add multi data segment support for read.FCSheader RGLab/ncdfFlow#47

RGLab · Jul 31, 2019 · dce6fde · dce6fde
1 parent ec6421d
commit dce6fde
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Showing 3 changed files with 27 additions and 10 deletions.
diff --git a/R/IO.R b/R/IO.R
@@ -41,7 +41,7 @@ isFCSfile <- function(files)
 #' @param path Directory where to look for the files.
 #' @param keyword An optional character vector that specifies the FCS keyword
 #' to read.
-#' @param emptyValue see \code{link[flowCore]{read.FCS}}
+#' @param ... other arguments passed to \code{link[flowCore]{read.FCS}}
 #' 
 #' @return A list of character vectors. Each element of the list correspond to
 #' one FCS file.
@@ -60,7 +60,7 @@ isFCSfile <- function(files)
 #' samp
 #' 
 #' @export
-read.FCSheader <- function(files, path=".", keyword=NULL, emptyValue = TRUE)
+read.FCSheader <- function(files, path=".", keyword=NULL, ...)
 {
 
     stopifnot(is.character(files), length(files)>=1, files!="")
@@ -69,7 +69,7 @@ read.FCSheader <- function(files, path=".", keyword=NULL, emptyValue = TRUE)
         files = file.path(path, files)
     res <- lapply(files, function(file){
 
-                              thisRes <- try(header(file, emptyValue = emptyValue), silent = TRUE)
+                              thisRes <- try(header(file, ...), silent = TRUE)
                               if(class(thisRes) == "try-error"){
                                 stop(thisRes, file)
                               }else
@@ -81,10 +81,10 @@ read.FCSheader <- function(files, path=".", keyword=NULL, emptyValue = TRUE)
     res
 }
 
-header <- function(files,emptyValue=TRUE){
+header <- function(files, ...){
     con <- file(files, open="rb")
-    offsets <- readFCSheader(con)
-    txt     <- readFCStext(con, offsets,emptyValue=emptyValue)
+    offsets <- findOffsets(con, ...)
+    txt     <- readFCStext(con, offsets, ...)
     close(con)
     txt
 }
@@ -478,7 +478,7 @@ readFCSgetPar <- function(x, pnam, strict=TRUE)
 ## ==========================================================================
 ## Find all data sections in a file and record their offsets.
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-findOffsets <- function(con,emptyValue=TRUE, dataset, ...)
+findOffsets <- function(con,emptyValue=TRUE, dataset = NULL, ...)
 {
     offsets <- readFCSheader(con)
     offsets <- matrix(offsets, nrow = 1, dimnames = list(NULL, names(offsets)))
@@ -629,7 +629,7 @@ readFCSheader <- function(con, start=0)
 ## ==========================================================================
 ## parse FCS file text section
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-readFCStext <- function(con, offsets,emptyValue, cpp = TRUE, ...)
+readFCStext <- function(con, offsets,emptyValue = TRUE, cpp = TRUE, ...)
 {
 
     seek(con, offsets["textstart"])

diff --git a/man/read.FCSheader.Rd b/man/read.FCSheader.Rd
diff --git a/tests/testthat/test-IO.R b/tests/testthat/test-IO.R
@@ -11,6 +11,23 @@ rownames(expectPD) <- paste0(rownames(expectPD), ".fcs")
 tmpdir <- tempfile()
 
 write.flowSet(fs, tmpdir)
+
+
+test_that("read.FCSheader--multi data segment", {
+  dataPath <- "~/rglab/workspace/flowCore/misc/"
+  filename  <- file.path(dataPath, "multi-datasegment.fcs")
+  skip_if_not(file.exists(filename))
+
+  expect_warning(txt <- read.FCSheader(filename)[[1]], "39 additional data")
+  expect_equal(txt[['$TOT']], "1244")
+
+  txt <- read.FCSheader(filename, dataset = 1)[[1]]
+  expect_equal(txt[['$TOT']], "1244")
+
+  txt <- read.FCSheader(filename, dataset = 10)[[1]]
+  expect_equal(txt[['$TOT']], "955")
+
+})
 test_that("write.FCS--write correct $BEGINDATA",{
 
         mat <- matrix(1:30,ncol = 3, dimnames = list(NULL, letters[1:3]))