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-
registration", # line break at
+ "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 427bdab..0000000
Binary files a/brainglobe_registration/resources/brainglobe.png and /dev/null differ
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>
-"""
-
-
-def _docs_links_widget(parent: QWidget = None):
- _docs_links_html = """
-
-
Website
- Source
-
- """ # 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("brainglobe-registration
"))
- 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