From noreply at r-forge.r-project.org  Tue Dec  2 09:13:10 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  2 Dec 2014 09:13:10 +0100 (CET)
Subject: [Zooimage-commits] r248 - in pkg/zooimage: . R inst/etc man
Message-ID: <20141202081310.E6EA3183D55@r-forge.r-project.org>

Author: phgrosjean
Date: 2014-12-02 09:13:10 +0100 (Tue, 02 Dec 2014)
New Revision: 248

Modified:
   pkg/zooimage/DESCRIPTION
   pkg/zooimage/NEWS
   pkg/zooimage/R/correction.R
   pkg/zooimage/R/import.R
   pkg/zooimage/R/planktonSorter.R
   pkg/zooimage/R/utilities.R
   pkg/zooimage/inst/etc/ZooImageManual.pdf
   pkg/zooimage/man/correctError.Rd
   pkg/zooimage/man/import.Rd
   pkg/zooimage/man/zooimage.package.Rd
Log:
Upgrade to version 5.1.0

Modified: pkg/zooimage/DESCRIPTION
===================================================================
--- pkg/zooimage/DESCRIPTION	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/DESCRIPTION	2014-12-02 08:13:10 UTC (rev 248)
@@ -1,8 +1,8 @@
 Package: zooimage
 Type: Package
 Title: Analysis of numerical zooplankton images
-Version: 4.0-0
-Date: 2014-02-23
+Version: 5.1-0
+Date: 2014-12-02
 Author: Philippe Grosjean [aut, cre],
   Kevin Denis [aut]
 Authors at R: c(person("Philippe", "Grosjean", role = c("aut", "cre"),

Modified: pkg/zooimage/NEWS
===================================================================
--- pkg/zooimage/NEWS	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/NEWS	2014-12-02 08:13:10 UTC (rev 248)
@@ -1,5 +1,37 @@
 = zooimage News
 
+== Changes in zooimage 5.1-0
+
+* calcVars()/calcVarsVIS() and dropVars() are reworked to used only FIT_xxx
+  variables in case of use of the FlowCAM (and to calculated many derived vars
+  from there). This way, there is no need any more of a second image analysis
+  in ImageJ.
+  
+
+== Changes in zooimage 5.0-0
+
+* importFlowCAM() and readFlowCAMlst() are reworked to create complete .zidb
+  files using all metadata from various version of Fluid Imaging's Visual
+  Spreadsheet software.
+  
+
+== Changes in zooimage 4.0-2
+
+* correctError() has now a mode argument allowing to run the analysis in 'demo'
+  and 'stat' mode, in addition to the default 'validation' mode
+  
+* The internal errorCorrection() function did not intialized ntrusted and
+  nsuspect in 'demo' mode
+  
+* New version of the user manual (explanations of the new functions).
+
+
+== Changes in zooimage 4.0-1
+
+* A bug (non initialisation of the confusion matrix) prevented to use
+  errorCorrection() in demo or stat mode. Corrected.
+
+
 == Changes in zooimage 4.0-0
 
 * Error correction functions added: correctError().

Modified: pkg/zooimage/R/correction.R
===================================================================
--- pkg/zooimage/R/correction.R	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/R/correction.R	2014-12-02 08:13:10 UTC (rev 248)
@@ -357,6 +357,10 @@
 	## data -- the dataset to study
 	if (missing(data) || !inherits(data, "ZIDat"))
 		stop("data must be a ZIdat object")
+## Temporary hack to eliminate possible unwanted columns!
+data$Id.1 <- NULL
+data$X.Item.1 <- NULL
+	
 	## classifier -- the classifier to use to classify particles
 	if (missing(classifier) || !inherits(classifier, "ZIClass"))
 		stop("classifier must be a ZIClass object")
@@ -451,8 +455,7 @@
 			if (is.null(testdir))
 				testdir <<- file.path(tempdir(),
 					noExtension(zidb))
-			if (file.exists(testdir)) {
-				
+			if (file.exists(testdir)) {			
 				res <- dlgMessage(paste("Temporary validation directory already",
 					"exists. Do we erase old data there?"), type = "okcancel")$res
 				if (res == "cancel")
@@ -462,6 +465,7 @@
 			dir.create(testdir, recursive = TRUE)
 			if (!file.exists(testdir))
 				stop("cannot create 'testdir'!")
+			testdir <<- normalizePath(testdir)
 			## Put required files there: create the planktonSorter directory
 			plSort <- file.path(testdir, "planktonSorter")
 			dir.create(plSort)
@@ -593,6 +597,8 @@
 		if (step < 1) {
 			## At first time, take a random subsample
 			## Same as considering everything as suspect
+#PhG			nsuspect <<- nobs
+#PhG			ntrusted <<- 0
 			sample.ids <- sample(1:nobs, size = sample.size)
 			corr$Step[sample.ids] <<- step
 			corr$RdValidated[sample.ids] <<- step
@@ -792,7 +798,8 @@
 		}
 		
 		## Error in the different fractions
-		if (mode != "validation") {
+#PhG		if (mode != "validation") {
+		if (mode == "stat") {
 			error <- validated != corr$Predicted
 			errInFract <- .errorInFractions(suspect = corr$Suspect,
 				error = error, validated = corr$Validated,
@@ -890,8 +897,10 @@
 			step.manual <<- TRUE
 		} else if (testset.validated) {
 			step.manual <<- FALSE
-			#getTest()
-			#correct()
+if (mode == "stat") {
+	getTest()
+	correct()
+}
 			cat(paste("Step", step + 1, "finished \n"))
 			step <<- step + 1
 		} else warning("You have to complete the validation first \n")
@@ -915,9 +924,9 @@
 
 	processDemo <- function () {
 		if (sample.size > 0) {
+#PhG			process()
+#PhG			validate()
 			process()
-			validate()
-			process()
 		} else cat("Correction done!\n")
 	}
 

Modified: pkg/zooimage/R/import.R
===================================================================
--- pkg/zooimage/R/import.R	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/R/import.R	2014-12-02 08:13:10 UTC (rev 248)
@@ -1,7 +1,22 @@
 ## ZooImage >= 3 importation routines
+## TODO:
+## - Import data with replicates as subdirs of one common dir
+## - Import grayscale data from a "grey" subdir of common dir, or in a first stage,
+##   do not use any subdir data that do not contain a .lst file (cf, data are
+##   in subdirs of "grey" dir)
+## - Warning: do not allow to mix, say 10x and 4x in the same sample! => check this!
+## - Replicates are AR.B25.2014-05-19.300A4X.01, .02, .03, ... => correct label from there?
+## - Use jpeg format for non color vignettes + check the difference in weight and
+##   speed of loading in R
+## - Calculate default concentration values, using $Fluid$TotalVolumeML assuming
+##   no dilution of the sample... SubPart is TotalVolumeML, SubCell = 1, VolIni = 1
+## - rajouter ?chelle de taille dans les vignettes
+## - Note: using jpeg instead of png: 10sec instead of 14sec, and 4.9Mb instead of 14.7Mb
+##   loading time for 25 vignettes faster too.
 
 #### Importation of FlowCAM data without image reanalysis ######################
 ## Read a FlowCAM .ctx file
+## TODO: add label everywhere in front of each table
 readFlowCAMctx <- function (ctx, stop.it = TRUE)
 {
 	## Check arguments
@@ -11,6 +26,10 @@
 		if (stop.it)
 			stop("'ctx' must be an existing (.ctx) file") else return(NULL)
 	
+	## Get the label from the directory containing the data
+	label <- basename(dirname(ctx))
+	if (label == ".") label <- basename(getwd())
+	
 	## Read .ctx data
 	dat <- scan(ctx, what = character(), sep = "\t", skip = 0,
 		blank.lines.skip = TRUE, flush = TRUE, quiet = TRUE, comment.char = "")
@@ -39,10 +58,12 @@
 	## We need these keys that may not be present in old .ctx files	
 	if (is.null(V$Fluid$TotalVolumeML)) {
 		## Volume calculation
+		cst <- V$Fluid$CalibConstant
+		if (is.null(cst)) cst <- V$Fluid$CalibrationConstant
 		Height <- (V$CaptureRegion$AcceptableBottom -
-			V$CaptureRegion$AcceptableTop) * V$Fluid$CalibConstant
+			V$CaptureRegion$AcceptableTop) * cst
 		Width <- (V$CaptureRegion$AcceptableRight -
-			V$CaptureRegion$AcceptableLeft) * V$Fluid$CalibConstant
+			V$CaptureRegion$AcceptableLeft) * cst
 		Area <- Height * Width
 		## Volume of one image
 		Volume <- (Area / (1e8)) * (V$Fluid$FlowCellDepth / 10000) # mL
@@ -72,6 +93,36 @@
 	if (length(secs) == 0) secs <- 0
 	V$RunTermination$MaxRunTime <- mins * 60 + secs
 	
+	## Possibly read also data from _notes.txt
+    notes <- sub("\\.ctx$", "_notes.txt", ctx)
+	if (file.exists(notes)) {
+		## TODO: parse key=value items
+		notesData <- readLines(notes, warn = FALSE)	
+		notesData <- paste(notesData, collapse = "\n") 
+	} else noteData <- ""
+	
+	## TODO: check there is no Fraction, Process and Subsample entries yet!
+	
+	## Add Fraction data
+	V$Fraction <- data.frame(Code = "", Min = -1, Max = -1)
+	
+	## Add Process information
+	useESD <- V$CaptureParameters$UseESDForCapture
+	if (is.null(useESD)) useECD <- FALSE else useECD <- useESD != 1
+	V$Process <- data.frame(Version = "1.0-0", Method = "Direct VS import",
+		MinSize = as.numeric(V$CaptureParameters$MinESD)/1000, # In mm
+		MaxSize = as.numeric(V$CaptureParameters$MaxESD)/1000, # In mm
+		UseECD = useECD)
+	
+	## Add Subsample information
+	## TODO: get this from _notes.txt... Here, assume using 10mL / 1L
+	
+	V$Subsample <- data.frame(SubPart = 0.01, SubMethod = 1,
+		CellPart = 1, Replicates = 1, VolIni = 1, VolPrec = 0.1)
+	
+	## Add Label in front of each table
+	V <- lapply(V, function (x) cbind(data.frame(Label = label), x))
+	
 	## Return the resulting list
 	V	
 }
@@ -125,7 +176,7 @@
 		cnames <- sub("Esd", "ESD", cnames)
 		cnames <- sub("FIT_Ch([1-9])_Width", "FIT_Ch\\1_TOF", cnames)
 		## We need to replace names by their zooimage equivalent
-		cnames[cnames == "FIT_Id"] <- "Id" # The only one not starting woth FIT_
+		cnames[cnames == "FIT_Id"] <- "Id" # The only one not starting with FIT_
 		cnames[cnames ==  "FIT_ABD_Area"] <-  "FIT_Area_ABD"
 		cnames[cnames == "FIT_ABD_Diameter"] <- "FIT_Diameter_ABD"
 		cnames[cnames == "FIT_ESD_Diameter"] <- "FIT_Diameter_ESD"
@@ -144,6 +195,9 @@
 		## Note: in comparison to old format, we have in addition:
 		#"FIT_Camera", "FIT_Fringe_Size", "FIT_Circle_Fit", "FIT_Ch1_Area",            
         #"FIT_Ch2_Area", "FIT_Ch3_Area"    
+		#
+		# Plus "FIT_Symmetry", "FIT_Circularity_Hu", "FIT_Intensity_Calimage",
+		# "FIT_Raw_Convex_Hull_Area", "FIT_Raw_Filled_Area"
 		
