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Loading_Functions.R
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Loading_Functions.R
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# The following contain peices from abfload, a package in R used to loading ABF Files. ---------
# It currently only works for ABFV1 files and fucntions from the package are tweaked below to work for both ABFV1 and ABFV2 files
BLOCK_SIZE <- 512
STRING_JUNK_PREFIX <- 44
abfloadv2 <- function ( filename=NULL )
{
if ( is.null(filename) )
{
filename <- file.choose()
}
result <- list()
fp <- file(filename, open="rb")
result$signature <- readChar(fp, nchars=4, useBytes=TRUE)
result$filename <- filename
if ( result$signature != "ABF2" )
{
close(fp)
stop("Only ABF2 files supported at present")
}
class(result) <- "abf2"
vb <- readBin(fp, what="integer", n=4, size=1)
result$version <- vb[4] + vb[3] * 0.1 + vb[2] * 0.01 + vb[1] * 0.001
result <- defRead(fp, header2Def, result)
result$startTime <- result$startTime * 0.001
# read the section index
result$sections <- list()
for ( sect.name in abfSections )
{
result$sections[[sect.name]] <- defRead ( fp, sectionInfo, repos=FALSE )
}
# read the strings section
seek(fp, where=result$sections$StringSection$blockIndex * BLOCK_SIZE + STRING_JUNK_PREFIX)
result$strings <- c(readBin(fp, "character", n=result$sections$StringSection$numEntries))
# read the epoch
seek(fp, where=result$section$EpochPerDACSection$blockIndex * BLOCK_SIZE + result$section$EpochPerDACSection$bytes)
result$epoch <- defRead(fp, abfEpochDacInfo, repos=FALSE)
# read the ADC defs
result$ADC <- list()
for ( ii in 1:result$sections$ADCSection$numEntries )
{
seek(fp, where=result$sections$ADCSection$blockIndex * BLOCK_SIZE + result$sections$ADCSection$bytes * (ii-1))
result$ADC[[ii]] <- defRead(fp, abfADCInfo, repos=FALSE)
result$ADC[[ii]]$name <- result$strings[result$ADC[[ii]]$ADCChannelNameIndex]
result$ADC[[ii]]$units <- result$strings[result$ADC[[ii]]$ADCUnitsIndex]
}
# read the protocol block
seek(fp, where=result$section$ProtocolSection$blockIndex * BLOCK_SIZE)
result$protocol <- defRead(fp, abfProtocolInfo, repos=FALSE)
##read the epochperdac
#seek(fp, where=result$section$EpochPerDacSection$blockIndex * BLOCK_SIZE)
#result$epoch <- defRead(fp, abfEpochDacInfo, repos=FALSE)
# and the tags, if any
result$rawTags <- list()
vLevel <- NA
vUnits <- ""
result$tags <- data.frame(time=0, level=vLevel, units=vUnits, comment="", vChange=TRUE)
if ( result$sections$TagSection$numEntries > 0 )
{
for ( ii in 1:result$sections$TagSection$numEntries )
{
seek(fp, where=result$sections$TagSection$blockIndex *
BLOCK_SIZE + result$sections$TagSection$bytes * (ii-1))
result$rawTags[[ii]] <- defRead(fp, abfTagInfo, repos=FALSE)
# this is purely empirical based on what I've seen in our own files
# I have no idea whether there's any more official scheme for this stuff
rmx <- regexec("[^']*'([^']+)' => ([^ ]+) ([^ ]+)", result$rawTags[[ii]]$comment)
result$rawTags[[ii]]$is.cmd <- rmx[[1]][1] != -1
tagTime <- result$rawTags[[ii]]$tagTime *
result$protocol$ADCSequenceInterval *
1e-6 / length(result$ADC)
if ( result$rawTags[[ii]]$is.cmd )
{
mxs <- regmatches(result$rawTags[[ii]]$comment, rmx)[[1]]
result$rawTags[[ii]]$cmd <- mxs[2]
result$rawTags[[ii]]$level <- as.numeric(mxs[3])
result$rawTags[[ii]]$units <- mxs[4]
vLevel <- result$rawTags[[ii]]$level
