def run(self):
accession_number = self.data["accession_number"]
patient_id = self.data["patient_id"]
accession_dir = "work/results/{}/{}".format(patient_id, accession_number)
if not os.path.exists(accession_dir):
os.makedirs(accession_dir)
dicom_series_to_nifti(self.data["images_dir"], accession_dir + "/source.nii.gz")
with self.output().open("w") as outfile:
outfile.write("Converted to nifti")
def test_resampling(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_dicom.dicom_series_to_nifti(
test_data.FAILING_ORHTOGONAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
self.assertTrue(os.path.isfile(results['NII_FILE']))
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_COMPRESSED)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_COMPRESSED)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.HITACHI_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.HITACHI_ANATOMICAL)[1]) is True
finally:
shutil.rmtree(tmp_output_dir)
settings.disable_validate_slicecount()
for key in inputFiles:
dicomFolderPath = key
outputFileName = inputFiles[ key ];
if (outputFileName in mapOfFileNames):
fileNo = mapOfFileNames[ outputFileName]
mapOfFileNames[outputFileName] = fileNo + 1
else:
mapOfFileNames.setdefault(outputFileName, 1)
outputFileName = outputFileName + "$$" + str(mapOfFileNames[ outputFileName])
print('***', dicomFolderPath)
print('--', outputDirectory, outputFileName)
outputFileName = outputFileName + ".nii.gz"
try:
convert_dicom.dicom_series_to_nifti(key, os.path.join(outputDirectory, outputFileName),
False)
except dicom2nifti.exceptions.ConversionValidationError:
print( " Error for file outputFileName", outputFileName )
print( 'completed' )
def readFromTextFile( inputFilePath):
inputFilesList = []
file1 = open(inputFilePath, 'r')
lines = file1.readlines()
count = 0
# Strips the newline character
for line in lines:
inputFilesList.append( line.strip() )
return inputFilesList
def test_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL, None, False)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_NON_ISOTROPIC,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_NON_ISOTROPIC)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.HITACHI_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.HITACHI_ANATOMICAL)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
shutil.rmtree(tmp_output_dir)