def setupWidgets(self):
"""
Set up the widgets and layouts for interface.
"""
dir_label = QLabel("Choose Directory:")
self.dir_line_edit = QLineEdit()
dir_button = QPushButton('...')
dir_button.setToolTip("Select file directory.")
dir_button.clicked.connect(self.setDirectory)
self.change_name_edit = QLineEdit()
self.change_name_edit.setToolTip(
"Files will be appended with numerical values.For example: filename <b> 01 </b >.jpg")
self.change_name_edit.setPlaceholderText("Change file names to...")
rename_button = QPushButton("Rename Files")
rename_button.setToolTip("Begin renaming files in directory.")
rename_button.clicked.connect(self.renameFiles)
file_exts = [".jpg", ".jpeg", ".png", ".gif", ".txt"]
# Create combo box for selecting file extensions.
ext_cb = QComboBox()
self.cb_value = file_exts[0]
ext_cb.setToolTip("Only files with this extension will be changed.")
ext_cb.addItems(file_exts)
ext_cb.currentTextChanged.connect(self.updateCbValue)
# Text edit is for displaying the file names as they are updated.
self.display_files_edit = QTextEdit()
self.display_files_edit.setReadOnly(True)
self.progress_bar = QProgressBar()
self.progress_bar.setValue(0)
# Set layout and widgets.
grid = QGridLayout()
grid.addWidget(dir_label, 0, 0)
grid.addWidget(self.dir_line_edit, 1, 0, 1, 2)
grid.addWidget(dir_button, 1, 2)
grid.addWidget(self.change_name_edit, 2, 0)
grid.addWidget(ext_cb, 2, 1)
grid.addWidget(rename_button, 2, 2)
grid.addWidget(self.display_files_edit, 3, 0, 1, 3)
grid.addWidget(self.progress_bar, 4, 0, 1, 3)
self.setLayout(grid)
class ImageFusionOptions(object):
"""
UI class that can be used by the AddOnOptions Class to allow the user
customise their input parameters for auto-registration.
"""
def __init__(self, window_options):
self.auto_image_fusion_frame = QtWidgets.QFrame()
self.window = window_options
self.moving_image = None
self.fixed_image = None
self.dict = {}
self.setupUi()
self.create_view()
self.get_patients_info()
def set_value(self, key, value):
"""
Stores values into a dictionary to the corresponding key.
Parameters
----------
key (Any):
value (Any):
"""
self.dict[key] = value
def create_view(self):
"""
Create a table to hold all the ROI creation by isodose entries.
"""
self.auto_image_fusion_frame.setVisible(False)
def setVisible(self, visibility):
"""
Custom setVisible function that will set the visibility of the GUI.
Args:
visibility (bool): flag for setting the GUI to visible
"""
self.auto_image_fusion_frame.setVisible(visibility)
def setupUi(self):
"""
Constructs the GUI and sets the limit of each input field.
"""
# Create a vertical Widget to hold Vertical Layout
self.vertical_layout_widget = QWidget()
self.vertical_layout = QtWidgets.QVBoxLayout()
# Create a Widget and set layout to a GridLayout
self.gridLayoutWidget = QWidget()
self.gridLayout = QtWidgets.QGridLayout(self.gridLayoutWidget)
self.gridLayout.setSizeConstraint(QLayout.SetDefaultConstraint)
self.gridLayout.setContentsMargins(0, 0, 0, 0)
self.gridLayout.setVerticalSpacing(0)
# Create horizontal spacer in the middle of the grid
hspacer = QtWidgets.QSpacerItem(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Minimum)
self.gridLayout.addItem(hspacer, 0, 5, 16, 1)
# Labels
self.fixed_image_label = QLabel("Fixed Image: ")
fixed_image_sizePolicy = QSizePolicy(QSizePolicy.Maximum,
QSizePolicy.Preferred)
fixed_image_sizePolicy.setHorizontalStretch(0)
fixed_image_sizePolicy.setVerticalStretch(0)
fixed_image_sizePolicy.setHeightForWidth(
self.fixed_image_label.sizePolicy().hasHeightForWidth())
self.fixed_image_label.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.fixed_image_placeholder \
= QLabel("This is a placeholder for fixed image")
self.fixed_image_placeholder.setWordWrap(False)
self.fixed_image_placeholder.setText(str(self.fixed_image))
self.fixed_image_placeholder.setMaximumSize(200, 50)
self.moving_image_label = QLabel("Moving Image: ")
moving_image_label_sizePolicy = QSizePolicy(QSizePolicy.Maximum,
QSizePolicy.Maximum)
moving_image_label_sizePolicy.setHorizontalStretch(0)
moving_image_label_sizePolicy.setVerticalStretch(0)
moving_image_label_sizePolicy.setHeightForWidth(
self.moving_image_label.sizePolicy().hasHeightForWidth())
self.moving_image_label.setSizePolicy(moving_image_label_sizePolicy)
self.moving_image_placeholder = QLabel("This is a placeholder")
self.moving_image_placeholder.setWordWrap(False)
self.moving_image_placeholder.setText(str(self.moving_image))
self.moving_image_placeholder.setMaximumSize(200, 50)
self.gridLayout.addWidget(self.fixed_image_label, 0, 0)
self.gridLayout.addWidget(self.fixed_image_placeholder, 0, 1)
self.gridLayout.addWidget(self.moving_image_label, 0, 2)
self.gridLayout.addWidget(self.moving_image_placeholder, 0, 3)
# Default Numbers
self.default_numbers_label = QLabel("Default Numbers")
self.default_numbers_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.default_numbers_label, 1, 0)
self.default_number_spinBox = QSpinBox(self.gridLayoutWidget)
self.default_number_spinBox.setRange(-2147483648, 2147483647)
self.default_number_spinBox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.default_number_spinBox.setToolTip(
"Default voxel value. Defaults to -1000.")
