finished abstracting image processing engine

all imagej related code has now been moved to ijimageengine.py

src/imageengine.py

@@ -39,7 +39,10 @@ class IImageEngine(ABC):
 
     @staticmethod
     def get_instance():
-        """Static access method."""
+        """Static access method.
+        :rtype IImageEngine:
+        """
+
         assert IImageEngine.__instance is not None
         return IImageEngine.__instance
 
@@ -50,7 +53,6 @@ class IImageEngine(ABC):
         :param str out_file_path: eg './white_estimate.tiff'
         """
 
-
     @abc.abstractmethod
     def compute_max(self, images_file_path):
         """Compute for each pixel position the maximum at this position in all input images.
@@ -59,3 +61,36 @@ class IImageEngine(ABC):
         :rtype IImage:
         """
 
+
+    @abc.abstractmethod
+    def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):
+        """
+        :param IImage image:
+        :param str operator: eg 'open'
+        :param str structuring_element_shape: eg 'square'
+        :param int structuring_element_radius:
+        """
+
+
+    @abc.abstractmethod
+    def replace_border(self, image, band_width):
+        """Overwrites the outer band of the image by duplicating the value of the pixels that touch this outer band
+
+        :param IImage image:
+        :param int band_width: width of the outer band, in pixels
+        :rtype IImage:
+
+        adaptation for the following code from matlab telemosToolbx's estimatedwhiteFluoImageTelemos function
+            outer = white_estimate;
+            white_estimate = white_estimate(4:(end-3),4:(end-3));
+            outer(1:3,4:(end-3))=repmat(white_estimate(1,:),3,1);  # top
+            outer((end-2):end,4:(end-3))=repmat(white_estimate(end,:),3,1); # bottom
+            outer(:,1:3)=repmat(outer(:,4),1,3); # left
+            outer(:,(end-2):end)=repmat(outer(:,end-3),1,3); # right
+            white_estimate = outer;
+            clear outer;
+        """
+        raise NotImplementedError()
+        return image
+
+

src/imagej/ijimageengine.py

@@ -22,6 +22,23 @@ class IJImage(IImage):
         raise NotImplementedError
 
 
+def imagej_run_image_command(image, command, options):
+    """performs the given imagej command on the given image
+
+    :param ImagePlus image:
+    :param str command: imagej command (eg "Gray Morphology")
+    :param str options: imagej options (eg "radius=1 type=square operator=open")
+
+    wrapper around IJ.run (https://imagej.nih.gov/ij/developer/api/ij/IJ.html#run-ij.ImagePlus-java.lang.String-java.lang.String-) which raises an exception on error
+    """
+    IJ.run(image, command, options)
+    error_message = IJ.getErrorMessage()
+    if error_message is not None:
+        raise Exception('The command "%s" with options "%s" failed because of the following error : %s' % (command, options, error_message))
+
+
+
+
 class IJImageEngine(IImageEngine):
 
     def missing(self):
@@ -34,7 +51,7 @@ class IJImageEngine(IImageEngine):
         """Computes for each pixel position the maximum at this position in all input images.
 
         :param list(str) images_file_path:
-        :rtype IJmage:
+        :rtype IJImage:
         """
         assert len(images_file_path) > 1
         max_image = IJ.openImage(images_file_path[0])
@@ -46,4 +63,35 @@ class IJImageEngine(IImageEngine):
             ic = ImageCalculator()
             ic.run("max", max_image, other_image)
         print('max_image', max_image)
-        return max_image
+        return IJImage(self, max_image)
+
+    def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):
+        """
+        :param IJImage image:
+        :param str operator: eg 'open'
+        :param str structuring_element_shape: eg 'square'
+        :param int structuring_element_radius:
+        """
+        assert operator not in ['fast open', 'fast erode'], "as of 13/09/2019, fast operators such as 'fast erode' seem broken in fiji (the resulting image is not at all similar to their slow equivalent)"
+        
+        processor = image.ij_image.getProcessor()
+        convert_to_byte = False
+        if processor.getBitDepth() != 8:
+            convert_to_byte = True
+            min_value = processor.getMin()
+            max_value = processor.getMax()
+            print("warning: downgrading image to byte as imagej's Gray Morphology processing doesn't handle 16bit images (range=[%d, %d])" % (min_value, max_value))
+            do_scaling = True
+            image.ij_image.setProcessor(processor.convertToByte(do_scaling))
+        print("before gray morphology")
+        assert structuring_element_radius < 11, "the radius of the structuring element is too big (%d); using it with Fiji's 'Gray Morphology' tool would result in very long computations." % structuring_element_radius
+        imagej_run_image_command(image.ij_image, "Gray Morphology", "radius=%d type=%s operator=%s" % (structuring_element_radius, structuring_element_shape, operator))
+        print("after gray morphology")
+
+
+    def replace_border(self, image, band_width):
+        raise NotImplementedError()
+        return image
+
+
+

src/preprocessing.py

@@ -1,74 +1,9 @@
 """preprocessing of synchrotron images based on telemosToolbox."""
 
