Nothing
R/NiftiFunctions.R
In arfS4: Activated Region Fitting, fMRI data analysis.
# NIFTI/ANALYZE Function Library
# Wouter D. Weeda, University of Amsterdam
###############################################################################
readHeader <- function(fileinf) {
## readHeader reads nifti header info from nii,img,hdr and gzipped exts.
## input is an object of class nifti.fileinfo (containing only file path, location, extension, gzippedness and endianness)
## output is an object of class nifti.header (which inherits nifti.fileinfo and adds values from nifti header file)
#open new header headinf
headinf=new('nifti.header',fileinf)
#open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
con <- gzfile(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',.nifti.header.extension(headinf),'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',.nifti.header.extension(headinf),sep=''),open='rb')
}
#if connection is open try and read header info (magicstring and headersize)
if(con) {
readin <- function(con,headinf) {
#read in all elements (independent of NIFTI or ANALYZE), strings with nuls are truncated #byte offset, type, descr.
.nifti.header.sizeof_hdr(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) # 0, int32, MUST BE 348
.nifti.header.data_type(headinf) <- rawToChar(readBin(con,raw(),n=10)) # 4, char[10]
.nifti.header.db_name(headinf) <- rawToChar(readBin(con,raw(),n=18)) # 14, char[18]
.nifti.header.extents(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) # 32, int32
.nifti.header.session_error(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian =.nifti.header.endian(headinf)) # 36, short
.nifti.header.regular(headinf) <- rawToChar(readBin(con,raw(),n=1)) # 38, char[1]
.nifti.header.dim_info(headinf) <- rawToChar(readBin(con,raw(),n=1)) # 39, char[1], MRI SLICE ORDERING
.nifti.header.dims(headinf) <- readBin(con,integer(),n=8,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 40, short[8], DATA ARRAY DIMENSIONS
.nifti.header.intent_p1(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) # 56, float, 1ST INTENT PARAMETER
.nifti.header.intent_p2(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) # 60, float, 2ND INTENT PARAMETER
.nifti.header.intent_p3(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) # 64, float, 3RD INTENT PARAMETER
.nifti.header.intent_code(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 68, short, NIFITINTENT CODE
.nifti.header.datatype(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 70, short, DEFINES DATA TYPE
.nifti.header.bitpix(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 72, short, NUMBER BITS PER VOXEL
.nifti.header.slice_start(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 74, short, FIRST SLICE INDEX
.nifti.header.pixdim(headinf) <- readBin(con,double(),n=8,size=4,endian=.nifti.header.endian(headinf)) # 76, float[8], GRID SPACINGS
.nifti.header.vox_offset(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #108, float, OFFSET INTO .NII FILE
.nifti.header.scl_slope(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #112, float, DATA SCALING: SLOPE
.nifti.header.scl_inter(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #116, float, DATA SCALING: INTERCEPT
.nifti.header.slice_end (headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) #120, short, LAST SLICE INDEX
.nifti.header.slice_code(headinf) <- readBin(con,integer(),size=1,n=1,signed=T,endian=.nifti.header.endian(headinf)) #122, integer[1], SLICE TIMING ORDER
.nifti.header.xyzt_units(headinf) <- readBin(con,integer(),size=1,n=1,signed=T,endian=.nifti.header.endian(headinf)) #123, integer[1], UNITS OF PIXDIM
.nifti.header.cal_max(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #124, float, MAX DISPLAY INTENSITY
.nifti.header.cal_min(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #128, float, MIN DISPLAY INTENSITY
.nifti.header.slice_duration(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #132, float, TIME FOR 1 SLICE
.nifti.header.toffset(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #136, float, TIME AXIS SHIFT
.nifti.header.glmax(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) #140, int32
.nifti.header.glmin(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) #144, int32
.nifti.header.descrip(headinf) <- rawToChar(readBin(con,raw(),n=80)) #148, char[80], TEXT
.nifti.header.aux_file(headinf) <- rawToChar(readBin(con,raw(),n=24)) #228, char[24], AUXILIARY FILENAME
.nifti.header.qform_code(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) #252, short, NIFITXFORM CODE
.nifti.header.sform_code(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) #254, short, NIFITXFORM CODE
.nifti.header.quatern_b(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #256, float, QUATERNION B PARAM
.nifti.header.quatern_c(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #260, float, QUATERNION C PARAM
.nifti.header.quatern_d(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #264, float, QUATERNION D PARAM
.nifti.header.qoffset_x(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #268, float, QUATERNION X SHIFT
.nifti.header.qoffset_y(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #272, float, QUATERNION Y SHIFT
.nifti.header.qoffset_z(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #276, float, QUATERNION Z SHIFT
.nifti.header.srow_x(headinf) <- readBin(con,double(),n=4,size=4,endian=.nifti.header.endian(headinf)) #280, float[4], 1ST ROW AFFINE TRANSFORM
.nifti.header.srow_y(headinf) <- readBin(con,double(),n=4,size=4,endian=.nifti.header.endian(headinf)) #296, float[4], 2ND ROW AFFINE TRANSFORM
.nifti.header.srow_z(headinf) <- readBin(con,double(),n=4,size=4,endian=.nifti.header.endian(headinf)) #312, float[4], 3RD ROW AFFINE TRANSFORM
.nifti.header.intent_name(headinf) <- rawToChar(readBin(con,raw(),n=16)) #328, char[16], NAME OR MEANING OF DATA
.nifti.header.magic(headinf) <- rawToChar(readBin(con,raw(),n=4)) #344, char[4], MAGICSTRING!