self.gridLayout.addWidget(self.default_number_spinBox, 1, 1)
# Final Interp
self.interp_order_label = QLabel("Final Interp")
self.interp_order_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.interp_order_label, 2, 0)
self.interp_order_spinbox = QSpinBox(self.gridLayoutWidget)
self.interp_order_spinbox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.interp_order_spinbox.setToolTip("The final interpolation order.")
self.gridLayout.addWidget(self.interp_order_spinbox, 2, 1)
# Metric
self.metric_label = QLabel("Metric")
self.metric_label.setAlignment(QtCore.Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.metric_label, 3, 0)
self.metric_comboBox = QComboBox()
self.metric_comboBox.addItem("correlation")
self.metric_comboBox.addItem("mean_squares")
self.metric_comboBox.addItem("mattes_mi")
self.metric_comboBox.addItem("joint_hist_mi")
self.metric_comboBox.setToolTip(
"The metric to be optimised during image registration.")
self.gridLayout.addWidget(self.metric_comboBox, 3, 1)
# Number of Iterations
self.no_of_iterations_label = QLabel("Number of Iterations")
self.no_of_iterations_label.setAlignment(Qt.AlignLeft
| Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.no_of_iterations_label, 4, 0)
self.no_of_iterations_spinBox = QSpinBox(self.gridLayoutWidget)
self.no_of_iterations_spinBox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.no_of_iterations_spinBox.setRange(0, 100)
self.no_of_iterations_spinBox.setToolTip(
"Number of iterations in each multi-resolution step.")
self.gridLayout.addWidget(self.no_of_iterations_spinBox, 4, 1)
# Shrink Factor
self.shrink_factor_label = QLabel("Shrink Factor")
self.shrink_factor_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.shrink_factor_label, 5, 0)
self.shrink_factor_qLineEdit = QLineEdit()
self.shrink_factor_qLineEdit.resize(
self.shrink_factor_qLineEdit.sizeHint().width(),
self.shrink_factor_qLineEdit.sizeHint().height())
self.shrink_factor_qLineEdit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[,]?[0-9]*[,]?[0-9]")))
self.shrink_factor_qLineEdit.setToolTip(
"The multi-resolution downsampling factors. Can be up to three "
"integer elements in an array. Example [8, 2, 1]")
self.gridLayout.addWidget(self.shrink_factor_qLineEdit, 5, 1)
# Optimiser
self.optimiser_label = QLabel("Optimiser")
self.optimiser_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.optimiser_label, 1, 2)
self.optimiser_comboBox = QComboBox(self.gridLayoutWidget)
self.optimiser_comboBox.addItem("lbfgsb")
self.optimiser_comboBox.addItem("gradient_descent")
self.optimiser_comboBox.addItem("gradient_descent_line_search")
self.optimiser_comboBox.setToolTip(
"The optimiser algorithm used for image registration.")
self.gridLayout.addWidget(self.optimiser_comboBox, 1, 3)
# Reg Method
self.reg_method_label = QLabel("Reg Method")
self.reg_method_label.setAlignment(QtCore.Qt.AlignLeft
| Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.reg_method_label, 2, 2)
self.reg_method_comboBox = QComboBox()
self.reg_method_comboBox.addItem("translation")
self.reg_method_comboBox.addItem("rigid")
self.reg_method_comboBox.addItem("similarity")
self.reg_method_comboBox.addItem("affine")
self.reg_method_comboBox.addItem("scaleversor")
self.reg_method_comboBox.addItem("scaleskewversor")
self.reg_method_comboBox.setToolTip(
"The linear transformation model to be used for image "
"registration.")
