def test_parse_dicom_folder(dicom_folder):
# given
p_kernel = PyPlanScoringKernel()
# when having a folder containing RS/RD/RP dicom
# then
p_kernel.parse_dicom_folder(dicom_folder)
assert p_kernel.dcm_files
def test_parse_empty_dicom_folder(tmpdir):
# given
p_kernel = PyPlanScoringKernel()
# when having a folder containing RS/RD/RP dicom
# then
with pytest.raises(FileNotFoundError):
p_kernel.parse_dicom_folder(tmpdir)
def test_setup_case(dicom_folder):
# given case files
rs_dvh = os.path.join(dicom_folder, 'RS.dcm')
file_path = os.path.join(dicom_folder, 'Scoring_criteria_2018.xlsx')
case_name = 'BiLateralLungSBRTCase'
# when instantiate
p_kernel = PyPlanScoringKernel()
p_kernel.setup_case(rs_dvh, file_path, case_name)
assert p_kernel.case is not None
def __init__(self, parent=None):
super(MainDialog, self).__init__(parent=parent)
self.setupUi(self)
self.folder_root = None
self.result = None
# calculation kernel
self.calc_kernel = PyPlanScoringKernel()
# Redirect STD out to
stdout = OutputWrapper(self, True)
stdout.outputWritten.connect(self.handle_output)
stderr = OutputWrapper(self, False)
stderr.outputWritten.connect(self.handle_output)
self.worker = Worker()
# connect Signal and Slots
self.set_conections()
self.save_reports_button.setEnabled(False)
self.textBrowser.setOpenExternalLinks(True)
def test_setup_dvh_calculation(dicom_folder, ini_file_path):
# given case files
rs_dvh = os.path.join(dicom_folder, 'RS.dcm')
file_path = os.path.join(dicom_folder, 'Scoring_criteria_2018.xlsx')
case_name = 'BiLateralLungSBRTCase'
# when instantiate
p_kernel = PyPlanScoringKernel()
# if not setup case before setup dvh calculator
p_kernel.setup_dvh_calculation(ini_file_path)
# then
assert p_kernel.dvh_calculator is None
# when setup case
p_kernel = PyPlanScoringKernel()
p_kernel.setup_case(rs_dvh, file_path, case_name)
p_kernel.setup_dvh_calculation(ini_file_path)
# then
assert p_kernel.dvh_calculator is not None
def test_calculate_dvh(dicom_folder, ini_file_path):
# given case files
rs_dvh = os.path.join(dicom_folder, 'RS.dcm')
file_path = os.path.join(dicom_folder, 'Scoring_criteria_2018.xlsx')
case_name = 'BiLateralLungSBRTCase'
# when instantiate
p_kernel = PyPlanScoringKernel()
p_kernel.parse_dicom_folder(dicom_folder)
p_kernel.setup_case(rs_dvh, file_path, case_name)
p_kernel.setup_dvh_calculation(ini_file_path)
p_kernel.setup_planing_item()
p_kernel.calculate_dvh()
assert p_kernel.dvh_data
def test_calc_plan_complexity(test_case, dicom_folder, ini_file_path):
# given case files
rs_dvh = os.path.join(dicom_folder, 'RS.dcm')
file_path = os.path.join(dicom_folder, 'Scoring_criteria_2018.xlsx')
case_name = 'BiLateralLungSBRTCase'
# when instantiate
p_kernel = PyPlanScoringKernel()
p_kernel.parse_dicom_folder(dicom_folder)
p_kernel.setup_case(rs_dvh, file_path, case_name)
p_kernel.setup_dvh_calculation(ini_file_path)
p_kernel.setup_planing_item()
# calculate plan complexity
p_kernel.calc_plan_complexity()
test_case.assertAlmostEqual(p_kernel.plan_complexity,
0.166503597706,
places=3)
def test_calc_plan_score(dicom_folder, ini_file_path):
# given case files
rs_dvh = os.path.join(dicom_folder, 'RS.dcm')
file_path = os.path.join(dicom_folder, 'Scoring_criteria_2018.xlsx')
case_name = 'BiLateralLungSBRTCase'
# when instantiate
p_kernel = PyPlanScoringKernel()
p_kernel.parse_dicom_folder(dicom_folder)
p_kernel.setup_case(rs_dvh, file_path, case_name)
p_kernel.setup_dvh_calculation(ini_file_path)
p_kernel.setup_planing_item()
p_kernel.calculate_dvh()
p_kernel.calc_plan_score()
assert not p_kernel._report_data_frame.empty
assert round(p_kernel._total_score) == round(90.01)
# save report data
p_kernel.save_report_data()
class MainDialog(QtGui.QMainWindow, PyPlanScoringBrainPTV.Ui_MainWindow):
def __init__(self, parent=None):
super(MainDialog, self).__init__(parent=parent)
self.setupUi(self)
self.folder_root = None
self.result = None
# calculation kernel
self.calc_kernel = PyPlanScoringKernel()
