From 193dc059a5f2dcc2123929357f040ec026a77a93 Mon Sep 17 00:00:00 2001
From: "Hannes F. Kuchelmeister" <hannes@kuchelmeister.org>
Date: Wed, 14 Jul 2021 11:03:16 +0200
Subject: [PATCH] add tile registration, however no all methods are implemented
 yet

---
 situr/image/situ_tile.py                | 10 ++++++++-
 situr/registration/__init__.py          |  3 +++
 situr/registration/tile_registration.py | 29 +++++++++++++++++++++++++
 3 files changed, 41 insertions(+), 1 deletion(-)
 create mode 100644 situr/registration/tile_registration.py

diff --git a/situr/image/situ_tile.py b/situr/image/situ_tile.py
index 131ef6d..9d8e215 100644
--- a/situr/image/situ_tile.py
+++ b/situr/image/situ_tile.py
@@ -21,10 +21,18 @@ class Tile:
                 SituImage(situ_image_list, nucleaus_channel=nucleaus_channel))
             self.round_transformations.append(IdentityRoundTransform())
 
-    def apply_transformations():
+    def apply_transformations(self):
         # TODO: implement (first apply channel transformations then round transformations)
         pass
 
+    def apply_channel_transformations(self):
+        # TODO: implement
+        pass
+
+    def apply_round_transformations(self):
+        # TODO: implement
+        pass
+
     def get_image_round(self, round):
         return self.images[round]
 
diff --git a/situr/registration/__init__.py b/situr/registration/__init__.py
index d8912c1..1d11602 100644
--- a/situr/registration/__init__.py
+++ b/situr/registration/__init__.py
@@ -1 +1,4 @@
 from .registration import Registration, RegistrationFunction, FilterregRegistrationFunction
+from .channel_registration import ChannelRegistration
+from .round_registration import RoundRegistration
+from .tile_registration import TileRegistration
diff --git a/situr/registration/tile_registration.py b/situr/registration/tile_registration.py
new file mode 100644
index 0000000..5d54ed0
--- /dev/null
+++ b/situr/registration/tile_registration.py
@@ -0,0 +1,29 @@
+from situr.image.situ_tile import Tile
+from situr.registration import RoundRegistration, ChannelRegistration, round_registration
+
+
+class CombinedRegistration:
+    def __init__(self, round_registration: RoundRegistration = RoundRegistration(), channel_registration: ChannelRegistration = ChannelRegistration(), reference_channel=0) -> None:
+        self.round_registration = round_registration
+        self.channel_registration = channel_registration
+
+    def do_registration_and_transform(self, tile: Tile):
+        """ This function applies the registration in the following order:
+            1. Register the channels for each round of each tile.
+            2. Apply transformations
+            3. Register the rounds
+            4. Apply transformation
+
+        Args:
+            tile (Tile): The tile that the registration and transformations are to be performed on.
+        """
+        # Do channel registration
+        for round in range(tile.get_roundcount()):
+            img = tile.get_image_round(round)
+            self.channel_registration
+
+        tile.apply_channel_transformations()
+
+        round_registration.do_round_registration(tile)
+
+        tile.apply_round_transformations()