def test_dvh_volume(self):
logger.info('Test_DVH test_dvh_volume')
tmpdirpath = tempfile.mkdtemp()
filenameStruct = wget.download(
"https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtstruct.dcm?inline=false",
out=tmpdirpath,
bar=None)
structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
filenameDose = wget.download(
"https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtdose.dcm?inline=false",
out=tmpdirpath,
bar=None)
doseImage = gt.read_3d_dicom([os.path.join(tmpdirpath, filenameDose)])
transformImage = gt.applyTransformation(input=doseImage,
neworigin=[-176, -320, -235])
aroi = gt.region_of_interest(structset, "PTV")
mask = aroi.get_mask(transformImage, corrected=False)
doseValues, volumePercentage = createDVH(transformImage,
mask,
bins=100,
useCm3=True)
self.assertTrue(np.all(volumePercentage >= 0))
self.assertTrue(np.all(volumePercentage <= 115120))
self.assertTrue(len(doseValues) == 100)
self.assertTrue(len(volumePercentage) == 100)
shutil.rmtree(tmpdirpath)
def test_dvh_compute_d(self):
logger.info('Test_DVH test_dvh_compute_d')
tmpdirpath = tempfile.mkdtemp()
filenameStruct = wget.download("https://github.com/OpenGATE/GateTools/raw/master/dataTest/rtstruct.dcm", out=tmpdirpath, bar=None)
structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
filenameDose = wget.download("https://github.com/OpenGATE/GateTools/raw/master/dataTest/rtdose.dcm", out=tmpdirpath, bar=None)
doseImage = gt.read_3d_dicom([os.path.join(tmpdirpath, filenameDose)])
transformImage = gt.applyTransformation(input=doseImage, neworigin=[-176, -320, -235])
aroi = gt.region_of_interest(structset, "PTV")
mask = aroi.get_mask(transformImage, corrected=False)
doseValues, volumePercentage = createDVH(transformImage, mask)
self.assertTrue(np.isclose(computeD(doseValues, volumePercentage, 95), 0.15428162737918327))
shutil.rmtree(tmpdirpath)
def test_dvh(self):
logger.info('Test_DVH test_dvh')
tmpdirpath = tempfile.mkdtemp()
filenameStruct = wget.download("https://github.com/OpenGATE/GateTools/raw/master/dataTest/rtstruct.dcm", out=tmpdirpath, bar=None)
structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
filenameDose = wget.download("https://github.com/OpenGATE/GateTools/raw/master/dataTest/rtdose.dcm", out=tmpdirpath, bar=None)
doseImage = gt.read_3d_dicom([os.path.join(tmpdirpath, filenameDose)])
transformImage = gt.applyTransformation(input=doseImage, neworigin=[-176, -320, -235])
aroi = gt.region_of_interest(structset, "PTV")
mask = aroi.get_mask(transformImage, corrected=False)
doseValues, volumePercentage = createDVH(transformImage, mask, bins=100)
self.assertTrue(np.allclose(doseValues, np.array([0.10095047205686569, 0.3028514161705971, 0.5047523528337479, 0.7066532969474792, 0.9085542261600494, 1.1104551553726196, 1.3123561143875122, 1.5142570734024048, 1.7161580324172974, 1.9180589318275452, 2.119959831237793, 2.3218607902526855, 2.523761749267578, 2.7256627082824707, 2.9275636672973633, 3.129464626312256, 3.3313655853271484, 3.533266544342041, 3.7351675033569336, 3.9370683431625366, 4.13896918296814, 4.340870141983032, 4.542771100997925, 4.744672060012817, 4.94657301902771, 5.1484739780426025, 5.350374937057495, 5.552275896072388, 5.75417685508728, 5.956077814102173, 6.157978773117065, 6.359879732131958, 6.561780691146851, 6.763681650161743, 6.965582609176636, 7.167483568191528, 7.369384527206421, 7.5712854862213135, 7.773186445236206, 7.9750871658325195, 8.176988124847412, 8.378889083862305, 8.580790042877197, 8.78269100189209, 8.984591960906982, 9.186492919921875, 9.388393878936768, 9.59029483795166, 9.792195796966553, 9.994096755981445, 10.195997714996338, 10.39789867401123, 10.599799633026123, 10.801700592041016, 11.003601551055908, 11.2055025100708, 11.407403469085693, 11.609304428100586, 11.811205387115479, 