Nothing
R/readIni.r
In PET: Simulation and Reconstruction of PET Images
Defines functions
readIni
readIni <- function(fileName, DebugLevel="Normal")
{
#
#
#
###############################################################
# check the value 'fileName' and DebugLevel
if(missing(fileName)) {
stop("The fileName has to be of type character. It contains the path to filename and the filename. The path containing the path relatively to the working-directory of your R-session or containig the full path to the file.")
}
if(!is.character(fileName))
stop("'fileName' have to be of type character.")
if (length(fileName) != 1)
stop("Please specify exactly one 'fileName'.")
if (file.access(fileName, 0))
stop("The file, '", fileName, "' doesn't exist.")
if (file.access(fileName, 4))
stop("No read permission for file '", fileName, "'.")
DL1 <- logDebug(DebugLevel)
DebugLevel <- DL1[[3]]
DL2 <- DL1[[2]]
DL1 <- DL1[[1]]
###############################################################
# Open connection
if (DL1)
cat("Open file: ",fileName, "\n")
con <- file(fileName, "rb")
on.exit(close(con)) # be careful ...
###############################################################
# Reading the INI-File
if (DL2)
cat("Reading INI-file.\n")
tmp <- readLines(con, n=1)
tmp <- unlist(strsplit(tmp, "=", fixed=TRUE))
tmp <- c(tmp[1],paste(tmp[2:length(tmp)], collapse="=" ))
if (!(tmp[1]=="mode")){
cat("The first line of the INI-file must contain the parameter mode and not '", tmp[1],"'. \n", sep="")
cat("See help to get more information about the structure of the file. \n")
stop()
} else {
mode <- tmp[2]
if (DL2)
cat("'mode' entry is set to '", mode, "' \n", sep="")
}
if (mode %in% c("FB", "BF", "CNF", "CBF", "CC", "CNC", "CBC", "Test", "ART", "EM", "CG")){
if (mode %in% c("FB", "BF", "CNF", "CBF", "CC", "CNC", "CBC", "Test")){
###########################################################
# direct reconstruction-method are used
# Initialisation a list with default values
leIniList <- 12
iniList <- list()
length(iniList) <- leIniList
names(iniList) <- c("mode", "rData", "XSamples", "YSamples", "Xmin", "Ymin",
"DeltaX", "DeltaY", "InterPol", "FilterTyp", "DebugLevel", "oData")
iniList$mode <- mode
iniList$InterPol <- 1
iniList$FilterTyp <- "Hamming"
iniList$DebugLevel <- DebugLevel
listNames <- names(iniList)
listNamesChar <- c("rData", "FilterTyp", "DebugLevel", "oData")
listNamesNumeric <- listNames[!(listNames %in% listNamesChar)]
} else {
###########################################################
# iterative reconstruction-method are used
# Initialisation a list with default values
leIniList <- 32
iniList <- list()
length(iniList) <- leIniList
names(iniList) <- c("mode", "rData", "XSamples", "YSamples", "StartImage", "UseFast",
"RadonKernel", "Iterations", "IterationsType", "SaveIterations",
"SaveIterationsName", "LowestALevel", "ConstrainMin", "ConstrainMax",
"Alpha", "Beta", "Regularization", "KernelFileSave",
"KernelFileName", "RefFileName", "ThetaSamples", "RhoSamples",
"ThetaMin", "RhoMin", "DeltaTheta", "DeltaRho", "Xmin", "Ymin",
"DeltaX", "DeltaY", "OverSamp", "DebugLevel")
iniList$mode <- mode
iniList$StartImage <- "None"
iniList$UseFast <- 1
iniList$RadonKernel <- "NN"
iniList$Iterations <- 20
iniList$IterationsType <- "random"
iniList$SaveIterations <- 0
iniList$SaveIterationsName <- ""
iniList$LowestALevel <- 0.0
iniList$ConstrainMin <- -1
iniList$ConstrainMax <- -1
iniList$Alpha <- 1.0
iniList$Beta <- 1.0
iniList$Regularization <- 0
iniList$KernelFileSave <- 0
iniList$KernelFileName <- ""
iniList$RefFileName <- "None"
iniList$OverSamp <- 0
iniList$DebugLevel <- DebugLevel
listNames <- names(iniList)
listNamesChar <- c("rData", "StartImage", "RadonKernel", "IterationsType",
"SaveIterationsName", "KernelFileName", "RefFileName",
"DebugLevel")
listNamesNumeric <- listNames[!(listNames %in% listNamesChar)]
}
tmp <- readLines(con, n=leIniList)
for (i in 1:length(tmp)){
tmp2 <- unlist(strsplit(tmp[i], "=", fixed=TRUE))
tmp2 <- c(tmp2[1],paste(tmp2[2:length(tmp2)], collapse="=" ))
if (tmp2[1] %in% listNames){
if (tmp2[1] %in% listNamesNumeric){
iniList[tmp2[1]] <- as.numeric(tmp2[2])
if (DL2) cat(tmp2[1], "entry is set to", tmp2[2], "\n")
} else {
iniList[tmp2[1]] <- tmp2[2]
if (DL2) cat(tmp2[1], " entry is set to '", tmp2[2], "'\n", sep="")
}
} else {
cat("WARNING: '", tmp2[1], "' is an illegal parameter and is ignored. \n", sep="")
}
}
if (mode %in% c("FB", "BF", "CNF", "CBF", "CC", "CNC", "CBC", "Test")){
###########################################################
# parameter checking for iterative reconstruction-method
# load rData
if (is.null(iniList$rData))
stop("'rData' entry missing in INI file.")
