From noreply at r-forge.r-project.org Thu Oct 1 10:16:26 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 1 Oct 2015 10:16:26 +0200 (CEST) Subject: [Zooimage-commits] r254 - in pkg/zooimage: . R man Message-ID: <20151001081627.0D200185979@r-forge.r-project.org> Author: phgrosjean Date: 2015-10-01 10:16:26 +0200 (Thu, 01 Oct 2015) New Revision: 254 Modified: pkg/zooimage/DESCRIPTION pkg/zooimage/NAMESPACE pkg/zooimage/NEWS pkg/zooimage/R/gui.R pkg/zooimage/man/correctError.Rd pkg/zooimage/man/gui.Rd pkg/zooimage/man/zooimage.package.Rd Log: Small bugs correction Modified: pkg/zooimage/DESCRIPTION =================================================================== --- pkg/zooimage/DESCRIPTION 2015-09-29 13:21:59 UTC (rev 253) +++ pkg/zooimage/DESCRIPTION 2015-10-01 08:16:26 UTC (rev 254) @@ -1,8 +1,8 @@ Package: zooimage Type: Package Title: Analysis of Numerical Zooplankton Images -Version: 5.4-1 -Date: 2015-09-29 +Version: 5.4-2 +Date: 2015-10-01 Author: Philippe Grosjean [aut, cre], Kevin Denis [aut], Guillaume Wacquet [aut] Authors at R: c(person("Philippe", "Grosjean", role = c("aut", "cre"), Modified: pkg/zooimage/NAMESPACE =================================================================== --- pkg/zooimage/NAMESPACE 2015-09-29 13:21:59 UTC (rev 253) +++ pkg/zooimage/NAMESPACE 2015-10-01 08:16:26 UTC (rev 254) @@ -28,6 +28,7 @@ # planktonSorter export(correctError) +export(activeLearning) # Zic export(zicCheck) @@ -176,6 +177,7 @@ export(validClass) export(vignettesClass) export(viewManual) +export(viewFrenchManual) export(viewResults) export(ZIDlg) # Not in menus yet! Modified: pkg/zooimage/NEWS =================================================================== --- pkg/zooimage/NEWS 2015-09-29 13:21:59 UTC (rev 253) +++ pkg/zooimage/NEWS 2015-10-01 08:16:26 UTC (rev 254) @@ -1,5 +1,13 @@ = zooimage News +== Changes in zooimage 5.4-2 + +* Correction of one bug in the function addVigsToTrain(). + +* The functions activeLearning() and viewFrenchManual() were not exported in + the NAMESPACE, but are required for the menus. Fixed. + + == Changes in zooimage 5.4-1 * Correction of various bugs by Guillaume Wacquet. Modified: pkg/zooimage/R/gui.R =================================================================== --- pkg/zooimage/R/gui.R 2015-09-29 13:21:59 UTC (rev 253) +++ pkg/zooimage/R/gui.R 2015-10-01 08:16:26 UTC (rev 254) @@ -758,7 +758,7 @@ if (ChgVigs[i] %in% RedundantVigs1) { status <- "Redundant" pathTrain1 <- Paths1[which(Vigs1 == ChgVigs[i])] - athTrain2 <- "" + pathTrain2 <- "" ChgToSave <- rbind(ChgToSave, cbind(nameChg, status, pathTrain1, pathTrain2)) } Modified: pkg/zooimage/man/correctError.Rd =================================================================== --- pkg/zooimage/man/correctError.Rd 2015-09-29 13:21:59 UTC (rev 253) +++ pkg/zooimage/man/correctError.Rd 2015-10-01 08:16:26 UTC (rev 254) @@ -2,6 +2,7 @@ \alias{correctError} \alias{addItemsToTrain} \alias{dropItemsToTrain} +\alias{activeLearning} \title{ The ZooImage error correction (manual validation) tools } \description{ @@ -16,6 +17,8 @@ addItemsToTrain(train, CtxSmp, add.mode = "SV+NSV", threshold = NA, dropItemsToTrain = dropItemsToTrain) dropItemsToTrain(train, cl, drop.nb) + +activeLearning(train, add.mode = "SV+NSV", threshold = NA) } \arguments{ Modified: pkg/zooimage/man/gui.Rd =================================================================== --- pkg/zooimage/man/gui.Rd 2015-09-29 13:21:59 UTC (rev 253) +++ pkg/zooimage/man/gui.Rd 2015-10-01 08:16:26 UTC (rev 254) @@ -5,6 +5,7 @@ \alias{closeAssistant} \alias{closeZooImage} \alias{viewManual} +\alias{viewFrenchManual} \alias{focusR} \alias{focusGraph} \alias{acquireImg} @@ -48,6 +49,7 @@ closeAssistant() closeZooImage() viewManual() +viewFrenchManual() focusR() focusGraph() acquireImg() Modified: pkg/zooimage/man/zooimage.package.Rd =================================================================== --- pkg/zooimage/man/zooimage.package.Rd 2015-09-29 13:21:59 UTC (rev 253) +++ pkg/zooimage/man/zooimage.package.Rd 2015-10-01 08:16:26 UTC (rev 254) @@ -16,8 +16,8 @@ \tabular{ll}{ Package: \tab zooimage\cr Type: \tab Package\cr - Version: \tab 5.4-1\cr - Date: \tab 2015-09-29\cr + Version: \tab 5.4-2\cr + Date: \tab 2015-10-01\cr License: \tab GPL 2 or above at your convenience.