Nothing
R/niftiFunctions.R
In arf3DS4: Activated Region Fitting, fMRI data analysis (3D).
Defines functions
getFileInfo
newFile
readHeader
readData
writeHeader
writeData
writeHeaderPart
writeDataPart
headToName
getIntent
fmri2array
bin2dec
xyzt2char
removeNullString
Documented in
fmri2array
readData
writeData
#############################################
# arf3DS4 S4 NIFTI FUNCTIONS #
# Wouter D. Weeda #
# University of Amsterdam #
#############################################
#[CONTAINS]
#getFileInfo
#newFile
#readHeader
#readData [user]
#writeHeader
#writeData [user]
#writeHeaderPart
#writeDataPart
#headToName
#getIntent
#fmri2array [user]
#bin2dec
#xyzt2char
getFileInfo <-
function(filename)
# getFileInfo sets file information (file path, location, extension, gzippedness and endianness)
{
#set separator
sp <- .Platform$file.sep
#check if only file else pre-append working directory
if(length(grep(sp,filename))==0) filename <- paste(getwd(),sp,filename,sep='')
#check if file exists
if(!file.exists(filename)) stop(paste('[getFileInfo] File',filename,'does noet exist!'))
#create new instance of class fileinfo
fileinf=new('nifti.fileinfo')
#split filename into path, name and extensions
fn <- strsplit(filename,sp)[[1]][length(strsplit(filename,sp)[[1]])]
#fsplit_name <- strsplit(tolower(fn),'\\.')[[1]]
fsplit_name <- strsplit(fn,'\\.')[[1]]
fsplit_path <- gsub(paste(sp,fn,sep=''),'',filename)
fname <- strsplit(fsplit_name[1],.Platform$file.sep)[[1]]
#set filename and path
.nifti.fileinfo.filename(fileinf) <- fname[length(fname)]
.nifti.fileinfo.fullpath(fileinf) <- fsplit_path
#check gzippedness and set extension
if(fsplit_name[length(fsplit_name)]=='gz') {
.nifti.fileinfo.gzipped(fileinf) <- TRUE
.nifti.fileinfo.extension(fileinf) <- fsplit_name[length(fsplit_name)-1]
} else {
.nifti.fileinfo.gzipped(fileinf) <- FALSE
.nifti.fileinfo.extension(fileinf) <- fsplit_name[length(fsplit_name)]
}
#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),sp,.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),sp,.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),sp,.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),sp,.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))
}
newFile <-
function(filename,templateHDR)
#set header info accordomg to a templateHeader
{
##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
sp <- .Platform$file.sep
#split filename into path, name and extensions
fn <- strsplit(filename,sp)[[1]][length(strsplit(filename,sp)[[1]])]
#fsplit_name <- strsplit(tolower(fn),'\\.')[[1]]
fsplit_name <- strsplit(fn,'\\.')[[1]]
fsplit_path <- gsub(paste(sp,fn,sep=''),'',filename)
fname <- strsplit(fsplit_name[1],.Platform$file.sep)[[1]]
#set filename and path
.nifti.header.filename(templateHDR) <- fname[length(fname)]
.nifti.header.fullpath(templateHDR) <- fsplit_path
#check gzippedness and set extension
if(fsplit_name[length(fsplit_name)]=='gz') {
.nifti.header.gzipped(templateHDR) <- TRUE
.nifti.header.extension(templateHDR) <- fsplit_name[length(fsplit_name)-1]
} else {
.nifti.header.gzipped(templateHDR) <- FALSE
.nifti.header.extension(templateHDR) <- fsplit_name[length(fsplit_name)]
}
# return header info object for created file
return(templateHDR)
}
readHeader <-
function(fileinf)
# readHeader reads nifti header info from nii,img,hdr and gzipped exts.
{
sp <- .Platform$file.sep
#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),sp,.nifti.header.filename(headinf),'.',.nifti.header.extension(headinf),'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),sp,.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 nulls 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(removeNullString(readBin(con,raw(),n=10))) # 4, char[10]
.nifti.header.db_name(headinf) <- rawToChar(removeNullString(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(removeNullString(readBin(con,raw(),n=1))) # 38, char[1]
.nifti.header.dim_info(headinf) <- rawToChar(removeNullString(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, raw[1], UNITS OF PIXDIM
.nifti.header.xyzt_units(headinf) <- rawToChar(removeNullString(readBin(con,raw(),n=1))) #123, raw[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(removeNullString(readBin(con,raw(),n=80))) #148, char[80], TEXT
.nifti.header.aux_file(headinf) <- rawToChar(removeNullString(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(removeNullString(readBin(con,raw(),n=16))) #328, char[16], NAME OR MEANING OF DATA
.nifti.header.magic(headinf) <- rawToChar(removeNullString(readBin(con,raw(),n=4))) #344, char[4], MAGICSTRING!