tmp <- unlist(strsplit(iniList$rData, ".", fixed=TRUE))
fformatRadon <- tmp[length(tmp)]
rfile <- iniList$rData
if (DL2) cat("\n")
iniList$rData <- readData(iniList$rData, DebugLevel)$Signal
if (DL2) cat("\n")
# If oData specified than loading oData
if (!(is.null(iniList$oData))){
tmp <- unlist(strsplit(iniList$oData, ".", fixed=TRUE))
fformatOrginal <- tmp[length(tmp)]
sfile <- iniList$oData
iniList$oData <- readData(iniList$oData, DebugLevel)
if (DL2) cat("\n")
}
##############################################
# checking the following parameters:
# XSamples, YSamples, XMin, YMin, DeltaX and DeltaY
if ( !(is.null(iniList$oData)) && fformatOrginal %in% c("pet", "fif", "dat")){
if(DL1) cat("Setting unknown parameters from '", sfile, "' \n", sep="")
# check XSamples
if(is.null(iniList$XSamples)){
iniList$XSamples <- iniList$oData$Header$SignalDim[[1]]
if(DL2)
cat("'XSamples' entry is set to", iniList$XSamples, "\n")
} else if (iniList$oData$Header$SignalDim[[1]] != iniList$XSamples){
if(DL2)
cat("Note: 'XSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check YSamples
if(is.null(iniList$YSamples)){
iniList$YSamples <- iniList$oData$Header$SignalDim[[2]]
if(DL2)
cat("'YSamples' entry is set to", iniList$YSamples, "\n")
} else if (iniList$oData$Header$SignalDim[[2]] != iniList$YSamples){
if(DL2)
cat("Note: 'YSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Xmin
if(is.null(iniList$Xmin)){
iniList$Xmin <- iniList$oData$Header$XYmin[[1]]
if(DL2)
cat("'Xmin' entry is set to", iniList$Xmin, "\n")
} else if (iniList$oData$Header$XYmin[[1]] != iniList$Xmin){
if(DL2)
cat("Note: 'Xmin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Ymin
if(is.null(iniList$Ymin)){
iniList$Ymin <- iniList$oData$Header$XYmin[[2]]
if(DL2)
cat("'Ymin' entry is set to", iniList$Ymin, "\n")
} else if (iniList$oData$Header$XYmin[[2]] != iniList$Ymin){
if(DL2)
cat("Note: 'Ymin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaX
if(is.null(iniList$DeltaX)){
iniList$DeltaX <- iniList$oData$Header$DeltaXY[[1]]
if(DL2)
cat("'DeltaX' entry is set to", iniList$DeltaX, "\n")
} else if (iniList$oData$Header$DeltaXY[[1]] != iniList$DeltaX){
if(DL2)
cat("Note: 'DeltaX' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaY
if(is.null(iniList$DeltaY)){
iniList$DeltaY <- iniList$oData$Header$DeltaXY[[2]]
if(DL2)
cat("'DeltaY' entry is set to", iniList$DeltaY, "\n")
} else if (iniList$oData$Header$DeltaXY[[2]] != iniList$DeltaY){
if(DL2)
cat("Note: 'DeltaY' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
iniList$oData <- iniList$oData$Signal
if(DL2) cat("\n")
} else if (!(is.null(iniList$oData))){
# check XSamples
if (is.null(iniList$XSamples))
iniList$XSamples <- nrow(iniList$oData)
# check YSamples
if (is.null(iniList$YSamples))
iniList$YSamples <- ncol(iniList$oData)
# check Xmin
if (is.null(iniList$Xmin))
iniList$Xmin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)*0.5*(iniList$XSamples-1)
# check Ymin
if (is.null(iniList$Ymin))
iniList$Ymin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)*0.5*(iniList$YSamples-1)
# check DeltaX
if (is.null(iniList$DeltaX))
iniList$DeltaX <- sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)
# check DeltaY
if (is.null(iniList$DeltaY))
iniList$DeltaY <- sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)
} else {
if(is.null(iniList$XSamples))
stop("'XSamples' entry missing in INI file")
if(is.null(iniList$YSamples))
stop("'YSamples' entry missing in INI file")
if(is.null(iniList$Xmin))
iniList$Xmin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)*0.5*(iniList$XSamples-1)
if(is.null(iniList$Ymin))
iniList$Ymin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)*0.5*(iniList$YSamples-1)
if(is.null(iniList$DeltaX))
iniList$DeltaX <- sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)
if(is.null(iniList$DeltaY))
iniList$DeltaY <- sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)
}
} else {
###########################################################
# parameter checking for iterative reconstruction-method
# load rData
if (is.null(iniList$rData))
stop("'rData' entry missing in INI file.")