 		## Read the data in
 		tab <- read.table(lst, header = FALSE, sep = "|", dec = ".", 
@@ -221,15 +275,38 @@
     tab$FIT_Blue_Green_Ratio <- tab$FIT_Avg_Blue / tab$FIT_Avg_Green
     tab$FIT_Red_Blue_Ratio <- tab$FIT_Avg_Red / tab$FIT_Avg_Blue
     tab$FIT_Ch2_Ch1_Ratio <- tab$FIT_Ch2_Peak / tab$FIT_Ch1_Peak
-    
-    ## Try to extract metadata from .ctx file, if it exists
+	
+	## Need label
+	label <- basename(dirname(lst))
+	if (label == ".") label <- basename(getwd())
+	
+	## Try to extract metadata from .ctx file, if it exists
     ctx <- sub("\\.lst$", ".ctx", lst)
 	if (read.ctx && file.exists(ctx)) {
 		ctxData <- readFlowCAMctx(ctx)
-		## TODO: return data in correct ZooImage format directly
-		attr(tab, "FlowCAM.metadata") <- ctxData
-    }
+    } else { # Use minimum default metadata
+		ctxData <- list(
+			Fraction = data.frame(Label = label, Code = "", Min = -1, Max = -1),
+			Process = data.frame(Label = label, Version = "1.0-0",
+				Method = "Direct VS import", MinSize = NA, MaxSize = NA, UseECD = NA),
+			Subsample = data.frame(Label = label, SubPart = 0.01, SubMethod = 1,
+				CellPart = 1, Replicates = 1, VolIni = 1, VolPrec = 0.1)
+		)
+	}
+	Sub <- ctxData$Subsample
 	
+	## Rework the table by renaming Id by Item, and prepending it with
+	## Label, Item and ECD and postpending it with Dil
+	n <- nrow(tab)
+	items <- tab$Id
+	tab$Id <- NULL
+	dil <- 1/(Sub$SubPart * Sub$CellPart * Sub$Replicates * Sub$VolIni)
+	tab <- cbind(data.frame(Label = rep(label, n), Item = items,
+		ECD = ecd(tab$FIT_Raw_Area)), tab, data.frame(Dil = rep(dil, n)))
+	
+	## Add metadata and change class of the object
+	attr(tab, "metadata") <- ctxData
+	class(tab) <- c("ZI3Dat", "ZIDat", "data.frame")
     tab
 }
 
@@ -240,44 +317,67 @@
 #res1 <- readFlowCAMlst(lstFile1)
 
 ## Temporary name!
-importFlowCAM <- function (lst, rgb.vigs = TRUE)
+importFlowCAM <- function (lst, rgb.vigs = TRUE,  type = "ZI3", replace = FALSE)
 {
+	## Check arguments
+    rgb.vigs <- isTRUE(as.logical(rgb.vigs))    
+    if (type != "ZI3") {
+        warning("only 'ZI3' is currently supported for 'type'")
+        return(invisible(FALSE))
+    }
+	
+	## Read metadata
 	dat <- readFlowCAMlst(lst, skip = 2, read.ctx = TRUE)
 	## Check results
 	if (!is.data.frame(dat) && NROW(dat) < 1)
 		stop("Problem while importing FlowCAM data, or empty series")
-	if (is.null(attr(dat, "FlowCAM.metadata")))
+	if (is.null(attr(dat, "metadata")))
 		stop("Problem while importing FlowCAM metadata from the .ctx file")
 	
-	## Create metadata from FlowCAM.metadatata
-	## TODO...
+	## Change dir to sample's parent directory
+    sampledir <- dirname(lst)
+    if (sampledir == ".") sampledir <- getwd()
+	label <- basename(sampledir)
+    parentdir <- dirname(sampledir)
+    #odir <- setwd(sampledir)
+    odir <- setwd(parentdir)
+    on.exit(setwd(odir))
 	
-	## ImportVignettes
-	#require(tiff)
-	#require(png)
+	## .zidb file is computed, and check if file already exists
+    zidbfile <- paste(sampledir, "zidb", sep = ".")
+    if (!isTRUE(as.logical(replace)) && file.exists(zidbfile)) {
+        return(invisible(TRUE))
+    }
 	
-	## List all tiff files in the directory (but exclude masks with _bin.tif)
-	sampledir <- dirname(lst)
-	odir <- setwd(sampledir)
-	on.exit(setwd(odir))
+	## Create the .zidb file
+    message("Creating the ZIDB file...")
+    filehashOption(defaultType = "DB1")
+    unlink(zidbfile)
+    dbCreate(zidbfile)
+    db <- dbInit(zidbfile)
+    dbInsert(db, ".ZI", 3)
+	if (isTRUE(rgb.vigs)) {
+		dbInsert(db, ".ImageType", "png")
+	} else {
+		dbInsert(db, ".ImageType", "jpeg")
+	}
+    
+    ## Add vignettes to the .zidb file
+    message("Adding vignettes to ZIDB file...")
 	
-	## Make sure zidbdir exists and is empty
-	## TODO: use a fresh dir, or erase existing one with user's acceptation
-	zidbdir <- file.path(dirname(sampledir), "_import", basename(sampledir))
-	if (file.exists(zidbdir) && dir(zidbdir) != 0)
-		stop("The destination dir already exists and is not empty!")
-	dir.create(zidbdir, recursive = TRUE, showWarnings = FALSE)
-	
-	tif <- dir(sampledir, pattern = "[0-9]\\.tif$", full.names = FALSE)
-	## Separate the list into collages and background calibration images
-	isCal <- grepl("^.*cal_image_[0-9]+\\.tif$", tif)
-	calFiles <- tif[isCal]
-	colFiles <- tif[!isCal]
-	## Check we have at least one image for each set
-	if (length(calFiles) == 0)
-		stop("No background calibration image found")
-	if (length(colFiles) == 0)
-		stop("No collages found")
+#    ## TODO: change this: do not use _import dir
+#    zidbdir <- file.path(dirname(sampledir), "_import", basename(sampledir))
+#    if (file.exists(zidbdir) && dir(zidbdir) != 0) 
+#        stop("The destination dir already exists and is not empty!")
+#    dir.create(zidbdir, recursive = TRUE, showWarnings = FALSE)
+    tif <- dir(sampledir, pattern = "[0-9]\\.tif$", full.names = TRUE)
+    isCal <- grepl("^.*cal_image_[0-9]+\\.tif$", tif)
+    calFiles <- tif[isCal]
+    colFiles <- tif[!isCal]
+    if (length(calFiles) == 0) 
+        stop("No background calibration image found")
+    if (length(colFiles) == 0) 
+        stop("No collages found")
 		
 	## Read all background calibration images into a list
 	cals <- list()
@@ -312,7 +412,7 @@
 		mat[coords[2]:coords[4], coords[1]:coords[3]]
 	
 	## Determine best gray level for background after substraction
-	gray <- attr(dat, "FlowCAM.metadata")$CaptureParameters$ThresholdLight
+	gray <- attr(dat, "metadata")$CaptureParameters$ThresholdLight
 	if (!length(gray)) {
 		warning("Unknown threshold gray level; using 40")
 		gray <- 40 # Target something like 40
@@ -327,7 +427,7 @@
 		## Do we need to load the next collage?
 		if (as.character(d$FIT_Filename) != colFile) {
 			filename <- as.character(d$FIT_Filename)
-			collage <- readTIFF(source = filename)
+			collage <- readTIFF(source = file.path(sampledir, filename))
 			colFile <- d$FIT_Filename
 			colFiles <- colFiles[colFiles != filename]
 			## If the image is RGB, we got three dimensions to reduce to two
@@ -373,14 +473,59 @@
 		}
 		
 		## Write this vignette
-		vigFile <- file.path(zidbdir,
-			sub("\\.tif$", paste0("_", i, ".png"), filename))
-		writePNG(image = vig2, target =  vigFile)
+#		vigFile <- file.path(zidbdir,
+#			sub("\\.tif$", paste0("_", i, ".png"), filename))
+#		writePNG(image = vig2, target =  vigFile)
+		#VigName <- sub("\\.tif$", paste0("_", i), filename)
+        VigName <- paste(label, i, sep = "_")
+		
+		## In case we use grayscale vignettes, use jpeg, otherwise, use png
+		if (isTRUE(rgb.vigs)) {
+			dbInsert(db, VigName, writePNG(image = vig2, target = raw()))
+		} else {
+			dbInsert(db, VigName, writeJPEG(image = vig2, target = raw(),
+				quality = 0.95))
+		}
 	}
 	
