Ok, no commits since a while. Last change was remake of init.R to improve readability.
Taha Ahmed
13 years ago
parent
70c39b9145
commit
f0ed360c0d
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source("/home/taha/chepec/chetex/common/R/common/ProvideSampleId.R")
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source("/home/taha/chepec/chetex/common/R/common/int2padstr.R")
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##################################################
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#################### OO2df #######################
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##################################################
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OO2df <- function(datafile) {
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## Description:
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##
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##
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##
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##
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## Usage:
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## OO2df(datafile)
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## Arguments:
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## datafile: text string with full path to TXT file
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## containing single or multiple data ranges
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## Value:
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## Dataframe with the following columns:
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## $ sampleid : chr
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## $ wavelength : num
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## $ counts : num
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## $
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## $
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## $
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## $
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## $
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## $
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## $
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## $
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## $
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## $
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## $ cps ?
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#
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# range.header.start.rexp <- "^; \\(Data for Range" #regexp
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# range.header.end.rexp <- "^_2THETA[^=]" #regexp
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range.data.start.rexp <- ">+Begin[\\s\\w]*<+"
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range.data.end.rexp <- ">+End[\\s\\w]*<+"
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# Read the input file
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dfile <- file(datafile, "r")
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# Note that readLines apparently completely skips empty lines.
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# That causes line numbers to not match between source and f vector.
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f <- readLines(dfile, n=-1) # read _all_ lines from data file
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close(dfile)
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# Fetch a sampleid for the current job
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sampleid <- ProvideSampleId(datafile)
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# # Look for header start rows
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# range.header.start.rows <- which(regexpr(range.header.start.rexp, f) == 1)
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# # Look for header end rows
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# range.header.end.rows <- which(regexpr(range.header.end.rexp, f) == 1)
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# Look for data start marker line
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range.data.start.rows <- which(regexpr(range.data.start.rexp, f, perl = TRUE) == 1) + 1
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# Look for data end marker line
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range.data.end.rows <- which(regexpr(range.data.end.rexp, f, perl = TRUE) == 1) - 1
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# Calculate number of ranges
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ranges.total <-
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ifelse(length(range.data.start.rows) == length(range.data.end.rows),
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length(range.data.start.rows),
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NA) #why would they not be equal?
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if (is.na(ranges.total)) {
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# Obviously something bad happened.
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# Do something about it. echo an error message perhaps.
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# But why would they not be equal?
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}
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# Header always precedes start of data
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range.header.end.rows <- range.data.start.rows - 2
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if (ranges.total > 1) {
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range.header.start.rows <- c(1, range.data.end.rows[2:length(range.data.end.rows)])
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} else {
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# Data in fact only contains one range
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range.header.start.rows <- 1
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}
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# Extract headers (as-is) and put them in a list (by range)
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headers.raw <- list()
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for (range in 1:ranges.total) {
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headers.raw[[range]] <- f[range.header.start.rows[range]:range.header.end.rows[range]]
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}
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####
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# Extract data (as-is) and put it an list (by range)
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data.raw <- list()
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for (range in 1:ranges.total) {
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data.raw[[range]] <- f[range.data.start.rows[range]:range.data.end.rows[range]]
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# Replace commas by dots
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data.raw[[range]] <- gsub(",", "\\.", data.raw[[range]])
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}
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# Specify header parameters to include in dataframe
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header.param.rexp <-
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c(DateTime = "^Date:",
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IntegrationTime = "^Integration Time \\(usec\\):",
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n_Averaged = "^Spectra Averaged:",
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Boxcar = "^Boxcar Smoothing:",
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CorrElectricDark = "^Correct for Electrical Dark:",
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StrobeLampEnabled = "^Strobe/Lamp Enabled:",
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CorrDetectorNonLin = "^Correct for Detector Non-linearity:",
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CorrStrayLight = "^Correct for Stray Light:",
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n_Pixels = "^Number of Pixels")
