36 lines
No EOL
1.3 KiB
Python
36 lines
No EOL
1.3 KiB
Python
"""
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SUM projection of tiled images
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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 = "projection"
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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+"/projection"
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logger1.info('Start Projecting Image at: ' + work_dir)
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image_type = it_wrapper.default_image_type()
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num_tiles_y = 3
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num_tiles_x = 3
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for jdx in range(num_tiles_y):
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for idx in range(num_tiles_x):
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label = str(idx) + "_" + str(jdx) +"_"+ str(idx+ num_tiles_x*jdx)
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input_path = work_dir + "/convert/itk_tile_" + label + ".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 SUM projection')
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project = it_wrapper.sum_projection(correct, image_type)
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output_image_type = it_wrapper.image_type_2d()
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logger1.info('Writing TIFF Stack')
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it_wrapper.write_image(output_path+"/sum_tile_" + label + ".tiff", output_image_type, project) |