registration:

- save original stack
- display first moving and ref images
- implement a StackableImage class WIP

src/napari_em_stack_reg/_widget.py

@@ -42,6 +42,7 @@
 
 # from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
+    QFrame,
     # QHBoxLayout,
     QLabel,
     # QMainWindow,
@@ -51,6 +52,9 @@
     QWidget,
 )
 
+from napari_em_stack_reg.tools.register import StackableImage
+
+
 if TYPE_CHECKING:
     import napari
 
@@ -65,25 +69,45 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self._stack_details = QLabel("No image layer found.")
         self._stack_details.setWordWrap(True)
 
-        self._begin_registration_button = QPushButton("Begin registration")
-        self._begin_registration_button.hide()
+        self._begin_button = QPushButton("Begin")
+        self._begin_button.hide()
 
         self._update_stack_details()
 
         self.setLayout(QVBoxLayout())
         self.layout().addWidget(self._stack_details)
-        self.layout().addWidget(self._begin_registration_button)
+
+        self._divider = QFrame()
+        self._divider.setFrameShape(QFrame.HLine)
+        self._divider.setFrameShadow(QFrame.Sunken)
+        self.layout().addWidget(self._divider)
+        self.layout().addWidget(self._begin_button)
 
         self._viewer.layers.events.inserted.connect(self._on_layer_inserted)
         self._viewer.layers.events.removed.connect(self._on_layer_removed)
 
+        self._begin_button.clicked.connect(self._on_begin_button_clicked)
+
     def _on_layer_inserted(self):
         self._update_stack_details()
-        self._begin_registration_button.show()
+        self._begin_button.show()
 
     def _on_layer_removed(self):
         self._update_stack_details()
-        self._begin_registration_button.hide()
+        self._begin_button.hide()
+
+    def _on_begin_button_clicked(self):
+        # print("Begin button clicked")
+
+        self._begin_button.hide()
+        stackable_img = StackableImage(self._viewer)
+        stackable_img.get_registration_images()
+
+        for layer in self._viewer.layers:
+            layer.events.transform.connect(self._on_transform_changed)
+
+    def _on_transform_changed(self, event):
+        print("Transform changed")
 
     def _update_stack_details(self):
         # print("this")

src/napari_em_stack_reg/tools/register.py

@@ -0,0 +1,70 @@
+import os
+
+import dask.array as da
+import numpy as np
+from napari.layers import Image
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import napari
+
+
+class StackableImage:
+    def __init__(self, viewer: "napari.viewer.Viewer"):
+        self._viewer = viewer
+        self._set_original_stack()
+
+        self._reference_index = 0
+        self._moving_index = 1
+        self._transforms = []
+
+    def _set_original_stack(self):
+        image_layer = next(
+            (
+                layer
+                for layer in self._viewer.layers
+                if isinstance(layer, Image)
+            ),
+            None,
+        )
+
+        if image_layer is not None:
+            if isinstance(image_layer.data, np.ndarray):
+                self._original_stack = da.from_array(image_layer.data)
+            elif isinstance(image_layer.data, da.Array):
+                self._original_stack = image_layer.data
+
+    def get_registration_images(self, reference_index: int = 0):
+        self._reference_img = self._original_stack[reference_index]
+        self._moving_img = self._original_stack[self._moving_index]
+
+        current_image_layer = next(
+            (
+                layer
+                for layer in self._viewer.layers
+                if isinstance(layer, Image)
+            ),
+            None,
+        )
+
+        if current_image_layer is not None:
+            self._viewer.layers.remove(current_image_layer)
+
+        # add reference image
+        self._viewer.add_image(
+            self._reference_img,
+            name=f"ref - slice {reference_index}",
+            blending="translucent_no_depth",
+            colormap="gray",
+        )
+
+        # add moving image
+        self._viewer.add_image(
+            self._moving_img,
+            name=f"moving - slice {self._moving_index}",
+            blending="translucent_no_depth",
+            colormap="gray",
+            opacity=0.5,
+        )
+
+        self._viewer.layers[-1].mode = "transform"