tmp <- unlist(strsplit(iniList$rData, ".", fixed=TRUE))
fformatRadon <- tmp[length(tmp)]
rfile <- iniList$rData
if (DL2) cat("\n")
iniList$rData <- readData(iniList$rData, DebugLevel)
if (DL2) cat("\n")
# If StartImage specified than loading StartImage
if (iniList$StartImage != "None" ){
tmp <- unlist(strsplit(iniList$StartImage, ".", fixed=TRUE))
fformatStart <- tmp[length(tmp)]
sfile <- iniList$StartImage
iniList$StartImage <- readData(iniList$StartImage, DebugLevel)
if (DL2) cat("\n")
}
##############################################
# checking the following parameters:
# XSamples, YSamples, XMin, YMin, DeltaX and DeltaY
if (iniList$StartImage != "None" && fformatStart %in% c("pet", "fif", "dat")){
if(DL1) cat("Setting unknown parameters from '", sfile, "' \n", sep="")
# check XSamples
if(is.null(iniList$XSamples)){
iniList$XSamples <- iniList$StartImage$Header$SignalDim[[1]]
if(DL2)
cat("'XSamples' entry is set to", iniList$XSamples, "\n")
} else if (iniList$StartImage$Header$SignalDim[[1]] != iniList$XSamples){
if(DL2)
cat("Note: 'XSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check YSamples
if(is.null(iniList$YSamples)){
iniList$YSamples <- iniList$StartImage$Header$SignalDim[[2]]
if(DL2)
cat("'YSamples' entry is set to", iniList$YSamples, "\n")
} else if (iniList$StartImage$Header$SignalDim[[2]] != iniList$YSamples){
if(DL2)
cat("Note: 'YSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Xmin
if(is.null(iniList$Xmin)){
iniList$Xmin <- iniList$StartImage$Header$XYmin[[1]]
if(DL2)
cat("'Xmin' entry is set to", iniList$Xmin, "\n")
} else if (iniList$StartImage$Header$XYmin[[1]] != iniList$Xmin){
if(DL2)
cat("Note: 'Xmin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Ymin
if(is.null(iniList$Ymin)){
iniList$Ymin <- iniList$StartImage$Header$XYmin[[2]]
if(DL2)
cat("'Ymin' entry is set to", iniList$Ymin, "\n")
} else if (iniList$StartImage$Header$XYmin[[2]] != iniList$Ymin){
if(DL2)
cat("Note: 'Ymin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaX
if(is.null(iniList$DeltaX)){
iniList$DeltaX <- iniList$StartImage$Header$DeltaXY[[1]]
if(DL2)
cat("'DeltaX' entry is set to", iniList$DeltaX, "\n")
} else if (iniList$StartImage$Header$DeltaXY[[1]] != iniList$DeltaX){
if(DL2)
cat("Note: 'DeltaX' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaY
if(is.null(iniList$DeltaY)){
iniList$DeltaY <- iniList$StartImage$Header$DeltaXY[[2]]
if(DL2)
cat("'DeltaY' entry is set to", iniList$DeltaY, "\n")
} else if (iniList$StartImage$Header$DeltaXY[[2]] != iniList$DeltaY){
if(DL2)
cat("Note: 'DeltaY' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
iniList$StartImage <- iniList$StartImage$Signal
if(DL2) cat("\n")
} else if (iniList$StartImage != "None"){
# check XSamples
if (is.null(iniList$XSamples))
iniList$XSamples <- nrow(iniList$StartImage)
# check YSamples
if (is.null(iniList$YSamples))
iniList$YSamples <- ncol(iniList$StartImage)
# check Xmin
if (is.null(iniList$Xmin))
iniList$Xmin <- -0.5*((iniList$XSamples)-1)
# check Ymin
if (is.null(iniList$Ymin))
iniList$Ymin <- -0.5*((iniList$YSamples)-1)
# check DeltaX
if (is.null(iniList$DeltaX))
iniList$DeltaX <- 1
# check DeltaY
if (is.null(iniList$DeltaY))
iniList$DeltaY <- 1
}
if(is.null(iniList$XSamples))
stop("'XSamples' entry missing in INI file")
if(is.null(iniList$YSamples))
stop("'YSamples' entry missing in INI file")
##############################################
# checking the following parameters:
# ThetaSamples, RhoSamples, ThetaMin, RhoMin, DeltaTheta and DeltaRho
if (fformatRadon %in% c("pet", "fif", "dat")){
if(DL1) cat("Setting unknown parameters from '", rfile, "' \n", sep="")