#close connection
close(con)
#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)<-'complex';.nifti.header.data.signed(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
{
sp <- .Platform$file.sep
#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),sp,.nifti.header.filename(headinf),'.',extension,'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),sp,.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))
} else stop('Unable to open connection')
#close connections
close(con)
#return datavector
return(invisible(data))
}
writeHeader <-
function(headinf)
#writeHeader writes header info to a .hdr file
{
sp <- .Platform$file.sep
.nifti.header.vox_offset(headinf) <- 0
## set correct extension
if(.nifti.header.extension(headinf)=='img') extension='hdr' else extension <- .nifti.header.extension(headinf)
## open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
fn <- paste(.nifti.header.fullpath(headinf),sp,.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),sp,.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
## write to .hdr file
if(extension=='hdr') con <- writeHeaderPart(con,headinf) else warning('Header info can only be written to .hdr files! No header info is written!')
close(con)
return(invisible(TRUE))
}
writeData <-
function(headinf,datavec=NULL)
#write data to a nifti file
{
## writeData writes both Header and Data info to a file
## input is headerinfo and datavector
## output is logical
sp <- .Platform$file.sep
if(is.null(datavec)) datavec = .fmri.data.datavec(headinf)
# 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),sp,.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),sp,.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
#set correct cal_min and cal_max
.nifti.header.cal_max(headinf) = max(datavec)
.nifti.header.cal_min(headinf) = min(datavec)
# for nii files write header and data in one connection (set offset of data as 352)
if(extension=='nii') {
.nifti.header.vox_offset(headinf) <- 352
con <- writeHeaderPart(con,headinf)
con <- writeDataPart(con,headinf,datavec)
}
# for img/hdr pairs write header to .hdr and data to .img
if(extension=='img') {
.nifti.header.vox_offset(headinf) <- 0
writeHeader(headinf)
con <- writeDataPart(con,headinf,datavec)
}
#close connection
close(con)
return(TRUE)
}
writeHeaderPart <-
function(con,headinf)
#writeHeaderPart of a nifti file
{
## 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(charToRaw(.nifti.header.xyzt_units(headinf)),con,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)
#write a datavector to nifti file
{
## 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)
}
headToName <-
function(headinf)
#turn header information to a filename
{
#if extension is nii
if(.nifti.header.extension(headinf)=='nii') {
if(.nifti.header.gzipped(headinf)) filename <- paste(.nifti.header.filename(headinf),'.nii.gz',sep='') else filename <- paste(.nifti.header.filename(headinf),'.nii',sep='')
}
#if extension is hdr
if(.nifti.header.extension(headinf)=='hdr') {
if(.nifti.header.gzipped(headinf)) filename <- paste(.nifti.header.filename(headinf),'.hdr.gz',sep='') else filename <- paste(.nifti.header.filename(headinf),'.hdr',sep='')
}
#if extension is img
if(.nifti.header.extension(headinf)=='img') {
if(.nifti.header.gzipped(headinf)) filename <- paste(.nifti.header.filename(headinf),'.img.gz',sep='') else filename <- paste(.nifti.header.filename(headinf),'.img',sep='')
}
#return filename
return(filename)
}
getIntent <-
function(code)
