[Zooimage-commits] r124 - pkg/zooimage/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 4 13:51:05 CEST 2009
Author: romain
Date: 2009-05-04 13:51:05 +0200 (Mon, 04 May 2009)
New Revision: 124
Modified:
pkg/zooimage/R/ZIClass.r
pkg/zooimage/R/gui.r
pkg/zooimage/R/utilities.r
pkg/zooimage/R/zid.r
pkg/zooimage/R/zim.r
Log:
ixed minor proble?\195?\185ms
Modified: pkg/zooimage/R/ZIClass.r
===================================================================
--- pkg/zooimage/R/ZIClass.r 2009-04-27 14:16:57 UTC (rev 123)
+++ pkg/zooimage/R/ZIClass.r 2009-05-04 11:51:05 UTC (rev 124)
@@ -47,9 +47,9 @@
# algorithm
algorithm <- algorithm[1]
algo.fun <- match.fun( algorithm )
- ZI.class <- algo.fun(Formula, data = df, ...),
+ ZI.class <- algo.fun(Formula, data = df, ...)
ZI.class <- structure( ZI.class,
- class = c("ZIClass", class(ZI.class))
+ class = c("ZIClass", class(ZI.class)),
algorithm = algorithm,
package = package,
calc.vars = CV,
Modified: pkg/zooimage/R/gui.r
===================================================================
--- pkg/zooimage/R/gui.r 2009-04-27 14:16:57 UTC (rev 123)
+++ pkg/zooimage/R/gui.r 2009-05-04 11:51:05 UTC (rev 124)
@@ -290,11 +290,10 @@
# }}}
# {{{ Img
-"acquireImg" <-
- function() {
- # Show an assitant dialog box allowing to choose between VueScan and a different
- # acquisition program... remember that setting in the registry under Windows
-
+#' Show an assitant dialog box allowing to choose between VueScan and a different
+#' acquisition program... remember that setting in the registry under Windows
+"acquireImg" <- function() {
+
# First read the registry to determine which software in recorded there...
Asoft <- getKey("AcquisitionSoftware", "VueScan")
if (Asoft == "VueScan") {
@@ -352,33 +351,46 @@
# Get a list of 'ZIEimport' objects currently loaded in memory
### TODO... Rework everything. What follows is old code!
- ImgFilters <- as.matrix(data.frame(title = c("Tiff image files (*.tif)",
- "Jpeg image files (*.jpg)", "Zooimage import extensions (Import_*.zie)", "Table and ImportTemplate.zie (*.txt)"), #, "FlowCAM zipped files (*.zfc)"),
+ ImgFilters <- as.matrix(data.frame(
+ title = c(
+ "Tiff image files (*.tif)",
+ "Jpeg image files (*.jpg)",
+ "Zooimage import extensions (Import_*.zie)",
+ "Table and ImportTemplate.zie (*.txt)"), #, "FlowCAM zipped files (*.zfc)"),
pattern = c("*.tif", "*.jpg", "Import_*.zie", "*.txt"))) #, "*.zfc")))
+
# Get last image type that was selected
Index <- as.numeric(getKey("ImageIndex", "1"))
+
# Get a list of images
Images <- choose.files(caption = "Select data to import...",
multi = TRUE, filters = ImgFilters, index = Index)
+
# Look if there is at least one image selected
- if (length(Images) == 0) return(invisible())
+ if (length(Images) == 0) {
+ return(invisible())
+ }
dir <- dirname(Images[1])
Images <- basename(Images)
+
+ has <- function( extension, pattern = extensionPattern(extension) ){
+ grepl( pattern, Images[1])
+ }
+
# Determine which kind of data it is
- if (regexpr("[.][zZ][fF][cC]$", Images[1]) > 0) {
- setKey("ImageIndex", "5")
+ if ( has( ".zfc" ) ){
+ setKey("ImageIndex", "5")
return(importFlowCamFiles(path = dir, ZFCfiles = Images, check = FALSE, show.log = TRUE))
- } else if (regexpr("^Import_.*[.]zie$", Images[1]) > 0) {
- pattern <- "[.][zZ][iI][eE]$"
- setKey("ImageIndex", "3")
- return(make.zie(path = dir, Filemap = Images[1], check = TRUE, show.log = TRUE))
- } else if (regexpr("[.][tT][xX][tT]$", Images[1]) > 0) {
- pattern <- "[.][tT][xX][tT]$"
- setKey("ImageIndex", "4")
- logProcess("Creating .zie file...")
- cat("Creating .zie file...\n")
- ziefile <- compile.zie(path = dir, Tablefile = Images[1])
- cat("...OK!\n")
+ } else if ( has( pattern = "^Import_.*[.]zie$") ) {
+ setKey("ImageIndex", "3")
+ return(make.zie(path = dir, Filemap = Images[1], check = TRUE, show.log = TRUE))
+ } else if ( has( "txt" ) ) {
+ pattern <- extensionPattern( ".txt" )
+ setKey("ImageIndex", "4")
+ logProcess("Creating .zie file...")
+ cat("Creating .zie file...\n")
+ ziefile <- compile.zie(path = dir, Tablefile = Images[1])
+ cat("...OK!\n")
res <- make.zie(path = dirname(ziefile), Filemap = basename(ziefile), check = TRUE, show.log = TRUE)
if (res) { # Everything is fine...
