def __init__(self):
self.batch_dir = Path.cwd().joinpath('test', 'batchtestdata')
self.dicom_structure = DICOMDirectorySearch.get_dicom_structure(
self.batch_dir, self.DummyProgressWindow, self.DummyProgressWindow)
self.iso_levels = self.get_iso_levels()
self.timestamp = BatchProcessingController.create_timestamp()
self.application = QApplication()
def test_batch_pyrad2pyradsr(test_object):
"""
Test that a DICOM file 'PyRadiomics-SR.dcm' is created from
Pyrad2Pyrad-SR.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Loop through patient datasets
for patient in test_object.get_patients():
# Get the files for the patient
cur_patient_files = \
BatchProcessingController.get_patient_files(patient)
# Create and setup the batch process
process = BatchProcessPyRad2PyRadSR(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files)
# Start the process
process.start()
# Get dataset directory
directory = process.patient_dict_container.path
# Get Pyradiomics SR, assert it exists
file_name = 'Pyradiomics-SR.dcm'
path = Path(directory).joinpath(file_name)
assert os.path.exists(str(path))
# Delete Pyradiomics SR
os.remove(path)
def test_batch_pyrad2csv(test_object):
"""
Test asserts creation of CSV as result of PyRad2CSV conversion.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Loop through patient datasets
for patient in test_object.get_patients():
cur_patient_files = BatchProcessingController.get_patient_files(
patient)
# Create and setup the Batch Process
process = BatchProcessPyRad2CSV(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files,
test_object.batch_dir)
# Target filename
filename = 'Pyradiomics_' + test_object.timestamp + '.csv'
# Set the filename
process.set_filename(filename)
# Start the process
process.start()
# Assert the resulting .csv file exists
assert os.path.isfile(
Path.joinpath(test_object.batch_dir, 'CSV', filename))
def test_batch_dvh2csv(test_object):
"""
Test asserts creation of CSV as result of DVH2CSV conversion.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Loop through patient datasets
for patient in test_object.get_patients():
cur_patient_files = BatchProcessingController.get_patient_files(
patient)
# Create and setup the Batch Process
process = BatchProcessDVH2CSV(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files,
str(test_object.batch_dir))
# Target filename
filename = 'DVHs_' + test_object.timestamp + '.csv'
# Set the filename
process.set_filename(filename)
# Start the process
process.start()
# Assert the resulting .csv file exists
assert os.path.isfile(
Path.joinpath(test_object.batch_dir, 'CSV', filename))
# Assert that there is DVH data in the RT Dose
rtdose = process.patient_dict_container.dataset['rtdose']
assert len(rtdose.DVHSequence) > 0
def test_batch_suv2roi(test_object):
"""
Test that at least 1 new ROI is created from SUV2ROI.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Loop through patient datasets
for patient in test_object.get_patients():
# Get the files for the patient
cur_patient_files = BatchProcessingController.get_patient_files(
patient)
# Create and setup the Batch Process
patient_weight = 70000
process = BatchProcessSUV2ROI(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files, patient_weight)
# Start the process
result = process.start()
if not result:
return
# Get rtss
rtss = process.patient_dict_container.dataset['rtss']
# Get ROIS from rtss
rois = []
for roi in rtss.StructureSetROISequence:
rois.append(roi.ROIName)
# Assert rtss contains new rois
difference = set(test_object.iso_levels) - set(rois)
assert len(difference) > 0
def test_batch_iso2roi(test_object):
"""
Test that at least 1 new ROI is created from ISO2ROI.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Loop through patient datasets
for patient in test_object.get_patients():
# Get the files for the patient
cur_patient_files = BatchProcessingController.get_patient_files(
patient)
# Create and setup the Batch Process
process = BatchProcessISO2ROI(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files)
# Start the process
result = process.start()
# Get rtss
if not result:
return
rtss = process.patient_dict_container.dataset['rtss']
# Get ROIS from rtss
rois = []
for roi in rtss.StructureSetROISequence:
rois.append(roi.ROIName)
# Assert rtss contains new rois
difference = set(test_object.iso_levels) - set(rois)