#close connection
closeAllConnections()
#set fmri data attributes for read in
if(.nifti.header.datatype(headinf)==0) { .nifti.header.data.type(headinf)<-'none';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==1) { .nifti.header.data.type(headinf)<-'raw';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==2) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==4) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==8) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==16) { .nifti.header.data.type(headinf)<-'double';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==32) { .nifti.header.data.type(headinf)<-'complex';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==64) { .nifti.header.data.type(headinf)<-'double';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==256) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==512) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==768) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==1024) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==1280) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==1536) { .nifti.header.data.type(headinf)<-'double';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==1792) { .nifti.header.data.type(headinf)<-'complex';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==2048) { .nifti.header.data.type(headinf)(headinf)<-'complex';.nifti.header.data.signed(headinf)(headinf)<-TRUE } else { stop('Datatype is unknown!') }
return(headinf)
}
#Read in Data with warning suppression
headinf <- suppressWarnings(readin(con,headinf))
} else {
stop('Unable to open connection.\n')
}
#return nifti.header object
return(invisible(headinf))
}
readData <- function(filename) {
## readData reads in nifti/analyze datafiles
## input is a filename to read from
## output is vector of data
#obtain header info
headinf <- readHeader(getFileInfo(filename))
## set correct extension
if(.nifti.header.extension(headinf)=='hdr') extension='img' else extension <- .nifti.header.extension(headinf)
#open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
con <- gzfile(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,sep=''),open='rb')
}
if(con) {
#create new vecdat object
data <- new('fmri.data',headinf)
#set length of data to read in
n=(.nifti.header.dims(headinf)[2]*.nifti.header.dims(headinf)[3]*.nifti.header.dims(headinf)[4]*.nifti.header.dims(headinf)[5]*(.nifti.header.bitpix(headinf)/8))
#read everthing before vox_offset
readBin(con,raw(),.nifti.header.vox_offset(headinf))
#read in data
.fmri.data.datavec(data) <- readBin(con, what=.nifti.header.data.type(headinf), n=n, size=(.nifti.header.bitpix(headinf)/8), signed=.nifti.header.data.signed(headinf), endian=.nifti.header.endian(headinf))
#close connections
closeAllConnections()
#return datavector
return(invisible(data))
} else stop('Unable to open connection')
}
getFileInfo <- function(filename) {
## getFileInfo sets file information (file path, location, extension, gzippedness and endianness)
## also changes to .hdr if a .img is called (and checks if img/hdr pairs exist)
## input is a filename (fullpath + name)
## outputs an object of class nifti.header
## calls readHeader to check nifti/analyze values
#check if file exists
if(!file.exists(filename)) stop(paste('File',filename,'does noet exist!'))
#create new instance of class fileinfo
fileinf=new('nifti.fileinfo')
#split filename into path, name and extensions
fsplit=strsplit(tolower(filename),'\\.')[[1]]
fname=strsplit(fsplit[1],.Platform$file.sep)[[1]]
#set filename and path
.nifti.fileinfo.filename(fileinf) <- fname[length(fname)]
.nifti.fileinfo.fullpath(fileinf) <- gsub(.nifti.fileinfo.filename(fileinf),'',fsplit[1])
#check gzippedness and set extension
if(fsplit[length(fsplit)]=='gz') {
.nifti.fileinfo.gzipped(fileinf) <- TRUE
.nifti.fileinfo.extension(fileinf) <- fsplit[length(fsplit)-1]
} else {
.nifti.fileinfo.gzipped(fileinf) <- FALSE
.nifti.fileinfo.extension(fileinf) <- fsplit[length(fsplit)]
}
#check valid files if img/hdr pair and if IMG try and open header
if(.nifti.fileinfo.extension(fileinf)=='img') {
if(.nifti.fileinfo.gzipped(fileinf)==TRUE) {
if(file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.hdr.gz',sep=''))) {
.nifti.fileinfo.extension(fileinf) <- 'hdr'
} else {
stop('No valid img/hdr pair found. HDR does not exist.\n')
}
} else {
if(file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.hdr',sep=''))) {
.nifti.fileinfo.extension(fileinf) <- 'hdr'
} else {
stop('No valid img/hdr pair found. HDR does not exist.\n')
}
}
}
if(.nifti.fileinfo.extension(fileinf)=='hdr') {
if(.nifti.fileinfo.gzipped(fileinf)==TRUE) {
if(!file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.img.gz',sep=''))) stop('No valid img/hdr pair found. IMG does not exist.\n')
} else {
if(!file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.img',sep=''))) stop('No valid img/hdr pair found. IMG does noet exist.\n')
}
}
#check nifti header. Returns fileinf of class nifti.header
headinfo=readHeader(fileinf)
#check if header size is 348 (if not try other endian)
if(.nifti.header.sizeof_hdr(headinfo)!=348) {
#change endian
if(.nifti.fileinfo.endian(fileinf)=='big') .nifti.fileinfo.endian(fileinf) <- 'little' else .nifti.fileinfo.endian(fileinf) <- 'big'
#check header again
headinfo=readHeader(fileinf)
if(.nifti.header.sizeof_hdr(headinfo)!=348) {
#header is of incorrect size
stop('Header is not of size 348 (even after swapping endian). File might not be of the correct format.\n')
}
}
#set filetype according to header info (not based on extension)
if(.nifti.header.magic(headinfo)=='n+1') {
.nifti.header.filetype(headinfo) <- 'nifti+1'
} else if(.nifti.header.magic(headinfo)=='ni1') {
.nifti.header.filetype(headinfo) <- 'nifti1'
} else if(.nifti.header.magic(headinfo)=='') {
.nifti.header.filetype(headinfo) <- 'analyze'
} else {
stop('Magicstring contains unknown characters. File might not be the correct format.\n')
}
#Returns object of class nifti.header
return(invisible(headinfo))
}
writeHeaderPart <- function(con,headinf) {
## writeHeaderPart writes nifti/analyze headerfiles
## input is connection,headerinfo,and datavec
## output is connection
#if connection is open try and read header info (magicstring and headersize)
if(con) {
#write all elements (independent of NIFTI or ANALYZE), watch String Truncation #byte offset, type, descr.
