User Interface Widgets¶

This section provides the documentation on the code behind DBS Guide.

Contents¶

Update Widget
Patient Directory Widget
Patient Info Widget
Frame Detection Widget
Registration Widget
Anatomical Fiducials Widget
Target Planning Widget
Intraoperative Planning Widget
Microelectrode Recordings Widget
Postoperative Info Widget
Postoperative Programming Widget
Data View Widget
Notes Widget

1. Update Widget (Status Bar)¶

Module for progress update

This module informs the user of the latest action that has been performed by the graphic user interface by updating the status bar at the top of the user interface.

class dbsGuideWidgets.wig_13_updateWidget.updateWidget(text)¶

Main updateWidget object

Sets up the status bar with the desired text.

Parameters:	text (String) – Text to be shown as the most recent update.

updateStatus(text)¶

Updates the status bar with text

Parameters:	text (String) – Text to be shown as the most recent update.

2. Patient Directory Widget¶

Module for defining patient directory.

This module allows the user to define the patient data directory.

class dbsGuideWidgets.wig_01_patientDirectoryWidget.patientDirectoryWidget(parameters)¶

Constructor - Main patientDirectoryWidget object

Initializes the patient directory widget.

Parameters:	parameters (Dictionary) – A dictionary of several important directory paths.

onRenameScansButtonGroupClicked(button)¶

Slot for Rename Scans button.

Parameters:	button (Macro - Integer) – The number that refers to the button that’s clicked

onUsePreviousValuesClicked(button)¶

Slot for Use Previous Values button.

Parameters:	button (Macro - Integer) – The number that refers to the button that’s clicked

patient_directory_setup()¶: Confiugres patient directory widget’s form.

3. Patient Info Widget¶

Module for providing information about the patient.

This module provides information about the date, the specific patient that is loaded, and the surgeon.

class dbsGuideWidgets.wig_02_patientInfoWidget.patientInfoWidget(parameters)¶

Constructor - Main patientInfoWidget

Initializes the patient info widget.

Parameters:	parameters (Dictionary) – A dictionary of several important directory paths.

onImplantedSidesButtonGroupClicked(button)¶

Slot for Implanted sides button.

Parameters:	button (Macro - Integer) – The number that refers to the button clicked

patient_info_setup()¶: Patient info widget setup.

selectedDateChanged()¶

Slot for date widget.

Updates the date widget and writes to file the date that has been selected by the user.

updateSurgeonName()¶

Slot for surgeon name widget.

Updates the surgeon name widget and writes to file the surgeon name that has been selected by the user.

4. Frame Detection Widget¶

Module for detecting the stereotactic frame.

This module allows the user to define the frame fiducials on the CT image.

class dbsGuideWidgets.wig_03_frameDetectionWidget.frameDetectionWidget(parameters)¶

Constructor - Main frameDetectionWidget object

Initializes the frame detection widget.

Parameters:	parameters (Dictionary) – A dictionary of several important directory paths.

calc_frame_fids_X(P1, P2, P3)¶

Calculates frame fiducial x-coordinates

Parameters:	P1 (float) – Point 1 P2 (float) – Point 2 P3 (float) – Point 3
Returns:	arrays of the top and bottom fiducials
Return type:	Numpy array

calc_frame_fids_Y(P1, P2, P3)¶

Calculates frame fiducial y-coordinates

Parameters:	P1 (float) – Point 1 P2 (float) – Point 2 P3 (float) – Point 3
Returns:	arrays of the top and bottom fiducials
Return type:	Numpy array

frame_detect_setup()¶

Setup function for frameDetectionWidget

This function sets up the frame detection widget with all the appropriate forms.

getFidCoords(fids)¶

Gets fiucial world coordinates.

Gets the world coordinates of the fiducial by looping through all fiducials in provided markups list node.

Parameters:	fids (vtkMRMLMarkupsFiducialNode) – markups list node
Returns:	fiducial coordinates
Return type:	list array

lineModel(scene, point1, point2, name, color)¶

Creates line model between two points

Creates a line model between two points and displays it.