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# Collect data and header parameters in dataframes, by range in a list
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data <- list()
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for (range in 1:ranges.total) {
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zz <- textConnection(data.raw[[range]], "r")
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data[[range]] <- data.frame(stringsAsFactors = FALSE,
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sampleid,
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int2padstr(range, "0", 3),
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matrix(scan(zz, what = character()), ncol = 2, byrow = T))
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close(zz)
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# Collect header parameters
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for (param in 1:length(header.param.rexp)) {
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data[[range]] <-
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cbind(stringsAsFactors = FALSE,
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data[[range]],
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# Matches any word, digit, plus, or minus character
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# surrounded by parentheses at the end of the string
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sub("\\s\\([\\w\\d\\+\\-]+\\)$", "",
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strsplit(headers.raw[[range]][which(regexpr(unname(header.param.rexp[param]),
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headers.raw[[range]]) == 1)], ": ")[[1]][2],
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perl = TRUE))
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}
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names(data[[range]]) <-
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c("sampleid", "range", "wavelength", "intensity", names(header.param.rexp))
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}
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# Create a unified dataframe
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data.df <- data[[1]]
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if (ranges.total > 1) {
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for (range in 2:ranges.total) {
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data.df <- rbind(data.df, data[[range]])
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}
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}
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# Convert the DateTime column to more legibly (and compact) format
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data.df$DateTime <-
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format(as.POSIXct(gsub("\\s[A-Z]{4}\\s", " ", data.df$Date),
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format = "%a %b %d %H:%M:%S %Y"),
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format = "%Y-%m-%d %H:%M:%S")
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# Convert wavelength and intensity to numeric format
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mode(data.df$wavelength) <- "numeric"
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mode(data.df$intensity) <- "numeric"
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return(data.df)
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}
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@ -0,0 +1,154 @@
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source("/home/taha/chepec/chetex/common/R/common/ProvideSampleId.R")
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source("/home/taha/chepec/chetex/common/R/common/int2padstr.R")
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##################################################
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#!!!!!!!!!!!!!!!!!# mraw2df #!!!!!!!!!!!!!!!!!!!!#
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##################################################
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mraw2df <- function(txtfile) {
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## Description:
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## Reads TXT files with one or multiple ranges (XRD commander "save as txt")
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## Extracts both data (thth, intensity) and parameters
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## Usage:
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## mraw2df(txtfile)
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## Arguments:
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## txtfile: text string with full path to TXT file, which may
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## containing single or multiple data ranges
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## Value:
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## Dataframe with the following columns:
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## $ sampleid : chr
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## $ thth : num
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## $ counts (or cps) : num
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## $ steptime : num
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## $ stepsize : num
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## $ theta : num
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## $ khi : num
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## $ phi : num
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## $ x : num
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## $ y : num
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## $ z : num
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## $ divergence : num
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## $ antiscatter : num
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## $ cps (or counts) : num
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#
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range.header.start.rexp <- "^; \\(Data for Range" #regexp
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range.header.end.rexp <- "^_2THETA[^=]" #regexp
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# Read the input multirange file
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ufile <- file(uxdfile, "r")
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# Note that readLines apparently completely skips empty lines.
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# In that case line numbers do not match between source and f.
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f <- readLines(ufile, n=-1) #read _all_ lines from UXD file
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close(ufile)
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# Fetch a sampleid for the current job
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sampleid <- ProvideSampleId(uxdfile)
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# Look for header start rows
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range.header.start.rows <- which(regexpr(range.header.start.rexp, f) == 1)
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# Look for header end rows
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range.header.end.rows <- which(regexpr(range.header.end.rexp, f) == 1)
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# Calculate number of ranges
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ranges.total <-
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ifelse(length(range.header.start.rows) == length(range.header.end.rows),
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length(range.header.start.rows),
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NA) #why would they not be equal?
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if (is.na(ranges.total)) {
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# Obviously something bad happened.
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# Do something about it. echo an error message perhaps.
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# But why would they not be equal?
