Index (IGTPrototypingTool API)

A B C D E F G H I L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractImageSource - Class in inputOutput: builds an interface to other teams and enables to get a Matrix, establishes a connection to the device and disconnects the connection
AbstractImageSource() - Constructor for class inputOutput.AbstractImageSource
AbstractTrackingDataSource - Class in inputOutput
AbstractTrackingDataSource() - Constructor for class inputOutput.AbstractTrackingDataSource
add(Vector3D) - Method in class util.Vector3D: Adds a vector to the current vector Returns a new Vector
addDataToSeries1(XYChart.Data<Double, Double>) - Method in class userinterface.TrackingDataDisplay
addDataToSeries2(XYChart.Data<Double, Double>) - Method in class userinterface.TrackingDataDisplay
addDataToSeries3(XYChart.Data<Double, Double>) - Method in class userinterface.TrackingDataDisplay
addIOpenIgtOnPacket(IOpenIgtPacketListener) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
addIOpenIgtOnPacket(IOpenIgtPacketListener) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
addLocal(Vector3D) - Method in class util.Vector3D: Adds a vector to the current vector Modifies the current vector
addMeasurement(Measurement) - Method in class algorithm.Tool: Adds a measurement to the list
addMessage(MessageHandler) - Method in class org.medcare.igtl.network.MessageQueueManager: add a new request to the request queue
addPathVisualisation() - Method in class algorithm.VisualizationManager: Select a .mps file created from MITK to add two targets to the visualisation One is the entry point and the other represents the target point
addRequest(byte[]) - Method in class org.medcare.igtl.network.RequestQueueManager: add a new request to the request queue
addResponse(ResponseHandler) - Method in class org.medcare.igtl.network.ResponseQueueManager: add a new response to the response queue
addSTLFile() - Method in class controller.VisualizationController: Method to add one or more STL Files to the existing ones
addSTLModels() - Method in class algorithm.VisualizationManager: Adds one or multiple stl files to the existing ones for the visualisation
addSTLToTreeView() - Method in class controller.VisualizationController: Adds the name of the stl file to the tree view
addTrackerToTreeView(List<Tool>) - Method in class controller.VisualizationController: Adds the Tracker to the Tree View
addVisualizationToRoot(Group) - Method in class algorithm.Tool: Helper method for adding the projection and the cone to the visualisation group
algorithm - package algorithm: Team Algorithm was responsible for processing the data and statistical evaluations.
ALL - Static variable in class org.medcare.igtl.messages.PositionMessage
App - Class in mainMethod
App() - Constructor for class mainMethod.App
APPLICATION_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
APPLICATION_IO_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
APPLICATION_UNKNOWNHOST_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
asArray() - Method in class util.Matrix3D
autoCaptureToggleButton - Variable in class controller.AutoTrackController
AutoTrackController - Class in controller
AutoTrackController() - Constructor for class controller.AutoTrackController
AverageMeasurement - Class in algorithm
AverageMeasurement() - Constructor for class algorithm.AverageMeasurement

B

BoxPlot - Class in algorithm
BoxPlot() - Constructor for class algorithm.BoxPlot
bytesArray - Variable in class org.medcare.igtl.messages.OpenIGTMessage
BytesArray - Class in org.medcare.igtl.util: ** For reading/writing binary fields
BytesArray() - Constructor for class org.medcare.igtl.util.BytesArray: ** Destination Constructor **

C

calculateRoi(Mat, boolean) - Static method in class algorithm.MatHelper: Calculates the region of interest.
CAM_MOVEMENT - Static variable in class algorithm.VisualizationManager: Determines how much the camera moves
CameraContainer - Class in shapes: A class to handle the camera movement more easily.
CameraContainer(boolean) - Constructor for class shapes.CameraContainer
capabilityList - Variable in class org.medcare.igtl.network.MessageHandler
CapabilityMessage - Class in org.medcare.igtl.messages: ** This class create an Capability object from bytes received or help to generate bytes to send from it
CapabilityMessage(String) - Constructor for class org.medcare.igtl.messages.CapabilityMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
CapabilityMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.CapabilityMessage: ** Constructor to be used to create message from received data
captureProgressSpinner - Variable in class controller.AutoTrackController
captureRateComboBox - Variable in class controller.AutoTrackController
CartesianSpacePosition - Class in org.medcare.robot
CartesianSpacePosition() - Constructor for class org.medcare.robot.CartesianSpacePosition
CartesianSpacePosition(double[][], double[]) - Constructor for class org.medcare.robot.CartesianSpacePosition
changeConsoleOutput() - Static method in class util.CustomLogger: Enable/disable console output
changeDataService(DataService) - Method in class algorithm.TrackingService: Sets the reference to the data service.
changeTimeline(Timeline) - Method in class algorithm.TrackingService: Sets the reference to the timeline object.
changeTrackingSource(AbstractTrackingDataSource) - Method in class algorithm.TrackingService: Sets the reference to the tracking source.
checkBounds(ArrayList<STLModel>) - Method in class algorithm.Tool: Checks for collision and changes tracker color accordingly Color red implies a collision with the model was detected Color green implies no collision was detected
checkConnection() - Method in class inputOutput.OIGTImageSource: This method is for checking the connection while the application is running by calling the isConnected() method from OpenIGTConnection.
checkTargets() - Method in class algorithm.Tool: Method to check if the projection intersects a target and if so, change the color of the target Color red implies an intersection between the projection and the target Color green implies no intersection was detected
clearData() - Method in class userinterface.TrackingDataDisplay
clearSTLModelsAndPaths() - Method in class algorithm.VisualizationManager: Clears all stl models and paths from the visualisation
client - Variable in class org.medcare.igtl.network.GenericClientResponseHandler
ClientSample - Class in sample
ClientSample() - Constructor for class sample.ClientSample
close() - Method in class controller.AutoTrackController
close() - Method in interface controller.Controller
close() - Method in class controller.InfoController
close() - Method in class controller.MainController: Close application
close() - Method in class controller.MeasurementController
close() - Method in class controller.SettingsController
close() - Method in class controller.ThrombectomyController
close() - Method in class controller.TrackingDataController
close() - Method in class controller.VideoController
close() - Method in class controller.VisualizationController
closeConnection() - Method in class algorithm.ImageDataManager
closeConnection() - Method in class algorithm.ImageDataProcessor
closeConnection() - Method in class inputOutput.AbstractImageSource: disconnects the connection to the device
closeConnection() - Method in class inputOutput.AbstractTrackingDataSource
closeConnection() - Method in class inputOutput.CSVFileReader
closeConnection() - Method in class inputOutput.FilestreamSource: sets isConnected = false
closeConnection() - Method in class inputOutput.LivestreamSource: closes connection to the device and sets isConnected = false
closeConnection() - Method in class inputOutput.OIGTImageSource: This method is for closing the connection.
closeConnection() - Method in class inputOutput.OIGTTrackingDataSource
closeLogger() - Static method in class util.CustomLogger: Stop stream to log file
coneIsVisible() - Method in class algorithm.Tool: Return if cone is visible
connect() - Method in class inputOutput.OIGTTrackingDataSource
CONNECTED - Enum constant in enum class org.medcare.igtl.network.OpenIGTServer.ServerStatus
CONNECTED - Enum constant in enum class org.medcare.igtl.network.ServerThread.ClientStatus
connectionProgressSpinner - Variable in class controller.AutoTrackController
connectToSource() - Method in class controller.VideoController: The connection to an image source is created according to the selected option of the choice box.
consoleOutput - Variable in class controller.SettingsController
controller - package controller: This package contains controller classes for UI elements that are defined in view package.
Controller - Interface in controller
ControllerCollector - Class in util
COORDINATE_LPS - Static variable in class org.medcare.igtl.messages.ImageMessage
COORDINATE_RAS - Static variable in class org.medcare.igtl.messages.ImageMessage
crc64(byte[], int, long) - Static method in class org.medcare.igtl.util.BytesArray: Calculates CRC from a byte buffer based on the polynom specified in ECMA-182.
crc64(byte[], long) - Method in class org.medcare.igtl.util.BytesArray: ** Calculate a crc value Adds from a complete byte array to the data checksum.
CrcException - Exception Class in org.medcare.igtl.util
CrcException() - Constructor for exception class org.medcare.igtl.util.CrcException: Constructs a FormatException with no detail message.
CrcException(String) - Constructor for exception class org.medcare.igtl.util.CrcException: Constructs a FormatException with the specified detail message
CSVFileReader - Class in inputOutput: This class reads in a 'CSV-file containing a variation of tools and coordinates of their position in a room.
CSVFileReader(Reader) - Constructor for class inputOutput.CSVFileReader: Constructs a CSVFileReader from a Reader object.
CSVFileReader(String) - Constructor for class inputOutput.CSVFileReader: Constructs a CSVFileReader by reading a file from the filesystem.
CustomLogger - Class in util
CustomLogger() - Constructor for class util.CustomLogger

D

DataArrayMessage - Class in org.medcare.igtl.messages
DataArrayMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.DataArrayMessage: This is a stub class for how the Array Data message is to be implemented
DataService - Class in algorithm: The class DataService represents the interface to team 1 Access to calculation with trackingdata over DataProcessor.
DataService() - Constructor for class algorithm.DataService
DataService(AbstractTrackingDataSource) - Constructor for class algorithm.DataService
decodeDouble(byte[], int) - Method in class org.medcare.igtl.util.BytesArray: ** Decodes a double value from bytes, using IEEE 754 format **
decodeLong(byte[], int, boolean) - Method in class org.medcare.igtl.util.BytesArray: ** Decodes a long value from bytes **
decodeTimeStamp(byte[]) - Method in class org.medcare.igtl.util.BytesArray: Will read a 8 bytes array and return it as a milli sec time stamp.
destroy() - Method in class org.medcare.igtl.network.MessageQueueManager: stop the thread
destroy() - Method in class org.medcare.igtl.network.RequestQueueManager: stop the thread
destroy() - Method in class org.medcare.igtl.network.ResponseQueueManager: stop the thread
determinant() - Method in class util.Matrix3D: Returns the determinant.
deviceName - Variable in class org.medcare.igtl.messages.OpenIGTMessage
DISCONNECTED - Enum constant in enum class org.medcare.igtl.network.OpenIGTServer.ServerStatus
DISCONNECTED - Enum constant in enum class org.medcare.igtl.network.ServerThread.ClientStatus
distTo(Vector3D) - Method in class util.Vector3D: Get the distance from the current vector to another vector
divisionsProperty() - Method in class shapes.TrackingCone
dot(Vector3D) - Method in class util.Vector3D: Returns the scalar product of this and another vector
DTYPE_SCALAR - Static variable in class org.medcare.igtl.messages.ImageMessage
DTYPE_VECTOR - Static variable in class org.medcare.igtl.messages.ImageMessage

E

editImagePosition(ImageScatterChart) - Method in class controller.ThrombectomyController: displays position and scale of the selected chart's image enables manually setting position and scale of that image
encodeDouble(int, double) - Method in class org.medcare.igtl.util.BytesArray: ** Encodes a double value into bytes ** ** @param len The number of bytes to encode the value to ** @param val The value to encode **
encodeLong(int, long, boolean) - Method in class org.medcare.igtl.util.BytesArray: ** Encodes a long value into bytes ** ** @param len The number of bytes to encode the value to ** @param val The value to encode ** @param signed true if signed false if unsigned **
encodeTimeStamp(long) - Method in class org.medcare.igtl.util.BytesArray: Encodes a time in millisec in a 8 bytes array **
encodeTimeStamp(long, long) - Method in class org.medcare.igtl.util.BytesArray: Encodes a time in millisec in a 8 bytes array **
ENDIAN_BIG - Static variable in class org.medcare.igtl.messages.ImageMessage
ENDIAN_LITTLE - Static variable in class org.medcare.igtl.messages.ImageMessage
equals(TempTool) - Method in class inputOutput.TempTool: Compares two tools against one another for equality
equals(Object) - Method in class util.Matrix3D
equals(Object) - Method in class util.Quaternion
equals(Object) - Method in class util.Vector3D
error(String, Exception, int) - Method in class org.medcare.igtl.util.ErrorManager: Method to manage errors
errorManager - Variable in class org.medcare.igtl.network.OpenIGTClient
errorManager - Variable in class org.medcare.igtl.network.OpenIGTServer
errorManager - Variable in class org.medcare.igtl.network.ServerThread
ErrorManager - Class in org.medcare.igtl.util
ErrorManager() - Constructor for class org.medcare.igtl.util.ErrorManager: Default ErrorManager constructor.
exit - Variable in class inputOutput.AbstractImageSource
ExportMeasurement - Class in inputOutput
ExportMeasurement(String, double, double, double, double, double, double, double, double) - Constructor for class inputOutput.ExportMeasurement

