R/dicom.R

In oro.dicom: Rigorous - DICOM Input / Output

##
## Copyright (c) 2010-2014, Brandon Whitcher
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## $Id: $
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dicomInfo <- function(fname, endian="little", flipud=TRUE, skip128=TRUE,
                      DICM=TRUE, skipSequence=FALSE, pixelData=TRUE,
                      warn=-1, debug=FALSE) {
  readDICOMFile(fname, endian=endian, flipud=flipud, 
                skipSequence=skipSequence, pixelData=pixelData,
                warn=warn, debug=debug)
}

dicomSeparate <- function(path, verbose=FALSE, counter=100, recursive=TRUE,
                          exclude=NULL, ...) {
  readDICOM(path, recursive=recursive, exclude=exclude, verbose=verbose,
            counter=counter, ...)
}

readDICOM <- function(path, recursive=TRUE, exclude=NULL, verbose=FALSE,
                      counter, ...) {
  if (length(list.files(path)) == 0 && file.exists(path)) {
    filenames <- path
  } else {
    if (recursive) {
      filenames <- list.files(path, full.names=TRUE, recursive=TRUE)
    } else {
      filenames <- list.files(path, full.names=TRUE)
    }
  }
  if (! is.null(exclude)) {
    filenames <- grep(exclude, filenames, ignore.case=TRUE, value=TRUE,
                      invert=TRUE)
  }
  nfiles <- length(filenames)
  nch <- nchar(as.character(nfiles))
  headers <- images <- vector("list", nfiles)
  names(images) <- names(headers) <- filenames
  if (verbose) {
    cat(" ", nfiles, "files to be processed by readDICOM()", fill=TRUE)
    tpb <- txtProgressBar(min=0, max=nfiles, style=3)
  }
  for (i in 1:nfiles) {
    if (verbose) {
      setTxtProgressBar(tpb, i)
    }
    dcm <- readDICOMFile(filenames[i], ...)
    images[[i]] <- dcm$img
    headers[[i]] <- dcm$hdr
  }
  if (verbose) {
    close(tpb)
  }
  list(hdr=headers, img=images)
}