redo registration to be more generic

situr/registration/__init__.py

@@ -0,0 +1 @@
+from .registration import Registration, RegistrationFunction, FilterregRegistrationFunction

situr/registration/channel_registration.py

@@ -1,34 +1,9 @@
-import abc
+from situr.registration import Registration
-import open3d as o3
-from probreg import filterreg
-from situr.image import extend_dim
-
-from situr.transformation import ScaleRotateTranslateChannelTransform
 
 
-class ChannelRegistration:
+class ChannelRegistration(Registration):
-    __metaclass__ = abc.ABCMeta
+    def do_channel_registration(self, situ_img, reference_channel=0):
-
-    def do_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
-
-    @abc.abstractmethod
-    def register_single_channel(self, peaks_data, reference_peaks):
-        """Performs the channel registration on an image. Expects the peaks in each image as input."""
-        raise NotImplementedError(
-            self.__class__.__name__ + '.register_single_channel')
-
-
-class FilterregChannelRegistration(ChannelRegistration):
-    def register_single_channel(self, data_peaks, reference_peaks):
-        source = o3.geometry.PointCloud()
-        source.points = o3.utility.Vector3dVector(extend_dim(data_peaks))
-        target = o3.geometry.PointCloud()
-        target.points = o3.utility.Vector3dVector(extend_dim(reference_peaks))
-
-        registration_method = filterreg.registration_filterreg
-        tf_param, _, _ = filterreg.registration_filterreg(source, target)
-
-        return ScaleRotateTranslateChannelTransform(transform_matrix=tf_param.rot[0:2, 0:2], scale=tf_param.scale, offset=tf_param.t[0:2])

situr/registration/registration.py

@@ -0,0 +1,35 @@
+import abc
+import open3d as o3
+from probreg import filterreg
+
+from situr.image import extend_dim
+from situr.transformation import ScaleRotateTranslateChannelTransform
+
+
+class RegistrationFunction:
+    __metaclass__ = abc.ABCMeta
+
+    def __init__(self, transormation_type=ScaleRotateTranslateChannelTransform):
+        self.transormation_type = transormation_type
+
+    @abc.abstractmethod
+    def do_registration(self, data_peaks, reference_peaks):
+        raise NotImplementedError(self.__class__.__name__ + '.do_registration')
+
+
+class FilterregRegistrationFunction(RegistrationFunction):
+    def do_registration(self, data_peaks, reference_peaks):
+        source = o3.geometry.PointCloud()
+        source.points = o3.utility.Vector3dVector(extend_dim(data_peaks))
+        target = o3.geometry.PointCloud()
+        target.points = o3.utility.Vector3dVector(extend_dim(reference_peaks))
+
+        registration_method = filterreg.registration_filterreg
+        tf_param, _, _ = filterreg.registration_filterreg(source, target)
+
+        return self.transormation_type(transform_matrix=tf_param.rot[0:2, 0:2], scale=tf_param.scale, offset=tf_param.t[0:2])
+
+
+class Registration:
+    def __init__(self, registration_function):
+        self.registration_function = registration_function

situr/registration/round_registration.py

@@ -0,0 +1,6 @@
+class RoundRegistration:
+    def do_round_registration(self, situ_tile, reference_channel=0):
+        # For each channel (except nucleus) compute transform compared to reference_channel
+        # Add Channel transformation to Channel
+        # TODO: implement
+        pass