def test_base_object():
empty = Delivery._empty()
assert empty.monitor_units == tuple()
collection = {field: getattr(empty, field) for field in empty._fields}
dummy = Delivery(**collection)
def test_object_consistency():
empty = Delivery._empty()
filtered = empty._filter_cps()
assert isinstance(filtered.monitor_units, tuple)
filtered._metersets(0, 0)
def test_round_trip_dcm2dd2dcm(loaded_dicom_dataset):
original = loaded_dicom_dataset
delivery_data = Delivery.from_dicom(original, FRACTION_GROUP)
processed = delivery_data.to_dicom(original)
single_fraction_group = convert_to_one_fraction_group(
original, FRACTION_GROUP)
original_gantry_angles = get_gantry_angles_from_dicom(
single_fraction_group)
assert num_of_control_points(
single_fraction_group) == num_of_control_points(processed)
assert maintain_order_unique(
delivery_data.gantry) == original_gantry_angles
processed_gantry_angles = get_gantry_angles_from_dicom(processed)
assert original_gantry_angles == processed_gantry_angles
assert source_to_surface_distances(
single_fraction_group) == source_to_surface_distances(processed)
assert first_mlc_positions(single_fraction_group) == first_mlc_positions(
processed)
assert str(single_fraction_group) == str(processed)
def test_fraction_group_number(loaded_dicom_dataset,
logfile_delivery_data: Delivery):
expected = FRACTION_GROUP
result = logfile_delivery_data._fraction_number(loaded_dicom_dataset)
assert result == expected
def test_mudensity_agreement(loaded_dicom_dataset, logfile_delivery_data):
dicom_delivery_data = Delivery.from_dicom(loaded_dicom_dataset, FRACTION_GROUP)
dicom_mu_density = dicom_delivery_data.mudensity(grid_resolution=5)
logfile_mu_density = logfile_delivery_data.mudensity(grid_resolution=5)
diff = logfile_mu_density - dicom_mu_density
max_diff = np.max(np.abs(diff))
std_diff = np.std(diff)
try:
assert max_diff < 4.1
assert std_diff < 0.4
except AssertionError:
max_val = np.max([np.max(logfile_mu_density), np.max(dicom_mu_density)])
plt.figure()
plt.pcolormesh(dicom_mu_density, vmin=0, vmax=max_val)
plt.colorbar()
plt.figure()
plt.pcolormesh(logfile_mu_density, vmin=0, vmax=max_val)
plt.colorbar()
plt.figure()
plt.pcolormesh(
logfile_mu_density - dicom_mu_density,
vmin=-max_diff,
vmax=max_diff,
cmap="bwr",
)
plt.colorbar()
plt.show()
raise
def test_round_trip_dd2dcm2dd(loaded_dicom_dataset, logfile_delivery_data: Delivery):
original = logfile_delivery_data._filter_cps()
template = loaded_dicom_dataset
dicom = original.to_dicom(template)
processed = Delivery.from_dicom(dicom, FRACTION_GROUP)
assert np.all(
np.around(original.monitor_units, 2) == np.around(processed.monitor_units, 2)
)
assert np.all(np.around(original.gantry, 2) == np.around(processed.gantry, 2))
assert np.all(np.around(original.mlc, 2) == np.around(processed.mlc, 2))
assert np.all(np.around(original.jaw, 2) == np.around(processed.jaw, 2))
# Collimator not currently handled appropriately
assert np.all(
np.around(original.collimator, 2) == np.around(processed.collimator, 2)
)
from pymedphys.dicom import get_gantry_angles_from_dicom
input_directory = 'input'
output_directory = 'output'
grid_resolution = 5 / 3
gantry_angle_tolerance = 3
image_dpi = 254
trf_filepaths = glob(os.path.join(input_directory, '*.trf'))
dicom_filepaths = glob(os.path.join(input_directory, '*.dcm'))
filepath_mu_density_map: Dict[str, np.ndarray] = {}
filepath_mu_density_diff_map: Dict[str, np.ndarray] = {}
for trf_filepath in trf_filepaths:
trf_delivery: Delivery = Delivery.from_logfile(trf_filepath).filter_cps()
trf_filename = os.path.basename(trf_filepath)
for dicom_filepath in dicom_filepaths:
dicom_dataset = pydicom.dcmread(dicom_filepath,
force=True,
stop_before_pixels=True)
try:
dicom_deliveries = Delivery.load_all_fractions(dicom_dataset)
except AttributeError:
print("{} does not appear to be an RT DICOM plan, "
"skipping...".format(dicom_filepath))
continue
for fraction_number, dicom_delivery_raw in dicom_deliveries.items():
dicom_delivery = dicom_delivery_raw.filter_cps()
from pymedphys import Delivery
input_directory = "input"
output_directory = "output"
trf_filepaths = glob(os.path.join(input_directory, "*.trf"))
dicom_filepaths = glob(os.path.join(input_directory, "*.dcm"))
for filepath in trf_filepaths:
print("Preparing to convert {}".format(filepath))
filename = os.path.basename(filepath)
output_filepath = os.path.join(output_directory, "{}.dcm".format(filename))
print("Loading log file")
delivery_data = Delivery.from_logfile(filepath)
print("Converting log file to RT Plan DICOM")
for dicom_filepath in dicom_filepaths:
dicom_template = pydicom.dcmread(dicom_filepath, force=True)
try:
created_dicom = delivery_data.to_dicom(dicom_template)
print("{} appears to be an RT DICOM plan with appropriate "
"angle meterset combination, using this one.".format(
dicom_filepath))
continue
except AttributeError:
print("{} does not appear to be an RT DICOM plan, "
"skipping...".format(dicom_filepath))
print("Saving newly created RT Plan DICOM")
def mu_density_from_delivery_data(delivery_data: pymedphys.Delivery, grid_resolution=1):
grid_xx, grid_yy = pymedphys.mudensity.grid(grid_resolution=grid_resolution)
mu_density = delivery_data.mudensity(grid_resolution=grid_resolution)
return grid_xx, grid_yy, mu_density
def logfile_delivery_data():
return Delivery.from_logfile(LOGFILE_FILEPATH)
def logfile_delivery_data():
path = get_file_in_dir(DIR_TO_TEST, "imrt.trf")
return Delivery.from_logfile(path)
import pymedphys
from pymedphys import Delivery
# trf file read
trf_file = 'C:/GitFolder/VMAT-QA-metrics/MU intensity/MonacoHDMLC.trf'
delivery = Delivery.from_logfile(trf_file)
trf_mu_density = delivery.mudensity() # This is the "fluence"
grid = pymedphys.mudensity.grid()
pymedphys.mudensity.display(grid, trf_mu_density) # plot the MU density
# dicom file read
# dicom_rtplan_filepath = 'C:/GitFolder/VMAT-QA-metrics/example/test_case/VMAT1Arc/0028_VMAT202003181arc.dcm'
# fraction_number = 28
# delivery = Delivery.from_dicom_file(dicom_rtplan_filepath, fraction_number)
# dcm_mudensity = delivery.mudensity() # This is the "fluence"
# plot the comparison
# subplot(1,2,1)
# plt.imshow(trf_mu_density)
# plt.title('TRF file (Elekta Log file)')
# subplot(1,2,2)
# plt.imshow(dcm_mudensity)
# plt.title('DCM file (Monaco Plan file)')
# plt.colorbar()
# plt.show()