#get Nifti Intent code
{
intent = 'Unkown code'
#statistics
if(as.numeric(code)==2) intent = 'correlation'
if(as.numeric(code)==3) intent = 't-test'
if(as.numeric(code)==4) intent = 'F-test'
if(as.numeric(code)==5) intent = 'z-score'
if(as.numeric(code)==6) intent = 'chisq'
if(as.numeric(code)==7) intent = 'beta'
if(as.numeric(code)==8) intent = 'binom'
if(as.numeric(code)==9) intent = 'gamma'
if(as.numeric(code)==10) intent = 'poisson'
if(as.numeric(code)==11) intent = 'normal'
if(as.numeric(code)==12) intent = 'F-test nonc'
if(as.numeric(code)==13) intent = 'chisq nonc'
if(as.numeric(code)==14) intent = 'logistic'
if(as.numeric(code)==15) intent = 'laplace'
if(as.numeric(code)==16) intent = 'uniform'
if(as.numeric(code)==17) intent = 't-test nonc'
if(as.numeric(code)==18) intent = 'weibull'
if(as.numeric(code)==19) intent = 'Chi'
if(as.numeric(code)==20) intent = 'invgauss'
if(as.numeric(code)==21) intent = 'extval (p-val)'
if(as.numeric(code)==22) intent = 'p-value'
if(as.numeric(code)==23) intent = 'logpval'
if(as.numeric(code)==24) intent = 'log10pval'
#Non-stat
if(as.numeric(code)==1001) intent = 'estimate'
if(as.numeric(code)==1002) intent = 'label'
if(as.numeric(code)==1003) intent = 'neuroname'
if(as.numeric(code)==1004) intent = 'genmatrix'
if(as.numeric(code)==1005) intent = 'symmatrix'
if(as.numeric(code)==1006) intent = 'displacement'
if(as.numeric(code)==1007) intent = 'vector'
if(as.numeric(code)==1008) intent = 'pointset'
if(as.numeric(code)==1009) intent = 'triangle'
if(as.numeric(code)==1010) intent = 'quaternion'
if(as.numeric(code)==1011) intent = 'dimless'
#gifti
if(as.numeric(code)==2001) intent = 'timeseries'
if(as.numeric(code)==2002) intent = 'node'
if(as.numeric(code)==2003) intent = 'rgb-triplet'
if(as.numeric(code)==2004) intent = 'rgba-vector'
if(as.numeric(code)==2005) intent = 'shape'
return(intent)
}
fmri2array <- function(fmridat)
#converts a fmri.data object to an array
{
dx = .fmri.data.dims(fmridat)[2]
dy = .fmri.data.dims(fmridat)[3]
dz = .fmri.data.dims(fmridat)[4]
dt = .fmri.data.dims(fmridat)[5]
out = .fmri.data.datavec(fmridat)
if(.fmri.data.dims(fmridat)[1]==3) dim(out) = c(dx,dy,dz)
if(.fmri.data.dims(fmridat)[1]==4) dim(out) = c(dx,dy,dz,dt)
return(out)
}
bin2dec <-
function(binvec)
#calculate decimal value for a binary vector
{
value = as.integer(binvec[1])
if(length(binvec)>1) {
for(i in 2:(length(binvec))) {
temp = value
value = temp*2+as.integer(binvec[i])
}
}
return(as.integer(value))
}
xyzt2char <-
function(char)
#convert a xyzt_unit raw element to space and time
{
if(!is.character(char)) return(paste('xyzt_units not decipherable.'))
bitvec = rawToBits(charToRaw(char))
space = rev(bitvec[1:3])
time = rev(bitvec[4:6])
space_int = bin2dec(space)
time_int = bin2dec(time)*8
space_char = 'unknown'
if(space_int==1) space_char = 'meters'
if(space_int==2) space_char = 'millimeters'
if(space_int==3) space_char = 'micrometers'
int = 'unknown'
if(time_int==8) time_char = 'seconds'
if(time_int==16) time_char = 'milliseconds'
if(time_int==24) time_char = 'microseconds'
if(time_int==32) time_char = 'Hertz'
if(time_int==40) time_char = 'ppm'
if(time_int==48) time_char = 'rad/sec'
return(paste('xyz in ',space_char,' | time in ',time_char,'\n',sep=''))
}
removeNullString <- function(raw)
#remove embedded and trailing nullstrings
{
rm = which(raw==0)
if(length(rm)>0) raw = raw[-rm]
return(raw)
}
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arf3DS4 documentation built on May 2, 2019, 8:19 a.m.
