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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| from brainglobe_space import AnatomicalSpace | ||
| from napari.layers import Image, Labels, Points | ||
| from napari.utils.notifications import show_info | ||
| from napari.viewer import Viewer | ||
| from qtpy.QtWidgets import ( | ||
| QComboBox, | ||
| QFormLayout, | ||
| QGroupBox, | ||
| QHBoxLayout, | ||
| QPushButton, | ||
| QWidget, | ||
| ) | ||
|
|
||
|
|
||
| class Reorient(QWidget): | ||
| """Widget to reorient images to a standard anatomical space.""" | ||
|
|
||
| def __init__(self, napari_viewer: Viewer, parent=None): | ||
| super().__init__(parent=parent) | ||
| self.viewer = napari_viewer | ||
| self.setLayout(QFormLayout()) | ||
|
|
||
| self._create_reorient_group() | ||
|
|
||
| def _create_reorient_group(self): | ||
| self.reorient_groupbox = QGroupBox("Reorient to standard space") | ||
| self.reorient_groupbox.setLayout(QFormLayout()) | ||
| self.layout().addRow(self.reorient_groupbox) | ||
|
|
||
| avail_labels = AnatomicalSpace.lims_labels | ||
|
|
||
| # Enter labels for source space | ||
| source_origin_row = QHBoxLayout() | ||
| self.source_origin1 = QComboBox(parent=self.reorient_groupbox) | ||
| self.source_origin1.addItems(avail_labels) | ||
| self.source_origin1.setCurrentIndex(0) | ||
| source_origin_row.addWidget(self.source_origin1) | ||
| self.source_origin2 = QComboBox(parent=self.reorient_groupbox) | ||
| self.source_origin2.addItems(avail_labels) | ||
| self.source_origin2.setCurrentIndex(2) | ||
| source_origin_row.addWidget(self.source_origin2) | ||
| self.source_origin3 = QComboBox(parent=self.reorient_groupbox) | ||
| self.source_origin3.addItems(avail_labels) | ||
| self.source_origin3.setCurrentIndex(5) | ||
| source_origin_row.addWidget(self.source_origin3) | ||
| self.reorient_groupbox.layout().addRow( | ||
| "Source origin:", source_origin_row | ||
| ) | ||
|
|
||
| # Enter labels for target space | ||
| target_origin_row = QHBoxLayout() | ||
| self.target_origin1 = QComboBox(parent=self.reorient_groupbox) | ||
| self.target_origin1.addItems(avail_labels) | ||
| self.target_origin1.setCurrentIndex(1) | ||
| target_origin_row.addWidget(self.target_origin1) | ||
| self.target_origin2 = QComboBox(parent=self.reorient_groupbox) | ||
| self.target_origin2.addItems(avail_labels) | ||
| self.target_origin2.setCurrentIndex(2) | ||
| target_origin_row.addWidget(self.target_origin2) | ||
| self.target_origin3 = QComboBox(parent=self.reorient_groupbox) | ||
| self.target_origin3.addItems(avail_labels) | ||
| self.target_origin3.setCurrentIndex(5) | ||
| target_origin_row.addWidget(self.target_origin3) | ||
| self.reorient_groupbox.layout().addRow( | ||
| "Target origin:", target_origin_row | ||
| ) | ||
|
|
||
| self.reorient_button = QPushButton( | ||
| "Reorient selected layers", parent=self.reorient_groupbox | ||
| ) | ||
| self.reorient_button.clicked.connect(self.reorient_layers) | ||
| self.reorient_groupbox.layout().addRow(self.reorient_button) | ||
|
|
||
| def reorient_layers(self): | ||
| """Reorient selected layers to the target space.""" | ||
| selected_layers = self.viewer.layers.selection | ||
| selected_stacks = [ | ||
| layer | ||
| for layer in selected_layers | ||
| if isinstance(layer, Image) or isinstance(layer, Labels) | ||
| ] | ||
| selected_points = [ | ||
| layer for layer in selected_layers if isinstance(layer, Points) | ||
| ] | ||
|
|
||
| if not selected_layers: | ||
| show_info("No layers selected. Select layers to reorient.") | ||
| return | ||
|
|
||
| source_origin = [ | ||
| self.source_origin1.currentText(), | ||
| self.source_origin2.currentText(), | ||
| self.source_origin3.currentText(), | ||
| ] | ||
| target_origin = [ | ||
| self.target_origin1.currentText(), | ||
| self.target_origin2.currentText(), | ||
| self.target_origin3.currentText(), | ||
| ] | ||
| source_origin = "".join(source_origin) | ||
| target_origin = "".join(target_origin) | ||
|
|
||
| for layer in selected_points: | ||
| if not selected_stacks: | ||
| show_info( | ||
| "Cannot reorient Points layer alone. Please select " | ||
| "at least one Image or Labels layer along with the " | ||
| "Points layer." | ||
| ) | ||
| return | ||
| source_stack_shape = selected_stacks[0].data.shape | ||
| source_space = AnatomicalSpace( | ||
| source_origin, shape=source_stack_shape | ||
| ) | ||
| layer.data = source_space.map_points_to(target_origin, layer.data) | ||
| layer.name = f"{layer.name}_space-{target_origin}" | ||
|
|
||
| for layer in selected_stacks: | ||
| interp_order = 0 if isinstance(layer, Labels) else 3 | ||
| source_space = AnatomicalSpace( | ||
| source_origin, shape=layer.data.shape | ||
| ) | ||
| layer.data = source_space.map_stack_to( | ||
| target_origin, layer.data, interp_order=interp_order | ||
| ) | ||
| layer.name = f"{layer.name}_orig-{target_origin}" | ||
|
|
||
| show_info("Layers reoriented to target space.") |
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