File: FieldTrip.py

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"""
FieldTrip buffer (V1) client in pure Python

(C) 2010 S. Klanke
"""

# We need socket, struct, and numpy
import socket
import struct
import numpy

VERSION = 1
PUT_HDR = 0x101
PUT_DAT = 0x102
PUT_EVT = 0x103
PUT_OK = 0x104
PUT_ERR = 0x105
GET_HDR = 0x201
GET_DAT = 0x202
GET_EVT = 0x203
GET_OK = 0x204
GET_ERR = 0x205
FLUSH_HDR = 0x301
FLUSH_DAT = 0x302
FLUSH_EVT = 0x303
FLUSH_OK = 0x304
FLUSH_ERR = 0x305
WAIT_DAT = 0x402
WAIT_OK = 0x404
WAIT_ERR = 0x405

DATATYPE_CHAR = 0
DATATYPE_UINT8 = 1
DATATYPE_UINT16 = 2
DATATYPE_UINT32 = 3
DATATYPE_UINT64 = 4
DATATYPE_INT8 = 5
DATATYPE_INT16 = 6
DATATYPE_INT32 = 7
DATATYPE_INT64 = 8
DATATYPE_FLOAT32 = 9
DATATYPE_FLOAT64 = 10
DATATYPE_UNKNOWN = 0xFFFFFFFF

CHUNK_UNSPECIFIED = 0
CHUNK_CHANNEL_NAMES = 1
CHUNK_CHANNEL_FLAGS = 2
CHUNK_RESOLUTIONS = 3
CHUNK_ASCII_KEYVAL = 4
CHUNK_NIFTI1 = 5
CHUNK_SIEMENS_AP = 6
CHUNK_CTF_RES4 = 7
CHUNK_NEUROMAG_FIF = 8

# List for converting FieldTrip datatypes to Numpy datatypes
numpyType = ['int8', 'uint8', 'uint16', 'uint32', 'uint64',
             'int8', 'int16', 'int32', 'int64', 'float32', 'float64']
# Corresponding word sizes
wordSize = [1, 1, 2, 4, 8, 1, 2, 4, 8, 4, 8]
# FieldTrip data type as indexed by numpy dtype.num
# this goes  0 => nothing, 1..4 => int8, uint8, int16, uint16, 7..10 =>
# int32, uint32, int64, uint64  11..12 => float32, float64
dataType = [-1, 5, 1, 6, 2, -1, -1, 7, 3, 8, 4, 9, 10]


def serialize(A):
    """
    Returns Fieldtrip data type and string representation of the given
    object, if possible.
    """
    if isinstance(A, str):
        return (0, A)

    if isinstance(A, numpy.ndarray):
        dt = A.dtype
        if not(dt.isnative) or dt.num < 1 or dt.num >= len(dataType):
            return (DATATYPE_UNKNOWN, None)

        ft = dataType[dt.num]
        if ft == -1:
            return (DATATYPE_UNKNOWN, None)

        if A.flags['C_CONTIGUOUS']:
            # great, just use the array's buffer interface
            return (ft, str(A.data))

        # otherwise, we need a copy to C order
        AC = A.copy('C')
        return (ft, str(AC.data))

    if isinstance(A, int):
        return (DATATYPE_INT32, struct.pack('i', A))

    if isinstance(A, float):
        return (DATATYPE_FLOAT64, struct.pack('d', A))

    return (DATATYPE_UNKNOWN, None)


class Chunk:

    def __init__(self):
        self.type = 0
        self.size = 0
        self.buf = ''


class Header:

