From fdec5467bdc58ded56797e17ef400412f3826c18 Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Thu, 18 Jan 2024 11:08:50 +0000
Subject: [PATCH 01/10] Moving from tabs to a dropdown style widget (#25)

* Fixed contents margins

* Added brainglobe-utils as dependency

* Added min dependency version for brainglobe-utils
---
 brainglobe_registration/napari.yaml           |  2 +-
 .../registration_widget.py                    | 38 ++++++++-----------
 pyproject.toml                                |  1 +
 3 files changed, 17 insertions(+), 24 deletions(-)

diff --git a/brainglobe_registration/napari.yaml b/brainglobe_registration/napari.yaml
index a5c3aaa..818695e 100644
--- a/brainglobe_registration/napari.yaml
+++ b/brainglobe_registration/napari.yaml
@@ -8,7 +8,7 @@ contributions:
   sample_data:
     - key: example
       display_name: Sample Brain Slice
-      uri: src/brainglobe_registration/resources/sample_hipp.tif
+      uri: brainglobe_registration/resources/sample_hipp.tif
   widgets:
     - command: brainglobe-registration.make_registration_widget
       display_name: BrainGlobe Registration
diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index ddecb4a..f98e0da 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -13,14 +13,11 @@
 import numpy as np
 from bg_atlasapi import BrainGlobeAtlas
 from bg_atlasapi.list_atlases import get_downloaded_atlases
+from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
 from napari.viewer import Viewer
-from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
-    QGroupBox,
     QPushButton,
     QTabWidget,
-    QVBoxLayout,
-    QWidget,
 )
 from skimage.segmentation import find_boundaries
 
@@ -44,9 +41,10 @@
 )
 
 
-class RegistrationWidget(QWidget):
+class RegistrationWidget(CollapsibleWidgetContainer):
     def __init__(self, napari_viewer: Viewer):
         super().__init__()
+        self.setContentsMargins(10, 10, 10, 10)
 
         self._viewer = napari_viewer
         self._atlas: BrainGlobeAtlas = None
@@ -84,16 +82,6 @@ def __init__(self, napari_viewer: Viewer):
         else:
             self._moving_image = None
 
-        self.setLayout(QVBoxLayout())
-        self.layout().addWidget(header_widget())
-
-        self.main_tabs = QTabWidget(parent=self)
-        self.main_tabs.setTabPosition(QTabWidget.West)
-
-        self.settings_tab = QGroupBox()
-        self.settings_tab.setLayout(QVBoxLayout())
-        self.parameters_tab = QTabWidget()
-
         self.get_atlas_widget = SelectImagesView(
             available_atlases=self._available_atlases,
             sample_image_names=self._sample_images,
@@ -133,13 +121,17 @@ def __init__(self, napari_viewer: Viewer):
         self.run_button.clicked.connect(self._on_run_button_click)
         self.run_button.setEnabled(False)
 
-        self.settings_tab.layout().addWidget(self.get_atlas_widget)
-        self.settings_tab.layout().addWidget(self.adjust_moving_image_widget)
-        self.settings_tab.layout().addWidget(self.transform_select_view)
-        self.settings_tab.layout().addWidget(self.run_button)
-        self.settings_tab.layout().setAlignment(Qt.AlignTop)
+        self.add_widget(header_widget(), collapsible=False)
+        self.add_widget(self.get_atlas_widget, widget_title="Select Images")
+        self.add_widget(
+            self.adjust_moving_image_widget, widget_title="Adjust Sample Image"
+        )
+        self.add_widget(
+            self.transform_select_view, widget_title="Select Transformations"
+        )
 
         self.parameter_setting_tabs_lists = []
+        self.parameters_tab = QTabWidget()
 
         for transform_type in self.transform_params:
             new_tab = RegistrationParameterListView(
@@ -150,10 +142,10 @@ def __init__(self, napari_viewer: Viewer):
             self.parameters_tab.addTab(new_tab, transform_type)
             self.parameter_setting_tabs_lists.append(new_tab)
 
-        self.main_tabs.addTab(self.settings_tab, "Settings")
-        self.main_tabs.addTab(self.parameters_tab, "Parameters")
+        self.add_widget(self.parameters_tab, widget_title="Advanced Settings")
+        self.add_widget(self.run_button, collapsible=False)
 
-        self.layout().addWidget(self.main_tabs)
+        self.layout().itemAt(1).widget().collapse(animate=False)
 
     def _on_atlas_dropdown_index_changed(self, index):
         # Hacky way of having an empty first dropdown
diff --git a/pyproject.toml b/pyproject.toml
index aeb282b..63db406 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,7 @@ classifiers = [
 dependencies = [
     "napari>=0.4.18",
     "bg-atlasapi",
+    "brainglobe-utils>=0.3.4",
     "numpy",
     "qtpy",
     "itk-elastix",

From a09d4e69a487145f89e4a05b4973d6149f30da0c Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Mon, 5 Feb 2024 15:44:41 +0000
Subject: [PATCH 02/10] 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
---
 .../registration_widget.py                    | 54 +++++++++++++--
 .../widgets/adjust_moving_image_view.py       | 53 ++++++++++++---
 .../widgets/transform_select_view.py          | 12 ++--
 tests/test_adjust_moving_image_view.py        | 29 ++++++++
 tests/test_parameter_list_view.py             | 12 ++--
 tests/test_registration_widget.py             | 67 +++++++++++++++++++
 6 files changed, 202 insertions(+), 25 deletions(-)

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index f98e0da..67ab52f 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/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",
+            )
diff --git a/brainglobe_registration/widgets/adjust_moving_image_view.py b/brainglobe_registration/widgets/adjust_moving_image_view.py
index 4740e25..c7ba3fd 100644
--- a/brainglobe_registration/widgets/adjust_moving_image_view.py
+++ b/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(),
+        )
diff --git a/brainglobe_registration/widgets/transform_select_view.py b/brainglobe_registration/widgets/transform_select_view.py
index eba8c32..d141816 100644
--- a/brainglobe_registration/widgets/transform_select_view.py
+++ b/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:
diff --git a/tests/test_adjust_moving_image_view.py b/tests/test_adjust_moving_image_view.py
index e56107e..fb2dc41 100644
--- a/tests/test_adjust_moving_image_view.py
+++ b/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)]
diff --git a/tests/test_parameter_list_view.py b/tests/test_parameter_list_view.py
index 00a701f..cabbfce 100644
--- a/tests/test_parameter_list_view.py
+++ b/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(
@@ -65,7 +65,7 @@ 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(
@@ -73,12 +73,12 @@ def test_parameter_list_view_cell_change_last_row_no_param(
 ):
     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(
@@ -86,11 +86,11 @@ def test_parameter_list_view_cell_change_last_row_no_value(
 ):
     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
diff --git a/tests/test_registration_widget.py b/tests/test_registration_widget.py
index aa91594..2b74c98 100644
--- a/tests/test_registration_widget.py
+++ b/tests/test_registration_widget.py
@@ -65,3 +65,70 @@ def test_sample_dropdown_index_changed_with_valid_index(
         registration_widget._moving_image.name
         == registration_widget._sample_images[1]
     )
+
+
+def test_scale_moving_image_no_atlas(
+    make_napari_viewer_with_images, registration_widget, mocker
+):
+    mocked_show_error = mocker.patch(
+        "brainglobe_registration.registration_widget.show_error"
+    )
+    registration_widget._atlas = None
+    registration_widget.adjust_moving_image_widget.scale_image_signal.emit(
+        10, 10
+    )
+    mocked_show_error.assert_called_once_with(
+        "Sample image or atlas not selected. "
+        "Please select a sample image and atlas before scaling"
+    )
+
+
+def test_scale_moving_image_no_sample_image(
+    make_napari_viewer_with_images, registration_widget, mocker
+):
+    mocked_show_error = mocker.patch(
+        "brainglobe_registration.registration_widget.show_error"
+    )
+    registration_widget._moving_image = None
+    registration_widget.adjust_moving_image_widget.scale_image_signal.emit(
+        10, 10
+    )
+    mocked_show_error.assert_called_once_with(
+        "Sample image or atlas not selected. "
+        "Please select a sample image and atlas before scaling"
+    )
+
+
+@pytest.mark.parametrize(
+    "x_scale_factor, y_scale_factor",
+    [
+        (0.5, 0.5),
+        (1.0, 1.0),
+        (2.0, 2.0),
+        (0.5, 1.0),
+        (1.0, 0.5),
+    ],
+)
+def test_scale_moving_image(
+    make_napari_viewer_with_images,
+    registration_widget,
+    mocker,
+    x_scale_factor,
+    y_scale_factor,
+):
+    mock_atlas = mocker.patch(
+        "brainglobe_registration.registration_widget.BrainGlobeAtlas"
+    )
+    mock_atlas.resolution = [20, 20, 20]
+    registration_widget._atlas = mock_atlas
+
+    current_size = registration_widget._moving_image.data.shape
+    registration_widget.adjust_moving_image_widget.scale_image_signal.emit(
+        mock_atlas.resolution[1] * x_scale_factor,
+        mock_atlas.resolution[2] * y_scale_factor,
+    )
+
+    assert registration_widget._moving_image.data.shape == (
+        current_size[0] * y_scale_factor,
+        current_size[1] * x_scale_factor,
+    )