F

fh - Variable in class org.medcare.igtl.util.ErrorManager
FILE - Enum constant in enum class inputOutput.VideoSource
FilestreamSource - Class in inputOutput: provides the footage from a file with these formats: mp4, avi, mkv, mov, 3GP, mpg, jpg and png
FilestreamSource(String) - Constructor for class inputOutput.FilestreamSource: constructs a new FilestreamSource object with the transmitted path.
flip2d - Variable in class inputOutput.TransformationMatrix: Factors for flipping (mirroring) the image
fontSizeInput - Variable in class controller.SettingsController
forDevice(int) - Static method in class inputOutput.LivestreamSource
FormatManager - Class in util: This class defines custom formats to use in this project.
FormatManager() - Constructor for class util.FormatManager
fps - Variable in class inputOutput.AbstractImageSource
fps - Variable in class inputOutput.OpenIGTLinkConnection
frameMatrix - Variable in class inputOutput.AbstractImageSource
FrameTransformation - Class in org.medcare.robot
FrameTransformation(double[][]) - Constructor for class org.medcare.robot.FrameTransformation
freezeVisualization() - Method in class controller.TrackingDataController
fromDegreeAngles(double[]) - Method in class util.Quaternion: Sets the quaternion from the specified Tait-Bryan angles, applying the rotations in x-z-y extrinsic order or y-z'-x" intrinsic order.
fromDegreeAngles(double, double, double) - Method in class util.Quaternion: Sets the quaternion from three angles in degree
fromRadiansAngles(double[]) - Method in class util.Quaternion: Sets the quaternion from the specified Tait-Bryan angles, applying the rotations in x-z-y extrinsic order or y-z'-x" intrinsic order.
fromRadiansAngles(double, double, double) - Method in class util.Quaternion: Sets the quaternion from the specified Tait-Bryan angles, applying the rotations in x-z-y extrinsic order or y-z'-x" intrinsic order.
fromRotationMatrix(Matrix3D) - Method in class util.Quaternion: Sets the quaternion from a rotation matrix with the specified elements.

