Add option to scale sample image (#26)

* Fixed contents margins

* Scaling of sample image added to adjust moving image dropdown

* Added brainglobe-utils as dependency

* Added error message when no images selected

* Added tests for scaling

* Added tests to check multiple scale_factors

* Cache the moving image data to allow scaling image multiple times

* Fixed tests by removing (0,0) case add guard in _on_scale_image in registration_widget.py

* Fixed tests

* Add docstring to _on_scale_moving_image

* Replaced all curr_ variable names with current_

* Added units to pixel size selection, set max range to be 100

brainglobe_registration/registration_widget.py

@@ -14,12 +14,14 @@
 from bg_atlasapi import BrainGlobeAtlas
 from bg_atlasapi.list_atlases import get_downloaded_atlases
 from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
+from napari.utils.notifications import show_error
 from napari.viewer import Viewer
 from qtpy.QtWidgets import (
     QPushButton,
     QTabWidget,
 )
 from skimage.segmentation import find_boundaries
+from skimage.transform import rescale
 
 from brainglobe_registration.elastix.register import run_registration
 from brainglobe_registration.utils.brainglobe_logo import header_widget
@@ -49,6 +51,7 @@ def __init__(self, napari_viewer: Viewer):
         self._viewer = napari_viewer
         self._atlas: BrainGlobeAtlas = None
         self._moving_image = None
+        self._moving_image_data_backup = None
 
         self.transform_params: dict[str, dict] = {
             "rigid": {},
@@ -101,10 +104,12 @@ def __init__(self, napari_viewer: Viewer):
         self.adjust_moving_image_widget.adjust_image_signal.connect(
             self._on_adjust_moving_image
         )
-
         self.adjust_moving_image_widget.reset_image_signal.connect(
             self._on_adjust_moving_image_reset_button_click
         )
+        self.adjust_moving_image_widget.scale_image_signal.connect(
+            self._on_scale_moving_image
+        )
 
         self.transform_select_view = TransformSelectView()
         self.transform_select_view.transform_type_added_signal.connect(
@@ -151,11 +156,11 @@ def _on_atlas_dropdown_index_changed(self, index):
         # Hacky way of having an empty first dropdown
         if index == 0:
             if self._atlas:
-                curr_atlas_layer_index = find_layer_index(
+                current_atlas_layer_index = find_layer_index(
                     self._viewer, self._atlas.atlas_name
                 )
 
-                self._viewer.layers.pop(curr_atlas_layer_index)
+                self._viewer.layers.pop(current_atlas_layer_index)
                 self._atlas = None
                 self.run_button.setEnabled(False)
                 self._viewer.grid.enabled = False
@@ -166,11 +171,11 @@ def _on_atlas_dropdown_index_changed(self, index):
         atlas = BrainGlobeAtlas(atlas_name)
 
         if self._atlas:
-            curr_atlas_layer_index = find_layer_index(
+            current_atlas_layer_index = find_layer_index(
                 self._viewer, self._atlas.atlas_name
             )
 
-            self._viewer.layers.pop(curr_atlas_layer_index)
+            self._viewer.layers.pop(current_atlas_layer_index)
         else:
             self.run_button.setEnabled(True)
 
@@ -189,6 +194,7 @@ def _on_sample_dropdown_index_changed(self, index):
             self._viewer, self._sample_images[index]
         )
         self._moving_image = self._viewer.layers[viewer_index]
+        self._moving_image_data_backup = self._moving_image.data.copy()
 
     def _on_adjust_moving_image(self, x: int, y: int, rotate: float):
         adjust_napari_image_layer(self._moving_image, x, y, rotate)
@@ -299,3 +305,41 @@ def _on_default_file_selection_change(
     def _on_sample_popup_about_to_show(self):
         self._sample_images = get_image_layer_names(self._viewer)
         self.get_atlas_widget.update_sample_image_names(self._sample_images)
+
+    def _on_scale_moving_image(self, x: float, y: float):
+        """
+        Scale the moving image to have resolution equal to the atlas.
+
+        Parameters
+        ----------
+        x : float
+            Moving image x pixel size (> 0.0).
+        y : float
+            Moving image y pixel size (> 0.0).
+
+        Will show an error if the pixel sizes are less than or equal to 0.
+        Will show an error if the moving image or atlas is not selected.
+        """
+        if x <= 0 or y <= 0:
+            show_error("Pixel sizes must be greater than 0")
+            return
+
+        if self._moving_image and self._atlas:
+            if self._moving_image_data_backup is None:
+                self._moving_image_data_backup = self._moving_image.data.copy()
+
+            x_factor = x / self._atlas.resolution[0]
+            y_factor = y / self._atlas.resolution[1]
+
+            self._moving_image.data = rescale(
+                self._moving_image_data_backup,
+                (y_factor, x_factor),
+                mode="constant",
+                preserve_range=True,
+                anti_aliasing=True,
+            )
+        else:
+            show_error(
+                "Sample image or atlas not selected. "
+                "Please select a sample image and atlas before scaling",
+            )

brainglobe_registration/widgets/adjust_moving_image_view.py

@@ -14,8 +14,8 @@ class AdjustMovingImageView(QWidget):
     A QWidget subclass that provides controls for adjusting the moving image.
 