writeBin(as.integer(.nifti.header.sizeof_hdr(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 0, int32, MUST BE 348
writeBin(charToRaw(.nifti.header.data_type(headinf)),con,endian=.nifti.header.endian(headinf)) # 4, char[10]
writeBin(raw(10-nchar(.nifti.header.data_type(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.db_name(headinf)),con,endian=.nifti.header.endian(headinf)) # 14, char[18]
writeBin(raw(18-nchar(.nifti.header.db_name(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(as.integer(.nifti.header.extents(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 32, int32
writeBin(as.integer(.nifti.header.session_error(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 36, short
writeBin(charToRaw(.nifti.header.regular(headinf)),con,endian=.nifti.header.endian(headinf)) # 38, char[1]
writeBin(raw(1-nchar(.nifti.header.regular(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.dim_info(headinf)),con,endian=.nifti.header.endian(headinf)) # 39, char[1], MRI SLICE ORDERING
writeBin(raw(1-nchar(.nifti.header.dim_info(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(as.integer(.nifti.header.dims(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 40, short[8], DATA ARRAY DIMENSIONS
writeBin(as.double(.nifti.header.intent_p1(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 56, float, 1ST INTENT PARAMETER
writeBin(as.double(.nifti.header.intent_p2(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 60, float, 2ND INTENT PARAMETER
writeBin(as.double(.nifti.header.intent_p3(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 64, float, 3RD INTENT PARAMETER
writeBin(as.integer(.nifti.header.intent_code(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 68, short, NIFITINTENT CODE
writeBin(as.integer(.nifti.header.datatype(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 70, short, DEFINES DATA TYPE
writeBin(as.integer(.nifti.header.bitpix(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 72, short, NUMBER BITS PER VOXEL
writeBin(as.integer(.nifti.header.slice_start(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 74, short, FIRST SLICE INDEX
writeBin(as.double(.nifti.header.pixdim(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 76, float[8], GRID SPACINGS
writeBin(as.double(.nifti.header.vox_offset(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #108, float, OFFSET INTO .NII FILE
writeBin(as.double(.nifti.header.scl_slope(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #112, float, DATA SCALING: SLOPE
writeBin(as.double(.nifti.header.scl_inter(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #116, float, DATA SCALING: INTERCEPT
writeBin(as.integer(.nifti.header.slice_end (headinf)),con,size=2,endian=.nifti.header.endian(headinf)) #120, short, LAST SLICE INDEX
writeBin(as.integer(.nifti.header.slice_code(headinf)),con,size=1,endian=.nifti.header.endian(headinf)) #122, integer[1], SLICE TIMING ORDER
writeBin(as.integer(.nifti.header.xyzt_units(headinf)),con,size=1,endian=.nifti.header.endian(headinf)) #123, integer[1], UNITS OF PIXDIM
writeBin(as.double(.nifti.header.cal_max(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #124, float, MAX DISPLAY INTENSITY
writeBin(as.double(.nifti.header.cal_min(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #128, float, MIN DISPLAY INTENSITY
writeBin(as.double(.nifti.header.slice_duration(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #132, float, TIME FOR 1 SLICE
writeBin(as.double(.nifti.header.toffset(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #136, float, TIME AXIS SHIFT
writeBin(as.integer(.nifti.header.glmax(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #140, int32
writeBin(as.integer(.nifti.header.glmin(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #144, int32
writeBin(charToRaw(.nifti.header.descrip(headinf)),con,endian=.nifti.header.endian(headinf)) #148, char[80], TEXT
writeBin(raw(80-nchar(.nifti.header.descrip(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.aux_file(headinf)),con,endian=.nifti.header.endian(headinf)) #228, char[24], AUXILIARY FILENAME
writeBin(raw(24-nchar(.nifti.header.aux_file(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(as.integer(.nifti.header.qform_code(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) #252, short, NIFITXFORM CODE
writeBin(as.integer(.nifti.header.sform_code(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) #254, short, NIFITXFORM CODE
writeBin(as.double(.nifti.header.quatern_b(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #256, float, QUATERNION B PARAM
writeBin(as.double(.nifti.header.quatern_c(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #260, float, QUATERNION C PARAM
writeBin(as.double(.nifti.header.quatern_d(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #264, float, QUATERNION D PARAM
writeBin(as.double(.nifti.header.qoffset_x(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #268, float, QUATERNION X SHIFT
writeBin(as.double(.nifti.header.qoffset_y(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #272, float, QUATERNION Y SHIFT
writeBin(as.double(.nifti.header.qoffset_z(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #276, float, QUATERNION Z SHIFT
writeBin(as.double(.nifti.header.srow_x(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #280, float[4], 1ST ROW AFFINE TRANSFORM
writeBin(as.double(.nifti.header.srow_y(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #296, float[4], 2ND ROW AFFINE TRANSFORM
writeBin(as.double(.nifti.header.srow_z(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #312, float[4], 3RD ROW AFFINE TRANSFORM
writeBin(charToRaw(.nifti.header.intent_name(headinf)),con,endian=.nifti.header.endian(headinf)) #328, char[16], NAME OR MEANING OF DATA
writeBin(raw(16-nchar(.nifti.header.intent_name(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.magic(headinf)),con,endian=.nifti.header.endian(headinf)) #344, char[4], MAGICSTRING!
