def make_png(self):
"""Create mask for each structure for all patients."""
print(f"Structure(s) to export: {self.structures}")
print(f"Patient(s) identification : {self.patients}")
for index, path_patient in enumerate(self.patient_paths):
patient_id = self.patients[index]
print(f"Exporting {index + 1} ({patient_id}) on {len(self.patients)}")
nii_output = os.path.join(path_patient, "output")
_, not_missing = self.find_structures(index)
dcmrtstruct2nii(self.rs_paths[index], path_patient, nii_output, not_missing, False, mask_foreground_value=1)
nii_maks = [nii_mask for nii_mask in os.listdir(nii_output) if nii_mask.startswith('mask')]
for nii in nii_maks:
nii_object = nib.load(os.path.join(nii_output, nii))
name = os.path.splitext(nii)[0].split("_")[1].replace("-", " ")
self.nii_to_png(name, nii_object, patient_id)
ct_nii_object = nib.load(os.path.join(nii_output, "image.nii"))
self.nii_to_png("ct", ct_nii_object, patient_id)
print(f"Export done")
def rtstruct2nii(rtstruct_file, original_dcm, output_path):
try:
dcmrtstruct2nii(rtstruct_file, original_dcm, output_path)
except Exception as e:
print(e)
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_tb(exc_traceback)
sys.exit(1)
try:
os.chdir(output_path)
for file in glob.glob("mask*.gz"):
print(file)
mask_nii_gz = file
mask_nii = os.path.splitext(mask_nii_gz)[0]
print(mask_nii)
with gzip.open(os.path.join(output_path, mask_nii_gz),
'r') as f_in, open(
os.path.join(output_path, mask_nii),
'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
except Exception as error:
print(error)
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_tb(exc_traceback)
sys.exit(1)
def test_bmia_stwstrategyhn1(tmpdir):
dataset = Path(tmpdir / 'stwstrategyhn1')
dcmrtstruct2niidir = Path(tmpdir / 'dcmrtstruct2nii')
dcmrtstruct2niidir.mkdir(exist_ok=True)
counter = 0
subjects = list_subjects_stwstrategyhn1()
numsubjects = len(subjects)
for subject in subjects:
counter += 1
print(f'Comparing {subject.label} {counter}/{numsubjects}')
subject_dir = Path(dataset / subject.label)
download_subject(subject, subject_dir)
rtstructs = list(
subject_dir.glob('*/scans/*/resources/secondary/files/*'))
if len(rtstructs) > 1 or len(rtstructs) <= 0:
assert False, f'> 1 RTSTRUCT or <= 0 RTSTRUCT found for subject {subject.label}, something changed in the dataset?'
rtstruct = rtstructs[0]
dicoms = list(subject_dir.glob('*/scans/*/resources/DICOM/files'))
if len(dicoms) > 1 or len(dicoms) <= 0:
assert False, f'> 1 DICOM or <= 0 DICOM found for subject {subject.label}, something changed in the dataset?'
dicom = dicoms[0]
subjoutdir = Path(dcmrtstruct2niidir / subject.label)
subjoutdir.mkdir(exist_ok=True)
dcmrtstruct2nii(rtstruct, dicom, subjoutdir)
niicounter = 0
for nii in subjoutdir.glob('*.nii.gz'):
niicounter += 1
niftis = list(subject_dir.glob(f'**/{nii.name}'))
if len(niftis) > 1 or len(niftis) <= 0:
assert False, f'> 1 niftis or <= 0 niftis {nii.name} found for subject {subject.label}, something changed in the dataset?'
nii_stwstrategyhn1 = niftis[0]
diff = diffnii(nii, nii_stwstrategyhn1)
if not (diff['similarity'] > .95 and diff['similarity'] < 1.05):
assert False, f'niftis not equal {diff["similarity"]}, {nii}:{nii_stwstrategyhn1} data: {diff}'
print(f"Compared {niicounter} NiFTI's for subject {subject.label}")
# cleanup, GitHub runners only have ~14 GB of space
shutil.rmtree(subjoutdir)
shutil.rmtree(subject_dir)
assert True
def dcmrtstruct2niiLoop(currStruct):
try:
# Extract the structure and convert to Nifti
# We do not want convert_original_dicom=True for all structures as this will add a lot of time.
# Do this only for BODY as this structure is always present. It has nothing to do with the structure itself for enabling convert_original_dicom=True.