Parameters:	scene (Nodes) – MRML scene point1 (array) – point 1 of the line point2 (array) – point 2 of the line name (String) – name of the line model color (Tuple) – color of the line model

onCrosshairToggleFrameButton()¶

Slot for Turn On Crosshairs button.

Toggles crosshairs ON/OFF.

onFrameFidButtonGroup(button)¶: Slot for buttons within the frame fiducial button group.

onFrameFidConfirmButton()¶

Slot for Confirm Frame Fiducials button.

Saves frame fiducials as 3D Slicer nodes and writes to patient directory as .vtk files. Finally, the frame .vtk files are displayed.

onFrameFidVolumeCBox(rerun=False)¶

Slot for Fiducial Volume box.

Displays the brain scan of the patient corresponding to the fiducial volume selected.

The list of available volumes:

3D T1 weighted (3D-T1W)
Fast spin echo T2 weighted coronal view (FSEcor_T2w)
Fast spin echo T2 weighted transverse view (FSEtra_T2W)
3D electodes T1 weighted (3DELECTRODE_T1w)
Fast spin echo T2 weighted saggital view (FSEsag_T2w)
CT scan with frame (ctFrame)

onP1pointClick(enabled)¶

Slot for Point 1 fiducial placement click.

Locks the point and records its coordinates.

Parameters:	enabled (Boolean) – whether the point has been clicked onto the scan or not

onShowFrameLegendButton()¶

Slot for Show Frame Fiducial Legend button.

Displays frame fiducial legend.

5. Registration Widget¶

Module for running registration of nifti files.

This module runs FSL flirt registration.

class dbsGuideWidgets.wig_04_registrationWidget.registrationWidget(regLogic, parameters)¶

Constructor - Main registrationWidget object

Initializes the registration widget.

Parameters:	regLogic – Registration logic paramters – A dictionary of several important directory paths.

linear_registration_setup()¶

Class setup function for widget.

This function sets up the registration widget.

onCTFrameVolCBox()¶: Slot for CT Frame Volume: combo box

onDeleteVolume()¶: Slot for Delete Highlighted Volumes button

onReferenceVolCBox()¶: Slot for Reference Volume: combo box

onRunRegistrationButton()¶: Slot for Run Registration button

6. Anatomical Fiducials Widget¶

Module for placing anatomical fiducials.

This module allows the user to define several anatomical fiducial points. These points include AC, PC, and midline points.

class dbsGuideWidgets.wig_05_anatomicalFiducialsWidget.anatomicalFiducialsWidget(parameters)¶

Constructor - Main anatomicalFiducialsWidget object

Initializes the Anatomical Fiducials widget.

Parameters:	paramters – A dictionary of several important directory paths.

acpc_point_setup()¶: Sets up the* Anatomical Fiducials widget.

getFidCoords(fids)¶

Gets the coordinates for fiducials.

Return rasCoord:
Parameters:	fids (array) – fiducials to get coordinates for
	The coordinates

onACPCTransformCBox()¶: Slot for Select Transform: combo box

onACPointClick(enabled)¶

Slot for AC point clicked.

Parameters:	enabled (boolean) – if the AC point is clicked

onAcpcTransformButton()¶: Slot for Run ACPC Transform button

onAddMidlineButton()¶: Slot for Add Midline button.

onCrosshairToggleButton()¶: Slot for Turn On Crosshairs button.

onFidConfirmButton()¶: Slot for Confirm Fiducials button.

onFidVolumeCBox()¶: Slot for Fiducial Volume: combo box.

onMid1PointClick(enabled)¶

Slot for Mid1 point clicked.

Parameters:	enabled (boolean) – if the Mid1 point is clicked

onMid2PointClick(enabled)¶

Slot for Mid2 point clicked.

Parameters:	enabled (boolean) – if the Mid2 point is clicked

onMidlineFidButtonGroup(button)¶

Slots for buttons in the midline fiducial button group

Parameters:	button (Integer) – button that was clicked

onPCPointClick(enabled)¶

Slot for PC point clicked.

Parameters:	enabled (boolean) – if the PC point is clicked

onRemoveMidlineButton()¶: Slot for Remove Midline button.

7. Target Planning Widget¶

Module for target planning.

