def test_dicom2nifti_rename_dicom2nifti_output():
dicom_dir = sd.unzip_t1()
nifti_file = sd.setup_nifti("2_t2_tse_coronal_512.nii.gz", unzip=True)
type = "dicom2nifti"
conversion = MagicMock()
conversion.ext = NIFTI_TYPE
orig_dir = Path("orig_dir")
roi_dir = Path(dicom_dir)
output_dir = Path(sd.WORKING_DIR)
converter = Converters.BaseConverter.factory(
type_=type,
orig_dir=orig_dir,
roi_dir=roi_dir,
output_dir=output_dir,
conversion=conversion,
)
converter.rename_dicom2nifti_output("test_output")
old_file = os.path.join(sd.WORKING_DIR, "2_t2_tse_coronal_512.nii")
new_file = os.path.join(sd.WORKING_DIR, "test_output.nii")
assert not os.path.exists(old_file)
assert os.path.exists(new_file)
sd.clean_working_dir()
def test_DicomRoiCollector_get_current_study_series_uid():
orig_dir = sd.unzip_t1()
fw_client = MagicMock()
file_object = MagicMock()
collector = Collectors.DicomRoiCollector(fw_client=fw_client,
orig_dir=orig_dir,
file_object=file_object)
studyInstance, seriesInstance = collector.get_current_study_series_uid()
assert studyInstance == sd.T2_PHANTOM_STUDY_UID
assert seriesInstance == sd.T2_PHANTOM_SERIES_UID
sd.clean_working_dir()
def test_PrepDicom_move_dicoms_to_workdir_zipped():
prepper = Preppers.PrepDicom(work_dir=sd.WORKING_DIR,
input_file_path=sd.DICOM_TEST_DATA)
prepper.move_dicoms_to_workdir()
expected_dir = prepper.orig_dir
print(expected_dir)
assert os.path.exists(expected_dir)
ndicoms = glob.glob(os.path.join(expected_dir, "*.dcm"))
assert len(ndicoms) == sd.NUM_DICOMS
sd.clean_working_dir()
def test_dcm2niix_nifti():
sd.clean_working_dir()
input_file = sd.get_zipped_t1()
work_dir = Path(sd.WORKING_DIR) / "work"
work_dir.mkdir(exist_ok=True)
output_dir = Path(sd.WORKING_DIR) / "output"
output_dir.mkdir(exist_ok=True)
fw = flywheel.Client()
# Get configuration, acquisition, and file info
file_id = "626037fe7cc96261fa295c75"
file_obj = fw.get_file(file_id)
# destination_type = "nrrd" if config.get("save_NRRD") else "nifti"
input_file = Path(input_file)
destination_type = "nifti"
combine = False
bitmask = False
method = "dcm2niix"
exporter = MeasurementExport(
fw_client=fw,
fw_file=file_obj,
work_dir=work_dir,
output_dir=output_dir,
input_file_path=input_file,
dest_file_type=destination_type,
combine=combine,
bitmask=bitmask,
method=method,
)
ohifviewer_info, labels, affine = exporter.process_file()
globpath = output_dir / "*"
output_files = glob.glob(globpath.as_posix())
assert len(output_files) == 3
output_files = [os.path.basename(a) for a in output_files]
doggy = [d for d in output_files if d.startswith("ROI_Doggy")]
potato = [d for d in output_files if d.startswith("ROI_Potato")]
lesion = [d for d in output_files if d.startswith("ROI_Lesion")]
assert len(doggy) == 1
assert len(potato) == 1
assert len(lesion) == 1
sd.clean_working_dir()
def test_PrepDicom_copy_dicoms_for_export():
unziped_dir = sd.unzip_t1()
prepper = Preppers.PrepDicom(work_dir=sd.WORKING_DIR,
input_file_path=sd.DICOM_TEST_DATA)
prepper.orig_dir = unziped_dir
prepper.copy_dicoms_for_export()
expected_dir = prepper.output_dir
ndicoms = glob.glob(os.path.join(expected_dir, "*.dcm"))
assert expected_dir != unziped_dir
assert os.path.exists(expected_dir)
assert len(ndicoms) == sd.NUM_DICOMS
sd.clean_working_dir()
def test_dicom2nifti_guess_dicom2nifti_outputname():
dicom_dir = sd.unzip_t1()
type = "dicom2nifti"
conversion = MagicMock()
conversion.ext = "ext"
output_filename = os.path.join(sd.WORKING_DIR, "output_filename")
orig_dir = Path("orig_dir")
roi_dir = Path(dicom_dir)
output_dir = Path("output_dir")
converter = Converters.BaseConverter.factory(
type_=type,
orig_dir=orig_dir,
roi_dir=roi_dir,
output_dir=output_dir,
conversion=conversion,
)
base_filename = converter.guess_dicom2nifti_outputname()
assert base_filename == "2_t2_tse_coronal_512"
sd.clean_working_dir()
def test_cleanup():
sd.clean_working_dir()