 	## Create zidb
 	## TODO...
-	dat
+	#dat
+	    message("Adding data from ZIM files to ZIDB file...")
+#    for (i in 1:length(Zims)) {
+#        Zim <- Zims[i]
+#        ZimName <- sub("\\.zim$", "", basename(Zim))
+#        ZimSize <- file.info(Zim)$size
+#        if (is.na(ZimSize)) {
+#            warning("file '", Zim, "' not found or of null length")
+#            return(invisible(FALSE))
+#        }
+#        dbInsert(db, ZimName, readBin(Zim, "raw", ZimSize + 100))
+#    }
+    
+    ## Adding metadata and particles' attributes to the .zidb file
+    ## TODO: SampleData come from a DESCRIPTION. zis file???
+	## Here, use a default format
+	smpdat <- data.frame(Label = label, Station = NA, Data = NA, Time = NA,
+		TimeZone = NA, Latitude = NA, Longitude = NA, CorrdsPrec = NA,
+		Operator = NA, Note = NA) # TODO: add note from FlowCAM data!!!
+	class(smpdat) <- c("ZIDesc", "data.frame")
+	
+	message("Adding sample data to ZIDB file...")
+    dbInsert(db, ".SampleData", smpdat)
+	
+    message("Adding R data to ZIDB file...")
+#    zidat <- file.path(zidir, paste0(basename(zidir), "_dat1.RData"))
+#    obj <- load(zidat)
+#    if (length(obj) != 1) {
+#        warning("Error loading ", zidat)
+#        return(invisible(FALSE))
+#    }
+    dbInsert(db, ".Data", dat)
+#    if (isTRUE(as.logical(delete.source))) 
+#        unlink(zidir, recursive = TRUE)
+    message("-- Done! --")
+    invisible(TRUE)
 }
 
 ## Example

Modified: pkg/zooimage/R/planktonSorter.R
===================================================================
--- pkg/zooimage/R/planktonSorter.R	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/R/planktonSorter.R	2014-12-02 08:13:10 UTC (rev 248)
@@ -205,7 +205,7 @@
 
 planktonSorterValidate <- function (path, query, body, ...) {
     if (!length(body)) return()
-	
+
 	## Special cases "iterate>>> " or "done>>> "
 	if (substring(body, 1, 11) == "iterate>>> ") {
 		res <- substring(body, 12)
@@ -282,7 +282,7 @@
 #</body>
 #</html>', url, url)
 
-correctError <- function(zidb, classifier, data = zidbDatRead(zidb),
+correctError <- function(zidb, classifier, data = zidbDatRead(zidb), mode = "validation",
 fraction = 0.05, sample.min = 100, grp.min = 2, random.sample = 0.1,
 algorithm = "rf", diff.max = 0.2, prop.bio = NULL, reset = TRUE,
 result = NULL) {
@@ -333,13 +333,16 @@
 	}
 	
 	## Create this object in TempEnv()
-	ec <- errorCorrection (data, classifier, zidb = zidb, mode = "validation",
+	ec <- errorCorrection (data, classifier, zidb = zidb, mode = mode,
 		fraction = fraction, sample.min = sample.min, grp.min = grp.min,
 		random.sample = random.sample, algorithm = algorithm,
 		diff.max = diff.max, prop.bio = prop.bio, testdir = testdir, id = Name,
 		result = result, envir = parent.frame())
-	assignTemp(Name, ec)
+	if (mode != "stat") assignTemp(Name, ec)
 	
 	## Start its first iteration...
 	ec$iterate()
+	
+	## Return the object
+	ec
 }

Modified: pkg/zooimage/R/utilities.R
===================================================================
--- pkg/zooimage/R/utilities.R	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/R/utilities.R	2014-12-02 08:13:10 UTC (rev 248)
@@ -107,7 +107,7 @@
 			"FIT_Avg_Blue", "FIT_PPC", "FIT_Ch1_Peak", "FIT_Ch1_TOF",
 			"FIT_Ch2_Peak", "FIT_Ch2_TOF", "FIT_Ch3_Peak", "FIT_Ch3_TOF",
 			"FIT_SaveX", "FIT_SaveY", "FIT_PixelW", "FIT_PixelH",
-			"FIT_CaptureX", "FIT_CaptureY", "FIT_Edge_Gradient",    
+			"FIT_CaptureX", "FIT_CaptureY", # Keep this one?"FIT_Edge_Gradient",    
 			"FIT_Source_Image", "FIT_Calibration_Image", "FIT_High_U32",
 			"FIT_Low_U32", "FIT_Total", "FIT_Red_Green_Ratio",
 			"FIT_Blue_Green_Ratio", "FIT_Red_Blue_Ratio",   
@@ -116,7 +116,21 @@
 			"FIT_Ch1_Area", "FIT_Ch2_Area", "FIT_Ch3_Area",         
 			"FIT_TimeStamp1", "FIT_Source_Image.1",
 			"X.Item.1", "FeretAngle", "Count",
-			"Skew", "Kurt", "Solidity")) # Last 3: NAs with multiple ROIs
+			"Skew", "Kurt", "Solidity", # Last 3: NAs with multiple ROIs
+			
+			## Added in zooimage v.5:
+            "FIT_Filename", "FIT_Feret_Min_Angle", "FIT_Feret_Max_Angle",
+			
+			## This is somehow redundant with other variables
+			"FIT_Raw_Area", "FIT_Raw_Perim", "FIT_Raw_Convex_Perim",
+			"FIT_Raw_Feret_Max", "FIT_Raw_Feret_Min", "FIT_Raw_Feret_Mean",
+			"FIT_Diameter_ABD", # This one is indeed ECD
+			
+            ## Found in format 17 of a color FlowCAM (from KAUST)
+            ## and not used yet
+            "FIT_Symmetry", "FIT_Circularity_Hu", "FIT_Intensity_Calimage",
+            "FIT_Raw_Convex_Hull_Area", "FIT_Raw_Filled_Area"
+		))
 	as.character(res)
 }
 
@@ -127,8 +141,105 @@
 	## This is the calculation of derived variables
 	## Note that you can make your own version of this function for more
 	## calculated variables!
+
+## calcVarsVIS() also included here to keep track of it in the ZIClass object!
+## Calculate derived variables... FlowCAM's Visual Spreadsheet
+calcVarsVIS <- function (x, drop.vars = NULL, drop.vars.def = dropVars()) 
+{
+    ## Use only FIT_xxx vars, andderived attributes (26 attributes in total):
+	## ECD, FIT_Area_ABD, FIT_Length, FIT_Width, FIT_Diameter_ESD,
+	## FIT_Perimeter, FIT_Convex_Perimeter, FIT_Intensity, FIT_Sigma_Intensity,
+	## FIT_Compactness, FIT_Elongation, FIT_Sum_Intensity, FIT_Roughness,
+	## FIT_Edge_Gradient, FIT_Volume_ABD, FIT_Volume_ESD, FIT_Aspect_Ratio,
+	## FIT_Transparency, EdgeRange, CV, MeanFDia, Transp2, FeretRoundness,
+	## EdgeCV, EdgeSDNorm & Perim_Ratio 
 	
 	## A small hack to correct some 0 (which can be problematic in further calcs)
+	noZero <- function(x) {
+        x[x == 0] <- 1e-09
+        x
+    }
+	
+	## Euclidean distance between two points
+	distance <- function (x, y)
+		sqrt(x^2 + y^2)
+	
+    ## All FIT_Raw_xxx vars have their counterpart resized in um:
+	## FIT_Raw_Area -> FIT_Diameter_ABD
+	## FIT_Raw_Feret_Max -> FIT_Length
+	## FIT_Raw_Feret_Min -> FIT_Width
+	## FIT_Raw_Feret_Mean -> FIT_Diameter_ESD
+	## FIT_Raw_Perim -> FIt_Perimeter
+	## FIT_Raw_Convex_Perim -> FIt_Convex_Perimeter
+	## (=> all FIT_Raw_xxx should be eliminated in dropVars()!)
+	
+	## (re)calculate ECD from FIT_DIameter_ABD (was once calc from FIT_Raw_Area)
+	x$ECD <- noZero(x$FIT_Diameter_ABD)
+	x$FIT_Area_ABD <- noZero(x$FIT_Area_ABD)
+    x$FIT_Length <- noZero(x$FIT_Length)
+    x$FIT_Width <- noZero(x$FIT_Width)
+	x$FIT_Diameter_ESD <- noZero(x$FIT_Diameter_ESD)
+	x$FIT_Perimeter <- noZero(x$FIT_Perimeter)
+	x$FIT_Convex_Perimeter <- noZero(x$FIT_Convex_Perimeter)
+	x$FIT_Intensity <- noZero(x$FIT_Intensity)
+	x$FIT_Sigma_Intensity <- noZero(x$FIT_Sigma_Intensity)
+	x$FIT_Sum_Intensity <- noZero(x$FIT_Sum_Intensity)
+	x$FIT_Compactness <- noZero(x$FIT_Compactness)
+	x$FIT_Elongation <- noZero(x$FIT_Elongation)
+	x$FIT_Roughness <- noZero(x$FIT_Roughness)
+	x$FIT_Aspect_Ratio <- noZero(x$FIT_Aspect_Ratio)
+	x$FIT_Volume_ABD <- noZero(x$FIT_Volume_ABD)
+	x$FIT_Volume_ESD <- noZero(x$FIT_Volume_ESD)
+	x$FIT_Transparency <- noZero(x$FIT_Transparency)
+	x$FIT_Edge_Gradient <- noZero(x$FIT_Edge_Gradient)
+	
+	
+	## Additional calculated variables
+    # This is FIT_Aspect_Ratio! x$ARFeret <- x$FIT_Width/x$FIT_Length
+    x$EdgeRange <- abs(x$FIT_Intensity - x$FIT_Edge_Gradient)
+    x$CV <- x$FIT_Sigma_Intensity/x$FIT_Intensity * 100
+    x$MeanFDia <- (x$FIT_Length + x$FIT_Width) / 2
+    x$Transp2 <- 1 - (x$FIT_Diameter_ABD/x$MeanFDia)
+    x$Transp2[x$Transp2 < 0] <- 0
+    x$FeretRoundness <- 4 * x$FIT_Area_ABD/(pi * sqrt(x$FIT_Length))
+    x$Circ. <- 4 * pi * x$FIT_Area_ABD / sqrt(x$FIT_Perimeter) # ImageJ calculation
+    x$EdgeCV <- x$FIT_Sigma_Intensity/x$FIT_Edge_Gradient * 100
+    x$EdgeSDNorm <- x$FIT_Intensity/x$EdgeRange
+    x$Perim_Ratio <- x$FIT_Convex_Perimeter / x$FIT_Perimeter 
+    
+	## Eliminate variables that are not predictors... and use Id as rownames
+	Id <- x$Id
+    if (length(Id)) rownames(x) <- Id
+    
+	## Variables to drop
+	## For those samples treated with FIT_VIS in ImageJ, we need to get rid of
+	## the ImageJ variables
+	x$Area <- NULL
+	x$Mean <- NULL
+	x$StdDev <- NULL
+	x$Mode <- NULL
+	x$Min <- NULL
+	x$Max <- NULL
+	x$Perim. <- NULL
+	x$Major <- NULL
+	x$Minor <- NULL
+	x$Circ. <- NULL
+	x$Feret <- NULL
+	x$IntDen <- NULL
+	x$Median <- NULL
+	
+	dropAll <- unique(as.character(c(drop.vars, drop.vars.def)))
+    for (dropVar in dropAll) x[[dropVar]] <- NULL
+    
+	## Return the recalculated data frame
+	x
+}
+	
+	## For data from the FlowCAM, we use a specific function
+	if (any(names(x) == "FIT_Length"))
+		return(calcVarsVIS(x, drop.vars = drop.vars, drop.vars.def = drop.vars.def))
+	
+	## A small hack to correct some 0 (which can be problematic in further calcs)
 	noZero <- function (x) {
 		x[x == 0] <- 0.000000001
 		x
@@ -184,7 +295,15 @@
 ## Calculate derived variables... FlowCAM's Visual Spreadsheet
 calcVarsVIS <- function (x, drop.vars = NULL, drop.vars.def = dropVars()) 
 {
-    ## A small hack to correct some 0 (which can be problematic in further calcs)
+    ## Use only FIT_xxx vars, andderived attributes (26 attributes in total):
+	## ECD, FIT_Area_ABD, FIT_Length, FIT_Width, FIT_Diameter_ESD,
+	## FIT_Perimeter, FIT_Convex_Perimeter, FIT_Intensity, FIT_Sigma_Intensity,
+	## FIT_Compactness, FIT_Elongation, FIT_Sum_Intensity, FIT_Roughness,
+	## FIT_Edge_Gradient, FIT_Volume_ABD, FIT_Volume_ESD, FIT_Aspect_Ratio,
+	## FIT_Transparency, EdgeRange, CV, MeanFDia, Transp2, FeretRoundness,
+	## EdgeCV, EdgeSDNorm & Perim_Ratio 
+	
+	## A small hack to correct some 0 (which can be problematic in further calcs)
 	noZero <- function(x) {
         x[x == 0] <- 1e-09
         x
@@ -194,11 +313,38 @@
 	distance <- function (x, y)
 		sqrt(x^2 + y^2)
 	
