add channel transformations into situ_image class

situr/image/situ_image.py

@@ -3,6 +3,8 @@ from PIL import Image, ImageDraw
 from skimage import img_as_float
 from skimage.feature import blob_dog
 
+from situr.transformation.channel_transformation import IdentityChannelTransform
+
 
 def extend_dim(array):
     ones = np.ones((array.shape[0], 1))
@@ -33,12 +35,23 @@ class SituImage:
         self.files = file_list
         self.data = None
         self.nucleaus_channel = nucleaus_channel
+        self.channel_transformations = [
+            IdentityChannelTransform() for file in file_list
+        ]
 
     def get_data(self):
         if self.data is None:
             self._load_image()
+            # TODO: apply transformations
         return self.data
 
+    def apply_transformations():
+        # TODO: implement
+        pass
+
+    def set_channel_transformation(self, channel, transformation):
+        self.channel_transformations[channel] = transformation
+
     def get_channel_count(self):
         return self.get_data().shape[0]
 
@@ -110,6 +123,8 @@ class SituImage:
         Returns:
             np.array: The peaks found by this method as np.array of shape (n, 2)
         '''
+        # TODO: think of a better way to declare peak finding parameters (so they don't need to be passedaround as much)
+
         img = img_as_float(self.get_data()[channel, focus_level, :, :])
         peaks = blob_dog(img, min_sigma=min_sigma,
                          max_sigma=max_sigma, threshold=threshold)

situr/registration/channel_registration.py

@@ -1,9 +1,15 @@
 from situr.registration import Registration
+from situr.transformation import IdentityChannelTransform
 
 
 class ChannelRegistration(Registration):
     def do_channel_registration(self, situ_img, reference_channel=0):
         # For each channel (except nucleus) compute transform compared to reference_channel
         # Add Channel transformation to Channel
-        # TODO: implement
-        pass
+        reference_peaks = situ_img.get_channel_peaks(reference_channel)
+        for channel in range(situ_img.get_channel_count()):
+            if channel != situ_img.nucleaus_channel and channel != reference_channel:
+                current_channel_peaks = situ_img.get_channel_peaks(channel)
+                transformation = self.registration_function.do_registration(
+                    current_channel_peaks, reference_peaks)
+                situ_img.set_channel_transformation(channel, transformation)

situr/transformation/__init__.py

@@ -1 +1 @@
-from .channel_transformation import ChannelTransform, ScaleRotateTranslateChannelTransform
+from .channel_transformation import ChannelTransform, IdentityChannelTransform, ScaleRotateTranslateChannelTransform

situr/transformation/channel_transformation.py

@@ -13,6 +13,10 @@ class ChannelTransform:
             self.__class__.__name__ + '.apply_transformation')
 
 
+class IdentityChannelTransform(ChannelTransform):
+    def apply_transformation(self, situ_img, channel):
+        pass
+
 class ScaleRotateTranslateChannelTransform(ChannelTransform):
     def __init__(self, transform_matrix, scale=1, offset=np.array([0, 0])):
         # TODO: check