def create_change_default_directory_frame(self):
config = Configuration()
default_directory = None
try:
default_directory = config.get_default_directory()
except SqlError:
config.set_up_config_db()
QtWidgets.QMessageBox.critical(
self.window, "Config file error",
"""Failed to access configuration file.
\nConfiguration file recreated with no default directory.
\nPlease update your default directory.""")
self.window.change_default_directory_frame = QtWidgets.QFrame()
self.window.change_default_directory_frame.setVisible(False)
self.change_default_directory_vertical_layout = QtWidgets.QVBoxLayout()
self.change_default_directory_prompt = QtWidgets.QLabel()
self.change_default_directory_prompt.setAlignment(QtCore.Qt.AlignLeft)
self.change_default_directory_prompt.setVisible(True)
self.change_default_directory_prompt.setText(
"Default directory's path:")
self.change_default_directory_vertical_layout.addWidget(
self.change_default_directory_prompt)
# Create a horizontal box to hold the input box for the
# directory and the choose button
self.change_default_directory_input_horizontal_box = \
QtWidgets.QHBoxLayout()
# Create a textbox to contain the path to the directory that
# contains the DICOM files
self.change_default_directory_input_box = \
UIChangeDefaultDirDragAndDropEvent(self)
self.change_default_directory_input_box.setCursorPosition(0)
self.change_default_directory_input_box.setText(default_directory)
self.change_default_directory_input_horizontal_box.addWidget(
self.change_default_directory_input_box)
# Create a choose button to open the file dialog
self.change_default_directory_button = QtWidgets.QPushButton()
self.change_default_directory_button.setText("Change")
self.change_default_directory_button.resize(
self.change_default_directory_button.sizeHint().width(),
self.change_default_directory_input_box.height())
self.change_default_directory_button.setCursor(
QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.change_default_directory_input_horizontal_box.addWidget(
self.change_default_directory_button)
self.change_default_directory_button.clicked.connect(
self.change_button_clicked)
# Create a widget to hold the input fields
self.change_default_directory_input_widget = QtWidgets.QWidget()
self.change_default_directory_input_horizontal_box.setStretch(0, 4)
self.change_default_directory_input_widget.setLayout(
self.change_default_directory_input_horizontal_box)
self.change_default_directory_vertical_layout.addWidget(
self.change_default_directory_input_widget, 1, QtCore.Qt.AlignTop)
self.window.change_default_directory_frame.setLayout(
self.change_default_directory_vertical_layout)
def init_first_time_window_config(request):
configuration = Configuration('TestFirstTimeWelcomeWindow.db')
db_file_path = os.environ['USER_HIDDEN'] + 'TestFirstTimeWelcomeWindow.db'
configuration.set_db_file_path(db_file_path)
def tear_down():
if os.path.isfile(db_file_path):
os.remove(db_file_path)
request.addfinalizer(tear_down)
def test_get_default_directory(init_sqlite_config):
configuration = Configuration()
new_default_dir = "/home/test/dir"
# Insert new default dir
init_sqlite_config.execute("""INSERT INTO configuration (id, default_dir)
VALUES (1, "%s");""" % new_default_dir)
init_sqlite_config.commit()
# Get default dir from configuration object
result = configuration.get_default_directory()
# Compare the value returned from get_default_directory() and the value from database
assert result == new_default_dir
def test_update_default_directory(init_sqlite_config):
configuration = Configuration()
new_default_dir = "/home/test/dir"
# Update default_dir with configuration object
configuration.update_default_directory(new_default_dir)
# Select default dir from the database
cursor = init_sqlite_config.cursor()
cursor.execute("SELECT default_dir FROM CONFIGURATION WHERE id = 1")
record = cursor.fetchone()
# Check if the value from database is equal to the one that we want to update into
assert record[0] == new_default_dir
def init_sqlite_config(request):
configuration = Configuration('TestSqliteConfig.db')
db_file_path = os.environ['USER_HIDDEN'] + 'TestSqliteConfig.db'
configuration.set_db_file_path(db_file_path)
connection = sqlite3.connect(db_file_path)
def tear_down():
connection.close()
if os.path.isfile(db_file_path):
os.remove(db_file_path)
request.addfinalizer(tear_down)
return connection
def save_options(self):
"""
Saves options selected in the first time welcome window.
