98 lines
3.6 KiB
Python
98 lines
3.6 KiB
Python
"""Image processing using imagej.
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"""
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from imageengine import IImage, IImageEngine
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from ij import IJ
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from ij.plugin import ImageCalculator
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class IJImage(IImage):
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def __init__(self, image_engine, ij_image):
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"""
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:param IJImageEngine image_engine:
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:param ImagePlus ij_image:
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"""
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self.image_engine = image_engine
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self.ij_image = ij_image
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def width(self):
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raise NotImplementedError
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def height(self):
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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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pass
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def save_as_tiff(self, image, out_file_path):
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IJ.saveAsTiff(image.ij_image, out_file_path)
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def compute_max(self, images_file_path):
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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 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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print('max_image', max_image)
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for image_file_path in images_file_path[2:-1]:
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other_image = IJ.openImage(image_file_path)
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print('other_image', other_image)
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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 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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