G

generateMatrixButton - Variable in class controller.AutoTrackController
GenericClientResponseHandler - Class in org.medcare.igtl.network
GenericClientResponseHandler(Header, byte[], OpenIGTClient, IOpenIgtPacketListener) - Constructor for class org.medcare.igtl.network.GenericClientResponseHandler
GenericIGTLinkClient - Class in org.medcare.igtl.network
GenericIGTLinkClient(String, int) - Constructor for class org.medcare.igtl.network.GenericIGTLinkClient
GenericIGTLinkClient.Sender - Class in org.medcare.igtl.network
GenericIGTLinkServer - Class in org.medcare.igtl.network
GenericIGTLinkServer(int) - Constructor for class org.medcare.igtl.network.GenericIGTLinkServer
GenericIGTLinkServer.Sender - Class in org.medcare.igtl.network
GenericMessageNodeHandler - Class in org.medcare.igtl.network
GenericMessageNodeHandler() - Constructor for class org.medcare.igtl.network.GenericMessageNodeHandler
GenericServerResponseHandler - Class in org.medcare.igtl.network
GenericServerResponseHandler(Header, byte[], ServerThread, IOpenIgtPacketListener) - Constructor for class org.medcare.igtl.network.GenericServerResponseHandler
get(int, int) - Method in class util.Matrix3D: Returns the element at the position i,j in the matrix
get1DFloatData() - Method in class org.medcare.igtl.messages.NDArrayMessage
getAccuracy(double, AverageMeasurement, AverageMeasurement) - Static method in class algorithm.TrackingDataProcessor: This method computes the distance of two average points.
getAccuracyRotation(Quaternion, Measurement, Measurement) - Static method in class algorithm.TrackingDataProcessor: This method gets a quaternion (four double values) and two measurements.
getAlive() - Method in class org.medcare.igtl.network.ServerThread
getAverageMeasurement() - Method in class algorithm.Tool: This method computes the mean of the passed values.
getAverageMeasurement(String) - Method in class algorithm.DataService: This method checks if the tool exists and returns the average measurement of all collected data of that tool
getAverageRotation() - Method in class algorithm.Tool: This method computes the average rotation.
getBody() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** body.
getBody() - Method in class org.medcare.igtl.network.MessageHandler
getBody() - Method in class org.medcare.igtl.network.ResponseHandler
getBody_size() - Method in class org.medcare.igtl.util.Header: ** Size of body in bytes.
getBoxPlot() - Method in class algorithm.AverageMeasurement
getBoxPlot(List<Double>) - Static method in class algorithm.TrackingDataProcessor: This method calculates the values for a boxplot.
getBufferedImage() - Method in class org.medcare.igtl.util.IGTImage
getBytes() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** Bytes to be sent.
getBytes() - Method in class org.medcare.igtl.util.BytesArray: ** Return a byte array representing the data
getBytes() - Method in class org.medcare.igtl.util.Header: ** this header bytes.
getBytes(int) - Method in class org.medcare.igtl.util.BytesArray: ** Read length of bytes from the bytesArray **
getBytesArray() - Method in class org.medcare.igtl.util.Header: ** ByteArray which contain header bytes.
getCapability() - Method in class org.medcare.igtl.network.MessageHandler: ** Gets the ArrayList of Types implemented in this Handler
getCapability() - Method in class org.medcare.igtl.network.ResponseHandler: ** Gets the ArrayList of Types implemented in this Handler
GetCapabilityData() - Method in class org.medcare.igtl.messages.CapabilityMessage: ** To get capability_data byte array **
getCapabilityList() - Method in class org.medcare.igtl.network.ResponseHandler
GetCapabilityList() - Method in class org.medcare.igtl.messages.CapabilityMessage: ** To get capabilityList ArrayList **
GetCapabilityMessage - Class in org.medcare.igtl.messages: ** This class create a GetCapability object from bytes received or help to generate bytes to send from it
GetCapabilityMessage(String) - Constructor for class org.medcare.igtl.messages.GetCapabilityMessage: ** Constructor to be used to create message to send them with this constructor you must use method CreateBody and then getBytes to send them **
GetCapabilityMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.GetCapabilityMessage: ** Constructor to be used to create message from received data
getCode() - Method in class org.medcare.igtl.messages.StatusMessage: ** To get client or server code **
getCode() - Method in class org.medcare.igtl.util.Status: ** To get client or server status code **
getControllers() - Method in class util.ControllerCollector
getCoordinate() - Method in class inputOutput.TempTool: This returns the current coordinates of this tool as an 3D Point
getCrc() - Method in class org.medcare.igtl.util.Header: ** 64 bit CRC for body data.
getCurrentStatus() - Method in class org.medcare.igtl.network.OpenIGTServer
getDataManager() - Method in class algorithm.DataService
getDataMatrix() - Method in class org.medcare.igtl.messages.DataArrayMessage
getDataProcessor() - Method in class algorithm.ImageDataManager
getDataSeries1() - Method in class userinterface.TrackingDataDisplay
getDataSeries2() - Method in class userinterface.TrackingDataDisplay
getDataSeries3() - Method in class userinterface.TrackingDataDisplay
getDataService() - Method in class algorithm.TrackingService: Returns the reference to the data service
getDataType() - Method in class org.medcare.igtl.util.Header: ** Type name of data **
getDeviceName() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** Unique device name.
getDeviceName() - Method in class org.medcare.igtl.util.Header: ** Unique device name.
getDimensions() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image dimensions **
getDivisions() - Method in class shapes.TrackingCone: Gets the value of the divisions property.
getDouble(int) - Method in class org.medcare.igtl.util.BytesArray: ** Read a double value from bytesArray, using IEEE 754 format **
getEncoding() - Method in class org.medcare.igtl.messages.StringMessage
getEndian() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image Endian of image scalar **
getError() - Method in class algorithm.Measurement
getErrorName() - Method in class org.medcare.igtl.messages.StatusMessage: ** To get errorName subCode **
getErrorName() - Method in class org.medcare.igtl.util.Status: ** To get client or server status code **
getErrors() - Method in class algorithm.AverageMeasurement
getErrors() - Method in class algorithm.BoxPlot
getErrors(Vector3D) - Method in class algorithm.Tool: This method calculates errors and saves them in a list.
getExceptionNumber() - Static method in class inputOutput.CSVFileReader
getFilePath() - Method in class algorithm.ImageDataProcessor
getFPS() - Method in class inputOutput.OIGTImageSource: This method returns the frames per second.
getHeader() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** header.
getHeader() - Method in class org.medcare.igtl.network.MessageHandler
getHeader() - Method in class org.medcare.igtl.network.ResponseHandler
getHeight() - Method in class shapes.TrackingCone: Gets the value of the height property.
getImageData() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get image_data byte array **
getImageDataByte() - Method in class inputOutput.OpenIGTLinkConnection: This method is for getting the current image data.
getImageDataSize() - Method in class org.medcare.igtl.messages.ImageMessage
getImageHeader() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get image_header byte array **
getImageMessage() - Method in class inputOutput.OIGTImageSource: This method is getting the current ImageMessage if it's needed.
getImageMessage() - Method in class inputOutput.OpenIGTLinkConnection: This method is for getting the current ImageMessage.
GetImageMessage - Class in org.medcare.igtl.messages: ** This class create a GetImage object from bytes received or help to generate bytes to send from it
GetImageMessage(String) - Constructor for class org.medcare.igtl.messages.GetImageMessage: ** Constructor to be used to create message to send them with this constructor you must use method CreateBody and then getBytes to send them **
GetImageMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.GetImageMessage: ** Constructor to be used to create message from received data
getImagePoints2d() - Method in class inputOutput.TransformationMatrix: Provides the image points as OpenCV-Matrix Only uses the first two coordinates of the point (2D)
getImagePoints3d() - Method in class inputOutput.TransformationMatrix: Provides the image points as OpenCV-Matrix Uses three point coordinates, to calculate in 3D
getImageScalarType() - Method in class inputOutput.OIGTImageSource: This method returns information about the type of ImageMessage.
getImageSize() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image Size **
getImageType() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image image type **
getIndex() - Method in class org.medcare.igtl.util.BytesArray: ** Gets the current read/write index return@ The index
getInstance() - Static method in class algorithm.TrackingService: Returns the instance.
getInstance() - Static method in class util.ControllerCollector
getIv() - Method in class userinterface.ImageScatterChart
getJitter() - Method in class algorithm.AverageMeasurement: The method getJitter computes the root mean square error.
getKeepAlive() - Method in class org.medcare.igtl.network.OpenIGTServer
getLastToolList() - Method in class inputOutput.AbstractTrackingDataSource
getLength() - Method in class org.medcare.igtl.messages.StringMessage
getLengthSquaredFromColumn(int) - Method in class util.Matrix3D: Gets the sum of all number squared in a column
getLogger() - Method in class org.medcare.igtl.util.ErrorManager: Method to get Logger used by this ErrorManager
getLong(int) - Method in class org.medcare.igtl.util.BytesArray: ** Read a long value from bytesArray **
getMag() - Method in class util.Vector3D: Gets the magnitude of the vector
getMatrix() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image matrix **
getMatrix() - Method in class org.medcare.igtl.messages.TransformMessage: ** To get Image matrix **
getMatrixString(Matrix3D) - Static method in class util.TransformNR: Gets the matrix string.
getMax() - Method in class algorithm.BoxPlot
getMeasurement() - Method in class algorithm.Tool: Returns a list of measurements
getMedian() - Method in class algorithm.BoxPlot
getMeshView() - Method in class shapes.STLModel
getMessage() - Method in class org.medcare.igtl.messages.StringMessage
getMessageHandler(Header, byte[], ServerThread) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
getMessageHandler(Header, byte[], ServerThread) - Method in class org.medcare.igtl.network.OpenIGTServer: ** To get message Handler
getMin() - Method in class algorithm.BoxPlot
getName() - Method in class algorithm.Tool: Returns the name of the tool
getName() - Method in class inputOutput.TempTool: This returns the name of the current tool
getName() - Method in class shapes.STLModel
getNextData(int) - Method in class algorithm.TrackingDataManager: The method getNextData calls method update, which is from inputOutput, creates from return value of update a measurement and adds this tool
getNextMat() - Method in class inputOutput.AbstractImageSource: provides the next Matrix for a further use
getNextMat() - Method in class inputOutput.FilestreamSource: Transmits the matrix of the picture
getNextMat() - Method in class inputOutput.LivestreamSource: Transmits the matrix of the picture
getNextMat() - Method in class inputOutput.OIGTImageSource: This method is getting the imgData as byte array (with a length of rows*cols), and then it is converted to a Mat object from OpenCV by using put(int row, int col, byte[]).
getNormals() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image normals **
getNormals() - Method in class org.medcare.robot.RasSpacePosition
getOpenIGT_Queue() - Method in class org.medcare.igtl.network.MessageQueueManager
getOpenIGTClient() - Method in class org.medcare.igtl.network.ResponseHandler
getOrigin() - Method in class inputOutput.OIGTImageSource: This method returns information about the origin of ImageMessage.
getOrigin() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image origin **
getPerspectiveCamera() - Method in class shapes.CameraContainer
getPos() - Method in class algorithm.Measurement
getPos() - Method in class shapes.TrackingCone
getPosition() - Method in class org.medcare.igtl.messages.PositionMessage: ** To get Image position **
getPosition() - Method in class org.medcare.igtl.messages.TransformMessage: ** To get Image origin **
getPositionArray() - Method in class util.TransformNR: Gets the position array.
getPositionData() - Method in class org.medcare.igtl.messages.PositionMessage: ** To get position_data byte array **
GetPositionMessage - Class in org.medcare.igtl.messages: ** This class create a GetPosition object from bytes received or help to generate bytes to send from it
GetPositionMessage(String) - Constructor for class org.medcare.igtl.messages.GetPositionMessage: ** Constructor to be used to create message to send them with this constructor you must use method CreateBody and then getBytes to send them **
GetPositionMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.GetPositionMessage: ** Constructor to be used to create message from received data
getPositionVector() - Method in class org.medcare.robot.CartesianSpacePosition
getQ1() - Method in class algorithm.BoxPlot
getQ3() - Method in class algorithm.BoxPlot
getQuaternion() - Method in class org.medcare.igtl.messages.PositionMessage: ** To get Image quaternion **
getRadius() - Method in class shapes.TrackingCone: Gets the value of the radius property.
getResponseHandler(Header, byte[]) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
getResponseHandler(Header, byte[]) - Method in class org.medcare.igtl.network.OpenIGTClient: ** To get response Handler
getRotation() - Method in class algorithm.Measurement
getRotation() - Method in class util.TransformNR: Gets the rotation.
getRotationError() - Method in class algorithm.AverageMeasurement
getRotationJitter() - Method in class algorithm.AverageMeasurement
getRotationJitter() - Method in class algorithm.Tool: This method computes the Jitter of a Rotation.
getRotationMat() - Method in class inputOutput.TransformationMatrix: Converts the rotation matrix array into an OpenCV-Matrix
getRotationMatrix() - Method in class org.medcare.robot.CartesianSpacePosition
getRotationMatrix() - Method in class util.TransformNR: Gets the rotation matrix.
getRotationMatrixArray() - Method in class org.medcare.igtl.messages.TransformMessage: ** To get Image normals **
getRotationMatrixArray() - Method in class util.TransformNR: Gets the rotation matrix array.
getRotationR() - Method in class inputOutput.TempTool: This returns the current Quaternion rotation of this tool
getRotationX() - Method in class inputOutput.TempTool: This returns the current Quaternion rotation around the X-axis of this tool
getRotationY() - Method in class inputOutput.TempTool: This returns the current Quaternion rotation around the Y-axis of this tool
getRotationZ() - Method in class inputOutput.TempTool: This returns the current Quaternion rotation around the Z-axis of this tool
getScalarType() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image scalar type **
getScaleMat() - Method in class inputOutput.TransformationMatrix: Converts the scale vector array into an OpenCV-Matrix
getServerThread() - Method in class org.medcare.igtl.network.OpenIGTServer
getSize() - Method in class org.medcare.igtl.util.BytesArray: ** For an output/write bytesArray, returns the number of bytes written.
getSleepTime() - Method in class org.medcare.igtl.network.MessageQueueManager: ** Gets the current sleep time value return@ The sleep time value
getSleepTime() - Method in class org.medcare.igtl.network.RequestQueueManager: ** Gets the current sleep time value return@ The sleep time value
getSleepTime() - Method in class org.medcare.igtl.network.ResponseQueueManager: ** Gets the current sleep time value return@ The sleep time value
getSource() - Method in class algorithm.TrackingDataManager
getSpacing() - Method in class inputOutput.OIGTImageSource: This method returns information about spacing of ImageMessage.
getSpacing() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get Image spacing **
getSphere() - Method in class shapes.Target
getStatus() - Method in class org.medcare.igtl.messages.StatusMessage: ** To get client or server status **
getStatus() - Method in class org.medcare.igtl.network.OpenIGTClient: ** To set server status **
getStatus() - Method in class org.medcare.igtl.network.ResponseHandler: ** To set client status **
getStatus() - Method in class org.medcare.igtl.network.ServerThread: ** To set server status **
getStatusData() - Method in class org.medcare.igtl.messages.StatusMessage: ** To get status_data byte array **
GetStatusMessage - Class in org.medcare.igtl.messages: ** This class create a GetStatus object from bytes received or help to generate bytes to send from it
GetStatusMessage(String) - Constructor for class org.medcare.igtl.messages.GetStatusMessage: ** Constructor to be used to create message to send them with this constructor you must use method CreateBody and then getBytes to send them **
GetStatusMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.GetStatusMessage: ** Constructor to be used to create message from received data
getStatusString() - Method in class org.medcare.igtl.messages.StatusMessage: ** To get statusString subCode **
getStatusString() - Method in class org.medcare.igtl.util.Status: ** To get client or server status code **
getSTLModels() - Method in class algorithm.VisualizationManager: Get all currently loaded stl models
getString(int) - Method in class org.medcare.igtl.util.BytesArray: ** Converts the byte array to a String based on the US-ASCII character set.
getString(int, boolean) - Method in class org.medcare.igtl.util.BytesArray: ** Read a string from the bytesArray.
getSubCode() - Method in class org.medcare.igtl.messages.StatusMessage: ** To get Image subCode **
getSubCode() - Method in class org.medcare.igtl.util.Status: ** To get client or server status code **
getSubDimensions() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get SubVolume dimensions **
getSubOffset() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get SubVolume offset **
getSubVolumeImageSize() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get SubVolume Size **
getTimeline() - Method in class algorithm.TrackingService: Returns the reference to the timeline
getTimestamp() - Method in class algorithm.Measurement
getTimestamp() - Method in class inputOutput.TempTool: This returns the current timestamp of this tool
getTimeStamp() - Static method in class org.medcare.igtl.util.Header: ** TimeStamp or 0 if unused.
getToolByName(String) - Method in class algorithm.DataService: This method checks if the tool exists.
getToolDataList() - Method in class inputOutput.OpenIGTLinkConnection
getToolMeasures() - Method in class algorithm.TrackingDataManager
getToolname() - Method in class algorithm.Measurement
getToolName() - Method in class userinterface.TrackingDataDisplay
getToolNames() - Method in class inputOutput.CSVFileReader
getTotalFrameNumber() - Method in class inputOutput.FilestreamSource: returns the frame total number of the selected file.
getTrace() - Method in class util.Matrix3D: Gets the trace (the sum of the diagonal) of the matrix
getTrackingDataSource() - Method in class algorithm.TrackingService: Returns the reference to the tracking source
getTrackingPoints2d() - Method in class inputOutput.TransformationMatrix: Provides the tracking points as OpenCV-Matrix Only uses the first two coordinates of the point (2D)
getTrackingPoints3d() - Method in class inputOutput.TransformationMatrix: Provides the tracking points as OpenCV-Matrix Uses three point coordinates, to calculate in 3D
getTransform() - Method in class org.medcare.igtl.util.IGTImage
getTransformationMatrix() - Method in class util.TransformNR: Gets the matrix transform.
getTransformData() - Method in class org.medcare.igtl.messages.TransformMessage: ** To get transform_data byte array **
getTransformMatOpenCvEstimated2d() - Method in class inputOutput.TransformationMatrix: Calculates a transformation matrix by the provided raw points Uses OpenCV's estimate-method based on RANSAC method Uses only the x,y coordinates of the points and hence only calculates a 2D projection matrix
getTransformMatOpenCvEstimated3d() - Method in class inputOutput.TransformationMatrix: Calculates a transformation matrix by the provided raw points Uses OpenCV's estimate-method based on RANSAC method Uses x,y,z coordinates of the points and hence calculates a 3D projection matrix
getTransformMatProjectionTransform() - Method in class inputOutput.TransformationMatrix: Calculates a transformation matrix by the provided raw points.
getTransformMatProjectionTransform(float[][], float[][]) - Static method in class algorithm.ProjectiveTransformation: Calculates a transformation matrix by the provided raw points.
getTransformMatrix() - Method in class org.medcare.robot.FrameTransformation
GetTransformMessage - Class in org.medcare.igtl.messages: ** This class create a GetTransform object from bytes received or help to generate bytes to send from it
GetTransformMessage(String) - Constructor for class org.medcare.igtl.messages.GetTransformMessage: ** Constructor to be used to create message to send them with this constructor you must use method CreateBody and then getBytes to send them **
GetTransformMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.GetTransformMessage: ** Constructor to be used to create message from received data
getTranslationMat() - Method in class inputOutput.TransformationMatrix: Converts the translation vector array into an OpenCV-Matrix
getTxTransform(String) - Method in class inputOutput.OpenIGTLinkConnection: The methods below are not used during a connection over MITK
getTxTransform(String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: Request for a transform for transmition to IGT
getTxTransform(String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: Request for a TransformNR for transmition to IGT
getTxTransform(String) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: Request for a transform for transmition to IGT
getTxTransform(String) - Method in class sample.ClientSample
getTxTransform(String) - Method in class sample.ServerSample
getULong(int) - Method in class org.medcare.igtl.util.BytesArray: ** Read an unsigned long value from bytesArray **
getValid() - Method in class inputOutput.TempTool: This returns the current activity status of this tool
getVersion() - Method in class org.medcare.igtl.network.MessageQueueManager: ** Gets the current version return@ The version value
getVersion() - Method in class org.medcare.igtl.network.RequestQueueManager: ** Gets the current version return@ The version value
getVersion() - Method in class org.medcare.igtl.network.ResponseQueueManager: ** Gets the current version return@ The version value
getVersion() - Method in class org.medcare.igtl.util.Header: ** Version number.
getW() - Method in class util.Quaternion: Returns the w (real) component.
getX() - Method in class util.Quaternion: Returns the x component.
getX() - Method in class util.TransformNR: Gets the x.
getX() - Method in class util.Vector3D: Return the x component of the vector
getY() - Method in class util.Quaternion: Returns the y component.
getY() - Method in class util.TransformNR: Gets the y.
getY() - Method in class util.Vector3D: Return the y component of the vector
getZ() - Method in class util.Quaternion: Returns the z component.
getZ() - Method in class util.TransformNR: Gets the z.
getZ() - Method in class util.Vector3D: Return the z component of the vector

H

hashCode() - Method in class util.Matrix3D
hashCode() - Method in class util.Quaternion
hashCode() - Method in class util.Vector3D
Header - Class in org.medcare.igtl.util: ** For reading/writing OpenIGTLink headers
Header(byte[]) - Constructor for class org.medcare.igtl.util.Header: ** Destination Constructor **
Header(long, String, String, byte[]) - Constructor for class org.medcare.igtl.util.Header: ** Destination Constructor **
Header(long, String, String, long, long, long) - Constructor for class org.medcare.igtl.util.Header: ** Destination Constructor **
heightProperty() - Method in class shapes.TrackingCone

