Find centre of rotation

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/docs_build_and_deploy.yml

@@ -1,4 +1,4 @@
-name: Build Sphinx docs and deploy to GitHub Pages
+name: Docs
 
 # Generate the documentation on all merges to main, all pull requests, or by
 # manual workflow dispatch. The build job can be used as a CI check that the
@@ -12,23 +12,35 @@ on:
     tags:
       - '*'
   pull_request:
+  merge_group:
   workflow_dispatch:
 
 jobs:
+  linting:
+    # scheduled workflows should not run on forks
+    if: (${{ github.event_name == 'schedule' }} && ${{ github.repository_owner == 'neuroinformatics-unit' }} && ${{ github.ref == 'refs/heads/main' }}) || (${{ github.event_name != 'schedule' }})
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
   build_sphinx_docs:
     name: Build Sphinx Docs
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/build_sphinx_docs@v2
+      - uses: neuroinformatics-unit/actions/build_sphinx_docs@main
+        with:
+          python-version: 3.11
+          use-make: true
 
   deploy_sphinx_docs:
     name: Deploy Sphinx Docs
     needs: build_sphinx_docs
     permissions:
       contents: write
-    if: github.event_name == 'push' && github.ref_type == 'tag'
+    if: (github.event_name == 'push' && github.ref_type == 'tag') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/deploy_sphinx_docs@v2
+      - uses: neuroinformatics-unit/actions/deploy_sphinx_docs@main
         with:
           secret_input: ${{ secrets.GITHUB_TOKEN }}
+          use-make: true

.github/workflows/test_and_deploy.yml

@@ -7,6 +7,7 @@ on:
     tags:
       - '*'
   pull_request:
+  merge_group:
 
 jobs:
   linting:
@@ -27,20 +28,23 @@ jobs:
     strategy:
       matrix:
         # Run all supported Python versions on linux
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest]
-        # Include one windows and macos run
+        # Include 1 Intel macos (13) and 1 M1 macos (latest) and 1 Windows run
         include:
+        - os: macos-13
+          python-version: "3.11"
         - os: macos-latest
-          python-version: "3.10"
+          python-version: "3.11"
         - os: windows-latest
-          python-version: "3.10"
+          python-version: "3.11"
 
     steps:
       # 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

derotation/analysis/full_rotation_pipeline.py → derotation/analysis/full_derotation_pipeline.py

@@ -14,7 +14,7 @@
 from sklearn.mixture import GaussianMixture
 from tifffile import imsave
 
-from derotation.derotate_by_line import rotate_an_image_array_line_by_line
+from derotation.derotate_by_line import derotate_an_image_array_line_by_line
 from derotation.load_data.custom_data_loaders import (
     get_analog_signals,
     read_randomized_stim_table,
@@ -56,7 +56,7 @@
         - saving the masked image stack
         """
         self.process_analog_signals()
-        rotated_images = self.rotate_frames_line_by_line()
+        rotated_images = self.derotate_frames_line_by_line()
         masked = self.add_circle_mask(rotated_images, self.mask_diameter)
         self.save(masked)
         self.save_csv_with_derotation_data()
@@ -168,14 +168,20 @@
         self.debugging_plots = self.config["debugging_plots"]
 
         if self.debugging_plots:
-            self.debug_plots_folder = self.config["paths_write"][
-                "debug_plots_folder"
-            ]
+            self.debug_plots_folder = Path(
+                self.config["paths_write"]["debug_plots_folder"]
+            )
             Path(self.debug_plots_folder).mkdir(parents=True, exist_ok=True)
 
         logging.info(f"Dataset {self.filename_raw} loaded")
         logging.info(f"Filename: {self.filename}")
 
+        self.center_of_rotation = (
+            self.num_lines_per_frame // 2,
+            self.num_lines_per_frame // 2,
+        )
+        self.hooks = {}
+
     ### ----------------- Analog signals processing pipeline ------------- ###
     def process_analog_signals(self):
         """From the analog signals (frame clock, line clock, full rotation,
@@ -790,26 +796,39 @@
         plt.savefig(self.debug_plots_folder / "rotation_angles.png")
 
     ### ----------------- Derotation ----------------- ###
-    def rotate_frames_line_by_line(self) -> np.ndarray:
-        """Rotates the image stack line by line, using the rotation angles
-        by line calculated from the analog signals.
-
-        Description of the algorithm:
-        - takes one line from the image stack
-        - creates a new image with only that line
-        - rotates the line by the given angle
-        - substitutes the line in the new image
-        - adds the new image to the rotated image stack
-
-        Edge cases and how they are handled:
-        - the rotation starts in the middle of the image -> the previous lines
-        are copied from the first frame
-        - the rotation ends in the middle of the image -> the remaining lines
-        are copied from the last frame
-
-        Before derotation, it finds the image offset, which is the peak of
-        the gaussian mixture model fitted to the image histogram. It is
-        useful to fill in the blank pixels that appear during the derotation.
+
+    def plot_max_projection_with_center(self):
+        """Plots the maximum projection of the image stack with the center
+        of rotation.
+        This plot will be saved in the debug_plots folder.
+        Please inspect it to check that the center of rotation is correctly
+        placed.
+        """
+        logging.info("Plotting max projection with center...")
+
+        max_projection = np.max(self.image_stack, axis=0)
+
+        fig, ax = plt.subplots(1, 1, figsize=(5, 5))
+
+        ax.imshow(max_projection, cmap="gray")
+        ax.scatter(
+            self.center_of_rotation[0],
+            self.center_of_rotation[1],
+            color="red",
+            marker="x",
+        )
+
+        ax.spines["top"].set_visible(False)
+        ax.spines["right"].set_visible(False)
+
+        ax.axis("off")
+
+        plt.savefig(self.debug_plots_folder / "max_projection_with_center.png")
+
+    def derotate_frames_line_by_line(self) -> np.ndarray:
+        """Wrapper for the function `derotate_an_image_array_line_by_line`.
+        Before calling the function, it finds the F0 image offset with
+        `find_image_offset`.
 
         Returns
         -------
@@ -818,12 +837,22 @@
         """
         logging.info("Starting derotation by line...")
 
+        if self.debugging_plots:
+            self.plot_max_projection_with_center()
+
         offset = self.find_image_offset(self.image_stack[0])
 
-        rotated_image_stack = rotate_an_image_array_line_by_line(
+        rotated_image_stack = derotate_an_image_array_line_by_line(
             self.image_stack,
             self.rot_deg_line,
             blank_pixels_value=offset,
+            center=self.center_of_rotation,
+            plotting_hook_line_addition=self.hooks.get(
+                "plotting_hook_line_addition"
+            ),
+            plotting_hook_image_completed=self.hooks.get(
+                "plotting_hook_image_completed"
+            ),
         )
 
         logging.info("✨ Image stack rotated ✨")