def setup_planing_item(self):
if self.dcm_files is not None and self.case is not None:
if self.dvh_calculator is not None:
# TODO refactor this into abstractions
plan_dcm = PyDicomParser(filename=self.dcm_files['rtplan'])
dose_dcm = PyDicomParser(filename=self.dcm_files['rtdose'])
plan_dict = plan_dcm.GetPlan()
dose_3d = dose_dcm.get_dose_3d()
self._planning_item = PyPlanningItem(plan_dict, self.case,
dose_3d,
self.dvh_calculator)
def test_gk_dvh():
# Given
slicer_dvh_file = r'C:\Users\Victor\Dropbox\Plan_Competition_Project\tests\tests_data\gk_plan\SLICER_RT_DVH.csv'
plan_folder = r'C:\Users\Victor\Dropbox\Plan_Competition_Project\tests\tests_data\gk_plan'
slicer_dvh = read_slicer_dvh(slicer_dvh_file)
# strip columns names
slicer_dvh.columns = [
'Skull Value', 'CerebelarDir', 'FrontalEsq ', 'Tumor', 'Tumor 2',
'Tumor 3', 'Tumor 4', 'Tumor 5'
]
dcm_files, flag = get_participant_folder_data(plan_folder)
plan_dict = PyDicomParser(filename=dcm_files['rtplan']).GetPlan()
structures = PyDicomParser(filename=dcm_files['rtss']).GetStructures()
rd_dcm = PyDicomParser(filename=dcm_files['rtdose'])
dose = rd_dcm.get_dose_3d()
structures_py = [
PyStructure(s, end_cap=s['thickness'] / 2)
for k, s in structures.items()
]
grid = (0.1, 0.1, 0.1)
dvh_pyplan = {}
for s in structures_py[:-1]:
dvh_calci = DVHCalculation(s, dose, calc_grid=grid)
dvh_l = dvh_calci.calculate(verbose=True)
dvh_pyplan[dvh_l['name']] = dvh_l
# plot_dvh(dvh_l, dvh_l['name'])
for target_name, dvh_calc in dvh_pyplan.items():
dose_t5 = slicer_dvh.index
t5 = slicer_dvh.loc[:, target_name].values
x_calc = np.arange(len(dvh_calc['data'])) * float(dvh_calc['scaling'])
py_t5 = dvh_calc['data']
plt.plot(dose_t5, t5, label='Slicer-RT')
plt.plot(x_calc, py_t5, label='PyPlanScoring')
plt.title(target_name)
plt.legend()
plt.show()
def test_dvh_comparisson(setup_calculation_options):
# Given plan DVH
folder = os.path.join(DATA_DIR, 'lungSBRT')
# parse DICOM folder
# plan_folder = r'C:\Users\Victor\Dropbox\Plan_Competition_Project\tests\tests_data\pinnacle\plan1'
plan_folder = r'C:\Users\Victor\Dropbox\Plan_Competition_Project\tests\tests_data\pinnacle\plan2'
dcm_files, flag = get_participant_folder_data(plan_folder)
rs_dvh = os.path.join(folder, 'RS.dcm')
plan_dict = PyDicomParser(filename=dcm_files['rtplan']).GetPlan()
# structures = PyDicomParser(filename=dcm_files['rtss']).GetStructures()
structures = PyDicomParser(filename=rs_dvh).GetStructures()
rd_dcm = PyDicomParser(filename=dcm_files['rtdose'])
dose = rd_dcm.get_dose_3d()
# criteria file
file_path = os.path.join(folder, 'Scoring_criteria.xlsx')
criteria = pd.read_excel(file_path, sheet_name='BiLateralLungSBRTCase')
# setup RT case
rt_case_tmp = RTCase("SBRT", 123, structures, criteria)
dvh_calc = DVHCalculator(rt_case_tmp, setup_calculation_options)
# when calculate DVH using pyplanScoring
planning_obj = PyPlanningItem(plan_dict, rt_case_tmp, dose, dvh_calc)
planning_obj.calculate_dvh()
# for k, v in planning_obj.dvh_data.items():
# plot_dvh(v, v['name'])
# plt.show()
# # Calculating the score
plan_eval = PlanEvaluation()
plan_eval.criteria = criteria
df = plan_eval.eval_plan(planning_obj)
raw_score = df['Raw score'].sum()
pass
# planIQ dvh
dvh_ref_path = '/home/victor/Dropbox/Plan_Competition_Project/tests/tests_data/ptv_based_SRS/PTV Based - PlanIQ DVH - Eclipse VMAT - Body included - Ahmad March 24.txt'
plan_iq_dvh = read_planiq_dvh(dvh_ref_path)
# compare against SLICER DV
plan_folder = r'/home/victor/Dropbox/Plan_Competition_Project/tests/tests_data/ptv_based_SRS'
# dcm_files, flag = get_participant_folder_data(plan_folder)
rtss = r'/home/victor/Dropbox/Plan_Competition_Project/tests/tests_data/ptv_based_SRS/RS.1.2.246.352.205.5644208623194161296.369175407993399980.dcm'
rt_dose = '/home/victor/Dropbox/Plan_Competition_Project/tests/tests_data/ptv_based_SRS/RD.1.2.246.352.71.7.584747638204.1898898.20180324182516.dcm'
ini_file = '/home/victor/Dropbox/Plan_Competition_Project/gui/cases/BrainMetSRSCase/PyPlanScoring.ini'
setup_calculation_options = get_calculation_options(ini_file)
structures = PyDicomParser(filename=rtss).GetStructures()
rd_dcm = PyDicomParser(filename=rt_dose)
dose = rd_dcm.get_dose_3d()
plan_dict = {}
# criteria file
file_path = '/home/victor/Dropbox/Plan_Competition_Project/tests/tests_data/ptv_based_SRS/Scoring_criteria.xlsx'
criteria = pd.read_excel(file_path, sheet_name='BrainSRS')
# setup RT case
rt_case_tmp = RTCase("SRS", 123, structures, criteria)
dvh_calc = DVHCalculator(rt_case_tmp, setup_calculation_options)
# when calculate DVH using pyplanScoring
planning_obj = PyPlanningItem(plan_dict, rt_case_tmp, dose, dvh_calc)
planning_obj.calculate_dvh()
# # Calculating the score