From 1b664b6dd3349973a13e68acd3f2d8a7618c504a Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Fri, 26 Jul 2024 13:30:38 +0100
Subject: [PATCH 03/10] Allow free rotation of the atlas (#36)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* 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

* Atlas rotation working using scipy

* Pitch, yaw, roll implemented using one affine transform

* Dask loading for both the reference atlas and the rotation

* Added a 'Reset Atlas' button, blocked while dask computes the rotation to avoid race conditions

* Rotate atlas button also greyed out while daks processes the rotation

* Use the update upload_pypi action (#29)

See https://github.com/neuroinformatics-unit/movement/pull/108

* Added elastix Logs directory to .gitignore

* Fixed tests

* Moved run_registration to be imported just as run button is clicked to avoid long boot times

* Atlas rotation works again (might relate to napari 0.4.19

* Added test for atlas_rotation_signal from AdjustMovingImage view

* [pre-commit.ci] pre-commit autoupdate (#30)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.2.0)
- [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/23.12.1...24.1.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#31)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.0...v0.3.5)
- [github.com/psf/black: 24.1.1 → 24.3.0](https://github.com/psf/black/compare/24.1.1...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Import header from brainglobe-utils (#33)

* import header from brainglobe-utils

* split package name over two lines

* remove brainglobe png from manifest

* add brainglobe-utils dependency

* Update requirements (#34)

* import header from brainglobe-utils

* split package name over two lines

* remove brainglobe png from manifest

* add brainglobe-utils dependency

* Switched from bg-atlasapi to brainglobe-atlasapi

* Added lxml_html_clean explicitly to requirements

* Pinned itk to 5.4rc2 for now as 5.4rc3 cased a seg fault

* Undo itk pin

---------

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

* add codecov token (#35)

* Added tests for calculate_rotated_bounding_box

* Fixed docstrings for functions in utils.py

* Keep track of napari layers for the atlas and atlas annotations in the napari widget class

* Added tests for atlas rotation

* Fixed pre-commit

* Add test for reset_atlas in adjust_moving_image_view

* Add caching

* Update the function calls in test_adjust_moving_image_view

* Apply suggestions from code review

Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>

* Applied suggestions from code review

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Applied suggestions from code review

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
---
 .github/workflows/test_and_deploy.yml         |  27 ++-
 .gitignore                                    |   3 +
 .pre-commit-config.yaml                       |   6 +-
 MANIFEST.in                                   |   1 -
 brainglobe_registration/elastix/register.py   |   2 +-
 .../registration_widget.py                    | 214 +++++++++++++++---
 .../resources/brainglobe.png                  | Bin 21216 -> 0 bytes
 .../utils/brainglobe_logo.py                  |  46 ----
 brainglobe_registration/utils/utils.py        |  72 +++++-
 .../widgets/adjust_moving_image_view.py       |  83 +++++--
 pyproject.toml                                |  11 +-
 tests/conftest.py                             |   4 +-
 tests/test_adjust_moving_image_view.py        |  46 +++-
 tests/test_registration_widget.py             |  82 +++++++
 tests/test_utils.py                           |  30 +++
 15 files changed, 508 insertions(+), 119 deletions(-)
 delete mode 100644 brainglobe_registration/resources/brainglobe.png
 delete mode 100644 brainglobe_registration/utils/brainglobe_logo.py

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index c00e554..de1d2d5 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -47,10 +47,28 @@ jobs:
         with:
           qt: true
 
+      # cache atlases needed by the tests
+      - name: Cache Atlases
+        id: atlas-cache
+        uses: actions/cache@v3
+        with:
+          path: | # ensure we don't cache any interrupted atlas download and extraction!
+            ~/.brainglobe/*
+            !~/.brainglobe/atlas.tar.gz
+          key: ${{ runner.os }}-cached-atlases
+          enableCrossOsArchive: false # ~ and $HOME evaluate to different places across OSs!
+
+      - if: ${{ steps.atlas-cache.outputs.cache-hit == 'true' }}
+        name: List files in brainglobe data folder # good to be able to sanity check that user data is as expected
+        run: |
+          ls -af ~/.brainglobe/
+
+
       # Run tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
 
   build_sdist_wheels:
     name: Build source distribution
@@ -66,11 +84,6 @@ jobs:
     needs: [build_sdist_wheels]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
-      with:
-        name: artifact
-        path: dist
-    - uses: pypa/gh-action-pypi-publish@v1.5.0
+    - uses: neuroinformatics-unit/actions/upload_pypi@v2
       with:
-        user: __token__
-        password: ${{ secrets.TWINE_API_KEY }}
+        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}
diff --git a/.gitignore b/.gitignore
index 73d56d3..08e97e3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -82,3 +82,6 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
+
+# Elastix related files
+/Logs/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6ffb785..f719a01 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,15 +17,15 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.9
+      rev: v0.3.5
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.12.1
+      rev: 24.3.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.8.0
+      rev: v1.9.0
       hooks:
           - id: mypy
             additional_dependencies:
diff --git a/MANIFEST.in b/MANIFEST.in
index b0e8711..902dcc4 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -3,7 +3,6 @@ include README.md
 include .napari-hub/DESCRIPTION.md
 include .napari-hub/config.yml
 include brainglobe_registration/napari.yaml
-include brainglobe_registration/resources/brainglobe.png
 exclude .pre-commit-config.yaml
 
 recursive-include brainglobe_registration/parameters *.txt
diff --git a/brainglobe_registration/elastix/register.py b/brainglobe_registration/elastix/register.py
index 955ed44..d04d918 100644
--- a/brainglobe_registration/elastix/register.py
+++ b/brainglobe_registration/elastix/register.py
@@ -2,7 +2,7 @@
 
 import itk
 import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import BrainGlobeAtlas
 
 
 def get_atlas_by_name(atlas_name: str) -> BrainGlobeAtlas:
diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index 67ab52f..35016fd 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -9,13 +9,21 @@
 """
 
 from pathlib import Path
+from typing import Optional
 
+import dask.array as da
+import napari.layers
 import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
-from bg_atlasapi.list_atlases import get_downloaded_atlases
+import numpy.typing as npt
+from brainglobe_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi.list_atlases import get_downloaded_atlases
 from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
+from brainglobe_utils.qtpy.logo import header_widget
+from dask_image.ndinterp import affine_transform as dask_affine_transform
+from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_error
 from napari.viewer import Viewer
+from pytransform3d.rotations import active_matrix_from_angle
 from qtpy.QtWidgets import (
     QPushButton,
     QTabWidget,
@@ -24,9 +32,9 @@
 from skimage.transform import rescale
 
 from brainglobe_registration.elastix.register import run_registration
-from brainglobe_registration.utils.brainglobe_logo import header_widget
 from brainglobe_registration.utils.utils import (
     adjust_napari_image_layer,
+    calculate_rotated_bounding_box,
     find_layer_index,
     get_image_layer_names,
     open_parameter_file,
@@ -49,9 +57,11 @@ def __init__(self, napari_viewer: Viewer):
         self.setContentsMargins(10, 10, 10, 10)
 
         self._viewer = napari_viewer
-        self._atlas: BrainGlobeAtlas = None
-        self._moving_image = None
-        self._moving_image_data_backup = None
+        self._atlas: Optional[BrainGlobeAtlas] = None
+        self._atlas_data_layer: Optional[napari.layers.Image] = None
+        self._atlas_annotations_layer: Optional[napari.layers.Labels] = None
+        self._moving_image: Optional[napari.layers.Image] = None
+        self._moving_image_data_backup: Optional[npt.NDArray] = None
 
         self.transform_params: dict[str, dict] = {
             "rigid": {},
@@ -110,6 +120,12 @@ def __init__(self, napari_viewer: Viewer):
         self.adjust_moving_image_widget.scale_image_signal.connect(
             self._on_scale_moving_image
         )
+        self.adjust_moving_image_widget.atlas_rotation_signal.connect(
+            self._on_adjust_atlas_rotation
+        )
+        self.adjust_moving_image_widget.reset_atlas_signal.connect(
+            self._on_atlas_reset
+        )
 
         self.transform_select_view = TransformSelectView()
         self.transform_select_view.transform_type_added_signal.connect(
@@ -126,10 +142,17 @@ def __init__(self, napari_viewer: Viewer):
         self.run_button.clicked.connect(self._on_run_button_click)
         self.run_button.setEnabled(False)
 
