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_write_dicom(self):
logger.info('Test_Write_Dicom test_write_dicom')
image = createImageExample()
tmpdirpath = tempfile.mkdtemp()
itk.imwrite(image, os.path.join(tmpdirpath, "input.mhd"))
filenameDcm = wget.download("https://github.com/OpenGATE/GateTools/raw/master/dataTest/rtdose.dcm", out=tmpdirpath, bar=None)
writeDicom(image, dicom = os.path.join(tmpdirpath, filenameDcm), output = os.path.join(tmpdirpath, "output.dcm"))
convertedDicom = gt.read_3d_dicom([os.path.join(tmpdirpath, "output.dcm")])
itk.imwrite(convertedDicom, os.path.join(tmpdirpath, "output.mhd"))
with open(os.path.join(tmpdirpath, "output.mhd"),"rb") as fnew:
bytesNew = fnew.read()
new_hash = hashlib.sha256(bytesNew).hexdigest()
self.assertTrue("65fc74e082eb4a69b60c289435564488956ba73bb274637fe0969c2152176308" == new_hash)
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_image_from_dicom(db, dicom_series, dicom_path):
'''
Convert one Dicom image to MHD image
'''
# modality
modality = dicom_series['modality']
#Try guessing pixel unit from dicom
try:
ds = pydicom.read_file(dicom_path)
unit = ds[0x0054, 0x1001].value
if unit == "BQML":
pixel_unit = 'Bq/mL'
else:
pixel_unit = unit
except:
# guess pixel unit FIXME --> check dicom tag ?
pixel_unit = 'undefined'
if modality == 'CT':
pixel_unit = 'HU'
if modality == 'NM':
pixel_unit = 'counts'
if modality == 'RTDOSE':
pixel_unit = 'Gy'
# get dicom files
files = syd.get_dicom_series_files(db, dicom_series)
if len(files) == 0:
s = 'Error, no file associated with this dicom serie'
syd.raise_except(s)
# get folder
folder = dicom_series['folder']
folder = os.path.join(db.absolute_data_folder, folder)
acquisition_id = int(
os.path.basename(os.path.dirname(folder)).split('_')[1])
suid = dicom_series['series_uid']
PixelType = itk.ctype('float')
Dimension = 3
namesGenerator = itk.GDCMSeriesFileNames.New()
namesGenerator.SetUseSeriesDetails(False)
namesGenerator.AddSeriesRestriction("0008|0021")
namesGenerator.SetGlobalWarningDisplay(False)
namesGenerator.SetDirectory(folder)
seriesUID = namesGenerator.GetSeriesUIDs()
fileNames = namesGenerator.GetFileNames(seriesUID[0])
# read dicom image
if len(fileNames) > 1:
itk_image = gt.read_dicom(fileNames)
else:
itk_image = gt.read_3d_dicom(fileNames)
# pixel_type (ignored)
# pixel_type = image.GetPixelIDTypeAsString()
# GetNumberOfComponentsPerPixel
# convert: assume only 2 type short for CT and float for everything else
pixel_type = 'float'
if modality == 'CT':
pixel_type = 'signed_short'
InputImageType = itk.Image[itk.F, Dimension]
OutputImageType = itk.Image[itk.SS, Dimension]
castImageFilter = itk.CastImageFilter[InputImageType,
OutputImageType].New()
castImageFilter.SetInput(itk_image)
castImageFilter.Update()
itk_image = castImageFilter.GetOutput()
# else:
# pixel_type = 'float'
# try:
# itk_image = sitk.Cast(itk_image, sitk.sitkFloat32)
# except:
# s = 'Cannot cast image. Ignoring '+str(dicom_series)
# warning(s)
# return None
# injection ?
injid = None
if 'injection_id' in dicom_series:
injid = dicom_series.injection_id
# create Image
#syd.update_nested_one(db, dicom_series)
labels = ''
if 'labels' in dicom_series:
labels = dicom_series.labels
dicom_study = syd.find_one(db['DicomStudy'],
id=dicom_series.dicom_study_id)
patient = syd.find_one(db['Patient'], id=dicom_study.patient_id)
img = {
'patient_id': patient.id,
'injection_id': injid,
'dicom_series_id': dicom_series.id,
'acquisition_id': acquisition_id,
'pixel_type': pixel_type,
'pixel_unit': pixel_unit,
'frame_of_reference_uid': dicom_series.frame_of_reference_uid,
'modality': modality,
'acquisition_date': dicom_series.acquisition_date,
'labels': labels
}
# insert the image in the db
img = syd.insert_new_image(db, img, itk_image)
# write the mhd file
p = syd.get_image_filename(db, img)
itk.imwrite(itk_image, p)
return img