print("T2 dir found.") pathROI = analasisysdir + "ROI/" if os.path.isdir(pathROI): print("ROI dir found.") infos = info_file_parser(analasisysdir + "info2.txt") timeflag = timeflagconverter_string2int(infos["time"]) ypT = int(infos["ypT"]) ypT2 = int(infos["ypT2"]) # # data, ROI = read_files(pathT2, pathROI, args.verbose, True) freader = FileReader(pathT2, pathROI, args.verbose) try: data, ROI = freader.read(raw=True) except NotImplementedError: data = freader.readUsingGDCM(raw=True) ROI = freader.readROI() except ValueError: print("Data not read. Check folders") continue roinorm=False if args.verbose: print("dicom file read") if args.norm: myroifilename = analasisysdir + "roinormmuscle.myroi" roireader = roiFileHandler(args.verbose) myroisnorm, roisnormSetted = roireader.read(myroifilename)
if os.path.isdir(pathT2): print("T2 dir found.") pathROI = analasisysdir + "ROI/" if os.path.isdir(pathROI): print("ROI dir found.") infos = info_file_parser(analasisysdir + "info.txt") timeflag[0] = timeflagconverter_string2int(infos["time"]) ypT[0] = int(infos["ypT"]) # # data, ROI = read_files(pathT2, pathROI, args.verbose, True) freader = FileReader(pathT2, pathROI, args.verbose) try: data, ROI = freader.read(raw=True) except NotImplementedError: data = freader.readUsingGDCM(raw=True) ROI = freader.readROI() except ValueError: continue roinorm=False if args.verbose: print("dicom file read") if args.norm: myroifilename = analasisysdir + "roinormmuscle.myroi" roireader = roiFileHandler(args.verbose) myroisnorm, roisnormSetted = roireader.read(myroifilename)
pathROI = analasisysdir + "ROI/" if os.path.isdir(pathROI): print("ROI dir found.") infos = info_file_parser(analasisysdir + "info2.txt") timeflag[0] = timeflagconverter_string2int(infos["time"]) ypT[0] = int(infos["ypT"]) ypT2[0] = int(infos["ypT2"]) # # data, ROI = read_files(pathT2, pathROI, args.verbose, True) freader = FileReader(pathT2, pathROI, args.verbose) try: data, ROI = freader.read(raw=True) except NotImplementedError: # data = freader.readUsingGDCM(raw=True) dataTMP = freader.readUsingGDCM(raw=False) data = dataTMP[:,:,:,0] ROI = freader.readROI() except ValueError: continue roinorm=False if args.verbose: print("dicom file read") if args.norm: myroifilename = analasisysdir + "roinormmuscle.myroi" roireader = roiFileHandler(args.verbose) myroisnorm, roisnormSetted = roireader.read(myroifilename)