R Package Documentation
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Defines functions getFileInfo newFile readHeader readData writeHeader writeData writeHeaderPart writeDataPart headToName getIntent fmri2array bin2dec xyzt2char removeNullString
Documented in fmri2array readData writeData
#############################################
# arf3DS4 S4 NIFTI FUNCTIONS #
# Wouter D. Weeda #
# University of Amsterdam #
#############################################
#[CONTAINS]
#getFileInfo
#newFile
#readHeader
#readData [user]
#writeHeader
#writeData [user]
#writeHeaderPart
#writeDataPart
#headToName
#getIntent
#fmri2array [user]
#bin2dec
#xyzt2char
getFileInfo <-
function(filename)
# getFileInfo sets file information (file path, location, extension, gzippedness and endianness)
{
#set separator
sp <- .Platform$file.sep
#check if only file else pre-append working directory
if(length(grep(sp,filename))==0) filename <- paste(getwd(),sp,filename,sep='')
#check if file exists
if(!file.exists(filename)) stop(paste('[getFileInfo] File',filename,'does noet exist!'))
#create new instance of class fileinfo
fileinf=new('nifti.fileinfo')
#split filename into path, name and extensions
fn <- strsplit(filename,sp)[[1]][length(strsplit(filename,sp)[[1]])]
#fsplit_name <- strsplit(tolower(fn),'\\.')[[1]]
fsplit_name <- strsplit(fn,'\\.')[[1]]
fsplit_path <- gsub(paste(sp,fn,sep=''),'',filename)
fname <- strsplit(fsplit_name[1],.Platform$file.sep)[[1]]
#set filename and path
.nifti.fileinfo.filename(fileinf) <- fname[length(fname)]
.nifti.fileinfo.fullpath(fileinf) <- fsplit_path
#check gzippedness and set extension
if(fsplit_name[length(fsplit_name)]=='gz') {
.nifti.fileinfo.gzipped(fileinf) <- TRUE
.nifti.fileinfo.extension(fileinf) <- fsplit_name[length(fsplit_name)-1]
} else {
.nifti.fileinfo.gzipped(fileinf) <- FALSE
.nifti.fileinfo.extension(fileinf) <- fsplit_name[length(fsplit_name)]
}
#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),sp,.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),sp,.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),sp,.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),sp,.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))
}
newFile <-
function(filename,templateHDR)
#set header info accordomg to a templateHeader
{
##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
sp <- .Platform$file.sep
#split filename into path, name and extensions
fn <- strsplit(filename,sp)[[1]][length(strsplit(filename,sp)[[1]])]
#fsplit_name <- strsplit(tolower(fn),'\\.')[[1]]
fsplit_name <- strsplit(fn,'\\.')[[1]]
fsplit_path <- gsub(paste(sp,fn,sep=''),'',filename)
fname <- strsplit(fsplit_name[1],.Platform$file.sep)[[1]]
#set filename and path
.nifti.header.filename(templateHDR) <- fname[length(fname)]
.nifti.header.fullpath(templateHDR) <- fsplit_path
#check gzippedness and set extension
if(fsplit_name[length(fsplit_name)]=='gz') {
.nifti.header.gzipped(templateHDR) <- TRUE
.nifti.header.extension(templateHDR) <- fsplit_name[length(fsplit_name)-1]
} else {
.nifti.header.gzipped(templateHDR) <- FALSE
.nifti.header.extension(templateHDR) <- fsplit_name[length(fsplit_name)]
}
# return header info object for created file
return(templateHDR)
}
readHeader <-
function(fileinf)
# readHeader reads nifti header info from nii,img,hdr and gzipped exts.
{
sp <- .Platform$file.sep
#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),sp,.nifti.header.filename(headinf),'.',.nifti.header.extension(headinf),'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),sp,.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 nulls 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(removeNullString(readBin(con,raw(),n=10))) # 4, char[10]
.nifti.header.db_name(headinf) <- rawToChar(removeNullString(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(removeNullString(readBin(con,raw(),n=1))) # 38, char[1]
.nifti.header.dim_info(headinf) <- rawToChar(removeNullString(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, raw[1], UNITS OF PIXDIM
.nifti.header.xyzt_units(headinf) <- rawToChar(removeNullString(readBin(con,raw(),n=1))) #123, raw[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(removeNullString(readBin(con,raw(),n=80))) #148, char[80], TEXT
.nifti.header.aux_file(headinf) <- rawToChar(removeNullString(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(removeNullString(readBin(con,raw(),n=16))) #328, char[16], NAME OR MEANING OF DATA
.nifti.header.magic(headinf) <- rawToChar(removeNullString(readBin(con,raw(),n=4))) #344, char[4], MAGICSTRING!