# check ThetaSamples
if(is.null(iniList$ThetaSamples)){
iniList$ThetaSamples <- iniList$rData$Header$SignalDim[[1]]
if(DL2)
cat("'ThetaSamples' entry is set to", iniList$ThetaSamples, "\n")
} else if (iniList$rData$Header$SignalDim[[1]] != iniList$ThetaSamples){
if(DL2)
cat("Note: 'ThetaSamples' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check RhoSamples
if(is.null(iniList$RhoSamples)){
iniList$RhoSamples <- iniList$rData$Header$SignalDim[[2]]
if(DL2)
cat("'RhoSamples' entry is set to", iniList$RhoSamples, "\n")
} else if (iniList$rData$Header$SignalDim[[2]] != iniList$RhoSamples){
if(DL2)
cat("Note: 'RhoSamples' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check ThetaMin
if(is.null(iniList$ThetaMin)){
iniList$ThetaMin <- iniList$rData$Header$XYmin[[1]]
if(DL2)
cat("'ThetaMin' entry is set to", iniList$ThetaMin, "\n")
} else if (iniList$rData$Header$XYmin[[1]] != iniList$ThetaMin){
if(DL2)
cat("Note: 'ThetaMin' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check RhoMin
if(is.null(iniList$RhoMin)){
iniList$RhoMin <- iniList$rData$Header$XYmin[[2]]
if(DL2)
cat("'RhoMin' entry is set to", iniList$RhoMin, "\n")
} else if (iniList$rData$Header$XYmin[[2]] != iniList$RhoMin){
if(DL2)
cat("Note: 'RhoMin' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaTheta
if(is.null(iniList$DeltaTheta)){
iniList$DeltaTheta <- iniList$rData$Header$DeltaXY[[1]]
if(DL2)
cat("'DeltaTheta' entry is set to", iniList$DeltaTheta, "\n")
} else if (iniList$rData$Header$DeltaXY[[1]] != iniList$DeltaTheta){
if(DL2)
cat("Note: 'DeltaTheta' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaRho
if(is.null(iniList$DeltaRho)){
iniList$DeltaRho <- iniList$rData$Header$DeltaXY[[2]]
if(DL2)
cat("'DeltaRho' entry is set to", iniList$DeltaRho, "\n")
} else if (iniList$rData$Header$DeltaXY[[2]] != iniList$DeltaRho){
if(DL2)
cat("Note: 'DeltaRho' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
iniList$rData <- iniList$rData$Signal
if(DL2) cat("\n")
} else {
# check ThetaSamples
if (is.null(iniList$ThetaSamples))
iniList$ThetaSamples <- nrow(iniList$rData)
# check RhoSamples
if (is.null(iniList$RhoSamples))
iniList$RhoSamples <- ncol(iniList$rData)
# check ThetaMin
if (is.null(iniList$ThetaMin))
iniList$ThetaMin <- 0
# check RhoMin
if (is.null(iniList$RhoMin))
iniList$RhoMin <- -0.5*((2*round(sqrt(iniList$XSamples^2+iniList$YSamples^2)/2)+1)-1)
# check DeltaTheta
if (is.null(iniList$DeltaTheta))
iniList$DeltaTheta <- pi/(iniList$ThetaSamples)
# check DeltaRho
if (is.null(iniList$DeltaRho))
iniList$DeltaRho <- (2*abs(iniList$RhoMin)+1)/iniList$RhoSamples
}
}
if(is.null(iniList$XSamples))
stop("'XSamples' entry missing in INI file")
if(is.null(iniList$YSamples))
stop("'YSamples' entry missing in INI file")
if(is.null(iniList$Xmin))
iniList$Xmin <- -0.5*((iniList$XSamples)-1)
if(is.null(iniList$Ymin))
iniList$Ymin <- -0.5*((iniList$YSamples)-1)
if(is.null(iniList$DeltaX))
iniList$DeltaX <- 1
if(is.null(iniList$DeltaY))
iniList$DeltaY <- 1
} else
stop("mode='", mode,"' don't be supported. See help to 'iradon' or 'iradonIT' to get more information about mode.", sep="")
return(iniList)
}
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Defines functions readIni
readIni <- function(fileName, DebugLevel="Normal")
{
#
#
#
###############################################################
# check the value 'fileName' and DebugLevel
if(missing(fileName)) {
stop("The fileName has to be of type character. It contains the path to filename and the filename. The path containing the path relatively to the working-directory of your R-session or containig the full path to the file.")
