change channel registration to be performed on tiles

situr/registration/__init__.py

@@ -1,5 +1,5 @@
 from .registration import Registration, RegistrationFunction, FilterregRegistrationFunction
-from .channel_registration import ChannelRegistration
+from .channel_registration import SituImageChannelRegistration, ChannelRegistration, AcrossRoundChannelRegistration
 from .round_registration import RoundRegistration, AllChannelRoundRegistration
 from .tile_registration import CombinedRegistration
 from .peak_finder import PeakFinder, PeakFinderDifferenceOfGaussian

situr/registration/channel_registration.py

@@ -1,10 +1,13 @@
+import numpy as np
+from situr.image import situ_image
+
+from situr.image.situ_tile import Tile
 from situr.registration.peak_finder import PeakFinder, PeakFinderDifferenceOfGaussian
 from situr.image.situ_image import SituImage
 from situr.registration import Registration, RegistrationFunction, FilterregRegistrationFunction
 
 
-class ChannelRegistration(Registration):
-
+class SituImageChannelRegistration(Registration):
     def do_channel_registration(self, situ_img: SituImage, reference_channel: int = 0):
         # For each channel (except nucleus) compute transform compared to reference_channel
         # Add Channel transformation to Channel
@@ -16,4 +19,38 @@ class ChannelRegistration(Registration):
                     situ_img, channel)
                 transformation = self.registration_function.do_registration(
                     current_channel_peaks, reference_peaks)
-                situ_img.set_channel_transformation(channel, transformation)
+                situ_img.set_channel_transformation(
+                    channel, transformation)
+
+
+class ChannelRegistration(Registration):
+    def do_channel_registration(self, tile: Tile, reference_channel: int = 0):
+        registration = SituImageChannelRegistration()
+        # For each channel (except nucleus) compute transform compared to reference_channel
+        # Add Channel transformation to Channel
+        for round in range(tile.get_round_count()):
+            situ_img = tile.get_round(round)
+            registration.do_channel_registration(situ_img, reference_channel)
+
+
+class AcrossRoundChannelRegistration(ChannelRegistration):
+    def do_channel_registration(self, tile: Tile, reference_channel: int = 0):
+        reference_peaks = []
+        for round in range(tile.get_round_count()):
+            reference_peaks.append(self.peak_finder.get_channel_peaks(
+                tile.get_round(round), reference_channel))
+        reference_peaks = np.concatenate(reference_peaks, axis=0)
+        for channel in range(tile.get_channel_count()):
+            if channel != tile.get_round(0).nucleaus_channel and channel != reference_channel:
+                current_channel_peaks = []
+                for round in range(tile.get_round_count()):
+                    current_channel_peaks.append(
+                        self.peak_finder.get_channel_peaks(tile.get_round(round), channel))
+                current_channel_peaks = np.concatenate(
+                    current_channel_peaks, axis=0)
+
+                transformation = self.registration_function.do_registration(
+                    current_channel_peaks, reference_peaks)
+                for round in range(tile.get_round_count()):
+                    tile.get_round(round).set_channel_transformation(
+                        channel, transformation)

situr/registration/tile_registration.py

@@ -17,10 +17,7 @@ class CombinedRegistration:
         Args:
             tile (Tile): The tile that the registration and transformations are to be performed on.
         """
-        # Do channel registration
-        for round in range(tile.get_round_count()):
-            img = tile.get_round(round)
-            self.channel_registration.do_channel_registration(img)
+        self.channel_registration.do_channel_registration(tile)
 
         tile.apply_channel_transformations()