writeBin(raw(4-nchar(.nifti.header.magic(headinf))),con,endian=.nifti.header.endian(headinf))
if(.nifti.header.vox_offset(headinf)>348) for(i in 1:(.nifti.header.vox_offset(headinf)-348)) writeBin(as.integer(0),size=1,con,endian=.nifti.header.endian(headinf))
} else {
stop('Unable to open connection.\n')
}
#return nifti.header object
return(con)
}
writeDataPart <- function(con,headinf,datavec) {
## writeDataPart writes nifti/analyze datafiles
## input is connection,headerinfo,and datavec
## output is connection
#write data to connection
if(con) {
mode(datavec) <- .nifti.header.data.type(headinf)
writeBin(datavec,con,size=(.nifti.header.bitpix(headinf)/8))
} else stop('Unable to open connection')
#return TRUE
return(con)
}
writeHeader <- function(headinf) {
##writeHeader writes header info to a .hdr file
## input is headerinfo
## output is logical
## set correct extension
if(.nifti.header.extension(headinf)=='img') extension='hdr' else extension <- .nifti.header.extension(headinf)
## open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
fn <- paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
## write to .hdr file
if(extension=='hdr') con <- writeHeaderPart(con,headinf) else warning('Header info can only be written to .hdr files! No header info is written!')
close(con)
return(TRUE)
}
writeData <- function(headinf,datavec) {
## writeData writes both Header and Data info to a file
## input is headerinfo and datavector
## output is logical
# set correct extension
if(.nifti.header.extension(headinf)=='hdr') extension='img' else extension <- .nifti.header.extension(headinf)
#open files based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
fn <- paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
# for nii files write header and data in one connection
if(extension=='nii') {
con <- writeHeaderPart(con,headinf)
con <- writeDataPart(con,headinf,datavec)
}
# for img/hdr pairs write header to .hdr and data to .img
if(extension=='img') {
writeHeader(headinf)
con <- writeDataPart(con,headinf,datavec)
}
#close connection
close(con)
return(TRUE)
}
newFile <- function(filename,templateHDR) {
##newFile creates a new file of the given filename (and directories it should be in if they not exist)
## input is a filename (full) and template headerinfo
## output is headerInfo of the newly created file
#split filename into path, name and extensions
fsplit=strsplit(tolower(filename),'\\.')[[1]]
fname=strsplit(fsplit[1],'/')[[1]]
#set filename and path
.nifti.header.filename(templateHDR) <- fname[length(fname)]
.nifti.header.fullpath(templateHDR) <- gsub(.nifti.header.filename(templateHDR),'',fsplit[1])
#check gzippedness and set extension
if(fsplit[length(fsplit)]=='gz') {
.nifti.header.gzipped(templateHDR) <- TRUE
.nifti.header.extension(templateHDR) <- fsplit[length(fsplit)-1]
} else {
.nifti.header.gzipped(templateHDR) <- FALSE
.nifti.header.extension(templateHDR) <- fsplit[length(fsplit)]
}
#create dirs if necessary
if(!file.exists(.nifti.header.fullpath(templateHDR))) dir.create(.nifti.header.fullpath(templateHDR))
# warn if file already exists
#if(file.exists(filename)) warning(paste('File',.nifti.header.filename(templateHDR),'already exists, overwriting.'))
# if nii, create one file
if(.nifti.header.extension(templateHDR)=='nii') {
file.create(filename)
}
# if img/hdr create two files
if(.nifti.header.extension(templateHDR)=='img' | .nifti.header.extension(templateHDR)=='hdr') {
if(.nifti.header.gzipped(templateHDR)==TRUE) {
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.hdr.gz',sep=''))
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.img.gz',sep=''))
}
if(.nifti.header.gzipped(templateHDR)==FALSE) {
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.hdr',sep=''))
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.img',sep=''))
}
}
# return header info object for created file
return(templateHDR)
}
Try the arfS4 package in your browser
Any scripts or data that you put into this service are public.
arfS4 documentation built on May 2, 2019, 6:14 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# NIFTI/ANALYZE Function Library
# Wouter D. Weeda, University of Amsterdam
###############################################################################
readHeader <- function(fileinf) {
## readHeader reads nifti header info from nii,img,hdr and gzipped exts.
## input is an object of class nifti.fileinfo (containing only file path, location, extension, gzippedness and endianness)
## output is an object of class nifti.header (which inherits nifti.fileinfo and adds values from nifti header file)
#open new header headinf
headinf=new('nifti.header',fileinf)
#open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
con <- gzfile(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',.nifti.header.extension(headinf),'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',.nifti.header.extension(headinf),sep=''),open='rb')
}
#if connection is open try and read header info (magicstring and headersize)
if(con) {
readin <- function(con,headinf) {
#read in all elements (independent of NIFTI or ANALYZE), strings with nuls are truncated #byte offset, type, descr.
