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##################################################
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################### pdf2df #######################
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##################################################
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pdf2df <- function(pdffile) {
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# Function for extracting information from ICDD PDF XML-files
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# For example the PDF files produced by the PDF database at Angstrom's X-ray lab
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# NOTE: sometimes intensity values are specified as less than some value.
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# In those cases, the lt sign will be preserved in the column int.Tex.
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# The intensity column, on the other hand, is numeric and so strips off the lt sign.
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# ARGS: pdffile (complete path and filename to PDF file)
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# VALUE: dataframe with 9 columns:
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# thth angles (numeric),
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# d (numeric),
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# h index (numeric),
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# k index (numeric),
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# l index (numeric),
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# hkl indices (string),
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# hkl.TeX indices formatted for LaTeX (string),
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# intensity (numeric),
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# int.TeX intensity formatted for LaTeX (string)
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# attr: This function sets the following attributes:
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# ApplicationName,
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# ApplicationVersion,
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# pdfNumber,
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# chemicalformula,
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# empiricalformula,
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# wavelength
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#
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require(XML)
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doc <- xmlTreeParse(pdffile)
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pdf <- xmlRoot(doc)
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rmchar <- "[^0-9]"
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#
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angles <- data.frame(NULL)
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for (i in 1:length(pdf[["graphs"]][["stick_series"]])) {
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angles <- rbind(angles, data.frame(stringsAsFactors = FALSE,#
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thth = as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["theta"]])),
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d = as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["da"]])),
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h = as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["h"]])),
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k = as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["k"]])),
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l = as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["l"]])),
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hkl = paste(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["h"]]),
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xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["k"]]),
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xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["l"]]), sep = ""),
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hkl.TeX = paste("\\mbox{$", ifelse(as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["h"]])) < 0,
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paste("\\bar{", abs(as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["h"]]))),
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"}", sep = ""),
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xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["h"]])),
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"\\,", ifelse(as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["k"]])) < 0,
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paste("\\bar{", abs(as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["k"]]))),
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"}", sep = ""),
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xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["k"]])),
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"\\,", ifelse(as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["l"]])) < 0,
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paste("\\bar{", abs(as.numeric(xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["l"]]))),
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"}", sep = ""),
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xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["l"]])),
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"$}", sep = "", collapse = ""),
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intensity = as.numeric(gsub(rmchar, "", xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["intensity"]]))),
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int.TeX = paste("{", xmlValue(pdf[["graphs"]][["stick_series"]][[i]][["intensity"]]), "}", sep = "")
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))
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}
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#
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attr(angles, "ApplicationName") <- xmlAttrs(pdf)[[1]]
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attr(angles, "ApplicationVersion") <- xmlAttrs(pdf)[[2]]
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attr(angles, "pdfNumber") <- xmlValue(pdf[["pdf_data"]][["pdf_number"]])
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attr(angles, "chemicalformula") <- gsub("[ ]", "", xmlValue(pdf[["pdf_data"]][["chemical_formula"]]))
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attr(angles, "empiricalformula") <- gsub("[ ]", "", xmlValue(pdf[["pdf_data"]][["empirical_formula"]]))
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attr(angles, "wavelength") <- as.numeric(xmlValue(pdf[["graphs"]][["wave_length"]]))
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# Caution: Do not subset. Subsetting causes all attributes to be lost.
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return(angles)
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}
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