now the _remove_particles method is complete

added an average filter so that it is now equivalent to the matlab code it's based on.

src/imageengine.py

@@ -61,6 +61,13 @@ class IImageEngine(ABC):
         :rtype IImage:
         """
 
+    @abc.abstractmethod
+    def mean_filter(self, image, radius):
+        """Each pixel becomes an average of its neighbours within the given radius
+
+        :param IImage image:
+        :param int radius: in pixels
+        """
 
     @abc.abstractmethod
     def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):

src/imagej/ijimageengine.py

@@ -144,6 +144,10 @@ class IJImageEngine(IImageEngine):
         print('max_image', max_image)
         return IJImage(self, max_image)
 
+    def mean_filter(self, image, radius):
+        """Implement interface method."""
+        IJ.run(image.ij_image, "Mean...", "radius=%d" % radius)
+
     def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):
         """
         :param IJImage image:
@@ -154,8 +158,8 @@ class IJImageEngine(IImageEngine):
         # we use opencv version because imagej's slow version is way too slow for big values of structuring_element_radius
         perform_gray_morphology_with_ijopencv(image, operator, structuring_element_shape, structuring_element_radius)
 
-
     def replace_border(self, image, band_width):
+        """Implement interface method."""
         raise NotImplementedError()
         return image
 

src/preprocessing.py

@@ -20,6 +20,9 @@ class WhiteEstimator(object):
         IImageEngine.get_instance().perform_gray_morphology(white_estimate, operator='open', structuring_element_shape='square', structuring_element_radius=(self.open_size + 1) / 2)
         IImageEngine.get_instance().perform_gray_morphology(white_estimate, operator='close', structuring_element_shape='square', structuring_element_radius=(self.close_size + 1) / 2)
 
+        IImageEngine.get_instance().mean_filter(white_estimate, radius=(self.average_size + 1) / 2)
+
+
     def estimate_white(self, sequences, channel_ids, dark=None):
         """Estimation of the white fluorescence image shape of synchrotron light from experimental images of Telemos microscope.