.nifti.header.sizeof_hdr(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) # 0, int32, MUST BE 348
.nifti.header.data_type(headinf) <- rawToChar(readBin(con,raw(),n=10)) # 4, char[10]
.nifti.header.db_name(headinf) <- rawToChar(readBin(con,raw(),n=18)) # 14, char[18]
.nifti.header.extents(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) # 32, int32
.nifti.header.session_error(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian =.nifti.header.endian(headinf)) # 36, short
.nifti.header.regular(headinf) <- rawToChar(readBin(con,raw(),n=1)) # 38, char[1]
.nifti.header.dim_info(headinf) <- rawToChar(readBin(con,raw(),n=1)) # 39, char[1], MRI SLICE ORDERING
.nifti.header.dims(headinf) <- readBin(con,integer(),n=8,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 40, short[8], DATA ARRAY DIMENSIONS
.nifti.header.intent_p1(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) # 56, float, 1ST INTENT PARAMETER
.nifti.header.intent_p2(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) # 60, float, 2ND INTENT PARAMETER
.nifti.header.intent_p3(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) # 64, float, 3RD INTENT PARAMETER
.nifti.header.intent_code(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 68, short, NIFITINTENT CODE
.nifti.header.datatype(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 70, short, DEFINES DATA TYPE
.nifti.header.bitpix(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 72, short, NUMBER BITS PER VOXEL
.nifti.header.slice_start(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) # 74, short, FIRST SLICE INDEX
.nifti.header.pixdim(headinf) <- readBin(con,double(),n=8,size=4,endian=.nifti.header.endian(headinf)) # 76, float[8], GRID SPACINGS
.nifti.header.vox_offset(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #108, float, OFFSET INTO .NII FILE
.nifti.header.scl_slope(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #112, float, DATA SCALING: SLOPE
.nifti.header.scl_inter(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #116, float, DATA SCALING: INTERCEPT
.nifti.header.slice_end (headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) #120, short, LAST SLICE INDEX
.nifti.header.slice_code(headinf) <- readBin(con,integer(),size=1,n=1,signed=T,endian=.nifti.header.endian(headinf)) #122, integer[1], SLICE TIMING ORDER
.nifti.header.xyzt_units(headinf) <- readBin(con,integer(),size=1,n=1,signed=T,endian=.nifti.header.endian(headinf)) #123, integer[1], UNITS OF PIXDIM
.nifti.header.cal_max(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #124, float, MAX DISPLAY INTENSITY
.nifti.header.cal_min(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #128, float, MIN DISPLAY INTENSITY
.nifti.header.slice_duration(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #132, float, TIME FOR 1 SLICE
.nifti.header.toffset(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #136, float, TIME AXIS SHIFT
.nifti.header.glmax(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) #140, int32
.nifti.header.glmin(headinf) <- readBin(con,integer(),n=1,size=4,signed=T,endian=.nifti.header.endian(headinf)) #144, int32
.nifti.header.descrip(headinf) <- rawToChar(readBin(con,raw(),n=80)) #148, char[80], TEXT
.nifti.header.aux_file(headinf) <- rawToChar(readBin(con,raw(),n=24)) #228, char[24], AUXILIARY FILENAME
.nifti.header.qform_code(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) #252, short, NIFITXFORM CODE
.nifti.header.sform_code(headinf) <- readBin(con,integer(),n=1,size=2,signed=T,endian=.nifti.header.endian(headinf)) #254, short, NIFITXFORM CODE
.nifti.header.quatern_b(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #256, float, QUATERNION B PARAM
.nifti.header.quatern_c(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #260, float, QUATERNION C PARAM
.nifti.header.quatern_d(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #264, float, QUATERNION D PARAM
.nifti.header.qoffset_x(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #268, float, QUATERNION X SHIFT
.nifti.header.qoffset_y(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #272, float, QUATERNION Y SHIFT
.nifti.header.qoffset_z(headinf) <- readBin(con,double(),n=1,size=4,endian=.nifti.header.endian(headinf)) #276, float, QUATERNION Z SHIFT
.nifti.header.srow_x(headinf) <- readBin(con,double(),n=4,size=4,endian=.nifti.header.endian(headinf)) #280, float[4], 1ST ROW AFFINE TRANSFORM
.nifti.header.srow_y(headinf) <- readBin(con,double(),n=4,size=4,endian=.nifti.header.endian(headinf)) #296, float[4], 2ND ROW AFFINE TRANSFORM
.nifti.header.srow_z(headinf) <- readBin(con,double(),n=4,size=4,endian=.nifti.header.endian(headinf)) #312, float[4], 3RD ROW AFFINE TRANSFORM
.nifti.header.intent_name(headinf) <- rawToChar(readBin(con,raw(),n=16)) #328, char[16], NAME OR MEANING OF DATA
.nifti.header.magic(headinf) <- rawToChar(readBin(con,raw(),n=4)) #344, char[4], MAGICSTRING!
