30 lines
999 B
Python
30 lines
999 B
Python
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"""
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Median filter on chosen image
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"""
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import logging
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from code.image.tools import it_wrapper
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import code.image.settings
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if __name__ == "__main__":
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# Do setup
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tool_name = "median"
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work_dir, image_data = code.image.settings.do_setup(tool_name)
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logger1 = logging.getLogger('processing.'+tool_name)
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output_path = work_dir+"/median"
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logger1.info('Start Filtering Image at: ' + work_dir)
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image_type = it_wrapper.default_image_type()
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input_path = work_dir + "/convert/itk_tile_0_2_6.tiff"
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logger1.info("Reading the image: " +input_path + " into ITK")
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reader = it_wrapper.read_image(input_path, image_type)
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correct = it_wrapper.correct_spacing(reader, image_type, image_data["VoxelSizeZ"])
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logger1.info('Doing Median Filter')
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median_filter = it_wrapper.median_filter(correct, image_type, 1)
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logger1.info('Writing TIFF Stack')
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it_wrapper.write_image(output_path+"/itk_tile_0_2_6.tiff", image_type, median_filter)
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