\cr } } From noreply at r-forge.r-project.org Fri Oct 9 17:46:50 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 9 Oct 2015 17:46:50 +0200 (CEST) Subject: [Zooimage-commits] r255 - in pkg/zooimage: . R inst/gui/errorcorrection man Message-ID: <20151009154650.4D6B1187107@r-forge.r-project.org> Author: phgrosjean Date: 2015-10-09 17:46:49 +0200 (Fri, 09 Oct 2015) New Revision: 255 Modified: pkg/zooimage/DESCRIPTION pkg/zooimage/NAMESPACE pkg/zooimage/NEWS pkg/zooimage/R/ZIRes.R pkg/zooimage/R/gui.R pkg/zooimage/TODO pkg/zooimage/inst/gui/errorcorrection/server.R pkg/zooimage/man/ZIRes.Rd pkg/zooimage/man/gui.Rd pkg/zooimage/man/zooimage.package.Rd Log: Cells counting per colonies Modified: pkg/zooimage/DESCRIPTION =================================================================== --- pkg/zooimage/DESCRIPTION 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/DESCRIPTION 2015-10-09 15:46:49 UTC (rev 255) @@ -1,8 +1,8 @@ Package: zooimage Type: Package Title: Analysis of Numerical Zooplankton Images -Version: 5.4-2 -Date: 2015-10-01 +Version: 5.4-3 +Date: 2015-10-09 Author: Philippe Grosjean [aut, cre], Kevin Denis [aut], Guillaume Wacquet [aut] Authors at R: c(person("Philippe", "Grosjean", role = c("aut", "cre"), Modified: pkg/zooimage/NAMESPACE =================================================================== --- pkg/zooimage/NAMESPACE 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/NAMESPACE 2015-10-09 15:46:49 UTC (rev 255) @@ -172,6 +172,7 @@ export(optInOutDecimalSep) export(processImg) export(processSamples) +export(processSamplesWithCells) export(removeObjects) export(saveObjects) export(validClass) Modified: pkg/zooimage/NEWS =================================================================== --- pkg/zooimage/NEWS 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/NEWS 2015-10-09 15:46:49 UTC (rev 255) @@ -1,5 +1,10 @@ = zooimage News +== Changes in zooimage 5.4-3 + +* Cells counting per colonies (per particles) is now provided. + + == Changes in zooimage 5.4-2 * Correction of one bug in the function addVigsToTrain(). Modified: pkg/zooimage/R/ZIRes.R =================================================================== --- pkg/zooimage/R/ZIRes.R 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/R/ZIRes.R 2015-10-09 15:46:49 UTC (rev 255) @@ -103,33 +103,12 @@ } ## Calculate abundances, biomasses and size spectra per class in a sample -#processSample <- function (x, sample, keep = NULL, detail = NULL, classes = "both", -#header = c("Abd", "Bio"), cells = NULL, biomass = NULL, breaks = NULL) processSample <- function (x, sample, keep = NULL, detail = NULL, classes = "both", -header = c("Abd", "Bio"), biomass = NULL, breaks = NULL) +header = c("Abd", "Bio"), cells = NULL, 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) - - ## Do we compute the number of cells and the ECD per cell? - ## But see version hereunder! -#### TODO: compute ECD using number of cells per colonies! -#### if (!is.null(cells)) { -#### x$Nb_cells <- computeNbCells(x, cells) -#### x$ECD_cells <- ecd(x$FIT_Area_ABD, x$Nb_cells) -#### } -#### PhG: here, computation before argument checking is not good! -#### PhG: cells points to a file. Not good! We ask for a specific object instead - - ## Do we compute the number of cells and the ECD per cell? - ## PhG: should not rely on a filehere! -#### if (!is.null(cells) && file.exists(cells)) { -#### ## Must be a ZICell model here! predict() iterates on all items -#### ## of the list to compute cells for all classes! -#### x$Nb_cells <- predict(cells, x) -#### x$ECD_cells <- ecd(x$FIT_Area_ABD, x$Nb_cells) -####} - + ## Check arguments if (missing(sample)) { sample <- unique(sampleInfo(x$Label, type = "sample", ext = "")) @@ -157,6 +136,16 @@ return(NULL) } + ## Do we compute the number of cells and the ECD per cell? + ## TODO: should not rely on a file here (use a predict() method of a ZICell object)! + if (!is.null(cells) && file.exists(cells)) { +#### ## Must be a ZICell model here! predict() iterates on all items +#### ## of the list to compute cells for all classes! +#### x$Nb_cells <- predict(cells, x) + x$Nbr_cells <- cellCompute(x, cells) + x$ECD_cells <- ecd(x$FIT_Area_ABD, x$Nb_cells) + } + ## Extract only data for a given sample allSamples <- unique(sampleInfo(x$Label, type = "sample", ext = "")) if (!sample %in% allSamples){ @@ -330,7 +319,7 @@ '[total]' = apply(spectrum, 2, sum)) } - ## Eliminate all ine except total if detail is not provided + ## Eliminate all lines except total if detail is not provided if (!length(detail)) spectrum <- spectrum[NROW(spectrum), , drop = FALSE] @@ -344,8 +333,8 @@ } processSampleAll <- function (path = ".", zidbfiles, ZIClass = NULL, keep = NULL, -detail = NULL, classes = "both", header = c("Abd", "Bio"), biomass = NULL, -breaks = NULL) +detail = NULL, classes = "both", header = c("Abd", "Bio"), cells = NULL, +biomass = NULL, breaks = NULL) { ## First, switch to that directory if (!checkDirExists(path)) return(invisible(FALSE)) @@ -382,8 +371,8 @@ ## Process that one sample and merge with the rest res <- rbind(res, processSample(dat, keep = keep, detail = detail, - classes = classes, header = header, biomass = biomass, - breaks = breaks)) + classes = classes, header = header, cells = cells, + biomass = biomass, breaks = breaks)) } progress(101) # Clear progression indicator message(" -- Done! --") Modified: pkg/zooimage/R/gui.R =================================================================== --- pkg/zooimage/R/gui.R 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/R/gui.R 2015-10-09 15:46:49 UTC (rev 255) @@ -30,8 +30,8 @@ menuAddItem(ZIname, "Interactive UI", "ZIUI()") menuAddItem(ZIname, "--", "") menuAddItem(ZIname, "Online help", 'help("zooimage")') - menuAddItem(ZIname, "Manual (English version)", "viewManual()") - menuAddItem(ZIname, "Manual (French version)", "viewFrenchManual()") + menuAddItem(ZIname, "Manual (English version)", "viewManual()") + menuAddItem(ZIname, "Manual (French version)", "viewFrenchManual()") menuAddItem(ZIname, "Web site", 'browseURL("http://www.sciviews.org/zooimage")') menuAddItem(ZIname, "--", "") @@ -48,7 +48,7 @@ menuAddItem("Analyze", "-", "") menuAddItem("Analyze", "Make training set...", "makeTrain()") menuAddItem("Analyze", "Add vignettes to training set", "addVigsToTrain()") - menuAddItem("Analyze", "Differences between two training sets", "compTrain()") + menuAddItem("Analyze", "Differences between two training sets", "compTrain()") menuAddItem("Analyze", "Count cells in colonies...", "countCellsGUI()") menuAddItem("Analyze", "Read training set...", "collectTrain()") menuAddItem("Analyze", "Make classifier...", "makeClass()") @@ -60,6 +60,7 @@ menuAddItem("Analyze", "--", "") menuAddItem("Analyze", "Edit samples description", "editDescription()") menuAddItem("Analyze", "Process samples...", "processSamples()") + menuAddItem("Analyze", "Process samples with cells counting...", "processSamplesWithCells()") menuAddItem("Analyze", "View results...", "viewResults()") menuAddItem("Analyze", "Export results...", "exportResults()") @@ -234,20 +235,20 @@ } else browseURL(manual) } -viewFrenchManual <- function () -{ - manual <- file.path(getTemp("ZIetc"), "ZooImageManual_french.pdf") - pdfviewer <- getOption( "pdfviewer" ) - if (!is.null(pdfviewer)) { - if (.Platform$OS.type == "windows") { - shell.exec(manual) - } else { - system(paste(shQuote(getOption("pdfviewer")), shQuote(manual)), - wait = FALSE) - } - } else browseURL(manual) -} - +viewFrenchManual <- function () +{ + manual <- file.path(getTemp("ZIetc"), "ZooImageManual_french.pdf") + pdfviewer <- getOption( "pdfviewer" ) + if (!is.null(pdfviewer)) { + if (.Platform$OS.type == "windows") { + shell.exec(manual) + } else { + system(paste(shQuote(getOption("pdfviewer")), shQuote(manual)), + wait = FALSE) + } + } else browseURL(manual) +} + focusR <- function () { ## Switch the focus to the R console @@ -590,7 +591,7 @@ if (!length(subdir)) return(invisible(NULL)) ## Ask for the .zid files - zidfiles <- selectFile(type = "ZidZidb", multiple = TRUE, quote = FALSE) + zidfiles <- selectFile(type = "ZidZidb", multiple = TRUE, quote = FALSE) if (!length(zidfiles)) return(invisible(NULL)) ## Prepare the training set @@ -758,7 +759,7 @@ if (ChgVigs[i] %in% RedundantVigs1) { status <- "Redundant" pathTrain1 <- Paths1[which(Vigs1 == ChgVigs[i])] - pathTrain2 <- "" + pathTrain2 <- "" ChgToSave <- rbind(ChgToSave, cbind(nameChg, status, pathTrain1, pathTrain2)) } @@ -1145,19 +1146,19 @@ if (!length(ZIT) || (length(ZIT) == 1 && ZIT == "")) return(invisible(NULL)) - ## Call activeLearning (for augmentation of training set) - train <- activeLearning(train = get(ZIT, envir = .GlobalEnv), - add.mode = "SV+NSV", threshold = NA) -# ## Call contextSelection (for selection of contextual samples) -# CtxSmp <- contextSelection() -# if (length(CtxSmp) < 1) { -# warning("No contextual samples selected! Initial training set will be used...") -# } else { -# ## Call addItemsToTrain (for augmentation of the training set) -# train <- addItemsToTrain(train = get(ZIT, envir = .GlobalEnv), -# CtxSmp = CtxSmp, add.mode = "SV+NSV", threshold = NA, -# dropItemsToTrain = dropItemsToTrain) -# } + ## Call activeLearning (for augmentation of training set) + train <- activeLearning(train = get(ZIT, envir = .GlobalEnv), + add.mode = "SV+NSV", threshold = NA) +# ## Call contextSelection (for selection of contextual samples) +# CtxSmp <- contextSelection() +# if (length(CtxSmp) < 1) { +# warning("No contextual samples selected! Initial training set will be used...") +# } else { +# ## Call addItemsToTrain (for augmentation of the training set) +# train <- addItemsToTrain(train = get(ZIT, envir = .GlobalEnv), +# CtxSmp = CtxSmp, add.mode = "SV+NSV", threshold = NA, +# dropItemsToTrain = dropItemsToTrain) +# } #.assignGlobal(ZIT, train) classifier <- ZIClass(Class ~ ., data = train[!(names(train) %in% "AddedItems")], method = "mlRforest", calc.vars = calcVars, ntree = 200, cv.k = 10) @@ -1219,10 +1220,47 @@ assignTemp("ZI.LastZIS", zisfile) } -processSamples <- function() +processSamplesWithCells <- function() { + ## Ask for a "cells" file with data required to compute the number of cells + ## per colonies (per particles) + cells <- getTemp("ZI.LastCells") + if (is.null(cells) || !file.exists(cells)) + cells <- "" + ## Ask for the cells file + if (cells != "") { + cells <- dlgOpen(default = cells, title = "Select a cells counting RDS file", + filters = matrix(c("Cells counting RDS file", ".rds"), + ncol = 2, byrow = TRUE))$res + } else if (file.exists(file.path(getwd(), "cells.rds"))) { + zisfile <- dlgOpen(default = file.path(getwd(), "cells.RData"), + title = "Select a cells counting RDS file", + filters = matrix(c("Cells counting file", ".rds"), + ncol = 2, byrow = TRUE))$res + } else { + zisfile <- dlgOpen(title = "Select a cells counting RDS file", + filters = matrix(c("Cells counting file", ".rds"), + ncol = 2, byrow = TRUE))$res + } + if (!length(cells)) return(invisible(NULL)) + + ## Remember