}
if(!is.character(fileName))
stop("'fileName' have to be of type character.")
if (length(fileName) != 1)
stop("Please specify exactly one 'fileName'.")
if (file.access(fileName, 0))
stop("The file, '", fileName, "' doesn't exist.")
if (file.access(fileName, 4))
stop("No read permission for file '", fileName, "'.")
DL1 <- logDebug(DebugLevel)
DebugLevel <- DL1[[3]]
DL2 <- DL1[[2]]
DL1 <- DL1[[1]]
###############################################################
# Open connection
if (DL1)
cat("Open file: ",fileName, "\n")
con <- file(fileName, "rb")
on.exit(close(con)) # be careful ...
###############################################################
# Reading the INI-File
if (DL2)
cat("Reading INI-file.\n")
tmp <- readLines(con, n=1)
tmp <- unlist(strsplit(tmp, "=", fixed=TRUE))
tmp <- c(tmp[1],paste(tmp[2:length(tmp)], collapse="=" ))
if (!(tmp[1]=="mode")){
cat("The first line of the INI-file must contain the parameter mode and not '", tmp[1],"'. \n", sep="")
cat("See help to get more information about the structure of the file. \n")
stop()
} else {
mode <- tmp[2]
if (DL2)
cat("'mode' entry is set to '", mode, "' \n", sep="")
}
if (mode %in% c("FB", "BF", "CNF", "CBF", "CC", "CNC", "CBC", "Test", "ART", "EM", "CG")){
if (mode %in% c("FB", "BF", "CNF", "CBF", "CC", "CNC", "CBC", "Test")){
###########################################################
# direct reconstruction-method are used
# Initialisation a list with default values
leIniList <- 12
iniList <- list()
length(iniList) <- leIniList
names(iniList) <- c("mode", "rData", "XSamples", "YSamples", "Xmin", "Ymin",
"DeltaX", "DeltaY", "InterPol", "FilterTyp", "DebugLevel", "oData")
iniList$mode <- mode
iniList$InterPol <- 1
iniList$FilterTyp <- "Hamming"
iniList$DebugLevel <- DebugLevel
listNames <- names(iniList)
listNamesChar <- c("rData", "FilterTyp", "DebugLevel", "oData")
listNamesNumeric <- listNames[!(listNames %in% listNamesChar)]
} else {
###########################################################
# iterative reconstruction-method are used
# Initialisation a list with default values
leIniList <- 32
iniList <- list()
length(iniList) <- leIniList
names(iniList) <- c("mode", "rData", "XSamples", "YSamples", "StartImage", "UseFast",
"RadonKernel", "Iterations", "IterationsType", "SaveIterations",
"SaveIterationsName", "LowestALevel", "ConstrainMin", "ConstrainMax",
"Alpha", "Beta", "Regularization", "KernelFileSave",
"KernelFileName", "RefFileName", "ThetaSamples", "RhoSamples",
"ThetaMin", "RhoMin", "DeltaTheta", "DeltaRho", "Xmin", "Ymin",
"DeltaX", "DeltaY", "OverSamp", "DebugLevel")
iniList$mode <- mode
iniList$StartImage <- "None"
iniList$UseFast <- 1
iniList$RadonKernel <- "NN"
iniList$Iterations <- 20
iniList$IterationsType <- "random"
iniList$SaveIterations <- 0
iniList$SaveIterationsName <- ""
iniList$LowestALevel <- 0.0
iniList$ConstrainMin <- -1
iniList$ConstrainMax <- -1
iniList$Alpha <- 1.0
iniList$Beta <- 1.0
iniList$Regularization <- 0
iniList$KernelFileSave <- 0
iniList$KernelFileName <- ""
iniList$RefFileName <- "None"
iniList$OverSamp <- 0
iniList$DebugLevel <- DebugLevel
listNames <- names(iniList)
listNamesChar <- c("rData", "StartImage", "RadonKernel", "IterationsType",
"SaveIterationsName", "KernelFileName", "RefFileName",
"DebugLevel")
listNamesNumeric <- listNames[!(listNames %in% listNamesChar)]
}
tmp <- readLines(con, n=leIniList)
for (i in 1:length(tmp)){
tmp2 <- unlist(strsplit(tmp[i], "=", fixed=TRUE))
tmp2 <- c(tmp2[1],paste(tmp2[2:length(tmp2)], collapse="=" ))
if (tmp2[1] %in% listNames){
if (tmp2[1] %in% listNamesNumeric){
iniList[tmp2[1]] <- as.numeric(tmp2[2])
if (DL2) cat(tmp2[1], "entry is set to", tmp2[2], "\n")
} else {
iniList[tmp2[1]] <- tmp2[2]
if (DL2) cat(tmp2[1], " entry is set to '", tmp2[2], "'\n", sep="")
}
} else {
cat("WARNING: '", tmp2[1], "' is an illegal parameter and is ignored. \n", sep="")
}
}
if (mode %in% c("FB", "BF", "CNF", "CBF", "CC", "CNC", "CBC", "Test")){
###########################################################
# parameter checking for iterative reconstruction-method
# load rData
if (is.null(iniList$rData))
stop("'rData' entry missing in INI file.")
