def read_mff_event(filePath, hdr):
import numpy as np
from xml.dom.minidom import parse
import os.path
from mff.mff_micros2Sample import mff_micros2Sample
import glob
import os
from mff.mff_getSummaryInfo import mff_getSummaryInfo
from mff.ns2pyTime import ns2pyTime
from mff.mff_micros2Sample import mff_micros2Sample
from mff.samples2EpochSample import samples2EpochSample
if hdr == None:
summaryInfo = mff_getSummaryInfo(filePath)
else:
summaryInfo = hdr['orig']
# Pull the information about the epochs out of the summary info
epochBeginSamps = summaryInfo['epochBeginSamps']
epochNumSamps = summaryInfo['epochNumSamps']
epochFirstBlocks = summaryInfo['epochFirstBlocks']
epochLastBlocks = summaryInfo['epochLastBlocks']
infofile = filePath + '/info.xml'
infotime = parse(infofile)
beginTime = infotime.getElementsByTagName(
'recordTime')[0].firstChild.data.encode()
bTime = ns2pyTime(beginTime)
numEpochs = len(epochBeginSamps)
events = []
eventInds = np.zeros((numEpochs, 2), dtype='i')
eventInd = 0
for p in range(numEpochs):
origp = [0, 0, 'metadata', {}]
eventp = [
'break ' + summaryInfo['epochType'],
summaryInfo['epochBeginSamps'][p], summaryInfo['epochLabels'][p],
[], summaryInfo['epochNumSamps'][p], [], origp
]
events.append(eventp)
eventInds[eventInd, :] = [eventp[1], eventInd]
eventInd = eventInd + 1
for file in glob.glob(filePath + "/Events_*.xml"):
eventsfile = file
eventsListObj = parse(eventsfile)
trackname = eventsListObj.getElementsByTagName(
'name')[0].firstChild.data.encode()
eventsList = eventsListObj.getElementsByTagName('event')
numEvents = eventsList.length
for p in range(numEvents):
theEvent = eventsList[p]
eventTime = theEvent.getElementsByTagName(
'beginTime')[0].firstChild.data.encode()
eTime = ns2pyTime(eventTime)
eventTimeInMicros = (eTime - bTime).microseconds
out = mff_micros2Sample(eventTimeInMicros, summaryInfo['sampRate'])
eventTimeInSamples = int(out[0])
sampleRemainder = int(out[1])
eventTimeInEpochSamples = samples2EpochSample(eventTimeInSamples,
epochBeginSamps,
epochNumSamps)
if eventTimeInEpochSamples >= 0:
keylist = theEvent.getElementsByTagName('key')
eventkeycount = len(keylist)
keyp = []
for q in range(eventkeycount):
theKey = keylist[q]
theKeyCode = theKey.getElementsByTagName(
'keyCode')[0].firstChild.data.encode()
theKeyData = theKey.getElementsByTagName(
'data')[0].firstChild.data.encode()
theKeyData1 = theKey.getElementsByTagName('data')
theKeyData0 = theKeyData1[0] # print theKeyData0.toxml()
a = theKeyData0.attributes["dataType"]
theKeyDatatype = a.value.encode()
theKeyq = [theKeyCode, int(theKeyData), theKeyDatatype, '']
keyp.append(theKeyq)
duration = int(
theEvent.getElementsByTagName('duration')
[0].firstChild.data.encode())
out = mff_micros2Sample(duration, summaryInfo['sampRate'])
origp = [sampleRemainder, int(out[1]), trackname, keyp]
eventp = [
theEvent.getElementsByTagName('code')
[0].firstChild.data.encode(), eventTimeInEpochSamples, 0, [],
int(out[0]), [], origp
]
events.append(eventp)
eventIndp = np.array([eventp[1], eventInd], dtype='i').reshape(
(1, 2))
eventInds = np.concatenate((eventInds, eventIndp), axis=0)
eventInd = eventInd + 1
eventInds0 = eventInds[eventInds[:, 0].argsort()]
sortedEvents = events
for p in range(eventInd):
nextEventInd = eventInds0[p, 1]
sortedEvents[p] = events[nextEventInd]
events = sortedEvents
return events
def read_mff_event(filePath, hdr):
import numpy as np
from xml.dom.minidom import parse
import os.path
from mff.mff_micros2Sample import mff_micros2Sample
import glob
import os
from mff.mff_getSummaryInfo import mff_getSummaryInfo
from mff.ns2pyTime import ns2pyTime
from mff.mff_micros2Sample import mff_micros2Sample
from mff.samples2EpochSample import samples2EpochSample
if hdr == None :
summaryInfo = mff_getSummaryInfo(filePath)