#close connection
closeAllConnections()
#set fmri data attributes for read in
if(.nifti.header.datatype(headinf)==0) { .nifti.header.data.type(headinf)<-'none';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==1) { .nifti.header.data.type(headinf)<-'raw';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==2) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==4) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==8) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==16) { .nifti.header.data.type(headinf)<-'double';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==32) { .nifti.header.data.type(headinf)<-'complex';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==64) { .nifti.header.data.type(headinf)<-'double';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==256) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==512) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==768) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==1024) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==1280) { .nifti.header.data.type(headinf)<-'integer';.nifti.header.data.signed(headinf)<-FALSE } else
if(.nifti.header.datatype(headinf)==1536) { .nifti.header.data.type(headinf)<-'double';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==1792) { .nifti.header.data.type(headinf)<-'complex';.nifti.header.data.signed(headinf)<-TRUE } else
if(.nifti.header.datatype(headinf)==2048) { .nifti.header.data.type(headinf)(headinf)<-'complex';.nifti.header.data.signed(headinf)(headinf)<-TRUE } else { stop('Datatype is unknown!') }
return(headinf)
}
#Read in Data with warning suppression
headinf <- suppressWarnings(readin(con,headinf))
} else {
stop('Unable to open connection.\n')
}
#return nifti.header object
return(invisible(headinf))
}
readData <- function(filename) {
## readData reads in nifti/analyze datafiles
## input is a filename to read from
## output is vector of data
#obtain header info
headinf <- readHeader(getFileInfo(filename))
## set correct extension
if(.nifti.header.extension(headinf)=='hdr') extension='img' else extension <- .nifti.header.extension(headinf)
#open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
con <- gzfile(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,sep=''),open='rb')
}
if(con) {
#create new vecdat object
data <- new('fmri.data',headinf)
#set length of data to read in
n=(.nifti.header.dims(headinf)[2]*.nifti.header.dims(headinf)[3]*.nifti.header.dims(headinf)[4]*.nifti.header.dims(headinf)[5]*(.nifti.header.bitpix(headinf)/8))
#read everthing before vox_offset
readBin(con,raw(),.nifti.header.vox_offset(headinf))
#read in data
.fmri.data.datavec(data) <- readBin(con, what=.nifti.header.data.type(headinf), n=n, size=(.nifti.header.bitpix(headinf)/8), signed=.nifti.header.data.signed(headinf), endian=.nifti.header.endian(headinf))
#close connections
closeAllConnections()
#return datavector
return(invisible(data))
} else stop('Unable to open connection')
}
getFileInfo <- function(filename) {
## getFileInfo sets file information (file path, location, extension, gzippedness and endianness)
## also changes to .hdr if a .img is called (and checks if img/hdr pairs exist)
## input is a filename (fullpath + name)
## outputs an object of class nifti.header
## calls readHeader to check nifti/analyze values
#check if file exists
if(!file.exists(filename)) stop(paste('File',filename,'does noet exist!'))
#create new instance of class fileinfo
fileinf=new('nifti.fileinfo')
#split filename into path, name and extensions
fsplit=strsplit(tolower(filename),'\\.')[[1]]
fname=strsplit(fsplit[1],.Platform$file.sep)[[1]]
#set filename and path
.nifti.fileinfo.filename(fileinf) <- fname[length(fname)]
.nifti.fileinfo.fullpath(fileinf) <- gsub(.nifti.fileinfo.filename(fileinf),'',fsplit[1])
#check gzippedness and set extension
if(fsplit[length(fsplit)]=='gz') {
.nifti.fileinfo.gzipped(fileinf) <- TRUE
.nifti.fileinfo.extension(fileinf) <- fsplit[length(fsplit)-1]
} else {
.nifti.fileinfo.gzipped(fileinf) <- FALSE
.nifti.fileinfo.extension(fileinf) <- fsplit[length(fsplit)]
}
#check valid files if img/hdr pair and if IMG try and open header
if(.nifti.fileinfo.extension(fileinf)=='img') {
if(.nifti.fileinfo.gzipped(fileinf)==TRUE) {
if(file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.hdr.gz',sep=''))) {
.nifti.fileinfo.extension(fileinf) <- 'hdr'
} else {
stop('No valid img/hdr pair found. HDR does not exist.\n')
}
} else {
if(file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.hdr',sep=''))) {
.nifti.fileinfo.extension(fileinf) <- 'hdr'
} else {
stop('No valid img/hdr pair found. HDR does not exist.\n')
}
}
}
if(.nifti.fileinfo.extension(fileinf)=='hdr') {
if(.nifti.fileinfo.gzipped(fileinf)==TRUE) {
if(!file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.img.gz',sep=''))) stop('No valid img/hdr pair found. IMG does not exist.\n')
} else {
if(!file.exists(paste(.nifti.fileinfo.fullpath(fileinf),.nifti.fileinfo.filename(fileinf),'.img',sep=''))) stop('No valid img/hdr pair found. IMG does noet exist.\n')
}
}
#check nifti header. Returns fileinf of class nifti.header
headinfo=readHeader(fileinf)
#check if header size is 348 (if not try other endian)
if(.nifti.header.sizeof_hdr(headinfo)!=348) {
#change endian
if(.nifti.fileinfo.endian(fileinf)=='big') .nifti.fileinfo.endian(fileinf) <- 'little' else .nifti.fileinfo.endian(fileinf) <- 'big'
#check header again
headinfo=readHeader(fileinf)
if(.nifti.header.sizeof_hdr(headinfo)!=348) {
#header is of incorrect size
stop('Header is not of size 348 (even after swapping endian). File might not be of the correct format.\n')
}
}
#set filetype according to header info (not based on extension)
if(.nifti.header.magic(headinfo)=='n+1') {
.nifti.header.filetype(headinfo) <- 'nifti+1'
} else if(.nifti.header.magic(headinfo)=='ni1') {
.nifti.header.filetype(headinfo) <- 'nifti1'
} else if(.nifti.header.magic(headinfo)=='') {
.nifti.header.filetype(headinfo) <- 'analyze'
} else {
stop('Magicstring contains unknown characters. File might not be the correct format.\n')
}
#Returns object of class nifti.header
return(invisible(headinfo))
}
writeHeaderPart <- function(con,headinf) {
## writeHeaderPart writes nifti/analyze headerfiles
## input is connection,headerinfo,and datavec
## output is connection
#if connection is open try and read header info (magicstring and headersize)
if(con) {
#write all elements (independent of NIFTI or ANALYZE), watch String Truncation #byte offset, type, descr.