vUnits <- result$rawTags[[ii]]$units
result$tags <- rbind(result$tags,
data.frame(time=tagTime,
level=vLevel,
units=vUnits,
comment="",
vChange=TRUE,
stringsAsFactors=FALSE))
}
else
{
result$comments <- rbind(result$comments,
data.frame(time=tagTime,
comment=paste(unlist(strsplit(result$rawTags[[ii]]$comment,
" +")),
collapse=" "),
stringsAsFactors=FALSE))
result$tags <- rbind(result$tags,
data.frame(time=tagTime,
level=vLevel,
units=vUnits,
comment=paste(unlist(strsplit(result$rawTags[[ii]]$comment,
" +")),
collapse=" "),
vChange=FALSE,
stringsAsFactors=FALSE))
}
}
}
# OK, now we need to read the data
if ( result$dataFormat == 0 )
{
dataSz <- 2
dataType <- "integer"
}
else if ( result$dataFormat == 1 )
{
dataSz <- 4
dataType <- "numeric"
}
else
{
warning(paste("unknown data format", result$dataFormat, "- data section not read"))
close(fp)
invisible(result)
}
headOffset <- result$sections$DataSection$blockIndex * BLOCK_SIZE
#si <- result$protocol$ADCSequenceInterval
if ( result$protocol$operationMode == 5 )
{
# gap free mode - this is our primary goal
#result$dataPtsPerChannel <- result$sections$DataSection$numEntries / length(result$ADC)
seek(fp, where=headOffset)
result$rawdata <- readBin(fp, what=dataType, size=dataSz, n=result$sections$DataSection$numEntries)
result$traces <- matrix(result$rawdata, nrow=length(result$ADC))
result$s <- 0:(dim(result$traces)[2]-1) * (result$protocol$ADCSequenceInterval * 1e-6)
# scale int data by ADC settings
if ( result$dataFormat == 0 )
{
for ( ii in 1:length(result$ADC) )
{
adc <- result$ADC[[ii]]
result$ADC[[ii]]$scaleFactor <- result$protocol$ADCRange /
(result$protocol$ADCResolution *
adc$instScaleFactor *
adc$signalGain *
adc$ADCProgGain *
adc$teleAddGain)
result$ADC[[ii]]$offset <- adc$instOffset - adc$signalOffset
result$traces[ii,] <- result$traces[ii,] * result$ADC[[ii]]$scaleFactor + result$ADC[[ii]]$offset
}
}
}
else
{
warning(paste("unsupported data mode", result$protocol$operationMode, "- data section not read"))
}
close(fp)
invisible(result)
}
defRead <- function ( fp, def, result=NULL, origin=0, repos=TRUE )
{
if ( is.null(result) )
result <- list()
for ( ii in 1:length(def$field) )
{
if (repos) { seek(fp, where=def$offset[ii]+origin) }
if ( def$type[ii]=="uint32" )
{
# R does not support unsigned long, so we have to fudge this to double
lo <- readBin(fp, what="integer", size=2, signed=FALSE)
hi <- readBin(fp, what="integer", size=2, signed=FALSE)
result[[def$field[ii]]] <- 65536.0 * hi + lo
}
else if ( def$type[ii]=="string" )
{
result[[def$field[ii]]] <- readChar(fp, nchars=def$bytes[ii], useBytes=TRUE)
}
else if ( def$type[ii]=="skip" )
{
seek(fp, where=def$bytes[ii], origin="current")
}
else
{
result[[def$field[ii]]] <- readBin(fp, what=def$type[ii], size=def$bytes[ii])
}
}
invisible(result)
}
# Required variables ------------------------------------------------------
padNA <- function (mydata, rowsneeded, first = TRUE)
{
temp1 = colnames(mydata)
rowsneeded = rowsneeded - nrow(mydata)
temp2 = setNames(
data.frame(matrix(rep(NA, length(temp1) * rowsneeded),
ncol = length(temp1))), temp1)
if (isTRUE(first)) rbind(mydata, temp2)
else rbind(temp2, mydata)
}
dotnames <- function(...) {
vnames <- as.list(substitute(list(...)))[-1L]
vnames <- unlist(lapply(vnames,deparse), FALSE, FALSE)
vnames
}
Cbind <- function(..., first = TRUE) {
Names <- dotnames(...)