I

identity() - Static method in class util.Matrix3D: Static method for clearly creating an identity matrix
IGenericOpenIGTLinkNode - Interface in org.medcare.igtl.network
ignoreDimension - Variable in class inputOutput.TransformationMatrix: Assuming that rotation, translation and scale matrix uses 3 dimension, we skip this dimension in order to use it for 2D
IGTImage - Class in org.medcare.igtl.util
IGTImage(ImageMessage) - Constructor for class org.medcare.igtl.util.IGTImage
IGTL_CAPABILITY_TYPE_LENGTH - Static variable in class org.medcare.igtl.messages.CapabilityMessage
IGTL_IMAGE_HEADER_SIZE - Static variable in class org.medcare.igtl.messages.ImageMessage
IGTL_IMAGE_HEADER_VERSION - Static variable in class org.medcare.igtl.messages.ImageMessage
IGTL_POSITION_MESSAGE_DEFAULT_SIZE - Static variable in class org.medcare.igtl.messages.PositionMessage
IGTL_POSITION_MESSAGE_POSITON_ONLY_SIZE - Static variable in class org.medcare.igtl.messages.PositionMessage
IGTL_POSITION_MESSAGE_WITH_QUATERNION3_SIZE - Static variable in class org.medcare.igtl.messages.PositionMessage
IGTL_STATUS_ERROR_NAME_LENGTH - Static variable in class org.medcare.igtl.messages.StatusMessage
IGTL_STATUS_HEADER_SIZE - Static variable in class org.medcare.igtl.messages.StatusMessage
IGTL_TRANSFORM_SIZE - Static variable in class org.medcare.igtl.messages.TransformMessage
ImageDataManager - Class in algorithm: builds an interface to other teams, includes distance measurement and conversion from matrix in bufferedimage
ImageDataManager() - Constructor for class algorithm.ImageDataManager
ImageDataProcessor - Class in algorithm: ImageDataProcessor accesses AbstractImageSource to control the connection and read images.
ImageDataProcessor() - Constructor for class algorithm.ImageDataProcessor
ImageMessage - Class in org.medcare.igtl.messages: ** This class create an Image object from bytes received or help to generate bytes to send from it
ImageMessage(String) - Constructor for class org.medcare.igtl.messages.ImageMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
ImageMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.ImageMessage: ** Constructor to be used to create message from received data
imagePoints - Variable in class inputOutput.TransformationMatrix: The raw measurements of the image points (landmarks in image coordinates)
ImageScatterChart - Class in userinterface
ImageScatterChart(NumberAxis, NumberAxis) - Constructor for class userinterface.ImageScatterChart
ImageWriter - Class in inputOutput: saves the imported frames as Mat Objects (OpenCV).
ImageWriter() - Constructor for class inputOutput.ImageWriter
InfoController - Class in controller
InfoController() - Constructor for class controller.InfoController
init() - Method in class algorithm.Tool: Method to initialize the attributes of the tool
initialize(URL, ResourceBundle) - Method in class controller.AutoTrackController
initialize(URL, ResourceBundle) - Method in class controller.InfoController
initialize(URL, ResourceBundle) - Method in class controller.MainController
initialize(URL, ResourceBundle) - Method in class controller.MeasurementController
initialize(URL, ResourceBundle) - Method in class controller.SettingsController
initialize(URL, ResourceBundle) - Method in class controller.ThrombectomyController
initialize(URL, ResourceBundle) - Method in class controller.TrackingDataController
initialize(URL, ResourceBundle) - Method in class controller.VideoController
initialize(URL, ResourceBundle) - Method in class controller.VisualizationController
initSensorCurve(XYChart.Series<Number, Number>) - Method in class userinterface.PlottableImage
injectStatusLabel(Label) - Method in class algorithm.VisualizationManager
injectStatusLabel(Label) - Method in interface controller.Controller
injectStatusLabel(Label) - Method in class controller.MeasurementController
injectStatusLabel(Label) - Method in class controller.ThrombectomyController
injectStatusLabel(Label) - Method in class controller.TrackingDataController
injectStatusLabel(Label) - Method in class controller.VideoController
injectStatusLabel(Label) - Method in class controller.VisualizationController
injectTrackingDataController(TrackingDataController) - Method in class controller.VisualizationController
injectVisualizationController(VisualizationController) - Method in class controller.TrackingDataController
injectVisualizationManager(VisualizationManager) - Method in class controller.TrackingDataController
injectVisualizationManager(VisualizationManager) - Method in class controller.VisualizationController
inputOutput - package inputOutput: This package contains classes for input and output of data streams.
interrupt() - Method in class org.medcare.igtl.network.OpenIGTClient: Interrupt this thread
interrupt() - Method in class org.medcare.igtl.network.ServerThread: Interrupt this thread
intersectsTarget(Target, Vector3D) - Method in class shapes.NeedleProjection: Function which determines if the projection intersects with a target, which is represented by a sphere
invert() - Method in class util.Matrix3D: Method to return the inverse of a matrix
IOpenIgtPacketListener - Interface in org.medcare.igtl.network
isConnected - Variable in class inputOutput.AbstractImageSource
isConnected() - Method in class algorithm.ImageDataProcessor
isConnected() - Method in class inputOutput.OpenIGTLinkConnection: This method is for checking the connection while the application is running.
isConnected() - Method in class org.medcare.igtl.network.OpenIGTClient
isConnected() - Method in class org.medcare.igtl.network.OpenIGTServer
isConsoleOn() - Static method in class util.CustomLogger
isEmpty(Mat) - Static method in class algorithm.MatHelper: Returns whether the provided Row/Column is empty.
isIdentity() - Method in class util.Quaternion: Compares with the identity quaternion, without distinguishing -0 from 0.
isRepeatModeOn() - Method in class inputOutput.CSVFileReader
isVisible() - Method in class shapes.STLModel

L

LENGTH - Static variable in class org.medcare.igtl.util.Header
licensesArea - Variable in class controller.InfoController
LISTENING - Enum constant in enum class org.medcare.igtl.network.OpenIGTServer.ServerStatus
LIVESTREAM - Enum constant in enum class inputOutput.VideoSource
LivestreamSource - Class in inputOutput: provides the livestream footage from a webcam, ultrasound device or any other suitable devices.
lm - Variable in class org.medcare.igtl.util.ErrorManager
loadCSVFile() - Method in class controller.TrackingDataController: load CSV file with tracking data created by MITK workbench
loadFromJSON(String) - Static method in class inputOutput.TransformationMatrix: Loads the attributes from a file
loadLastSTLModels() - Method in class algorithm.VisualizationManager: Loads the previously used stl files for visualisation
loadNextData(int) - Method in class algorithm.DataService: The method loadNextData gets a number of how much data should be reloaded.
loadNextData(int, boolean) - Method in class algorithm.DataService
loadTransformationMatrix() - Method in class algorithm.Tool
logger - Variable in class org.medcare.igtl.util.ErrorManager

M

main(String[]) - Static method in class mainMethod.StartClass
main(String[]) - Static method in class org.medcare.igtl.util.Tests: Main method of the class.
main(String[]) - Static method in class sample.ClientSample
main(String[]) - Static method in class sample.ServerSample
MainController - Class in controller
MainController() - Constructor for class controller.MainController
mainMethod - package mainMethod: This package contains the application's main method.
makeIdentityMatrix() - Method in class util.Matrix3D: Makes an identity matrix.
makeIdentityQuaternion() - Method in class util.Quaternion: Sets all components to zero except w, which is set to 1.
manageError(String, Exception, int) - Method in class org.medcare.igtl.network.GenericClientResponseHandler
manageError(String, Exception, int) - Method in class org.medcare.igtl.network.GenericServerResponseHandler
manageError(String, Exception, int) - Method in class org.medcare.igtl.network.MessageHandler: manage error this method must be adapted for each use
manageError(String, Exception, int) - Method in class org.medcare.igtl.network.ResponseHandler: manage error this method must be adapted for each use
Mat2BufferedImage(Mat) - Static method in class algorithm.ImageDataProcessor
Mat2Image(Mat, String) - Static method in class algorithm.ImageDataProcessor
MatHelper - Class in algorithm
MatHelper() - Constructor for class algorithm.MatHelper
Matrix3D - Class in util: This class is based on the class Matrix3f from https://github.com/jMonkeyEngine/jmonkeyengine/blob/master/jme3-core/src/main/java/com/jme3/math/Matrix3f.java
Matrix3D() - Constructor for class util.Matrix3D: Instantiates an identity matrix (diagonals = 1, other elements = 0).
Matrix3D(double[]) - Constructor for class util.Matrix3D: Instantiates a matrix with specified elements.
Matrix3D(double[][]) - Constructor for class util.Matrix3D
Matrix3D(Matrix3D) - Constructor for class util.Matrix3D: Instantiates a copy of the matrix argument.
matToArray(Mat) - Static method in class algorithm.MatHelper: Converts an OpenCV-Mat to a double array
MAX_UINT - Static variable in class org.medcare.igtl.util.BytesArray
Measurement - Class in algorithm
Measurement() - Constructor for class algorithm.Measurement
Measurement(TempTool) - Constructor for class algorithm.Measurement
MeasurementController - Class in controller
MeasurementController() - Constructor for class controller.MeasurementController
MESSAGE_CRC_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
MESSAGE_ERROR - Static variable in class org.medcare.igtl.util.ErrorManager
MESSAGE_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
MESSAGE_HANDLER_ERROR - Static variable in class org.medcare.igtl.util.ErrorManager
MESSAGE_INTERRUPTED_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
MESSAGE_NOT_MANAGED - Static variable in class org.medcare.igtl.util.ErrorManager
MESSAGE_PB_RESULT - Static variable in class org.medcare.igtl.util.ErrorManager
MessageHandler - Class in org.medcare.igtl.network: Perform request corresponding to the message received performRequest methods must be adapted corresponding to the need of each use User must adapt Capability list, to be able to send the right capability list and to have a correct error management for incorrect capability request
MessageHandler(Header, byte[], ServerThread) - Constructor for class org.medcare.igtl.network.MessageHandler: Default MessageQueueManager constructor.
MessageQueueManager - Class in org.medcare.igtl.network: One MessageQueueManager is created by each ServerThread to add MessageHandler to MessageQueueManager queue as soon as they receive messages.
MessageQueueManager(ServerThread) - Constructor for class org.medcare.igtl.network.MessageQueueManager: Default MessageQueueManager constructor.
move(Vector3D) - Method in class shapes.CameraContainer: Moves the position vector by adding a new one to it and updates the position of the camera
mult(double) - Method in class util.Matrix3D: Method to mutliply all values of the current matrix with a scalar
mult(Vector3D) - Method in class util.Matrix3D
multLocal(double) - Method in class util.Vector3D: Scalar multiply the current vector with a number Changes the current vector

N

NDArrayMessage - Class in org.medcare.igtl.messages: ** This class create an NDArray object from bytes received or help to generate bytes to send from it
NDArrayMessage(String) - Constructor for class org.medcare.igtl.messages.NDArrayMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
NDArrayMessage(String, byte, byte, short[], float[]) - Constructor for class org.medcare.igtl.messages.NDArrayMessage
NDArrayMessage(String, float[]) - Constructor for class org.medcare.igtl.messages.NDArrayMessage
NDArrayMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.NDArrayMessage: ** Constructor to be used to create message from received data
NeedleProjection - Class in shapes: This class represents the projection of the needle, so a straight path in front of the needle.
NeedleProjection() - Constructor for class shapes.NeedleProjection
next_crc(long, byte) - Method in class org.medcare.igtl.util.BytesArray: Calculates the next crc value.
norm() - Method in class util.Quaternion: Returns the norm, defined as the dot product of the quaternion with itself.

