSet
 
 if TYPE_CHECKING:
@@ -36,29 +37,49 @@ def enabled(self, enabled: bool) -> None:
         self.events.enabled()
 
     def _on_enable(self):
+
+        # check if the validated labels layer is set
+        validated_labels_layer_set = self._curator_model._ortho_viewers is not None
+
         # add the lables layer events
         self._selected_labels.events.changed.connect(self._on_selection_changed)
         self._curator_model.labels_layer.mouse_drag_callbacks.append(
             self._on_click_selection
         )
 
         # add the validated labels layer events
-        self._selected_validated_labels.events.changed.connect(
-            self._on_selection_changed
-        )
-        self._curator_model.validated_labels_layer.mouse_drag_callbacks.append(
-            self._on_click_selection
-        )
+        if self._curator_model.validated_labels_layer is not None:
+            self._selected_validated_labels.events.changed.connect(
+                self._on_selection_changed
+            )
+            self._curator_model.validated_labels_layer.mouse_drag_callbacks.append(
+                self._on_click_selection
+            )
 
+        labels_layer_name = self._curator_model.labels_layer.name
+        if validated_labels_layer_set:
+            validated_labels_layer_name = (
+                self._curator_model.validated_labels_layer.name
+            )
+        if validated_labels_layer_set:
+            for viewer in self._curator_model._ortho_viewers:
+                viewer.layers[labels_layer_name].mouse_drag_callbacks.append(
+                    self._on_click_selection
+                )
+                if validated_labels_layer_set:
+                    viewer.layers[
+                        validated_labels_layer_name
+                    ].mouse_drag_callbacks.append(self._on_click_selection)
         # set the labels layer coloring mode
         self._curator_model.labels_layer.color_mode = "direct"
-        self._curator_model.labels_layer.color = (
-            self._curator_model._colormap_manager._default_colormap
-        )
 
-        self._curator_model.validated_labels_layer.color_mode = "direct"
-        self._curator_model.validated_labels_layer.color = (
-            self._curator_model._colormap_manager._default_colormap
+        if validated_labels_layer_set:
+            self._curator_model.validated_labels_layer.color_mode = "direct"
+
+        # set the colormaps
+        self._set_all_labels_colormamaps(
+            labels_colormap=self._curator_model._colormap_manager._default_colormap,
+            validated_labels_colormap=self._curator_model._colormap_manager._default_colormap,
         )
 
     def _on_disable(self):
@@ -76,9 +97,9 @@ def _on_click_selection(self, layer: napari.layers.Labels, event: Event):
             world=True,
         )
 
-        if layer is self._curator_model.labels_layer:
+        if layer.name == self._curator_model.labels_layer.name:
             selection_set = self._selected_labels
-        elif layer is self._curator_model.validated_labels_layer:
+        elif layer.name == self._curator_model.validated_labels_layer.name:
             selection_set = self._selected_validated_labels
         else:
             return
@@ -100,18 +121,98 @@ def _on_selection_changed(self, event: Event):
         if not self.enabled:
             # don't do anything if not curating
             return
+
+        selected_labels = event.source
         # get the indices of the validated labels
-        self._curator_model.labels_layer.color = (
+        new_colormap = (
             self._curator_model._colormap_manager.create_highlighted_colormap(
-                list(self._selected_labels)
+                list(selected_labels)
             )
         )
 
-        self._curator_model.validated_labels_layer.color = (
-            self._curator_model._colormap_manager.create_highlighted_colormap(
-                list(self._selected_validated_labels)
+        if selected_labels is self._selected_labels:
+            self._set_labels_layer_colormap(
+                labels_colormap=new_colormap,
             )
-        )
+        elif selected_labels is self._selected_validated_labels:
+            self._set_validated_labels_layer_colormap(labels_colormap=new_colormap)
+        else:
+            raise ValueError("unknown selction model")
+
+    def _set_all_labels_colormamaps(
+        self,
+        labels_colormap: Dict[int, np.ndarray],
+        validated_labels_colormap: Dict[int, np.ndarray],
+    ) -> None:
+        """Set the label colormaps for all viewers"""
+        self._set_labels_layer_colormap(labels_colormap)
+        self._set_validated_labels_layer_colormap(validated_labels_colormap)
+
+    def _set_labels_layer_colormap(
+        self, labels_colormap: Dict[int, np.ndarray]
+    ) -> None:
+        self._curator_model.labels_layer.color = labels_colormap
+
+        if self._curator_model._ortho_viewers is None:
+            # we can return early if there aren't orthoviewers
+            return
+
+        # update the orthoviewers
+        labels_layer_name = self._curator_model.labels_layer.name
+
+        for viewer in self._curator_model._ortho_viewers:
+            viewer.layers[labels_layer_name].color = labels_colormap
+
+        # # set the main viewers
+        # self._fast_set_labels_colormap(layer=self._curator_model.labels_layer, colormap=labels_colormap)
+        #
+        # if self._curator_model._ortho_viewers is None:
+        #     # we can return early if there aren't orthoviewers
+        #     return
+        #
+        # # update the orthoviewers
+        # labels_layer_name = self._curator_model.labels_layer.name
+        #
+        # for viewer in self._curator_model._ortho_viewers:
+        #     self._fast_set_labels_colormap(
+        #         layer=viewer.layers[labels_layer_name],
+        #         colormap=labels_colormap
+        #     )
+
+    def _set_validated_labels_layer_colormap(
+        self, labels_colormap: Dict[int, np.ndarray]
+    ) -> None:
+        if self._curator_model.validated_labels_layer is not None:
+            self._curator_model.validated_labels_layer.color = labels_colormap
+
+        if self._curator_model._ortho_viewers is None:
+            # we can return early if there aren't orthoviewers
+            return
+
+        # update the orthoviewers
+        validated_labels_layer_name = self._curator_model.validated_labels_layer.name
+        for viewer in self._curator_model._ortho_viewers:
+            viewer.layers[validated_labels_layer_name].color = labels_colormap
+
+    def _fast_set_labels_colormap(self, layer, colormap):
+        if layer._background_label not in colormap:
+            colormap[layer._background_label] = np.array([0, 0, 0, 0])
+        if None not in colormap:
+            colormap[None] = np.array([0, 0, 0, 1])
+
+        # colors = {
+        #     label: transform_color(color_str)[0]
+        #     for label, color_str in colormap.items()
+        # }
+
+        layer._color = colormap
+        # set the colormap
+        custom_colormap, label_color_index = color_dict_to_colormap(layer.color)
+        #
+        # # layer._colormap = custom_colormap
+        # # layer._label_color_index = label_color_index
+        # #
+        # # layer._selected_color = layer.get_color(layer.selected_label)
 