assert len(difference) > 0
# An rtss.dcm is being created during this batch test - this is
# because the existing RTSTRUCT in DICOM-RT-02 does not match the
# rest of the dataset. We need to delete this, or future tests
# will fail.
rtss_path = test_object.batch_dir.joinpath("DICOM-RT-02", "rtss.dcm")
os.remove(rtss_path)
def test_batch_roi_name_to_fma_id(test_object):
"""
Test asserts an ROI changes name and one is deleted.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Get RTSS file path, count number of ROIs
rtss_path = None
for root, dirs, files in os.walk(test_object.batch_dir, topdown=True):
for name in files:
try:
ds = dcmread(os.path.join(root, name))
if ds.SOPClassUID == '1.2.840.10008.5.1.4.1.1.481.3':
rtss_path = os.path.join(root, name)
break
except (InvalidDicomError, FileNotFoundError):
pass
# Assert rtss exists
assert rtss_path is not None
assert os.path.exists(rtss_path)
for patient in test_object.get_patients():
# Get the files for the patient
cur_patient_files = BatchProcessingController.get_patient_files(
patient)
# Create and setup the Batch Process
process = BatchProcessROIName2FMAID(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files)
# Start the process
status = process.start()
assert status
# Assert no ROIs called Lungs exists
ds = dcmread(rtss_path)
for roi in ds.StructureSetROISequence:
assert roi.ROIName != 'Lungs'
def setup_ui(self, batch_window_instance):
"""
Sets up the UI for the batch processing window.
"""
# Get the appropriate stylesheet
if platform.system() == 'Darwin':
self.stylesheet_path = "res/stylesheet.qss"
else:
self.stylesheet_path = "res/stylesheet-win-linux.qss"
self.stylesheet = open(resource_path(self.stylesheet_path)).read()
# Create class variables
self.file_path = "Select file path..."
# Label font
label_font = QtGui.QFont()
label_font.setPixelSize(14)
# Set the window icon
window_icon = QtGui.QIcon()
window_icon.addPixmap(
QtGui.QPixmap(resource_path("res/images/icon.ico")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
# Set window properties
batch_window_instance.setObjectName("BatchWindowInstance")
batch_window_instance.setWindowIcon(window_icon)
batch_window_instance.setWindowTitle("Batch Processing")
batch_window_instance.resize(840, 530)
# == Directory widgets
# Directory label
dir_label_text = "Select directory to perform batch processing on:"
self.dir_info_label = QtWidgets.QLabel(dir_label_text)
self.dir_info_label.setFont(label_font)
# Directory line edit
self.directory_input = QtWidgets.QLineEdit()
self.directory_input.setText(self.file_path)
self.directory_input.textChanged.connect(self.line_edit_changed)
self.directory_input.setStyleSheet(self.stylesheet)
# Label to display file search status
self.search_progress_label = QtWidgets.QLabel("No directory is "
"currently selected.")
self.search_progress_label.setFont(label_font)
# Browse button
self.browse_button = QtWidgets.QPushButton("Change")
self.browse_button.setObjectName("NormalButton")
self.browse_button.setStyleSheet(self.stylesheet)
# == Tab widgets
# Tab widget
self.tab_widget = CheckableTabWidget()
self.tab_widget.tabBar().setObjectName("batch-tabs")
self.tab_widget.setStyleSheet(self.stylesheet)
# Tabs
self.iso2roi_tab = ISO2ROIOptions()
self.suv2roi_tab = SUV2ROIOptions()
self.dvh2csv_tab = DVH2CSVOptions()
self.pyrad2csv_tab = PyRad2CSVOptions()
self.pyrad2pyradSR_tab = Pyrad2PyradSROptions()
self.csv2clinicaldatasr_tab = CSV2ClinicalDataSROptions()
self.clinicaldatasr2csv_tab = ClinicalDataSR2CSVOptions()
self.batchnamecleaning_tab = ROINameCleaningOptions()
self.batchname2fma_tab = ROIName2FMAIDOptions()
# Add tabs to tab widget
self.tab_widget.addTab(self.iso2roi_tab, "ISO2ROI")
self.tab_widget.addTab(self.suv2roi_tab, "SUV2ROI")
self.tab_widget.addTab(self.dvh2csv_tab, "DVH2CSV")
self.tab_widget.addTab(self.pyrad2csv_tab, "PyRad2CSV")
self.tab_widget.addTab(self.pyrad2pyradSR_tab, "Pyrad2Pyrad-SR")
self.tab_widget.addTab(self.csv2clinicaldatasr_tab,
"CSV2ClinicalData-SR")
self.tab_widget.addTab(self.clinicaldatasr2csv_tab,
"ClinicalData-SR2CSV")
self.tab_widget.addTab(self.batchnamecleaning_tab, "ROI Name Cleaning")
self.tab_widget.addTab(self.batchname2fma_tab, "ROI Name to FMA ID")
# == Bottom widgets
# Info text
info_text = "Batch Processing will be performed on datasets in the "
info_text += "selected directory."