O

OIGTImageSource - Class in inputOutput: provides the basic functionalities for the application like opening and closing the connection, and an image converted to a Mat object from OpenCV.
OIGTImageSource() - Constructor for class inputOutput.OIGTImageSource: This constructor is used when the user doesn't enter an ip address or a port number.
OIGTTrackingDataSource - Class in inputOutput: this class makes it possible to connect with OpenIGTLink so the tracking data of the tools (coordinates, rotation, name, etc.) can be transfered directly without saving it in a CSV-file in advance
OIGTTrackingDataSource() - Constructor for class inputOutput.OIGTTrackingDataSource
on_browseOutputDirectory() - Method in class controller.AutoTrackController: Action that is called when the user wants to set an output directory
on_doAutoCapture() - Method in class controller.AutoTrackController: Called, when the "Auto Capture" Button is toggled (on or off)
on_doSingleCapture() - Method in class controller.AutoTrackController: Called when the "Single Capture" Button is pressed.
on_generateMatrix() - Method in class controller.AutoTrackController
on_importMatrix() - Method in class controller.AutoTrackController: Called, when "Import Matrix" Button is pressed.
on_openOutputDirectory() - Method in class controller.AutoTrackController: Action that is called when the user wants to open the output directory
on_reloadMatrix() - Method in class controller.AutoTrackController: Reloads the matrix from the last given path (so it's easier to change from the outside)
onConnectButtonClicked() - Method in class controller.TrackingDataController: Connect via OpenIGTLink.
onGetStatus(String) - Method in class inputOutput.OpenIGTLinkConnection
onGetStatus(String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: Request for status from IGT/Slicer
onGetStatus(String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: Request for status from IGT/Slicer
onGetStatus(String) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: Request for status from IGT/Slicer
onGetStatus(String) - Method in class sample.ClientSample
onGetStatus(String) - Method in class sample.ServerSample
onMouseClicked(double, double) - Method in interface userinterface.PlottableImageCallback
onNDArrayMessage(NDArrayMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkClient.Sender
onNDArrayMessage(NDArrayMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkServer.Sender
onRxDataArray(String, Matrix3D) - Method in class inputOutput.OpenIGTLinkConnection
onRxDataArray(String, Matrix3D) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: This is the handler for an array of raw data in an array
onRxDataArray(String, Matrix3D) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: This is the handler for an array of raw data in an array
onRxDataArray(String, Matrix3D) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: This is the handler for an array of raw data in an array
onRxDataArray(String, Matrix3D) - Method in class sample.ClientSample
onRxDataArray(String, Matrix3D) - Method in class sample.ServerSample
onRxImage(String, ImageMessage) - Method in class inputOutput.OpenIGTLinkConnection: This method is receiving an image as ImageMessage from the server, while it is running in the background during the connection.
onRxImage(String, ImageMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: This is a handler for an Image sent from IGT packet
onRxImage(String, ImageMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: This is a handler for an Image sent from IGT packet
onRxImage(String, ImageMessage) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: This is a handler for an Image sent from IGT packet
onRxImage(String, ImageMessage) - Method in class sample.ClientSample
onRxImage(String, ImageMessage) - Method in class sample.ServerSample
onRxNDArray(String, float[]) - Method in class inputOutput.OpenIGTLinkConnection
onRxNDArray(String, float[]) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
onRxNDArray(String, float[]) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
onRxNDArray(String, float[]) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: THis is a request for an array of data
onRxNDArray(String, float[]) - Method in class sample.ClientSample
onRxNDArray(String, float[]) - Method in class sample.ServerSample
onRxString(String, String) - Method in class inputOutput.OpenIGTLinkConnection
onRxString(String, String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: This is the handler for a String packet
onRxString(String, String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: This is the handler for a String packet
onRxString(String, String) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: This is the handler for a String packet
onRxString(String, String) - Method in class sample.ClientSample
onRxString(String, String) - Method in class sample.ServerSample
onRxTransform(String, TransformNR) - Method in class inputOutput.OpenIGTLinkConnection
onRxTransform(String, TransformNR) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: This method will be called by the IGT server when a transform is received.
onRxTransform(String, TransformNR) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: This method will be called by the IGT server when a TransformNR is received.
onRxTransform(String, TransformNR) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: This method will be called by the IGT server when a transform is received.
onRxTransform(String, TransformNR) - Method in class sample.ClientSample
onRxTransform(String, TransformNR) - Method in class sample.ServerSample
onStatus(StatusMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkClient.Sender
onStatus(StatusMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkServer.Sender
onStringMessage(StringMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkClient.Sender
onStringMessage(StringMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkServer.Sender
onTaskSpaceUpdate(PositionMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkClient.Sender
onTaskSpaceUpdate(PositionMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkServer.Sender
onTrackingSourceChanged(boolean, boolean, boolean) - Method in interface algorithm.TrackingServiceObserver: This method is triggered once a reference to one of the attributes of the TrackingService changed
onTransformMessage(TransformMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkClient.Sender
onTransformMessage(TransformMessage) - Method in class org.medcare.igtl.network.GenericIGTLinkServer.Sender
onTxDataArray(String) - Method in class inputOutput.OpenIGTLinkConnection
onTxDataArray(String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: THis is a request for an array of data
onTxDataArray(String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: THis is a request for an array of data
onTxDataArray(String) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: THis is a request for an array of data
onTxDataArray(String) - Method in class sample.ClientSample
onTxDataArray(String) - Method in class sample.ServerSample
onTxNDArray(String) - Method in class inputOutput.OpenIGTLinkConnection
onTxNDArray(String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
onTxNDArray(String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
onTxNDArray(String) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: THis is a request for an array of data
onTxNDArray(String) - Method in class sample.ClientSample
onTxNDArray(String) - Method in class sample.ServerSample
onTxString(String) - Method in class inputOutput.OpenIGTLinkConnection
onTxString(String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient: This is the request handler for a String packet
onTxString(String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer: This is the request handler for a String packet
onTxString(String) - Method in interface org.medcare.igtl.network.IOpenIgtPacketListener: This is the request handler for a String packet
onTxString(String) - Method in class sample.ClientSample
onTxString(String) - Method in class sample.ServerSample
openAboutView() - Method in class controller.MainController: Creates a dialogue to display some information about the application
openConnection() - Method in class inputOutput.AbstractImageSource: establishes a connection to the device
openConnection() - Method in class inputOutput.FilestreamSource: initializes a new VideoCapture object using the path.
openConnection() - Method in class inputOutput.LivestreamSource: initializes a new VideoCapture object using the deviceID.
openConnection() - Method in class inputOutput.OIGTImageSource: This method is starting the connection by creating an object of OpenIGTConnection.
openConnection(VideoSource) - Method in class algorithm.ImageDataManager
openConnection(VideoSource) - Method in class algorithm.ImageDataProcessor
openConnection(VideoSource, int) - Method in class algorithm.ImageDataManager
openConnection(VideoSource, int) - Method in class algorithm.ImageDataProcessor: Sets the type of image source depending on parameters source and deviceId and prepares the connection.
openIGT_Queue - Variable in class org.medcare.igtl.network.RequestQueueManager
openIGT_Queue - Variable in class org.medcare.igtl.network.ResponseQueueManager
OpenIGTClient - Class in org.medcare.igtl.network: The class can be used by first connecting to a server sending requests comming from the requestQueue, listening for response and adding response to the responsqueue
OpenIGTClient(String, int, ErrorManager) - Constructor for class org.medcare.igtl.network.OpenIGTClient: Default OpenIGTClient constructor.
OPENIGTCLIENT_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
OPENIGTCLIENT_IO_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
OPENIGTCLIENT_UNKNOWNHOST_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
OPENIGTLINK - Enum constant in enum class inputOutput.VideoSource
OpenIGTLinkConnection - Class in inputOutput: builds a connection based on OpenIGTLink for tracking data and image data.
OpenIGTLinkConnection() - Constructor for class inputOutput.OpenIGTLinkConnection: This constructor establishes a connection to a OpenIGTLink server using the default ip-address and port.
OpenIGTLinkConnection(String, int) - Constructor for class inputOutput.OpenIGTLinkConnection: An IP-address and a port number is needed for the connection.
OpenIGTLinkConnection.ToolData - Class in inputOutput
openIGTMessage - Variable in class org.medcare.igtl.network.GenericClientResponseHandler
openIGTMessage - Variable in class org.medcare.igtl.network.GenericMessageNodeHandler
openIGTMessage - Variable in class org.medcare.igtl.network.GenericServerResponseHandler
OpenIGTMessage - Class in org.medcare.igtl.messages: ** All messages will have to extend this class
OpenIGTMessage(String) - Constructor for class org.medcare.igtl.messages.OpenIGTMessage: ** Constructor to be used to create message to getBytes to send them **
OpenIGTMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.OpenIGTMessage: ** Constructor to be used to build messages from incoming bytes **
OpenIGTServer - Class in org.medcare.igtl.network: The class can be used to create a server listening a port Messages received will be queued and proceed
OpenIGTServer(int, ErrorManager) - Constructor for class org.medcare.igtl.network.OpenIGTServer: Default MessageQueueManager constructor.
OPENIGTSERVER_IO_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
OpenIGTServer.ServerStatus - Enum Class in org.medcare.igtl.network
org.medcare.igtl.messages - package org.medcare.igtl.messages
org.medcare.igtl.network - package org.medcare.igtl.network
org.medcare.igtl.util - package org.medcare.igtl.util
org.medcare.robot - package org.medcare.robot
origin() - Method in class org.medcare.robot.RasSpacePosition
outputPathButton - Variable in class controller.AutoTrackController
outputPathField - Variable in class controller.AutoTrackController

P

packBody() - Method in class org.medcare.igtl.messages.CapabilityMessage: ** To create body from image_header and image_data SetCapabilityData must have called first
packBody() - Method in class org.medcare.igtl.messages.DataArrayMessage
packBody() - Method in class org.medcare.igtl.messages.GetCapabilityMessage: ** To create body to get bytes to send
packBody() - Method in class org.medcare.igtl.messages.GetImageMessage: ** To create body to get bytes to send
packBody() - Method in class org.medcare.igtl.messages.GetPositionMessage: ** To create body to get bytes to send
packBody() - Method in class org.medcare.igtl.messages.GetStatusMessage: ** To create body to get bytes to send
packBody() - Method in class org.medcare.igtl.messages.GetTransformMessage: ** To create body to get bytes to send
packBody() - Method in class org.medcare.igtl.messages.ImageMessage: ** To create body from image_header and image_data SetImageHeader and SetImageData must have called first
packBody() - Method in class org.medcare.igtl.messages.NDArrayMessage
packBody() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** To create body from image_header and image_data SetImageHeader and SetImageData must have called first
packBody() - Method in class org.medcare.igtl.messages.PositionMessage: ** To create body from image_header and image_data SetPositionData must have called first
packBody() - Method in class org.medcare.igtl.messages.StatusMessage: ** To create body from image_header and image_data SetStatusData must have called first
packBody() - Method in class org.medcare.igtl.messages.StringMessage
packBody() - Method in class org.medcare.igtl.messages.TransformMessage: ** To create body from image_header and image_data SetTransformData must have called first
parseXMLStringMessage(String) - Static method in class inputOutput.OpenIGTLinkConnection
parseXMLStringMessage(String) - Static method in class sample.ClientSample
path - Variable in class inputOutput.ImageWriter
perform(String) - Method in class org.medcare.igtl.network.GenericClientResponseHandler
perform(String) - Method in class org.medcare.igtl.network.GenericServerResponseHandler
perform(String) - Method in class org.medcare.igtl.network.MessageHandler: Perform the request job this method must be adapted for each use
perform(String) - Method in class org.medcare.igtl.network.ResponseHandler: Perform the response job this method must be adapted for each use
perform(String, Header, byte[], IOpenIgtPacketListener) - Method in class org.medcare.igtl.network.GenericMessageNodeHandler
performRequest() - Method in class org.medcare.igtl.network.MessageHandler: Perform the request job on the message performRequest methods must be corresponding to the need of each use
performResponse() - Method in class org.medcare.igtl.network.ResponseHandler: Perform the response job performResponse methods must be adapted corresponding to the need of each use
Persistence - Class in util
Persistence() - Constructor for class util.Persistence
PlottableImage - Class in userinterface
PlottableImage(NumberAxis, NumberAxis) - Constructor for class userinterface.PlottableImage
PlottableImageCallback - Interface in userinterface
position - Static variable in class org.medcare.igtl.messages.PositionMessage
POSITION_ONLY - Static variable in class org.medcare.igtl.messages.PositionMessage
PositionMessage - Class in org.medcare.igtl.messages: ** This class create an Position object from bytes received or help to generate bytes to send from it
PositionMessage(String, double[], Quaternion) - Constructor for class org.medcare.igtl.messages.PositionMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
PositionMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.PositionMessage: ** Constructor to be used to create message from received data
printBytes(byte[]) - Static method in class org.medcare.igtl.util.BytesArray
printDoubleDataArray(double[][]) - Method in class org.medcare.igtl.messages.TransformMessage
printPos() - Method in class algorithm.Tool: Helper method to print the current position
projectionIsVisible() - Method in class algorithm.Tool: Return if projection is visible
ProjectiveTransformation - Class in algorithm
ProjectiveTransformation() - Constructor for class algorithm.ProjectiveTransformation
pushNDArrayMessage(String, float[]) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
pushNDArrayMessage(String, float[]) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
pushPose(String, TransformNR) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
pushPose(String, TransformNR) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
pushStatus(String, int, int, String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
pushStatus(String, int, int, String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
pushStatus(String, int, int, String, String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
pushStatus(String, int, int, String, String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
pushStringMessage(String, String) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
pushStringMessage(String, String) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
pushTransformMessage(String, TransformNR) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
pushTransformMessage(String, TransformNR) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
putByte(byte) - Method in class org.medcare.igtl.util.BytesArray: ** Write an array of bytes to the bytesArray **
putBytes(byte[]) - Method in class org.medcare.igtl.util.BytesArray: ** Write an array of bytes to the bytesArray **
putBytes(byte[], int) - Method in class org.medcare.igtl.util.BytesArray: ** Write an array of bytes to the bytesArray **
putBytes(byte[], int, int) - Method in class org.medcare.igtl.util.BytesArray: ** Write an array of bytes to the bytesArray **
putCrc(byte[], int, long) - Method in class org.medcare.igtl.util.BytesArray: ** Calculate and Add a crc value to the bytesArray **
putDouble(double, int) - Method in class org.medcare.igtl.util.BytesArray: ** Add a double value to the bytesArray **
putLong(long, int) - Method in class org.medcare.igtl.util.BytesArray: ** Add a long value to the bytesArray **
putShort(short) - Method in class org.medcare.igtl.util.BytesArray: ** Add a short value to the bytesArray **
putString(String) - Method in class org.medcare.igtl.util.BytesArray: ** Add a string to the bytesArray.
putTimeStamp() - Method in class org.medcare.igtl.util.BytesArray: ** Calculate Add a timestamp value to the bytesArray ** ** @return The long value of timeStamp
putTimeStamp(float) - Method in class org.medcare.igtl.util.BytesArray: ** Add a timestamp value to the bytesArray ** ** @param t float timestamp n ** @return The number of bytes written
putULong(long, int) - Method in class org.medcare.igtl.util.BytesArray: ** Add a unsigned long value to the bytesArray.