last file used + assignTemp("ZI.LastCells", cells) + + ## Call .processSamples() using this file... + .processSamples(cells) +} + +## Just delegate to .processSamples() without providing a cells file to do +## the computation without cells counting +processSamples <- function () + .processSamples() + +.processSamples <- function(cells = NULL) +{ ## Ask for a description.zis file, look at all samples described there - ## Calculate abundances, total and partial size spectra and possibly biomasses + ## Calculate abundances, total and partial size spectra and possibly number + ## of cells per colonies (per particles) and biomasses ## Get the last edited description.zis file ## Get a possibly saved directory as default one zisfile <- getTemp("ZI.LastZIS") Modified: pkg/zooimage/TODO =================================================================== --- pkg/zooimage/TODO 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/TODO 2015-10-09 15:46:49 UTC (rev 255) @@ -1,3 +1,5 @@ = zooimage - TODO list * There is a calibrate() method in vegan => use a different name here + +* Check authors everywhere and adjust (in particular for Guillaume Wacquet) Modified: pkg/zooimage/inst/gui/errorcorrection/server.R =================================================================== --- pkg/zooimage/inst/gui/errorcorrection/server.R 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/inst/gui/errorcorrection/server.R 2015-10-09 15:46:49 UTC (rev 255) @@ -82,7 +82,7 @@ # .ZI$Train <- addItemsToTrain(.ZI$Train, CtxSmp, # dropItemsToTrain = dropItemsToTrain) # } - .ZI$Train <- activeLearning(.ZI$Train) + .ZITrain <- activeLearning(.ZITrain) assign(.ZIClass, eval(parse(text = .ZI$classifcmd))) if (file.exists(DemoFile)) { # Run in demo mode res <- load(DemoFile) @@ -173,7 +173,7 @@ #assign(ResData, processSample(dat2, keep = NULL, detail = detail, # biomass = .ZI$biovolume, breaks = .ZI$breaks, classes = "Class")) ## With cellModels... - assign(ResData, processSample(dat2, keep = NULL, detail = detail, cellModels = .ZI$cellModelsfile, + assign(ResData, processSample(dat2, keep = NULL, detail = detail, cells = .ZI$cellModelsfile, biomass = .ZI$biovolume, breaks = .ZI$breaks, classes = "Class")) ## Save it save(list = ResData, file = ResFile) Modified: pkg/zooimage/man/ZIRes.Rd =================================================================== --- pkg/zooimage/man/ZIRes.Rd 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/man/ZIRes.Rd 2015-10-09 15:46:49 UTC (rev 255) @@ -11,10 +11,12 @@ and they collect them together in a 'ZIRes' object. } \usage{ -processSample(x, sample, keep = NULL, detail = NULL, classes = "both", - header = c("Abd", "Bio"), biomass = NULL, breaks = NULL) -processSampleAll(path = ".", zidbfiles, ZIClass = NULL, keep = NULL, detail = NULL, - classes = "both", header = c("Abd", "Bio"), biomass = NULL, breaks = NULL) +processSample(x, sample, keep = NULL, + detail = NULL, classes = "both", header = c("Abd", "Bio"), + cells = NULL, biomass = NULL, breaks = NULL) +processSampleAll(path = ".", zidbfiles, ZIClass = NULL, keep = NULL, + detail = NULL, classes = "both", header = c("Abd", "Bio"), + cells = NULL, biomass = NULL, breaks = NULL) \method{print}{ZIRes}(x, \dots) \method{rbind}{ZIRes}(\dots, deparse.level = 1) @@ -38,6 +40,8 @@ defined. One can also specify the name of another factor variable in \code{x}. } \item{header}{ a character vector with one or two strings to use as headers for, respectively, abundances and biomasses. } + \item{cells}{ the path to an .rds file containing cells counting models, as used + by \code{cellCompute()}. } \item{biomass}{ a specification for biomass conversion. Can be \code{NULL} (by default) for turning off biomass calculation, or a numeric vector of three values P1, P2 and P3 (same biomass for all classes with Bio = P1 * ECD^P3 + P2), Modified: pkg/zooimage/man/gui.Rd =================================================================== --- pkg/zooimage/man/gui.Rd 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/man/gui.Rd 2015-10-09 15:46:49 UTC (rev 255) @@ -26,6 +26,7 @@ \alias{validClass} \alias{editDescription} \alias{processSamples} +\alias{processSamplesWithCells} \alias{viewResults} \alias{exportResults} \alias{loadObjects} @@ -70,6 +71,7 @@ validClass() editDescription() processSamples() +processSamplesWithCells() viewResults() exportResults loadObjects() Modified: pkg/zooimage/man/zooimage.package.Rd =================================================================== --- pkg/zooimage/man/zooimage.package.Rd 2015-10-01 08:16:26 UTC (rev 254) +++ pkg/zooimage/man/zooimage.package.Rd 2015-10-09 15:46:49 UTC (rev 255) @@ -16,8 +16,8 @@ \tabular{ll}{ Package: \tab zooimage\cr Type: \tab Package\cr - Version: \tab 5.4-2\cr - Date: \tab 2015-10-01\cr + Version: \tab 5.4-3\cr + Date: \tab 2015-10-09\cr License: \tab GPL 2 or above at your convenience.\cr } } From noreply at r-forge.r-project.org Tue Oct 27 15:54:04 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 27 Oct 2015 15:54:04 +0100 (CET) Subject: [Zooimage-commits] r256 - in pkg/zooimage: . R inst/gui/errorcorrection Message-ID: <20151027145404.86C28184543@r-forge.r-project.org> Author: phgrosjean Date: 2015-10-27 15:54:03 +0100 (Tue, 27 Oct 2015) New Revision: 256 Modified: pkg/zooimage/NEWS pkg/zooimage/R/gui.R pkg/zooimage/inst/gui/errorcorrection/server.R Log: Use .zidb in processSamples() Modified: pkg/zooimage/NEWS =================================================================== --- pkg/zooimage/NEWS 2015-10-09 15:46:49 UTC (rev 255) +++ pkg/zooimage/NEWS 2015-10-27 14:54:03 UTC (rev 256) @@ -4,7 +4,9 @@ * Cells counting per colonies (per particles) is now provided. +* processSamples() now look for .zidb files instead of .zid files. + == Changes in zooimage 5.4-2 * Correction of one bug in the function addVigsToTrain(). Modified: pkg/zooimage/R/gui.R =================================================================== --- pkg/zooimage/R/gui.R 2015-10-09 15:46:49 UTC (rev 255) +++ pkg/zooimage/R/gui.R 2015-10-27 14:54:03 UTC (rev 256) @@ -1357,13 +1357,13 @@ if (!length(smplist) || smplist == "") stop("No sample found in the description file!") - ## Are there corresponding .zid files for all samples? + ## Are there corresponding .zidb files for all samples? zisdir <- dirname(zisfile) if (zisdir == ".") zisdir <- getwd() - zidfiles <- file.path(zisdir, paste(smplist, ".zid", sep = "")) - if (!all(file.exists(zidfiles)) || - !all(regexpr("[.][zZ][iI][dD]$", zidfiles) > 0)) - stop("One or more .zid files do not exist or is invalid!") + zidbfiles <- file.path(zisdir, paste(smplist, ".zidb", sep = "")) + if (!all(file.exists(zidbfiles)) || + !all(regexpr("[.][zZ][iI][dD][bB]$", zidbfiles) > 0)) + stop("One or more .zidb files do not exist or is invalid!") ## Get a classifier ZIC <- getTemp("ZI.ClassName") @@ -1413,7 +1413,6 @@ biomass = conv, breaks = brks) ## TODO: possibly export result in a file... - ## Assign this result to the variable .assignGlobal(name, res) ## Remember the name of the variable Modified: pkg/zooimage/inst/gui/errorcorrection/server.R =================================================================== --- pkg/zooimage/inst/gui/errorcorrection/server.R 2015-10-09 15:46:49 UTC (rev 255) +++ pkg/zooimage/inst/gui/errorcorrection/server.R 2015-10-27 14:54:03 UTC (rev 256) @@ -79,7 +79,7 @@ # warning("No contextual samples selected! Initial training set will be used.") # } else { # ## TODO: merge with activeLearningGUI -# .ZI$Train <- addItemsToTrain(.ZI$Train, CtxSmp, +# .ZITrain <- addItemsToTrain(.ZITrain, CtxSmp, # dropItemsToTrain = dropItemsToTrain) # } .ZITrain <- activeLearning(.ZITrain)