Welcome to pygtlink’s documentation!¶

Introduction to pygtlink library!¶

An introduction to pygtlink library

Package Documentation¶

class pygtlink.IgtlHeader¶

Bases: object

pack(endian='>')¶

unpack(binary_header, endian='>')¶

class pygtlink.MessageBase¶

Bases: object

Implementation of the base message. Base class for all king of messages

Variables:

header (bytearray) – A pointer to the byte array for the serialized header. To prevent large copy of the byte array in the Pack() function, header byte array is concatenated to the byte array for the body.
body (bytearray) – A pointer to the byte array for the serialized body. To prevent large copy of the byte array in the Pack() function, header byte array is concatenated to the byte array for the header.
_messageSize (int) – The size of the message
_bodySize (int) – The size of the body to be read. This function must be called after the message header is set.
_messageType (str) – The message type
_headerVersion (int) – An unsigned short for the message format version
_deviceName (str) – A character string for the device name (message name).
_timeStampSec (uint64) – A time stamp (second) for message creation. It consists of fields for seconds (m_TimeStampSec)and fractions of a second (m_TimeStampSecFraction).
_timeStampFraction (uint64) – A time stamp (second) for message creation. It consists of fields for seconds (m_TimeStampSec)and fractions of a second (m_TimeStampSecFraction).
_isHeaderUnpacked (bool) – Unpacking (deserialization) status for the header
_isBodyUnpacked (bool) – Unpacking (deserialization) status for the body
_isBodyPacked (bool) – Packing (deserialization) status for the body

copyHeader(messageBase)¶

Copies the unpacked header from another message

Parameters:	messageBase (pygtlink.MessageBase) – message from which to copy the header

getBodyCrc()¶

Gets the message body crc

Returns:	The body crc

getBodySizeToRead()¶

Gets the size of the body to be read. This function must be called after the message header is set. Same as: getPackBodySize()

Returns:	The body size to read

getDeviceName()¶

Gets the device name

Returns:	The message device name

static getHeaderSize()¶

Gets the igtl message header size (same for all messages)

Returns:	The igtl message header size

getHeaderVersion()¶

Gets the message version number

Returns:	The message header version

getMessageType()¶

Gets the device type

Returns:	The message type

getPackBodySize()¶

Gets the size of the message body.

Returns:	The body size

getPackSize()¶

Gets the size of the serialized message

Returns:	The message size

getTimeStamp()¶

Gets the message timestamp

Returns:	The timestamp in seconds since the epoch as a floating point number. The epoch is the point where the time starts, and is platform dependent. For Unix, the epoch is January 1, 1970, 00:00:00 (UTC). To find out what the epoch is on a given platform, look at time.gmtime(0).

getTimeStampSecFrac()¶

Gets the message timestamp

Returns:	The timestamp expressed in second and fraction

initBuffer()¶: Initializes the message

isHeaderUnpacked()¶

pack()¶

Serializes the header and body based on the member variables. PackContent() must be implemented in the child class.

Returns:	0 in case of error, 1 if the message was successfully packed

setDeviceName(device_name)¶

Sets the device name

Parameters:	device_name (str) – The device name to set

setHeaderVersion(header_version)¶

Sets the message version number

Parameters:	header_version (int) – The header version to set

setMessageType(msg_type)¶

Sets the device (message) type

Parameters:	msg_type (str) – The message type to set

setTimeStamp(timestamp)¶

Sets the message timestamp

Parameters:	timestamp (int) – timestamp in seconds since the epoch as a floating point number. The epoch is the point where the time starts, and is platform dependent. For Unix, the epoch is January 1, 1970, 00:00:00 (UTC). To find out what the epoch is on a given platform, look at time.gmtime(0). Can be obtained using the python function time.time() from the time module

unpack(crccheck=0)¶

Unpack() deserializes the header and/or body, extracting data from the byte stream. If the header has already been deserialized, Unpack() deserializes only the body part. UnpackBody() must be implemented to deserialize the body part. Unpack() performs 64-bit CRC check, when crccheck = 1.

Parameters: crccheck (int) – The body crccheck

Returns:

The unpacking result, i.e.

Code	Meaning
UNPACK_UNDEF	Nothing deserialized
UNPACK_HEADER	The header has been deserialized.
UNPACK_BODY	The body has been deserialized.