# Redirect STD out to
stdout = OutputWrapper(self, True)
stdout.outputWritten.connect(self.handle_output)
stderr = OutputWrapper(self, False)
stderr.outputWritten.connect(self.handle_output)
self.worker = Worker()
# connect Signal and Slots
self.set_conections()
self.save_reports_button.setEnabled(False)
self.textBrowser.setOpenExternalLinks(True)
def handle_output(self, text, stdout):
# self.listWidget.addItem(text)
self.textBrowser.insertPlainText(str(text))
def set_conections(self):
self.action_developer.triggered.connect(self.about)
self.import_button.clicked.connect(self.on_import)
self.save_reports_button.clicked.connect(self.on_save)
self.worker.worker_finished.connect(self.worker_done)
def worker_done(self, obj):
self.calc_kernel = obj
self.calc_kernel.save_dvh_data(self.name)
self.calc_kernel.save_report_data(self.name)
total_score = self.calc_kernel.total_score
self.textBrowser.insertPlainText('Total score: %1.2f \n' % total_score)
self.textBrowser.insertPlainText('---------- Metrics -------------\n')
# Pretty print
print(self.calc_kernel.report)
print()
if self.complexity_check_box.isChecked():
self.textBrowser.insertPlainText(
'---------- Complexity metric -------------\n')
# try:
self.calc_kernel.calc_plan_complexity()
self.calc_kernel.save_complexity_figure_per_beam()
self.textBrowser.insertPlainText(
"Aperture complexity: %1.3f [mm-1]:\n" %
self.calc_kernel.plan_complexity)
txt = 'It is a Python 3.x port of the Eclipse ESAPI plug-in script.\n' \
'As such, it aims to contain the complete functionality of the aperture complexity analysis\n'
self.textBrowser.insertPlainText(txt)
self.textBrowser.insertPlainText("Reference: ")
self.textBrowser.insertHtml(
"<a href=\"https://github.com/umro/Complexity\" > https://github.com/umro/Complexity</a>"
)
self.textBrowser.insertPlainText('\n')
# except:
# print("Aperture complexity is valid only in linac-based dynamic treatments - (IMRT/VMAT)")
def setup_case(self, file_path, case_name, ini_file_path, rs_dvh=''):
if not rs_dvh:
rs_dvh = self.calc_kernel.dcm_files[
'rtss'] # TODO add folder DVH file
self.calc_kernel.setup_case(rs_dvh, file_path, case_name)
self.calc_kernel.setup_dvh_calculation(ini_file_path)
self.calc_kernel.setup_planing_item()
def on_import(self):
self.textBrowser.clear()
self.name = self.lineEdit.text()
if self.name:
self.folder_root = QtGui.QFileDialog.getExistingDirectory(
self,
"Select the directory containing only: RP and RD Dicom RT dose files from one plan",
QtCore.QDir.currentPath())
if self.folder_root:
dcm_files, flag = self.calc_kernel.parse_dicom_folder(
self.folder_root)
if flag:
# setup case using global variables
self.setup_case(criteria_file, case_name, ini_file_path,
rs_dvh)
self.worker.set_calc_kernel(self.calc_kernel)
self.textBrowser.insertPlainText(
'Loaded - DICOM-RT Files: \n')
txt = [os.path.split(v)[1] for k, v in dcm_files.items()]
for t in txt:
self.textBrowser.insertPlainText(str(t) + '\n')
self.save_reports_button.setEnabled(True)
else:
msg = "<p>missing Dicom Files: " + str(dcm_files)
QtGui.QMessageBox.critical(self, "Missing Data", msg,
QtGui.QMessageBox.Abort)
else:
msg = "Please set the output file name"
QtGui.QMessageBox.critical(self, "Missing Data", msg,
QtGui.QMessageBox.Abort)
def on_save(self):
self.textBrowser.insertPlainText(
'------------- Calculating DVH and score --------------\n')
self.worker.start()
def about(self):
txt = "PyPlanScoring - 2018 - RT Plan Competition: %s \n" \
"Be the strongest link in the radiotherapy chain\n" \
"https://radiationknowledge.org \n" \
"Author: %s\n" \
"Copyright (C) 2017 - 2018 Victor Gabriel Leandro Alves, All rights reserved\n" \
"Platform details: Python %s on %s\n" \
"This program aims to calculate_integrate an approximate score.\n" \
"your final score may be different due to structure boundaries and dose interpolation uncertainties\n" \
"%s" \
% (__version__, __author__, platform.python_version(), platform.system(), __license__)
QtGui.QMessageBox.about(self, 'Information', txt)