This module provides target planning capabilities for the surgeon.

class dbsGuideWidgets.wig_06_targetPlanningWidget.targetPlanningWidget(parameters)¶

Constructor - Main targetPlanningWidget object

Initiates the targetPlanningWidget

Parameters:	paramters – A dictionary of several important directory paths.

get_model_point(node)¶

Gets model point.

Return point_Ras:
Parameters:	node – the node for which the model point is requested
	the model point

norm_vec(P1, P2)¶

Creates a normal vector between two points.

Parameters:	P1 (Array - coordinates) – Point 1 P2 (Array - coordinates) – Point 2
Return NormVec:	The normal vector

onCrosshairTogglePlanningButton()¶: Slot for Turn On Crosshairs button

onFrameSliderValueChanged(newValue)¶

Slot for Entry to Target slider

Parameters:	newValue (Integer) – the new value tha the slider is set to

onLeftButtonGroupClicked(button)¶

Slot for Left Plan - Plot Planned Lead button group.

Parameters:	button (Integer) – id of the button clicked

onLeftElecModelButtonGroup()¶: Slot for electrode type in Left Plan - Electrode:

onLeftEntryCoordConfirmButton()¶: Slot for confirming left entry coordinates

onLeftEntryJumpButton()¶: Slot for Jump to... button under Left Plan - Entry:

onLeftEntryMoveButton()¶: Slot for when the Left Plan - Entry button is moved.

onLeftEntryPointClick(enabled)¶

Slot for Left Plan - Entry: point button clicked

Parameters:	enabled (Boolean) – status of button enabled

onLeftMERTracksButton(button)¶

Slot for Left Plan - Plot MER Tracks button group.

Parameters:	button (Integer) – id of the button clicked

onLeftTargetCoordConfirmButton()¶: Slot for Confirm Left Plan button under Left Plan

onLeftTargetJumpButton()¶: Slot for Jump to... button under Left Plan - Target:

onLeftTargetMoveButton()¶: Slot for when the Left Plan - Target button is moved.

onLeftTargetPlanningExpand(collapsed)¶

Slot for when Left Plan collapsible button is expanded.

Parameters:	collapsed (Boolean) – the state of the button (collapsed or not)

onLeftTargetPointClick(enabled)¶

Slot for Left Plan - Target: point button clicked

Parameters:	enabled (Boolean) – status of button enabled

onMouseMovedPlanning(observer, eventid)¶

Slot for when the the cross hair node has been relocated.

Parameters:	observer – observer eventid – event ID

onPlannedPreopConfirmButton(button)¶

Slot for Planned Preop Confirm button

Parameters:	button (Integer) – ID of button

onPlanningVolumeCBox()¶: Slot for Planning Volume combo box.

onProbeEyeCBox()¶: Slot for Probe Eye Model combo box.

onProbeEyeClose()¶: Slot for Close Probe's Eye button.

onRightButtonGroupClicked(button)¶

Slot for Right Plan - Plot Planned Lead button group.

Parameters:	button (Integer) – id of the button clicked

onRightElecModelButtonGroup()¶: Slot for electrode type in Right Plan - Electrode:

onRightEntryCoordConfirmButton()¶: Slot for confirming right entry coordinates

onRightEntryJumpButton()¶: Slot for Jump to... button under Right Plan - Entry:

onRightEntryMoveButton()¶: Slot for when the Right Plan - Entry button is moved.

onRightEntryPointClick(enabled)¶

Slot for Right Plan - Entry: point button clicked

Parameters:	enabled (Boolean) – status of button enabled

onRightMERTracksButton(button)¶

Slot for Right Plan - Plot MER Tracks button group.

Parameters:	button (Integer) – id of the button clicked

onRightTargetCoordConfirmButton()¶: Slot for Confirm Left Plan button under Left Plan

onRightTargetJumpButton()¶: Slot for Jump to... button under Right Plan - Target:

onRightTargetMoveButton()¶: Slot for when the Right Plan - Target button is moved.

onRightTargetPlanningExpand(collapsed)¶

Slot for when Right Plan collapsible button is expanded.