-        self.add_widget(header_widget(), collapsible=False)
+        self.add_widget(
+            header_widget(
+                "brainglobe-<br>registration",  # line break at <br>
+                "Registration with Elastix",
+                github_repo_name="brainglobe-registration",
+            ),
+            collapsible=False,
+        )
         self.add_widget(self.get_atlas_widget, widget_title="Select Images")
         self.add_widget(
-            self.adjust_moving_image_widget, widget_title="Adjust Sample Image"
+            self.adjust_moving_image_widget, widget_title="Prepare Images"
         )
         self.add_widget(
             self.transform_select_view, widget_title="Select Transformations"
@@ -162,13 +185,14 @@ def _on_atlas_dropdown_index_changed(self, index):
 
                 self._viewer.layers.pop(current_atlas_layer_index)
                 self._atlas = None
+                self._atlas_data_layer = None
+                self._atlas_annotations_layer = None
                 self.run_button.setEnabled(False)
                 self._viewer.grid.enabled = False
 
             return
 
         atlas_name = self._available_atlases[index]
-        atlas = BrainGlobeAtlas(atlas_name)
 
         if self._atlas:
             current_atlas_layer_index = find_layer_index(
@@ -179,14 +203,41 @@ def _on_atlas_dropdown_index_changed(self, index):
         else:
             self.run_button.setEnabled(True)
 
-        self._viewer.add_image(
-            atlas.reference,
+        self._atlas = BrainGlobeAtlas(atlas_name)
+        dask_reference = da.from_array(
+            self._atlas.reference,
+            chunks=(
+                1,
+                self._atlas.reference.shape[1],
+                self._atlas.reference.shape[2],
+            ),
+        )
+        dask_annotations = da.from_array(
+            self._atlas.annotation,
+            chunks=(
+                1,
+                self._atlas.annotation.shape[1],
+                self._atlas.annotation.shape[2],
+            ),
+        )
+
+        contrast_max = np.max(
+            dask_reference[dask_reference.shape[0] // 2]
+        ).compute()
+        self._atlas_data_layer = self._viewer.add_image(
+            dask_reference,
             name=atlas_name,
             colormap="gray",
             blending="translucent",
+            contrast_limits=[0, contrast_max],
+            multiscale=False,
+        )
+        self._atlas_annotations_layer = self._viewer.add_labels(
+            dask_annotations,
+            name="Annotations",
+            visible=False,
         )
 
-        self._atlas = BrainGlobeAtlas(atlas_name=atlas_name)
         self._viewer.grid.enabled = True
 
     def _on_sample_dropdown_index_changed(self, index):
@@ -197,18 +248,31 @@ def _on_sample_dropdown_index_changed(self, index):
         self._moving_image_data_backup = self._moving_image.data.copy()
 
     def _on_adjust_moving_image(self, x: int, y: int, rotate: float):
+        if not self._moving_image:
+            show_error(
+                "No moving image selected. "
+                "Please select a moving image before adjusting"
+            )
+            return
         adjust_napari_image_layer(self._moving_image, x, y, rotate)
 
     def _on_adjust_moving_image_reset_button_click(self):
+        if not self._moving_image:
+            show_error(
+                "No moving image selected. "
+                "Please select a moving image before adjusting"
+            )
+            return
         adjust_napari_image_layer(self._moving_image, 0, 0, 0)
 
     def _on_run_button_click(self):
+
         current_atlas_slice = self._viewer.dims.current_step[0]
 
         result, parameters, registered_annotation_image = run_registration(
-            self._atlas.reference[current_atlas_slice, :, :],
+            self._atlas_data_layer.data[current_atlas_slice, :, :],
             self._moving_image.data,
-            self._atlas.annotation[current_atlas_slice, :, :],
+            self._atlas_annotations_layer.data[current_atlas_slice, :, :],
             self.transform_selections,
         )
 
@@ -311,7 +375,7 @@ 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
@@ -324,22 +388,114 @@ def _on_scale_moving_image(self, x: float, y: float):
             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()
+        if not (self._moving_image and self._atlas):
+            show_error(
+                "Sample image or atlas not selected. "
+                "Please select a sample image and atlas before scaling",
+            )
+            return
+
+        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]
 
-            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,
+        )
 
-            self._moving_image.data = rescale(
-                self._moving_image_data_backup,
-                (y_factor, x_factor),
-                mode="constant",
-                preserve_range=True,
-                anti_aliasing=True,
+    def _on_adjust_atlas_rotation(self, pitch: float, yaw: float, roll: float):
+        if not (
+            self._atlas
+            and self._atlas_data_layer
+            and self._atlas_annotations_layer
+        ):
+            show_error(
+                "No atlas selected. Please select an atlas before rotating"
             )
-        else:
+            return
+
+        # Create the rotation matrix
+        roll_matrix = active_matrix_from_angle(0, np.deg2rad(roll))
+        pitch_matrix = active_matrix_from_angle(2, np.deg2rad(pitch))
+        yaw_matrix = active_matrix_from_angle(1, np.deg2rad(yaw))
+
+        rot_matrix = roll_matrix @ pitch_matrix @ yaw_matrix
+
+        full_matrix = np.eye(4)
+        full_matrix[:-1, :-1] = rot_matrix
+
+        # Translate the origin to the center of the image
+        origin = np.asarray(self._atlas.reference.shape) // 2
+        translate_matrix = np.eye(4)
+        translate_matrix[:-1, -1] = origin
+
+        bounding_box = calculate_rotated_bounding_box(
+            self._atlas.reference.shape, full_matrix
+        )
+        new_translation = np.asarray(bounding_box) // 2
+        post_rotate_translation = np.eye(4)
+        post_rotate_translation[:3, -1] = -new_translation
+
+        # Combine the matrices. The order of operations is:
+        # 1. Translate the origin to the center of the image
+        # 2. Rotate the image
+        # 3. Translate the origin back to the top left corner
+        transform_matrix = (
+            translate_matrix @ full_matrix @ post_rotate_translation
+        )
+
+        self._atlas_data_layer.data = dask_affine_transform(
+            self._atlas.reference,
+            transform_matrix,
+            order=2,
+            output_shape=bounding_box,
+            output_chunks=(2, bounding_box[1], bounding_box[2]),
+        )
+
+        self._atlas_annotations_layer.data = dask_affine_transform(
+            self._atlas.annotation,
+            transform_matrix,
+            order=0,
+            output_shape=bounding_box,
+            output_chunks=(2, bounding_box[1], bounding_box[2]),
+        )
+
+        # Resets the viewer grid to update the grid to the new atlas
+        self._viewer.reset_view()
+
+        worker = self.compute_atlas_rotation(self._atlas_data_layer.data)
+        worker.returned.connect(self.set_atlas_layer_data)
+        worker.start()
+
+    @thread_worker
+    def compute_atlas_rotation(self, dask_array: da.Array):
+        self.adjust_moving_image_widget.reset_atlas_button.setEnabled(False)
+        self.adjust_moving_image_widget.adjust_atlas_rotation.setEnabled(False)
+
+        computed_array = dask_array.compute()
+
+        self.adjust_moving_image_widget.reset_atlas_button.setEnabled(True)
+        self.adjust_moving_image_widget.adjust_atlas_rotation.setEnabled(True)
+
+        return computed_array
+
+    def set_atlas_layer_data(self, new_data):
+        self._atlas_data_layer.data = new_data
+
+    def _on_atlas_reset(self):
+        if not self._atlas:
             show_error(
-                "Sample image or atlas not selected. "
-                "Please select a sample image and atlas before scaling",
+                "No atlas selected. Please select an atlas before resetting"
             )
+            return
+
+        self._atlas_data_layer.data = self._atlas.reference
+        self._atlas_annotations_layer.data = self._atlas.annotation
+        self._viewer.grid.enabled = False
+        self._viewer.grid.enabled = True
diff --git a/brainglobe_registration/resources/brainglobe.png b/brainglobe_registration/resources/brainglobe.png
deleted file mode 100644
index 427bdaba9b89f967c183f4a998e7e642df50600d..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/brainglobe_registration/utils/brainglobe_logo.py b/brainglobe_registration/utils/brainglobe_logo.py
deleted file mode 100644
index e387adb..0000000
--- a/brainglobe_registration/utils/brainglobe_logo.py
+++ /dev/null
@@ -1,46 +0,0 @@
-from importlib.resources import files
-
-from qtpy.QtWidgets import QGroupBox, QHBoxLayout, QLabel, QVBoxLayout, QWidget
-
-brainglobe_logo = files("brainglobe_registration").joinpath(
-    "resources/brainglobe.png"
-)
-
-_logo_html = f"""
-<h1>
-<img src="{brainglobe_logo}"width="100">
-<\h1>
-"""
-
-
-def _docs_links_widget(parent: QWidget = None):
-    _docs_links_html = """
-    <h3>
-    <p><a href="https://brainglobe.info" style="color:gray;">Website</a></p>
-    <p><a href="https://github.com/brainglobe/brainglobe-registration" style="color:gray;">Source</a></p>
-    </h3>
-    """  # noqa: E501
-    docs_links_widget = QLabel(_docs_links_html, parent=parent)
-    docs_links_widget.setOpenExternalLinks(True)
-    return docs_links_widget
-
-
-def _logo_widget(parent: QWidget = None):
-    return QLabel(_logo_html, parent=None)
-
-
-def header_widget(parent: QWidget = None):
-    box = QGroupBox(parent)
-    box.setFlat(True)
-    box.setLayout(QVBoxLayout())
-    box.layout().addWidget(QLabel("<h2>brainglobe-registration</h2>"))
-    subbox = QGroupBox(parent)
-    subbox.setFlat(True)
-    subbox.setLayout(QHBoxLayout())
-    subbox.layout().setSpacing(0)
-    subbox.layout().setContentsMargins(0, 0, 0, 0)
-    subbox.setStyleSheet("border: 0;")
-    subbox.layout().addWidget(_logo_widget(parent=box))
-    subbox.layout().addWidget(_docs_links_widget(parent=box))
-    box.layout().addWidget(subbox)
-    return box
diff --git a/brainglobe_registration/utils/utils.py b/brainglobe_registration/utils/utils.py
index 48d0933..2bb9891 100644
--- a/brainglobe_registration/utils/utils.py
+++ b/brainglobe_registration/utils/utils.py
@@ -1,8 +1,9 @@
 from pathlib import Path
-from typing import List
+from typing import Dict, List, Tuple
 
