taha
/
R-common
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Re-wrote muxd2df() from scratch.

Browse Source 
To make it able to include parameters as well as data in the returned df.
muxd2df() now works satisfactorily, outputs parameters such as steptime,
theta, and cps as well as thth and counts.
Other minor changes mostly updates of source file pointers.
master
Taha Ahmed 13 years ago
parent b976bd3fa4
commit b55af5d478
6 changed files with 159 additions and 8 deletions
Show Stats Download Patch File Download Diff File

2
AUTOLAB/amp2df.R
Unescape Escape View File

@ -1,4 +1,4 @@
source("/home/taha/chepec/chetex/common/R/common.R")
source("/home/taha/chepec/chetex/common/R/common/ProvideSampleId.R")
##################################################
#################### amp2df ######################

146
XRD-TF/muxd2df.R
Unescape Escape View File

@ -1,7 +1,151 @@
source("/home/taha/chepec/chetex/common/R/common/ProvideSampleId.R")
##################################################
################### muxd2df ######################
##################################################
muxd2df <- function(uxdfile) {
## Description:
## Reads UXD files with multiple ranges (converted using XCH v1.0)
## Extracts both data (thth, intensity) and parameters
## Also automatically calculates cps is counts are present, and vice versa
## (note that this depends on specific strings in the UXD format).
## Usage:
## muxd2df(uxdfile)
## Arguments:
## uxdfile: text string with full path to UXD file
## Value:
## Dataframe with the following columns:
## $ sampleid : chr
## $ thth : num
## $ counts (or cps) : num
## $ steptime : num
## $ stepsize : num
## $ theta : num
## $ khi : num
## $ phi : num
## $ x : num
## $ y : num
## $ z : num
## $ divergence : num
## $ antiscatter : num
## $ cps (or counts) : num
#
range.header.start.rexp <- "^; \\(Data for Range" #regexp
range.header.end.rexp <- "^_2THETA[^=]" #regexp
# Read the input multirange file
ufile <- file(uxdfile, "r")
# Note that readLines apparently completely skips empty lines.
# In that case line numbers do not match between source and f.
f <- readLines(ufile, n=-1) #read _all_ lines from UXD file
close(ufile)
# Fetch a sampleid for the current job
sampleid <- ProvideSampleId(uxdfile)
# Look for header start rows
range.header.start.rows <- which(regexpr(range.header.start.rexp, f) == 1)
# Look for header end rows
range.header.end.rows <- which(regexpr(range.header.end.rexp, f) == 1)
# Calculate number of ranges
ranges.total <- ifelse(length(range.header.start.rows) == length(range.header.end.rows), length(range.header.start.rows), NA)
if (is.na(ranges.total)) {
# Obviously something bad happened.
# Do something about it. echo an error message perhaps.
}
# Determine whether we have COUNTS or COUNTS PER SECOND in current UXD-file
# Assuming it is the same for all ranges in this job (a safe assumption).
if (f[range.header.end.rows][1] == "_2THETACOUNTS") {
# we got counts
counts.flag <- TRUE
cps.flag <- FALSE
}
if (f[range.header.end.rows][1] == "_2THETACPS") {
# we got counts per second
counts.flag <-FALSE
cps.flag <- TRUE
}
# Extract headers (as-is) and put them in a list (by range)
headers.raw <- list()
for (range in 1:ranges.total) {
headers.raw[[range]] <- f[range.header.start.rows[range]:range.header.end.rows[range]]
}
# Data always start on the row after header end
range.data.start.rows <- range.header.end.rows + 1
# Data end rows precedes header with one row, except for the first range
range.data.end.rows <- c(range.header.start.rows[2:length(range.header.start.rows)] - 1, length(f))
# Extract data (as-is) and put it an list (by range)
data.raw <- list()
for (range in 1:ranges.total) {
data.raw[[range]] <- f[range.data.start.rows[range]:range.data.end.rows[range]]
}
# Specify header parameters to include in dataframe
header.param.rexp <- c(steptime = "^_STEPTIME=",
stepsize = "^_STEPSIZE=",
theta = "^_THETA=",
khi = "^_KHI=",
phi = "^_PHI=",
x = "^_X=",
y = "^_Y=",
z = "^_Z=",
divergence = "^_DIVERGENCE=",
antiscatter = "^_ANTISCATTER=")
# Collect data and header parameters in dataframes, by range in a list
data <- list()
for (range in 1:ranges.total) {
zz <- textConnection(data.raw[[range]], "r")
data[[range]] <- data.frame(stringsAsFactors = F,
sampleid,
matrix(scan(zz, what = numeric()), ncol = 2, byrow = T))
close(zz)
# Collect header parameters
for (param in 1:length(header.param.rexp)) {
data[[range]] <- cbind(data[[range]],
as.numeric(strsplit(headers.raw[[range]][which(regexpr(unname(header.param.rexp[param]),
headers.raw[[range]]) == 1)], "=")[[1]][2]))
}
names(data[[range]]) <- c("sampleid", "thth", ifelse(counts.flag, "counts", "cps"), names(header.param.rexp))
}
# Calculate the other of the pair counts <-> cps
if (counts.flag) {
for (range in 1:ranges.total) {
data[[range]] <- cbind(data[[range]], cps = data[[range]]$counts / data[[range]]$steptime)
}
}
if (cps.flag) {
for (range in 1:ranges.total) {
data[[range]] <- cbind(data[[range]], counts = data[[range]]$cps * data[[range]]$steptime)
}
}
# Return a unified dataframe
data.df <- data[[1]]
for (range in 2:ranges.total) {
data.df <- rbind(data.df, data[[range]])
}
return(data.df)
}
#### OLD VERSION - DEPRECATE
##################################################
################### muxd2df ######################
##################################################
muxd2df <- function(uxdfile, range.descriptor) {
muxd2df.old <- function(uxdfile, range.descriptor) {
# Function that reads an UXD file which contains several ranges
# (created in a programmed run, for example)
# Arguments

