R/readHeaderFunctions.R
In vagnerfonseca/edf: Reading EDF(+) and BDF(+) Files
# DF(+)/BDF(+) file header reading functions
#
# Purpose : Reading .edf(+) & .bdf file headers
#
# Copyright : (C) 2015-2016, Vis Consultancy, the Netherlands
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with edfReader package for R. If not, see <http://www.gnu.org/licenses/>.
#
# Acknowledgement :
# This package has used code from:
# - edf.R version 0.3 (27-11-2013) from Fabien Feschet,
# http://data-auvergne.fr/cloud/index.php/s/WYmFEDZylFWJzNs
# - the work of Henelius Andreas as of July 2015, https://github.com/bwrc/edf
#
# History :
# Oct15 - Created
# Feb16 - Version 1.0.0
# Mar16 - Version 1.1.0 support for non-unique signals labels
# & sub second start data from data record
# Apr16 - Version 1.1.1, no changes
# ------------------------------------------------------------------------------
# read EDF header
# ------------------------------------------------------------------------------
#' Read EDF(+) or BDF(+) file header
#'
#' The function reads the header of an EDF (European Data Format) file, an EDF+ file,
#' an BDF file, or an BDF+ file
#'
#' @param fileName The full path to the EDF(+)/BDF(+) file to be read.
#' @return an object of class ebdfHeader
#'
#' @section Details:
#' The object returned contains also an object of class ebdfSHeaders.
#' Both objects ebdfHeader and ebdfSHeaders have supporting S3 print and summary functions.\cr
#' For object details see the package vignette.
#'
#' @section Acknowledgement:
#' This package has used code from:
#' \itemize{
#' \item edf.R version 0.3 (27-11-2013), http://feschet.fr/?p=11
#' \item the work of Henelius Andreas as of July 2015, https://github.com/bwrc/edf
#' }
#' @seealso
#' \code{\link{edfReader}}, \code{\link{readEdfSignals}}\cr
#' For the vignette use the console command:\cr
#' \code{vignette('edfReaderVignette', package = "edfReader")}\cr
#' or click on \code{Index} below.
#' @aliases readBdfHeader
#' @examples
#' # Examples from the vignette
#' libDir <- system.file ("extdata", package="edfReader")
#' # a continuous recording
#' CFile <- paste (libDir, '/edfPlusC.edf', sep='')
#' CHdr <- readEdfHeader (CFile)
#' CHdr # print the header
#' summary (CHdr) # print a header summary
#' str (CHdr) # look to the details
#' CHdr$sHeaders # print the signal headers
#' summary(CHdr$sHeaders) # print a signal headers summary
#' str(CHdr$sHeaders) # look to the signal header details
#' # for a discontinuous recording
#' DFile <- paste (libDir, '/bdfPlusD.bdf', sep='')
#' # and proceed as above to read the header and to show the results
#' @export
readEdfHeader <- function (fileName) {
# open the file
if (file.exists (fileName)) inFile <- file(fileName, "rb", encoding="UTF-16LE")
else stop (paste ("File '", fileName, "' doesn't exists.", sep=''))
hdr <- list()
class (hdr) <- "ebdfHeader"
hdr$fileName <- fileName
hdr$fileType = ''
version <- readBin (inFile, integer(), n=1, size=1, signed=FALSE , endian="little")
eVersion <- version
if (version[1] == 48) { # ascii 48 = 0
hdr$version <- '0' # always 0, see specs
spaces <- readChar(inFile, 7, TRUE) # read the other 7 bytes, should be 7 ' '
if (spaces != ' ') stop (paste ("File '", fileName, "' is not an EDF or BDF file.", sep=''))
hdr$fileType = 'EDF'
} else if (version[1] == 255) { # possibly a bdf file
hdr$fileType <- 'BDF'
otherVersion <- gsub ("[[:space:]]*$", "", readChar(inFile, 7, TRUE))
if (otherVersion == "BIOSEMI") {
hdr$version <- paste('"', version,'"', otherVersion, sep='')
} else {
stop (paste ("File '", fileName, "' is not an EDF or BDF file.", sep=''))
}
} else stop (paste ("File '", fileName, "' is not an EDF or BDF file.", sep=''))
hdr$patient <- gsub ("[[:space:]]*$", "", readChar(inFile, 80, TRUE)) # local patient identification
hdr$recordingId <- gsub ("[[:space:]]*$", "", readChar(inFile, 80, TRUE)) # local recording identification
dateTimeSring <- readChar(inFile, 16, TRUE)
if (substr(dateTimeSring, 11, 11) == ':') {
substr(dateTimeSring, 11, 11) <- '.'
substr(dateTimeSring, 14, 14) <- '.'
