WIP 3D cropping

brainglobe_registration/registration_widget.py

@@ -42,6 +42,7 @@
 from brainglobe_registration.widgets.adjust_moving_image_view import (
     AdjustMovingImageView,
 )
+from brainglobe_registration.widgets.crop_atlas_view import CropAtlasView
 from brainglobe_registration.widgets.parameter_list_view import (
     RegistrationParameterListView,
 )
@@ -110,6 +111,18 @@ def __init__(self, napari_viewer: Viewer):
             self._on_sample_popup_about_to_show
         )
 
+        self.crop_atlas_widget = CropAtlasView(parent=self)
+
+        self.crop_atlas_widget.crop_x_signal.connect(
+            self._on_crop_atlas_x_signal
+        )
+        self.crop_atlas_widget.crop_y_signal.connect(
+            self._on_crop_atlas_y_signal
+        )
+        self.crop_atlas_widget.crop_z_signal.connect(
+            self._on_crop_atlas_z_signal
+        )
+
         self.adjust_moving_image_widget = AdjustMovingImageView(parent=self)
         self.adjust_moving_image_widget.adjust_image_signal.connect(
             self._on_adjust_moving_image
@@ -151,6 +164,7 @@ def __init__(self, napari_viewer: Viewer):
             collapsible=False,
         )
         self.add_widget(self.get_atlas_widget, widget_title="Select Images")
+        self.add_widget(self.crop_atlas_widget, widget_title="Crop Atlas")
         self.add_widget(
             self.adjust_moving_image_widget, widget_title="Prepare Images"
         )
@@ -236,6 +250,27 @@ def _on_atlas_dropdown_index_changed(self, index):
         )
 
         self._viewer.grid.enabled = True
+        self.crop_atlas_widget.set_ranges(*self._atlas.reference.shape[-1::-1])
+        self.clipping_planes = [
+            {"position": (0, 0, 0), "normal": (1, 0, 0), "enabled": False},
+            {
+                "position": (self._atlas.reference.shape[2], 0, 0),
+                "normal": (-1, 0, 0),
+                "enabled": False,
+            },
+            {"position": (0, 0, 0), "normal": (0, 1, 0), "enabled": False},
+            {
+                "position": (0, self._atlas.reference.shape[1], 0),
+                "normal": (0, -1, 0),
+                "enabled": False,
+            },
+            {"position": (0, 0, 0), "normal": (0, 0, 1), "enabled": False},
+            {
+                "position": (0, 0, self._atlas.reference.shape[0]),
+                "normal": (0, 0, -1),
+                "enabled": False,
+            },
+        ]
 
     def _on_sample_dropdown_index_changed(self, index):
         viewer_index = find_layer_index(
@@ -262,6 +297,63 @@ def _on_adjust_moving_image_reset_button_click(self):
             return
         adjust_napari_image_layer(self._moving_image, 0, 0, 0)
 
+    def _on_crop_atlas_x_signal(self, start: int, end: int):
+        if not (self._atlas_data_layer and self._atlas_annotations_layer):
+            show_error(
+                "No atlas selected. Please select an atlas before cropping"
+            )
+            return
+
+        self.clipping_planes[4]["enabled"] = True
+        self.clipping_planes[4]["position"] = (0, 0, start)
+        self.clipping_planes[5]["enabled"] = True
+        self.clipping_planes[5]["position"] = (0, 0, end)
+
+        self._atlas_data_layer.experimental_clipping_planes = (
+            self.clipping_planes
+        )
+        self._atlas_annotations_layer.experimental_clipping_planes = (
+            self.clipping_planes
+        )
+
+    def _on_crop_atlas_y_signal(self, start: int, end: int):
+        if not (self._atlas_data_layer and self._atlas_annotations_layer):
+            show_error(
+                "No atlas selected. Please select an atlas before cropping"
+            )
+            return
+
+        self.clipping_planes[2]["enabled"] = True
+        self.clipping_planes[2]["position"] = (0, start, 0)
+        self.clipping_planes[3]["enabled"] = True
+        self.clipping_planes[3]["position"] = (0, end, 0)
+
+        self._atlas_data_layer.experimental_clipping_planes = (
+            self.clipping_planes
+        )
+        self._atlas_annotations_layer.experimental_clipping_planes = (
+            self.clipping_planes
+        )
+
+    def _on_crop_atlas_z_signal(self, start: int, end: int):
+        if not (self._atlas_data_layer and self._atlas_annotations_layer):
+            show_error(
+                "No atlas selected. Please select an atlas before cropping"
+            )
+            return
+
+        self.clipping_planes[0]["enabled"] = True
+        self.clipping_planes[0]["position"] = (start, 0, 0)
+        self.clipping_planes[1]["enabled"] = True
+        self.clipping_planes[1]["position"] = (end, 0, 0)
+
+        self._atlas_data_layer.experimental_clipping_planes = (
+            self.clipping_planes
+        )
+        self._atlas_annotations_layer.experimental_clipping_planes = (
+            self.clipping_planes
+        )
+
     def _on_run_button_click(self):
 