else:
summaryInfo = hdr['orig']
# Pull the information about the epochs out of the summary info
epochBeginSamps = summaryInfo['epochBeginSamps']
epochNumSamps = summaryInfo['epochNumSamps']
epochFirstBlocks = summaryInfo['epochFirstBlocks']
epochLastBlocks = summaryInfo['epochLastBlocks']
infofile = filePath+'/info.xml'
infotime = parse(infofile)
beginTime = infotime.getElementsByTagName('recordTime')[0].firstChild.data.encode()
bTime = ns2pyTime(beginTime)
numEpochs = len(epochBeginSamps)
events = []
eventInds = np.zeros((numEpochs,2), dtype='i')
eventInd = 0
for p in range(numEpochs):
origp = [0, 0, 'metadata',{}]
eventp = ['break '+ summaryInfo['epochType'],
summaryInfo['epochBeginSamps'][p],
summaryInfo['epochLabels'][p], [],
summaryInfo['epochNumSamps'][p], [], origp ]
events.append(eventp)
eventInds[eventInd,:] = [eventp[1], eventInd]
eventInd = eventInd+1
for file in glob.glob(filePath+"/Events_*.xml"):
eventsfile = file
eventsListObj = parse(eventsfile)
trackname = eventsListObj.getElementsByTagName('name')[0].firstChild.data.encode()
eventsList = eventsListObj.getElementsByTagName('event')
numEvents = eventsList.length
for p in range(numEvents):
theEvent= eventsList[p]
eventTime = theEvent.getElementsByTagName('beginTime')[0].firstChild.data.encode()
eTime = ns2pyTime(eventTime)
eventTimeInMicros = (eTime-bTime).microseconds
out = mff_micros2Sample(eventTimeInMicros,summaryInfo['sampRate'])
eventTimeInSamples = int(out[0])
sampleRemainder = int(out[1])
eventTimeInEpochSamples= samples2EpochSample(eventTimeInSamples, epochBeginSamps, epochNumSamps)
if eventTimeInEpochSamples >= 0:
keylist = theEvent.getElementsByTagName('key')
eventkeycount = len(keylist)
keyp = []
for q in range(eventkeycount):
theKey = keylist[q]
theKeyCode = theKey.getElementsByTagName('keyCode')[0].firstChild.data.encode()
theKeyData = theKey.getElementsByTagName('data')[0].firstChild.data.encode()
theKeyData1 = theKey.getElementsByTagName('data')
theKeyData0 = theKeyData1[0] # print theKeyData0.toxml()
a = theKeyData0.attributes["dataType"]
theKeyDatatype = a.value.encode()
theKeyq = [theKeyCode, int(theKeyData), theKeyDatatype,'']
keyp.append(theKeyq)
duration = int(theEvent.getElementsByTagName('duration')[0].firstChild.data.encode())
out = mff_micros2Sample(duration, summaryInfo['sampRate'])
origp =[sampleRemainder, int(out[1]), trackname, keyp]
eventp=[theEvent.getElementsByTagName('code')[0].firstChild.data.encode(),eventTimeInEpochSamples,0, [], int(out[0]), [], origp]
events.append(eventp)
eventIndp = np.array([eventp[1], eventInd], dtype='i').reshape((1,2))
eventInds = np.concatenate((eventInds,eventIndp), axis=0)
eventInd = eventInd+1
eventInds0 = eventInds[eventInds[:,0].argsort()]
sortedEvents = events
for p in range(eventInd):
nextEventInd = eventInds0[p,1]
sortedEvents[p] = events[nextEventInd]
events = sortedEvents
return events
def getEpochInfos(filePath, sampRate):
import numpy as np
from xml.dom.minidom import parse
import os.path
from mff.mff_micros2Sample import mff_micros2Sample
##------------------------------------------------------------------------------
epochfile = filePath+'/epochs.xml'
epochList = parse(epochfile)
epochs = epochList.getElementsByTagName('epoch')
numEpochs = epochs.length
epochBeginSamps = np.zeros((numEpochs), dtype='i8')
epochNumSamps = np.zeros((numEpochs), dtype='i8')
epochFirstBlocks = np.zeros((numEpochs), dtype='i8')
epochLastBlocks = np.zeros((numEpochs), dtype='i8')
epochTime0 = np.zeros((numEpochs), dtype='i8')
epochLabels = [None]*numEpochs #np.zeros((numEpochs), dtype='S50')
epochSubjects = []
epochFilenames = []
epochSegStatus = [None]*numEpochs #np.zeros((numEpochs), dtype='S50')
multiSubj = False
for p in range(numEpochs):
anEpoch = epochs[p]