 import napari
 import numpy as np
+import numpy.typing as npt
 from pytransform3d.rotations import active_matrix_from_angle
 
 
@@ -20,7 +21,7 @@ def adjust_napari_image_layer(
     https://forum.image.sc/t/napari-3d-rotation-center-change-and-scaling/66347/5
 
     Parameters
-    ----------
+    ------------
     image_layer : napari.layers.Layer
         The napari image layer to be adjusted.
     x : int
@@ -31,7 +32,7 @@ def adjust_napari_image_layer(
         The angle of rotation in degrees.
 
     Returns
-    -------
+    --------
     None
     """
     image_layer.translate = (y, x)
@@ -46,7 +47,7 @@ def adjust_napari_image_layer(
     image_layer.affine = transform_matrix
 
 
-def open_parameter_file(file_path: Path) -> dict:
+def open_parameter_file(file_path: Path) -> Dict:
     """
     Opens the parameter file and returns the parameter dictionary.
 
@@ -56,13 +57,13 @@ def open_parameter_file(file_path: Path) -> dict:
     The values are stripped of any trailing ")" and leading or trailing quotes.
 
     Parameters
-    ----------
+    ------------
     file_path : Path
         The path to the parameter file.
 
     Returns
-    -------
-    dict
+    --------
+    Dict
         A dictionary containing the parameters from the file.
     """
     with open(file_path, "r") as f:
@@ -94,5 +95,62 @@ def find_layer_index(viewer: napari.Viewer, layer_name: str) -> int:
 def get_image_layer_names(viewer: napari.Viewer) -> List[str]:
     """
     Returns a list of the names of the napari image layers in the viewer.
+
+    Parameters
+    ------------
+    viewer : napari.Viewer
+        The napari viewer containing the image layers.
+
+    Returns
+    --------
+    List[str]
+        A list of the names of the image layers in the viewer.
     """
     return [layer.name for layer in viewer.layers]
+
+
+def calculate_rotated_bounding_box(
+    image_shape: Tuple[int, int, int], rotation_matrix: npt.NDArray
+) -> Tuple[int, int, int]:
+    """
+    Calculates the bounding box of the rotated image.
+
+    This function calculates the bounding box of the rotated image given the
+    image shape and rotation matrix. The bounding box is calculated by
+    transforming the corners of the image and finding the minimum and maximum
+    values of the transformed corners.
+
+    Parameters
+    ------------
+    image_shape : Tuple[int, int, int]
+        The shape of the image.
+    rotation_matrix : npt.NDArray
+        The rotation matrix.
+
+    Returns
+    --------
+    Tuple[int, int, int]
+        The bounding box of the rotated image.
+    """
+    corners = np.array(
+        [
+            [0, 0, 0, 1],
+            [image_shape[0], 0, 0, 1],
+            [0, image_shape[1], 0, 1],
+            [0, 0, image_shape[2], 1],
+            [image_shape[0], image_shape[1], 0, 1],
+            [image_shape[0], 0, image_shape[2], 1],
+            [0, image_shape[1], image_shape[2], 1],
+            [image_shape[0], image_shape[1], image_shape[2], 1],
+        ]
+    )
+
+    transformed_corners = rotation_matrix @ corners.T
+    min_corner = np.min(transformed_corners, axis=1)
+    max_corner = np.max(transformed_corners, axis=1)
+
+    return (
+        int(np.round(max_corner[0] - min_corner[0])),
+        int(np.round(max_corner[1] - min_corner[1])),
+        int(np.round(max_corner[2] - min_corner[2])),
+    )
diff --git a/brainglobe_registration/widgets/adjust_moving_image_view.py b/brainglobe_registration/widgets/adjust_moving_image_view.py
index c7ba3fd..111951d 100644
--- a/brainglobe_registration/widgets/adjust_moving_image_view.py
+++ b/brainglobe_registration/widgets/adjust_moving_image_view.py
@@ -1,4 +1,4 @@
-from qtpy.QtCore import Signal
+from qtpy.QtCore import Qt, Signal
 from qtpy.QtWidgets import (
     QDoubleSpinBox,
     QFormLayout,
@@ -35,10 +35,16 @@ class AdjustMovingImageView(QWidget):
         reset_image_signal.
     _on_scale_image_button_click():
         Emits the scale_image_signal with the entered pixel sizes.
+    _on_adjust_atlas_rotation():
+        Emits the atlas_rotation_signal with the entered pitch, yaw, and roll.
+    _on_atlas_reset():
+        Resets the pitch, yaw, and roll to 0 and emits the atlas_reset_signal.
     """
 
     adjust_image_signal = Signal(int, int, float)
     scale_image_signal = Signal(float, float)
+    atlas_rotation_signal = Signal(float, float, float)
+    reset_atlas_signal = Signal()
     reset_image_signal = Signal()
 
     def __init__(self, parent=None):
@@ -53,22 +59,44 @@ def __init__(self, parent=None):
         super().__init__(parent=parent)
 
         self.setLayout(QFormLayout())
+        self.layout().setLabelAlignment(Qt.AlignLeft)
 