writeBin(as.integer(.nifti.header.sizeof_hdr(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 0, int32, MUST BE 348
writeBin(charToRaw(.nifti.header.data_type(headinf)),con,endian=.nifti.header.endian(headinf)) # 4, char[10]
writeBin(raw(10-nchar(.nifti.header.data_type(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.db_name(headinf)),con,endian=.nifti.header.endian(headinf)) # 14, char[18]
writeBin(raw(18-nchar(.nifti.header.db_name(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(as.integer(.nifti.header.extents(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 32, int32
writeBin(as.integer(.nifti.header.session_error(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 36, short
writeBin(charToRaw(.nifti.header.regular(headinf)),con,endian=.nifti.header.endian(headinf)) # 38, char[1]
writeBin(raw(1-nchar(.nifti.header.regular(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.dim_info(headinf)),con,endian=.nifti.header.endian(headinf)) # 39, char[1], MRI SLICE ORDERING
writeBin(raw(1-nchar(.nifti.header.dim_info(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(as.integer(.nifti.header.dims(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 40, short[8], DATA ARRAY DIMENSIONS
writeBin(as.double(.nifti.header.intent_p1(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 56, float, 1ST INTENT PARAMETER
writeBin(as.double(.nifti.header.intent_p2(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 60, float, 2ND INTENT PARAMETER
writeBin(as.double(.nifti.header.intent_p3(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 64, float, 3RD INTENT PARAMETER
writeBin(as.integer(.nifti.header.intent_code(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 68, short, NIFITINTENT CODE
writeBin(as.integer(.nifti.header.datatype(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 70, short, DEFINES DATA TYPE
writeBin(as.integer(.nifti.header.bitpix(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 72, short, NUMBER BITS PER VOXEL
writeBin(as.integer(.nifti.header.slice_start(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) # 74, short, FIRST SLICE INDEX
writeBin(as.double(.nifti.header.pixdim(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) # 76, float[8], GRID SPACINGS
writeBin(as.double(.nifti.header.vox_offset(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #108, float, OFFSET INTO .NII FILE
writeBin(as.double(.nifti.header.scl_slope(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #112, float, DATA SCALING: SLOPE
writeBin(as.double(.nifti.header.scl_inter(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #116, float, DATA SCALING: INTERCEPT
writeBin(as.integer(.nifti.header.slice_end (headinf)),con,size=2,endian=.nifti.header.endian(headinf)) #120, short, LAST SLICE INDEX
writeBin(as.integer(.nifti.header.slice_code(headinf)),con,size=1,endian=.nifti.header.endian(headinf)) #122, integer[1], SLICE TIMING ORDER
writeBin(as.integer(.nifti.header.xyzt_units(headinf)),con,size=1,endian=.nifti.header.endian(headinf)) #123, integer[1], UNITS OF PIXDIM
writeBin(as.double(.nifti.header.cal_max(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #124, float, MAX DISPLAY INTENSITY
writeBin(as.double(.nifti.header.cal_min(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #128, float, MIN DISPLAY INTENSITY
writeBin(as.double(.nifti.header.slice_duration(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #132, float, TIME FOR 1 SLICE
writeBin(as.double(.nifti.header.toffset(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #136, float, TIME AXIS SHIFT
writeBin(as.integer(.nifti.header.glmax(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #140, int32
writeBin(as.integer(.nifti.header.glmin(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #144, int32
writeBin(charToRaw(.nifti.header.descrip(headinf)),con,endian=.nifti.header.endian(headinf)) #148, char[80], TEXT
writeBin(raw(80-nchar(.nifti.header.descrip(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.aux_file(headinf)),con,endian=.nifti.header.endian(headinf)) #228, char[24], AUXILIARY FILENAME
writeBin(raw(24-nchar(.nifti.header.aux_file(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(as.integer(.nifti.header.qform_code(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) #252, short, NIFITXFORM CODE
writeBin(as.integer(.nifti.header.sform_code(headinf)),con,size=2,endian=.nifti.header.endian(headinf)) #254, short, NIFITXFORM CODE
writeBin(as.double(.nifti.header.quatern_b(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #256, float, QUATERNION B PARAM
writeBin(as.double(.nifti.header.quatern_c(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #260, float, QUATERNION C PARAM
writeBin(as.double(.nifti.header.quatern_d(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #264, float, QUATERNION D PARAM
writeBin(as.double(.nifti.header.qoffset_x(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #268, float, QUATERNION X SHIFT
writeBin(as.double(.nifti.header.qoffset_y(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #272, float, QUATERNION Y SHIFT
writeBin(as.double(.nifti.header.qoffset_z(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #276, float, QUATERNION Z SHIFT
writeBin(as.double(.nifti.header.srow_x(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #280, float[4], 1ST ROW AFFINE TRANSFORM
writeBin(as.double(.nifti.header.srow_y(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #296, float[4], 2ND ROW AFFINE TRANSFORM
writeBin(as.double(.nifti.header.srow_z(headinf)),con,size=4,endian=.nifti.header.endian(headinf)) #312, float[4], 3RD ROW AFFINE TRANSFORM
writeBin(charToRaw(.nifti.header.intent_name(headinf)),con,endian=.nifti.header.endian(headinf)) #328, char[16], NAME OR MEANING OF DATA
writeBin(raw(16-nchar(.nifti.header.intent_name(headinf))),con,endian=.nifti.header.endian(headinf))
writeBin(charToRaw(.nifti.header.magic(headinf)),con,endian=.nifti.header.endian(headinf)) #344, char[4], MAGICSTRING!