tmp <- unlist(strsplit(iniList$rData, ".", fixed=TRUE))
fformatRadon <- tmp[length(tmp)]
rfile <- iniList$rData
if (DL2) cat("\n")
iniList$rData <- readData(iniList$rData, DebugLevel)$Signal
if (DL2) cat("\n")
# If oData specified than loading oData
if (!(is.null(iniList$oData))){
tmp <- unlist(strsplit(iniList$oData, ".", fixed=TRUE))
fformatOrginal <- tmp[length(tmp)]
sfile <- iniList$oData
iniList$oData <- readData(iniList$oData, DebugLevel)
if (DL2) cat("\n")
}
##############################################
# checking the following parameters:
# XSamples, YSamples, XMin, YMin, DeltaX and DeltaY
if ( !(is.null(iniList$oData)) && fformatOrginal %in% c("pet", "fif", "dat")){
if(DL1) cat("Setting unknown parameters from '", sfile, "' \n", sep="")
# check XSamples
if(is.null(iniList$XSamples)){
iniList$XSamples <- iniList$oData$Header$SignalDim[[1]]
if(DL2)
cat("'XSamples' entry is set to", iniList$XSamples, "\n")
} else if (iniList$oData$Header$SignalDim[[1]] != iniList$XSamples){
if(DL2)
cat("Note: 'XSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check YSamples
if(is.null(iniList$YSamples)){
iniList$YSamples <- iniList$oData$Header$SignalDim[[2]]
if(DL2)
cat("'YSamples' entry is set to", iniList$YSamples, "\n")
} else if (iniList$oData$Header$SignalDim[[2]] != iniList$YSamples){
if(DL2)
cat("Note: 'YSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Xmin
if(is.null(iniList$Xmin)){
iniList$Xmin <- iniList$oData$Header$XYmin[[1]]
if(DL2)
cat("'Xmin' entry is set to", iniList$Xmin, "\n")
} else if (iniList$oData$Header$XYmin[[1]] != iniList$Xmin){
if(DL2)
cat("Note: 'Xmin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Ymin
if(is.null(iniList$Ymin)){
iniList$Ymin <- iniList$oData$Header$XYmin[[2]]
if(DL2)
cat("'Ymin' entry is set to", iniList$Ymin, "\n")
} else if (iniList$oData$Header$XYmin[[2]] != iniList$Ymin){
if(DL2)
cat("Note: 'Ymin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaX
if(is.null(iniList$DeltaX)){
iniList$DeltaX <- iniList$oData$Header$DeltaXY[[1]]
if(DL2)
cat("'DeltaX' entry is set to", iniList$DeltaX, "\n")
} else if (iniList$oData$Header$DeltaXY[[1]] != iniList$DeltaX){
if(DL2)
cat("Note: 'DeltaX' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaY
if(is.null(iniList$DeltaY)){
iniList$DeltaY <- iniList$oData$Header$DeltaXY[[2]]
if(DL2)
cat("'DeltaY' entry is set to", iniList$DeltaY, "\n")
} else if (iniList$oData$Header$DeltaXY[[2]] != iniList$DeltaY){
if(DL2)
cat("Note: 'DeltaY' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
iniList$oData <- iniList$oData$Signal
if(DL2) cat("\n")
} else if (!(is.null(iniList$oData))){
# check XSamples
if (is.null(iniList$XSamples))
iniList$XSamples <- nrow(iniList$oData)
# check YSamples
if (is.null(iniList$YSamples))
iniList$YSamples <- ncol(iniList$oData)
# check Xmin
if (is.null(iniList$Xmin))
iniList$Xmin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)*0.5*(iniList$XSamples-1)
# check Ymin
if (is.null(iniList$Ymin))
iniList$Ymin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)*0.5*(iniList$YSamples-1)
# check DeltaX
if (is.null(iniList$DeltaX))
iniList$DeltaX <- sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)
# check DeltaY
if (is.null(iniList$DeltaY))
iniList$DeltaY <- sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)
} else {
if(is.null(iniList$XSamples))
stop("'XSamples' entry missing in INI file")
if(is.null(iniList$YSamples))
stop("'YSamples' entry missing in INI file")
if(is.null(iniList$Xmin))
iniList$Xmin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)*0.5*(iniList$XSamples-1)
if(is.null(iniList$Ymin))
iniList$Ymin <- -sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)*0.5*(iniList$YSamples-1)
if(is.null(iniList$DeltaX))
iniList$DeltaX <- sqrt(0.5)*(ncol(iniList$rData)/iniList$XSamples)
if(is.null(iniList$DeltaY))
iniList$DeltaY <- sqrt(0.5)*(ncol(iniList$rData)/iniList$YSamples)
}
} else {
###########################################################
# parameter checking for iterative reconstruction-method
# load rData
if (is.null(iniList$rData))
stop("'rData' entry missing in INI file.")
