def parse_coordinates(xmlfile, desc): """Read the 'Position' sheet from the Imaris XML file. Returns ------- coordinates : [(x, y, z)] List of 3-tuples of floats, representing the coordinates. """ log.warn('Reading %s file: %s' % (desc, xmlfile.name)) imsxml = ImarisXML(xmlfile) coordinates = imsxml.coordinates('Position') log.warn("- %s objects: %s" % (desc, len(coordinates))) return coordinates
#!/usr/bin/python from imaris_xml import ImarisXML from log import log log.setLevel(20) basedir = 'TESTDATA/spots_distances/' infile = basedir + 'spots_red_multi_ws-all.xml' outfile = basedir + 'result_ImarisXML_sp_red_mult_all.txt' # test with filehandle: XML = ImarisXML(open(infile)) # test with string: XML = ImarisXML(infile) res = XML.celldata('Position') output = open(outfile, 'w') output.write(str(res)) print('Written results to "%s"' % outfile)