def test_streamlit_gui():
pymedphys.zip_data_paths("mu-density-gui-e2e-data.zip",
extract_directory=HERE)
with process("poetry run pymedphys gui", cwd=HERE, shell=True) as _:
subprocess.check_call("yarn", cwd=HERE, shell=True)
subprocess.check_call("yarn cypress run", cwd=HERE, shell=True)
def test_cypress():
pymedphys.zip_data_paths("mu-density-gui-e2e-data.zip",
extract_directory=HERE)
pymedphys.zip_data_paths(
"dummy-ct-and-struct.zip",
extract_directory=HERE.joinpath("cypress", "fixtures"),
)
with process("poetry run pymedphys gui", cwd=HERE, shell=True) as _:
subprocess.check_call("yarn", cwd=HERE, shell=True)
subprocess.check_call("yarn cypress run", cwd=HERE, shell=True)
def test_delivery_from_monaco():
data_paths = pymedphys.zip_data_paths("tel-dicom-pairs.zip")
dir_names = {path.parent.name for path in data_paths}
assert len(dir_names) >= 2
for dir_name in dir_names:
if dir_name in DIRS_TO_SKIP:
continue
current_paths = [
path for path in data_paths if path.parent.name == dir_name
]
tel_path = get_file_type(current_paths, "tel.1", exact_match=True)
dcm_path = get_file_type(current_paths, "dcm")
delivery_dcm = pymedphys.Delivery.from_dicom(pydicom.read_file(
str(dcm_path), force=True),
fraction_number=1)
delivery_monaco = pymedphys.Delivery.from_monaco(tel_path)
assert np.allclose(delivery_monaco.mu, delivery_dcm.mu, atol=0.01)
assert np.allclose(delivery_monaco.gantry,
delivery_dcm.gantry,
atol=0.01)
assert np.allclose(delivery_monaco.collimator,
delivery_dcm.collimator,
atol=0.01)
assert np.allclose(delivery_monaco.mlc, delivery_dcm.mlc, atol=0.1)
assert np.allclose(delivery_monaco.jaw, delivery_dcm.jaw, atol=0.01)
def test_structure_dedupe():
data_paths = pymedphys.zip_data_paths("structure-deduplication.zip")
input_paths = [path for path in data_paths if path.parent.name == "input"]
for input_path in input_paths:
input_dcm = pydicom.read_file(str(input_path), force=True)
baseline_path = input_path.parent.parent.joinpath(
"baseline", input_path.name)
baseline_dcm = pydicom.read_file(str(baseline_path), force=True)
assert str(input_dcm) != str(baseline_dcm)
roi_contour_sequences = input_dcm.ROIContourSequence
for item in roi_contour_sequences:
pymedphys.dicom.merge_contours(item, inplace=True)
assert str(input_dcm) == str(baseline_dcm)
with tempfile.TemporaryDirectory() as temp_dir:
output_filename = str(pathlib.Path(temp_dir).joinpath("temp.dcm"))
command = "pymedphys dicom merge-contours".split() + [
str(input_path),
output_filename,
]
subprocess.check_call(command)
cli_dcm = pydicom.read_file(output_filename, force=True)
assert str(cli_dcm) == str(baseline_dcm)
def get_file_within_data_zip(zip_name, file_name):
dose_data_files = pymedphys.zip_data_paths(zip_name)
path_match = [path for path in dose_data_files if path.name == file_name]
assert len(path_match) == 1
return str(path_match[0])
def get_file_in_dir(directory, filename):
all_paths = pymedphys.zip_data_paths("delivery_test_data.zip")
filtered = [
path
for path in all_paths
if path.parent.name == directory and path.name == filename
]
assert len(filtered) == 1
return str(filtered[0])
def test_lossless_jpeg():
testing_data = pymedphys.zip_data_paths("lossless_jpeg_test.zip")
input_jpg = [path for path in testing_data if path.name == "input.jpg"][0]
output_ppm = [path for path in testing_data
if path.name == "output.ppm"][0]
reference = imageio.imread(output_ppm)
with tempfile.TemporaryDirectory() as tmpdirname:
output_file = pathlib.Path(tmpdirname).joinpath("output.ppm")
pymedphys._losslessjpeg.convert_lossless_jpeg( # pylint: disable = protected-access
input_jpg, output_file)
result = imageio.imread(output_file)
assert np.all(reference == result)
def test_end_to_end():
edge_lengths = [20, 20]
image_paths = pymedphys.zip_data_paths("wlutz_images.zip")
results = pymedphys._wlutz.iview.batch_process( # pylint:disable = protected-access
image_paths,
edge_lengths,
display_figure=False)
reference_dataframe = pd.read_csv(HERE.joinpath("end_to_end.csv"))
assert np.max(
np.abs(results["Rotation"] - reference_dataframe["Rotation"])) <= 0.1
assert (np.max(
np.max(
np.abs(
results.drop(columns=["Rotation"]) -
reference_dataframe.drop(columns=["Rotation"])))) <= 0.05)
def test_conversions():
data_paths = pymedphys.zip_data_paths("trf-references-and-baselines.zip")
files_with_references = [
path for path in data_paths
if path.parent.name == "with_reference" and path.suffix == ".trf"
]
assert len(files_with_references) >= 5
files_without_references = [
path for path in data_paths
if path.parent.name == "with_baseline" and path.suffix == ".trf"
]
assert len(files_without_references) >= 4
with tempfile.TemporaryDirectory() as output_directory:
for filepath in files_with_references:
convert_and_check_against_reference(filepath, output_directory)
for filepath in files_without_references:
convert_and_check_against_baseline(filepath, output_directory)
def download_and_extract_demo_data(cwd):
pymedphys.zip_data_paths("mu-density-gui-e2e-data.zip",
extract_directory=cwd)
def dataset():
path = pymedphys.zip_data_paths("dicom-to-delivery-issue-#1047.zip")[0]
return pydicom.dcmread(path)