epochBegin = int(anEpoch.getElementsByTagName('beginTime')[0].firstChild.data)
epochEnd = int(anEpoch.getElementsByTagName('endTime')[0].firstChild.data)
epochBeginSamps[p] = mff_micros2Sample(epochBegin, sampRate)[0]
epochTime0[p] = epochBeginSamps[p]
epochNumSamps[p] = mff_micros2Sample(epochEnd, sampRate)[0]- epochBeginSamps[p]
epochFirstBlocks[p] = int(anEpoch.getElementsByTagName('firstBlock')[0].firstChild.data)
epochLastBlocks[p] = int(anEpoch.getElementsByTagName('lastBlock')[0].firstChild.data)
epochLabels[p] = 'epoch'
epochType = 'cnt'
totalNumSegs = 0
##------------------------------------------------------------------------------------
categfile = filePath+'/categories.xml'
if os.path.isfile(categfile):
epochType = 'seg'
categList = parse(categfile)
cats = categList.getElementsByTagName('cat')
numCategs = cats.length
multiSubj = False
if os.path.exists(filePath+'/subjects'):
multiSubj = True
for p in range(numCategs):
aCateg = cats[p]
segList = aCateg.getElementsByTagName('segments')
numSegs = segList.length
for q in range(numSegs):
aSeg = segList[q]
keyListArray = aSeg.getElementsByTagName('keyCode')
numKeys = keyListArray.length
numSubjs = 0
for r in range(numKeys):
aKey = keyListArray[r]
if aKey.firstChild.data.encode() == 'subj':
numSubjs = numSubjs + 1
if multiSubj:
epochSubjects = [None]*numEpochs #np.zeros((numEpochs), dtype='S50')
epochFilenames = [None]*numEpochs #np.zeros((numEpochs), dtype='S50')
for p in range(numCategs):
aCateg = cats[p]
categLabel = aCateg.getElementsByTagName('name')[0].firstChild.data #.encode()
segList = aCateg.getElementsByTagName('seg')
numSegs = segList.length
totalNumSegs = totalNumSegs + numSegs
for q in range(numSegs):
aSeg = segList[q]
segBegin = int(aSeg.getElementsByTagName('beginTime')[0].firstChild.data)
segBeginSamp = int(mff_micros2Sample(segBegin, sampRate)[0])
segInd = np.where(epochBeginSamps == segBeginSamp)[0]
epochSegStatus[segInd[0]] = aSeg.getAttribute('status')
epochLabels[segInd[0]] = categLabel
time0 = int(aSeg.getElementsByTagName('evtBegin')[0].firstChild.data)
time0Samp = mff_micros2Sample(time0, sampRate)[0]
time0Samp = time0Samp - segBeginSamp
epochTime0[segInd[0]] = time0Samp
if multiSubj:
keyListArray = aSeg.getElementsByTagName('keyCode')
numKeys = keyListArray.length
dataListArray = aSeg.getElementsByTagName('data')
for r in range(numKeys):
aKey = keyListArray[r]
aData = dataListArray[r]
subject = None
filename = None
if aData.firstChild != None:
if aKey.firstChild.data.encode() =='subj':
subject = aData.firstChild.data #.encode()
elif aKey.firstChild.data.encode() == 'FILE':
filename = aData.firstChild.data.encode()
epochSubjects[segInd[0]] = subject
epochFilenames[segInd[0]] = filename
if (multiSubj and len(set(epochFilenames))==1 and len(set(epochSubjects)) == 1):
epochSubjects = []
epochFilenames = []
multiSubj = False
##------------------------------------------------------------------------------------
epochInfo = {'epochType':epochType, 'epochBeginSamps':epochBeginSamps,
'epochNumSamps':epochNumSamps, 'epochFirstBlocks':epochFirstBlocks,
'epochLastBlocks':epochLastBlocks, 'epochLabels':epochLabels,
'epochTime0':epochTime0, 'multiSubj':multiSubj, 'epochSubjects':epochSubjects,
'epochFilenames':epochFilenames, 'epochSegStatus':epochSegStatus}
return epochInfo
def getEpochInfos(filePath, sampRate):
import numpy as np
from xml.dom.minidom import parse
import os.path
from mff.mff_micros2Sample import mff_micros2Sample
##------------------------------------------------------------------------------
epochfile = filePath + '/epochs.xml'
epochList = parse(epochfile)
epochs = epochList.getElementsByTagName('epoch')
numEpochs = epochs.length
epochBeginSamps = np.zeros((numEpochs), dtype='i8')