datalist <- setNames(list(...), Names)
nrows <- max(sapply(datalist, function(x)
ifelse(is.null(dim(x)), length(x), nrow(x))))
datalist <- lapply(seq_along(datalist), function(x) {
z <- datalist[[x]]
if (is.null(dim(z))) {
z <- setNames(data.frame(z), Names[x])
} else {
if (is.null(colnames(z))) {
colnames(z) <- paste(Names[x], sequence(ncol(z)), sep = "_")
} else {
colnames(z) <- paste(Names[x], colnames(z), sep = "_")
}
}
padNA(z, rowsneeded = nrows, first = first)
})
do.call(cbind, datalist)
}
header2Def <- data.frame(
field=c("headerSize", "episodes", "startDate", "startTime",
"stopwatchTime", "fileType", "dataFormat", "nScan",
"CRCEnable", "fileCRC", "fileGUID", "creatorVersion",
"creatorNameIndex", "modifierVersion", "modifierNameIndex", "protocolPathIndex"),
offset=c(8, 12, 16, 20,
24, 28, 30, 32,
34, 36, 40, 56,
60, 64, 68, 72),
type=c("uint32", "uint32", "uint32", "uint32",
"uint32", "integer", "integer", "integer",
"integer", "uint32", "uint32", "uint32",
"uint32", "uint32", "uint32", "uint32"),
bytes=c(4, 4, 4, 4,
4, 2, 2, 2,
2, 4, 4, 4,
4, 4, 4, 4),
stringsAsFactors=FALSE
)
# sections
abfSections <- c(
"ProtocolSection",
"ADCSection",
"DACSection",
"EpochSection",
"ADCPerDACSection",
"EpochPerDACSection",
"UserListSection",
"StatsRegionSection",
"MathSection",
"StringSection",
"DataSection",
"TagSection",
"ScopeSection",
"DeltaSection",
"VoiceTagSection",
"SynchArraySection",
"AnnotationSection",
"StatsSection"
)
sectionInfo <- data.frame(
field=c("blockIndex", "bytes", "numEntries"),
type=c("uint32", "uint32", "integer"),
bytes=c(4,4,8),
stringsAsFactors=FALSE
)
abfProtocolInfo <- data.frame(
field=c("operationMode", "ADCSequenceInterval", "fileCompressionEnabled", "unused",
"fileCompressionRatio", "synchTimeUnit", "secondsPerRun", "samplesPerEpisode",
"pretriggerSamples", "episodesPerRun", "runsPerTrial", "nTrials",
"averagingMode", "undoRunCount", "firstEpInRun", "triggerThreshold",
"triggerSource", "triggerAction", "triggerPolarity", "scopeOutputInterval",
"episodeStartToStart", "runStartToStart", "averageCount", "trialStartToStart",
"autoTriggerStrategy", "firstRunDelay", "channelStatsStrategy", "samplesPerTrace",
"startDisplayNum", "finishDisplayNum", "showPNRawData", "statsPeriod",
"statsMeasurements", "statsSaveStrategy", "ADCRange", "DACRange",
"ADCResolution", "DACResolution", "experimentType", "manualInfoStrategy",
"commentsEnable", "fileCommentIndex", "autoAnalyseEnable", "signalType",
"digitalEnable", "activeDACChannel", "digitalHolding", "digitalInterEpisode",
"digitalDACChannel", "digitalTrainActiveLogic", "statsEnable", "statsClearStrategy",
"levelHysteresis", "timeHysteresis", "allowExternalTags", "averageAlgorithm",
"averageWeighting", "undoPromptStrategy", "trialTriggerSource", "statsDisplayStrategy",
"externalTagType", "scopeTriggerOut", "LTPType", "alternateDACOutputState",
"alternateDigitalOutputState", "cellID1", "cellID2", "cellID3",
"digitizerADCs", "digitizerDACs", "digitizerTotalDigOuts", "digitizerSynchDigOuts",
"digitizerType"),
type=c("integer", "numeric", "logical", "skip",
"uint32", "numeric", "numeric", "integer",
"integer", "integer", "integer", "integer",
"integer", "integer", "integer", "numeric",