    """Class for storing header information in the FieldTrip buffer format"""

    def __init__(self):
        self.nChannels = 0
        self.nSamples = 0
        self.nEvents = 0
        self.fSample = 0.0
        self.dataType = 0
        self.chunks = {}
        self.labels = []

    def __str__(self):
        return ('Channels.: %i\nSamples..: %i\nEvents...: %i\nSampFreq.: '
                '%f\nDataType.: %s\n'
                % (self.nChannels, self.nSamples, self.nEvents,
                   self.fSample, numpyType[self.dataType]))


class Event:
    """Class for storing events in the FieldTrip buffer format"""

    def __init__(self, S=None):
        if S is None:
            self.type = ''
            self.value = ''
            self.sample = 0
            self.offset = 0
            self.duration = 0
        else:
            self.deserialize(S)

    def __str__(self):
        return ('Type.....: %s\nValue....: %s\nSample...: %i\nOffset...: '
                '%i\nDuration.: %i\n' % (str(self.type), str(self.value),
                                         self.sample, self.offset,
                                         self.duration))

    def deserialize(self, buf):
        bufsize = len(buf)
        if bufsize < 32:
            return 0

        (type_type, type_numel, value_type, value_numel, sample,
         offset, duration, bsiz) = struct.unpack('IIIIIiiI', buf[0:32])

        self.sample = sample
        self.offset = offset
        self.duration = duration

        st = type_numel * wordSize[type_type]
        sv = value_numel * wordSize[value_type]

        if bsiz + 32 > bufsize or st + sv > bsiz:
            raise IOError(
                'Invalid event definition -- does not fit in given buffer')

        raw_type = buf[32:32 + st]
        raw_value = buf[32 + st:32 + st + sv]

        if type_type == 0:
            self.type = raw_type
        else:
            self.type = numpy.ndarray(
                (type_numel), dtype=numpyType[type_type], buffer=raw_type)

        if value_type == 0:
            self.value = raw_value
        else:
            self.value = numpy.ndarray(
                (value_numel), dtype=numpyType[value_type], buffer=raw_value)

        return bsiz + 32

    def serialize(self):
        """
        Returns the contents of this event as a string, ready to
        send over the network, or None in case of conversion problems.
        """
        type_type, type_buf = serialize(self.type)
        if type_type == DATATYPE_UNKNOWN:
            return None
        type_size = len(type_buf)
        type_numel = type_size / wordSize[type_type]

        value_type, value_buf = serialize(self.value)
        if value_type == DATATYPE_UNKNOWN:
            return None
        value_size = len(value_buf)
        value_numel = value_size / wordSize[value_type]

        bufsize = type_size + value_size

        S = struct.pack('IIIIIiiI', type_type, type_numel, value_type,
                        value_numel, int(self.sample), int(self.offset),
                        int(self.duration), bufsize)
        return S + type_buf + value_buf


class Client:

    """Class for managing a client connection to a FieldTrip buffer."""

    def __init__(self):
        self.isConnected = False
        self.sock = []

    def connect(self, hostname, port=1972):
        """
        connect(hostname [, port]) -- make a connection, default port is
        1972.
        """
        self.sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
        self.sock.connect((hostname, port))
        self.sock.setblocking(True)
        self.isConnected = True

    def disconnect(self):
        """disconnect() -- close a connection."""
        if self.isConnected:
            self.sock.close()
            self.sock = []
            self.isConnected = False

    def sendRaw(self, request):
        """Send all bytes of the string 'request' out to socket."""
        if not(self.isConnected):
            raise IOError('Not connected to FieldTrip buffer')

        N = len(request)
        nw = self.sock.send(request)
        while nw < N:
            nw += self.sock.send(request[nw:])

    def sendRequest(self, command, payload=None):
        if payload is None:
            request = struct.pack('HHI', VERSION, command, 0)
        else:
            request = struct.pack(
                'HHI', VERSION, command, len(payload)) + payload
        self.sendRaw(request)

    def receiveResponse(self, minBytes=0):
        """
        Receive response from server on socket 's' and return it as
        (status,bufsize,payload).
        """

        resp_hdr = self.sock.recv(8)
        while len(resp_hdr) < 8:
            resp_hdr += self.sock.recv(8 - len(resp_hdr))