self.info_label = QtWidgets.QLabel(info_text)
self.info_label.setFont(label_font)
# Back button
self.back_button = QtWidgets.QPushButton("Exit")
self.back_button.setObjectName("BatchExitButton")
self.back_button.setMaximumWidth(80)
self.back_button.setStyleSheet(self.stylesheet)
self.back_button.setProperty("QPushButtonClass", "fail-button")
# Begin button
self.begin_button = QtWidgets.QPushButton("Begin")
self.begin_button.setObjectName("BeginButton")
self.begin_button.setMaximumWidth(100)
self.begin_button.setStyleSheet(self.stylesheet)
self.begin_button.setProperty("QPushButtonClass", "success-button")
self.begin_button.setEnabled(False)
# == Set layout
# Create layouts
self.layout = QtWidgets.QVBoxLayout()
self.directory_layout = QtWidgets.QGridLayout()
self.middle_layout = QtWidgets.QVBoxLayout()
self.bottom_layout = QtWidgets.QGridLayout()
# Add top text
self.layout.addWidget(self.dir_info_label)
# Add directory widgets
self.directory_layout.addWidget(self.directory_input)
self.directory_layout.addWidget(self.browse_button, 0, 1)
self.directory_layout.addWidget(self.search_progress_label, 1, 0)
self.layout.addLayout(self.directory_layout)
# Add middle widgets (patient count, tabs)
self.middle_layout.addWidget(self.tab_widget)
self.layout.addLayout(self.middle_layout)
# Add bottom widgets (buttons)
self.bottom_layout.addWidget(self.info_label, 0, 0, 2, 4)
self.bottom_layout.addWidget(self.back_button, 2, 2, 1, 1)
self.bottom_layout.addWidget(self.begin_button, 2, 3, 1, 1)
self.layout.addLayout(self.bottom_layout)
# Connect buttons to functions
self.browse_button.clicked.connect(self.show_file_browser)
self.begin_button.clicked.connect(self.confirm_button_clicked)
self.back_button.clicked.connect(
lambda: QtCore.QCoreApplication.exit(0))
# Set window layout
batch_window_instance.setLayout(self.layout)
# Create batch processing controller, enable the processing
self.batch_processing_controller = BatchProcessingController()
class UIBatchProcessingWindow(object):
"""
This class contains the user interface for the batch processing
window.
"""
def setup_ui(self, batch_window_instance):
"""
Sets up the UI for the batch processing window.
"""
# Get the appropriate stylesheet
if platform.system() == 'Darwin':
self.stylesheet_path = "res/stylesheet.qss"
else:
self.stylesheet_path = "res/stylesheet-win-linux.qss"
self.stylesheet = open(resource_path(self.stylesheet_path)).read()
# Create class variables
self.file_path = "Select file path..."
# Label font
label_font = QtGui.QFont()
label_font.setPixelSize(14)
# Set the window icon
window_icon = QtGui.QIcon()
window_icon.addPixmap(
QtGui.QPixmap(resource_path("res/images/icon.ico")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
# Set window properties
batch_window_instance.setObjectName("BatchWindowInstance")
batch_window_instance.setWindowIcon(window_icon)
batch_window_instance.setWindowTitle("Batch Processing")
batch_window_instance.resize(840, 530)
# == Directory widgets
# Directory label
dir_label_text = "Select directory to perform batch processing on:"
self.dir_info_label = QtWidgets.QLabel(dir_label_text)
self.dir_info_label.setFont(label_font)
# Directory line edit
self.directory_input = QtWidgets.QLineEdit()
self.directory_input.setText(self.file_path)
self.directory_input.textChanged.connect(self.line_edit_changed)
self.directory_input.setStyleSheet(self.stylesheet)
# Label to display file search status
self.search_progress_label = QtWidgets.QLabel("No directory is "
"currently selected.")
