finished abstracting image processing engine
all imagej related code has now been moved to ijimageengine.py
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@ -39,7 +39,10 @@ class IImageEngine(ABC):
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@staticmethod
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def get_instance():
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"""Static access method."""
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"""Static access method.
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:rtype IImageEngine:
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"""
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assert IImageEngine.__instance is not None
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return IImageEngine.__instance
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@ -50,7 +53,6 @@ class IImageEngine(ABC):
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:param str out_file_path: eg './white_estimate.tiff'
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"""
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@abc.abstractmethod
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def compute_max(self, images_file_path):
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"""Compute for each pixel position the maximum at this position in all input images.
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@ -59,3 +61,36 @@ class IImageEngine(ABC):
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:rtype IImage:
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"""
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@abc.abstractmethod
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def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):
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"""
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:param IImage image:
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:param str operator: eg 'open'
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:param str structuring_element_shape: eg 'square'
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:param int structuring_element_radius:
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"""
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@abc.abstractmethod
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def replace_border(self, image, band_width):
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"""Overwrites the outer band of the image by duplicating the value of the pixels that touch this outer band
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:param IImage image:
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:param int band_width: width of the outer band, in pixels
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:rtype IImage:
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adaptation for the following code from matlab telemosToolbx's estimatedwhiteFluoImageTelemos function
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outer = white_estimate;
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white_estimate = white_estimate(4:(end-3),4:(end-3));
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outer(1:3,4:(end-3))=repmat(white_estimate(1,:),3,1); # top
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outer((end-2):end,4:(end-3))=repmat(white_estimate(end,:),3,1); # bottom
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outer(:,1:3)=repmat(outer(:,4),1,3); # left
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outer(:,(end-2):end)=repmat(outer(:,end-3),1,3); # right
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white_estimate = outer;
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clear outer;
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"""
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raise NotImplementedError()
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return image
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@ -22,6 +22,23 @@ class IJImage(IImage):
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raise NotImplementedError
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def imagej_run_image_command(image, command, options):
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"""performs the given imagej command on the given image
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:param ImagePlus image:
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:param str command: imagej command (eg "Gray Morphology")
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:param str options: imagej options (eg "radius=1 type=square operator=open")
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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
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"""
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IJ.run(image, command, options)
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error_message = IJ.getErrorMessage()
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if error_message is not None:
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raise Exception('The command "%s" with options "%s" failed because of the following error : %s' % (command, options, error_message))
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class IJImageEngine(IImageEngine):
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def missing(self):
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@ -34,7 +51,7 @@ class IJImageEngine(IImageEngine):
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"""Computes for each pixel position the maximum at this position in all input images.
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:param list(str) images_file_path:
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:rtype IJmage:
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:rtype IJImage:
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"""
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assert len(images_file_path) > 1
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max_image = IJ.openImage(images_file_path[0])
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@ -46,4 +63,35 @@ class IJImageEngine(IImageEngine):
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ic = ImageCalculator()
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ic.run("max", max_image, other_image)
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print('max_image', max_image)
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return max_image
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return IJImage(self, max_image)
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def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):
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"""
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:param IJImage image:
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:param str operator: eg 'open'
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:param str structuring_element_shape: eg 'square'
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:param int structuring_element_radius:
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"""
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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)"
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processor = image.ij_image.getProcessor()
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convert_to_byte = False
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if processor.getBitDepth() != 8:
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convert_to_byte = True
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min_value = processor.getMin()
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max_value = processor.getMax()
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print("warning: downgrading image to byte as imagej's Gray Morphology processing doesn't handle 16bit images (range=[%d, %d])" % (min_value, max_value))
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do_scaling = True
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image.ij_image.setProcessor(processor.convertToByte(do_scaling))
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print("before gray morphology")
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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
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imagej_run_image_command(image.ij_image, "Gray Morphology", "radius=%d type=%s operator=%s" % (structuring_element_radius, structuring_element_shape, operator))
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print("after gray morphology")
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def replace_border(self, image, band_width):
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raise NotImplementedError()
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return image
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@ -1,74 +1,9 @@
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"""preprocessing of synchrotron images based on telemosToolbox."""