-    x$FIT_Area_ABD <- noZero(x$FIT_Area_ABD)
-    x$FIT_Perimeter <- noZero(x$FIT_Perimeter)
+    ## All FIT_Raw_xxx vars have their counterpart resized in um:
+	## FIT_Raw_Area -> FIT_Diameter_ABD
+	## FIT_Raw_Feret_Max -> FIT_Length
+	## FIT_Raw_Feret_Min -> FIT_Width
+	## FIT_Raw_Feret_Mean -> FIT_Diameter_ESD
+	## FIT_Raw_Perim -> FIt_Perimeter
+	## FIT_Raw_Convex_Perim -> FIt_Convex_Perimeter
+	## (=> all FIT_Raw_xxx should be eliminated in dropVars()!)
+	
+	## (re)calculate ECD from FIT_DIameter_ABD (was once calc from FIT_Raw_Area)
+	x$ECD <- noZero(x$FIT_Diameter_ABD)
+	x$FIT_Area_ABD <- noZero(x$FIT_Area_ABD)
     x$FIT_Length <- noZero(x$FIT_Length)
     x$FIT_Width <- noZero(x$FIT_Width)
-    x$ARFeret <- x$FIT_Width/x$FIT_Length
+	x$FIT_Diameter_ESD <- noZero(x$FIT_Diameter_ESD)
+	x$FIT_Perimeter <- noZero(x$FIT_Perimeter)
+	x$FIT_Convex_Perimeter <- noZero(x$FIT_Convex_Perimeter)
+	x$FIT_Intensity <- noZero(x$FIT_Intensity)
+	x$FIT_Sigma_Intensity <- noZero(x$FIT_Sigma_Intensity)
+	x$FIT_Sum_Intensity <- noZero(x$FIT_Sum_Intensity)
+	x$FIT_Compactness <- noZero(x$FIT_Compactness)
+	x$FIT_Elongation <- noZero(x$FIT_Elongation)
+	x$FIT_Roughness <- noZero(x$FIT_Roughness)
+	x$FIT_Aspect_Ratio <- noZero(x$FIT_Aspect_Ratio)
+	x$FIT_Volume_ABD <- noZero(x$FIT_Volume_ABD)
+	x$FIT_Volume_ESD <- noZero(x$FIT_Volume_ESD)
+	x$FIT_Transparency <- noZero(x$FIT_Transparency)
+	x$FIT_Edge_Gradient <- noZero(x$FIT_Edge_Gradient)
+	
+	
+	## Additional calculated variables
+    # This is FIT_Aspect_Ratio! x$ARFeret <- x$FIT_Width/x$FIT_Length
     x$EdgeRange <- abs(x$FIT_Intensity - x$FIT_Edge_Gradient)
     x$CV <- x$FIT_Sigma_Intensity/x$FIT_Intensity * 100
     x$MeanFDia <- (x$FIT_Length + x$FIT_Width) / 2
@@ -215,6 +361,22 @@
     if (length(Id)) rownames(x) <- Id
     
 	## Variables to drop
+	## For those samples treated with FIT_VIS in ImageJ, we need to get rid of
+	## the ImageJ variables
+	x$Area <- NULL
+	x$Mean <- NULL
+	x$StdDev <- NULL
+	x$Mode <- NULL
+	x$Min <- NULL
+	x$Max <- NULL
+	x$Perim. <- NULL
+	x$Major <- NULL
+	x$Minor <- NULL
+	x$Circ. <- NULL
+	x$Feret <- NULL
+	x$IntDen <- NULL
+	x$Median <- NULL
+	
 	dropAll <- unique(as.character(c(drop.vars, drop.vars.def)))
     for (dropVar in dropAll) x[[dropVar]] <- NULL
     

Modified: pkg/zooimage/inst/etc/ZooImageManual.pdf
===================================================================
(Binary files differ)

Modified: pkg/zooimage/man/correctError.Rd
===================================================================
--- pkg/zooimage/man/correctError.Rd	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/man/correctError.Rd	2014-12-02 08:13:10 UTC (rev 248)
@@ -6,7 +6,7 @@
   Open a web page for manual validation and error correction of predicted abundances in samples.
 }
 \usage{
-correctError(zidb, classifier, data = zidbDatRead(zidb),
+correctError(zidb, classifier, data = zidbDatRead(zidb), mode = "validation",
 fraction = 0.05, sample.min = 100, grp.min = 2, random.sample = 0.1,
 algorithm = "rf", diff.max = 0.2, prop.bio = NULL, reset = TRUE,
 result = NULL)
@@ -16,6 +16,12 @@
   \item{zidb}{ Path to a Zidb file. }
   \item{classifier}{ A ZIClass object appropriate for this sample and the desired classification. }
   \item{data}{ A ZIDat or a ZITest object matching that sample (by default, it is the ZIDat object contained in the zidb file). }
+  \item{mode}{ The mode to use for error correction. By default, \code{mode = "validation"},
+    where particles are manually validated. \code{mode = "demo"} is the same one, but it sorts particles
+    according to the Class variable in data, ignoring changes made in the user interface (so that one
+    can explain the logic of the process without care about how particles are manually resorted).
+    Finally, \code{mode = "stat"} do not display the user interface at all and calculates all steps
+    directly to show gain from the process from 0 to 100\% of the particles validated. }
   \item{fraction}{ The fraction of items to validate at each step (1/20th by default). }
   \item{sample.min}{ Minimal number of items to take at each step. }
   \item{grp.min}{ Minimal number of items to take for each group, on average. }

Modified: pkg/zooimage/man/import.Rd
===================================================================
--- pkg/zooimage/man/import.Rd	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/man/import.Rd	2014-12-02 08:13:10 UTC (rev 248)
@@ -12,7 +12,7 @@
 \usage{
 readFlowCAMctx(ctx, stop.it = TRUE)
 readFlowCAMlst(lst, skip = 2, read.ctx = TRUE)
-importFlowCAM(lst, rgb.vigs = TRUE)
+importFlowCAM(lst, rgb.vigs = TRUE,  type = "ZI3", replace = FALSE)
 }
 
 \arguments{
@@ -26,6 +26,10 @@
   \item{read.ctx}{ should we also read the .ctx file with \code{readFlowCAMctx()}? }
   \item{rgb.vigs}{ do we build color vignettes that mix OD, visual and mask in the
     three RGB channels? }
+  \item{type}{ the type of \code{.zidb} file to create. Currently, only supports
+    \code{type = "ZI3"} (defaulf value). }
+  \item{replace}{ a boolean indicating if an existing \code{.zidb} file should
+    be replaced by a new one. }
 }
 
 \value{

Modified: pkg/zooimage/man/zooimage.package.Rd
===================================================================
--- pkg/zooimage/man/zooimage.package.Rd	2014-03-02 12:32:42 UTC (rev 247)
+++ pkg/zooimage/man/zooimage.package.Rd	2014-12-02 08:13:10 UTC (rev 248)
@@ -16,8 +16,8 @@
   \tabular{ll}{
     Package: \tab zooimage\cr
     Type: \tab Package\cr
-    Version: \tab 4.0-0\cr
-    Date: \tab 2014-02-25\cr
+    Version: \tab 5.1-0\cr
+    Date: \tab 2014-12-02\cr
     License: \tab GPL 2 or above at your convenience.\cr
   }
   Everytime you publish results that use ZooImage, you must place a reference


From noreply at r-forge.r-project.org  Sun Dec  7 08:40:32 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  7 Dec 2014 08:40:32 +0100 (CET)
Subject: [Zooimage-commits] r249 - in pkg: . zooimage zooimage/R
	zooimage/inst/gui zooimage/inst/gui/errorcorrection zooimage/man
Message-ID: <20141207074033.0A8BA1805B3@r-forge.r-project.org>