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}
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# Determine whether we have COUNTS or COUNTS PER SECOND in current UXD-file
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# Assuming it is the same for all ranges in this job (a safe assumption).
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if (f[range.header.end.rows][1] == "_2THETACOUNTS") {
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# we got counts
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counts.flag <- TRUE
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cps.flag <- FALSE
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}
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if (f[range.header.end.rows][1] == "_2THETACPS") {
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# we got counts per second
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counts.flag <-FALSE
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cps.flag <- TRUE
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}
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# Extract headers (as-is) and put them in a list (by range)
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headers.raw <- list()
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for (range in 1:ranges.total) {
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headers.raw[[range]] <- f[range.header.start.rows[range]:range.header.end.rows[range]]
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}
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# Data always start on the row after header end
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range.data.start.rows <- range.header.end.rows + 1
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# Data end rows precedes header with one row, except for the first range
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# But only if data contained more than one range, obviously. Let's make the code check for that
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if (ranges.total > 1) {
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range.data.end.rows <- c(range.header.start.rows[2:length(range.header.start.rows)] - 1, length(f))
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} else {
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# Data in fact only contains one range
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range.data.end.rows <- length(f)
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}
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####
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# Extract data (as-is) and put it an list (by range)
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data.raw <- list()
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for (range in 1:ranges.total) {
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data.raw[[range]] <- f[range.data.start.rows[range]:range.data.end.rows[range]]
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}
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# Specify header parameters to include in dataframe
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header.param.rexp <- c(steptime = "^_STEPTIME=",
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stepsize = "^_STEPSIZE=",
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theta = "^_THETA=",
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khi = "^_KHI=",
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phi = "^_PHI=",
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x = "^_X=",
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y = "^_Y=",
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z = "^_Z=",
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divergence = "^_DIVERGENCE=",
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antiscatter = "^_ANTISCATTER=")
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# Collect data and header parameters in dataframes, by range in a list
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data <- list()
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for (range in 1:ranges.total) {
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zz <- textConnection(data.raw[[range]], "r")
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data[[range]] <- data.frame(stringsAsFactors = F,
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sampleid,
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int2padstr(range, "0", 3),
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matrix(scan(zz, what = numeric()), ncol = 2, byrow = T))
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close(zz)
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# Collect header parameters
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for (param in 1:length(header.param.rexp)) {
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data[[range]] <- cbind(data[[range]],
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as.numeric(strsplit(headers.raw[[range]][which(regexpr(unname(header.param.rexp[param]),
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headers.raw[[range]]) == 1)], "=")[[1]][2]))
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}
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names(data[[range]]) <-
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c("sampleid", "range", "thth", ifelse(counts.flag, "counts", "cps"), names(header.param.rexp))
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}
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# Calculate the other of the pair counts <-> cps
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if (counts.flag) {
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for (range in 1:ranges.total) {
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data[[range]] <- cbind(data[[range]], cps = data[[range]]$counts / data[[range]]$steptime)
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}
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}
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if (cps.flag) {
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for (range in 1:ranges.total) {
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data[[range]] <- cbind(data[[range]], counts = data[[range]]$cps * data[[range]]$steptime)
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}
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}
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# Return a unified dataframe
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data.df <- data[[1]]
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if (ranges.total > 1) {
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for (range in 2:ranges.total) {
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data.df <- rbind(data.df, data[[range]])
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}
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}
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return(data.df)
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}
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@ -1,13 +1,10 @@
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# To source a bunch of files in the same directory
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sourceDir <- function(path, trace = TRUE) {
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for (nm in list.files(path, pattern = "\\.[Rr]$")) {
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if(trace) {
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cat(nm,":")
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}
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source(file.path(path, nm))
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if(trace) {
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cat("\n")
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}
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lsDir <- list.files(path, pattern = "\\.[Rr]$")
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for (i in lsDir) {
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if(trace) {cat(i, ":")}
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source(file.path(path, i))
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if(trace) {cat("\n")}
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}
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}
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}
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