        (version, command, bufsize) = struct.unpack('HHI', resp_hdr)

        if version != VERSION:
            self.disconnect()
            raise IOError('Bad response from buffer server - disconnecting')

        if bufsize > 0:
            payload = self.sock.recv(bufsize)
            while len(payload) < bufsize:
                payload += self.sock.recv(bufsize - len(payload))
        else:
            payload = None
        return (command, bufsize, payload)

    def getHeader(self):
        """
        getHeader() -- grabs header information from the buffer an returns
        it as a Header object.
        """

        self.sendRequest(GET_HDR)
        (status, bufsize, payload) = self.receiveResponse()

        if status == GET_ERR:
            return None

        if status != GET_OK:
            self.disconnect()
            raise IOError('Bad response from buffer server - disconnecting')

        if bufsize < 24:
            self.disconnect()
            raise IOError('Invalid HEADER packet received (too few bytes) - '
                          'disconnecting')

        (nchans, nsamp, nevt, fsamp, dtype,
         bfsiz) = struct.unpack('IIIfII', payload[0:24])

        H = Header()
        H.nChannels = nchans
        H.nSamples = nsamp
        H.nEvents = nevt
        H.fSample = fsamp
        H.dataType = dtype

        if bfsiz > 0:
            offset = 24
            while offset + 8 < bufsize:
                (chunk_type, chunk_len) = struct.unpack(
                    'II', payload[offset:offset + 8])
                offset += 8
                if offset + chunk_len > bufsize:
                    break
                H.chunks[chunk_type] = payload[offset:offset + chunk_len]
                offset += chunk_len

            if CHUNK_CHANNEL_NAMES in H.chunks:
                L = H.chunks[CHUNK_CHANNEL_NAMES].split(b'\0')
                numLab = len(L)
                if numLab >= H.nChannels:
                    H.labels = [x.decode('utf-8') for x in L[0:H.nChannels]]

        return H

    def putHeader(self, nChannels, fSample, dataType, labels=None,
                  chunks=None):
        haveLabels = False
        extras = ''
        if not(labels is None):
            serLabels = ''
            try:
                for n in range(0, nChannels):
                    serLabels += labels[n] + '\0'
            except:
                raise ValueError('Channels names (labels), if given,'
                                 ' must be a list of N=numChannels strings')

            extras = struct.pack('II', CHUNK_CHANNEL_NAMES,
                                 len(serLabels)) + serLabels
            haveLabels = True

        if not(chunks is None):
            for chunk_type, chunk_data in chunks:
                if haveLabels and chunk_type == CHUNK_CHANNEL_NAMES:
                    # ignore channel names chunk in case we got labels
                    continue
                extras += struct.pack('II', chunk_type,
                                      len(chunk_data)) + chunk_data

        sizeChunks = len(extras)

        hdef = struct.pack('IIIfII', nChannels, 0, 0,
                           fSample, dataType, sizeChunks)
        request = struct.pack('HHI', VERSION, PUT_HDR,
                              sizeChunks + len(hdef)) + hdef + extras
        self.sendRaw(request)
        (status, bufsize, resp_buf) = self.receiveResponse()
        if status != PUT_OK:
            raise IOError('Header could not be written')

    def getData(self, index=None):
        """
        getData([indices]) -- retrieve data samples and return them as a
        Numpy array, samples in rows(!). The 'indices' argument is optional,
        and if given, must be a tuple or list with inclusive, zero-based
        start/end indices.
        """

        if index is None:
            request = struct.pack('HHI', VERSION, GET_DAT, 0)
        else:
            indS = int(index[0])
            indE = int(index[1])
            request = struct.pack('HHIII', VERSION, GET_DAT, 8, indS, indE)
        self.sendRaw(request)

        (status, bufsize, payload) = self.receiveResponse()
        if status == GET_ERR:
            return None

        if status != GET_OK:
            self.disconnect()
            raise IOError('Bad response from buffer server - disconnecting')

        if bufsize < 16:
            self.disconnect()
            raise IOError('Invalid DATA packet received (too few bytes)')