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from ij import IJ
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from ij.plugin import ImageCalculator
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from catalog import ImageCatalog, Sequence
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from imageengine import IImageEngine
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from imagej.ijimageengine import IJImageEngine, IJImage
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def imagej_run_image_command(image, command, options):
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"""performs the given imagej command on the given image
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:param ImagePlus image:
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:param str command: imagej command (eg "Gray Morphology")
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:param str options: imagej options (eg "radius=1 type=square operator=open")
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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
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"""
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IJ.run(image, command, options)
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error_message = IJ.getErrorMessage()
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if error_message is not None:
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raise Exception('The command "%s" with options "%s" failed because of the following error : %s' % (command, options, error_message))
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def compute_max(images_file_path):
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image_engine = IJImageEngine()
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return image_engine.compute_max(images_file_path)
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def replace_border(image, band_width):
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"""Overwrites the outer band of the image by duplicating the value of the pixels that touch this outer band
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:param ImagePlus image:
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:param int band_width: width of the outer band, in pixels
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:rtype ImagePlus:
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adaptation for the following code from matlab telemosToolbx's estimatedwhiteFluoImageTelemos function
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outer = white_estimate;
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white_estimate = white_estimate(4:(end-3),4:(end-3));
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outer(1:3,4:(end-3))=repmat(white_estimate(1,:),3,1); # top
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outer((end-2):end,4:(end-3))=repmat(white_estimate(end,:),3,1); # bottom
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outer(:,1:3)=repmat(outer(:,4),1,3); # left
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outer(:,(end-2):end)=repmat(outer(:,end-3),1,3); # right
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white_estimate = outer;
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clear outer;
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"""
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raise NotImplementedError()
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return image
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def perform_gray_morphology(image, operator, structuring_element_shape, structuring_element_radius):
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"""
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:param ImagePlus image:
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:param str operator: eg 'open'
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:param str structuring_element_shape: eg 'square'
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:param int structuring_element_radius:
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"""
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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)"
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processor = image.getProcessor()
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convert_to_byte = False
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if processor.getBitDepth() != 8:
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convert_to_byte = True
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min_value = processor.getMin()
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max_value = processor.getMax()
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print("warning: downgrading image to byte as imagej's Gray Morphology processing doesn't handle 16bit images (range=[%d, %d])" % (min_value, max_value))
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do_scaling = True
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image.setProcessor(processor.convertToByte(do_scaling))
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print("before gray morphology")
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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
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imagej_run_image_command(image, "Gray Morphology", "radius=%d type=%s operator=%s" % (structuring_element_radius, structuring_element_shape, operator))
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print("after gray morphology")
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class WhiteEstimator(object):
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@ -82,8 +17,8 @@ class WhiteEstimator(object):
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self.average_size = average_size
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def _remove_particles(self, white_estimate):
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perform_gray_morphology(white_estimate, operator='open', structuring_element_shape='square', structuring_element_radius=(self.open_size + 1) / 2)
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perform_gray_morphology(white_estimate, operator='close', structuring_element_shape='square', structuring_element_radius=(self.close_size + 1) / 2)
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IImageEngine.get_instance().perform_gray_morphology(white_estimate, operator='open', structuring_element_shape='square', structuring_element_radius=(self.open_size + 1) / 2)
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IImageEngine.get_instance().perform_gray_morphology(white_estimate, operator='close', structuring_element_shape='square', structuring_element_radius=(self.close_size + 1) / 2)
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def estimate_white(self, sequences, channel_ids, dark=None):
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"""Estimation of the white fluorescence image shape of synchrotron light from experimental images of Telemos microscope.
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@ -190,11 +125,11 @@ class WhiteEstimator(object):
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for z_index in range(sequence.num_slices):
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images_file_path.append(sequence.get_image_file_path(channel_index, frame_index, z_index))
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white_estimate = compute_max(images_file_path)
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white_estimate = IImageEngine.get_instance().compute_max(images_file_path)
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# modify spurious pixels on the side of the images
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try:
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replace_border(white_estimate, 3)
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IImageEngine.get_instance().replace_border(white_estimate, 3)
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except NotImplementedError as error:
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print('warning: replace_outer_frame is not implemented yet')
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@ -333,7 +268,7 @@ def test_preprocessing(raw_images_root_path):
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white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
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# find_white_reference_image(white_estimate, sequence.get_white())
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print(white_estimate)
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IImageEngine.get_instance().save_as_tiff( IJImage( IImageEngine.get_instance(), white_estimate ), './white_estimate.tiff' )
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IImageEngine.get_instance().save_as_tiff( white_estimate, './white_estimate.tiff' )
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print('end')
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if __name__ == '__main__':
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