def convert_nifti_to_zipped_dicom_rt(nifti_file: Path, reference_series: Path,
scratch_folder: Path,
config: SegmentationModelBase) -> Path:
"""
Given a Nifti file and a reference DICOM series, create zip file containing a DICOM-RT file.
Calls rtconvert with the given Nifti file, reference DICOM series and configuration from
config to create a DICOM-RT file in the scratch folder. This is then zipped and a path to
the zip returned.
:param nifti_file: Path to Nifti file.
:param reference_series: Path to folder containing reference DICOM series.
:param scratch_folder: Scratch folder to extract files into.
:param config: Model config.
:return: Path to DICOM-RT file.
"""
dicom_rt_file = scratch_folder / nifti_file.with_suffix(".dcm").name
(stdout,
stderr) = rtconvert(in_file=nifti_file,
reference_series=reference_series,
out_file=dicom_rt_file,
struct_names=config.ground_truth_ids_display_names,
struct_colors=[
convert_rgb_colour_to_hex(rgb)
for rgb in config.colours
],
fill_holes=config.fill_holes)
# Log stdout, stderr from DICOM-RT conversion.
logging.debug("stdout: %s", stdout)
logging.debug("stderr: %s", stderr)
dicom_rt_zip_file = dicom_rt_file.with_suffix(dicom_rt_file.suffix +
'.zip')
with zipfile.ZipFile(dicom_rt_zip_file, 'w') as dicom_rt_zip:
dicom_rt_zip.write(dicom_rt_file, dicom_rt_file.name)
return dicom_rt_zip_file
def test_rtconvert() -> None:
"""
Test calling RTConvert for the test data.
"""
(stdout, stderr) = rtconvert(in_file=TestNiftiSegmentationLocation,
reference_series=TestDicomVolumeLocation,
out_file=TestOutputFile,
struct_names=StructureNames,
struct_colors=StructureColors,
fill_holes=FillHoles,
roi_interpreted_types=ROIInterpretedTypes,
manufacturer=Manufacturer,
interpreter=Interpreter,
modelId=ModelId)
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == ''
assert "Successfully written" in stdout
assert TestOutputFile.is_file()
with open(TestOutputFile, 'rb') as infile:
ds = dcmread(infile)
assert ds is not None
# Check the modality
assert ds.Modality == 'RTSTRUCT'
assert ds.Manufacturer == Manufacturer
assert ds.SoftwareVersions == ModelId
assert len(ds.StructureSetROISequence) == len(StructureNames)
for i, item in enumerate(StructureNames):
assert ds.StructureSetROISequence[i].ROINumber == i + 1
assert ds.StructureSetROISequence[i].ROIName == item
assert Interpreter in ds.RTROIObservationsSequence[
i].ROIInterpreter
assert ds.RTROIObservationsSequence[i].RTROIInterpretedType == (
'' if ROIInterpretedTypes[i] == 'None' else
ROIInterpretedTypes[i])
assert len(ds.ROIContourSequence) == len(StructureNames)
for i, item in enumerate(StructureNames):
assert ds.ROIContourSequence[i].ReferencedROINumber == i + 1
assert ds.ROIContourSequence[i].ROIDisplayColor == _parse_rgb(
StructureColors[i])
def convert_nifti_to_zipped_dicom_rt(nifti_file: Path, reference_series: Path,
scratch_folder: Path,
config: SegmentationModelBase,
dicom_rt_zip_file_name: str,
model_id: str) -> Path:
"""
Given a Nifti file and a reference DICOM series, create zip file containing a DICOM-RT file.
Calls rtconvert with the given Nifti file, reference DICOM series and configuration from
config to create a DICOM-RT file in the scratch folder. This is then zipped and a path to
the zip returned.
:param nifti_file: Path to Nifti file.
:param reference_series: Path to folder containing reference DICOM series.
:param scratch_folder: Scratch folder to extract files into.
:param config: Model config.
:param dicom_rt_zip_file_name: Target DICOM-RT zip file name, ending in .dcm.zip.
:param model_id: The AzureML model ID <model_name>:<ID>
:return: Path to DICOM-RT file.
"""
dicom_rt_file_path = scratch_folder / Path(
dicom_rt_zip_file_name).with_suffix("")
(stdout,
stderr) = rtconvert(in_file=nifti_file,
reference_series=reference_series,
out_file=dicom_rt_file_path,
struct_names=config.ground_truth_ids_display_names,
struct_colors=[
convert_rgb_colour_to_hex(rgb)
for rgb in config.colours
],
fill_holes=config.fill_holes,
roi_interpreted_types=config.roi_interpreted_types,
manufacturer=config.manufacturer,
interpreter=config.interpreter,
modelId=model_id)
# Log stdout, stderr from DICOM-RT conversion.
logging.debug("stdout: %s", stdout)
logging.debug("stderr: %s", stderr)
dicom_rt_zip_file_path = scratch_folder / dicom_rt_zip_file_name
with zipfile.ZipFile(dicom_rt_zip_file_path, 'w') as dicom_rt_zip:
dicom_rt_zip.write(dicom_rt_file_path, dicom_rt_file_path.name)
return dicom_rt_zip_file_path