Author: phgrosjean
Date: 2014-12-07 08:40:31 +0100 (Sun, 07 Dec 2014)
New Revision: 249

Added:
   pkg/zooimage/inst/gui/errorcorrection/
   pkg/zooimage/inst/gui/errorcorrection/global.R
   pkg/zooimage/inst/gui/errorcorrection/server.R
   pkg/zooimage/inst/gui/errorcorrection/ui.R
Removed:
   pkg/zooimage.Rcheck/
Modified:
   pkg/zooimage/DESCRIPTION
   pkg/zooimage/NAMESPACE
   pkg/zooimage/NEWS
   pkg/zooimage/R/ZIRes.R
   pkg/zooimage/R/ZITrain.R
   pkg/zooimage/R/gui.R
   pkg/zooimage/R/import.R
   pkg/zooimage/R/utilities.R
   pkg/zooimage/R/zid.R
   pkg/zooimage/R/zidb.R
   pkg/zooimage/man/gui.Rd
Log:
Changes in the GUI

Modified: pkg/zooimage/DESCRIPTION
===================================================================
--- pkg/zooimage/DESCRIPTION	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/DESCRIPTION	2014-12-07 07:40:31 UTC (rev 249)
@@ -11,7 +11,7 @@
   email = "kevin.denis at umons.ac.be"))
 Maintainer: Philippe Grosjean <phgrosjean at sciviews.org>
 Depends: R (>= 2.14.0), svMisc (>= 0.9-67), svDialogs (>= 0.9-53), mlearning
-Imports: filehash, jpeg, png, tiff, utils, digest, tools
+Imports: filehash, jpeg, png, tiff, utils, digest, tools, shiny
 Suggests: rJava, mlbench
 Description: ZooImage is a free (open source) solution for analyzing digital
 	images of zooplankton. In combination with ImageJ, a free image analysis

Modified: pkg/zooimage/NAMESPACE
===================================================================
--- pkg/zooimage/NAMESPACE	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/NAMESPACE	2014-12-07 07:40:31 UTC (rev 249)
@@ -21,6 +21,7 @@
 #import(RWeka)
 import(mlearning)
 #import(party)
+import(shiny)
 
 # planktonSorter
 export(correctError)
@@ -164,6 +165,7 @@
 export(ZIDlg)
 # Not in menus yet!
 #export(subpartZIDat)
+export(ZIUI)
 
 # GUI-Utilities
 export(selectGroups)

Modified: pkg/zooimage/NEWS
===================================================================
--- pkg/zooimage/NEWS	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/NEWS	2014-12-07 07:40:31 UTC (rev 249)
@@ -7,6 +7,8 @@
   from there). This way, there is no need any more of a second image analysis
   in ImageJ.
   
+* A new UI for error correction using shiny.
+  
 
 == Changes in zooimage 5.0-0
 

Modified: pkg/zooimage/R/ZIRes.R
===================================================================
--- pkg/zooimage/R/ZIRes.R	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/R/ZIRes.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -106,6 +106,9 @@
 processSample <- function (x, sample, keep = NULL, detail = NULL, classes = "both",
 header = c("Abd", "Bio"), biomass = NULL, breaks = NULL)
 {
+	## Fix ECD in case of FIT_VIS data
+	if ("FIT_Area_ABD" %in% names(x)) x$ECD <- ecd(x$FIT_Area_ABD)
+	
 	## Check arguments
 	if (missing(sample)) {
 		sample <- unique(sampleInfo(x$Label, type = "sample", ext = ""))
@@ -208,7 +211,7 @@
 			x$P2 <- biomass[2]
 			x$P3 <- biomass[3]
 		} else stop("wrong 'biomass', must be NULL, a vector of 3 values or a data frame with Class, P1, P2 and P3")
-		if(!is.numeric(x$ECD)) stop("'ECD' required for biomasses")
+		if (!is.numeric(x$ECD)) stop("'ECD' required for biomasses")
 		x$BioWeight <- (x$P1 * x$ECD^x$P3 + x$P2) * x$Dil
 	}
 	

Modified: pkg/zooimage/R/ZITrain.R
===================================================================
--- pkg/zooimage/R/ZITrain.R	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/R/ZITrain.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -380,6 +380,8 @@
 
 	## Rename Dat in df
 	df <- Dat
+	## Fix ECD in case of FIT_VIS data
+	if ("FIT_Area_ABD" %in% names(df)) df$ECD <- ecd(df$FIT_Area_ABD)
 	## Problem if there is no remaining row in the data frame
 	if (nrow(df) == 0) {
 		warning("No valid item found (no vignettes with valid measurement data)")

Modified: pkg/zooimage/R/gui.R
===================================================================
--- pkg/zooimage/R/gui.R	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/R/gui.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -27,6 +27,8 @@
 	menuAddItem(ZIname, "List objects", "listObjects()")
 	menuAddItem(ZIname, "Remove objects", "removeObjects()")
 	menuAddItem(ZIname, "-", "")
+	menuAddItem(ZIname, "Interactive UI", "ZIUI()")
+	menuAddItem(ZIname, "--", "")
 	menuAddItem(ZIname, "Online help", 'help("zooimage")')
 	menuAddItem(ZIname, "Manual", "viewManual()")
 	menuAddItem(ZIname,
@@ -1345,3 +1347,16 @@
 #    res <- subpartThreshold(ZIDat = zid, Filter = threshold)
 #    return(res)
 #}
+
+
+################################################################################
+## New User Interface using Shiny for error correction
+ZIUI <- function () {
+	#appdir <- system.file("gui", "errorcorrection", package = "zooimage")
+	#runApp(appdir)
+	res <- dlgOpen(title = "Select one R method file",
+		filters = dlgFilters[c("R", "All"), ])$res
+	if (length(res)) {
+		source(res, chdir = TRUE)
+	}
+}
\ No newline at end of file

Modified: pkg/zooimage/R/import.R
===================================================================
--- pkg/zooimage/R/import.R	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/R/import.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -302,7 +302,7 @@
 	tab$Id <- NULL
 	dil <- 1/(Sub$SubPart * Sub$CellPart * Sub$Replicates * Sub$VolIni)
 	tab <- cbind(data.frame(Label = rep(label, n), Item = items,
-		ECD = ecd(tab$FIT_Raw_Area)), tab, data.frame(Dil = rep(dil, n)))
+		ECD = ecd(tab$FIT_Area_ABD)), tab, data.frame(Dil = rep(dil, n)))
 	
 	## Add metadata and change class of the object
 	attr(tab, "metadata") <- ctxData

Modified: pkg/zooimage/R/utilities.R
===================================================================
--- pkg/zooimage/R/utilities.R	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/R/utilities.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -112,7 +112,7 @@
 			"FIT_Low_U32", "FIT_Total", "FIT_Red_Green_Ratio",
 			"FIT_Blue_Green_Ratio", "FIT_Red_Blue_Ratio",   
 			"FIT_Ch2_Ch1_Ratio", "FIT_Ch4_Peak", "FIT_Ch4_TOF", "FIT_Timestamp1",
-			"FIT_Timestamp2", "FIT_Camera", "FIT_FringSize", "FIT_CircleFit",
+			"FIT_Timestamp2", "FIT_Camera", "FIT_FringSize",
 			"FIT_Ch1_Area", "FIT_Ch2_Area", "FIT_Ch3_Area",         
 			"FIT_TimeStamp1", "FIT_Source_Image.1",
 			"X.Item.1", "FeretAngle", "Count",
@@ -129,7 +129,8 @@
             ## Found in format 17 of a color FlowCAM (from KAUST)
             ## and not used yet
             "FIT_Symmetry", "FIT_Circularity_Hu", "FIT_Intensity_Calimage",
-            "FIT_Raw_Convex_Hull_Area", "FIT_Raw_Filled_Area"
+            "FIT_Raw_Convex_Hull_Area", "FIT_Raw_Filled_Area",
+			"FIT_CircleFit", "FIT_Edge_Gradient"
 		))
 	as.character(res)
 }
@@ -150,9 +151,8 @@
 	## ECD, FIT_Area_ABD, FIT_Length, FIT_Width, FIT_Diameter_ESD,
 	## FIT_Perimeter, FIT_Convex_Perimeter, FIT_Intensity, FIT_Sigma_Intensity,
 	## FIT_Compactness, FIT_Elongation, FIT_Sum_Intensity, FIT_Roughness,
-	## FIT_Edge_Gradient, FIT_Volume_ABD, FIT_Volume_ESD, FIT_Aspect_Ratio,
-	## FIT_Transparency, EdgeRange, CV, MeanFDia, Transp2, FeretRoundness,
-	## EdgeCV, EdgeSDNorm & Perim_Ratio 
+	## FIT_Volume_ABD, FIT_Volume_ESD, FIT_Aspect_Ratio, FIT_Transparency,
+	## CV, MeanFDia, Transp2, FeretRoundness & Perim_Ratio 
 	
 	## A small hack to correct some 0 (which can be problematic in further calcs)
 	noZero <- function(x) {
@@ -174,7 +174,7 @@
 	## (=> all FIT_Raw_xxx should be eliminated in dropVars()!)
 	
