NaviNIBS.Navigator.Model.Tools module

class NaviNIBS.Navigator.Model.Tools.Tool(key, usedFor, label=None, trackerKey=None, isActive=True, doRenderTool=True, doRenderTracker=True, doShowTrackingState=True, romFilepath=None, trackerStlFilepath=None, toolStlFilepath=None, filepathsRelTo='<userDataDir>', toolToTrackerTransf=None, toolStlToToolTransf=None, trackerStlToTrackerTransf=None, toolColor=None, trackerColor=None, toolOpacity=None, trackerOpacity=None, installPath=None, sessionPath=None, initialTrackerPose=None, initialTrackerPoseRelativeTo='world', toolToTrackerTransfHistory=NOTHING)

Bases: GenericCollectionDictItem[str]

Parameters:

• _key

• _usedFor

• _label – Optional “nice” label for display. If not specified, key will be used instead. Label does not need to be unique, but could be confusing in some GUI displays if multiple tools with the same label are shown.

• _trackerKey – Optional key to match up to tracking data. If not specified, key will be used instead.

• _isActive – Whether to actively use for tracking/pointing

• _doRenderTool – Whether to show tool in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doRenderTracker – Whether to show tracker in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doShowTrackingState – Whether to include this tool in tracking status widget(s). To actually show, must not also be excluded by other hide filters on the widget.

• _romFilepath – Path to a .rom file describing optical marker positions on a rigid body tracker, as used by NDI Polaris systems.

• _trackerStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tracker.

• _toolStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tool.

• _filepathsRelTo – Can be one of: - '<install>': relative to NaviNIBS install dir - '<userDataDir>': relative to user data dir - '<session>': relative to session file - absolute path

• _toolToTrackerTransf – Used for aligning actual tool position to Polaris-reported tracker position (e.g. actual coil to coil tracker, or actual pointer to uncalibrated pointer tracker)

• _toolStlToToolTransf – Used for visualization of tool surface mesh only; can be used to align mesh with actual tool orientation

• _trackerStlToTrackerTransf

• _toolColor

• _trackerColor – Note: some surf file formats (e.g. .ply) allow specifying color of elements within the file; if color is None here and colors are available in the surf file, those colors will be used.

• _toolOpacity

• _trackerOpacity

• _installPath

• _sessionPath

• _initialTrackerPose – For defining initial pose of tool, e.g. for tools that never get a camera-reported position, or for a default (simulated) position when a camera is not connected.

• _initialTrackerPoseRelativeTo

• _toolToTrackerTransfHistory

_usedFor: str

_label: tp.Optional[str]

Optional “nice” label for display. If not specified, key will be used instead. Label does not need to be unique, but could be confusing in some GUI displays if multiple tools with the same label are shown.

_trackerKey: tp.Optional[str]

Optional key to match up to tracking data. If not specified, key will be used instead.

_isActive: bool

Whether to actively use for tracking/pointing

_doRenderTool: bool

Whether to show tool in camera view, etc. To actually render, a valid pose and mesh must be available.

_doRenderTracker: bool

Whether to show tracker in camera view, etc. To actually render, a valid pose and mesh must be available.

_doShowTrackingState: bool

Whether to include this tool in tracking status widget(s). To actually show, must not also be excluded by other hide filters on the widget.

_romFilepath: tp.Optional[str]

Path to a .rom file describing optical marker positions on a rigid body tracker, as used by NDI Polaris systems.

_trackerStlFilepath: tp.Optional[str]

Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tracker.

_toolStlFilepath: tp.Optional[str]

Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tool.

_filepathsRelTo: str

Can be one of:

• '<install>': relative to NaviNIBS install dir

• '<userDataDir>': relative to user data dir

• '<session>': relative to session file

• absolute path

_toolToTrackerTransf: tp.Optional[np.ndarray]

Used for aligning actual tool position to Polaris-reported tracker position (e.g. actual coil to coil tracker, or actual pointer to uncalibrated pointer tracker)

_toolStlToToolTransf: tp.Optional[np.ndarray]

Used for visualization of tool surface mesh only; can be used to align mesh with actual tool orientation

_trackerStlToTrackerTransf: tp.Optional[np.ndarray]

_toolColor: str | None

_trackerColor: str | None

Note: some surf file formats (e.g. .ply) allow specifying color of elements within the file; if color is None here and colors are available in the surf file, those colors will be used.