     This widget provides controls for adjusting the x and y offsets and
-    rotation of the moving image. It emits signals when the image is adjusted
-    or reset.
+    rotation of the moving image. It emits signals when the image is adjusted,
+    scaled, or reset.
 
     Attributes
     ----------
@@ -33,9 +33,12 @@ class AdjustMovingImageView(QWidget):
     _on_reset_image_button_click():
         Resets the x and y offsets and rotation to 0 and emits the
         reset_image_signal.
+    _on_scale_image_button_click():
+        Emits the scale_image_signal with the entered pixel sizes.
     """
 
     adjust_image_signal = Signal(int, int, float)
+    scale_image_signal = Signal(float, float)
     reset_image_signal = Signal()
 
     def __init__(self, parent=None):
@@ -54,15 +57,27 @@ def __init__(self, parent=None):
         offset_range = 2000
         rotation_range = 360
 
-        self.adjust_moving_image_x = QSpinBox()
+        self.adjust_moving_image_voxel_size_x = QDoubleSpinBox(parent=self)
+        self.adjust_moving_image_voxel_size_x.setDecimals(2)
+        self.adjust_moving_image_voxel_size_x.setRange(0.01, 100.00)
+        self.adjust_moving_image_voxel_size_y = QDoubleSpinBox(parent=self)
+        self.adjust_moving_image_voxel_size_y.setDecimals(2)
+        self.adjust_moving_image_voxel_size_y.setRange(0.01, 100.00)
+        self.scale_moving_image_button = QPushButton()
+        self.scale_moving_image_button.setText("Scale Image")
+        self.scale_moving_image_button.clicked.connect(
+            self._on_scale_image_button_click
+        )
+
+        self.adjust_moving_image_x = QSpinBox(parent=self)
         self.adjust_moving_image_x.setRange(-offset_range, offset_range)
         self.adjust_moving_image_x.valueChanged.connect(self._on_adjust_image)
 
-        self.adjust_moving_image_y = QSpinBox()
+        self.adjust_moving_image_y = QSpinBox(parent=self)
         self.adjust_moving_image_y.setRange(-offset_range, offset_range)
         self.adjust_moving_image_y.valueChanged.connect(self._on_adjust_image)
 
-        self.adjust_moving_image_rotate = QDoubleSpinBox()
+        self.adjust_moving_image_rotate = QDoubleSpinBox(parent=self)
         self.adjust_moving_image_rotate.setRange(
             -rotation_range, rotation_range
         )
@@ -71,15 +86,26 @@ def __init__(self, parent=None):
             self._on_adjust_image
         )
 
-        self.adjust_moving_image_reset_button = QPushButton(parent=self)
+        self.adjust_moving_image_reset_button = QPushButton()
         self.adjust_moving_image_reset_button.setText("Reset Image")
         self.adjust_moving_image_reset_button.clicked.connect(
             self._on_reset_image_button_click
         )
 
-        self.layout().addRow(QLabel("Adjust the moving image: "))
-        self.layout().addRow("X offset:", self.adjust_moving_image_x)
-        self.layout().addRow("Y offset:", self.adjust_moving_image_y)
+        self.layout().addRow(QLabel("Adjust the moving image scale:"))
+        self.layout().addRow(
+            "Sample image X pixel size (\u03BCm / pixel):",
+            self.adjust_moving_image_voxel_size_x,
+        )
+        self.layout().addRow(
+            "Sample image Y pixel size (\u03BCm / pixel):",
+            self.adjust_moving_image_voxel_size_y,
+        )
+        self.layout().addRow(self.scale_moving_image_button)
+
+        self.layout().addRow(QLabel("Adjust the sample image position:"))
+        self.layout().addRow("X offset (pixels):", self.adjust_moving_image_x)
+        self.layout().addRow("Y offset (pixels):", self.adjust_moving_image_y)
         self.layout().addRow(
             "Rotation (degrees):", self.adjust_moving_image_rotate
         )
@@ -106,3 +132,12 @@ def _on_reset_image_button_click(self):
         self.adjust_moving_image_rotate.setValue(0)
 
         self.reset_image_signal.emit()
+
+    def _on_scale_image_button_click(self):
+        """
+        Emit the scale_image_signal with the entered pixel sizes.
+        """
+        self.scale_image_signal.emit(
+            self.adjust_moving_image_voxel_size_x.value(),
+            self.adjust_moving_image_voxel_size_y.value(),
+        )

brainglobe_registration/widgets/transform_select_view.py

@@ -169,7 +169,7 @@ def _on_transform_type_change(self, index):
             self.file_selections[index].setCurrentIndex(0)
 