 	## (re)calculate ECD from FIT_DIameter_ABD (was once calc from FIT_Raw_Area)
-	x$ECD <- noZero(x$FIT_Diameter_ABD)
+	x$ECD <- noZero(ecd(x$FIT_Area_ABD))
 	x$FIT_Area_ABD <- noZero(x$FIT_Area_ABD)
     x$FIT_Length <- noZero(x$FIT_Length)
     x$FIT_Width <- noZero(x$FIT_Width)
@@ -191,20 +191,20 @@
 	x$FIT_Volume_ABD <- noZero(x$FIT_Volume_ABD)
 	x$FIT_Volume_ESD <- noZero(x$FIT_Volume_ESD)
 	x$FIT_Transparency <- noZero(x$FIT_Transparency)
-	x$FIT_Edge_Gradient <- noZero(x$FIT_Edge_Gradient)
 	
-	
 	## Additional calculated variables
     # This is FIT_Aspect_Ratio! x$ARFeret <- x$FIT_Width/x$FIT_Length
-    x$EdgeRange <- abs(x$FIT_Intensity - x$FIT_Edge_Gradient)
+    ## For later on:
+	#x$EdgeRange <- abs(x$FIT_Intensity - x$FIT_Edge_Gradient)
     x$CV <- x$FIT_Sigma_Intensity/x$FIT_Intensity * 100
     x$MeanFDia <- (x$FIT_Length + x$FIT_Width) / 2
     x$Transp2 <- 1 - (x$FIT_Diameter_ABD/x$MeanFDia)
     x$Transp2[x$Transp2 < 0] <- 0
     x$FeretRoundness <- 4 * x$FIT_Area_ABD/(pi * sqrt(x$FIT_Length))
     x$Circ. <- 4 * pi * x$FIT_Area_ABD / sqrt(x$FIT_Perimeter) # ImageJ calculation
-    x$EdgeCV <- x$FIT_Sigma_Intensity/x$FIT_Edge_Gradient * 100
-    x$EdgeSDNorm <- x$FIT_Intensity/x$EdgeRange
+    ## For later on:
+	#x$EdgeCV <- x$FIT_Sigma_Intensity/x$FIT_Edge_Gradient * 100
+    #x$EdgeSDNorm <- x$FIT_Intensity/x$EdgeRange
     x$Perim_Ratio <- x$FIT_Convex_Perimeter / x$FIT_Perimeter 
     
 	## Eliminate variables that are not predictors... and use Id as rownames

Modified: pkg/zooimage/R/zid.R
===================================================================
--- pkg/zooimage/R/zid.R	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/R/zid.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -521,11 +521,18 @@
     rownames(allmes) <- 1:nrow(allmes)
     Names <- names(allmes)
     
-	## Calculate an ECD from Area if there is not one yet
-    if (!"ECD" %in% Names && "Area" %in% Names) {
-        ECD <- ecd(allmes$Area)
-        allmes <- data.frame(allmes[, 1:2], ECD = ECD, allmes[, 3:ncol(allmes)])
-    }
+	## Calculate an ECD from Area (or FIT_Area_ABD) if there is not one yet
+    if (!"ECD" %in% Names) {
+		if ("FIT_Area_ABD" %in% Names) { # This is FlowCAM data!
+			ECD <- ecd(allmes$FIT_Area_ABD)
+			allmes <- data.frame(allmes[, 1:2], ECD = ECD,
+				allmes[, 3:ncol(allmes)])
+		} else if ("Area" %in% Names) { # All other cases
+			ECD <- ecd(allmes$Area)
+			allmes <- data.frame(allmes[, 1:2], ECD = ECD,
+				allmes[, 3:ncol(allmes)])
+		}
+	}
     attr(allmes, "metadata") <- allmeta
     class(allmes) <- c("ZI3Dat", "ZIDat", "data.frame")
     ZI.sample <- allmes
@@ -585,6 +592,10 @@
 	ZI.sample <- NULL
 	load(rdata)
 	
+	## Fix ECD in case of FIT_VIS data
+	if ("FIT_Area_ABD" %in% names(ZI.sample))
+		ZI.sample$ECD <- ecd(ZI.sample$FIT_Area_ABD)
+	
 	## Delete the file
 	if (deletefile) {
 		unlink(rdata)

Modified: pkg/zooimage/R/zidb.R
===================================================================
--- pkg/zooimage/R/zidb.R	2014-12-02 08:13:10 UTC (rev 248)
+++ pkg/zooimage/R/zidb.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -125,7 +125,10 @@
 		warning("Error loading ", zidat)
 		return(invisible(FALSE))
 	}
-    dbInsert(db, ".Data", get(obj))
+    dat <- get(obj)
+	## Fix ECD in case of FIT_VIS data
+	if ("FIT_Area_ABD" %in% names(dat)) dat$ECD <- ecd(dat$FIT_Area_ABD)
+	dbInsert(db, ".Data", dat)
 
 	## Do we delete sources?
     if (isTRUE(as.logical(delete.source)))
@@ -429,8 +432,12 @@
 	db2env(dbInit(zidbfile))
 
 ## Read only Rdata file from a .zidb database
-zidbDatRead <- function (zidbfile)
-	zidbLink(zidbfile)$.Data
+zidbDatRead <- function (zidbfile) {
+	res <- zidbLink(zidbfile)$.Data
+	## Fix ECD in case of FIT_VIS data
+	if ("FIT_Area_ABD" %in% names(res)) res$ECD <- ecd(res$FIT_Area_ABD)
+	res
+}
 
 ## Read only the sample data
 zidbSampleRead <- function (zidbfile)

Added: pkg/zooimage/inst/gui/errorcorrection/global.R
===================================================================
--- pkg/zooimage/inst/gui/errorcorrection/global.R	                        (rev 0)
+++ pkg/zooimage/inst/gui/errorcorrection/global.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -0,0 +1,128 @@
+## Zoo/PhytoImage simplified analysis UI (run the application)
+## Copyright (c) 2014, Philippe Grosjean (Philippe.Grosjean at umons.ac.be)
+## TODO: allow for placing samples in subdirs + use tree view 
+
+## Get the working directory
+if (!exists(".ZI"))
+    stop("You must run this app from within a method script!")
+inidir <- dirname(.ZI$wdir)
+cat("Directory:", inidir, "\n")
+
+## Used to print a report after exiting the shiny app
+print.reportObj <- function (x, ...) {
+    line <- paste0(c("\n", rep('-', getOption("width")), "\n"))
+    cat(line, paste0(x, collapse = "\n"), line, sep = "")
+    invisible(x)
+}
+
+## Additional functions required by the UI
+## Same a headerPanel, but taking less space, using h5 instead of h1
+smallHeaderPanel <- function (title, windowTitle = title) {
+    tagList(tags$head(tags$title(windowTitle)), div(class = "span12", 
+        style = "padding: 2px 0px;", strong(title)))
+}
+
+#smallTitlePanel <- function (title, windowTitle = title) {
+#    tagList(tags$head(tags$title(windowTitle)), h5(style = "padding: 2px 0px;", 
+#        title))
+#}
+
+## Define UI for default process using a config .R script in zooimage
+## TODO: change the title according to actual name and version of the software
+## TODO: translate UI strings (English and French interfaces)
+uiTitle <- paste0("Zoo/PhytoImage version 5.1-0 (UMONS/IFREMER rephy release) - ",
+    .ZI$method, " - ", .ZI$user)
+
+
+### List all available methods
+#Methods <- dir(file.path(inidir, "_analyses"), pattern = "\\.R$")
+#if (!length(Methods)) stop("No methods defined in that directory")
+### Eliminate .R
+#Methods <- sub("\\.R$", "", Methods)
+#Methods <- .ZI$method
+
+### Prepare for first method
+#source(paste(file.path(inidir, "_analyses", .ZI$method), "R", sep = "."), chdir = TRUE)
+
+## List all samples currently available
+listSamples <- function (path, method, unanalyzed.only = FALSE) {
+    res <- dir(path)
+    if (!length(res)) return(character(0))
+    ## Eliminate hidden dirs and files (starting with "_")
+    res <- res[substr(res, 1, 1) != "_"]
+    if (!length(res)) return(character(0))
+    ## Keep only dirs or .zidb files
+    res <- res[grepl("\\.zidb$", res) | file.info(file.path(inidir, res))$isdir]
+    if (!length(res)) return(character(0))
+    ## Copy res to files, and eliminate .zidb extensions from res
+    files <- rev(res)
+    res <- rev(sub("\\.zidb$", "", res))
+    ## Where there is a dir and a .zidb file for the same sample, eliminate dir
+    keep <- !duplicated(res)
+    ## Select files and dir, rereverting rev and files
+    res <- rev(res[keep])
+    if (!length(res)) return(character(0))
+    files <- rev(files[keep])
+    ## Determine which sample is imported (has a .zidb file)
+    imp <- grepl("\\.zidb$", files)
+    ## Determine if some of these files are already processed 
+    proc <- dir(file.path(path, "_analyses", method),
+        pattern = "\\_valid.RData$")
+    if (length(proc)) {
+        ## Keep only those items that are in res
+        procsmp <- sub("_valid\\.RData$", "", proc)
+        proc <- (res %in% procsmp)
+    } else proc <- rep(FALSE, length(res))
+    ## Create names with smp [ ]/[I]/[A]
+    status <- rep("[ ]", length(res))
+    status[imp] <- "[I]"
+    status[proc] <- "[A]"
+    nms <- paste(status, res)
+  
+    ## If keep unanalyzed only, select corresponding items
+    #    if (isTRUE(as.logical(unanalyzed.only))) {
+    #        res <- res[!proc]
+    #        nms <- nms[!proc]
+    #        files <- files[!proc]
+    #        imp <- imp[!proc]
+    #    }
+  
+    ## Create a list with samples, files and processed
+    list(samples = res, names = nms,  files = files, imported = imp,
+        analyzed = proc)
+}
+AllSamples <- listSamples(inidir, method = .ZI$method)
+
+
+
+calcSample <- function (Sample, input, output, session)
+{
+    ## Is this sample already imported?
+    ## Try to import it anyway with replace = FALSE
+    if (file.exists(file.path(inidir, Sample))) {
+        ## Get .lst file first
+        Lst <- dir(file.path(inidir, Sample), pattern = "\\.lst$",
+            full.names = TRUE)[1]
+        if (length(Lst)) {
+            res <- try(importFlowCAM(Lst, rgb.vigs = FALSE, replace = FALSE),
+                silent = TRUE)
+            if (inherits(res, "try-error")) {
+                stop("Error importing sample", Sample)
+            } else { # Update list
+                Method <- .ZI$method #input$method
+                AllSamples <- listSamples(inidir, method = Method)
+                #, input$newonlyCheck)
+                ## Is this sample validated?
+                ## TODO: if reimported => backup validation data and clear it now!
+                if (file.exists(file.path(inidir, "_analyses", Method,
+                    paste(Sample, "valid.RData", sep = "_")))) {
+                    tag <- "[A]"
+                } else tag <- "[I]"
+        
+                updateSelectInput(session, "sample", choices = AllSamples$names,
+                    selected = paste(tag, Sample))
+            }
+        }
+    }
+}
+

