Squashed commit of the following:

commit 6c75b50
Author: alessandrofelder <[email protected]>
Date:   Mon Jul 10 14:54:23 2023 +0100

    make a napari-MPL widget

commit 50af5aa
Merge: b23c008 dd681ce
Author: lauraporta <[email protected]>
Date:   Mon Jul 10 14:11:17 2023 +0100

    Merge branch 'derotation-01' into napari-matplotlib

commit b23c008
Author: alessandrofelder <[email protected]>
Date:   Mon Jul 10 14:07:05 2023 +0100

    dummy napari plotting widget

commit dd681ce
Author: lauraporta <[email protected]>
Date:   Mon Jul 10 12:50:24 2023 +0100

    Refactor plots and other methods

commit 4b8596f
Author: lauraporta <[email protected]>
Date:   Mon Jul 10 12:24:48 2023 +0100

    Update pyproject.toml

commit cd4d14f
Author: lauraporta <[email protected]>
Date:   Mon Jul 10 12:01:20 2023 +0100

    Move part of the analysis code in methods in other files - analog preprocessing - extraction of rotation angles

commit a233b24
Author: lauraporta <[email protected]>
Date:   Mon Jul 10 11:04:28 2023 +0100

    Add new plotting of centroids

commit 0be6a4b
Author: lauraporta <[email protected]>
Date:   Thu Jun 29 18:57:52 2023 +0200

    Add improvements in the optimization algorithms for centroid location and derotation angles

commit 2776f7c
Author: lauraporta <[email protected]>
Date:   Wed Jun 28 21:41:23 2023 +0200

    Add functioning algorithm to optimize rotation degrees

commit 3c63528
Author: lauraporta <[email protected]>
Date:   Wed Jun 28 14:33:09 2023 +0200

    Add changes to gitignore

commit 5c73d88
Author: lauraporta <[email protected]>
Date:   Mon Jun 26 17:38:05 2023 +0200

    Optimization v1

commit 6c0e0ca
Author: lauraporta <[email protected]>
Date:   Mon Jun 26 17:37:54 2023 +0200

    Improve plots

commit 510db18
Author: lauraporta <[email protected]>
Date:   Mon Jun 26 17:37:32 2023 +0200

    Clean up

commit 7b4748e
Author: lauraporta <[email protected]>
Date:   Mon Jun 26 17:36:43 2023 +0200

    Add libraries to pyproject.toml

commit 0bac20f
Author: lauraporta <[email protected]>
Date:   Fri Jun 23 13:39:35 2023 +0100

    Add draft pipeline to find centroid

commit 2c42d39
Author: lauraporta <[email protected]>
Date:   Thu Jun 22 16:50:26 2023 +0100

    Visualize effects of derotation and correct some errors

commit 8c843f6
Author: lauraporta <[email protected]>
Date:   Thu Jun 22 15:03:20 2023 +0100

    Add working logic to calculate the rotation degree for each frame

commit 9708a17
Author: lauraporta <[email protected]>
Date:   Tue Jun 20 16:22:21 2023 +0100

    Linting

commit 52bea43
Author: lauraporta <[email protected]>
Date:   Tue Jun 20 16:21:03 2023 +0100

    Add draft logic to fit the rotation degree changes to curve [not working]

commit 4f2a0e3
Author: lauraporta <[email protected]>
Date:   Tue Jun 20 14:53:58 2023 +0100

    Get the rotation angle per tick

commit 2cf3636
Author: lauraporta <[email protected]>
Date:   Tue Jun 20 13:50:25 2023 +0100

    Assign correct sign for rotation

commit e3be111
Author: lauraporta <[email protected]>
Date:   Tue Jun 20 13:20:19 2023 +0100

    Find optimal threshold for frames

Author: lauraporta

derotation/napari.yaml

@@ -0,0 +1,10 @@
+name: derotation
+display_name: Neuroinformatics derotation tools
+contributions:
+  commands:
+    - id: derotation.make_plotting_widget
+      python_name: derotation.plotting:Plotting
+      title: Make Plotting Widget
+  widgets:
+    - command: derotation.make_plotting_widget
+      display_name: NIU derotation plotting

derotation/plotting.py

@@ -0,0 +1,40 @@
+from typing import Optional
+
+import numpy as np
+from napari.viewer import Viewer
+from napari_matplotlib.base import SingleAxesWidget
+from qtpy.QtWidgets import (
+    QPushButton,
+    QVBoxLayout,
+    QWidget,
+)
+
+
+class DerotationCanvas(SingleAxesWidget):
+    def __init__(
+        self,
+        napari_viewer: Viewer,
+        parent: Optional[QWidget] = None,
+    ):
+        super().__init__(napari_viewer, parent=parent)
+        self.angles_over_time = np.sin(np.linspace(0, 10, 100))
+        self._update_layers(None)
+
+    def draw(self):
+        self.axes.plot(self.angles_over_time, color="red")
+        self.axes.set_title(f"z={self.current_z}")
+        self.axes.axvline(self.current_z)
+
+
+class Plotting(QWidget):
+    def __init__(self, napari_viewer: Viewer):
+        super().__init__()
+
+        self._viewer = napari_viewer
+        self.setLayout(QVBoxLayout())
+        self.button = QPushButton()
+        self.button.setText("Make plot")
+        self.layout().addWidget(self.button)
+
+        self.mpl_widget = DerotationCanvas(self._viewer)
+        self.layout().addWidget(self.mpl_widget)

setup.cfg

@@ -0,0 +1,3 @@
+[options.entry_points]
+napari.manifest =
+    brainglobe-napari = derotation:napari.yaml