self.search_progress_label.setFont(label_font)
# Browse button
self.browse_button = QtWidgets.QPushButton("Change")
self.browse_button.setObjectName("NormalButton")
self.browse_button.setStyleSheet(self.stylesheet)
# == Tab widgets
# Tab widget
self.tab_widget = CheckableTabWidget()
self.tab_widget.tabBar().setObjectName("batch-tabs")
self.tab_widget.setStyleSheet(self.stylesheet)
# Tabs
self.iso2roi_tab = ISO2ROIOptions()
self.suv2roi_tab = SUV2ROIOptions()
self.dvh2csv_tab = DVH2CSVOptions()
self.pyrad2csv_tab = PyRad2CSVOptions()
self.pyrad2pyradSR_tab = Pyrad2PyradSROptions()
self.csv2clinicaldatasr_tab = CSV2ClinicalDataSROptions()
self.clinicaldatasr2csv_tab = ClinicalDataSR2CSVOptions()
self.batchnamecleaning_tab = ROINameCleaningOptions()
self.batchname2fma_tab = ROIName2FMAIDOptions()
# Add tabs to tab widget
self.tab_widget.addTab(self.iso2roi_tab, "ISO2ROI")
self.tab_widget.addTab(self.suv2roi_tab, "SUV2ROI")
self.tab_widget.addTab(self.dvh2csv_tab, "DVH2CSV")
self.tab_widget.addTab(self.pyrad2csv_tab, "PyRad2CSV")
self.tab_widget.addTab(self.pyrad2pyradSR_tab, "Pyrad2Pyrad-SR")
self.tab_widget.addTab(self.csv2clinicaldatasr_tab,
"CSV2ClinicalData-SR")
self.tab_widget.addTab(self.clinicaldatasr2csv_tab,
"ClinicalData-SR2CSV")
self.tab_widget.addTab(self.batchnamecleaning_tab, "ROI Name Cleaning")
self.tab_widget.addTab(self.batchname2fma_tab, "ROI Name to FMA ID")
# == Bottom widgets
# Info text
info_text = "Batch Processing will be performed on datasets in the "
info_text += "selected directory."
self.info_label = QtWidgets.QLabel(info_text)
self.info_label.setFont(label_font)
# Back button
self.back_button = QtWidgets.QPushButton("Exit")
self.back_button.setObjectName("BatchExitButton")
self.back_button.setMaximumWidth(80)
self.back_button.setStyleSheet(self.stylesheet)
self.back_button.setProperty("QPushButtonClass", "fail-button")
# Begin button
self.begin_button = QtWidgets.QPushButton("Begin")
self.begin_button.setObjectName("BeginButton")
self.begin_button.setMaximumWidth(100)
self.begin_button.setStyleSheet(self.stylesheet)
self.begin_button.setProperty("QPushButtonClass", "success-button")
self.begin_button.setEnabled(False)
# == Set layout
# Create layouts
self.layout = QtWidgets.QVBoxLayout()
self.directory_layout = QtWidgets.QGridLayout()
self.middle_layout = QtWidgets.QVBoxLayout()
self.bottom_layout = QtWidgets.QGridLayout()
# Add top text
self.layout.addWidget(self.dir_info_label)
# Add directory widgets
self.directory_layout.addWidget(self.directory_input)
self.directory_layout.addWidget(self.browse_button, 0, 1)
self.directory_layout.addWidget(self.search_progress_label, 1, 0)
self.layout.addLayout(self.directory_layout)
# Add middle widgets (patient count, tabs)
self.middle_layout.addWidget(self.tab_widget)
self.layout.addLayout(self.middle_layout)
# Add bottom widgets (buttons)
self.bottom_layout.addWidget(self.info_label, 0, 0, 2, 4)
self.bottom_layout.addWidget(self.back_button, 2, 2, 1, 1)
self.bottom_layout.addWidget(self.begin_button, 2, 3, 1, 1)
self.layout.addLayout(self.bottom_layout)
# Connect buttons to functions
self.browse_button.clicked.connect(self.show_file_browser)
self.begin_button.clicked.connect(self.confirm_button_clicked)
self.back_button.clicked.connect(
lambda: QtCore.QCoreApplication.exit(0))
# Set window layout
batch_window_instance.setLayout(self.layout)
# Create batch processing controller, enable the processing
self.batch_processing_controller = BatchProcessingController()
def show_file_browser(self):
"""
Show the file browser for selecting a folder for the Onko
default directory.
"""
# Open a file dialog and return chosen directory
folder = \
QtWidgets.QFileDialog.getExistingDirectory(None,
'Choose Directory ..',
'')
# If chosen directory is nothing (user clicked cancel) set to
# user home
if folder == "":
folder = expanduser("~")
# Update file path
self.file_path = folder
# Update directory text
self.directory_input.setText(self.file_path)
def line_edit_changed(self):
"""
When the line edit box is changed, update related fields,
start searching the directory.