Added: pkg/zooimage/inst/gui/errorcorrection/server.R
===================================================================
--- pkg/zooimage/inst/gui/errorcorrection/server.R	                        (rev 0)
+++ pkg/zooimage/inst/gui/errorcorrection/server.R	2014-12-07 07:40:31 UTC (rev 249)
@@ -0,0 +1,397 @@
+## Zoo/PhytoImage simplified analysis UI (server code)
+## Copyright (c) 2014, Philippe Grosjean (Philippe.Grosjean at umons.ac.be)
+## TODO: allow for placing samples in subdirs + use tree view
+## TODO: add "Stat" button for fully validated samples 
+## TODO: translate server messages (English and French interfaces)
+## TODO: allow downloading the data with something like:
+## In server.R:
+#output$downloadData <- downloadHandler(
+#  filename = function() {
+#    paste('data-', Sys.Date(), '.csv', sep='')
+#  },
+#  content = function(file) {
+#    write.csv(data, file)
+#  }
+#)
+#
+## In ui.R:
+#downloadLink('downloadData', 'Download')
+## 
+## - Use includeMarkdown()
+##
+## - Use renderDataTable(), e.g.,
+## Pass a callback function to DataTables using I()
+#renderDataTable(iris, options = list(
+#  iDisplayLength = 5,
+#  fnInitComplete = I("function(oSettings, json) {alert('Done.');}")
+#))
+
+shinyServer(function (input, output, session) {
+    
+    doAnalysis <- reactive({
+        generalMessage <- function(message) {
+            paste0("______________________________________________________________________",
+                #"\n?chantillons totaux:    ", length(AllSamples$names),
+                "\n?chantillons ? traiter: ", sum(!AllSamples$analyzed),
+                "\n?chantillons analys?s:  ", sum(AllSamples$analyzed),
+                "\n\n", message, "\n",
+                "______________________________________________________________________\n")
+        }
+        
+        if (input$goButton == 0)
+            return(generalMessage("(Auncun ?chantillon n'a encore ?t? analys? au cours de cette session)."))
+        isolate({
+            Sample <- substring(input$sample, 5)
+            ZIDB <- file.path(inidir, paste(Sample, "zidb", sep = "."))
+            ## Determine if we already got some data...
+            ## First look at "demo" data _valid0.RData
+            DemoFile <- file.path(inidir, "_analyses", .ZI$method, #input$method,
+                paste(Sample, "valid0.RData", sep = "_"))
+            SampleFile <- file.path(inidir, "_analyses", .ZI$method, #input$method,
+                paste(Sample, "valid.RData", sep = "_"))
+            MetaFile <- file.path(inidir, "_analyses", .ZI$method, #input$method,
+                paste(Sample, "valid.txt", sep = "_"))
+            ResFile <- file.path(inidir, "_analyses", .ZI$method, #input$method,
+                paste(Sample, "res.RData", sep = "_"))
+            
+            ValidData <- paste(Sample, "valid", sep = "_")
+            ResData <- paste(Sample, "res", sep = "_")
+            if (exists(ValidData, inherits = FALSE)) rm(list = ValidData)
+            if (file.exists(DemoFile)) { # Run in demo mode
+                res <- load(DemoFile)
+                DemoData <- get(res)
+                rm(list = res)
+                ce <- correctError(zidb = ZIDB, classifier = .ZIClass,
+                    data = DemoData, mode = "demo")
+                ## Note: we save just nothing, because we are in demo mode?
+                ## or do we save data?
+            } else {
+                ## Are there some data already available?
+                if (file.exists(SampleFile)) { # Reanalyze the sample
+                    res <- load(SampleFile)
+                    SampleData <- get(res)
+                    rm(list = res)
+                    ce <- correctError(zidb = ZIDB, classifier = .ZIClass,
+                        data = SampleData)
+                } else { # Nothing available: start from scratch
+                    ce <- correctError(zidb = ZIDB, classifier = .ZIClass)
+                }
+                
+            } #x <- "Demo found" else x <- "Demo not found"
+            
+            
+            ## Backup sample and metadata files if they exist
+            if (file.exists(SampleFile))
+                file.copy(SampleFile, paste(SampleFile, "bak", sep = "."))
+            unlink(SampleFile)
+            if (file.exists(MetaFile))
+                file.copy(MetaFile, paste(MetaFile, "bak", sep = "."))
+            unlink(MetaFile)
+            if (file.exists(ResFile))
+                file.copy(ResFile, paste(ResFile, "bak", sep = "."))
+            unlink(ResFile)
+            
+            ## The following code fails while we are still validating items...
+            ## TODO: associate name of validator + date
+            res <- try(save(list = ValidData, file = SampleFile), silent = TRUE)
+            while (inherits(res, "try-error")) {
+                Sys.sleep(0.5) # Wait 1/2 sec
+                res <- try(save(list = ValidData, file = SampleFile),
+                    silent = TRUE)
+            }
+            ## Save associated metadata
+            cat("zooimage version: 5.1.0\n", file = MetaFile)
+            cat("method: ", .ZI$method, "\n", sep = "",
+                file = MetaFile, append = TRUE)
+            cat("user: ", .ZI$user, "\n", sep = "",
+                file = MetaFile, append = TRUE)
+            cat("date: ", as.character(Sys.time()), "\n", sep = "",
+                file = MetaFile, append = TRUE)
+            cat("training set: ", .ZI$train, "\n", sep = "",
+                file = MetaFile, append = TRUE)
+            ## should be../ more
+            #cat("training file: ", .ZI$trainfile, "\n", sep = "",
+            #    file = MetaFile, append = TRUE)
+            cat("classifier: ", .ZI$classif, "\n", sep = "",
+                file = MetaFile, append = TRUE)
+            ## should be../ more
+            #cat("classifier file: ", .ZI$classifile, "\n", sep = "",
+            #    file = MetaFile, append = TRUE)
+            cat("classifier cmd: ", .ZI$classifcmd, "\n", sep = "",
+                file = MetaFile, append = TRUE)
+            cat("size breaks: ", paste(.ZI$breaks, collapse = "-"), "\n", sep = "",
+                file = MetaFile, append = TRUE)
+            cat("biovolume conversion: \n", sep = "",
+                file = MetaFile, append = TRUE)
+            write.table(.ZI$biovolume, sep = "\t", dec = ".", row.names = FALSE,
+                col.names = TRUE, file = MetaFile, append = TRUE)
+                        
+            ## Calculate results for this sample
+            dat2 <- get(ValidData)
+            cl <- levels(dat2$Class) # All classes
+            ## We used first uppercase for classes of interest, thus:
+            cl <- cl[grepl("^[A-Z]", cl)]
+            ## Now, we also want to calculate separate abundances for most abundant classes
+            ## i.e., those with at least 50 individuals measured
+            detail <- cl[cl %in% levels(dat2$Class)[table(dat2$Class) >= 50]]
+            ## Calculate results for this sample
+            ## TODO: correct the bug with keep = cl => replacement has different number of rows
+            #assign(ResData, processSample(dat2, keep = cl, detail = detail,
+            #    biomass = .ZI$biovolume, breaks = .ZI$breaks, classes = "Class"))
+            assign(ResData, processSample(dat2, keep = NULL, detail = detail,
+                biomass = .ZI$biovolume, breaks = .ZI$breaks, classes = "Class"))
+            ## Save it
+            save(list = ResData, file = ResFile)
+
+            ## Report success            
+            x <- paste("(L'?chantillon", Sample, "vient d'?tre analys?).")
+            
+            Method <- .ZI$method #input$method
+            AllSamples <- listSamples(inidir, method = Method)
+            
+            if (file.exists(file.path(inidir, "_analyses", Method,
+                paste(Sample, "valid.RData", sep = "_")))) {
+                tag <- "[A]"
+            } else tag <- "[I]"
+                    
+            updateSelectInput(session, "sample", choices = AllSamples$names,
+                selected = paste(tag, Sample))
+            
+            return(generalMessage(x))
+        })
+    })
+
+    #output$generalSummary <- renderText({
+    #  if (input$stopButton) { # Manage clean closing of the page
+    #    ## R?activer R
+    #    ## TODO: change this code to get the name of R application under Mac OS X
+    #    GUI <- .Platform$GUI
+    #    if (GUI == "Rgui") { # Code for RGui under Windows
+    #        try(bringToTop(-1), silent = TRUE)
+    #    } else if (GUI == "AQUA") { # Code for R/R64/SciViews R64.app
+    #        ## This works from Mac OS X 10.5 Leopard:
+    #        try(system("osascript -e 'tell application id \"Rgui\" to activate'",
+    #            ignore.stdout = TRUE, ignore.stderr = TRUE), silent = TRUE)
+    #        #try(system("osascript -e 'tell application \"R\" to activate'",
+    #        #    ignore.stdout = TRUE, ignore.stderr = TRUE), silent = TRUE)
+    #        #try(system("osascript -e 'tell application \"R64\" to activate'",
+    #        #    ignore.stdout = TRUE, ignore.stderr = TRUE), silent = TRUE)
+    #        #try(system("osascript -e 'tell application \"SciViews R64\" to activate'",
+    #        #    ignore.stdout = TRUE, ignore.stderr = TRUE), silent = TRUE)
+    #    } else if (grepl("^mac", .Platform$pkgType)) { # Try code for Terminal.app
+    #        try(system("osascript -e 'tell application \"Terminal\" to activate'",
+    #            ignore.stdout = TRUE, ignore.stderr = TRUE), silent = TRUE)
+    #    }
+    #    
+    #    ## Stop the application, returning a short report of what was done
+    #    report <- structure("Content of my report here...", class = "reportObj")
+    #    stopApp(report)
+    #    
+    #    ## Indicate the app is disconnected
+    #    paste(strong(em("Application d?connect?e!")))
+    #  
+    #  } else { # Indicate number of samples to process and number analyzed
+    #    ## TODO: make this reactive to the change to the list of samples
+    #    paste(em("A traiter:"), strong(em(sum(!AllSamples$analyzed))),
+    #      em(" -  analys?s:"), strong(em(sum(AllSamples$analyzed))))
+    #  }
+    #})
+    
+    output$sampleSummary <- renderPrint(width = 80, {
+      if (input$stopButton) {
+        #updateTabsetPanel(session, "mainTabset", selected = "R?sum?")
+      } else {
+            ## Also update the list of samples, depending on both method and newonlyCheck
+         #   AllSamples <- listSamples(inidir, method = .ZI$method, input$newonlyCheck)
+         #   updateSelectInput(session, "sample", choices = AllSamples$names)
+            Sample <- substring(input$sample, 5)
+            calcSample(Sample, input, output, session)
+            ## Link to the .zidb file and provide a summary of this sample
+            cat("===", Sample, "===\n")
+            ZIDB <- file.path(inidir, paste(Sample, "zidb", sep = "."))
+            Dat <- zidbDatRead(ZIDB)
+            cat("?chantillon contenant", nrow(Dat), "particules num?ris?es.\n")
+            if (substr(input$sample, 1, 3) == "[A]") {
+                ## Get analysis statistics about this sample
+                #if (!exists("SampleData")) {
+                    ## Download the data!
+                    SampleFile <- file.path(inidir, "_analyses", .ZI$method, #input$method,
+                        paste(Sample, "valid.RData", sep = "_"))
+                    if (file.exists(SampleFile)) {
+                        res <- load(SampleFile)
+                        SampleData <- get(res)
+                        rm(list = res)
+                    }
+                #}
+                res <- try(print(table(SampleData$Class)), silent = TRUE)
+                if (inherits(res, "try-error"))
+                    cat("\nStatistiques d'analyse pour l'?chantillon non disponibles\n")
+            } else cat("\nCet ?chantillon n'est pas encore analys? avec la m?thode '", .ZI$method, "'.", sep = "")
+            #head(Dat)
+            #print(summary(Dat[, c("ECD")]))
+            #print(attr(Dat, "metadata"))
+            #plot(Dat$Area, Dat$Perim.)
+            #cat("Ici, le r?sum? de", Sample)
+            cat("\n", doAnalysis())
+        }
+    })
+    
+    output$sampleTable <- renderDataTable(options = list(pageLength = 50), {  #renderTable({
+        if (input$stopButton) {
+            updateTabsetPanel(session, "mainTabset", selected = "R?sum?")
+        } else {
+            doAnalysis()
+            Sample <- substring(input$sample, 5)
+            calcSample(Sample, input, output, session)
+            ## Link to the .zidb file and provide a summary of this sample
+            #cat("===", Sample, "===\n")
+            ZIDB <- file.path(inidir, paste(Sample, "zidb", sep = "."))
+            
+            ## Depending if the file is analyzed or not, we look at the
+            ## ZITest or ZIDat object
+            if (substr(input$sample, 1, 3) == "[A]") {
+                ## Get analysis statistics about this sample
+                #if (!exists("SampleData")) {
+                    ## Download the data!
+                    SampleFile <- file.path(inidir, "_analyses", .ZI$method, #input$method,
+                        paste(Sample, "valid.RData", sep = "_"))
+                    if (file.exists(SampleFile)) {
+                        res <- load(SampleFile)
+                        SampleData <- get(res)
+                        rm(list = res)
+                    }
+                #}
+                res <- try(Dat50 <- head(SampleData, n = 50), silent = TRUE)
+                if (inherits(res, "try-error")) {
+                    Dat <- zidbDatRead(ZIDB)
+                    Dat50 <- head(Dat, n = 50)
+                    Dat50b <- Dat50
+                    Dat50b$Label <- NULL
+                    Dat50b$Item <- NULL
+                    Dat50b$ECD <- NULL
+                    data.frame(Label = Dat50$Label, Item = Dat50$Item,
+                        ECD = Dat50$ECD, Dat50b)
+                } else {
+                    Dat50b <- Dat50
+                    Dat50b$Label <- NULL
+                    Dat50b$Item <- NULL
+                    Dat50b$ECD <- NULL
+                    Dat50b$Class <- NULL
+                    Dat50b$Predicted <- NULL
+                    Dat50b$Id <- NULL
+                    Dat50b$Id.1 <- NULL
+                    data.frame(Label = Dat50$Label, Item = Dat50$Item,
+                        ECD = Dat50$ECD, Class = Dat50$Class, Dat50b)
+                        #Dat50$Predicted,Dat50$ECD, Dat50b)
+                }
+            } else {
+                Dat <- zidbDatRead(ZIDB)
+                Dat50 <- head(Dat, n = 50)
+                Dat50b <- Dat50
+                Dat50b$Label <- NULL
+                Dat50b$Item <- NULL
+                Dat50b$ECD <- NULL
+                data.frame(Label = Dat50$Label, Item = Dat50$Item,
+                    ECD = Dat50$ECD, Dat50b)
+            }
+        }
+    })
+    
+    output$samplePlot <- renderPlot({
+        if (input$stopButton) {
+            updateTabsetPanel(session, "mainTabset", selected = "R?sum?")
+        } else {
+            
+            ## This is only in shiny 0.10.2!!
+            #withProgress(message = 'Calculation in progress',
+            #    detail = '...', value = 0, {
+            #    for (i in 1:15) {
+            #        incProgress(1/15, detail = paste0("...", i, "/15"))
+            #        Sys.sleep(0.25)
+            #    }
+            #})
+            
+            Sample <- substring(input$sample, 5)
+            calcSample(Sample, input, output, session)
+            ## Link to the .zidb file and provide a summary of this sample
+            #cat("===", Sample, "===\n")
+            ZIDB <- file.path(inidir, paste(Sample, "zidb", sep = "."))
+            Dat <- zidbDatRead(ZIDB)
+            hist(Dat$ECD, col = "cornsilk", breaks = "FD",
+                main = "Distribution de la taille des particules",
+                xlab = "ECD", ylab = "Fr?quences")
+        }
+    })
+    
+    output$vignettesPlot <- renderPlot({
+        if (input$stopButton) {
+            updateTabsetPanel(session, "mainTabset", selected = "R?sum?")
+        } else {
+            Sample <- substring(input$sample, 5)
+            calcSample(Sample, input, output, session)
+            ## Link to the .zidb file and provide a summary of this sample
+            #cat("===", Sample, "===\n")
+            ZIDB <- file.path(inidir, paste(Sample, "zidb", sep = "."))
+            DB <- zidbLink(ZIDB)
+            Items <- ls(DB) # Contains data in *_dat1 and vignettes in *_nn
+            ## Eliminate items that are not vignettes
+            noVig <- grep("_dat1", Items)
+            if (length(noVig)) Vigs <- Items[-noVig] else Vigs <- Items
+            ## Display a 5*5 thumbnail of the first 25 vignettes
+            zidbPlotNew(Sample)
+            ImgType <- DB$.ImageType
+            for (i in 1:30)
+                zidbDrawVignette(DB[[Vigs[i]]], type = ImgType, item = i,
+                    nx = 6, ny = 5)
+        }
+    })
+    
+    output$sampleResults <- renderPrint({
+        if (input$stopButton) {
+            updateTabsetPanel(session, "mainTabset", selected = "R?sum?")
+        } else {
+            ## Also update the list of samples, depending on both method and newonlyCheck
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/zooimage -r 249