tmp <- unlist(strsplit(iniList$rData, ".", fixed=TRUE))
fformatRadon <- tmp[length(tmp)]
rfile <- iniList$rData
if (DL2) cat("\n")
iniList$rData <- readData(iniList$rData, DebugLevel)
if (DL2) cat("\n")
# If StartImage specified than loading StartImage
if (iniList$StartImage != "None" ){
tmp <- unlist(strsplit(iniList$StartImage, ".", fixed=TRUE))
fformatStart <- tmp[length(tmp)]
sfile <- iniList$StartImage
iniList$StartImage <- readData(iniList$StartImage, DebugLevel)
if (DL2) cat("\n")
}
##############################################
# checking the following parameters:
# XSamples, YSamples, XMin, YMin, DeltaX and DeltaY
if (iniList$StartImage != "None" && fformatStart %in% c("pet", "fif", "dat")){
if(DL1) cat("Setting unknown parameters from '", sfile, "' \n", sep="")
# check XSamples
if(is.null(iniList$XSamples)){
iniList$XSamples <- iniList$StartImage$Header$SignalDim[[1]]
if(DL2)
cat("'XSamples' entry is set to", iniList$XSamples, "\n")
} else if (iniList$StartImage$Header$SignalDim[[1]] != iniList$XSamples){
if(DL2)
cat("Note: 'XSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check YSamples
if(is.null(iniList$YSamples)){
iniList$YSamples <- iniList$StartImage$Header$SignalDim[[2]]
if(DL2)
cat("'YSamples' entry is set to", iniList$YSamples, "\n")
} else if (iniList$StartImage$Header$SignalDim[[2]] != iniList$YSamples){
if(DL2)
cat("Note: 'YSamples' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Xmin
if(is.null(iniList$Xmin)){
iniList$Xmin <- iniList$StartImage$Header$XYmin[[1]]
if(DL2)
cat("'Xmin' entry is set to", iniList$Xmin, "\n")
} else if (iniList$StartImage$Header$XYmin[[1]] != iniList$Xmin){
if(DL2)
cat("Note: 'Xmin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check Ymin
if(is.null(iniList$Ymin)){
iniList$Ymin <- iniList$StartImage$Header$XYmin[[2]]
if(DL2)
cat("'Ymin' entry is set to", iniList$Ymin, "\n")
} else if (iniList$StartImage$Header$XYmin[[2]] != iniList$Ymin){
if(DL2)
cat("Note: 'Ymin' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaX
if(is.null(iniList$DeltaX)){
iniList$DeltaX <- iniList$StartImage$Header$DeltaXY[[1]]
if(DL2)
cat("'DeltaX' entry is set to", iniList$DeltaX, "\n")
} else if (iniList$StartImage$Header$DeltaXY[[1]] != iniList$DeltaX){
if(DL2)
cat("Note: 'DeltaX' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaY
if(is.null(iniList$DeltaY)){
iniList$DeltaY <- iniList$StartImage$Header$DeltaXY[[2]]
if(DL2)
cat("'DeltaY' entry is set to", iniList$DeltaY, "\n")
} else if (iniList$StartImage$Header$DeltaXY[[2]] != iniList$DeltaY){
if(DL2)
cat("Note: 'DeltaY' is different between '", fileName, "' and '", sfile, "'. INI-file is preferred. \n", sep="")
}
iniList$StartImage <- iniList$StartImage$Signal
if(DL2) cat("\n")
} else if (iniList$StartImage != "None"){
# check XSamples
if (is.null(iniList$XSamples))
iniList$XSamples <- nrow(iniList$StartImage)
# check YSamples
if (is.null(iniList$YSamples))
iniList$YSamples <- ncol(iniList$StartImage)
# check Xmin
if (is.null(iniList$Xmin))
iniList$Xmin <- -0.5*((iniList$XSamples)-1)
# check Ymin
if (is.null(iniList$Ymin))
iniList$Ymin <- -0.5*((iniList$YSamples)-1)
# check DeltaX
if (is.null(iniList$DeltaX))
iniList$DeltaX <- 1
# check DeltaY
if (is.null(iniList$DeltaY))
iniList$DeltaY <- 1
}
if(is.null(iniList$XSamples))
stop("'XSamples' entry missing in INI file")
if(is.null(iniList$YSamples))
stop("'YSamples' entry missing in INI file")
##############################################