             if index >= len(self.transform_type_selections) - 1:
-                curr_length = self.rowCount()
+                current_length = self.rowCount()
                 self.setRowCount(self.rowCount() + 1)
 
                 self.transform_type_selections.append(QComboBox())
@@ -180,7 +180,7 @@ def _on_transform_type_change(self, index):
                     self.transform_type_signaller.map
                 )
                 self.transform_type_signaller.setMapping(
-                    self.transform_type_selections[-1], curr_length
+                    self.transform_type_selections[-1], current_length
                 )
 
                 self.file_selections.append(QComboBox())
@@ -191,14 +191,16 @@ def _on_transform_type_change(self, index):
                     self.file_signaller.map
                 )
                 self.file_signaller.setMapping(
-                    self.file_selections[-1], curr_length
+                    self.file_selections[-1], current_length
                 )
 
                 self.setCellWidget(
-                    curr_length, 0, self.transform_type_selections[curr_length]
+                    current_length,
+                    0,
+                    self.transform_type_selections[current_length],
                 )
                 self.setCellWidget(
-                    curr_length, 1, self.file_selections[curr_length]
+                    current_length, 1, self.file_selections[current_length]
                 )
 
         else:

tests/test_adjust_moving_image_view.py

@@ -14,6 +14,12 @@ def adjust_moving_image_view() -> AdjustMovingImageView:
     return adjust_moving_image_view
 
 
+def test_init(qtbot, adjust_moving_image_view):
+    qtbot.addWidget(adjust_moving_image_view)
+
+    assert adjust_moving_image_view.layout().rowCount() == 9
+
+
 @pytest.mark.parametrize(
     "x_value, expected",
     [
@@ -94,3 +100,26 @@ def test_reset_image_button_click(qtbot, adjust_moving_image_view):
     assert adjust_moving_image_view.adjust_moving_image_x.value() == 0
     assert adjust_moving_image_view.adjust_moving_image_y.value() == 0
     assert adjust_moving_image_view.adjust_moving_image_rotate.value() == 0
+
+
+@pytest.mark.parametrize(
+    "x_scale, y_scale",
+    [(2.5, 2.5), (10, 20), (10.221, 10.228)],
+)
+def test_scale_image_button_click(
+    qtbot, adjust_moving_image_view, x_scale, y_scale
+):
+    qtbot.addWidget(adjust_moving_image_view)
+
+    with qtbot.waitSignal(
+        adjust_moving_image_view.scale_image_signal, timeout=1000
+    ) as blocker:
+        adjust_moving_image_view.adjust_moving_image_voxel_size_x.setValue(
+            x_scale
+        )
+        adjust_moving_image_view.adjust_moving_image_voxel_size_y.setValue(
+            y_scale
+        )
+        adjust_moving_image_view.scale_moving_image_button.click()
+
+    assert blocker.args == [round(x_scale, 2), round(y_scale, 2)]

tests/test_parameter_list_view.py

@@ -56,7 +56,7 @@ def test_parameter_list_view_cell_change(parameter_list_view, qtbot):
 def test_parameter_list_view_cell_change_last_row(parameter_list_view, qtbot):
     qtbot.addWidget(parameter_list_view)
 
-    curr_row_count = parameter_list_view.rowCount()
+    current_row_count = parameter_list_view.rowCount()
     last_row_index = len(param_dict)
 
     parameter_list_view.setItem(
@@ -65,32 +65,32 @@ def test_parameter_list_view_cell_change_last_row(parameter_list_view, qtbot):
     parameter_list_view.setItem(last_row_index, 1, QTableWidgetItem("true"))
 
     assert parameter_list_view.param_dict["TestParameter"] == ["true"]
-    assert parameter_list_view.rowCount() == curr_row_count + 1
+    assert parameter_list_view.rowCount() == current_row_count + 1
 
 
 def test_parameter_list_view_cell_change_last_row_no_param(
     parameter_list_view, qtbot
 ):
     qtbot.addWidget(parameter_list_view)
 
-    curr_row_count = parameter_list_view.rowCount()
+    current_row_count = parameter_list_view.rowCount()
     last_row_index = len(param_dict)
 
     parameter_list_view.setItem(last_row_index, 1, QTableWidgetItem("true"))
 
-    assert parameter_list_view.rowCount() == curr_row_count
+    assert parameter_list_view.rowCount() == current_row_count
 
 
 def test_parameter_list_view_cell_change_last_row_no_value(
     parameter_list_view, qtbot
 ):
     qtbot.addWidget(parameter_list_view)
 
-    curr_row_count = parameter_list_view.rowCount()
+    current_row_count = parameter_list_view.rowCount()
     last_row_index = len(param_dict)
 
     parameter_list_view.setItem(
         last_row_index, 0, QTableWidgetItem("TestParameter")
     )
 
-    assert parameter_list_view.rowCount() == curr_row_count
+    assert parameter_list_view.rowCount() == current_row_count