"""
self.file_path = self.directory_input.text()
self.dvh2csv_tab.set_dvh_output_location(self.file_path, False)
self.pyrad2csv_tab.set_pyrad_output_location(self.file_path, False)
self.begin_button.setEnabled(False)
self.batch_processing_controller.set_dicom_structure(None)
self.batch_processing_controller.load_patient_files(
self.file_path, self.search_progress, self.search_completed)
def search_progress(self, progress_update):
"""
Changed the progress label
:param progress_update: current progress of file search
"""
self.search_progress_label.setText("Loading selected directory... ( "
"%s files searched)" %
progress_update)
def search_completed(self, dicom_structure):
"""
Called when patient files are loaded
:param dicom_structure: DICOMStructure
"""
if dicom_structure:
self.batch_processing_controller.set_dicom_structure(
dicom_structure)
self.begin_button.setEnabled(True)
self.search_progress_label.setText("%s patients found." %
len(dicom_structure.patients))
# Update tables
self.suv2roi_tab.populate_table(dicom_structure)
# Update the batch name cleaning table
batch_directory = self.directory_input.text()
self.batchnamecleaning_tab.populate_table(dicom_structure,
batch_directory)
else:
self.search_progress_label.setText("No patients were found.")
self.batch_processing_controller.set_dicom_structure(None)
def confirm_button_clicked(self):
"""
Executes when the confirm button is clicked.
"""
processes = [
'iso2roi', 'suv2roi', 'dvh2csv', 'pyrad2csv', 'pyrad2pyrad-sr',
'csv2clinicaldata-sr', 'clinicaldata-sr2csv', 'roinamecleaning',
'roiname2fmaid'
]
selected_processes = []
suv2roi_weights = self.suv2roi_tab.get_patient_weights()
# Return if SUV2ROI weights is None. Alert user weights are incorrect.
if suv2roi_weights is None:
self.show_invalid_weight_dialog()
return
# Get the selected processes
for i in range(self.tab_widget.count()):
if self.tab_widget.isChecked(i):
selected_processes.append(processes[i])
# Save the changed settings
self.iso2roi_tab.save_isodoses()
file_directories = {
"batch_path":
self.file_path,
"dvh_output_path":
self.dvh2csv_tab.get_dvh_output_location(),
"pyrad_output_path":
self.pyrad2csv_tab.get_pyrad_output_location(),
'clinical_data_input_path':
self.csv2clinicaldatasr_tab.get_csv_input_location(),
'clinical_data_output_path':
self.clinicaldatasr2csv_tab.get_csv_output_location()
}
# Setup the batch processing controller
self.batch_processing_controller.set_file_paths(file_directories)
self.batch_processing_controller.set_processes(selected_processes)
self.batch_processing_controller.set_suv2roi_weights(suv2roi_weights)
# Set batch ROI name cleaning options if selected
if 'roinamecleaning' in selected_processes:
# Get ROIs, datasets, options
name_cleaning_options = {}
roi_name_table = self.batchnamecleaning_tab.table_roi
for i in range(roi_name_table.rowCount()):
# Get current ROI name and what to do with it
roi_name = roi_name_table.item(i, 0).text()
option = roi_name_table.cellWidget(i, 1).currentIndex()
# Get new name text
if isinstance(roi_name_table.cellWidget(i, 2),
ROINameCleaningPrefixEntryField):
new_name = roi_name[0:3] \
+ roi_name_table.cellWidget(i, 2).text()
# Remove any whitespace, replace with underscores
new_name = '_'.join(new_name.split())
else:
new_name = roi_name_table.cellWidget(i, 2).currentText()
# Get the dataset(s) the ROI is in
dataset_list = []
dataset_combo_box = roi_name_table.cellWidget(i, 3)
rtss_path = self.directory_input.text()
for index in range(dataset_combo_box.count()):
dataset_list.append(rtss_path +
dataset_combo_box.itemText(index))
if roi_name not in name_cleaning_options.keys():
name_cleaning_options[roi_name] = []
for item in dataset_list:
name_cleaning_options[roi_name].append(
[option, new_name, item])
# Set batch name cleaning parameters in the batch processing
# controller.
self.batch_processing_controller.set_name_cleaning_options(
name_cleaning_options)
# Enable processing
self.batch_processing_controller.start_processing()
def show_invalid_weight_dialog(self):
"""
Shows a dialog informing the user that an entered weight in the
SUV2ROI tab is invalid (either negative or not a number).