Q

quaternion - Variable in class org.medcare.igtl.messages.PositionMessage
Quaternion - Class in util
Quaternion() - Constructor for class util.Quaternion: Creates an identity quaternion: all components are zero except x0, which is set to 1.
Quaternion(double[]) - Constructor for class util.Quaternion: Creates a quaternion from Tait-Bryan angles, applying the rotations in x-z-y extrinsic order or y-z'-x" intrinsic order.
Quaternion(double, double, double, double) - Constructor for class util.Quaternion: Creates a quaternion with the specified components.
Quaternion(Matrix3D) - Constructor for class util.Quaternion

R

radiusProperty() - Method in class shapes.TrackingCone
RasSpacePosition - Class in org.medcare.robot
RasSpacePosition() - Constructor for class org.medcare.robot.RasSpacePosition
RasSpacePosition(double[][], double[]) - Constructor for class org.medcare.robot.RasSpacePosition
readBufImg() - Method in class algorithm.ImageDataManager
readImg() - Method in class algorithm.ImageDataManager
readImg() - Method in class algorithm.ImageDataProcessor: Reads an image from video source and crops it.
readMat() - Method in class algorithm.ImageDataManager
readMat() - Method in class algorithm.ImageDataProcessor
readStlSaveFile() - Static method in class util.Persistence
register(Controller) - Method in class util.ControllerCollector
registerController() - Method in interface controller.Controller
registerImageClickedHandler(PlottableImageCallback) - Method in class userinterface.PlottableImage
registerObserver(TrackingServiceObserver) - Method in class algorithm.TrackingService: Register an observer.
regMatrixImportButton - Variable in class controller.AutoTrackController
regMatrixStatusBox - Variable in class controller.AutoTrackController
removeIOpenIgtOnPacket(IOpenIgtPacketListener) - Method in class org.medcare.igtl.network.GenericIGTLinkClient
removeIOpenIgtOnPacket(IOpenIgtPacketListener) - Method in class org.medcare.igtl.network.GenericIGTLinkServer
REQUEST_ERROR - Static variable in class org.medcare.igtl.util.ErrorManager
REQUEST_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
REQUEST_INTERRUPT_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
REQUEST_RESULT_ERROR - Static variable in class org.medcare.igtl.util.ErrorManager
REQUEST_TYPE_NOT_FOUND - Static variable in class org.medcare.igtl.util.ErrorManager
RequestQueueManager - Class in org.medcare.igtl.network: RequestQueueManager create its own OpenIGTClient connected to one OpenIGTServer.
RequestQueueManager(OpenIGTClient) - Constructor for class org.medcare.igtl.network.RequestQueueManager: Default RequestQueueManager constructor.
resetView() - Method in class algorithm.VisualizationManager: Helper Method used to recenter the view to its original position
RESPONSE_CRC_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
RESPONSE_ERROR - Static variable in class org.medcare.igtl.util.ErrorManager
RESPONSE_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
RESPONSE_HANDLER_ERROR - Static variable in class org.medcare.igtl.util.ErrorManager
RESPONSE_INTERRUPTED_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
RESPONSE_NOT_MANAGED - Static variable in class org.medcare.igtl.util.ErrorManager
RESPONSE_PB_RESULT - Static variable in class org.medcare.igtl.util.ErrorManager
ResponseHandler - Class in org.medcare.igtl.network: Perform response data corresponding to the message received performResponse methods must be adapted corresponding to the need of each use User must adapt Capability list, to be able to send the right capability list and to have a correct error management for incorrect capability request User must use SetStatus method so it value correspond to the real status of the client.
ResponseHandler(Header, byte[], OpenIGTClient) - Constructor for class org.medcare.igtl.network.ResponseHandler: Default ResponseHandler constructor.
ResponseQueueManager - Class in org.medcare.igtl.network: Each OpenIGTClient create its own ResponseQueueManager to queue response they get from server.
ResponseQueueManager(ErrorManager) - Constructor for class org.medcare.igtl.network.ResponseQueueManager: Default ResponseQueueManager constructor.
restartMeasurements() - Method in class algorithm.DataService: Restarts all measurements: resets the internal list of tools.
restartMeasurements() - Method in class algorithm.TrackingDataManager: Restarts all measurements: resets the internal list of tools.
rotateMatrix(Matrix3D) - Method in class shapes.NeedleProjection: Rotates the needle projection through a given rotation matrix
rotateMatrix(Matrix3D) - Method in class shapes.TrackingCone
rotation3d - Variable in class inputOutput.TransformationMatrix: The rotation matrix, provided by MITK
run() - Method in class org.medcare.igtl.network.GenericIGTLinkClient.Sender
run() - Method in class org.medcare.igtl.network.GenericIGTLinkServer.Sender
run() - Method in class org.medcare.igtl.network.MessageQueueManager: Starts the thread and process requests in queue
run() - Method in class org.medcare.igtl.network.OpenIGTClient: Reader thread.
run() - Method in class org.medcare.igtl.network.RequestQueueManager: Starts the thread and process requests in queue
run() - Method in class org.medcare.igtl.network.ResponseQueueManager: Starts the thread reading responses and adding them to the responseQueue
run() - Method in class org.medcare.igtl.network.ServerThread: Reader thread.