         current_atlas_slice = self._viewer.dims.current_step[0]
@@ -465,6 +557,10 @@ def _on_adjust_atlas_rotation(self, pitch: float, yaw: float, roll: float):
             output_chunks=(2, bounding_box[1], bounding_box[2]),
         )
 
+        self.crop_atlas_widget.set_ranges(
+            *self._atlas_data_layer.data.shape[-1::-1]
+        )
+
         worker = self.compute_atlas_rotation(self._atlas_data_layer.data)
         worker.returned.connect(self.set_atlas_layer_data)
         worker.start()

brainglobe_registration/widgets/crop_atlas_view.py

@@ -0,0 +1,58 @@
+from qtpy.QtCore import Qt, Signal
+from qtpy.QtWidgets import QLabel, QVBoxLayout, QWidget
+from superqt import QLabeledRangeSlider
+
+
+class CropAtlasView(QWidget):
+    crop_z_signal = Signal(int, int)
+    crop_y_signal = Signal(int, int)
+    crop_x_signal = Signal(int, int)
+
+    def __init__(self, parent=None):
+        super().__init__(parent=parent)
+        self.setLayout(QVBoxLayout())
+
+        self.x_slider = QLabeledRangeSlider(Qt.Orientation.Horizontal)
+        self.y_slider = QLabeledRangeSlider(Qt.Orientation.Horizontal)
+        self.z_slider = QLabeledRangeSlider(Qt.Orientation.Horizontal)
+
+        self.set_ranges(100, 100, 100)
+
+        self.layout().addWidget(QLabel("Crop X"))
+        self.layout().addWidget(self.x_slider)
+        self.layout().addWidget(QLabel("Crop Y"))
+        self.layout().addWidget(self.y_slider)
+        self.layout().addWidget(QLabel("Crop Z"))
+        self.layout().addWidget(self.z_slider)
+
+        self.x_slider.sliderMoved.connect(self._on_crop_x)
+        self.y_slider.sliderMoved.connect(self._on_crop_y)
+        self.z_slider.sliderMoved.connect(self._on_crop_z)
+        # Emits twice, but if not connected, editing text doesn't emit signal
+        # via sliderMoved
+        self.x_slider.editingFinished.connect(self._on_crop_x)
+        self.y_slider.editingFinished.connect(self._on_crop_y)
+        self.z_slider.editingFinished.connect(self._on_crop_z)
+
+    def set_ranges(self, x_max, y_max, z_max):
+        self.x_slider.setRange(0, x_max - 1)
+        self.x_slider.setValue((0, x_max - 1))
+        self.y_slider.setRange(0, y_max - 1)
+        self.y_slider.setValue((0, y_max - 1))
+        self.z_slider.setRange(0, z_max - 1)
+        self.z_slider.setValue((0, z_max - 1))
+
+    def _on_crop_x(self):
+        self.crop_x_signal.emit(
+            self.x_slider.value()[0], self.x_slider.value()[1]
+        )
+
+    def _on_crop_y(self):
+        self.crop_y_signal.emit(
+            self.y_slider.value()[0], self.y_slider.value()[1]
+        )
+
+    def _on_crop_z(self):
+        self.crop_z_signal.emit(
+            self.z_slider.value()[0], self.z_slider.value()[1]
+        )