_toolOpacity: float | None

_trackerOpacity: float | None

_installPath: tp.Optional[str]

_sessionPath: tp.Optional[str]

property label

property labelIsSet

property trackerKey

property trackerKeyIsSet

property usedFor

property isActive

property doRenderTool

property doRenderTracker

property doShowTrackingState

property romFilepath

property toolStlFilepath

property trackerStlFilepath

property filepathsRelTo

property filepathsRelToKey

property sessionPath

property toolToTrackerTransf

property toolStlToToolTransf

property trackerStlToTrackerTransf

property trackerColor

property toolColor

property trackerOpacity

property toolOpacity

property toolToTrackerTransfHistory

property trackerSurf

property toolSurf

property initialTrackerPose

property initialTrackerPoseRelativeTo

asDict()

Return type:

Dict[str, Any]

classmethod fromDict(d, sessionPath=None)

sigKeyAboutToChange: Signal

sigKeyChanged: Signal

sigItemAboutToChange: Signal

This signal includes the key of the item, and optionally a list of keys of attributes about to change; if second arg is None, all attributes should be assumed to be about to change.

Not emitted when key changed (use sigKeyAboutToChange instead!)

sigItemChanged: Signal

This signal includes the key of the item, and optionally a list of keys of changed attributes; if second arg is None, all attributes should be assumed to have changed.

Not emitted when key changed (use sigKeyChanged instead!)

class NaviNIBS.Navigator.Model.Tools.SubjectTracker(key, label=None, trackerKey=None, isActive=True, doRenderTool=True, doRenderTracker=True, doShowTrackingState=True, romFilepath=None, trackerStlFilepath=None, toolStlFilepath=None, filepathsRelTo='<userDataDir>', toolToTrackerTransf=None, toolStlToToolTransf=None, trackerStlToTrackerTransf=None, toolColor=None, trackerColor=None, toolOpacity=None, trackerOpacity=None, installPath=None, sessionPath=None, initialTrackerPose=None, initialTrackerPoseRelativeTo='world', toolToTrackerTransfHistory=NOTHING, usedFor='subject')

Bases: Tool

Parameters:

• _key

• _label – Optional “nice” label for display. If not specified, key will be used instead. Label does not need to be unique, but could be confusing in some GUI displays if multiple tools with the same label are shown.

• _trackerKey – Optional key to match up to tracking data. If not specified, key will be used instead.

• _isActive – Whether to actively use for tracking/pointing

• _doRenderTool – Whether to show tool in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doRenderTracker – Whether to show tracker in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doShowTrackingState – Whether to include this tool in tracking status widget(s). To actually show, must not also be excluded by other hide filters on the widget.

• _romFilepath – Path to a .rom file describing optical marker positions on a rigid body tracker, as used by NDI Polaris systems.

• _trackerStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tracker.

• _toolStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tool.

• _filepathsRelTo – Can be one of: - '<install>': relative to NaviNIBS install dir - '<userDataDir>': relative to user data dir - '<session>': relative to session file - absolute path

• _toolToTrackerTransf – Used for aligning actual tool position to Polaris-reported tracker position (e.g. actual coil to coil tracker, or actual pointer to uncalibrated pointer tracker)

• _toolStlToToolTransf – Used for visualization of tool surface mesh only; can be used to align mesh with actual tool orientation

• _trackerStlToTrackerTransf

• _toolColor

• _trackerColor – Note: some surf file formats (e.g. .ply) allow specifying color of elements within the file; if color is None here and colors are available in the surf file, those colors will be used.

• _toolOpacity

• _trackerOpacity

• _installPath

• _sessionPath

• _initialTrackerPose – For defining initial pose of tool, e.g. for tools that never get a camera-reported position, or for a default (simulated) position when a camera is not connected.

• _initialTrackerPoseRelativeTo

• _toolToTrackerTransfHistory

• _usedFor

property toolToTrackerTransf

class NaviNIBS.Navigator.Model.Tools.CoilTool(key, label=None, trackerKey=None, isActive=True, doRenderTool=True, doRenderTracker=True, doShowTrackingState=True, romFilepath=None, trackerStlFilepath=None, toolStlFilepath=None, filepathsRelTo='<userDataDir>', toolToTrackerTransf=None, toolStlToToolTransf=None, trackerStlToTrackerTransf=None, toolColor=None, trackerColor=None, toolOpacity=None, trackerOpacity=None, installPath=None, sessionPath=None, initialTrackerPose=None, initialTrackerPoseRelativeTo='world', toolToTrackerTransfHistory=NOTHING, usedFor='coil')

Bases: Tool

Parameters:

• _key

• _label – Optional “nice” label for display. If not specified, key will be used instead. Label does not need to be unique, but could be confusing in some GUI displays if multiple tools with the same label are shown.