if currStruct == 'BODY' or currStruct == 'External':
dcmrtstruct2nii(patRTStructFile, patCTFolder, tempOutFolder, structures=currStruct, gzip=True, mask_background_value=0, mask_foreground_value=1, convert_original_dicom=True)
else:
dcmrtstruct2nii(patRTStructFile, patCTFolder, tempOutFolder, structures=currStruct, gzip=True, mask_background_value=0, mask_foreground_value=1, convert_original_dicom=False)
except:
print('An exception occurred in dcmrtstruct2nii data extraction for struct ' + str(currStruct))
print(patRTStructFile)
print(list_rt_structs(patRTStructFile))
# Write to error log file,
myInference.write2log(outFileNameErrors, 'An exception occurred in dcmrtstruct2nii data extraction for struct ' + str(currStruct))
def patLargeDataLoop(patNr, patient):
# Create new random seed
# Important for parallell threading
R=np.random.RandomState()
# Create random large integer
# Use it to name the folders
randPatValue = R.randint(100000000000, 999999999999)
# Patient folder where data files are originally contained
patFolderPath = allPatFolder + '/' + patient
# Move RS struct file that is not a CT Dicom file to another folder
# otherwise dcmstruct2nii will not accept it
RTStructFolderName = moveRTStructFile(patFolderPath)
# Move CT files to a subdirectory under the patient
CTFolderName = moveCTFiles(patFolderPath)
# Patient folder where CT files now are contained
patCTFolderPath = allPatFolder + '/' + patient +'/' + CTFolderName
# Get RT struct file name
RTStructFile = getRTStructFile(patFolderPath + '/' + RTStructFolderName)
# Define whole path for RT struct file
patRTStructFile = patFolderPath + '/' + RTStructFolderName + '/' + RTStructFile
# Define patient output folder
patOutFolderPath = outFolder + '/' + str(randPatValue)
# Get list of all structures present
structListExported = list_rt_structs(patRTStructFile)
# Convert the RT structs to Nifty format
# This is performed by targeting each individual structure at a time in a loop.
# This is slower but safer.
# In this way we can isolate exceptions to individual structures and not break
# the process of dcmrtstruc2nii which happens otherwise. This avoids modification of the
# dcmrtstruc2nii source code and allows us in retrospect to see if missing data was important or not.
# Failed objects are due to the fact that the structures are not completed or simply empty in Eclipse.
for structNr, currStruct in enumerate(structListExported):
try:
# Extract the structure and convert to Nifty
# We do not want convert_original_dicom=True for all structures as this will add a lot of time.
# Do this only for BODY as this structure is always present. It has nothing to do with the structure itself for enabling convert_original_dicom=True.
if currStruct == 'BODY':
print(patient + ' ' + str(randPatValue))
dcmrtstruct2nii(patRTStructFile, patCTFolderPath, patOutFolderPath, structures=currStruct, gzip=True, mask_background_value=0, mask_foreground_value=1, convert_original_dicom=True)
else:
dcmrtstruct2nii(patRTStructFile, patCTFolderPath, patOutFolderPath, structures=currStruct, gzip=True, mask_background_value=0, mask_foreground_value=1, convert_original_dicom=False)
except:
print("Exception when extracting " + currStruct + ' for ' + patient + ' ' + str(randPatValue))
def make(self):
"""Create structures and convert the CT in nii format for each subject."""
print(f"Structure(s) to export: {self.structures}")
print(f"Patient(s) identification : {self.patients}")
for index, path_patient in enumerate(self.patient_paths):
patient_id = self.patients[index]
print(
f"Exporting {index + 1} ({patient_id}) on {len(self.patients)}"
)
nii_output = os.path.join(self.export_path, patient_id)
missing, not_missing = self.find_structures(index)
if len(missing) == 0 or self.force:
dcmrtstruct2nii(self.rs_paths[index],
path_patient,
nii_output,
not_missing,
False,
mask_foreground_value=1)
nii_maks = [
nii_mask for nii_mask in os.listdir(nii_output)
if nii_mask.startswith('mask')
]
for nii in nii_maks:
name = os.path.splitext(nii)[0].split("_")[1].replace(
"-", " ")
os.rename(os.path.join(nii_output, nii),
os.path.join(nii_output, name + '.nii'))
os.rename(os.path.join(nii_output, "image.nii"),
os.path.join(nii_output, "ct.nii"))
else:
print(f"Skip {patient_id} because of missing structure(s)")
print("Export done")
def convertitoreRTstDCtoNII(PathDicom_RT,PathDicom_CT,output_path):
return dcmrtstruct2nii(PathDicom_RT, PathDicom_CT, output_path,structures=None,gzip=False,mask_background_value=0, mask_foreground_value=1,convert_original_dicom=True)
#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Fri Jun 14 09:13:56 2019 @author: leonardo """ from dcmrtstruct2nii import dcmrtstruct2nii RT='/home/leonardo/Scrivania/paziente_prova/CSI+Boost/RTst_2011-09-29_075800_TomoTherapy.Patient.Disease_TomoTherapy.Structure.Set_n1__00000/1.2.826.0.1.3680043.2.200.868401404.495.96056.551.dcm' PathDicom_DOSE='/home/leonardo/Scrivania/paziente_prova/CSI+Boost/RTDOSE_2011-09-29_075800_TomoTherapy.Patient.Disease_TomoTherapy.Planned.Dose_n1__00000' output_path='/home/leonardo/Scrivania/paziente_prova/RT_2_nii_(DOSE)/' dcmrtstruct2nii(RT,PathDicom_DOSE,output_path,structures=None,gzip=False,mask_background_value=0,mask_foreground_value=1,convert_original_dicom=True)