Parameters:	collapsed (Boolean) – the state of the button (collapsed or not)

onRightTargetPointClick(enabled)¶

Slot for Right Plan - Target: point button clicked

Parameters:	enabled (Boolean) – status of button enabled

onSelectAllLeftMERClicked(button)¶

Slot for All button in Left Plan - MER Tracks

Parameters:	button (Boolean) – status of button being clicked

onSelectAllRightMERClicked(button)¶

Slot for All button in Right Plan - MER Tracks

Parameters:	button (Boolean) – status of button being clicked

onUpdateCrosshairPlanning()¶: Slot for Update Crosshairs button

reslice_on_path(p0, pN, orientation=0)¶

Modifies the slice node to be resliced on a specific path

Parameters:	p0 (array - coordinates) – point 0 pN (array - coordinates) – point N orientation (Integer) – the orientation, default set to 0

target_planning_setup()¶: Sets up the Target Planning widget.

8. Intraoperative Planning Widget¶

Module for intraoperative planning.

This module provides manipulation of the pre-operative plan during the operation.

class dbsGuideWidgets.wig_07_intraopPlanningWidget.intraopPlanningWidget(parameters)¶

Constructor - Main intraopPlanningWidget object

Initializes the Intraoperative Planning widget.

intraop_planning_setup()¶: Sets up the intraoperative planning widget.

onLeftButtonGroupIntraopClicked(button)¶

Slot for selection of Plot Planned Lead under Left Plan

Parameters:	button (Integer) – id of button clicked

onLeftIntraopPlanningExpand(collapsed)¶

Slot for Left Plan collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onLeftMERTracksIntraopButton(button)¶

Slot for selection of Plot MER Tracks under Left Plan

Parameters:	button (Integer) – id of button clicked

onLeftTrajUsedButtonGroup()¶: Slot for selection of Trajectory used under Left Plan

onNotesWidgetExpand(collapsed)¶

Slot for Intraoperative Notes collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onRightButtonGroupIntraopClicked(button)¶

Slot for selection of Plot Planned Lead under Right Plan

Parameters:	button (Integer) – id of button clicked

onRightIntraopPlanningExpand(collapsed)¶

Slot for Right Plan collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onRightMERTracksIntraopButton(button)¶

Slot for selection of Plot MER Tracks under Right Plan

Parameters:	button (Integer) – id of button clicked

onRightTrajUsedButtonGroup()¶: Slot for selection of Trajectory used under Right Plan

onUpdatePlannedLeads(button)¶

Slot for Update Plan buttons

Parameters:	button (Integer) – id of button clicked -2 for left, -3 for right

9. Microelectrode Recordings Widget¶

Module for intraoperative microelectrode recordings.

This module allows input of recordings depths of the target nucleus using intraoperaive microelectrode recordings.

class dbsGuideWidgets.wig_08_intraopMicroelectrodeWidget.intraopMicroelectrodeWidget(parameters)¶

intraop_microelectrode_setup()¶: Sets up the intraoperative microelectrode recordings widget display configuration.

onIntraopMERConfirmButton(button)¶

Slot for Confirm MER button.

Parameters:	button (Integer) – id of button clicked

onLeftMERActivityPlotClicked(button)¶

Slot for selection of Plot MER Tracks under Left Plan

Parameters:	button (Integer) – id of button clicked

onLeftMicroelectrodeExpand(collapsed)¶

Slot for Left Plan collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onLeftTrajNoMERButton(button)¶

Slot for trajectory used under Left Plan

Parameters:	button (Integer) – id of button clicked

onNotesWidgetExpand(collapsed)¶

Slot for Microelctrode Recordings Notes collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onRightMERActivityPlotClicked(button)¶

Slot for selection of Plot MER Tracks under Right Plan

Parameters:	button (Integer) – id of button clicked

onRightMicroelectrodeExpand(collapsed)¶

Slot for Right Plan collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onRightTrajNoMERButton(button)¶

Slot for trajectory used under Right Plan

Parameters:	button (Integer) – id of button clicked

10. Postoperative Info Widget¶

Module for post-operative electrode localization.

