make more classes abstract

situr/image/situ_image.py

@@ -1,3 +1,4 @@
+import abc
 import numpy as np
 from PIL import Image, ImageDraw
 from skimage import img_as_float
@@ -17,7 +18,17 @@ def remove_dim(array: np.ndarray):
     return array[:, :-1]
 
 
-class PeakFinderDifferenceOfGaussian:
+class PeakFinder:
+    __metaclass__ = abc.ABCMeta
+
+    @abc.abstractmethod
+    def find_peaks(self, img_array: np.ndarray) -> np.ndarray:
+        """Finds the peaks in the input image"""
+        raise NotImplementedError(
+            self.__class__.__name__ + '.find_peaks')
+
+
+class PeakFinderDifferenceOfGaussian(PeakFinder):
     def __init__(self, min_sigma=0.75, max_sigma=3, threshold=0.1):
         self.min_sigma = min_sigma
         self.max_sigma = max_sigma
@@ -44,22 +55,21 @@ class SituImage:
         A list of lists. Each inner list corresponds to one focus level. Its contents correspons to a file for each channel.
     nucleaus_channel : int
         tells which channel is used for showing where the cell nucleuses are.
+    peak_finder : 
     """
 
-    def __init__(self, file_list: List[List[str]], nucleaus_channel: int = 4):
+    def __init__(self, file_list: List[List[str]], nucleaus_channel: int = 4, peak_finder: PeakFinder = PeakFinderDifferenceOfGaussian()):
         self.files = file_list
         self.data = None
         self.nucleaus_channel = nucleaus_channel
         self.channel_transformations = [
             IdentityChannelTransform() for file in file_list
         ]
-        self.peak_finder = PeakFinderDifferenceOfGaussian()
-        # TODO: make peak finder a constructor argument
+        self.peak_finder = peak_finder
 
     def get_data(self) -> np.ndarray:
         if self.data is None:
             self._load_image()
-            # TODO: apply transformations
         return self.data
 
     def apply_transformations(self):

situr/registration/registration.py

@@ -33,5 +33,6 @@ class FilterregRegistrationFunction(RegistrationFunction):
 
 
 class Registration:
+    __metaclass__ = abc.ABCMeta
     def __init__(self, registration_function: RegistrationFunction):
         self.registration_function = registration_function

situr/transformation/transformation.py

@@ -1,2 +1,4 @@
+import abc
+
 class Transform:
-    pass
+    __metaclass__ = abc.ABCMeta