S

s - Variable in class org.medcare.igtl.network.GenericIGTLinkServer
sample - package sample
saveImage(BufferedImage, String) - Method in class inputOutput.ImageWriter: This method is for saving one single Image given as a parameter on the computer.
saveToJSON(File) - Method in class inputOutput.TransformationMatrix: Writes the current configuration into a JSON file
saveVideo(String, int, int, int) - Method in class inputOutput.ImageWriter: This method needs a filename, frames-per-second and width and height of the matrix for creating an object of VideoWriter.
scalarMultiplyColumn(int, double) - Method in class util.Matrix3D: Sets the element at the position i,j in the matrix
scaleVector3d - Variable in class inputOutput.TransformationMatrix: Scaling vector (applied in the respective dimensions)
scheduleReloadMatrix() - Method in class algorithm.VisualizationManager: This will set a flag that makes tools reload the transformation matrix from source on the next update
searchForMoreVideos - Variable in class controller.SettingsController
sendBytes(byte[]) - Method in class org.medcare.igtl.network.OpenIGTClient: Sends bytes
sendBytes(byte[]) - Method in class org.medcare.igtl.network.ServerThread: Sends bytes
Sender() - Constructor for class org.medcare.igtl.network.GenericIGTLinkClient.Sender
Sender() - Constructor for class org.medcare.igtl.network.GenericIGTLinkServer.Sender
sendMessage(OpenIGTMessage) - Method in class org.medcare.igtl.network.OpenIGTClient
sendMessage(OpenIGTMessage) - Method in class org.medcare.igtl.network.OpenIGTServer: Sends a message up the link
sendMessage(OpenIGTMessage) - Method in class org.medcare.igtl.network.ServerThread
sendMessage(Header, byte[]) - Method in class org.medcare.igtl.network.OpenIGTClient
sendMessage(Header, byte[]) - Method in class org.medcare.igtl.network.ServerThread
ServerSample - Class in sample
ServerSample() - Constructor for class sample.ServerSample
serverThread - Variable in class org.medcare.igtl.network.MessageHandler
ServerThread - Class in org.medcare.igtl.network: OpenIGTServer create one ServerThread for each client making a connection.
ServerThread(Socket, OpenIGTServer) - Constructor for class org.medcare.igtl.network.ServerThread: Default ServerThread constructor.
SERVERTHREAD_ABNORMAL_ANSWER - Static variable in class org.medcare.igtl.util.ErrorManager
SERVERTHREAD_IO_EXCEPTION - Static variable in class org.medcare.igtl.util.ErrorManager
ServerThread.ClientStatus - Enum Class in org.medcare.igtl.network
set(double, double, double, double) - Method in class util.Quaternion: Sets all 4 components to specified values.
set(int, double) - Method in class util.Vector3D: Method to set the vectors components
set(int, int, double) - Method in class util.Matrix3D: Sets the element at the position i,j in the matrix
set(Matrix3D) - Method in class util.Matrix3D: Copies the matrix argument.
set(Quaternion) - Method in class util.Quaternion: Copies all 4 components from another quaternion.
set1D_FloatData() - Method in class org.medcare.igtl.messages.NDArrayMessage
set1D_FloatData(float[]) - Method in class org.medcare.igtl.messages.NDArrayMessage
setAlive(boolean) - Method in class org.medcare.igtl.network.ServerThread
setBody(byte[]) - Method in class org.medcare.igtl.messages.OpenIGTMessage
setBody(byte[]) - Method in class org.medcare.igtl.network.MessageHandler
setBody(byte[]) - Method in class org.medcare.igtl.network.ResponseHandler
setBottomCrop(int) - Method in class algorithm.ImageDataProcessor
setBoxPlot(BoxPlot) - Method in class algorithm.AverageMeasurement
SetCapabilityData(byte[]) - Method in class org.medcare.igtl.messages.CapabilityMessage: ** To extract capabilityList capability_data byte array
SetCapabilityData(ArrayList<String>) - Method in class org.medcare.igtl.messages.CapabilityMessage: ** To create capability_data from capabilityList and to get the byte array to send
setCapabilityList(ArrayList<String>) - Method in class org.medcare.igtl.network.ResponseHandler
setCode(int) - Method in class org.medcare.igtl.util.Status: ** To set client or server status code
setCode(long) - Method in class org.medcare.igtl.messages.StatusMessage: ** To set client or server code
setColor(String) - Method in class shapes.STLModel: A method to set the color of the model.
setColor(PhongMaterial) - Method in class shapes.STLModel
setConeColor(PhongMaterial) - Method in class algorithm.Tool: Method to set the color of the cone
setConeSize(double) - Method in class algorithm.Tool: Method to set the size of the cone
setConeVisibility(boolean) - Method in class algorithm.Tool: Method to set the visibility of the cone
setCurrentStatus(OpenIGTServer.ServerStatus) - Method in class org.medcare.igtl.network.OpenIGTServer
setData(double, double, double, double, double, double, double, double, double, String) - Method in class inputOutput.TempTool: This is the set method for all tool values.
setDataManager(TrackingDataManager) - Method in class algorithm.DataService
setDimensions(long[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image dimensions
setDimensions(long, long, long) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image dimensions
setDivisions(int) - Method in class shapes.TrackingCone: Sets the value of the divisions property.
setEndian(long) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image Endian of image scalar (default is ENDIAN_BIG)
setError(double) - Method in class algorithm.Measurement
setErrorNamee(String) - Method in class org.medcare.igtl.util.Status: ** To set client or server status errorName
setErrors(List<Double>) - Method in class algorithm.AverageMeasurement
setErrors(List<Double>) - Method in class algorithm.BoxPlot
setFilePath(String) - Method in class algorithm.ImageDataProcessor
setFrameTransformation(double[][], double[]) - Method in class org.medcare.robot.CartesianSpacePosition
setHeader(Header) - Method in class org.medcare.igtl.messages.OpenIGTMessage
setHeader(Header) - Method in class org.medcare.igtl.network.MessageHandler
setHeader(Header) - Method in class org.medcare.igtl.network.ResponseHandler
setHeight(double) - Method in class shapes.TrackingCone: Sets the value of the height property.
setImage(Image) - Method in class userinterface.PlottableImage
setImageData(byte[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To Set image_data byte array **
setImageDataByte(byte[]) - Method in class inputOutput.OpenIGTLinkConnection: This method is for setting an image data in the form of a byte.
setImageHeader(byte[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To extract image characteristics from image_header byte array
setImageHeader(long[], double[], double[][], long[], long[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To create image_header from image carateristics and to get the byte array to send
setImageHeader(long, long, long, long, long, long[], double[], double[][], long[], long[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To create image_header from image carateristics and to get the byte array to send
setImageMessage(ImageMessage) - Method in class inputOutput.OpenIGTLinkConnection: This method is for setting an ImageMessage.
setImageType(long) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image image type
setIndex(int) - Method in class org.medcare.igtl.util.BytesArray: ** Resets the read/write index to the specified value **
setIp(String) - Method in class inputOutput.OpenIGTLinkConnection
setIv(ImageView) - Method in class userinterface.ImageScatterChart: sets imageview and adds listeners so size and position can be changed
setIvSize() - Method in class controller.VideoController: Change ImageView size.
setKeepAlive(boolean) - Method in class org.medcare.igtl.network.OpenIGTServer
setLeftCrop(int) - Method in class algorithm.ImageDataProcessor
setLogger(Logger) - Method in class org.medcare.igtl.util.ErrorManager: Method to set Logger used by this ErrorManager
setMag(double) - Method in class util.Vector3D: Sets the magnitude of the vector
setMatrix(double[][]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image matrix
setMatrix(double[][]) - Method in class org.medcare.igtl.messages.TransformMessage: ** To set Image matrix
setMatrix(double[], double[][]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image matrix
setMatrix(double[], double[][]) - Method in class org.medcare.igtl.messages.TransformMessage: ** To set Image matrix
setMatrix(double[], double[], double[], double[]) - Method in class org.medcare.igtl.messages.TransformMessage: ** To set Image matrix
setMatrix(double[], double[], double[], double[], double[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image matrix
setMax(double) - Method in class algorithm.BoxPlot
setMedian(double) - Method in class algorithm.BoxPlot
setMeshGroup(Group) - Method in class algorithm.VisualizationManager: Sets the reference to the MeshGroup.
setMeshView(MeshView) - Method in class shapes.STLModel
setMin(double) - Method in class algorithm.BoxPlot
setName(String) - Method in class algorithm.Tool: Sets the name of the tool
setName(String) - Method in class shapes.STLModel
setOpenIGT_Queue(ConcurrentLinkedQueue<MessageHandler>) - Method in class org.medcare.igtl.network.MessageQueueManager
setOpenIGTClient(OpenIGTClient) - Method in class org.medcare.igtl.network.ResponseHandler
setOrigin(double[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image origin
setOrigin(double, double, double) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image origin
setPane(ScrollPane) - Method in class algorithm.VisualizationManager: Sets the reference to the ScrollPane.
setPort(int) - Method in class inputOutput.OpenIGTLinkConnection
setPos(double, double, double) - Method in class shapes.Target
setPos(Vector3D) - Method in class algorithm.Measurement
setPos(Vector3D) - Method in class shapes.CameraContainer: Sets the new position of the vector and updates the position of the camera
setPosition(double[]) - Method in class org.medcare.igtl.messages.PositionMessage: ** To set Image position
setPosition(double[]) - Method in class org.medcare.igtl.messages.TransformMessage: ** To set Image origin
setPosition(double[][], double[]) - Method in class org.medcare.robot.RasSpacePosition
setPosition(double, double, double) - Method in class org.medcare.igtl.messages.PositionMessage: ** To set Image position
setPosition(double, double, double) - Method in class org.medcare.igtl.messages.TransformMessage: ** To set Image origin
setPositionData(byte[]) - Method in class org.medcare.igtl.messages.PositionMessage: ** To extract image characteristics from position_data byte array
setPositionData(double[], Quaternion, int) - Method in class org.medcare.igtl.messages.PositionMessage: ** To create position_data from image characteristics and to get the byte array to send
setProjectionVisibility(boolean) - Method in class algorithm.Tool: Method to set the visibility of the projection
setQ1(double) - Method in class algorithm.BoxPlot
setQ3(double) - Method in class algorithm.BoxPlot
setRadius(double) - Method in class shapes.TrackingCone: Sets the value of the radius property.
setRepeatMode(boolean) - Method in class inputOutput.CSVFileReader
setRightCrop(int) - Method in class algorithm.ImageDataProcessor
setRotation(Quaternion) - Method in class algorithm.Measurement
setRotation(Quaternion) - Method in class util.TransformNR: Sets the rotation.
setRotationError(Quaternion) - Method in class algorithm.AverageMeasurement
setRotationJitter(Quaternion) - Method in class algorithm.AverageMeasurement
setScalarType(long) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image scalar type
setScalarTypeToInt16() - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image scalar type to Int16 **
setScalarTypeToInt32() - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image scalar type to Int32 **
setScalarTypeToInt8() - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image scalar type to Int8 **
setScalarTypeToUint16() - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image scalar type to Uint16 **
setScalarTypeToUint32() - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image scalar type to Uint32 **
setScalarTypeToUint8() - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image scalar type to Uint8 **
setServerThread(ServerThread) - Method in class org.medcare.igtl.network.OpenIGTServer
setSleepTime(long) - Method in class org.medcare.igtl.network.MessageQueueManager: Sets the time the listener thread will wait between actions
setSleepTime(long) - Method in class org.medcare.igtl.network.RequestQueueManager: Sets the time the listener thread will wait between actions
setSleepTime(long) - Method in class org.medcare.igtl.network.ResponseQueueManager: Sets the time the listener thread will wait between actions
setSocketFactory(SocketFactory) - Method in class org.medcare.igtl.network.OpenIGTClient
setSource(AbstractTrackingDataSource) - Method in class algorithm.TrackingDataManager
setSourceConnected(Boolean) - Method in class controller.VisualizationController
setSpacing(double[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image spacing
setSpacing(float, float, float) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image spacing
setSphereColor(Color) - Method in class shapes.Target
setStatus(OpenIGTServer.ServerStatus) - Method in class org.medcare.igtl.network.ServerThread: ** To set server status
setStatus(Status) - Method in class org.medcare.igtl.messages.StatusMessage: ** To set client or server status
setStatus(Status) - Method in class org.medcare.igtl.network.OpenIGTClient: ** To set server status
setStatus(Status) - Method in class org.medcare.igtl.network.ResponseHandler: ** To set client status
setStatusData(byte[]) - Method in class org.medcare.igtl.messages.StatusMessage: ** To extract image characteristics from status_data byte array
setStatusData(Status) - Method in class org.medcare.igtl.messages.StatusMessage: ** To create status_data from server or client status and to get the byte array to send
setStatusLabel(Label) - Method in class controller.AutoTrackController: Enables the Main View to inject the status label at the bottom of the window
setStatusString(String) - Method in class org.medcare.igtl.util.Status: ** To set client or server status statusString
setSubCode(int) - Method in class org.medcare.igtl.util.Status: ** To set client or server status subCode
setSubVolume(int, int, int, int, int, int) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image dimensions
setSubVolume(long[], long[]) - Method in class org.medcare.igtl.messages.ImageMessage: ** To set Image dimensions
setTargets(LinkedList<Target>) - Method in class algorithm.Tool: Set the targets of the tool
setTimestamp(double) - Method in class algorithm.Measurement
SettingsController - Class in controller
SettingsController() - Constructor for class controller.SettingsController
setToolname(String) - Method in class algorithm.Measurement
setTopCrop(int) - Method in class algorithm.ImageDataProcessor
setTrackingDataSource(AbstractTrackingDataSource) - Method in class algorithm.DataService
setTransformData(byte[]) - Method in class org.medcare.igtl.messages.TransformMessage: ** To extract image characteristics from transform_data byte array
setTransformData(double[], double[][]) - Method in class org.medcare.igtl.messages.TransformMessage: ** To create transform_data from image characteristics and to get the byte array to send
setTransformMatrix(double[][]) - Method in class org.medcare.robot.FrameTransformation
setup() - Static method in class util.CustomLogger: Setup a log file in addition to standard console output
setValues(String, TransformNR) - Method in class inputOutput.OIGTTrackingDataSource: this method assigns the values of each tool to an object of a toollist
setVisible(boolean) - Method in class shapes.STLModel
setVisualizationRunning(Boolean) - Method in class controller.VisualizationController
setX(double) - Method in class util.TransformNR: Sets the x.
setY(double) - Method in class util.TransformNR: Sets the y.
setZ(double) - Method in class util.TransformNR: Sets the z.
shapes - package shapes
show() - Method in class algorithm.Tool: Method to update the current position of the tool and perform all necessary transformations on it
showFigure() - Method in class algorithm.VisualizationManager: Adds the Nodes and Controls to the Scene
singleCaptureButton - Variable in class controller.AutoTrackController
slerp(Quaternion, Quaternion, float) - Method in class util.Quaternion: Interpolates between the specified quaternions and stores the result in the current instance.
sourceChoiceBox - Variable in class controller.AutoTrackController
start(Stage) - Method in class mainMethod.App
StartClass - Class in mainMethod
StartClass() - Constructor for class mainMethod.StartClass
startListening(int) - Method in class org.medcare.igtl.network.OpenIGTServer
startServer(int) - Method in class org.medcare.igtl.network.OpenIGTServer
startVideo() - Method in class controller.VideoController: If an image source is connected, image transmission starts.
Status - Class in org.medcare.igtl.util
Status() - Constructor for class org.medcare.igtl.util.Status: Constructs a status object with default value STATUS_OK
Status(int) - Constructor for class org.medcare.igtl.util.Status: Constructs a a status object with the specified status code
Status(int, int, String, String) - Constructor for class org.medcare.igtl.util.Status: Constructs a a status object with the specified status code
STATUS_ACCESS_DENIED - Static variable in class org.medcare.igtl.util.Status
STATUS_BUSY - Static variable in class org.medcare.igtl.util.Status
STATUS_CHECKSUM_ERROR - Static variable in class org.medcare.igtl.util.Status
STATUS_CONFIG_ERROR - Static variable in class org.medcare.igtl.util.Status
STATUS_DISABLED - Static variable in class org.medcare.igtl.util.Status
STATUS_HARDWARE_FAILURE - Static variable in class org.medcare.igtl.util.Status
STATUS_INVALID - Static variable in class org.medcare.igtl.util.Status
STATUS_MANUAL_MODE - Static variable in class org.medcare.igtl.util.Status
STATUS_NOT_FOUND - Static variable in class org.medcare.igtl.util.Status
STATUS_NOT_PRESENT - Static variable in class org.medcare.igtl.util.Status
STATUS_NOT_READY - Static variable in class org.medcare.igtl.util.Status
STATUS_NUM_TYPES - Static variable in class org.medcare.igtl.util.Status
STATUS_OK - Static variable in class org.medcare.igtl.util.Status
STATUS_OVERFLOW - Static variable in class org.medcare.igtl.util.Status
STATUS_PANICK_MODE - Static variable in class org.medcare.igtl.util.Status
STATUS_RESOURCE_ERROR - Static variable in class org.medcare.igtl.util.Status
STATUS_SHUT_DOWN - Static variable in class org.medcare.igtl.util.Status
STATUS_TIME_OUT - Static variable in class org.medcare.igtl.util.Status
STATUS_UNKNOWN_ERROR - Static variable in class org.medcare.igtl.util.Status
STATUS_UNKNOWN_INSTRUCTION - Static variable in class org.medcare.igtl.util.Status
STATUS_UNKNOWN_VERSION - Static variable in class org.medcare.igtl.util.Status
StatusMessage - Class in org.medcare.igtl.messages: ** This class create an Status object from bytes received or help to generate bytes to send from it
StatusMessage(String) - Constructor for class org.medcare.igtl.messages.StatusMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
StatusMessage(String, int, int, String) - Constructor for class org.medcare.igtl.messages.StatusMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
StatusMessage(String, int, int, String, String) - Constructor for class org.medcare.igtl.messages.StatusMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
StatusMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.StatusMessage: ** Constructor to be used to create message from received data
STLModel - Class in shapes: This class represent a stl model.
STLModel(MeshView) - Constructor for class shapes.STLModel
STLModel(MeshView, String, String, boolean) - Constructor for class shapes.STLModel
stop() - Method in class inputOutput.OpenIGTLinkConnection: This method is for stopping the connection (the client).
stop() - Method in class mainMethod.App
stopClient() - Method in class org.medcare.igtl.network.GenericIGTLinkClient
STOPPED - Enum constant in enum class org.medcare.igtl.network.OpenIGTServer.ServerStatus
stopServer() - Method in class org.medcare.igtl.network.OpenIGTServer
stopUpdate() - Method in class inputOutput.CSVFileReader: TODO interrupt update loop without closing app completely
stopVideo() - Method in class controller.VideoController
StringMessage - Class in org.medcare.igtl.messages
StringMessage(String) - Constructor for class org.medcare.igtl.messages.StringMessage
StringMessage(String, String) - Constructor for class org.medcare.igtl.messages.StringMessage
StringMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.StringMessage
sub(Vector3D) - Method in class util.Vector3D: Subtracts the other vector from this one Returns a new Vecotr
subtract(Quaternion) - Method in class util.Quaternion: Subtracts the argument and returns difference as a new instance.