This module allows the user to define the location of the implanted electrodes using post-operative images (CT or MRI).

class dbsGuideWidgets.wig_09_postopElectrodeWidget.postopElectrodeWidget(parameters)¶

onActualElecPlotButton(button)¶

Slot for Update Activity button

Parameters:	button (Integer) – id of the button clicked (left/right side)

onCrosshairTogglePostButton()¶: Slot for Turn On Crosshairs button

onElecLBpointClick(enabled)¶

Slot for Elect Bot: point button clicked under Left Plan

Parameters:	enabled (Boolean) – status of button enabled

onElecLTpointClick(enabled)¶

Slot for Elect Top: point button clicked under Left Plan

Parameters:	enabled (Boolean) – status of button enabled

onElecRBpointClick(enabled)¶

Slot for Elect bot: point button clicked under Right Plan

Parameters:	enabled (Boolean) – status of button enabled

onElecRTpointClick(enabled)¶

Slot for Elect Top: point button clicked under Right Plan

Parameters:	enabled (Boolean) – status of button enabled

onElectrodeFidButton(button)¶

Slot for Electrode fiducial buttons

Parameters:	button (Integer) – button ID

onFidVolumeElecBox()¶: Slot for Fiducial Volume: combo box

onLeftActualElecButtonGroupClicked(button)¶

Slot for Plot Actual Lead: button group under Left Plan

Parameters:	button (Integer) – id of the button clicked

onLeftActualElectrodeExpand(collapsed)¶

Slot for Left Side collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onLeftActualMERTracksButtonGroupClicked(button)¶

Slot for Plot MER Tracks: button group under Left Plan

Parameters:	button (Integer) – id of the button clicked

onMouseMovedPost(observer, eventid)¶: Slot for when the the cross hair node has been relocated. :param observer: observer :param eventid: event ID

onNotesWidgetExpand(collapsed)¶

Slot for Postoperative Notes collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onPostopMERConfirmButton(button)¶

Slot for Confirm Electrode button

Parameters:	button (Integer) – id of the button clicked (right or left side)

onRightActualElecButtonGroupClicked(button)¶

Slot for Plot Actual Lead: button group under Right Plan

Parameters:	button (Integer) – id of the button clicked

onRightActualElectrodeExpand(collapsed)¶

Slot for Right Side collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onRightActualMERTracksButtonGroupClicked(button)¶

Slot for Plot MER Tracks: button group under Right Plan

Parameters:	button (Integer) – id of the button clicked

onUpdateCrosshairPost()¶: Slot for Update Crosshairs button

postop_setup()¶: Sets up the Postoperative Info widget display configuration.

11. Postoperative Programming Widget¶

Module for Postoperative Programming widget.

This module is used to program the visualization postoperative.

class dbsGuideWidgets.wig_11_postopProgrammingWidget.postopProgrammingWidget(parameters)¶

Constructor - Main dataVisualizationWidget object

Initiates the Data View widget

Parameters:	dataVisibility – Data visibility paramters – A dictionary of several important directory paths.

onLeftElecModelButtonGroup()¶: Slot for button group belonging to Electrode: under Left Electrode

onLeftElecNumberButtonGroup(button)¶: Slot for button group belonging to Channel: under Left Electrode

onLeftPostopProgrammingExpand(collapsed)¶

Slot for Left Electrode collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onLeftShowElectrodeDiagramButton()¶: Slot for Electrode Diagram button belonging to Left Electrode

onRightElecModelButtonGroup()¶: Slot for button group belonging to Electrode: under Right Electrode

onRightElecNumberButtonGroup(button)¶: Slot for button group belonging to Channel: under Right Electrode

onRightPostopProgrammingExpand(collapsed)¶

Slot for Right Electrode collapsible button.

Parameters:	collapsed (Boolean) – status of button - expanded/collapsed

onRightShowElectrodeDiagramButton()¶: Slot for Electrode Diagram button belonging to Right Electrode

postop_programming_setup()¶: Sets up the postoperative planning widget.

12. Data View Widget¶

Module for manipulating what data models are shown.