        (nchans, nsamp, datype, bfsiz) = struct.unpack('IIII', payload[0:16])

        if bfsiz < bufsize - 16 or datype >= len(numpyType):
            raise IOError('Invalid DATA packet received')

        raw = payload[16:bfsiz + 16]
        D = numpy.ndarray((nsamp, nchans), dtype=numpyType[datype], buffer=raw)

        return D

    def getEvents(self, index=None):
        """
        getEvents([indices]) -- retrieve events and return them as a list
        of Event objects. The 'indices' argument is optional, and if given,
        must be a tuple or list with inclusive, zero-based start/end indices.
        The 'type' and 'value' fields of the event will be converted to strings
        or Numpy arrays.
        """

        if index is None:
            request = struct.pack('HHI', VERSION, GET_EVT, 0)
        else:
            indS = int(index[0])
            indE = int(index[1])
            request = struct.pack('HHIII', VERSION, GET_EVT, 8, indS, indE)
        self.sendRaw(request)

        (status, bufsize, resp_buf) = self.receiveResponse()
        if status == GET_ERR:
            return []

        if status != GET_OK:
            self.disconnect()
            raise IOError('Bad response from buffer server - disconnecting')

        offset = 0
        E = []
        while 1:
            e = Event()
            nextOffset = e.deserialize(resp_buf[offset:])
            if nextOffset == 0:
                break
            E.append(e)
            offset = offset + nextOffset

        return E

    def putEvents(self, E):
        """
        putEvents(E) -- writes a single or multiple events, depending on
        whether an 'Event' object, or a list of 'Event' objects is
        given as an argument.
        """
        if isinstance(E, Event):
            buf = E.serialize()
        else:
            buf = ''
            num = 0
            for e in E:
                if not(isinstance(e, Event)):
                    raise 'Element %i in given list is not an Event' % num
                buf = buf + e.serialize()
                num = num + 1

        self.sendRequest(PUT_EVT, buf)
        (status, bufsize, resp_buf) = self.receiveResponse()

        if status != PUT_OK:
            raise IOError('Events could not be written.')

    def putData(self, D):
        """
        putData(D) -- writes samples that must be given as a NUMPY array,
        samples x channels. The type of the samples (D) and the number of
        channels must match the corresponding quantities in the FieldTrip
        buffer.
        """

        if not(isinstance(D, numpy.ndarray)) or len(D.shape) != 2:
            raise ValueError(
                'Data must be given as a NUMPY array (samples x channels)')

        nSamp = D.shape[0]
        nChan = D.shape[1]

        (dataType, dataBuf) = serialize(D)

        dataBufSize = len(dataBuf)

        request = struct.pack('HHI', VERSION, PUT_DAT, 16 + dataBufSize)
        dataDef = struct.pack('IIII', nChan, nSamp, dataType, dataBufSize)
        self.sendRaw(request + dataDef + dataBuf)

        (status, bufsize, resp_buf) = self.receiveResponse()
        if status != PUT_OK:
            raise IOError('Samples could not be written.')

    def poll(self):

        request = struct.pack('HHIIII', VERSION, WAIT_DAT, 12, 0, 0, 0)
        self.sendRaw(request)

        (status, bufsize, resp_buf) = self.receiveResponse()

        if status != WAIT_OK or bufsize < 8:
            raise IOError('Polling failed.')

        return struct.unpack('II', resp_buf[0:8])

    def wait(self, nsamples, nevents, timeout):
        request = struct.pack('HHIIII', VERSION, WAIT_DAT,
                              12, int(nsamples), int(nevents), int(timeout))
        self.sendRaw(request)

        (status, bufsize, resp_buf) = self.receiveResponse()

        if status != WAIT_OK or bufsize < 8:
            raise IOError('Wait request failed.')

        return struct.unpack('II', resp_buf[0:8])