     def merge_selected_labels(self):
         """Merge the selected label values.

src/morphometrics/_gui/label_curator/label_curator.py

@@ -1,6 +1,6 @@
 from enum import Enum
 from itertools import cycle
-from typing import Dict, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import glasbey
 import napari
@@ -48,7 +48,7 @@ def _initialize_colormaps(
         colors_default[:, 0:3] = colors_default[:, 0:3] * 0.7
 
         colors_default_cylcer = cycle(colors_default)
-        colormap_default = {i: next(colors_default_cylcer) for i in range(5000)}
+        colormap_default = {i: next(colors_default_cylcer) for i in range(2000)}
         colormap_default[0] = np.array([0, 0, 0, 0])
         colormap_default[None] = np.array([0, 0, 0, 1])
 
@@ -68,11 +68,13 @@ class LabelCurator:
     def __init__(
         self,
         viewer: napari.Viewer,
+        ortho_viewers: Optional[List[napari.Viewer]] = None,
         labels_layer: Optional[Labels] = None,
         validated_labels_layer: Optional[Labels] = None,
         mode: Union[CurationMode, str] = "paint",
     ):
         self._viewer = viewer
+        self._ortho_viewers = ortho_viewers
         self._mode = CurationMode(mode)
         self._labels_layer = None
         self._validated_labels_layer = None

src/morphometrics/_gui/label_curator/qt_label_curator.py

@@ -14,6 +14,7 @@
     QWidget,
 )
 
+from morphometrics._gui._qt.multiple_viewer_widget import MultipleViewerWidget
 from morphometrics._gui.label_curator.label_cleaning import LabelCleaningModel
 from morphometrics._gui.label_curator.label_curator import CurationMode, LabelCurator
 from morphometrics.label.image_utils import expand_selected_labels_using_crop
@@ -215,10 +216,15 @@ def _on_paint_enabled_changed(self, event: Event) -> None:
 
 
 class QtLabelingWidget(QWidget):
-    def __init__(self, viewer: napari.Viewer, parent: Optional[QWidget] = None):
+    def __init__(
+        self,
+        main_viewer: napari.Viewer,
+        ortho_viewers: Optional[List[napari.Viewer]] = None,
+        parent: Optional[QWidget] = None,
+    ):
         super().__init__(parent=parent)
-        self._viewer = viewer
-        self._model = LabelCurator(viewer=viewer)
+        self._viewer = main_viewer
+        self._model = LabelCurator(viewer=main_viewer, ortho_viewers=ortho_viewers)
 
         # make the label selection widget
         self._label_selection_widget = magicgui(
@@ -228,6 +234,12 @@ def __init__(self, viewer: napari.Viewer, parent: Optional[QWidget] = None):
             auto_call=True,
             call_button=None,
         )
+        self._viewer.layers.events.inserted.connect(
+            self._label_selection_widget.reset_choices
+        )
+        self._viewer.layers.events.removed.connect(
+            self._label_selection_widget.reset_choices
+        )
 
         # get the curation mode widget
         self.curation_mode_widget = QtLabelingModeWidget(curator_model=self._model)
@@ -254,3 +266,20 @@ def _get_valid_labels_layers(self, combo_box) -> List[napari.layers.Labels]:
             for layer in self._viewer.layers
             if isinstance(layer, napari.layers.Labels)
         ]
+
+
+class QtMultiCanvasLabelingWidget(MultipleViewerWidget):
+    def __init__(self, viewer: napari.Viewer):
+        super().__init__(viewer)
+        # self.flood_fill_widget = FloodFillWidget(
+        #     main_viewer=viewer, ortho_viewers=self.ortho_viewer_models
+        # )
+        # self.addWidget(self.flood_fill_widget)
+        self.labeling_widget = QtLabelingWidget(
+            main_viewer=viewer, ortho_viewers=self.ortho_viewer_models
+        )
+        self.addWidget(self.labeling_widget)
+
+        self.viewer.axes.visible = True
+        for model in self.ortho_viewer_models:
+            model.axes.visible = True