         offset_range = 2000
         rotation_range = 360
 
-        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.adjust_moving_image_pixel_size_x = QDoubleSpinBox(parent=self)
+        self.adjust_moving_image_pixel_size_x.setDecimals(3)
+        self.adjust_moving_image_pixel_size_x.setRange(0.001, 100.00)
+        self.adjust_moving_image_pixel_size_y = QDoubleSpinBox(parent=self)
+        self.adjust_moving_image_pixel_size_y.setDecimals(3)
+        self.adjust_moving_image_pixel_size_y.setRange(0.001, 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_atlas_pitch = QDoubleSpinBox(parent=self)
+        self.adjust_atlas_pitch.setSingleStep(0.1)
+        self.adjust_atlas_pitch.setRange(-rotation_range, rotation_range)
+
+        self.adjust_atlas_yaw = QDoubleSpinBox(parent=self)
+        self.adjust_atlas_yaw.setSingleStep(0.1)
+        self.adjust_atlas_yaw.setRange(-rotation_range, rotation_range)
+
+        self.adjust_atlas_roll = QDoubleSpinBox(parent=self)
+        self.adjust_atlas_roll.setSingleStep(0.1)
+        self.adjust_atlas_roll.setRange(-rotation_range, rotation_range)
+
+        self.adjust_atlas_rotation = QPushButton()
+        self.adjust_atlas_rotation.setText("Rotate Atlas")
+        self.adjust_atlas_rotation.clicked.connect(
+            self._on_adjust_atlas_rotation
+        )
+        self.reset_atlas_button = QPushButton()
+        self.reset_atlas_button.setText("Reset Atlas")
+        self.reset_atlas_button.clicked.connect(self._on_atlas_reset)
+
         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)
@@ -95,17 +123,24 @@ def __init__(self, parent=None):
         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.adjust_moving_image_pixel_size_x,
         )
         self.layout().addRow(
             "Sample image Y pixel size (\u03BCm / pixel):",
-            self.adjust_moving_image_voxel_size_y,
+            self.adjust_moving_image_pixel_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(QLabel("Adjust the atlas pitch and yaw: "))
+        self.layout().addRow("Pitch:", self.adjust_atlas_pitch)
+        self.layout().addRow("Yaw:", self.adjust_atlas_yaw)
+        self.layout().addRow("Roll:", self.adjust_atlas_roll)
+        self.layout().addRow(self.adjust_atlas_rotation)
+        self.layout().addRow(self.reset_atlas_button)
+
+        self.layout().addRow(QLabel("Adjust the moving image position: "))
+        self.layout().addRow("X offset:", self.adjust_moving_image_x)
+        self.layout().addRow("Y offset:", self.adjust_moving_image_y)
         self.layout().addRow(
             "Rotation (degrees):", self.adjust_moving_image_rotate
         )
@@ -138,6 +173,26 @@ 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(),
+            self.adjust_moving_image_pixel_size_x.value(),
+            self.adjust_moving_image_pixel_size_y.value(),
+        )
+
+    def _on_adjust_atlas_rotation(self):
+        """
+        Emit the atlas_rotation_signal with the entered pitch and yaw.
+        """
+        self.atlas_rotation_signal.emit(
+            self.adjust_atlas_pitch.value(),
+            self.adjust_atlas_yaw.value(),
+            self.adjust_atlas_roll.value(),
         )
+
+    def _on_atlas_reset(self):
+        """
+        Reset the pitch, yaw, and roll to 0 and emit the atlas_reset_signal.
+        """
+        self.adjust_atlas_yaw.setValue(0)
+        self.adjust_atlas_pitch.setValue(0)
+        self.adjust_atlas_roll.setValue(0)
+
+        self.reset_atlas_signal.emit()
diff --git a/pyproject.toml b/pyproject.toml
index 63db406..83e575c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,12 +24,15 @@ classifiers = [
 
 dependencies = [
     "napari>=0.4.18",
-    "bg-atlasapi",
-    "brainglobe-utils>=0.3.4",
+    "brainglobe-atlasapi",
+    "brainglobe-utils>=0.4.3",
+    "dask",
+    "dask-image",
+    "itk-elastix",
+    "lxml_html_clean",
     "numpy",
+    "pytransform3d",
     "qtpy",
-    "itk-elastix",
-    "pytransform3d"
 ]
 
 [project.urls]
diff --git a/tests/conftest.py b/tests/conftest.py
index a7708ef..df32c05 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -3,8 +3,8 @@
 
 import numpy as np
 import pytest
-from bg_atlasapi import BrainGlobeAtlas
-from bg_atlasapi import config as bg_config
+from brainglobe_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import config as bg_config
 from PIL import Image
 
 
diff --git a/tests/test_adjust_moving_image_view.py b/tests/test_adjust_moving_image_view.py
index fb2dc41..8eae56c 100644
--- a/tests/test_adjust_moving_image_view.py
+++ b/tests/test_adjust_moving_image_view.py
@@ -17,7 +17,7 @@ def adjust_moving_image_view() -> AdjustMovingImageView:
 def test_init(qtbot, adjust_moving_image_view):
     qtbot.addWidget(adjust_moving_image_view)
 
-    assert adjust_moving_image_view.layout().rowCount() == 9
+    assert adjust_moving_image_view.layout().rowCount() == 15
 
 
 @pytest.mark.parametrize(
@@ -104,7 +104,7 @@ def test_reset_image_button_click(qtbot, adjust_moving_image_view):
 
 @pytest.mark.parametrize(
     "x_scale, y_scale",
-    [(2.5, 2.5), (10, 20), (10.221, 10.228)],
+    [(2.5, 2.5), (10, 20), (10.2212, 10.2289)],
 )
 def test_scale_image_button_click(
     qtbot, adjust_moving_image_view, x_scale, y_scale
@@ -114,12 +114,48 @@ def test_scale_image_button_click(
     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(
+        adjust_moving_image_view.adjust_moving_image_pixel_size_x.setValue(
             x_scale
         )
-        adjust_moving_image_view.adjust_moving_image_voxel_size_y.setValue(
+        adjust_moving_image_view.adjust_moving_image_pixel_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)]
+    assert blocker.args == [round(x_scale, 3), round(y_scale, 3)]
+
+
+def test_atlas_rotation_changed(
+    qtbot,
+    adjust_moving_image_view,
+):
+    qtbot.addWidget(adjust_moving_image_view)
+
+    with qtbot.waitSignal(
+        adjust_moving_image_view.atlas_rotation_signal, timeout=1000
+    ) as blocker:
+        adjust_moving_image_view.adjust_atlas_pitch.setValue(10)
+        adjust_moving_image_view.adjust_atlas_yaw.setValue(20)
+        adjust_moving_image_view.adjust_atlas_roll.setValue(30)
+
+        adjust_moving_image_view.adjust_atlas_rotation.click()
+
+    assert blocker.args == [10, 20, 30]
+
+
+def test_atlas_reset_button_click(
+    qtbot,
+    adjust_moving_image_view,
+):
+    qtbot.addWidget(adjust_moving_image_view)
+
+    with qtbot.waitSignal(
+        adjust_moving_image_view.reset_atlas_signal, timeout=1000
+    ):
+        adjust_moving_image_view.reset_atlas_button.click()
+
+    assert (
+        adjust_moving_image_view.adjust_atlas_pitch.value() == 0
+        and adjust_moving_image_view.adjust_atlas_yaw.value() == 0
+        and adjust_moving_image_view.adjust_atlas_roll.value() == 0
+    )
diff --git a/tests/test_registration_widget.py b/tests/test_registration_widget.py
index 2b74c98..828c4aa 100644
--- a/tests/test_registration_widget.py
+++ b/tests/test_registration_widget.py
@@ -12,6 +12,29 @@ def registration_widget(make_napari_viewer_with_images):
     return widget
 
 
+@pytest.fixture()
+def registration_widget_with_example_atlas(make_napari_viewer_with_images):
+    """
+    Create an initialised RegistrationWidget with the "example_mouse_100um"
+    loaded.
+
+    Parameters
+    ------------
+    make_napari_viewer_with_images for testing
+        Fixture that creates a napari viewer
+    """
+    viewer = make_napari_viewer_with_images
+
+    widget = RegistrationWidget(viewer)
+
+    # Based on the downloaded atlases by the fixture in conftest.py,
+    # the example atlas will be in the third position.
+    example_atlas_index = 2
+    widget._on_atlas_dropdown_index_changed(example_atlas_index)
+
+    return widget
+
+
 def test_registration_widget(make_napari_viewer_with_images):
     widget = RegistrationWidget(make_napari_viewer_with_images)
 