}
hdr$startTime <- strptime(dateTimeSring, format="%d.%m.%y %H.%M.%S") # start date and time of recording
# proposed?: strptime(readChar(inFile, 16, TRUE), format="%d.%m.%y %H:%M:%S") # start date and time of recording
hdr$headerLength<- as.integer(readChar(inFile, 8, TRUE)) # number of bytes in header record
hdr$reserved <- gsub ("[[:space:]]*$", "", readChar(inFile, 44, TRUE)) # reserved
hdr$nRecords <- as.integer(readChar(inFile, 8, TRUE)) # number of data records
hdr$recordDuration <- as.numeric(readChar(inFile, 8, TRUE)) # duration of a data record, in seconds
hdr$nSignals <- as.integer(readChar(inFile, 4, TRUE)) # number of signals (ns) in data record
# get the signal headers
ns <- hdr$nSignals
label <- character (ns)
for (i in 1:ns) label[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=16, useBytes=TRUE))
transducerType <- character (ns)
for (i in 1:ns) transducerType[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=80, useBytes=TRUE))
physicalDim <- character (ns)
for (i in 1:ns) physicalDim[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=8, useBytes=TRUE))
physicalMin <- double (ns)
for (i in 1:ns) physicalMin[i] <- as.numeric (readChar (inFile, nchars=8, useBytes=TRUE))
physicalMax <- double (ns)
for (i in 1:ns) physicalMax[i] <- as.numeric (readChar (inFile, nchars=8, useBytes=TRUE))
digitalMin <- integer (ns)
for (i in 1:ns) digitalMin[i] <- as.integer (readChar (inFile, nchars=8, useBytes=TRUE))
digitalMax <- integer (ns)
for (i in 1:ns) digitalMax[i] <- as.integer (readChar (inFile, nchars=8, useBytes=TRUE))
preFilter <- character (ns)
for (i in 1:ns) preFilter[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=80, useBytes=TRUE))
samplesPerRecord <- integer (ns)
for (i in 1:ns) samplesPerRecord[i] <- as.integer (readChar (inFile, nchars=8, useBytes=TRUE))
reserved <- character (ns)
for (i in 1:ns) reserved[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=32, useBytes=TRUE))
close(inFile)
# derived attributes
if (hdr$recordDuration) sRate <- samplesPerRecord / hdr$recordDuration
else sRate <- NA # in EDF+ hdr$recordD may be zero
sLength <- samplesPerRecord * hdr$nRecords
hdr$recordedPeriod <- hdr$recordDuration * hdr$nRecords
hdr$sampleBits <- ifelse (hdr$fileType == 'EDF', 16, 24)
hdr$isPlus <- FALSE # not an EDF+ file
hdr$isContinuous<- TRUE # continuous recording, the default
if (hdr$reserved == 'EDF+C' | hdr$reserved == 'BDF+C'| hdr$reserved == 'EDF+D'| hdr$reserved == 'BDF+D') {
hdr$isPlus <- TRUE
if (hdr$reserved == 'EDF+D' | hdr$reserved == 'BDF+D') hdr$isContinuous <- FALSE
}
isAnnotation <- rep (FALSE, ns)
if (hdr$isPlus) for (i in 1:ns) {
if (label[i] == 'EDF Annotations' | label[i] == 'BDF Annotations') isAnnotation[i] <- TRUE
}
# physicaL = gain * digital + offset with:
# gain = (physicalMax - physicalMin) / (digitalMax - digitalMin)
# offset = physicalMax - gain * digitalMax
gain <- rep (1, ns)
offset <- rep (0, ns)
for (i in 1:ns) if (!isAnnotation[i]) {
if ((digitalMax[i] != digitalMin[i]) & (physicalMax[i] != physicalMin[i])) {
gain[i] <- (physicalMax[i] - physicalMin[i]) / (digitalMax[i] - digitalMin[i])
offset[i] <- physicalMax[i] - gain[i] * digitalMax[i]
}
}
# create signal data frame
hdr$sHeaders <- data.frame(label=label, transducerType=transducerType, physicalDim=physicalDim,
physicalMin=physicalMin, physicalMax=physicalMax,
digitalMin=digitalMin, digitalMax=digitalMax,
preFilter=preFilter, samplesPerRecord=samplesPerRecord,
reserved=reserved, gain=gain, offset=offset, sRate=sRate,
isAnnotation=isAnnotation, sLength=sLength, stringsAsFactors=FALSE)
signalNames <- label
for (sn in 1:length(signalNames)) {
if (signalNames[sn]=="") signalNames[sn] <- 'NA' # avoid empty names
}
for (sn in 1:length(signalNames)) {
equals <- signalNames == signalNames[sn]
