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)
if len(ROI) is not len(data):
print("skipping this analysis len(data)",len(data),"len(ROI)",len(ROI))
continue
patientsuffix = patID + infos["time"]
his, allhistos, histogiafatti,histogclm = make_histo(data,ROI,patientsuffix, args.verbose,roinorm,args.norm,args.icut,args.filter)
entropy_his, allentropy_his = make_histo_entropy(data,ROI,patientsuffix,
args.verbose)
nVoxel[0] = int(his.GetEntries())
mean[0] = his.GetMean()
stdDev[0] = his.GetStdDev()
skewness[0] = his.GetSkewness()
kurtosis[0] = his.GetKurtosis()
entropy_mean[0] = entropy_his.GetMean()
entropy_var[0] = entropy_his.GetStdDev()
if args.verbose:
print(patientID, timeflag[0], nVoxel[0], ypT[0], mean[0], stdDev[0], skewness[0], kurtosis[0])
his.Write()
entropy_his.Write()
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()
stdDev[0] = his.GetStdDev()
skewness[0] = his.GetSkewness()
kurtosis[0] = his.GetKurtosis()
if args.verbose:
print(patientID, timeflag[0], nVoxel[0], ypT[0], mean[0], stdDev[0], skewness[0], kurtosis[0])
his.Write()
for thishisto in allhistos:
if thishisto.GetEntries() >0:
nVoxelPF[nFette[0]] = int(thishisto.GetEntries())
meanPF[nFette[0]] = thishisto.GetMean()
stdDevPF[nFette[0]] = thishisto.GetStdDev()
skewnessPF[nFette[0]] = thishisto.GetSkewness()
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 "+lines[0]+ "is: "+timeflag[0])
raise NameError('OutOfRange')
his, allhistos, histogiafatti,histogclm = make_histo(data,ROI,patientsuffix,args.verbose,roinorm,args.norm,args.icut,args.filter)
nVoxel[0] = int(his.GetEntries())
mean[0] = his.GetMean()
stdDev[0] = his.GetStdDev()
skewness[0] = his.GetSkewness()
kurtosis[0] = his.GetKurtosis()
if args.verbose:
print(patientID, timeflag[0], nVoxel[0], ypT[0], mean[0], stdDev[0], skewness[0], kurtosis[0])
his.Write()
for thishisto in allhistos:
if thishisto.GetEntries() >0:
nVoxelPF[nFette[0]] = int(thishisto.GetEntries())
meanPF[nFette[0]] = thishisto.GetMean()
stdDevPF[nFette[0]] = thishisto.GetStdDev()
skewnessPF[nFette[0]] = thishisto.GetSkewness()
# for infileROI in infilesROI:
# dicomsROI.append(dicom.read_file(infileROI))
# for i, thisROI in enumerate(dicomsROI):
# pix_arr = thisROI.pixel_array
# ROI[i] = pix_arr.T
# for i, thisdicom in enumerate(dicoms):
# pix_arr = thisdicom.pixel_array
# data[i] = pix_arr.T
data, ROI = read_files(inpath,args.filterROI, args.verbose, True)
outfile= ROOT.TFile(outfname,"RECREATE")
his, allhistos = make_histo(data,ROI)
his.Write()
for thishisto in allhistos:
thishisto.Write()
# histograms = []
# for i, fetta, fettaROI in enumerate(zip(data,ROI)):
# if fettaROI.max() > 0 :
# histogram = make_histo(fetta, fettaROI)
# histogram.SetName("h"+str(i))
# histogram.SetTitle("h"+str(i))
# histogram.Write()
outfile.Write()
# dicomsROI.append(dicom.read_file(infileROI))
# for i, thisROI in enumerate(dicomsROI):
# pix_arr = thisROI.pixel_array
# ROI[i] = pix_arr.T
# for i, thisdicom in enumerate(dicoms):
# pix_arr = thisdicom.pixel_array
# data[i] = pix_arr.T
data, ROI = read_files(inpath, args.filterROI, args.verbose, True)
outfile = ROOT.TFile(outfname, "RECREATE")
if args.filterROI:
his, allhistos = make_histo(data, ROI)
his.Write()
else:
allhistos = make_histo_ofallpixels(data, "", args.verbose, args.normalize)
for thishisto in allhistos:
thishisto.Write()
# histograms = []
# for i, fetta, fettaROI in enumerate(zip(data,ROI)):
# if fettaROI.max() > 0 :
# histogram = make_histo(fetta, fettaROI)
# histogram.SetName("h"+str(i))
# histogram.SetTitle("h"+str(i))
# histogram.Write()
