def file_save(self): filename = QtGui.QFileDialog.getSaveFileName(self, 'Save File') writer = roiFileHandler() writer.dicomsPath = os.path.abspath(self.inpath) if not str(filename).endswith('.myroi'): filename = filename + ".myroi" writer.write(filename, self.rois, self.roisSetted)
def file_open(self): filename = QtGui.QFileDialog.getOpenFileName(self, 'Open File','ROI','ROI files (*.myroi)') reader = roiFileHandler() originalpath = reader.dicomsPath self.rois, self.roisSetted = reader.read(filename) self.updatemain() self.label2_roisSetted.setText("ROI setted: "+str(self.roisSetted))
def file_save(self): filename = QtGui.QFileDialog.getSaveFileName(self, 'Save File') writer = roiFileHandler() writer.dicomsPath = os.path.abspath(self.inpath) if not str(filename).endswith('.myroi'): filename = filename+".myroi" writer.write(filename, self.rois, self.roisSetted)
def file_open(self): filename = QtGui.QFileDialog.getOpenFileName(self, 'Open File', 'ROI', 'ROI files (*.myroi)') reader = roiFileHandler() originalpath = reader.dicomsPath self.rois, self.roisSetted = reader.read(filename) self.updatemain() self.label2_roisSetted.setText("ROI setted: " + str(self.roisSetted))
timeflag[0] = int(lines[3]) ypT[0] = int(lines[4]) # data, ROI = read_files(pathT2, pathROI, args.verbose, True) freader = FileReader(pathT2, pathROI, args.verbose) data, ROI = freader.read(True) roinorm = False if args.verbose: print("dicom file read") if args.norm: myroifilename = lines[5] roireader = roiFileHandler(args.verbose) myroisnorm, roisnormSetted = roireader.read(myroifilename) roinorm = myroi2roi(myroisnorm, data.shape, args.verbose) if args.verbose: print("norm file read") if args.verbose: print("data mean:", data.mean(), "min:", data.min(), "max:", data.max(), "shape:", data.shape) print("ROI mean:", ROI.mean(), "min:", ROI.min(), "max:", ROI.max(), "shape:", ROI.shape) patientsuffix = lines[0] + str(timeflag[0]) if timeflag[0] != 0 and timeflag[0] != 1 and timeflag[0] != 2: print( "ERROR: timeflag (0 for pre, 1 for int and 2 for post) of patient "
timeflag[0] = int(lines[3]) ypT[0] = int(lines[4]) # data, ROI = read_files(pathT2, pathROI, args.verbose, True) freader = FileReader(pathT2, pathROI, args.verbose) data, ROI = freader.read(True) roinorm=False if args.verbose: print("dicom file read") if args.norm: myroifilename = lines[5] roireader = roiFileHandler(args.verbose) myroisnorm, roisnormSetted = roireader.read(myroifilename) roinorm = myroi2roi(myroisnorm, data.shape, args.verbose) if args.verbose: print("norm file read") patientsuffix=lines[0]+str(timeflag[0]) if timeflag[0] != 0 and timeflag[0] != 1 and timeflag[0] != 2: print("ERROR: timeflag (0 for pre, 1 for int and 2 for post) of patient "+lines[0]+ "is: "+timeflag[0]) raise NameError('OutOfRange') his, allhistos, histogiafatti = make_histo(data,ROI,patientsuffix,args.verbose,roinorm,args.norm) nVoxel[0] = int(his.GetEntries()) mean[0] = his.GetMean()
if args.inputpath: inpath = args.inputpath if args.roi: myroifilename = args.roi if args.outfile: outfname = args.outfile out_file = open(outfname,"w") out_file.write("#layer \t max \t meaninroi \n") freader = FileReader(inpath, False, args.verbose) data, unusedROI = freader.read(True) roireader = roiFileHandler() rois, roisSetted = roireader.read(myroifilename) nFette = len(data) if nFette != len(rois): print("error: len rois = ",len(rois)," but len dicom=",nFette) for layer in xrange(0,nFette): thisroi = grid_points_in_poly(data[layer].shape, rois[layer]['points']) masked = data[layer]*thisroi maximum = data[layer].max() meaninroi = masked.mean() out_file.write(str(layer)+"\t"+str(maximum)+"\t"+str(meaninroi)+"\n") out_file.close()