97 lines
No EOL
3.8 KiB
Python
97 lines
No EOL
3.8 KiB
Python
"""
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Conversion of IMS/LSM/CZI files to OME and then Generic TIFFs
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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 utility
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import extract_zeiss_metadata
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import bftools_wrapper
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def extract_pixel_values_only(input_file, working_directory, channel=0, significant_bits=8):
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im = skimage.external.tifffile.imread(input_file)
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pixel_vals_only = im[0, :, 0, channel, :, :] # Strip excess data
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out_path = working_directory + "/" + os.path.splitext(os.path.basename(input_file))[0] + "_pixels_only.tiff"
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if significant_bits==8:
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skimage.external.tifffile.imsave(out_path, skimage.img_as_ubyte(pixel_vals_only))
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elif significant_bits==16:
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skimage.external.tifffile.imsave(out_path, skimage.img_as_uint(pixel_vals_only))
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else:
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# Let skiimage decide
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skimage.external.tifffile.imsave(out_path, pixel_vals_only)
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def do_conversion(input_file, output_file, channel = 0, series = 0):
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#
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# # Get the image metadata
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extract_zeiss_metadata.extract_metadata(input_file, os.getcwd() + "temp_metadata.xml")
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image_metadata = extract_zeiss_metadata.get_metadata_as_class(os.getcwd() + "temp_metadata.xml")
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#
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# # Choose the tile size
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tile_x = 1024
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tile_y = 1024
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# Black box JVM conversion via CLI. Be skeptical of outputs,
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# at least the Z-physical size is silently lost!!!
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bftools_wrapper.convert(input_file, output_file, tile_x, tile_y, channel, series)
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# Make versions with just XYZ pixel values for easier use in scikit-image/VTK etc.
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# DANGER, now all physical size is lost. Only trust physical sizes
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# in the standalone xml metadata file, obtained (and validated) using `extract_zeiss_metadata()`.
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# Collect the file names
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file_names = []
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for eachFile in os.listdir(output_file):
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if eachFile.endswith(".tiff"):
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file_names.append(output_file + "/" + eachFile)
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# Make a partial function for multiple arg mapping
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working_directory = output_file + "/Pixel_Values_Only/"
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if not os.path.exists(working_directory):
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os.makedirs(working_directory)
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significant_bits = int(image_metadata.Image[0].Pixels.SignificantBits)
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partial_extract_pixel_values_only = partial(extract_pixel_values_only,
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working_directory=working_directory,
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channel=channel,
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significant_bits=significant_bits)
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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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run_cpus = 1
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#pool = mp.Pool(processes = run_cpus)
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pool = mp.Pool(processes = 1)
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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('format_conversion.'+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_file", type=str, help='Input file in a ZEISS format.')
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parser.add_argument("-o", "--output_folder", type=str, help='Output Tiff Location.')
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args = parser.parse_args()
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logger1.info('Start Converting Image at: ' + args.input_file)
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do_conversion(args.input_file, args.output_folder, channel = 1, series = 0)
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logger1.info('Completed Processing') |