120 lines
No EOL
5.3 KiB
Python
120 lines
No EOL
5.3 KiB
Python
"""
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Convert to VTK. Use pvti files for final assembly.
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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 vtk
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import utility
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import extract_zeiss_metadata
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def do_conversion(file_attributes, working_directory):
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reader = vtk.vtkTIFFReader()
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reader.SetFileName(file_attributes["FileName"])
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reader.Update()
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image_data = reader.GetOutput()
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image_data.SetExtent(file_attributes["Extents"])
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image_data.SetSpacing(file_attributes["PhysicalSize"])
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out_path = working_directory + "/" + os.path.splitext(os.path.basename(file_attributes["FileName"]))[0] + ".vti"
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writer = vtk.vtkXMLImageDataWriter()
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writer.SetInputData(image_data)
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writer.SetFileName(out_path)
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writer.Write()
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def convert_to_vti(input_folder, metadata_file, tile_dimensions, downsample_dimensions):
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extract_zeiss_metadata.extract_metadata(metadata_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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num_x = int(math.floor(image_metadata.Image[0].Pixels.SizeX/tile_dimensions[0]))+1
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num_y = int(math.floor(image_metadata.Image[0].Pixels.SizeY/tile_dimensions[1]))+1
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size_x = int(math.floor(tile_dimensions[0]/downsample_dimensions[0]))+1
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size_y = int(math.floor(tile_dimensions[1]/downsample_dimensions[1]))+1
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size_z = int(math.floor(image_metadata.Image[0].Pixels.SizeZ/downsample_dimensions[2]))
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physical_x = float(image_metadata.Image[0].Pixels.PhysicalSizeX)*float(downsample_dimensions[0])
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physical_y = float(image_metadata.Image[0].Pixels.PhysicalSizeY)*float(downsample_dimensions[1])
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physical_z = float(image_metadata.Image[0].Pixels.PhysicalSizeZ)*float(downsample_dimensions[2])
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# Grab the file base name. Assume the input folder only has the tiff files we want to convert
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path_base_name = ""
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for eachFile in os.listdir(input_folder):
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if eachFile.endswith(".tiff"):
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loc_start_index = eachFile.find("_tile")
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if loc_start_index>-1:
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path_base_name = input_folder + "/" + eachFile[:loc_start_index]
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break
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file_attribute_collection = []
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for jdx in range(num_y):
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for idx in range(num_x):
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global_index = idx + jdx*num_x
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file_name = path_base_name + "_tile_X" + str(idx) + "_Y" + str(jdx) + "_ID_" + str(global_index)+"_pixels_only_downsampled.tiff"
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min_ext_x = idx*size_x
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min_ext_y = jdx*size_y
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max_ext_x = (idx+1)*size_x-1
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max_ext_y = (jdx+1)*size_y-1
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min_ext_z = 0
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max_ext_z = size_z-1
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if idx == num_x - 1:
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max_ext_x = int(math.floor(image_metadata.Image[0].Pixels.SizeX/downsample_dimensions[0]))+2
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if jdx == num_y - 1:
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max_ext_y = int(math.floor(image_metadata.Image[0].Pixels.SizeY/downsample_dimensions[1]))+2
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extents = [min_ext_x, max_ext_x, min_ext_y, max_ext_y, min_ext_z, max_ext_z]
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file_attributes = {}
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file_attributes["PhysicalSize"]= (physical_x, physical_y, physical_z)
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file_attributes["Extents"]= extents
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file_attributes["FileName"]= file_name
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file_attribute_collection.append(file_attributes)
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# Make a partial function for multiple arg mapping
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working_directory = os.getcwd() + "/VTK_Files/"
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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_conversion, working_directory=working_directory)
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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 = 1)
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pool.map(partial_extract_pixel_values_only, file_attribute_collection)
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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('tiff_to_vtk.'+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 converted.')
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parser.add_argument("-m", "--metadatafile", type=str, help='File with image metadata.')
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parser.add_argument("-tx", "--tile_x", type=int, help='X Tile size.')
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parser.add_argument("-ty", "--tile_y", type=int, help='Y Tile Size.')
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parser.add_argument("-dx", "--downsample_x", type=int, help='X Downsample Factor.', default=1)
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parser.add_argument("-dy", "--downsample_y", type=int, help='Y Downsample Factor.', default=1)
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parser.add_argument("-dz", "--downsample_z", type=int, help='Y Downsample Factor.', default=1)
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args = parser.parse_args()
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logger1.info('Start Converting Images to VTI at: ' + args.input_folder)
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convert_to_vti(args.input_folder, args.metadatafile, (args.tile_x, args.tile_y),
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(args.downsample_x, args.downsample_y, args.downsample_z))
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logger1.info('Completed Converting') |