If CRC check fails, Unpack() doesn’t deserialize the body, thus it doesn’t return UNPACK_BODY flag.

class pygtlink.ImageMessage2¶

Bases: pygtlink.igtl_message_base.MessageBase

The class implements the openIgtLink image message

Variables:

_dimensions (float) – A vector containing the numbers of voxels in i, j and k directions.
_spacing (float[3]) – A vector containing the spacings of the voxels in i, j and k directions.
_subDimensions (int[3]) – A vector containing the numbers of voxels of the subvolume in i, j and k directions.
_subOffset (int[3]) – A vector containing the offset (number of voxels) of the first voxel of the subvolume from the first voxel of the original image.
_matrix (nd.array) – A matrix representing the origin and the orientation of the image. The matrix is set to identity by default
_endian (int) – A variable for the Endian of the scalar values in the image.
_numComponents (int) – A variable for the number of components
_scalarType (int) – A variable for the scalar type of the voxels
_coordinate (int) – A variable for the used coordinate system

getCoordinateSystem()¶

Gets the coordinate system (COORDINATE_RAS or COORDINATE_LPS)

Returns:	The coordinate system (COORDINATE_RAS or COORDINATE_LPS)

getData()¶

Gets the image raw data

Returns:	The image raw data

getDimensions()¶

Gets image dimensions as a tuple of the numbers of pixels in i, j and k directions.

Returns:	number of pixels in i, j, k directions

getEndian(endian)¶

Gets the Endianess of the image scalars. (default is ENDIAN_BIG)

Returns:	The endianess of the image scalars

getImageSize()¶

Gets the size (length) of the byte array for the image data. The size is defined by: dimensions[0]*dimensions[1]*dimensions[2]*scalarSize*numComponents.

Returns:	The size of the byte array for the image data

getMatrix()¶

Gets the orientation and origin matrix.

Returns:	The 4x4 matrix representing the origin and the orientation of the image.

getNormals()¶

Gets the orientation of the image as an array of the normal vectors for the i, j and k indexes.

Returns:	The image orientation vector concatenated in a matrix per columns

getNumComponents()¶

Gets the number of components for each voxel.

Returns:	the number of components for each voxel.

getOrigin()¶

Gets the coordinates of the origin using an array of positions along the first (R or L), second (A or P) and the third (S) axes.

Returns:	list of origin coordinates

getScalarSize()¶

Gets the size of the scalar type used in the current image data.

Returns:	The size of the scalar type used in the current image data.

getScalarType()¶

Gets the image scalar type.

Returns:	the image scalar type

getSpacing()¶

Gets spacings as an array or list of spacing values in i, j and k directions.

Returns:	list of spacing values

getSubVolume()¶

Gets sub-volume dimensions and offset expressed in pixels in i, j, k directions

Returns:	dims[3], off[3] - 2 lists containing dimensions and offsets of the subvolume

getSubVolumeSize()¶

Gets the size (length) of the byte array for the subvolume image data. The size is defined by: subDimensions[0]*subDimensions[1]*subDimensions[2]*scalarSize*numComponents.

Returns:	The size (length) of the byte array for the subvolume image data.

setCoordinateSystem(coordSys)¶

Sets the coordinate system (COORDINATE_RAS or COORDINATE_LPS)

Parameters:	coordSys – The coordinate system (COORDINATE_RAS or COORDINATE_LPS)

setData(rawImgData)¶

Sets the image raw data

Parameters:	rawImgData – image raw data
Returns:	True if the data were correctly set, False otherwise

setDimensions(dimensions)¶

Sets image dimensions by an array of the numbers of pixels in i, j and k directions. SetDimensions() should be called prior to SetSubVolume(), since SetDimensions() sets subvolume parameters automatically assuming that subvolume = entire volume.

Parameters:	dimensions – element list, tuple or array - [rows, cols, channels]

setEndian(endian)¶

Sets the Endianess of the image scalars. (default is ENDIAN_BIG)

Parameters:	endian – Endianess of the image scalars

setMatrix(matrix)¶

Sets the orientation and origin matrix.

Parameters:	matrix – a 4x4 matrix representing the origin and the orientation of the image.

setNormals(m)¶

Sets the orientation of the image by an array of the normal vectors for the i, j and k indexes.

Parameters:	m – a 3x3 matrix containing the normal vectors stored in columns

setNumComponents(num)¶

Sets the number of components for each voxel.

Parameters:	num – number of components for each voxel

setOrigin(origin)¶

Sets the coordinates of the origin by an array of positions along the first (R or L), second (A or P) and the third (S) axes.

Param:	list or array with the origin coordinates

setScalarType(stype)¶

Sets the image scalar type. (to one of PixelType)

Parameters:	stype – image scalar type

setScalarTypeToInt16()¶: Sets the image scalar type to 16-bit integer.

setScalarTypeToInt32()¶: Sets the image scalar type to 32-bit integer.

setScalarTypeToInt8()¶: Sets the image scalar type to 8-bit integer.

setScalarTypeToUint16()¶: Sets the image scalar type to 16-bit unsigned integer.

setScalarTypeToUint32()¶: Sets the image scalar type to 32-bit unsigned integer.

setScalarTypeToUint8()¶: Sets the image scalar type to 8-bit unsigned integer.

setSpacing(spacing)¶

Sets spacings by an array or list of spacing values in i, j and k directions.