# checking the following parameters:
# ThetaSamples, RhoSamples, ThetaMin, RhoMin, DeltaTheta and DeltaRho
if (fformatRadon %in% c("pet", "fif", "dat")){
if(DL1) cat("Setting unknown parameters from '", rfile, "' \n", sep="")
# check ThetaSamples
if(is.null(iniList$ThetaSamples)){
iniList$ThetaSamples <- iniList$rData$Header$SignalDim[[1]]
if(DL2)
cat("'ThetaSamples' entry is set to", iniList$ThetaSamples, "\n")
} else if (iniList$rData$Header$SignalDim[[1]] != iniList$ThetaSamples){
if(DL2)
cat("Note: 'ThetaSamples' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check RhoSamples
if(is.null(iniList$RhoSamples)){
iniList$RhoSamples <- iniList$rData$Header$SignalDim[[2]]
if(DL2)
cat("'RhoSamples' entry is set to", iniList$RhoSamples, "\n")
} else if (iniList$rData$Header$SignalDim[[2]] != iniList$RhoSamples){
if(DL2)
cat("Note: 'RhoSamples' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check ThetaMin
if(is.null(iniList$ThetaMin)){
iniList$ThetaMin <- iniList$rData$Header$XYmin[[1]]
if(DL2)
cat("'ThetaMin' entry is set to", iniList$ThetaMin, "\n")
} else if (iniList$rData$Header$XYmin[[1]] != iniList$ThetaMin){
if(DL2)
cat("Note: 'ThetaMin' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check RhoMin
if(is.null(iniList$RhoMin)){
iniList$RhoMin <- iniList$rData$Header$XYmin[[2]]
if(DL2)
cat("'RhoMin' entry is set to", iniList$RhoMin, "\n")
} else if (iniList$rData$Header$XYmin[[2]] != iniList$RhoMin){
if(DL2)
cat("Note: 'RhoMin' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaTheta
if(is.null(iniList$DeltaTheta)){
iniList$DeltaTheta <- iniList$rData$Header$DeltaXY[[1]]
if(DL2)
cat("'DeltaTheta' entry is set to", iniList$DeltaTheta, "\n")
} else if (iniList$rData$Header$DeltaXY[[1]] != iniList$DeltaTheta){
if(DL2)
cat("Note: 'DeltaTheta' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
# check DeltaRho
if(is.null(iniList$DeltaRho)){
iniList$DeltaRho <- iniList$rData$Header$DeltaXY[[2]]
if(DL2)
cat("'DeltaRho' entry is set to", iniList$DeltaRho, "\n")
} else if (iniList$rData$Header$DeltaXY[[2]] != iniList$DeltaRho){
if(DL2)
cat("Note: 'DeltaRho' is different between '", fileName, "' and '", rfile, "'. INI-file is preferred. \n", sep="")
}
iniList$rData <- iniList$rData$Signal
if(DL2) cat("\n")
} else {
# check ThetaSamples
if (is.null(iniList$ThetaSamples))
iniList$ThetaSamples <- nrow(iniList$rData)
# check RhoSamples
if (is.null(iniList$RhoSamples))
iniList$RhoSamples <- ncol(iniList$rData)
# check ThetaMin
if (is.null(iniList$ThetaMin))
iniList$ThetaMin <- 0
# check RhoMin
if (is.null(iniList$RhoMin))
iniList$RhoMin <- -0.5*((2*round(sqrt(iniList$XSamples^2+iniList$YSamples^2)/2)+1)-1)
# check DeltaTheta
if (is.null(iniList$DeltaTheta))
iniList$DeltaTheta <- pi/(iniList$ThetaSamples)
# check DeltaRho
if (is.null(iniList$DeltaRho))
iniList$DeltaRho <- (2*abs(iniList$RhoMin)+1)/iniList$RhoSamples
}
}
if(is.null(iniList$XSamples))
stop("'XSamples' entry missing in INI file")
if(is.null(iniList$YSamples))
stop("'YSamples' entry missing in INI file")
if(is.null(iniList$Xmin))
iniList$Xmin <- -0.5*((iniList$XSamples)-1)
if(is.null(iniList$Ymin))
iniList$Ymin <- -0.5*((iniList$YSamples)-1)
if(is.null(iniList$DeltaX))
iniList$DeltaX <- 1
if(is.null(iniList$DeltaY))
iniList$DeltaY <- 1
} else
stop("mode='", mode,"' don't be supported. See help to 'iradon' or 'iradonIT' to get more information about mode.", sep="")
return(iniList)
}
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