From noreply at r-forge.r-project.org  Tue Dec  9 09:35:23 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  9 Dec 2014 09:35:23 +0100 (CET)
Subject: [Zooimage-commits] r250 - pkg/zooimage
Message-ID: <20141209083523.D256C1876DE@r-forge.r-project.org>

Author: marmayer
Date: 2014-12-09 09:35:23 +0100 (Tue, 09 Dec 2014)
New Revision: 250

Modified:
   pkg/zooimage/DESCRIPTION
Log:
Triggering a rebuild after it has been stuck for a few days.


Modified: pkg/zooimage/DESCRIPTION
===================================================================
--- pkg/zooimage/DESCRIPTION	2014-12-07 07:40:31 UTC (rev 249)
+++ pkg/zooimage/DESCRIPTION	2014-12-09 08:35:23 UTC (rev 250)
@@ -1,7 +1,7 @@
 Package: zooimage
 Type: Package
 Title: Analysis of numerical zooplankton images
-Version: 5.1-0
+Version: 5.1-1
 Date: 2014-12-02
 Author: Philippe Grosjean [aut, cre],
   Kevin Denis [aut]


From noreply at r-forge.r-project.org  Tue Dec  9 10:03:08 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  9 Dec 2014 10:03:08 +0100 (CET)
Subject: [Zooimage-commits] r251 - pkg/zooimage
Message-ID: <20141209090308.755311875E7@r-forge.r-project.org>

Author: marmayer
Date: 2014-12-09 10:03:08 +0100 (Tue, 09 Dec 2014)
New Revision: 251

Modified:
   pkg/zooimage/DESCRIPTION
Log:
Test to see if it rebuilds now


Modified: pkg/zooimage/DESCRIPTION
===================================================================
--- pkg/zooimage/DESCRIPTION	2014-12-09 08:35:23 UTC (rev 250)
+++ pkg/zooimage/DESCRIPTION	2014-12-09 09:03:08 UTC (rev 251)
@@ -1,7 +1,7 @@
 Package: zooimage
 Type: Package
 Title: Analysis of numerical zooplankton images
-Version: 5.1-1
+Version: 5.1-2
 Date: 2014-12-02
 Author: Philippe Grosjean [aut, cre],
   Kevin Denis [aut]


From noreply at r-forge.r-project.org  Tue Dec  9 10:07:58 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  9 Dec 2014 10:07:58 +0100 (CET)
Subject: [Zooimage-commits] r252 - pkg/zooimage
Message-ID: <20141209090758.D8A3018767B@r-forge.r-project.org>

Author: marmayer
Date: 2014-12-09 10:07:58 +0100 (Tue, 09 Dec 2014)
New Revision: 252

Modified:
   pkg/zooimage/DESCRIPTION
Log:
rebuild


Modified: pkg/zooimage/DESCRIPTION
===================================================================
--- pkg/zooimage/DESCRIPTION	2014-12-09 09:03:08 UTC (rev 251)
+++ pkg/zooimage/DESCRIPTION	2014-12-09 09:07:58 UTC (rev 252)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Analysis of numerical zooplankton images
 Version: 5.1-2
-Date: 2014-12-02
+Date: 2014-12-09
 Author: Philippe Grosjean [aut, cre],
   Kevin Denis [aut]
 Authors at R: c(person("Philippe", "Grosjean", role = c("aut", "cre"),