if (sum(equals) > 1) { # distinguish duplicates
suffix <- 1
for (en in which(equals)) {
# NOTE: This is not bullet proof "a-1, a, a" will result in "a-1, a-1, a-2".
newName <- paste(signalNames[en], '-', suffix, sep='')
while (sum(signalNames == newName)) {
suffix <- suffix +1
newName <- paste(signalNames[en], '-', suffix, sep='')
}
signalNames[en] <- paste(signalNames[en], '-', suffix, sep='')
suffix <- suffix +1
}
}
}
# if + file get secondfraction start form first data record
hdr$startSecondFraction <- 0
if (hdr$isPlus) {
hdr$startSecondFraction <- getStartSecondFraction (hdr)
hdr$startTime <- hdr$startTime + hdr$startSecondFraction
}
row.names (hdr$sHeaders) <- signalNames
class (hdr$sHeaders) <- c("ebdfSHeaders", "data.frame")
# perform a consistency check
if (hdr$isPlus & !sum(hdr$sHeaders$isAnnotation)) cat ('ERROR: The annotation signal is missing.')
hdr
}
getStartSecondFraction <- function (hdr) {
StartSecondFraction <- 0
nAnnots <- sum (hdr$sHeaders$isAnnotation)
if (hdr$isPlus & nAnnots) {
annotations1 <- which.max (hdr$sHeaders$isAnnotation)
inFile <- file(hdr$fileName, "rb", encoding="UTF-16LE")
readBin (inFile, 'raw', n=hdr$headerLength , size=1)
samples <- readNextDataRecord (hdr, inFile)
StartSecondFraction <- getAnnoRecordStartRT (samples[[annotations1]]) # the subsecond start time is in the first TAL in the first annotation signal
close(inFile)
}
StartSecondFraction
}
vagnerfonseca/edf documentation built on May 3, 2019, 2:41 p.m.
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# DF(+)/BDF(+) file header reading functions
#
# Purpose : Reading .edf(+) & .bdf file headers
#
# Copyright : (C) 2015-2016, Vis Consultancy, the Netherlands
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with edfReader package for R. If not, see <http://www.gnu.org/licenses/>.
#
# Acknowledgement :
# This package has used code from:
# - edf.R version 0.3 (27-11-2013) from Fabien Feschet,
# http://data-auvergne.fr/cloud/index.php/s/WYmFEDZylFWJzNs
# - the work of Henelius Andreas as of July 2015, https://github.com/bwrc/edf
#
# History :
# Oct15 - Created
# Feb16 - Version 1.0.0
# Mar16 - Version 1.1.0 support for non-unique signals labels
# & sub second start data from data record
# Apr16 - Version 1.1.1, no changes
# ------------------------------------------------------------------------------
# read EDF header
# ------------------------------------------------------------------------------
#' Read EDF(+) or BDF(+) file header
#'
#' The function reads the header of an EDF (European Data Format) file, an EDF+ file,
#' an BDF file, or an BDF+ file
#'
#' @param fileName The full path to the EDF(+)/BDF(+) file to be read.
#' @return an object of class ebdfHeader
#'
#' @section Details:
#' The object returned contains also an object of class ebdfSHeaders.
#' Both objects ebdfHeader and ebdfSHeaders have supporting S3 print and summary functions.\cr
#' For object details see the package vignette.
#'
#' @section Acknowledgement:
#' This package has used code from:
#' \itemize{
#' \item edf.R version 0.3 (27-11-2013), http://feschet.fr/?p=11
#' \item the work of Henelius Andreas as of July 2015, https://github.com/bwrc/edf
#' }
#' @seealso
#' \code{\link{edfReader}}, \code{\link{readEdfSignals}}\cr
#' For the vignette use the console command:\cr
#' \code{vignette('edfReaderVignette', package = "edfReader")}\cr
#' or click on \code{Index} below.