"""
self.filepath = self.first_time_welcome_input_box.text()
self.csv_path = self.clinical_data_csv_input_box.text()
if self.filepath == "" and self.csv_path == "":
QMessageBox.about(self, "Unable to proceed",
"No directories selected.")
elif not os.path.exists(self.filepath) or not \
os.path.exists(self.csv_path):
QMessageBox.about(self, "Unable to proceed",
"Directories do not exist")
else:
config = Configuration()
try:
config.update_default_directory(self.filepath)
# Update CSV path if it exists
if self.csv_path != "" and os.path.exists(self.csv_path):
config.update_clinical_data_csv_dir(self.csv_path)
except SqlError:
config.set_up_config_db()
QMessageBox.critical(
self, "Config file error",
"Failed to access configuration file.\nPlease try again.")
else:
self.configured.emit(self.filepath)
def test_error_handling(init_sqlite_config):
# Drop database file to reproduce SQL error
configuration = Configuration()
cursor = init_sqlite_config.cursor()
# Lock the database to trigger SqlError
cursor.execute("""PRAGMA locking_mode = EXCLUSIVE;""")
cursor.execute("""BEGIN EXCLUSIVE;""")
with pytest.raises(SqlError):
configuration.get_default_directory()
with pytest.raises(SqlError):
configuration.update_default_directory('')
def init_config(request):
configuration = Configuration('TestConfig.db')
db_file_path = os.environ['USER_HIDDEN'] + 'TestConfig.db'
configuration.set_db_file_path(db_file_path)
connection = sqlite3.connect(db_file_path)
configuration.update_default_directory("../testdata/DICOM-RT-TEST")
def tear_down():
connection.close()
if os.path.isfile(db_file_path):
os.remove(db_file_path)
request.addfinalizer(tear_down)
return connection
def init_config(request):
configuration = Configuration('TestConfig.db')
db_file_path = Path(
os.environ['USER_ONKODICOM_HIDDEN']).joinpath('TestConfig.db')
configuration.set_db_file_path(db_file_path)
connection = sqlite3.connect(db_file_path)
configuration.update_default_directory(Path.cwd().joinpath(
'test', 'testdata'))
def tear_down():
connection.close()
if os.path.isfile(db_file_path):
os.remove(db_file_path)
request.addfinalizer(tear_down)
return connection
def save_default_dir(self):
self.filepath = self.first_time_welcome_input_box.text()
if self.filepath == "":
QMessageBox.about(self, "Unable to proceed",
"No directory selected.")
elif not os.path.exists(self.filepath):
QMessageBox.about(self, "Unable to proceed",
"Directory does not exist")
else:
config = Configuration()
try:
config.update_default_directory(self.filepath)
except SqlError:
config.set_up_config_db()
QMessageBox.critical(
self, "Config file error",
"Failed to access configuration file.\nPlease try again.")
else:
self.configured.emit(self.filepath)
def import_clinical_data(self):
"""
Attempt to import clinical data from the CSV stored in the
program's settings database.
"""
# Return if there is no RTDOSE in the dataset
patient_dict_container = PatientDictContainer()
if 'rtdose' not in list(patient_dict_container.dataset.keys()):
message = "No RTDOSE found. Clinical data is only imported for " \
"datasets that include an RTDOSE."
attrib = QtWidgets.QTableWidgetItem("Warning")
value = QtWidgets.QTableWidgetItem(message)
self.table_cd.insertRow(0)
self.table_cd.setItem(0, 0, attrib)
self.table_cd.setItem(0, 1, value)
return
# Return if data has been imported from DICOM SR
if self.table_populated:
return
# Clear data dictionary and table
self.data_dict = {}
self.clear_table()
# Current patient's ID
patient_id = patient_dict_container.dataset[0].PatientID
# Try get the clinical data CSV file path
try:
config = Configuration()
file_path = config.get_clinical_data_csv_dir()
except SqlError:
# Write warning to table
message = "Failed to access configuration file."
attrib = QtWidgets.QTableWidgetItem("Warning")
value = QtWidgets.QTableWidgetItem(message)
self.table_cd.insertRow(0)
self.table_cd.setItem(0, 0, attrib)
self.table_cd.setItem(0, 1, value)
return
# Get CSV data
if file_path == "" or file_path is None \
or not os.path.exists(file_path):
# Clear table
self.clear_table()
# Write warning to table
message = "Clinical data CSV could not be found."
attrib = QtWidgets.QTableWidgetItem("Warning")
value = QtWidgets.QTableWidgetItem(message)
self.table_cd.insertRow(0)
self.table_cd.setItem(0, 0, attrib)
self.table_cd.setItem(0, 1, value)
return
with open(file_path, newline="") as stream:
data = list(csv.reader(stream))
# See if CSV data matches patient ID
patient_in_file = False
row_num = 0
for i, row in enumerate(data):
if row[0] == patient_id:
patient_in_file = True
row_num = i
break
# Return if patient's data not in the CSV file
if not patient_in_file:
# Clear table
self.clear_table()
# Write warning to table
message = "Patient clinical data not found in CSV."