Parameters:	spacing – array or list of spacing values

setSubVolume(dims, off)¶

Sets sub-volume dimensions and offset by arrays of the dimensions and the offset. SetDimensions(), since SetDimensions() reset the subvolume parameters automatically.

Parameters:	dims – 3-element list or array with the number of subvolume pixels in i, j, k directions off – 3-element list or array with the subvolume pixels offsets in i, j, k directions
Returns:	True if the subvolume is successfully specified, False if an invalid subvolume is specified.

class pygtlink.SensorMessage¶

Bases: pygtlink.igtl_message_base.MessageBase

Variables:	_larray (int) – The sensor array len (uint8) _status (int) – The status (uint8) _unit (int) – The unit (uint64) _data (list) – The sensor data (float64[Larray])

getData()¶

Gets sensor data

Returns:	The sensor data

getLength()¶

Gets sensor data length (num elements)

Returns:	The sensor data length

getStatus()¶

Gets sensor status

Returns:	The sensor status

getUnit()¶

Gets sensor data unit

Returns:	The sensor data unit

setData(data)¶

Sets sensor data

Parameters:	data – The list or array of sensor data

setLength(length)¶

Sets sensor data length (num elements)

Parameters:	length – The array or list of spacing values

setStatus(status)¶

Sets status

Parameters:	status – The status to be set

setUnit(unit)¶

Sets unit

Parameters:	unit – The sensor data unit to be set (must be an int)

class pygtlink.StatusMessage¶

Bases: pygtlink.igtl_message_base.MessageBase

Variables:	_code (int) – The command code (uint16) _subCode (int) – The command sub code (int64) _errorName (str) – The error name (char[20]) _message (str) – The error message (char[BODY_SIZE - 30])

getCode()¶

Gets the status code

Returns:	The status code

getErrorName()¶

Gets the status error name

Returns:	The status error name

getMessage()¶

Gets the status message

Returns:	The status message

getSubCode()¶

Gets the status subcode

Returns:	The status subcode

setCode(code)¶

Sets the status code

Parameters:	code – The status code to be set

setErrorName(errorName)¶

Sets the status error name

Parameters:	errorName – The status error name to be set

setMessage(message)¶

Sets the status message

Parameters:	message – The status message to be set

setSubCode(subCode)¶

Sets the status subcode

Parameters:	subCode – The status subcode

class pygtlink.PositionMessage¶

Bases: pygtlink.igtl_message_base.MessageBase

The class implements the openIgtLink position message

Variables:

_x (float) – The x component of the position
_y (float) – The y component of the position
_z (float) – The z component of the position
_ox (float) – The first component of the orientation quaternion
_oy (float) – The second component of the orientation quaternion
_oz (float) – The third component of the orientation quaternion
_w (float) – The fourth component of the orientation quaternion

getPosition()¶

Gets the position

Returns:	The position as a list [x, y, z]

getQuaternion()¶

Sets the quaternion

Returns:	The quaternion as a list [ox, oy, oz, w]

setPosition(pos)¶

Sets the position

Parameters:	pos – The position to be set. It can be a 3-element list or nd.array

setQuaternion(quat)¶

Sets the quaternion

Parameters:	quat – The quaternion to be set. It can be a 4-element list or nd.array

class pygtlink.SocketServer¶

Bases: object

Implementation of IGTL Server

Variables:	_serverSocket (socket.socket) – The server TCP socket listening for incoming connection _clientSocket (socket.socket) – The TCP socket the server opens with the client when a connection request is received over the _serverSocket _serverAddress (str) – The server address _serverPort (int) – The server port

kill()¶: Shut down the socket connection with the client and closes the server socket

receive(length)¶

Receives a message of <length> bytes from the IGTL client

Parameters:	length (int) – The length of the message to be received
Returns:	The received message (a byte string)

send(data)¶

Sends data to the IGTL client

Parameters:	data – the message to be sent (as a byte string)

setAddress(address, port)¶

Sets the Server address and port

Parameters:	address (str) – The server address to be set port (int) – The server port to be set

setTimeout(timeout=0)¶

Sets receive timeout

Parameters:	timeout (int) – The receive timeout to be set

start()¶: Creates the server socket and binds it with the server address set with setAddress()

waitForConnection()¶: Waits for a connection request to be sent from the client

class pygtlink.ClientSocket¶

Bases: object

Implementation of IGTL client

Variables:	_clientSocket (socket.socket) – The client TCP socket

connectToServer(serverAddress, port)¶

Connects to the IGTL server

Parameters:	serverAddress (str) – Server Address port (int) – Server Port

kill()¶: Shut down the connection and closes the socket

receive(length)¶

Receives a message of <length> bytes from the IGTL server

Parameters:	length (int) – The length of the message to be received
Returns:	The received message (a byte string)

send(data)¶

Sends data to the IGTL server

Parameters:	data – the message to be sent (as a byte string)

setTimeout(timeout=0)¶

Sets receive timeout

Parameters:	timeout (int) – The receive timeout to be set