epochNumSamps = np.zeros((numEpochs), dtype='i8')
epochFirstBlocks = np.zeros((numEpochs), dtype='i8')
epochLastBlocks = np.zeros((numEpochs), dtype='i8')
epochTime0 = np.zeros((numEpochs), dtype='i8')
epochLabels = [None] * numEpochs #np.zeros((numEpochs), dtype='S50')
epochSubjects = []
epochFilenames = []
epochSegStatus = [None] * numEpochs #np.zeros((numEpochs), dtype='S50')
multiSubj = False
for p in range(numEpochs):
anEpoch = epochs[p]
epochBegin = int(
anEpoch.getElementsByTagName('beginTime')[0].firstChild.data)
epochEnd = int(
anEpoch.getElementsByTagName('endTime')[0].firstChild.data)
epochBeginSamps[p] = mff_micros2Sample(epochBegin, sampRate)[0]
epochTime0[p] = epochBeginSamps[p]
epochNumSamps[p] = mff_micros2Sample(epochEnd,
sampRate)[0] - epochBeginSamps[p]
epochFirstBlocks[p] = int(
anEpoch.getElementsByTagName('firstBlock')[0].firstChild.data)
epochLastBlocks[p] = int(
anEpoch.getElementsByTagName('lastBlock')[0].firstChild.data)
epochLabels[p] = 'epoch'
epochType = 'cnt'
totalNumSegs = 0
##------------------------------------------------------------------------------------
categfile = filePath + '/categories.xml'
if os.path.isfile(categfile):
epochType = 'seg'
categList = parse(categfile)
cats = categList.getElementsByTagName('cat')
numCategs = cats.length
multiSubj = False
if os.path.exists(filePath + '/subjects'):
multiSubj = True
for p in range(numCategs):
aCateg = cats[p]
segList = aCateg.getElementsByTagName('segments')
numSegs = segList.length
for q in range(numSegs):
aSeg = segList[q]
keyListArray = aSeg.getElementsByTagName('keyCode')
numKeys = keyListArray.length
numSubjs = 0
for r in range(numKeys):
aKey = keyListArray[r]
if aKey.firstChild.data.encode() == 'subj':
numSubjs = numSubjs + 1
if multiSubj:
epochSubjects = [None
] * numEpochs #np.zeros((numEpochs), dtype='S50')
epochFilenames = [
None
] * numEpochs #np.zeros((numEpochs), dtype='S50')
for p in range(numCategs):
aCateg = cats[p]
categLabel = aCateg.getElementsByTagName(
'name')[0].firstChild.data #.encode()
segList = aCateg.getElementsByTagName('seg')
numSegs = segList.length
totalNumSegs = totalNumSegs + numSegs
for q in range(numSegs):
aSeg = segList[q]
segBegin = int(
aSeg.getElementsByTagName('beginTime')[0].firstChild.data)
segBeginSamp = int(mff_micros2Sample(segBegin, sampRate)[0])
segInd = np.where(epochBeginSamps == segBeginSamp)[0]
epochSegStatus[segInd[0]] = aSeg.getAttribute('status')
epochLabels[segInd[0]] = categLabel
time0 = int(
aSeg.getElementsByTagName('evtBegin')[0].firstChild.data)
time0Samp = mff_micros2Sample(time0, sampRate)[0]
time0Samp = time0Samp - segBeginSamp
epochTime0[segInd[0]] = time0Samp
if multiSubj:
keyListArray = aSeg.getElementsByTagName('keyCode')
numKeys = keyListArray.length
dataListArray = aSeg.getElementsByTagName('data')
for r in range(numKeys):
aKey = keyListArray[r]
aData = dataListArray[r]
subject = None
filename = None
if aData.firstChild != None:
if aKey.firstChild.data.encode() == 'subj':
subject = aData.firstChild.data #.encode()
elif aKey.firstChild.data.encode() == 'FILE':
filename = aData.firstChild.data.encode()
epochSubjects[segInd[0]] = subject
epochFilenames[segInd[0]] = filename
if (multiSubj and len(set(epochFilenames)) == 1
and len(set(epochSubjects)) == 1):
epochSubjects = []
epochFilenames = []
multiSubj = False
##------------------------------------------------------------------------------------
epochInfo = {
'epochType': epochType,
'epochBeginSamps': epochBeginSamps,
'epochNumSamps': epochNumSamps,
'epochFirstBlocks': epochFirstBlocks,
'epochLastBlocks': epochLastBlocks,
'epochLabels': epochLabels,
'epochTime0': epochTime0,
'multiSubj': multiSubj,
'epochSubjects': epochSubjects,
'epochFilenames': epochFilenames,
'epochSegStatus': epochSegStatus
}
return epochInfo
