From d9ab10461205def1bc74f4c778d8b53eaa132e92 Mon Sep 17 00:00:00 2001
From: "Hannes F. Kuchelmeister" <hannes@kuchelmeister.org>
Date: Wed, 14 Jul 2021 11:59:35 +0200
Subject: [PATCH] add type hints to transformations

---
 .../transformation/channel_transformation.py  | 17 +++++++---
 situr/transformation/round_transformation.py  | 31 ++++++++++++++++---
 2 files changed, 39 insertions(+), 9 deletions(-)

diff --git a/situr/transformation/channel_transformation.py b/situr/transformation/channel_transformation.py
index 7c9b783..48e0e5d 100644
--- a/situr/transformation/channel_transformation.py
+++ b/situr/transformation/channel_transformation.py
@@ -1,4 +1,5 @@
 import abc
+from situr.image.situ_image import SituImage
 import numpy as np
 import scipy
 
@@ -9,18 +10,26 @@ class ChannelTransform(Transform):
     __metaclass__ = abc.ABCMeta
 
     @abc.abstractmethod
-    def apply_transformation(self, situ_img, channel):
+    def apply_transformation(self, situ_img: SituImage, channel: int):
         """Performs a transformation on one channel, all focus_levels are transformed the same way"""
         raise NotImplementedError(
             self.__class__.__name__ + '.apply_transformation')
 
 
 class IdentityChannelTransform(ChannelTransform):
-    def apply_transformation(self, situ_img, channel):
+    def apply_transformation(self, situ_img: SituImage, channel: int):
         pass
 
+
 class ScaleRotateTranslateChannelTransform(ChannelTransform):
-    def __init__(self, transform_matrix, scale=1, offset=np.array([0, 0])):
+    def __init__(self, transform_matrix: np.ndarray, scale: float = 1, offset: np.ndarray = np.array([0, 0])):
+        """Constructor for a Transformation that supports rotation, translation and scaling on a channel
+
+        Args:
+            transform_matrix (np.ndarray): A matrix of shape (2,2)
+            scale (float, optional): The scale factor. Defaults to 1.
+            offset (np.ndarray, optional): The offset of shape (2,). Defaults to np.array([0, 0]).
+        """
         # TODO: check
         #   * transform matrix is 2x2
         #   * offset is array (2,)
@@ -28,7 +37,7 @@ class ScaleRotateTranslateChannelTransform(ChannelTransform):
         self.offset = offset
         self.scale = scale
 
-    def apply_tranformation(self, situ_img, channel):
+    def apply_tranformation(self, situ_img: SituImage, channel: int):
         channel_img = situ_img.get_channel(channel)
         focus_levels = channel_img.shape[0]
 
diff --git a/situr/transformation/round_transformation.py b/situr/transformation/round_transformation.py
index 14f6852..ea13ace 100644
--- a/situr/transformation/round_transformation.py
+++ b/situr/transformation/round_transformation.py
@@ -1,4 +1,5 @@
 import abc
+from situr.image.situ_tile import Tile
 import scipy
 import numpy as np
 from situr.image import situ_image
@@ -9,19 +10,39 @@ class RoundTransform(Transform):
     __metaclass__ = abc.ABCMeta
 
     @abc.abstractmethod
-    def apply_transformation(self, situ_tile, round):
-        """Performs a transformation on one round, all channels and focus_levels are transformed the same way"""
+    def apply_transformation(self, situ_tile: Tile, round: int):
+        """Performs a transformation on one round, all channels and focus_levels are transformed the same way
+
+        Args:
+            situ_tile (Tile): The tile the transformation is applied to.
+            round (int): The round that the transformation is to be applied to.
+
+        Raises:
+            NotImplementedError: This method is abstract and therefore raises an error
+        """
         raise NotImplementedError(
             self.__class__.__name__ + '.apply_transformation')
 
 
 class IdentityRoundTransform(RoundTransform):
-    def apply_transformation(self, situ_tile, round):
+    def apply_transformation(self, situ_tile: Tile, round: Tile):
+        """Performs the identity transformation (meaning no transformation)
+        Args:
+            situ_tile (Tile): The tile the transformation is applied to.
+            round (Tile): The round that the transformation is to be applied to.
+        """
         pass
 
 
 class ScaleRotateTranslateRoundTransform(RoundTransform):
-    def __init__(self, transform_matrix, scale=1, offset=np.array([0, 0])):
+    def __init__(self, transform_matrix: np.ndarray, scale: int = 1, offset: np.array = np.array([0, 0])):
+        """Constructor for a Transformation that supports rotation, translation and scaling on a channel
+
+        Args:
+            transform_matrix (np.ndarray): A matrix of shape (2,2)
+            scale (int, optional): The scale factor. Defaults to 1.
+            offset (np.array, optional): The offset of shape (2,). Defaults to np.array([0, 0]).
+        """
         # TODO: check
         #   * transform matrix is 2x2
         #   * offset is array (2,)
@@ -29,7 +50,7 @@ class ScaleRotateTranslateRoundTransform(RoundTransform):
         self.offset = offset
         self.scale = scale
 
-    def apply_tranformation(self, situ_tile, round):
+    def apply_tranformation(self, situ_tile: Tile, round: int):
         situ_image = situ_tile.get_image_round(round)
 
         for channel in range(situ_image.get_channel_count()):