#' @aliases readBdfHeader
#' @examples
#' # Examples from the vignette
#' libDir <- system.file ("extdata", package="edfReader")
#' # a continuous recording
#' CFile <- paste (libDir, '/edfPlusC.edf', sep='')
#' CHdr <- readEdfHeader (CFile)
#' CHdr # print the header
#' summary (CHdr) # print a header summary
#' str (CHdr) # look to the details
#' CHdr$sHeaders # print the signal headers
#' summary(CHdr$sHeaders) # print a signal headers summary
#' str(CHdr$sHeaders) # look to the signal header details
#' # for a discontinuous recording
#' DFile <- paste (libDir, '/bdfPlusD.bdf', sep='')
#' # and proceed as above to read the header and to show the results
#' @export
readEdfHeader <- function (fileName) {
# open the file
if (file.exists (fileName)) inFile <- file(fileName, "rb", encoding="UTF-16LE")
else stop (paste ("File '", fileName, "' doesn't exists.", sep=''))
hdr <- list()
class (hdr) <- "ebdfHeader"
hdr$fileName <- fileName
hdr$fileType = ''
version <- readBin (inFile, integer(), n=1, size=1, signed=FALSE , endian="little")
eVersion <- version
if (version[1] == 48) { # ascii 48 = 0
hdr$version <- '0' # always 0, see specs
spaces <- readChar(inFile, 7, TRUE) # read the other 7 bytes, should be 7 ' '
if (spaces != ' ') stop (paste ("File '", fileName, "' is not an EDF or BDF file.", sep=''))
hdr$fileType = 'EDF'
} else if (version[1] == 255) { # possibly a bdf file
hdr$fileType <- 'BDF'
otherVersion <- gsub ("[[:space:]]*$", "", readChar(inFile, 7, TRUE))
if (otherVersion == "BIOSEMI") {
hdr$version <- paste('"', version,'"', otherVersion, sep='')
} else {
stop (paste ("File '", fileName, "' is not an EDF or BDF file.", sep=''))
}
} else stop (paste ("File '", fileName, "' is not an EDF or BDF file.", sep=''))
hdr$patient <- gsub ("[[:space:]]*$", "", readChar(inFile, 80, TRUE)) # local patient identification
hdr$recordingId <- gsub ("[[:space:]]*$", "", readChar(inFile, 80, TRUE)) # local recording identification
dateTimeSring <- readChar(inFile, 16, TRUE)
if (substr(dateTimeSring, 11, 11) == ':') {
substr(dateTimeSring, 11, 11) <- '.'
substr(dateTimeSring, 14, 14) <- '.'
}
hdr$startTime <- strptime(dateTimeSring, format="%d.%m.%y %H.%M.%S") # start date and time of recording
# proposed?: strptime(readChar(inFile, 16, TRUE), format="%d.%m.%y %H:%M:%S") # start date and time of recording
hdr$headerLength<- as.integer(readChar(inFile, 8, TRUE)) # number of bytes in header record
hdr$reserved <- gsub ("[[:space:]]*$", "", readChar(inFile, 44, TRUE)) # reserved
hdr$nRecords <- as.integer(readChar(inFile, 8, TRUE)) # number of data records
hdr$recordDuration <- as.numeric(readChar(inFile, 8, TRUE)) # duration of a data record, in seconds
hdr$nSignals <- as.integer(readChar(inFile, 4, TRUE)) # number of signals (ns) in data record
# get the signal headers
ns <- hdr$nSignals
label <- character (ns)
for (i in 1:ns) label[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=16, useBytes=TRUE))
transducerType <- character (ns)
for (i in 1:ns) transducerType[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=80, useBytes=TRUE))
physicalDim <- character (ns)
for (i in 1:ns) physicalDim[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=8, useBytes=TRUE))
physicalMin <- double (ns)
for (i in 1:ns) physicalMin[i] <- as.numeric (readChar (inFile, nchars=8, useBytes=TRUE))
physicalMax <- double (ns)
for (i in 1:ns) physicalMax[i] <- as.numeric (readChar (inFile, nchars=8, useBytes=TRUE))
digitalMin <- integer (ns)
for (i in 1:ns) digitalMin[i] <- as.integer (readChar (inFile, nchars=8, useBytes=TRUE))
digitalMax <- integer (ns)
for (i in 1:ns) digitalMax[i] <- as.integer (readChar (inFile, nchars=8, useBytes=TRUE))