@@ -132,3 +155,62 @@ def test_scale_moving_image(
         current_size[0] * y_scale_factor,
         current_size[1] * x_scale_factor,
     )
+
+
+@pytest.mark.parametrize(
+    "pitch, yaw, roll, expected_shape",
+    [
+        (0, 0, 0, (132, 80, 114)),
+        (45, 0, 0, (150, 150, 114)),
+        (0, 45, 0, (174, 80, 174)),
+        (0, 0, 45, (132, 137, 137)),
+    ],
+)
+def test_on_adjust_atlas_rotation(
+    registration_widget_with_example_atlas,
+    pitch,
+    yaw,
+    roll,
+    expected_shape,
+):
+    reg_widget = registration_widget_with_example_atlas
+    atlas_shape = reg_widget._atlas.reference.shape
+
+    reg_widget._on_adjust_atlas_rotation(pitch, yaw, roll)
+
+    assert reg_widget._atlas_data_layer.data.shape == expected_shape
+    assert reg_widget._atlas_annotations_layer.data.shape == expected_shape
+    assert reg_widget._atlas.reference.shape == atlas_shape
+
+
+def test_on_adjust_atlas_rotation_no_atlas(registration_widget, mocker):
+    mocked_show_error = mocker.patch(
+        "brainglobe_registration.registration_widget.show_error"
+    )
+    registration_widget._on_adjust_atlas_rotation(10, 10, 10)
+    mocked_show_error.assert_called_once_with(
+        "No atlas selected. Please select an atlas before rotating"
+    )
+
+
+def test_on_atlas_reset(registration_widget_with_example_atlas):
+    reg_widget = registration_widget_with_example_atlas
+    atlas_shape = reg_widget._atlas.reference.shape
+    reg_widget._on_adjust_atlas_rotation(10, 10, 10)
+
+    reg_widget._on_atlas_reset()
+
+    assert reg_widget._atlas_data_layer.data.shape == atlas_shape
+    assert reg_widget._atlas.reference.shape == atlas_shape
+    assert reg_widget._atlas_annotations_layer.data.shape == atlas_shape
+
+
+def test_on_atlas_reset_no_atlas(registration_widget, mocker):
+    mocked_show_error = mocker.patch(
+        "brainglobe_registration.registration_widget.show_error"
+    )
+
+    registration_widget._on_atlas_reset()
+    mocked_show_error.assert_called_once_with(
+        "No atlas selected. Please select an atlas before resetting"
+    )
diff --git a/tests/test_utils.py b/tests/test_utils.py
index d857e09..89068e7 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -7,6 +7,7 @@
 
 from brainglobe_registration.utils.utils import (
     adjust_napari_image_layer,
+    calculate_rotated_bounding_box,
     find_layer_index,
     get_image_layer_names,
     open_parameter_file,
@@ -93,3 +94,32 @@ def test_get_image_layer_names(make_napari_viewer_with_images):
 
     assert len(layer_names) == 2
     assert layer_names == ["moving_image", "atlas_image"]
+
+
+@pytest.mark.parametrize(
+    "basis, rotation, expected_bounds",
+    [
+        (0, 0, (50, 100, 200)),
+        (0, 90, (50, 200, 100)),
+        (0, 180, (50, 100, 200)),
+        (0, 45, (50, 212, 212)),
+        (1, 0, (50, 100, 200)),
+        (1, 90, (200, 100, 50)),
+        (1, 180, (50, 100, 200)),
+        (1, 45, (177, 100, 177)),
+        (2, 0, (50, 100, 200)),
+        (2, 90, (100, 50, 200)),
+        (2, 180, (50, 100, 200)),
+        (2, 45, (106, 106, 200)),
+    ],
+)
+def test_calculate_rotated_bounding_box(basis, rotation, expected_bounds):
+    image_shape = (50, 100, 200)
+    rotation_matrix = np.eye(4)
+    rotation_matrix[:-1, :-1] = active_matrix_from_angle(
+        basis, np.deg2rad(rotation)
+    )
+
+    result_shape = calculate_rotated_bounding_box(image_shape, rotation_matrix)
+
+    assert result_shape == expected_bounds

From 538cdd27e4fefcdaf0e0eaaa8ff67bd45ef67e65 Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <igor.tatarnikov@gmail.com>
Date: Mon, 29 Jul 2024 11:03:19 +0100
Subject: [PATCH 04/10] Cleaned up a few things

---
 brainglobe_registration/elastix/register.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/brainglobe_registration/elastix/register.py b/brainglobe_registration/elastix/register.py
index d04d918..4a216f9 100644
--- a/brainglobe_registration/elastix/register.py
+++ b/brainglobe_registration/elastix/register.py
@@ -1,7 +1,8 @@
-from typing import List
+from typing import List, Tuple
 
 import itk
 import numpy as np
+import numpy.typing as npt
 from brainglobe_atlasapi import BrainGlobeAtlas
 
 
@@ -28,28 +29,30 @@ def run_registration(
     atlas_image,
     moving_image,
     annotation_image,
-    parameter_lists: List[tuple[str, dict]],
-) -> tuple[np.ndarray, itk.ParameterObject, np.ndarray]:
+    parameter_lists: List[Tuple[str, dict]],
+) -> Tuple[npt.NDArray, itk.ParameterObject, npt.NDArray]:
     """
     Run the registration process on the given images.
 
     Parameters
     ----------
-    atlas_image : np.ndarray
+    atlas_image : npt.NDArray
         The atlas image.
-    moving_image : np.ndarray
+    moving_image : npt.NDArray
         The moving image.
-    annotation_image : np.ndarray
+    annotation_image : npt.NDArray
         The annotation image.
     parameter_lists : List[tuple[str, dict]], optional
         The list of parameter lists, by default None
 
     Returns
     -------
-    np.ndarray
+    npt.NDArray
         The result image.
     itk.ParameterObject
         The result transform parameters.
+    npt.NDArray
+        The transformed annotation image.
     """
     # convert to ITK, view only
     atlas_image = itk.GetImageViewFromArray(atlas_image).astype(itk.F)

From 56a6f749d2e03e484f1a975f6b85c8beaba83478 Mon Sep 17 00:00:00 2001
From: saarah815 <63860766+saarah815@users.noreply.github.com>
Date: Tue, 6 Aug 2024 19:33:27 +0100
Subject: [PATCH 05/10] Mark 'Advanced Settings' as optional (#48)

---
 brainglobe_registration/registration_widget.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index 82e47e8..62b2437 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -175,7 +175,9 @@ def __init__(self, napari_viewer: Viewer):
             self.parameters_tab.addTab(new_tab, transform_type)
             self.parameter_setting_tabs_lists.append(new_tab)
 
-        self.add_widget(self.parameters_tab, widget_title="Advanced Settings")
+        self.add_widget(
+            self.parameters_tab, widget_title="Advanced Settings (optional)"
+        )
         self.add_widget(self.run_button, collapsible=False)
 
         self.layout().itemAt(1).widget().collapse(animate=False)

From ce8bdc533ae5b52f9dce5afc1677c42378c7e631 Mon Sep 17 00:00:00 2001
From: saarah815 <63860766+saarah815@users.noreply.github.com>
Date: Wed, 7 Aug 2024 10:25:58 +0100
Subject: [PATCH 06/10] Info message when running BrainGlobe Registration
 plugin with no atlas installed (#46)

* added error when no atlas found

* added error when no atlas found

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* changes to info message

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* parent_widget

* parent_widget

---------

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .../registration_widget.py                    |  8 +++----
 brainglobe_registration/utils/utils.py        | 21 +++++++++++++++++++
 2 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index 62b2437..edaffc9 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -24,10 +24,7 @@
 from napari.utils.notifications import show_error
 from napari.viewer import Viewer
 from pytransform3d.rotations import active_matrix_from_angle
-from qtpy.QtWidgets import (
-    QPushButton,
-    QTabWidget,
-)
+from qtpy.QtWidgets import QPushButton, QTabWidget
 from skimage.segmentation import find_boundaries
 from skimage.transform import rescale
 
@@ -35,6 +32,7 @@
 from brainglobe_registration.utils.utils import (
     adjust_napari_image_layer,
     calculate_rotated_bounding_box,
+    check_atlas_installed,
     find_layer_index,
     get_image_layer_names,
     open_parameter_file,
@@ -182,6 +180,8 @@ def __init__(self, napari_viewer: Viewer):
 
         self.layout().itemAt(1).widget().collapse(animate=False)
 