This module provides the user the capability of turning model data OFF/ON within the 3D view and slice view.

class dbsGuideWidgets.wig_10_dataVisualizationWidget.dataVisualizationWidget(dataVisibility, parameters)¶

Constructor - Main dataVisualizationWidget object

Initiates the Data View widget

Parameters:	dataVisibility – Data visibility paramters – A dictionary of several important directory paths.

data_view_setup()¶: Sets up the Data View widget display configuration

hex2rgb(hx)¶

Changes colour mode from HEX to RGB

Parameters:	color (string) – color in RGB
Return rgb:	the RGB equivalent of the given HEX
Return type:	Tuple

onActualContactButtonGroupClicked(button)¶

Slot for button group belonging to Electrode Contacts - Actual:

Parameters:	button (Integer) – ID of the button selected

onActualContactColorChange(color)¶

Slot for change in colour of Electrode Contacts - Actual:

Parameters:	color – the new color that was selected

onActualLeadButtonGroupClicked(button)¶

Slot for button group belonging to Electrode Leads - Actual:

Parameters:	button (Integer) – ID of the button selected

onActualLeadColorChange(color)¶

Slot for change in colour of Electrode Leads - Actual:

Parameters:	color – the new color that was selected

onActualMERActivityColorChange(color)¶

Slot for change in colour of MER Activity - Actual:

Parameters:	color – the new color that was selected

onActualMERSTNButtonGroupClicked(button)¶

Slot for button group belonging to MER Activity - Planned:

Parameters:	button (Integer) – ID of the button selected

onActualMERTrackColorChange(color)¶

Slot for change in colour of MER Trajectory - Actual:

Parameters:	color – the new color that was selected

onActualMERTracksButtonGroupClicked(button)¶

Slot for button group belonging to MER Trajectory - Actual:

Parameters:	button (Integer) – ID of the button selected

onPlannedContactButtonGroupClicked(button)¶

Slot for button group belonging to Electrode Contacts - Planned:

Parameters:	button (Integer) – ID of the button selected

onPlannedContactColorChange(color)¶

Slot for change in colour of Electrode Contacts - Planned:

Parameters:	color – the new color that was selected

onPlannedLeadButtonGroupClicked(button)¶

Slot for button group belonging to Electrode Leads - Planned:

Parameters:	button (Integer) – ID of the button selected

onPlannedLeadColorChange(color)¶

Slot for change in colour of Electrode Leads - Planned:

Parameters:	color – the new color that was selected

onPlannedMERActivityColorChange(color)¶

Slot for change in colour of MER Activity - Planned:

Parameters:	color – the new color that was selected

onPlannedMERSTNButtonGroupClicked(button)¶

Slot for button group belonging to MER Activity - Planned:

Parameters:	button (Integer) – ID of the button selected

onPlannedMERTrackColorChange(color)¶

Slot for change in colour of MER Trajectory - Planned:

Parameters:	color – the new color that was selected

onPlannedMERTracksButtonGroupClicked(button)¶

Slot for button group belonging to MER Trajectory - Planned:

Parameters:	button (Integer) – ID of the button selected

onSaveSceneButton()¶: Slot for Save Slicer Scene button.

rgbToHex(color)¶

Changes colour mode from RGB to HEX

Parameters:	color (tuple) – color in RGB
Return rgb2hex:	the HEX equivalent of the given RGB
Return type:	String

13. Notes Widget¶

Module for notes box

This module creates a notes box for the user interface and saves any typed notes to the patient data directory as a .txt file.

class dbsGuideWidgets.wig_12_notesWidget.notesWidget(parameters, plainText, title, extension)¶

Main NotesWidget object. Initializes the notes box with the desired title of the notes in the notes box. The notes box is closed/collapsed by default. If the user needs to enter notes, the user can expand the notes box and start typing.

Parameters:	parameters (Dictionary) – A dictionary of several important directory paths.` plainText – Text to be included inside text box by defualt. title (String) – Title of notes box collapsible button extension (String) – Text for file to be saved as.

notes_setup()¶

Sets up the notes widget

Connects the ‘save button’ with onSaveNotesButton.

onSaveNotesButton(button)¶

Slot for save button

Saves notes once Save button is clicked.

Parameters:	button (Boolean) – The status of the button.