• _trackerKey – Optional key to match up to tracking data. If not specified, key will be used instead.

• _isActive – Whether to actively use for tracking/pointing

• _doRenderTool – Whether to show tool in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doRenderTracker – Whether to show tracker in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doShowTrackingState – Whether to include this tool in tracking status widget(s). To actually show, must not also be excluded by other hide filters on the widget.

• _romFilepath – Path to a .rom file describing optical marker positions on a rigid body tracker, as used by NDI Polaris systems.

• _trackerStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tracker.

• _toolStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tool.

• _filepathsRelTo – Can be one of: - '<install>': relative to NaviNIBS install dir - '<userDataDir>': relative to user data dir - '<session>': relative to session file - absolute path

• _toolToTrackerTransf – Used for aligning actual tool position to Polaris-reported tracker position (e.g. actual coil to coil tracker, or actual pointer to uncalibrated pointer tracker)

• _toolStlToToolTransf – Used for visualization of tool surface mesh only; can be used to align mesh with actual tool orientation

• _trackerStlToTrackerTransf

• _toolColor

• _trackerColor – Note: some surf file formats (e.g. .ply) allow specifying color of elements within the file; if color is None here and colors are available in the surf file, those colors will be used.

• _toolOpacity

• _trackerOpacity

• _installPath

• _sessionPath

• _initialTrackerPose – For defining initial pose of tool, e.g. for tools that never get a camera-reported position, or for a default (simulated) position when a camera is not connected.

• _initialTrackerPoseRelativeTo

• _toolToTrackerTransfHistory

• _usedFor

property toolToTrackerTransf: ndarray | None

Override parent class to not assume identity transform by default. Unlike other tools, this will return None if no transform is set.

Return type:

Optional[ndarray]

class NaviNIBS.Navigator.Model.Tools.Pointer(key, label=None, trackerKey=None, isActive=True, doRenderTool=True, doRenderTracker=True, doShowTrackingState=True, romFilepath=None, trackerStlFilepath=None, toolStlFilepath=None, filepathsRelTo='<userDataDir>', toolToTrackerTransf=None, toolStlToToolTransf=None, trackerStlToTrackerTransf=None, toolColor=None, trackerColor=None, toolOpacity=None, trackerOpacity=None, installPath=None, sessionPath=None, initialTrackerPose=None, initialTrackerPoseRelativeTo='world', toolToTrackerTransfHistory=NOTHING, usedFor='pointer')

Bases: Tool

Parameters:

• _key

• _label – Optional “nice” label for display. If not specified, key will be used instead. Label does not need to be unique, but could be confusing in some GUI displays if multiple tools with the same label are shown.

• _trackerKey – Optional key to match up to tracking data. If not specified, key will be used instead.

• _isActive – Whether to actively use for tracking/pointing

• _doRenderTool – Whether to show tool in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doRenderTracker – Whether to show tracker in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doShowTrackingState – Whether to include this tool in tracking status widget(s). To actually show, must not also be excluded by other hide filters on the widget.

• _romFilepath – Path to a .rom file describing optical marker positions on a rigid body tracker, as used by NDI Polaris systems.

• _trackerStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tracker.

• _toolStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tool.

• _filepathsRelTo – Can be one of: - '<install>': relative to NaviNIBS install dir - '<userDataDir>': relative to user data dir - '<session>': relative to session file - absolute path

• _toolToTrackerTransf – Used for aligning actual tool position to Polaris-reported tracker position (e.g. actual coil to coil tracker, or actual pointer to uncalibrated pointer tracker)

• _toolStlToToolTransf – Used for visualization of tool surface mesh only; can be used to align mesh with actual tool orientation

• _trackerStlToTrackerTransf

• _toolColor

• _trackerColor – Note: some surf file formats (e.g. .ply) allow specifying color of elements within the file; if color is None here and colors are available in the surf file, those colors will be used.

• _toolOpacity

• _trackerOpacity

• _installPath

• _sessionPath

• _initialTrackerPose – For defining initial pose of tool, e.g. for tools that never get a camera-reported position, or for a default (simulated) position when a camera is not connected.