self.gridLayout.addWidget(self.reg_method_comboBox, 2, 3)
# Sampling Rate
self.sampling_rate_label = QLabel("Sampling Rate")
self.sampling_rate_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.sampling_rate_label, 3, 2)
self.sampling_rate_spinBox = QDoubleSpinBox(self.gridLayoutWidget)
self.sampling_rate_spinBox.setMinimum(0)
self.sampling_rate_spinBox.setMaximum(1)
self.sampling_rate_spinBox.setSingleStep(0.01)
self.sampling_rate_spinBox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.sampling_rate_spinBox.setToolTip("The fraction of voxels sampled "
"during each iteration.")
self.gridLayout.addWidget(self.sampling_rate_spinBox, 3, 3)
# Smooth Sigmas
self.smooth_sigma_label = QLabel("Smooth Sigma")
self.smooth_sigma_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.smooth_sigma_label, 4, 2)
self.smooth_sigmas_qLineEdit = QLineEdit()
self.smooth_sigmas_qLineEdit.resize(
self.smooth_sigmas_qLineEdit.sizeHint().width(),
self.smooth_sigmas_qLineEdit.sizeHint().height())
self.smooth_sigmas_qLineEdit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[,]?[0-9]*[,]?[0-9]")))
self.smooth_sigmas_qLineEdit.setToolTip(
"The multi-resolution smoothing kernal scale (Gaussian). Can be "
"up to three integer elements in an array. Example [4, 2, 1]")
self.gridLayout.addWidget(self.smooth_sigmas_qLineEdit, 4, 3)
# Label to hold warning labels.
self.warning_label = QLabel()
# Button for fast mode
self.fast_mode_button = QtWidgets.QPushButton("Fast Mode")
self.fast_mode_button.setCursor(
QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.fast_mode_button.clicked.connect(self.set_fast_mode)
# Add Widgets to the vertical layout
self.vertical_layout.addWidget(self.fast_mode_button)
self.vertical_layout.addWidget(self.gridLayoutWidget)
self.vertical_layout.addWidget(self.warning_label)
# Set layout of frame to the gridlayout widget
self.auto_image_fusion_frame.setLayout(self.vertical_layout)
def set_gridLayout(self):
"""
Set the UI based on the values taken from the JSON
"""
msg = ""
# If-Elif statements for setting the dict
# this can only be done in if-else statements.
if self.dict["reg_method"] == "translation":
self.reg_method_comboBox.setCurrentIndex(0)
elif self.dict["reg_method"] == "rigid":
self.reg_method_comboBox.setCurrentIndex(1)
elif self.dict["reg_method"] == "similarity":
self.reg_method_comboBox.setCurrentIndex(2)
elif self.dict["reg_method"] == "affine":
self.reg_method_comboBox.setCurrentIndex(3)
elif self.dict["reg_method"] == "scaleversor":
self.reg_method_comboBox.setCurrentIndex(4)
elif self.dict["reg_method"] == "scaleskewversor":
self.reg_method_comboBox.setCurrentIndex(5)
else:
msg += 'There was an error setting the reg_method value.\n'
self.warning_label.setText(msg)
if self.dict["metric"] == "coorelation":
self.metric_comboBox.setCurrentIndex(0)
elif self.dict["metric"] == "mean_squares":
self.metric_comboBox.setCurrentIndex(1)
elif self.dict["metric"] == "mattes_mi":
self.metric_comboBox.setCurrentIndex(2)
elif self.dict["metric"] == "joint_hist_mi":
self.metric_comboBox.setCurrentIndex(3)
else:
msg += 'There was an error setting the metric value.\n'
self.warning_label.setText(msg)
if self.dict["optimiser"] == "lbfgsb":
self.optimiser_comboBox.setCurrentIndex(0)
elif self.dict["optimiser"] == "gradient_descent":
self.optimiser_comboBox.setCurrentIndex(1)
elif self.dict["optimiser"] == "gradient_descent_line_search":
self.optimiser_comboBox.setCurrentIndex(2)
else:
msg += 'There was an error setting the optimiser value.\n'
self.warning_label.setText(msg)
# Check if all elements in list are ints
if all(isinstance(x, int) for x in self.dict["shrink_factors"]):