12.013106346130371, 12.215007305145264, 12.416908264160156, 12.618809223175049, 12.820710182189941, 13.022610664367676, 13.224511623382568, 13.426412582397461, 13.628313541412354, 13.830214500427246, 14.032115459442139, 14.234016418457031, 14.435917377471924, 14.637818336486816, 14.839719295501709, 15.041620254516602, 15.243521213531494, 15.445422172546387, 15.64732313156128, 15.849224090576172, 16.051124572753906, 16.253026008605957, 16.454927444458008, 16.656827926635742, 16.858728408813477, 17.060629844665527, 17.262531280517578, 17.464431762695312, 17.666332244873047, 17.868233680725098, 18.07013511657715, 18.272035598754883, 18.473936080932617, 18.675837516784668, 18.87773895263672, 19.079639434814453, 19.281539916992188, 19.483440399169922, 19.685341835021973, 19.887243270874023, 20.089143753051758])))
self.assertTrue(np.all(volumePercentage >= 0))
self.assertTrue(np.all(volumePercentage <= 100))
self.assertTrue(len(doseValues) == 100)
self.assertTrue(len(volumePercentage) == 100)
shutil.rmtree(tmpdirpath)
def insert_roi_from_struct(db, struct, crop):
"""
Insert an ROI from a DicomStruct file
"""
roi = Box()
res = []
series_id = struct['dicom_series_id']
dicom_series = syd.find_one(db['DicomSeries'], id=series_id)
acquisition = syd.find_one(db['Acquisition'],
id=dicom_series['acquisition_id'])
injection_id = acquisition['injection_id']
acquisition_id = dicom_series['acquisition_id']
injection = syd.find_one(db['Injection'], id=injection_id)
patient = syd.find_one(db['Patient'], id=injection['patient_id'])
### Getting the CT image path ###
image_ct = syd.find_one(db['Image'], dicom_series_id=series_id)
try:
file_img = syd.find_one(db['File'], id=image_ct['file_mhd_id'])
except:
print('Could not find the CT image in the database')
filename_img_ct = db.absolute_data_folder + '/' + file_img[
'folder'] + '/' + file_img['filename']
### Getting the DicomStruct dicom path ###
dicom_file = syd.find_one(db['DicomFile'], dicom_struct_id=struct['id'])
file_struct = syd.find_one(db['File'], id=dicom_file['file_id'])
filename_struct = db.absolute_data_folder + '/' + file_struct[
'folder'] + '/' + file_struct['filename']
### Verifying if the ROI already exists in the table ###
e = syd.find(db['Roi'], dicom_struct_id=struct['id'])
if e != []:
return {}
### Using GateTools to extract the image from the Dicom File ###
structset = pydicom.read_file(filename_struct)
img_ct = itk.imread(filename_img_ct, itk.F)
base_filename, extension = os.path.splitext(filename_img_ct)
roi_names = gt.list_roinames(structset)
roi_objs = list()
npbar = 0
pbar = None
for r in roi_names:
try:
aroi = gt.region_of_interest(structset, r)
if not aroi.have_mask():
tqdm.write(f'Mask for {r} not possible')
roi_objs.append(aroi)
except:
tqdm.write(f'Something is wrong with ROI {r}')
roi.remove(r)
if npbar > 0:
pbar = tqdm(total=npbar, leave=False)
for roiname, aroi in zip(roi_names, roi_objs):
try:
mask = aroi.get_mask(img_ct, corrected=False, pbar=pbar)
if crop:
mask = gt.image_auto_crop(mask, bg=0)
output_filename = base_filename + '_' + ''.join(
e for e in roiname if e.isalnum()) + '.mhd'
im = {
'patient_id': patient['id'],
'injection_id': injection_id,
'acquisition_id': acquisition_id,
'pixel_unit': 'binary',
'pixel_type': 'float',
'frame_of_reference_uid':
dicom_series['frame_of_reference_uid'],
'modality': 'RTSTRUCT',
'labels': roiname
}
im = syd.insert_write_new_image(db, im, mask)
roi = {
'dicom_struct_id': struct['id'],
'image_id': im['id'],
'frame_of_reference_uid': struct['frame_of_reference_uid'],
'name': roiname,
'labels': None
}
roi = syd.insert_one(db['Roi'], roi)
im['roi_id'] = roi['id']
res.append(roi)
syd.update_one(db['Image'], im)
syd.update_roi_characteristics(db, roi)
except:
tqdm.write(f'Error in {roiname, aroi}')
if npbar > 0:
pbar.close()
return res