Fix 2D collage not running because of 3D z range clamping.

docker/dev_environment/collageradiomics_examples/Dockerfile

@@ -2,7 +2,7 @@ FROM nathanhillyer/ml-base
 ENV LANG C.UTF-8
 RUN PIP_INSTALL="python -m pip install --upgrade --no-cache-dir --retries 10 --timeout 60" && \
     $PIP_INSTALL \
-        collageradiomics==0.2.5 \
+        collageradiomics==0.2.6 \
         Pillow \
         && \
     ldconfig && \

docker/dev_environment/collageradiomics_pip/Dockerfile

@@ -2,7 +2,7 @@ FROM nathanhillyer/ubuntu-base
 ENV LANG C.UTF-8
 RUN PIP_INSTALL="python -m pip install --upgrade --no-cache-dir --retries 10 --timeout 60" && \
     $PIP_INSTALL \
-        collageradiomics==0.2.5 \
+        collageradiomics==0.2.6 \
         && \
     ldconfig && \
     apt-get clean && \

module/VERSION

@@ -1 +1 @@
-0.2.5
+0.2.6

module/collageradiomics.py

@@ -368,7 +368,7 @@ def __init__(self,
             # in the case of a single 2D slice, give it a third dimension of unit length
             self._img_array = self._img_array.reshape(self._img_array.shape + (1,))
 
-        min_3D_slices = 3;
+        min_3D_slices = 3
         if self._img_array.shape[0] <  self._haralick_window_size or self._img_array.shape[1] < self._haralick_window_size or (self._is_3D and self._img_array.shape[2] < min_3D_slices):
             raise Exception(
                 f'Image is too small for a window size of {self._haralick_window_size} pixels.')
@@ -487,8 +487,8 @@ def calculate_haralick_textures(self, dominant_angles):
         if self.verbose_logging:
             print('starting haralick calculations...')
 
-        # We extended the dominant angles by one slice in each direction, so now we need to trim those off.
-        for z in range(1, depth - 1):
+        # In 3D, we extended the dominant angles by one slice in each direction, so now we need to trim those off if we are running in 3D.
+        for z in range(1, depth - 1) if self.is_3D else range(depth):
             for y,x in product(range(height), range(width)):
                 if self.mask_array[y,x,z]:
                     haralick_image[y,x,z,:] = self.calculate_haralick_feature_values(dominant_angles_binned[:,:,z], x, y)