103 lines
4.1 KiB
Python
103 lines
4.1 KiB
Python
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#!/usr/bin/env python
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"""
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Extract and Parse Metadata from IMS/LSM/CZI files.
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"""
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from argparse import ArgumentParser
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import os
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import subprocess
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import logging
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import utility
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import ome_schema
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def extract_metadata(input_path, output_path):
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"""
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Extract OME metadata from the input file and write it out as a nicely formatted xml using
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bftools. (http://www.openmicroscopy.org/site/support/bio-formats5.3/users/comlinetools/display.html)
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"""
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bf_tools_dir = os.getenv('BFTOOLS_DIR', os.getcwd()) + "/"
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command = bf_tools_dir +"showinf -omexml-only -nopix " + input_path + " | " + bf_tools_dir + "xmlindent > " + output_path
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p = subprocess.Popen(command, shell=True)
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p.wait()
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def get_metadata_as_class(input_xml_path):
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"""
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Return the OME metadata from the input XML file as a Python class. The class is automatically generated
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using pyxbgen (http://pyxb.sourceforge.net/pyxbgen_cli.html) and the current OME XML Schema
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(https://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd).
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If you need to use a newer schema you need to regenerate the file ome_schema.py by doing:
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pip install pyxb
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pyxbgen -m ome_schema -u https://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
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where the web address points to the new schema. You can then access the elements of the OME XML as
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instance attributes etc.
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"""
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xml = open(input_xml_path).read()
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image_metadata = ome_schema.CreateFromDocument(xml)
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return image_metadata
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def integer_color_to_rgb(color):
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"""
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Convert integer color to (r,g,b)
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"""
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return ((color >> 16) & 255, (color >> 8) & 255, color & 255)
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def print_metadata_overview(image_metadata):
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"""
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Print a reader-friendly metadata summary
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"""
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print "Number of Images: ", len(image_metadata.Image)
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print "Image '0' - Name: ", image_metadata.Image[0].Name
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print "Image '0' - Num Channels: ", image_metadata.Image[0].Pixels.SizeC
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print "Image '0' - Num Times: ", image_metadata.Image[0].Pixels.SizeT
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pixel_size_x = image_metadata.Image[0].Pixels.PhysicalSizeX
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pixel_size_y = image_metadata.Image[0].Pixels.PhysicalSizeY
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pixel_size_z = image_metadata.Image[0].Pixels.PhysicalSizeZ
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pixel_unit_x = image_metadata.Image[0].Pixels.PhysicalSizeXUnit
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pixel_unit_y = image_metadata.Image[0].Pixels.PhysicalSizeYUnit
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pixel_unit_z = image_metadata.Image[0].Pixels.PhysicalSizeZUnit
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print "Image '0' - Pixel Physical Size X: ", pixel_size_x, pixel_unit_x
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print "Image '0' - Pixel Physical Size Y: ", pixel_size_y, pixel_unit_y
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print "Image '0' - Pixel Physical Size Z: ", pixel_size_z, pixel_unit_z
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print "Image '0' - Pixel Size X: ", image_metadata.Image[0].Pixels.SizeX
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print "Image '0' - Pixel Size Y:", image_metadata.Image[0].Pixels.SizeY
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print "Image '0' - Pixel Size Z:", image_metadata.Image[0].Pixels.SizeZ
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print "Image '0' - Pixel Dimension Order: ", image_metadata.Image[0].Pixels.DimensionOrder
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print "Image '0' - Pixel Bits: ", image_metadata.Image[0].Pixels.SignificantBits
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for idx, eachChannel in enumerate(image_metadata.Image[0].Pixels.Channel):
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print "Image '0' - Channel " +str(idx) + " Color: ", integer_color_to_rgb(eachChannel.Color)
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if __name__ == "__main__":
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# Do setup
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tool_name = "extract_metadata"
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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_file", type=str, help='Output metadata file.')
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parser.add_argument("--verbose", type=bool, help='Output a simple metadata summary.')
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args = parser.parse_args()
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logger1.info('Reading Metadata At: ' + args.input_file)
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extract_metadata(args.input_file, args.output_file)
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if(args.verbose):
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image_metadata = get_metadata_as_class(args.output_file)
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print_metadata_overview(image_metadata)
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logger1.info('Completed Reading Metadata')
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