writeBin(raw(4-nchar(.nifti.header.magic(headinf))),con,endian=.nifti.header.endian(headinf))
if(.nifti.header.vox_offset(headinf)>348) for(i in 1:(.nifti.header.vox_offset(headinf)-348)) writeBin(as.integer(0),size=1,con,endian=.nifti.header.endian(headinf))
} else {
stop('Unable to open connection.\n')
}
#return nifti.header object
return(con)
}
writeDataPart <- function(con,headinf,datavec) {
## writeDataPart writes nifti/analyze datafiles
## input is connection,headerinfo,and datavec
## output is connection
#write data to connection
if(con) {
mode(datavec) <- .nifti.header.data.type(headinf)
writeBin(datavec,con,size=(.nifti.header.bitpix(headinf)/8))
} else stop('Unable to open connection')
#return TRUE
return(con)
}
writeHeader <- function(headinf) {
##writeHeader writes header info to a .hdr file
## input is headerinfo
## output is logical
## set correct extension
if(.nifti.header.extension(headinf)=='img') extension='hdr' else extension <- .nifti.header.extension(headinf)
## open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
fn <- paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
## write to .hdr file
if(extension=='hdr') con <- writeHeaderPart(con,headinf) else warning('Header info can only be written to .hdr files! No header info is written!')
close(con)
return(TRUE)
}
writeData <- function(headinf,datavec) {
## writeData writes both Header and Data info to a file
## input is headerinfo and datavector
## output is logical
# set correct extension
if(.nifti.header.extension(headinf)=='hdr') extension='img' else extension <- .nifti.header.extension(headinf)
#open files based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
fn <- paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
# for nii files write header and data in one connection
if(extension=='nii') {
con <- writeHeaderPart(con,headinf)
con <- writeDataPart(con,headinf,datavec)
}
# for img/hdr pairs write header to .hdr and data to .img
if(extension=='img') {
writeHeader(headinf)
con <- writeDataPart(con,headinf,datavec)
}
#close connection
close(con)
return(TRUE)
}
newFile <- function(filename,templateHDR) {
##newFile creates a new file of the given filename (and directories it should be in if they not exist)
## input is a filename (full) and template headerinfo
## output is headerInfo of the newly created file
#split filename into path, name and extensions
fsplit=strsplit(tolower(filename),'\\.')[[1]]
fname=strsplit(fsplit[1],'/')[[1]]
#set filename and path
.nifti.header.filename(templateHDR) <- fname[length(fname)]
.nifti.header.fullpath(templateHDR) <- gsub(.nifti.header.filename(templateHDR),'',fsplit[1])
#check gzippedness and set extension
if(fsplit[length(fsplit)]=='gz') {
.nifti.header.gzipped(templateHDR) <- TRUE
.nifti.header.extension(templateHDR) <- fsplit[length(fsplit)-1]
} else {
.nifti.header.gzipped(templateHDR) <- FALSE
.nifti.header.extension(templateHDR) <- fsplit[length(fsplit)]
}
#create dirs if necessary
if(!file.exists(.nifti.header.fullpath(templateHDR))) dir.create(.nifti.header.fullpath(templateHDR))
# warn if file already exists
#if(file.exists(filename)) warning(paste('File',.nifti.header.filename(templateHDR),'already exists, overwriting.'))
# if nii, create one file
if(.nifti.header.extension(templateHDR)=='nii') {
file.create(filename)
}
# if img/hdr create two files
if(.nifti.header.extension(templateHDR)=='img' | .nifti.header.extension(templateHDR)=='hdr') {
if(.nifti.header.gzipped(templateHDR)==TRUE) {
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.hdr.gz',sep=''))
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.img.gz',sep=''))
}
if(.nifti.header.gzipped(templateHDR)==FALSE) {
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.hdr',sep=''))
file.create(paste(.nifti.header.fullpath(templateHDR),.nifti.header.filename(templateHDR),'.img',sep=''))
}
}
# return header info object for created file
return(templateHDR)
}
Try the arfS4 package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.