From 29c95557553dd9bda01c7960557a10caed8a61ae Mon Sep 17 00:00:00 2001
From: "Hannes F. Kuchelmeister" <hannes@kuchelmeister.org>
Date: Mon, 12 Jul 2021 18:39:42 +0200
Subject: [PATCH] redo registration to be more generic

---
 situr/registration/__init__.py             |  1 +
 situr/registration/channel_registration.py | 33 +++-----------------
 situr/registration/registration.py         | 35 ++++++++++++++++++++++
 situr/registration/round_registration.py   |  6 ++++
 4 files changed, 46 insertions(+), 29 deletions(-)
 create mode 100644 situr/registration/registration.py
 create mode 100644 situr/registration/round_registration.py

diff --git a/situr/registration/__init__.py b/situr/registration/__init__.py
index e69de29..d8912c1 100644
--- a/situr/registration/__init__.py
+++ b/situr/registration/__init__.py
@@ -0,0 +1 @@
+from .registration import Registration, RegistrationFunction, FilterregRegistrationFunction
diff --git a/situr/registration/channel_registration.py b/situr/registration/channel_registration.py
index 576c339..be6050d 100644
--- a/situr/registration/channel_registration.py
+++ b/situr/registration/channel_registration.py
@@ -1,34 +1,9 @@
-import abc
-import open3d as o3
-from probreg import filterreg
-from situr.image import extend_dim
-
-from situr.transformation import ScaleRotateTranslateChannelTransform
+from situr.registration import Registration
 
 
-class ChannelRegistration:
-    __metaclass__ = abc.ABCMeta
-
-    def do_registration(self, situ_img, reference_channel=0):
+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
-
-    @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])
diff --git a/situr/registration/registration.py b/situr/registration/registration.py
new file mode 100644
index 0000000..19cc00c
--- /dev/null
+++ b/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
diff --git a/situr/registration/round_registration.py b/situr/registration/round_registration.py
new file mode 100644
index 0000000..3b0cb8f
--- /dev/null
+++ b/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