+        check_atlas_installed(self)
+
     def _on_atlas_dropdown_index_changed(self, index):
         # Hacky way of having an empty first dropdown
         if index == 0:
diff --git a/brainglobe_registration/utils/utils.py b/brainglobe_registration/utils/utils.py
index 2bb9891..e94faa7 100644
--- a/brainglobe_registration/utils/utils.py
+++ b/brainglobe_registration/utils/utils.py
@@ -4,7 +4,10 @@
 import napari
 import numpy as np
 import numpy.typing as npt
+from brainglobe_atlasapi.list_atlases import get_downloaded_atlases
+from brainglobe_utils.qtpy.dialog import display_info
 from pytransform3d.rotations import active_matrix_from_angle
+from qtpy.QtWidgets import QWidget
 
 
 def adjust_napari_image_layer(
@@ -154,3 +157,21 @@ def calculate_rotated_bounding_box(
         int(np.round(max_corner[1] - min_corner[1])),
         int(np.round(max_corner[2] - min_corner[2])),
     )
+
+
+def check_atlas_installed(parent_widget: QWidget):
+    """
+    Function checks if user has any atlases installed. If not, message box
+    appears in napari, directing user to download atlases via attached links.
+    """
+    available_atlases = get_downloaded_atlases()
+    if len(available_atlases) == 0:
+        display_info(
+            widget=parent_widget,
+            title="Information",
+            message="No atlases available. Please download atlas(es) "
+            "using <a href='https://brainglobe.info/documentation/"
+            "brainglobe-atlasapi/usage/command-line-interface.html'>"
+            "brainglobe-atlasapi</a> or <a href='https://brainglobe.info/"
+            "tutorials/manage-atlases-in-GUI.html'>brainrender-napari</a>",
+        )

From 88377a21be0e3b2723683d643b90c59cd2a87862 Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Fri, 9 Aug 2024 09:56:55 +0100
Subject: [PATCH 07/10] Clean up widget (#51)

* Cleaned up rogue widget duplication

* Added parent to parameters_tab
---
 brainglobe_registration/registration_widget.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index edaffc9..11e3752 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -93,11 +93,6 @@ def __init__(self, napari_viewer: Viewer):
         else:
             self._moving_image = None
 
-        self.main_tabs = QTabWidget(parent=self)
-        self.main_tabs.setTabPosition(QTabWidget.West)
-
-        self.parameters_tab = QTabWidget()
-
         self.get_atlas_widget = SelectImagesView(
             available_atlases=self._available_atlases,
             sample_image_names=self._sample_images,
@@ -162,7 +157,7 @@ def __init__(self, napari_viewer: Viewer):
         )
 
         self.parameter_setting_tabs_lists = []
-        self.parameters_tab = QTabWidget()
+        self.parameters_tab = QTabWidget(parent=self)
 
         for transform_type in self.transform_params:
             new_tab = RegistrationParameterListView(

From 5b55032a8043e597906d4abf50b061c82f147db2 Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Fri, 9 Aug 2024 16:37:21 +0100
Subject: [PATCH 08/10] Fix slow plugin loading (#54)

---
 brainglobe_registration/registration_widget.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index 11e3752..61a497c 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -28,7 +28,6 @@
 from skimage.segmentation import find_boundaries
 from skimage.transform import rescale
 
-from brainglobe_registration.elastix.register import run_registration
 from brainglobe_registration.utils.utils import (
     adjust_napari_image_layer,
     calculate_rotated_bounding_box,
@@ -268,6 +267,7 @@ def _on_adjust_moving_image_reset_button_click(self):
         adjust_napari_image_layer(self._moving_image, 0, 0, 0)
 
     def _on_run_button_click(self):
+        from brainglobe_registration.elastix.register import run_registration
 
         current_atlas_slice = self._viewer.dims.current_step[0]
 

From f690deaf6474663a3cca294c56ac6765619dd6f2 Mon Sep 17 00:00:00 2001
From: saarah815 <63860766+saarah815@users.noreply.github.com>
Date: Tue, 13 Aug 2024 14:26:50 +0100
Subject: [PATCH 09/10] Filter Images (#52)

* work_in_progress

* filter_images

* filter_images

* filter_images

* filter_images

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .../registration_widget.py                    | 26 +++++-
 brainglobe_registration/utils/utils.py        | 79 +++++++++++++++++++
 2 files changed, 102 insertions(+), 3 deletions(-)

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index 61a497c..acb72e7 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -24,7 +24,7 @@
 from napari.utils.notifications import show_error
 from napari.viewer import Viewer
 from pytransform3d.rotations import active_matrix_from_angle
-from qtpy.QtWidgets import QPushButton, QTabWidget
+from qtpy.QtWidgets import QCheckBox, QPushButton, QTabWidget
 from skimage.segmentation import find_boundaries
 from skimage.transform import rescale
 
@@ -32,6 +32,7 @@
     adjust_napari_image_layer,
     calculate_rotated_bounding_box,
     check_atlas_installed,
+    filter_plane,
     find_layer_index,
     get_image_layer_names,
     open_parameter_file,
@@ -135,6 +136,9 @@ def __init__(self, napari_viewer: Viewer):
             self._on_default_file_selection_change
         )
 
+        self.filter_checkbox = QCheckBox("Filter Images")
+        self.filter_checkbox.setChecked(False)
+
         self.run_button = QPushButton("Run")
         self.run_button.clicked.connect(self._on_run_button_click)
         self.run_button.setEnabled(False)
@@ -170,6 +174,9 @@ def __init__(self, napari_viewer: Viewer):
         self.add_widget(
             self.parameters_tab, widget_title="Advanced Settings (optional)"
         )
+
+        self.add_widget(self.filter_checkbox, collapsible=False)
+
         self.add_widget(self.run_button, collapsible=False)
 
         self.layout().itemAt(1).widget().collapse(animate=False)
@@ -271,9 +278,22 @@ def _on_run_button_click(self):
 
         current_atlas_slice = self._viewer.dims.current_step[0]
 
+        if self.filter_checkbox.isChecked():
+            atlas_layer = filter_plane(
+                self._atlas_data_layer.data[
+                    current_atlas_slice, :, :
+                ].compute()
+            )
+            moving_image_layer = filter_plane(self._moving_image.data)
+        else:
+            atlas_layer = self._atlas_data_layer.data[
+                current_atlas_slice, :, :
+            ]
+            moving_image_layer = self._moving_image.data
+
         result, parameters, registered_annotation_image = run_registration(
-            self._atlas_data_layer.data[current_atlas_slice, :, :],
-            self._moving_image.data,
+            atlas_layer,
+            moving_image_layer,
             self._atlas_annotations_layer.data[current_atlas_slice, :, :],
             self.transform_selections,
         )
diff --git a/brainglobe_registration/utils/utils.py b/brainglobe_registration/utils/utils.py
index e94faa7..858ebab 100644
--- a/brainglobe_registration/utils/utils.py
+++ b/brainglobe_registration/utils/utils.py
@@ -8,6 +8,8 @@
 from brainglobe_utils.qtpy.dialog import display_info
 from pytransform3d.rotations import active_matrix_from_angle
 from qtpy.QtWidgets import QWidget
+from scipy.ndimage import gaussian_filter
+from skimage import morphology
 
 
 def adjust_napari_image_layer(
@@ -175,3 +177,80 @@ def check_atlas_installed(parent_widget: QWidget):
             "brainglobe-atlasapi</a> or <a href='https://brainglobe.info/"
             "tutorials/manage-atlases-in-GUI.html'>brainrender-napari</a>",
         )
+
+
+def filter_plane(img_plane):
+    """
+    Apply a set of filter to the plane (typically to avoid overfitting details
+    in the image during registration)
+    The filter is composed of a despeckle filter using opening and a pseudo
+    flatfield filter
+
+    Originally from: [https://github.com/brainglobe/brainreg/blob/main
+    /brainreg/core/utils/preprocess.py]
+
+    Parameters
+    ----------
+    img_plane : np.array
+        A 2D array to filter
+
+    Returns
+    -------
+    np.array
+        Filtered image
+    """
+
+    img_plane = despeckle_by_opening(img_plane)
+    img_plane = pseudo_flatfield(img_plane)
+    return img_plane
+
+
+def despeckle_by_opening(img_plane, radius=2):
+    """
+    Despeckle the image plane using a grayscale opening operation
+
+    Originally from: [https://github.com/brainglobe/brainreg/blob/main
+    /brainreg/core/utils/preprocess.py]
+
+    Parameters
+    ----------
+    img_plane : np.array
+        The image to filter
+
+    radius: int
+        The radius of the opening kernel
+
+    Returns
+    -------
+    np.array
+        The despeckled image
+    """
+    kernel = morphology.disk(radius)
+    morphology.opening(img_plane, out=img_plane, footprint=kernel)
+    return img_plane
+
+
+def pseudo_flatfield(img_plane, sigma=5):
+    """
+    Pseudo flat field filter implementation using a de-trending by a
+    heavily gaussian filtered copy of the image.
+
+    Originally from: [https://github.com/brainglobe/brainreg/blob/main
+    /brainreg/core/utils/preprocess.py]
+
+    Parameters
+    ----------
+    img_plane : np.array
+        The image to filter
+
+    sigma : int
+        The sigma of the gaussian filter applied to the
+        image used for de-trending
+
+    Returns
+    -------
+    np.array
+        The pseudo flat field filtered image
+    """
+    filtered_img = gaussian_filter(img_plane, sigma)
+    return img_plane / (filtered_img + 1)