"""
button_reply = \
QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Warning,
"Invalid Patient Weight",
"Please enter a valid patient weight.",
QtWidgets.QMessageBox.StandardButton.Ok,
self)
button_reply.button(
QtWidgets.QMessageBox.StandardButton.Ok).setStyleSheet(
self.stylesheet)
button_reply.exec_()
def test_batch_clinicaldatasr2csv(test_object):
"""
Test asserts a CSV is created with dummy clinical data. Test deletes
CSV after running.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Get patient ID for dummy SR
patient_id = None
for root, dirs, files in os.walk(test_object.batch_dir, topdown=True):
if patient_id is not None:
break
for name in files:
try:
ds = dcmread(os.path.join(root, name))
if hasattr(ds, 'PatientID') \
and ds.SOPClassUID == '1.2.840.10008.5.1.4.1.1.2':
patient_id = ds.PatientID
break
except (InvalidDicomError, FileNotFoundError):
pass
# Assert a patient ID was found
assert patient_id is not None
# Create dummy SR
dcm_path = test_object.batch_dir.joinpath("Clinical-Data-SR.dcm")
text_data = "MD5Hash: " + patient_id + "\n"
text_data += "Age: 20\nNationality: Australian\n"
dicom_sr = DICOMStructuredReport.generate_dicom_sr(dcm_path, ds, text_data,
"CLINICAL-DATA")
dicom_sr.save_as(dcm_path)
# Assert dummy SR was created
assert os.path.exists(dcm_path)
# Reload patient (to get newly created SR)
patients = DICOMDirectorySearch.get_dicom_structure(
test_object.batch_dir, test_object.DummyProgressWindow,
test_object.DummyProgressWindow)
# Loop through each patient
for patient in patients.patients.values():
# Get current patient files
cur_patient_files = BatchProcessingController.get_patient_files(
patient)
# Create Batch Clinical Data SR to CSV object
process = \
BatchProcessClinicalDataSR2CSV(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files,
test_object.batch_dir)
# Start the process, assert it finished successfully
status = process.start()
assert status
# Assert CSV exists
csv_path = test_object.batch_dir.joinpath("ClinicalData.csv")
assert os.path.exists(csv_path)
# Assert data is correct in CSV
with open(csv_path, newline="") as stream:
data = list(csv.reader(stream))
stream.close()
assert data[0] == ["MD5Hash", "Age", "Nationality"]
assert data[1] == [patient_id, "20", "Australian"]
# Delete dummy CSV and SR
os.remove(csv_path)
os.remove(dcm_path)
def test_batch_csv2clinicaldatasr(test_object):
"""
Test asserts an SR is created with dummy clinical data. Test deletes
SR after running.
:param test_object: test_object function, for accessing the shared
TestObject object.
"""
# Get patient ID for dummy CSV
patient_id = None
for root, dirs, files in os.walk(test_object.batch_dir, topdown=True):
if patient_id is not None:
break
for name in files:
try:
ds = dcmread(os.path.join(root, name))
if hasattr(ds, 'PatientID'):
patient_id = ds.PatientID
break
except (InvalidDicomError, FileNotFoundError):
pass
assert patient_id is not None
# Create dummy CSV
csv_path = test_object.batch_dir.joinpath("dummy_cd.csv")
data = [['MD5Hash', 'Age', 'Nationality'],
[patient_id, '20', 'Australian']]
with open(csv_path, "w", newline="") as f:
writer = csv.writer(f)
writer.writerow(data[0])
writer.writerow(data[1])
f.close()
# Loop through each patient
for patient in test_object.get_patients():
# Get current patient files
cur_patient_files = BatchProcessingController.get_patient_files(
patient)
# Create Batch CSV to Clinical Data SR object
process = \
BatchProcessCSV2ClinicalDataSR(test_object.DummyProgressWindow,
test_object.DummyProgressWindow,
cur_patient_files,
csv_path)
# Start the process, assert it finished successfully
status = process.start()
assert status
# Assert SR exists
sr_path = test_object.batch_dir.joinpath("DICOM-RT-02",
"Clinical-Data-SR.dcm")
assert os.path.exists(sr_path)
# Assert data is correct in SR
text_data = "MD5Hash: " + patient_id + "\n"
text_data += "Age: 20\nNationality: Australian\n"
sr_ds = dcmread(sr_path)
assert sr_ds.SeriesDescription == "CLINICAL-DATA"
sr_text_data = sr_ds.ContentSequence[0].TextValue
assert text_data == sr_text_data
# Delete dummy CSV and SR
os.remove(csv_path)
os.remove(sr_path)