-from ij import IJ
-from ij.plugin import ImageCalculator
 from catalog import ImageCatalog, Sequence
 from imageengine import IImageEngine
 from imagej.ijimageengine import IJImageEngine, IJImage
 
-def imagej_run_image_command(image, command, options):
-    """performs the given imagej command on the given image
-
-    :param ImagePlus image:
-    :param str command: imagej command (eg "Gray Morphology")
-    :param str options: imagej options (eg "radius=1 type=square operator=open")
-
-    wrapper around IJ.run (https://imagej.nih.gov/ij/developer/api/ij/IJ.html#run-ij.ImagePlus-java.lang.String-java.lang.String-) which raises an exception on error
-    """
-    IJ.run(image, command, options)
-    error_message = IJ.getErrorMessage()
-    if error_message is not None:
-        raise Exception('The command "%s" with options "%s" failed because of the following error : %s' % (command, options, error_message))
-
-
-def compute_max(images_file_path):
-    image_engine = IJImageEngine()
-    return image_engine.compute_max(images_file_path)
-
-def replace_border(image, band_width):
-    """Overwrites the outer band of the image by duplicating the value of the pixels that touch this outer band
-
-    :param ImagePlus image:
-    :param int band_width: width of the outer band, in pixels
-    :rtype ImagePlus:
-
-    adaptation for the following code from matlab telemosToolbx's estimatedwhiteFluoImageTelemos function
-        outer = white_estimate;
-        white_estimate = white_estimate(4:(end-3),4:(end-3));
-        outer(1:3,4:(end-3))=repmat(white_estimate(1,:),3,1);  # top
-        outer((end-2):end,4:(end-3))=repmat(white_estimate(end,:),3,1); # bottom
-        outer(:,1:3)=repmat(outer(:,4),1,3); # left
-        outer(:,(end-2):end)=repmat(outer(:,end-3),1,3); # right
-        white_estimate = outer;
-        clear outer;
-    """
-    raise NotImplementedError()
-    return image
-
-
-def perform_gray_morphology(image, operator, structuring_element_shape, structuring_element_radius):
-    """
-    :param ImagePlus image:
-    :param str operator: eg 'open'
-    :param str structuring_element_shape: eg 'square'
-    :param int structuring_element_radius:
-    """
-    assert operator not in ['fast open', 'fast erode'], "as of 13/09/2019, fast operators such as 'fast erode' seem broken in fiji (the resulting image is not at all similar to their slow equivalent)"
-    
-    processor = image.getProcessor()
-    convert_to_byte = False
-    if processor.getBitDepth() != 8:
-        convert_to_byte = True
-        min_value = processor.getMin()
-        max_value = processor.getMax()
-        print("warning: downgrading image to byte as imagej's Gray Morphology processing doesn't handle 16bit images (range=[%d, %d])" % (min_value, max_value))
-        do_scaling = True
-        image.setProcessor(processor.convertToByte(do_scaling))
-    print("before gray morphology")
-    assert structuring_element_radius < 11, "the radius of the structuring element is too big (%d); using it with Fiji's 'Gray Morphology' tool would result in very long computations." % structuring_element_radius
-    imagej_run_image_command(image, "Gray Morphology", "radius=%d type=%s operator=%s" % (structuring_element_radius, structuring_element_shape, operator))
-    print("after gray morphology")
-
 
 class WhiteEstimator(object):
 
@@ -82,8 +17,8 @@ class WhiteEstimator(object):
         self.average_size = average_size
 
     def _remove_particles(self, white_estimate):
-        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='open', structuring_element_shape='square', structuring_element_radius=(self.open_size + 1) / 2)
-        perform_gray_morphology(white_estimate, operator='close', structuring_element_shape='square', structuring_element_radius=(self.close_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)
 
     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.
@@ -190,11 +125,11 @@ class WhiteEstimator(object):
                     for z_index in range(sequence.num_slices):
                         images_file_path.append(sequence.get_image_file_path(channel_index, frame_index, z_index))
 
-        white_estimate = compute_max(images_file_path)
+        white_estimate = IImageEngine.get_instance().compute_max(images_file_path)
         
         # modify spurious pixels on the side of the images
         try:
-            replace_border(white_estimate, 3)
+            IImageEngine.get_instance().replace_border(white_estimate, 3)
         except NotImplementedError as error:
             print('warning: replace_outer_frame is not implemented yet')
 
@@ -333,7 +268,7 @@ def test_preprocessing(raw_images_root_path):
     white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
     # find_white_reference_image(white_estimate, sequence.get_white())
     print(white_estimate)
-    IImageEngine.get_instance().save_as_tiff( IJImage( IImageEngine.get_instance(), white_estimate ), './white_estimate.tiff' )
+    IImageEngine.get_instance().save_as_tiff( white_estimate, './white_estimate.tiff' )
     print('end')
 
 if __name__ == '__main__':