75 lines
3 KiB
Python
75 lines
3 KiB
Python
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"""
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Downsample the tiffs for easier postprocessing
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"""
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import os
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import logging
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import math
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from argparse import ArgumentParser
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from functools import partial
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import multiprocessing as mp
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import skimage.external.tifffile
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import skimage.transform
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from skimage import exposure
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import utility
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def do_downsample(input_file, working_directory, downsample_ratios):
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im = skimage.external.tifffile.imread(input_file)
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downsampled = skimage.transform.downscale_local_mean(im, downsample_ratios)
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out_path = working_directory + "/" + os.path.splitext(os.path.basename(input_file))[0] + "_downsampled.tiff"
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scaled_image = exposure.rescale_intensity(downsampled, out_range=(0.0, 1.0))
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skimage.external.tifffile.imsave(out_path, skimage.img_as_ubyte(scaled_image))
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def downsample_tiffs(input_folder, downsample_ratios, channel = 0, series = 0):
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file_names = []
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dir_name = os.path.dirname(input_folder)
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for eachFile in os.listdir(input_folder):
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if eachFile.endswith(".tiff"):
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file_names.append(dir_name + "/" + eachFile)
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# Make a partial function for multiple arg mapping
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working_directory = os.getcwd() + "/Downsampled_X"+str(downsample_ratios[2]) + "_Y"+str(downsample_ratios[1])
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working_directory += "_Z"+str(downsample_ratios[0]) + "/"
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if not os.path.exists(working_directory):
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os.makedirs(working_directory)
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partial_extract_pixel_values_only = partial(do_downsample,
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working_directory=working_directory,
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downsample_ratios=downsample_ratios)
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# Limit to max 6 cpus
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num_available_cpus = mp.cpu_count()
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if num_available_cpus > 6:
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num_available_cpus = 6
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# Distribute across processes - Be conservative with available CPUs
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run_cpus = int(math.floor(num_available_cpus/2))
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if run_cpus == 0:
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run_cpus = 1
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#pool = mp.Pool(processes = run_cpus)
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pool = mp.Pool(processes = 3)
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pool.map(partial_extract_pixel_values_only, file_names)
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if __name__ == "__main__":
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# Do setup
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tool_name = "zeiss_to_tiff"
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utility.do_setup(tool_name)
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logger1 = logging.getLogger('downsample_tiffs.'+tool_name)
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# Suppress XML Parse warnings
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pyxb_logger = logging.getLogger('pyxb')
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pyxb_logger.setLevel(logging.CRITICAL)
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parser = ArgumentParser()
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parser.add_argument("-i", "--input_folder", type=str, help='Folder with tiffs to be downsampled.')
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parser.add_argument("-x", "--x_reduction", type=int, help='Factor reduction in x.', default=1)
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parser.add_argument("-y", "--y_reduction", type=int, help='Factor reduction in y.', default=1)
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parser.add_argument("-z", "--z_reduction", type=int, help='Factor reduction in z.', default=1)
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args = parser.parse_args()
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logger1.info('Start Downsampling Images at: ' + args.input_folder)
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downsample_ratios = (args.z_reduction, args.y_reduction, args.x_reduction)
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downsample_tiffs(args.input_folder, downsample_ratios)
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logger1.info('Completed Downsampling')
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