• _initialTrackerPoseRelativeTo

• _toolToTrackerTransfHistory

• _usedFor

class NaviNIBS.Navigator.Model.Tools.CalibrationPlate(key, label=None, trackerKey=None, isActive=True, doRenderTool=True, doRenderTracker=True, doShowTrackingState=True, romFilepath=None, trackerStlFilepath=None, toolStlFilepath=None, filepathsRelTo='<userDataDir>', toolToTrackerTransf=None, toolStlToToolTransf=None, trackerStlToTrackerTransf=None, toolColor=None, trackerColor=None, toolOpacity=None, trackerOpacity=None, installPath=None, sessionPath=None, initialTrackerPose=None, initialTrackerPoseRelativeTo='world', toolToTrackerTransfHistory=NOTHING, usedFor='calibration')

Bases: Tool

Parameters:

• _key

• _label – Optional “nice” label for display. If not specified, key will be used instead. Label does not need to be unique, but could be confusing in some GUI displays if multiple tools with the same label are shown.

• _trackerKey – Optional key to match up to tracking data. If not specified, key will be used instead.

• _isActive – Whether to actively use for tracking/pointing

• _doRenderTool – Whether to show tool in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doRenderTracker – Whether to show tracker in camera view, etc. To actually render, a valid pose and mesh must be available.

• _doShowTrackingState – Whether to include this tool in tracking status widget(s). To actually show, must not also be excluded by other hide filters on the widget.

• _romFilepath – Path to a .rom file describing optical marker positions on a rigid body tracker, as used by NDI Polaris systems.

• _trackerStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tracker.

• _toolStlFilepath – Path to a surface mesh file (e.g. .stl, .ply) for visualization of the tool.

• _filepathsRelTo – Can be one of: - '<install>': relative to NaviNIBS install dir - '<userDataDir>': relative to user data dir - '<session>': relative to session file - absolute path

• _toolToTrackerTransf – Used for aligning actual tool position to Polaris-reported tracker position (e.g. actual coil to coil tracker, or actual pointer to uncalibrated pointer tracker)

• _toolStlToToolTransf – Used for visualization of tool surface mesh only; can be used to align mesh with actual tool orientation

• _trackerStlToTrackerTransf

• _toolColor

• _trackerColor – Note: some surf file formats (e.g. .ply) allow specifying color of elements within the file; if color is None here and colors are available in the surf file, those colors will be used.

• _toolOpacity

• _trackerOpacity

• _installPath

• _sessionPath

• _initialTrackerPose – For defining initial pose of tool, e.g. for tools that never get a camera-reported position, or for a default (simulated) position when a camera is not connected.

• _initialTrackerPoseRelativeTo

• _toolToTrackerTransfHistory

• _usedFor

class NaviNIBS.Navigator.Model.Tools.ToolPositionsServerInfo(hostname='127.0.0.1', pubPort=18950, cmdPort=18951, type='IGTLink', doAutostart=True, initKwargs=NOTHING)

Bases: object

Parameters:

• _hostname

• _pubPort

• _cmdPort

• _type

• _doAutostart

• _initKwargs

_hostname: str

_pubPort: int

_cmdPort: int

_type: str

_doAutostart: bool

_initKwargs: dict[str, Any]

sigInfoChanged: Signal

property hostname

property pubPort

property cmdPort

property type

property doAutostart

property initKwargs

asDict()

Return type:

Dict[str, Any]

class NaviNIBS.Navigator.Model.Tools.Tools(items=NOTHING, positionsServerInfo=NOTHING, sessionPath=None)

Bases: GenericCollection[str, Tool]

Parameters:

• _items

• _positionsServerInfo

• _sessionPath

_positionsServerInfo: ToolPositionsServerInfo

_sessionPath: tp.Optional[str]

sigPositionsServerInfoChanged: Signal

includes list of keys of changed info attributes

addItemFromDict(toolDict)

property subjectTracker: SubjectTracker | None

Return type:

Optional[SubjectTracker]

property pointer: Pointer | None

Return type:

Optional[Pointer]

property calibrationPlate: CalibrationPlate | None

Return type:

Optional[CalibrationPlate]

property positionsServerInfo

property sessionPath

asList()

Return type:

List[Dict[str, Any]]

classmethod fromList(toolList, sessionPath=None)

Return type:

Tools

classmethod toolFromDict(toolDict, sessionPath=None)

Return type:

Tool