T

Target - Class in shapes: This class represents the target.
Target(double, double, double) - Constructor for class shapes.Target
TempTool - Class in inputOutput: This class is used as an object to temporary save the values of a tool, which are separated in CSVFileReader.
TempTool() - Constructor for class inputOutput.TempTool
tempToolList - Variable in class inputOutput.AbstractTrackingDataSource
Tests - Class in org.medcare.igtl.util: ** Utility to test util library/BytesArray crc64 and timestamp utilities and differents encoding/decoding
Tests() - Constructor for class org.medcare.igtl.util.Tests
ThrombectomyController - Class in controller
ThrombectomyController() - Constructor for class controller.ThrombectomyController
toDegreesAngles(double[]) - Method in class util.Quaternion: Converts to equivalent Tait-Bryan angles in degree
Tool - Class in algorithm: The class Tool represents the name of a tool, its respective measurements and the visualisation.
Tool() - Constructor for class algorithm.Tool
Tool(String) - Constructor for class algorithm.Tool
ToolData() - Constructor for class inputOutput.OpenIGTLinkConnection.ToolData
toolName - Variable in class inputOutput.ExportMeasurement
toRadiansAngles(double[]) - Method in class util.Quaternion: Converts to equivalent Tait-Bryan angles, to be applied in x-z-y intrinsic order or y-z'-x" extrinsic order, for instance by Quaternion.fromRadiansAngles(double[]) (double[])}.
toRotationMatrix() - Method in class util.Quaternion: Converts to an equivalent rotation matrix.
toString() - Method in class org.medcare.igtl.messages.CapabilityMessage: ** To get capability String **
toString() - Method in class org.medcare.igtl.messages.DataArrayMessage
toString() - Method in class org.medcare.igtl.messages.GetCapabilityMessage: ** To get capability String **
toString() - Method in class org.medcare.igtl.messages.GetImageMessage: ** To get get image String **
toString() - Method in class org.medcare.igtl.messages.GetPositionMessage: ** To get get Position String **
toString() - Method in class org.medcare.igtl.messages.GetStatusMessage: ** To get get Status String **
toString() - Method in class org.medcare.igtl.messages.GetTransformMessage: ** To get the get Transform String **
toString() - Method in class org.medcare.igtl.messages.ImageMessage: ** To get image String **
toString() - Method in class org.medcare.igtl.messages.NDArrayMessage
toString() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** To get message String **
toString() - Method in class org.medcare.igtl.messages.PositionMessage: ** To get position String **
toString() - Method in class org.medcare.igtl.messages.StatusMessage: ** To get status String **
toString() - Method in class org.medcare.igtl.messages.StringMessage
toString() - Method in class org.medcare.igtl.messages.TransformMessage: ** To get transform String **
toString() - Method in class org.medcare.igtl.util.BytesArray
toString() - Method in class org.medcare.igtl.util.Header
toString() - Method in class util.Matrix3D: Helper function to print the 3x3 matrix to the console
toString() - Method in class util.Quaternion: Helper function to print the values of the quaternion
toString() - Method in class util.TransformNR
toString() - Method in class util.Vector3D: Helper function to show the vector on the console
toString(Double) - Static method in class util.FormatManager
toString(Object) - Static method in class util.FormatManager
TrackingCone - Class in shapes: This class represents the cone of the tool
TrackingCone() - Constructor for class shapes.TrackingCone
TrackingCone(double, double) - Constructor for class shapes.TrackingCone
TrackingCone(int, double, double) - Constructor for class shapes.TrackingCone
trackingConnectedStatusBox - Variable in class controller.AutoTrackController
TrackingDataController - Class in controller
TrackingDataController() - Constructor for class controller.TrackingDataController
TrackingDataDisplay - Class in userinterface: This class stores the Series of one tool.
TrackingDataDisplay(String) - Constructor for class userinterface.TrackingDataDisplay
TrackingDataManager - Class in algorithm: The class TrackingDataManager represents the interface between the GUI and data from InputOutput.
TrackingDataManager() - Constructor for class algorithm.TrackingDataManager
TrackingDataProcessor - Class in algorithm: This class provides the methods for processing the measurements.
TrackingDataProcessor() - Constructor for class algorithm.TrackingDataProcessor
trackingPoints - Variable in class inputOutput.TransformationMatrix: The raw measurements of the tracker (landmarks in tracking coordinates)
TrackingService - Class in algorithm: This class is used to manage the access to the OpenIGTLink-Connection and therefore to the trackers.
TrackingServiceObserver - Interface in algorithm: Interface for defining a callback-method for being triggered upon a change in references in TrackingService.
TransformationMatrix - Class in inputOutput
TransformationMatrix() - Constructor for class inputOutput.TransformationMatrix
TransformMessage - Class in org.medcare.igtl.messages: ** This class create an Transform object from bytes received or help to generate bytes to send from it
TransformMessage(String) - Constructor for class org.medcare.igtl.messages.TransformMessage: ** Constructor to be used to create message to send them with this constructor you must use method SetImageHeader, then CreateBody and then getBytes to send them **
TransformMessage(String, double[], double[][]) - Constructor for class org.medcare.igtl.messages.TransformMessage
TransformMessage(Header, byte[]) - Constructor for class org.medcare.igtl.messages.TransformMessage: ** Constructor to be used to create message from received data
TransformNR - Class in util: The Class TransformNR.
TransformNR() - Constructor for class util.TransformNR: Instantiates a new transform nr.
TransformNR(double[], double[][]) - Constructor for class util.TransformNR: Instantiates a new transform nr.
TransformNR(double[], Quaternion) - Constructor for class util.TransformNR: Instantiates a new transform nr.
TransformNR(double, double, double, Quaternion) - Constructor for class util.TransformNR: Instantiates a new transform nr.
translationVector3d - Variable in class inputOutput.TransformationMatrix: The translation vector as provided by MITK
traverseNode(Node, StringBuffer) - Method in class sample.ServerSample
TYPE_FLOAT32 - Static variable in class org.medcare.igtl.messages.ImageMessage
TYPE_FLOAT64 - Static variable in class org.medcare.igtl.messages.ImageMessage
TYPE_INT16 - Static variable in class org.medcare.igtl.messages.ImageMessage
TYPE_INT32 - Static variable in class org.medcare.igtl.messages.ImageMessage
TYPE_INT8 - Static variable in class org.medcare.igtl.messages.ImageMessage
TYPE_UINT16 - Static variable in class org.medcare.igtl.messages.ImageMessage
TYPE_UINT32 - Static variable in class org.medcare.igtl.messages.ImageMessage
TYPE_UINT8 - Static variable in class org.medcare.igtl.messages.ImageMessage

U

Unpack() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** To control the checksum and unpack the body
unpackBody() - Method in class org.medcare.igtl.messages.CapabilityMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.DataArrayMessage
unpackBody() - Method in class org.medcare.igtl.messages.GetCapabilityMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.GetImageMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.GetPositionMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.GetStatusMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.GetTransformMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.ImageMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.NDArrayMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.OpenIGTMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.PositionMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.StatusMessage: ** To create body from body array
unpackBody() - Method in class org.medcare.igtl.messages.StringMessage
unpackBody() - Method in class org.medcare.igtl.messages.TransformMessage: ** To create body from body array
unregister(Controller) - Method in class util.ControllerCollector
unregisterController() - Method in interface controller.Controller
unsignedByteToShort(byte) - Method in class org.medcare.igtl.util.BytesArray: Converts an unsigned byte to a short.
update() - Method in class inputOutput.AbstractTrackingDataSource
update() - Method in class inputOutput.CSVFileReader: this returns an ArrayList containing as many tools as are listed in the CSV-file: when the CSV-file contains two tools then the method returns an ArrayList containing the objects of two tools
update() - Method in class inputOutput.OIGTTrackingDataSource
update() - Method in class shapes.CameraContainer: Updates the position of the camera to the position of the vector
update() - Method in class shapes.Target
updateDiagrams() - Method in class controller.TrackingDataController
updateTrackingInformation() - Method in class controller.AutoTrackController: Enables the Main View to inject the tracking data controller
use3dTransformCheckBox - Variable in class controller.AutoTrackController
userinterface - package userinterface: This package contains GUI elements.
util - package util: This package contains utility/helper classes for the IGTPrototypingTool project.

V

valueOf(String) - Static method in enum class inputOutput.VideoSource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.medcare.igtl.network.OpenIGTServer.ServerStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.medcare.igtl.network.ServerThread.ClientStatus: Returns the enum constant of this class with the specified name.
values() - Static method in enum class inputOutput.VideoSource: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.medcare.igtl.network.OpenIGTServer.ServerStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.medcare.igtl.network.ServerThread.ClientStatus: Returns an array containing the constants of this enum class, in the order they are declared.
vector - Variable in class util.Vector3D: The 3 components of the vector in an array
Vector3D - Class in util
Vector3D() - Constructor for class util.Vector3D: Create a vector where all components are set to zero
Vector3D(double[]) - Constructor for class util.Vector3D: Create a vector where the components are set to a 3-dimensional array
Vector3D(double, double, double) - Constructor for class util.Vector3D: Create a vector where the components are set to the parameters
VERSION - Static variable in class org.medcare.igtl.messages.OpenIGTMessage
verticalFG - Variable in class controller.SettingsController
VideoController - Class in controller
VideoController() - Constructor for class controller.VideoController
videoHeight - Variable in class controller.SettingsController
videoImagePlot - Variable in class controller.AutoTrackController
VideoSource - Enum Class in inputOutput
videoWidth - Variable in class controller.SettingsController
VisualizationController - Class in controller
VisualizationController() - Constructor for class controller.VisualizationController
VisualizationManager - Class in algorithm: This class is used to manage the 3D-Visualization.
VisualizationManager() - Constructor for class algorithm.VisualizationManager
visualizeCone() - Method in class algorithm.VisualizationManager
visualizeTracking() - Method in class algorithm.VisualizationManager: Visualizes the tracking tools by updating their position and rotation according to the tracking data read from CSV or IGT connection
visualizeTracking() - Method in class controller.TrackingDataController: Start the visualization of tracking data that is read from CSV or IGT connection

W

w - Variable in class util.Quaternion: The real component (x0).
WITH_QUATERNION3 - Static variable in class org.medcare.igtl.messages.PositionMessage
writeMat(Mat) - Method in class inputOutput.ImageWriter: This method is for saving the video by storing each Mat object that is received.
writeStlSaveFile(JSONObject) - Static method in class util.Persistence

X

x - Variable in class util.Quaternion: The 1st imaginary component (x1).
x_normalized - Variable in class inputOutput.ExportMeasurement
x_raw - Variable in class inputOutput.ExportMeasurement
x_shifted - Variable in class inputOutput.ExportMeasurement

Y

y - Variable in class util.Quaternion: The 2nd imaginary component (x2).
y_normalized - Variable in class inputOutput.ExportMeasurement
y_raw - Variable in class inputOutput.ExportMeasurement
y_shifted - Variable in class inputOutput.ExportMeasurement

Z

z - Variable in class util.Quaternion: The 3rd imaginary component (x3).
z_raw - Variable in class inputOutput.ExportMeasurement
z_shifted - Variable in class inputOutput.ExportMeasurement
zero() - Method in class util.Matrix3D: Method to return a matrix with only zeros
zero() - Static method in class util.Vector3D: Returns a zero vector (identity operation)

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