4
XRD-TF/pdf2df.R
Unescape Escape View File

@ -5,8 +5,8 @@ pdf2df <- function(pdffile) {
# Function for extracting information from ICDD PDF XML-files
# For example the PDF files produced by the PDF database at Angstrom's X-ray lab
# NOTE: sometimes intensity values are specified as less than some value.
# In those cases, this function simply strips the less-than character.
# (Perhaps not true, see the int.Tex column)
# In those cases, the lt sign will be preserved in the column int.Tex.
# The intensity column, on the other hand, is numeric and so strips off the lt sign.
# ARGS: pdffile (complete path and filename to PDF file)
# VALUE: dataframe with 9 columns:
# thth angles (numeric),

4
XRD-TF/scherrer.R
Unescape Escape View File

@ -1,3 +1,5 @@
source("/home/taha/chepec/chetex/common/R/common/as.radians.R")
##################################################
################## scherrer ######################
##################################################
@ -8,7 +10,7 @@ scherrer <- function(integralbreadth, thth, wavelength = 1.54056, shapeconstant
# wavelength - X-ray wavelength used (default 1.54056 A, Cu Ka)
# shapeconstant - Scherrer constant (default spherical, ~0.9)
# VALUE: vector with size parameters
## REQUIRES: as.radians(), source("/home/taha/chepec/chetex/common/R/common.R")
## REQUIRES: as.radians()
D <- (shapeconstant * wavelength) / (as.radians(integralbreadth) * cos(as.radians(thth)))
# cos() - angles must be in radians, not degrees!
return(D) #units of angstrom

6
common/ConvertRefPot.R
Unescape Escape View File

@ -1,6 +1,6 @@
source(SHE2AVS.R)
source(AVS2SHE.R)
source(ConvertRefPotEC.R)
source("/home/taha/chepec/chetex/common/R/common/SHE2AVS.R")
source("/home/taha/chepec/chetex/common/R/common/AVS2SHE.R")
source("/home/taha/chepec/chetex/common/R/common/ConvertRefPotEC.R")
##################################################
################# ConvertRefPot ##################

5
common/is.wholenumber.R
Unescape Escape View File

@ -0,0 +1,5 @@
# This function was copied from R's documentation (see ?is.integer).
is.wholenumber <- function(x, tol = .Machine$double.eps^0.5) {
abs(x - round(x)) < tol
}
Write Preview
Loading…
Cancel
Save