preFilter <- character (ns)
for (i in 1:ns) preFilter[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=80, useBytes=TRUE))
samplesPerRecord <- integer (ns)
for (i in 1:ns) samplesPerRecord[i] <- as.integer (readChar (inFile, nchars=8, useBytes=TRUE))
reserved <- character (ns)
for (i in 1:ns) reserved[i] <- gsub ("[[:space:]]*$", "", readChar(inFile, nchars=32, useBytes=TRUE))
close(inFile)
# derived attributes
if (hdr$recordDuration) sRate <- samplesPerRecord / hdr$recordDuration
else sRate <- NA # in EDF+ hdr$recordD may be zero
sLength <- samplesPerRecord * hdr$nRecords
hdr$recordedPeriod <- hdr$recordDuration * hdr$nRecords
hdr$sampleBits <- ifelse (hdr$fileType == 'EDF', 16, 24)
hdr$isPlus <- FALSE # not an EDF+ file
hdr$isContinuous<- TRUE # continuous recording, the default
if (hdr$reserved == 'EDF+C' | hdr$reserved == 'BDF+C'| hdr$reserved == 'EDF+D'| hdr$reserved == 'BDF+D') {
hdr$isPlus <- TRUE
if (hdr$reserved == 'EDF+D' | hdr$reserved == 'BDF+D') hdr$isContinuous <- FALSE
}
isAnnotation <- rep (FALSE, ns)
if (hdr$isPlus) for (i in 1:ns) {
if (label[i] == 'EDF Annotations' | label[i] == 'BDF Annotations') isAnnotation[i] <- TRUE
}
# physicaL = gain * digital + offset with:
# gain = (physicalMax - physicalMin) / (digitalMax - digitalMin)
# offset = physicalMax - gain * digitalMax
gain <- rep (1, ns)
offset <- rep (0, ns)
for (i in 1:ns) if (!isAnnotation[i]) {
if ((digitalMax[i] != digitalMin[i]) & (physicalMax[i] != physicalMin[i])) {
gain[i] <- (physicalMax[i] - physicalMin[i]) / (digitalMax[i] - digitalMin[i])
offset[i] <- physicalMax[i] - gain[i] * digitalMax[i]
}
}
# create signal data frame
hdr$sHeaders <- data.frame(label=label, transducerType=transducerType, physicalDim=physicalDim,
physicalMin=physicalMin, physicalMax=physicalMax,
digitalMin=digitalMin, digitalMax=digitalMax,
preFilter=preFilter, samplesPerRecord=samplesPerRecord,
reserved=reserved, gain=gain, offset=offset, sRate=sRate,
isAnnotation=isAnnotation, sLength=sLength, stringsAsFactors=FALSE)
signalNames <- label
for (sn in 1:length(signalNames)) {
if (signalNames[sn]=="") signalNames[sn] <- 'NA' # avoid empty names
}
for (sn in 1:length(signalNames)) {
equals <- signalNames == signalNames[sn]
if (sum(equals) > 1) { # distinguish duplicates
suffix <- 1
for (en in which(equals)) {
# NOTE: This is not bullet proof "a-1, a, a" will result in "a-1, a-1, a-2".
newName <- paste(signalNames[en], '-', suffix, sep='')
while (sum(signalNames == newName)) {
suffix <- suffix +1
newName <- paste(signalNames[en], '-', suffix, sep='')
}
signalNames[en] <- paste(signalNames[en], '-', suffix, sep='')
suffix <- suffix +1
}
}
}
# if + file get secondfraction start form first data record
hdr$startSecondFraction <- 0
if (hdr$isPlus) {
hdr$startSecondFraction <- getStartSecondFraction (hdr)
hdr$startTime <- hdr$startTime + hdr$startSecondFraction
}
row.names (hdr$sHeaders) <- signalNames
class (hdr$sHeaders) <- c("ebdfSHeaders", "data.frame")
# perform a consistency check
if (hdr$isPlus & !sum(hdr$sHeaders$isAnnotation)) cat ('ERROR: The annotation signal is missing.')
hdr
}
getStartSecondFraction <- function (hdr) {
StartSecondFraction <- 0
nAnnots <- sum (hdr$sHeaders$isAnnotation)
if (hdr$isPlus & nAnnots) {
annotations1 <- which.max (hdr$sHeaders$isAnnotation)
inFile <- file(hdr$fileName, "rb", encoding="UTF-16LE")
readBin (inFile, 'raw', n=hdr$headerLength , size=1)
samples <- readNextDataRecord (hdr, inFile)
StartSecondFraction <- getAnnoRecordStartRT (samples[[annotations1]]) # the subsecond start time is in the first TAL in the first annotation signal
close(inFile)
}
StartSecondFraction
}
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