#close connection
close(con)
#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)<-'complex';.nifti.header.data.signed(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
{
sp <- .Platform$file.sep
#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),sp,.nifti.header.filename(headinf),'.',extension,'.gz',sep=''),open='rb')
} else {
con <- file(paste(.nifti.header.fullpath(headinf),sp,.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))
} else stop('Unable to open connection')
#close connections
close(con)
#return datavector
return(invisible(data))
}
writeHeader <-
function(headinf)
#writeHeader writes header info to a .hdr file
{
sp <- .Platform$file.sep
.nifti.header.vox_offset(headinf) <- 0
## set correct extension
if(.nifti.header.extension(headinf)=='img') extension='hdr' else extension <- .nifti.header.extension(headinf)
## open based on gzippedness
if(.nifti.header.gzipped(headinf)==TRUE) {
fn <- paste(.nifti.header.fullpath(headinf),sp,.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),sp,.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
## write to .hdr file
if(extension=='hdr') con <- writeHeaderPart(con,headinf) else warning('Header info can only be written to .hdr files! No header info is written!')
close(con)
return(invisible(TRUE))
}
writeData <-
function(headinf,datavec=NULL)
#write data to a nifti file
{
## writeData writes both Header and Data info to a file
## input is headerinfo and datavector
## output is logical
sp <- .Platform$file.sep
if(is.null(datavec)) datavec = .fmri.data.datavec(headinf)
# 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),sp,.nifti.header.filename(headinf),'.',extension,'.gz',sep='')
con <- gzfile(fn,open='wb')
} else {
fn <-paste(.nifti.header.fullpath(headinf),sp,.nifti.header.filename(headinf),'.',extension,sep='')
con <- file(fn,open='wb')
}
#set correct cal_min and cal_max
.nifti.header.cal_max(headinf) = max(datavec)
.nifti.header.cal_min(headinf) = min(datavec)
# for nii files write header and data in one connection (set offset of data as 352)
if(extension=='nii') {
.nifti.header.vox_offset(headinf) <- 352
con <- writeHeaderPart(con,headinf)
con <- writeDataPart(con,headinf,datavec)
}
# for img/hdr pairs write header to .hdr and data to .img
if(extension=='img') {
.nifti.header.vox_offset(headinf) <- 0
writeHeader(headinf)
con <- writeDataPart(con,headinf,datavec)
}
#close connection
close(con)
return(TRUE)
}
writeHeaderPart <-
function(con,headinf)
#writeHeaderPart of a nifti file
{
## 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(charToRaw(.nifti.header.xyzt_units(headinf)),con,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)
#write a datavector to nifti file
{
## 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)
}
headToName <-
function(headinf)
#turn header information to a filename
{
#if extension is nii
if(.nifti.header.extension(headinf)=='nii') {
if(.nifti.header.gzipped(headinf)) filename <- paste(.nifti.header.filename(headinf),'.nii.gz',sep='') else filename <- paste(.nifti.header.filename(headinf),'.nii',sep='')
}
#if extension is hdr
if(.nifti.header.extension(headinf)=='hdr') {
if(.nifti.header.gzipped(headinf)) filename <- paste(.nifti.header.filename(headinf),'.hdr.gz',sep='') else filename <- paste(.nifti.header.filename(headinf),'.hdr',sep='')
}
#if extension is img
if(.nifti.header.extension(headinf)=='img') {
if(.nifti.header.gzipped(headinf)) filename <- paste(.nifti.header.filename(headinf),'.img.gz',sep='') else filename <- paste(.nifti.header.filename(headinf),'.img',sep='')
