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()