From 17435b1679a913d4ebe4ba772ddc102ddbd2f1d9 Mon Sep 17 00:00:00 2001
From: saarah815 <63860766+saarah815@users.noreply.github.com>
Date: Tue, 13 Aug 2024 15:14:15 +0100
Subject: [PATCH 10/10] Communicate napari layer deletions appropriately to the
 plugin (#49)

* layer_deletion

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* layer_deletion_edits

* Made pytest happy

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* updated_layer

* fixed manual vs automatic deletion

* fixed manual vs automatic deletion

* Refactored some old code to avoid duplication

* add comments

---------

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Co-authored-by: IgorTatarnikov <igor.tatarnikov@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .../registration_widget.py                    | 102 ++++++++++++++----
 .../widgets/select_images_view.py             |   7 +-
 2 files changed, 89 insertions(+), 20 deletions(-)

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
index acb72e7..4d0f367 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -18,9 +18,11 @@
 from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_atlasapi.list_atlases import get_downloaded_atlases
 from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
+from brainglobe_utils.qtpy.dialog import display_info
 from brainglobe_utils.qtpy.logo import header_widget
 from dask_image.ndinterp import affine_transform as dask_affine_transform
 from napari.qt.threading import thread_worker
+from napari.utils.events import Event
 from napari.utils.notifications import show_error
 from napari.viewer import Viewer
 from pytransform3d.rotations import active_matrix_from_angle
@@ -60,6 +62,8 @@ def __init__(self, napari_viewer: Viewer):
         self._atlas_annotations_layer: Optional[napari.layers.Labels] = None
         self._moving_image: Optional[napari.layers.Image] = None
         self._moving_image_data_backup: Optional[npt.NDArray] = None
+        self._automatic_deletion_flag = False
+        # Flag to differentiate between manual and automatic atlas deletion
 
         self.transform_params: dict[str, dict] = {
             "rigid": {},
@@ -136,6 +140,8 @@ def __init__(self, napari_viewer: Viewer):
             self._on_default_file_selection_change
         )
 
+        # Use decorator to connect to layer deletion event
+        self._connect_events()
         self.filter_checkbox = QCheckBox("Filter Images")
         self.filter_checkbox.setChecked(False)
 
@@ -183,33 +189,69 @@ def __init__(self, napari_viewer: Viewer):
 
         check_atlas_installed(self)
 
+    def _connect_events(self):
+        @self._viewer.layers.events.removed.connect
+        def _on_layer_deleted(event: Event):
+            if not self._automatic_deletion_flag:
+                self._handle_layer_deletion(event)
+
+    def _handle_layer_deletion(self, event: Event):
+        deleted_layer = event.value
+
+        # Check if the deleted layer is the moving image
+        if self._moving_image == deleted_layer:
+            self._moving_image = None
+            self._moving_image_data_backup = None
+            self._update_dropdowns()
+
+        # Check if deleted layer is the atlas reference / atlas annotations
+        if (
+            self._atlas_data_layer == deleted_layer
+            or self._atlas_annotations_layer == deleted_layer
+        ):
+            # Reset the atlas selection combobox
+            self.get_atlas_widget.reset_atlas_combobox()
+
+    def _delete_atlas_layers(self):
+        # Delete atlas reference layer if it exists
+        if self._atlas_data_layer in self._viewer.layers:
+            self._viewer.layers.remove(self._atlas_data_layer)
+
+        # Delete atlas annotations layer if it exists
+        if self._atlas_annotations_layer in self._viewer.layers:
+            self._viewer.layers.remove(self._atlas_annotations_layer)
+
+        # Clear atlas attributes
+        self._atlas = None
+        self._atlas_data_layer = None
+        self._atlas_annotations_layer = None
+        self.run_button.setEnabled(False)
+        self._viewer.grid.enabled = False
+
+    def _update_dropdowns(self):
+        # Extract the names of the remaining layers
+        layer_names = get_image_layer_names(self._viewer)
+        # Update the dropdowns in SelectImagesView
+        self.get_atlas_widget.update_sample_image_names(layer_names)
+
     def _on_atlas_dropdown_index_changed(self, index):
         # Hacky way of having an empty first dropdown
         if index == 0:
-            if self._atlas:
-                current_atlas_layer_index = find_layer_index(
-                    self._viewer, self._atlas.atlas_name
-                )
-
-                self._viewer.layers.pop(current_atlas_layer_index)
-                self._atlas = None
-                self._atlas_data_layer = None
-                self._atlas_annotations_layer = None
-                self.run_button.setEnabled(False)
-                self._viewer.grid.enabled = False
-
+            self._delete_atlas_layers()
             return
 
         atlas_name = self._available_atlases[index]
 
         if self._atlas:
-            current_atlas_layer_index = find_layer_index(
-                self._viewer, self._atlas.atlas_name
-            )
+            # Set flag to True when atlas is changed, not manually deleted
+            # Ensures atlas index does not reset to 0
+            self._automatic_deletion_flag = True
+            try:
+                self._delete_atlas_layers()
+            finally:
+                self._automatic_deletion_flag = False
 
-            self._viewer.layers.pop(current_atlas_layer_index)
-        else:
-            self.run_button.setEnabled(True)
+        self.run_button.setEnabled(True)
 
         self._atlas = BrainGlobeAtlas(atlas_name)
         dask_reference = da.from_array(
@@ -252,13 +294,19 @@ def _on_sample_dropdown_index_changed(self, index):
         viewer_index = find_layer_index(
             self._viewer, self._sample_images[index]
         )
+        if viewer_index == -1:
+            self._moving_image = None
+            self._moving_image_data_backup = None
+
+            return
+
         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):
         if not self._moving_image:
             show_error(
-                "No moving image selected. "
+                "No moving image selected."
                 "Please select a moving image before adjusting"
             )
             return
@@ -276,6 +324,22 @@ def _on_adjust_moving_image_reset_button_click(self):
     def _on_run_button_click(self):
         from brainglobe_registration.elastix.register import run_registration
 
+        if self._atlas_data_layer is None:
+            display_info(
+                widget=self,
+                title="Warning",
+                message="Please select an atlas before clicking 'Run'.",
+            )
+            return
+
+        if self._moving_image == self._atlas_data_layer:
+            display_info(
+                widget=self,
+                title="Warning",
+                message="Your moving image cannot be an atlas.",
+            )
+            return
+
         current_atlas_slice = self._viewer.dims.current_step[0]
 
         if self.filter_checkbox.isChecked():
diff --git a/brainglobe_registration/widgets/select_images_view.py b/brainglobe_registration/widgets/select_images_view.py
index 17bc737..ad9046c 100644
--- a/brainglobe_registration/widgets/select_images_view.py
+++ b/brainglobe_registration/widgets/select_images_view.py
@@ -98,7 +98,8 @@ def __init__(
 
     def update_sample_image_names(self, sample_image_names: List[str]):
         self.available_sample_dropdown.clear()
-        self.available_sample_dropdown.addItems(sample_image_names)
+        if len(sample_image_names) != 0:
+            self.available_sample_dropdown.addItems(sample_image_names)
 
     def _on_atlas_index_change(self):
         """
@@ -122,5 +123,9 @@ def _on_moving_image_index_change(self):
             self.available_sample_dropdown.currentIndex()
         )
 
+    def reset_atlas_combobox(self):
+        if self.available_atlas_dropdown is not None:
+            self.available_atlas_dropdown.setCurrentIndex(0)
+
     def _on_sample_popup_about_to_show(self):
         self.sample_image_popup_about_to_show.emit()