# Shrink_factors is stored as a list in JSON convert the list into
# a string.
shrink_factor_list_json = ', '.join(
str(e) for e in self.dict["shrink_factors"])
self.shrink_factor_qLineEdit.setText(shrink_factor_list_json)
else:
msg += 'There was an error setting the Shrink Factors value.\n'
self.warning_label.setText(msg)
# Check if all elements in list are ints
if all(isinstance(x, int) for x in self.dict["smooth_sigmas"]):
# Since smooth_sigma is stored as a list in JSON convert the list
# into a string.
smooth_sigma_list_json = ', '.join(
str(e) for e in self.dict["smooth_sigmas"])
self.smooth_sigmas_qLineEdit.setText(smooth_sigma_list_json)
else:
msg += 'There was an error setting the Smooth Sigmas value.\n'
self.warning_label.setText(msg)
try:
self.sampling_rate_spinBox.setValue(
float(self.dict["sampling_rate"]))
except ValueError:
msg += 'There was an error setting the Sampling Rate value.\n'
self.warning_label.setText(msg)
try:
self.interp_order_spinbox.setValue(int(self.dict["final_interp"]))
except ValueError:
msg += 'There was an error setting the Final Interp value.\n'
self.warning_label.setText(msg)
try:
self.no_of_iterations_spinBox.setValue(
int(self.dict["number_of_iterations"]))
except ValueError:
msg += 'There was an error setting the Number of iterations ' \
'value.\n'
self.warning_label.setText(msg)
try:
self.default_number_spinBox.setValue(
int(self.dict["default_value"]))
except ValueError:
msg += 'There was an error setting the Default Number'
self.warning_label.setText(msg)
def get_patients_info(self):
"""
Retrieve the patient's study description of the fixed image
and for the moving image (if it exists).
"""
patient_dict_container = PatientDictContainer()
if not patient_dict_container.is_empty():
filename = patient_dict_container.filepaths[0]
dicom_tree_slice = DicomTree(filename)
dict_tree = dicom_tree_slice.dict
try:
self.fixed_image = dict_tree["Series Instance UID"][0]
except:
self.fixed_image = ""
self.warning_label.setText(
'Couldn\'t find the series instance '
'UID for the Fixed Image.')
moving_dict_container = MovingDictContainer()
if not moving_dict_container.is_empty():
filename = moving_dict_container.filepaths[0]
dicom_tree_slice = DicomTree(filename)
dict_tree = dicom_tree_slice.dict
try:
self.moving_image = dict_tree["Series Instance UID"][0]
except:
self.moving_image = ""
self.warning_label.setText(
'Couldn\'t find the series instance '
'UID for the Moving Image.')
if moving_dict_container.is_empty() and self.moving_image != "":
self.moving_image = ""
self.fixed_image_placeholder.setText(str(self.fixed_image))
self.moving_image_placeholder.setText(str(self.moving_image))
def get_values_from_UI(self):
"""
Sets values from the GUI to the dict that will be used to store the
relevant parameters to imageFusion.json.
"""
self.dict["reg_method"] = str(self.reg_method_comboBox.currentText())
self.dict["metric"] = str(self.metric_comboBox.currentText())
self.dict["optimiser"] = str(self.optimiser_comboBox.currentText())
a_string = self.shrink_factor_qLineEdit.text().split(",")
a_int = list(map(int, a_string))
self.dict["shrink_factors"] = a_int
a_string = self.smooth_sigmas_qLineEdit.text().split(",")
a_int = list(map(int, a_string))
self.dict["smooth_sigmas"] = a_int
self.dict["sampling_rate"] = self.sampling_rate_spinBox.value()
self.dict["final_interp"] = self.interp_order_spinbox.value()
self.dict[
"number_of_iterations"] = self.no_of_iterations_spinBox.value()
self.dict["default_value"] = self.default_number_spinBox.value()
return self.dict
def check_parameter(self):
"""
Check the number of values of the smooth sigma and shrink factors of
that are parameters used for images fusion.
"""
len_smooth_sigmas = len(self.dict["smooth_sigmas"])
len_shrink_factor = len(self.dict["shrink_factors"])
if len_smooth_sigmas != len_shrink_factor:
raise ValueError
def set_fast_mode(self):
"""These settings are customised to be fast for images fusion."""
self.reg_method_comboBox.setCurrentIndex(1)
self.metric_comboBox.setCurrentIndex(1)
self.optimiser_comboBox.setCurrentIndex(1)
self.shrink_factor_qLineEdit.setText("8")
self.smooth_sigmas_qLineEdit.setText("10")
self.sampling_rate_spinBox.setValue(0.25)
self.interp_order_spinbox.setValue(2)
self.no_of_iterations_spinBox.setValue(50)
self.default_number_spinBox.setValue(-1000)