}
#return filename
return(filename)
}
getIntent <-
function(code)
#get Nifti Intent code
{
intent = 'Unkown code'
#statistics
if(as.numeric(code)==2) intent = 'correlation'
if(as.numeric(code)==3) intent = 't-test'
if(as.numeric(code)==4) intent = 'F-test'
if(as.numeric(code)==5) intent = 'z-score'
if(as.numeric(code)==6) intent = 'chisq'
if(as.numeric(code)==7) intent = 'beta'
if(as.numeric(code)==8) intent = 'binom'
if(as.numeric(code)==9) intent = 'gamma'
if(as.numeric(code)==10) intent = 'poisson'
if(as.numeric(code)==11) intent = 'normal'
if(as.numeric(code)==12) intent = 'F-test nonc'
if(as.numeric(code)==13) intent = 'chisq nonc'
if(as.numeric(code)==14) intent = 'logistic'
if(as.numeric(code)==15) intent = 'laplace'
if(as.numeric(code)==16) intent = 'uniform'
if(as.numeric(code)==17) intent = 't-test nonc'
if(as.numeric(code)==18) intent = 'weibull'
if(as.numeric(code)==19) intent = 'Chi'
if(as.numeric(code)==20) intent = 'invgauss'
if(as.numeric(code)==21) intent = 'extval (p-val)'
if(as.numeric(code)==22) intent = 'p-value'
if(as.numeric(code)==23) intent = 'logpval'
if(as.numeric(code)==24) intent = 'log10pval'
#Non-stat
if(as.numeric(code)==1001) intent = 'estimate'
if(as.numeric(code)==1002) intent = 'label'
if(as.numeric(code)==1003) intent = 'neuroname'
if(as.numeric(code)==1004) intent = 'genmatrix'
if(as.numeric(code)==1005) intent = 'symmatrix'
if(as.numeric(code)==1006) intent = 'displacement'
if(as.numeric(code)==1007) intent = 'vector'
if(as.numeric(code)==1008) intent = 'pointset'
if(as.numeric(code)==1009) intent = 'triangle'
if(as.numeric(code)==1010) intent = 'quaternion'
if(as.numeric(code)==1011) intent = 'dimless'
#gifti
if(as.numeric(code)==2001) intent = 'timeseries'
if(as.numeric(code)==2002) intent = 'node'
if(as.numeric(code)==2003) intent = 'rgb-triplet'
if(as.numeric(code)==2004) intent = 'rgba-vector'
if(as.numeric(code)==2005) intent = 'shape'
return(intent)
}
fmri2array <- function(fmridat)
#converts a fmri.data object to an array
{
dx = .fmri.data.dims(fmridat)[2]
dy = .fmri.data.dims(fmridat)[3]
dz = .fmri.data.dims(fmridat)[4]
dt = .fmri.data.dims(fmridat)[5]
out = .fmri.data.datavec(fmridat)
if(.fmri.data.dims(fmridat)[1]==3) dim(out) = c(dx,dy,dz)
if(.fmri.data.dims(fmridat)[1]==4) dim(out) = c(dx,dy,dz,dt)
return(out)
}
bin2dec <-
function(binvec)
#calculate decimal value for a binary vector
{
value = as.integer(binvec[1])
if(length(binvec)>1) {
for(i in 2:(length(binvec))) {
temp = value
value = temp*2+as.integer(binvec[i])
}
}
return(as.integer(value))
}
xyzt2char <-
function(char)
#convert a xyzt_unit raw element to space and time
{
if(!is.character(char)) return(paste('xyzt_units not decipherable.'))
bitvec = rawToBits(charToRaw(char))
space = rev(bitvec[1:3])
time = rev(bitvec[4:6])
space_int = bin2dec(space)
time_int = bin2dec(time)*8
space_char = 'unknown'
if(space_int==1) space_char = 'meters'
if(space_int==2) space_char = 'millimeters'
if(space_int==3) space_char = 'micrometers'
int = 'unknown'
if(time_int==8) time_char = 'seconds'
if(time_int==16) time_char = 'milliseconds'
if(time_int==24) time_char = 'microseconds'
if(time_int==32) time_char = 'Hertz'
if(time_int==40) time_char = 'ppm'
if(time_int==48) time_char = 'rad/sec'
return(paste('xyz in ',space_char,' | time in ',time_char,'\n',sep=''))
}
removeNullString <- function(raw)
#remove embedded and trailing nullstrings
{
rm = which(raw==0)
if(length(rm)>0) raw = raw[-rm]
return(raw)
}
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