attrib = QtWidgets.QTableWidgetItem("Warning")
value = QtWidgets.QTableWidgetItem(message)
self.table_cd.insertRow(0)
self.table_cd.setItem(0, 0, attrib)
self.table_cd.setItem(0, 1, value)
return
# Put patient data into dictionary
headings = data[0]
attribs = data[row_num]
for i, heading in enumerate(headings):
self.data_dict[heading] = attribs[i]
# Update table
self.populate_table()
# Save clinical data to DICOM SR
self.save_clinical_data()
os.environ["QT_AUTO_SCREEN_SCALE_FACTOR"] = "1"
app = QtWidgets.QApplication(sys.argv)
print("PDPI: " + str(app.primaryScreen().physicalDotsPerInch()))
# Set the font to Segoe UI, 9, when in windows OS
if platform.system() == 'Windows':
f = QFont("Segoe UI", 9)
app.setFont(f)
elif platform.system() == 'Darwin':
f = QFont("Helvetica Neue", 13)
app.setFont(f)
if len(sys.argv) > 1:
controller = Controller(default_directory=sys.argv[1])
controller.show_open_patient()
else:
# Get the default DICOM directory from SQLite database
# stored in a hidden directory in the user home directory
configuration = Configuration()
default_dir = configuration.get_default_directory()
if default_dir is None:
controller = Controller()
controller.show_first_time_welcome()
else:
controller = Controller(default_directory=default_dir)
controller.show_welcome()
sys.exit(app.exec_())
def create_change_clinical_data_csv_frame(self):
config = Configuration()
csv_dir = None
# Try get the clinical data CSV directory
try:
csv_dir = config.get_clinical_data_csv_dir()
except SqlError:
config.set_up_config_db()
QtWidgets.QMessageBox.critical(
self.window, "Config file error",
"""Failed to access configuration file.
\nConfiguration file recreated with no default directory.
\nPlease update your default directory.""")
# Clinical data prompt text
text = "Importing Clinical Data\n\nClinical data can be " \
"automatically imported into the DICOM image set. This " \
"requires a matching process which is strict (see the User " \
"Manual). The three requirements are detailed below:\n\n1. " \
"The Patient's Clinical Data must be stored in the Comma " \
"Separated Values (CSV) format, which any spreadsheet " \
"program can produce, including MS Excel.\n\n2. This CSV " \
"file must contain the patient's identifier in the first " \
"column, and that first column must be titled \"Patient_ID\"." \
"\n\n3. The entry in the first CSV column [\"Patient_ID\"] " \
"must match the patient identifier in the DICOM dataset.\n\n" \
"4. The CSV file must contain the ICD10 code in the second " \
"column, and that column must be named \"ICD10\"."
# Create the frame
self.window.clinical_data_csv_dir_frame = QtWidgets.QFrame()
self.window.clinical_data_csv_dir_frame.setVisible(False)
# Create the layout
self.clinical_data_csv_layout = QtWidgets.QVBoxLayout()
self.change_clinical_data_csv_dir_prompt = QtWidgets.QLabel()
self.change_clinical_data_csv_dir_prompt.setAlignment(
QtCore.Qt.AlignJustify)
self.change_clinical_data_csv_dir_prompt.setVisible(True)
self.change_clinical_data_csv_dir_prompt.setMaximumWidth(
self.window.clinical_data_csv_dir_frame.width() - 10)
self.change_clinical_data_csv_dir_prompt.setText(text)
self.change_clinical_data_csv_dir_prompt.setWordWrap(True)
self.clinical_data_csv_layout.addWidget(
self.change_clinical_data_csv_dir_prompt)
# Create a horizontal box to hold the input box for the
# directory and the choose button
self.clinical_data_csv_dir_input_layout = QtWidgets.QHBoxLayout()
# Create a textbox to contain the path to the directory that
# contains the DICOM files
self.clinical_data_csv_dir_input_box = \
UIChangeDefaultDirDragAndDropEvent(self)
self.clinical_data_csv_dir_input_box.setCursorPosition(0)
self.clinical_data_csv_dir_input_box.setText(csv_dir)
self.clinical_data_csv_dir_input_layout.addWidget(
self.clinical_data_csv_dir_input_box)
# Create a choose button to open the file dialog
self.clinical_data_csv_dir_button = QtWidgets.QPushButton()
self.clinical_data_csv_dir_button.setText("Change")
self.clinical_data_csv_dir_button.resize(
self.clinical_data_csv_dir_button.sizeHint().width(),
self.clinical_data_csv_dir_input_box.height())
self.clinical_data_csv_dir_button.setCursor(
QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.clinical_data_csv_dir_button.clicked.connect(
self.change_clinical_data_csv_button_clicked)
self.clinical_data_csv_dir_input_layout.addWidget(
self.clinical_data_csv_dir_button)
# Create a widget to hold the input fields
self.clinical_data_csv_dir_input_widget = QtWidgets.QWidget()
self.clinical_data_csv_dir_input_widget.setLayout(
self.clinical_data_csv_dir_input_layout)
self.clinical_data_csv_layout.addWidget(
self.clinical_data_csv_dir_input_widget)
self.clinical_data_csv_layout.addStretch(1)
# Set the frame's layout
self.window.clinical_data_csv_dir_frame.setLayout(
self.clinical_data_csv_layout)