nFette[0] = 0
if patientdir[-1]=='/':
patID = patientdir.split('/')[-2].replace('.','')
else:
patID = patientdir.split('/')[-1].replace('.','')
patientID[:63] = patID
print("working on patient: "+patientID)
print("in the directory: "+pathT2)
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
nFette = 0
if patientdir[-1]=='/':
patID = patientdir.split('/')[-2].replace('.','')
else:
patID = patientdir.split('/')[-1].replace('.','')
patientID = patID
print("working on patient: "+patientID)
print("in the directory: "+pathT2)
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 + "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
def check_dir(inputdir, verbose=False):
if verbose:
print("inputdir", inputdir)
table = []
patientdirs = glob.glob(inputdir + "*/")
for patientdir in patientdirs:
if verbose:
print(patientdir)
if patientdir[-1] == '/':
patID = patientdir.split('/')[-2].replace('.', '')
else:
patID = patientdir.split('/')[-1].replace('.', '')
if verbose:
print("id:", patID)
analasisysdirs = glob.glob(patientdir + "*/")
for analasisysdir in analasisysdirs:
patient = []
patient.append(patID)
if verbose:
print("\t", analasisysdir)
pathT2 = analasisysdir + "T2/"
pathROI = analasisysdir + "ROI/"
# freader = FileReader(pathT2, pathROI, args.verbose)
if verbose:
print("reading on patient: " + patID)
print("T2 directory: " + pathT2)
if os.path.isdir(pathT2):
dicomfiles = glob.glob(pathT2 + "/*.dcm")
allfiles = glob.glob(pathT2 + "/*")
patient.append(len(dicomfiles))
patient.append(len(allfiles) - len(dicomfiles))
else:
patient.append(0)
patient.append(0)
pathROI = analasisysdir + "ROI/"
if os.path.isdir(pathROI):
nrrdfiles = glob.glob(pathROI + "/*.nrrd")
if len(nrrdfiles) > 0:
fr = nrrdFileHandler(False)
nrrdROI = fr.read(nrrdfiles[0])
dicomfiles = glob.glob(pathROI + "/*.dcm")
allfiles = glob.glob(pathROI + "/*")
# patient.append(len(nrrdfiles))
patient.append(len(nrrdROI))
patient.append(len(dicomfiles))
patient.append(
len(allfiles) - len(dicomfiles) - len(nrrdfiles))
else:
patient.append(0)
patient.append(0)
patient.append(0)
else:
patient.append(0)
patient.append(0)
patient.append(0)
infofilename = analasisysdir + "info.txt"
if os.path.isfile(infofilename):
infos = info_file_parser(infofilename)
patient.append(infos["time"])
patient.append(infos["ypT"])
patient.append(infos["name"])
else:
patient.append("None")
patient.append("None")
patient.append("None")
table.append(patient)
return table
def check_dir(inputdir, verbose=False):
if verbose:
print("inputdir",inputdir)
table = []
patientdirs= glob.glob(inputdir+"*/")
for patientdir in patientdirs:
if verbose:
print(patientdir)
if patientdir[-1]=='/':
patID = patientdir.split('/')[-2].replace('.','')
else:
patID = patientdir.split('/')[-1].replace('.','')
if verbose:
print("id:",patID)
analasisysdirs=glob.glob(patientdir+"*/")
for analasisysdir in analasisysdirs:
patient = []
patient.append(patID)
if verbose:
print("\t",analasisysdir)
pathT2 = analasisysdir + "T2/"
pathROI = analasisysdir + "ROI/"
# freader = FileReader(pathT2, pathROI, args.verbose)
if verbose:
print("reading on patient: "+patID)
print("T2 directory: "+pathT2)
if os.path.isdir(pathT2):
dicomfiles = glob.glob(pathT2+"/*.dcm")
allfiles = glob.glob(pathT2+"/*")
patient.append(len(dicomfiles))
patient.append(len(allfiles)-len(dicomfiles))
else:
patient.append(0)
patient.append(0)
pathROI = analasisysdir + "ROI/"
if os.path.isdir(pathROI):
nrrdfiles = glob.glob(pathROI+"/*.nrrd")
if len(nrrdfiles) > 0 :
fr = nrrdFileHandler(False)
nrrdROI = fr.read(nrrdfiles[0])
dicomfiles = glob.glob(pathROI+"/*.dcm")
allfiles = glob.glob(pathROI+"/*")
# patient.append(len(nrrdfiles))
patient.append(len(nrrdROI))
patient.append(len(dicomfiles))
patient.append(len(allfiles)-len(dicomfiles)-len(nrrdfiles))
else:
patient.append(0)
patient.append(0)
patient.append(0)
else:
patient.append(0)
patient.append(0)
patient.append(0)
infofilename = analasisysdir + "info.txt"
if os.path.isfile(infofilename):
infos = info_file_parser(infofilename)
patient.append(infos["time"])
patient.append(infos["ypT"])
patient.append(infos["name"])
else:
patient.append("None")
patient.append("None")
patient.append("None")
table.append(patient)
return table