"integer", "integer", "integer", "numeric",
"numeric", "numeric", "integer", "numeric",
"integer", "numeric", "integer", "integer",
"integer", "integer", "integer", "numeric",
"integer", "integer", "numeric", "numeric",
"integer", "integer", "integer", "integer",
"integer", "integer", "integer", "integer",
"integer", "integer", "integer", "integer",
"integer", "integer", "integer", "integer",
"integer", "integer", "integer", "integer",
"numeric", "integer", "integer", "integer",
"integer", "integer", "integer", "integer",
"integer", "numeric", "numeric", "numeric",
"integer", "integer", "integer", "integer",
"integer"),
bytes=c(2, 4, 1, 3,
4, 4, 4, 4,
4, 4, 4, 4,
2, 2, 2, 4,
2, 2, 2, 4,
4, 4, 4, 4,
2, 4, 2, 4,
4, 4, 2, 4,
4, 2, 4, 4,
4, 4, 2, 2,
2, 4, 2, 2,
2, 2, 2, 2,
2, 2, 2, 2,
2, 4, 2, 2,
4, 2, 2, 2,
2, 2, 2, 2,
2, 4, 4, 4,
2, 2, 2, 2,
2),
stringsAsFactors=FALSE
)
abfEpochDacInfo <- data.frame(
field=c("nEpochNum", "nDACNum", "nEpochType", "fEpochInitLevel",
"fEpochLevelInc", "lEpochInitDuration", "lEpochDurationInc", "lEpochPulsePeriod",
"lEpochPulseWidth"),
type=c("integer", "integer", "integer", "numeric",
"numeric", "uint32", "uint32", "uint32",
"uint32"),
bytes=c(2, 2, 2, 8,
8, 4, 4, 4,
4),
stringsAsFactors=FALSE
)
abfMathInfo <- data.frame(
field=c("mathEnable", "mathExpression", "mathOperatorIndex", "mathUnitsIndex",
"mathUpperLimit", "mathLowerLimit", "mathADCNum1", "mathADCNum2",
"unused", "mathK1", "mathK2", "mathK3",
"mathK4", "mathK5", "mathK6"),
type=c("integer", "integer", "uint32", "uint32",
"numeric", "numeric", "integer", "integer",
"skip", "numeric", "numeric", "numeric",
"numeric", "numeric", "numeric"),
bytes=c(2, 2, 4, 4,
4, 4, 2, 2,
16, 4, 4, 4,
4, 4, 4),
stringsAsFactors=FALSE
)
abfADCInfo <- data.frame(
field=c("ADCNum", "teleEnable", "teleInstrument", "teleAddGain",
"teleFilter", "teleMembraneCap", "teleMode", "teleAccResist",
"ADCPtoLChannelMap", "ADCSamplingSeq", "ADCProgGain", "ADCDispAmp",
"ADCDispOffset", "instScaleFactor", "instOffset", "signalGain",
"signalOffset", "signalLowpass", "signalHighpass", "lowpassType",
"highpassType", "postprocLowpass", "postprocLowpassType", "enabledDuringPN",
"statsChannelPolarity", "ADCChannelNameIndex", "ADCUnitsIndex"),
type=c("integer", "integer", "integer", "numeric",
"numeric", "numeric", "integer", "numeric",
"integer", "integer", "numeric", "numeric",
"numeric", "numeric", "numeric", "numeric",
"numeric", "numeric", "numeric", "integer",
"integer", "numeric", "integer", "logical",
"integer", "integer", "integer"),
bytes=c(2, 2, 2, 4,
4, 4, 2, 4,
2, 2, 4, 4,
4, 4, 4, 4,
4, 4, 4, 1,
1, 4, 1, 1,
2, 4, 4),
stringsAsFactors=FALSE
)
abfTagInfo <- data.frame(
field=c("tagTime", "comment", "tagType", "annotIndex"),
type=c("integer", "string", "integer", "integer"),
bytes=c(4, 56, 2, 2),
stringsAsFactors=FALSE
)
abfEpochDacInfo <- data.frame(
field=c("nEpochNum", "nDACNum", "nEpochType", "fEpochInitLevel",
"fEpochLevelInc", "lEpochInitDuration", "lEpochDurationInc", "lEpochPulsePeriod",
"lEpochPulseWidth"),
type=c("integer", "integer", "integer", "numeric",
"numeric", "uint32", "uint32", "uint32",
"uint32"),
bytes=c(2, 2, 2, 4,
4, 8, 8, 8,
8),
stringsAsFactors=FALSE
)