# Move the table and copy the template to the '_raw' subdirectory too
@@ -386,27 +398,30 @@
tplfile <- file.path(path, Images[1])
file.rename(tplfile, file.path(path, "_raw", basename(tplfile)))
# Move also possibly the .xls equivalent
- xlsfile <- sub("\\.[tT][xX][tT]$", ".xls", tplfile)
- if (xlsfile != tplfile && file.exists(xlsfile))
+ xlsfile <- sub( pattern, ".xls", tplfile)
+ if (xlsfile != tplfile && file.exists(xlsfile)){
file.rename(xlsfile, file.path(path, "_raw", basename(xlsfile)))
+ }
file.rename(file.path(path, "ImportTemplate.zie"), file.path(path, "_raw", "ImportTemplate.zie"))
}
return(res)
- } else if (regexpr("[.][tT][iI][fF]$", Images[1]) > 0) {
- pattern <- "[.][tT][iI][fF]$"
+ } else if ( has( ".tif" ) ){
+ pattern <- extensionPattern (".tif" )
setKey("ImageIndex", "1")
- } else if (regexpr("[.][jJ][pP][gG]$", Images[1]) > 0) {
- pattern <- "[.][jJ][pP][gG]$"
+ } else if ( has( "jpg") ) {
+ pattern <- extensionPatter( "jpg" )
setKey("ImageIndex", "2")
} else stop("Unrecognized data type!")
+
# If there is no special treatment, just make all required .zim files for currently selected images
make.zim(dir = dir, pattern = pattern, images = Images, show.log = TRUE)
}
+# TODO: call the batch version of imagej zooimage plugins
"processImg" <- function() {
# Display a dialog box telling how to process images using ImageJ
# When the user clicks on 'OK', ImageJ is started... + the checkbox 'close R'
- res <- modalAssistant(paste(getTemp("ZIname"), "picture processing"),
+ res <- modalAssistant(paste(getTemp("ZIname"), "picture processing"),
c(paste("Once images are acquired and imported into", getTemp("ZIname")),
"(they have correct associated metadata), they must be",
"processed.",
@@ -421,8 +436,9 @@
# Analyze result
if (res == "ID_CANCEL") return(invisible())
# Start ImageJ
- if (!is.null(getOption("ImageEditor")))
+ if (!is.null(getOption("ImageEditor"))){
startPgm("ImageEditor", switchdir = TRUE, iconize = TRUE)
+ }
# Do we have to close R?
if (res == "1") q()
}
@@ -1060,5 +1076,19 @@
}
# }}}
+# {{{ ijplugin
+ijplugin <- function( zimfile,
+ ij.plugin = c("Scanner_Gray16", "MacroPhoto_Gray16", "Scanner_Color", "Microscope_Color" ) ){
+
+ cmd <- sprintf( 'java -Xmx900m -cp .:"%s":"%s" org.sciviews.zooimage.ZooImage %s "%s"',
+ system.file( "imagej", "ij.jar", package = "zooimage" ),
+ system.file( "imagej", "plugins", "_zooimage.jar", package = "zooimage" ),
+ ij.plugin,
+ zimfile )
+ # system( cmd, intern = TRUE )
+ cmd
+}
+# }}}
+
# :tabSize=4:indentSize=4:noTabs=false:folding=explicit:collapseFolds=1:
Modified: pkg/zooimage/R/utilities.r
===================================================================
--- pkg/zooimage/R/utilities.r 2009-04-27 14:16:57 UTC (rev 123)
+++ pkg/zooimage/R/utilities.r 2009-05-04 11:51:05 UTC (rev 124)
@@ -405,7 +405,7 @@
combine <- function( ..., .list = list(...) ){
force(.list)
mergefun <- function(x,y){
- if(all( sort(names(x)) == sort(names(y)) ){
+ if( all( sort(names(x)) == sort(names(y) ) ) ) {
rbind( x,y )
} else{
merge( x, y, all = TRUE )
Modified: pkg/zooimage/R/zid.r
===================================================================
--- pkg/zooimage/R/zid.r 2009-04-27 14:16:57 UTC (rev 123)
+++ pkg/zooimage/R/zid.r 2009-05-04 11:51:05 UTC (rev 124)
@@ -174,7 +174,6 @@
# Avoid collecting duplicate informations about fractions
fracdup <- duplicated(fractions)
-
results <- lapply( seq.int( 1, length(dat1files) ), function(i){
dat1path <- file.path(zidir, dat1files[i])
Modified: pkg/zooimage/R/zim.r
===================================================================
--- pkg/zooimage/R/zim.r 2009-04-27 14:16:57 UTC (rev 123)
+++ pkg/zooimage/R/zim.r 2009-05-04 11:51:05 UTC (rev 124)
@@ -282,7 +282,7 @@
# Note: use only the fraction, that is, SCS.xxxx-xx-xx.SS+F from SCS.xxxx-xx-xx.SS+Fnn)
# If there are duplicates, only extract first one
zimfiles <- sprintf( "%s.zim",
- get.sampleinfo(zipfiles, "fraction", ext = extensionPattern(".zip") )
+ get.sampleinfo(zipfiles, "fraction", ext = extensionPattern(".zip") ) )
keep <- !duplicated(zimfiles)
zimfiles <- zimfiles[keep]
zipfiles <- zipfiles[keep]
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