From noreply at r-forge.r-project.org Wed Feb 6 10:23:47 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 6 Feb 2013 10:23:47 +0100 (CET) Subject: [Zooimage-commits] r239 - in pkg/zooimage: . R man Message-ID: <20130206092347.DDDB71812ED@r-forge.r-project.org> Author: phgrosjean Date: 2013-02-06 10:23:47 +0100 (Wed, 06 Feb 2013) New Revision: 239 Modified: pkg/zooimage/DESCRIPTION pkg/zooimage/NEWS pkg/zooimage/R/gui.R pkg/zooimage/R/guiutils.R pkg/zooimage/man/zooimage.package.Rd Log: Assignment to .GlobalEnv through .assignGlobal() function Modified: pkg/zooimage/DESCRIPTION =================================================================== --- pkg/zooimage/DESCRIPTION 2013-01-30 18:21:42 UTC (rev 238) +++ pkg/zooimage/DESCRIPTION 2013-02-06 09:23:47 UTC (rev 239) @@ -1,8 +1,8 @@ Package: zooimage Type: Package Title: Analysis of numerical zooplankton images -Version: 3.0-1 -Date: 2012-12-21 +Version: 3.0-2 +Date: 2013-02-06 Author: Ph. Grosjean, K. Denis & R. Francois Maintainer: Ph. Grosjean Depends: R (>= 2.14.0), svMisc (>= 0.9-67), svDialogs (>= 0.9-53), mlearning Modified: pkg/zooimage/NEWS =================================================================== --- pkg/zooimage/NEWS 2013-01-30 18:21:42 UTC (rev 238) +++ pkg/zooimage/NEWS 2013-02-06 09:23:47 UTC (rev 239) @@ -1,5 +1,12 @@ = zooimage News +== Changes in zooimage 3.0-2 + +* Assignment to .GlobalEnv is strictly restricted to GUI operations, and only + following direct request by the end-user through an explicit dialog box. The + internal function .assignGlobal() is used for that purpose. + + == Changes in zooimage 3.0-1 * getTrain() was not able to collect data when attributes measured on samples Modified: pkg/zooimage/R/gui.R =================================================================== --- pkg/zooimage/R/gui.R 2013-01-30 18:21:42 UTC (rev 238) +++ pkg/zooimage/R/gui.R 2013-02-06 09:23:47 UTC (rev 239) @@ -560,13 +560,14 @@ return(invisible(NULL)) ## Ask for a name for this ZITrain object - name <- dlgInput("Name for the ZITrain object:", default = "ZItrain")$res + name <- dlgInput("Name for the ZITrain object to create in the global environment:", + default = "ZItrain")$res if (!length(name)) return(invisible(FALSE)) name <- make.names(name) # Make sure it is a valid name! - ## Get the training set and save it in .GlobalEnv under the given name + ## Get the training set and save it in .GlobalEnv under the provided name res <- getTrain(dir, creator = NULL, desc = NULL, keep_ = FALSE) - assign(name, res, envir = .GlobalEnv) + .assignGlobal(name, res) ## Remember the object name assignTemp("ZI.TrainName", name) @@ -659,7 +660,7 @@ if (!length(ZIT) || (length(ZIT) == 1 && ZIT == "")) return(invisible(NULL)) ## Ask for a name for this ZIClass object - name <- dlgInput("Name for the ZIClass object to create:", + name <- dlgInput("Name for the ZIClass object to create in the global environment:", default = "ZIclass")$res if (!length(name)) return(invisible(NULL)) name <- make.names(name) # Make sure it is a valid name! @@ -770,8 +771,9 @@ ## Calculate results using formula created by variables selection res <- ZIClass(form, data = get(ZIT, envir = .GlobalEnv), algorithm = algorithm) } + ## Store the resulting object + .assignGlobal(name, res) ## Print results - assign(name, res, envir = .GlobalEnv) print(res) cat("\n") ## Remember that ZIClass object @@ -1071,7 +1073,7 @@ brks <- eval(parse(text = brks)) ## Get a name for the variable containing results - name <- dlgInput("Name for the ZIRes object to create:", + name <- dlgInput("Name for the ZIRes object to create in the global environment:", default = "ZIres")$res if (!length(name)) return(invisible(NULL)) name <- make.names(name) @@ -1084,7 +1086,7 @@ ## Assign this result to the variable - assign(name, res, envir = .GlobalEnv) + .assignGlobal(name, res) ## Remember the name of the variable assignTemp("ZI.LastRES", name) } Modified: pkg/zooimage/R/guiutils.R =================================================================== --- pkg/zooimage/R/guiutils.R 2013-01-30 18:21:42 UTC (rev 238) +++ pkg/zooimage/R/guiutils.R 2013-02-06 09:23:47 UTC (rev 239) @@ -260,3 +260,9 @@ # tkwait.window(ZIAssist) # return(getTemp("ZIret")) } + +.assignGlobal <- function (x, value) +{ + G <- .GlobalEnv + assign(x = x, value = value, envir = G) +} Modified: pkg/zooimage/man/zooimage.package.Rd =================================================================== --- pkg/zooimage/man/zooimage.package.Rd 2013-01-30 18:21:42 UTC (rev 238) +++ pkg/zooimage/man/zooimage.package.Rd 2013-02-06 09:23:47 UTC (rev 239) @@ -16,8 +16,8 @@ \tabular{ll}{ Package: \tab zooimage\cr Type: \tab Package\cr - Version: \tab 3.0-1\cr - Date: \tab 2012-12-21\cr + Version: \tab 3.0-2\cr + Date: \tab 2013-02-06\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 Mon Feb 11 20:53:52 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 11 Feb 2013 20:53:52 +0100 (CET) Subject: [Zooimage-commits] r240 - in pkg/zooimage: . man Message-ID: <20130211195352.5ED7A184602@r-forge.r-project.org> Author: phgrosjean Date: 2013-02-11 20:53:51 +0100 (Mon, 11 Feb 2013) New Revision: 240 Modified: pkg/zooimage/DESCRIPTION pkg/zooimage/NEWS pkg/zooimage/man/zooimage.package.Rd Log: Minor changes to DESCRIPTION file of zooimage Modified: pkg/zooimage/DESCRIPTION =================================================================== --- pkg/zooimage/DESCRIPTION 2013-02-06 09:23:47 UTC (rev 239) +++ pkg/zooimage/DESCRIPTION 2013-02-11 19:53:51 UTC (rev 240) @@ -1,10 +1,10 @@ Package: zooimage Type: Package Title: Analysis of numerical zooplankton images -Version: 3.0-2 -Date: 2013-02-06 +Version: 3.0-3 +Date: 2013-02-11 Author: Ph. Grosjean, K. Denis & R. Francois -Maintainer: Ph. Grosjean +Maintainer: Philippe Grosjean Depends: R (>= 2.14.0), svMisc (>= 0.9-67), svDialogs (>= 0.9-53), mlearning Imports: filehash, jpeg, png, ipred, rpart, e1071, tree, utils Suggests: rJava, mlbench Modified: pkg/zooimage/NEWS =================================================================== --- pkg/zooimage/NEWS 2013-02-06 09:23:47 UTC (rev 239) +++ pkg/zooimage/NEWS 2013-02-11 19:53:51 UTC (rev 240) @@ -1,5 +1,10 @@ = zooimage News +== Changes in zooimage 3.0-3 + +* Minor adaptations to DESCRIPTION file. + + == Changes in zooimage 3.0-2 * Assignment to .GlobalEnv is strictly restricted to GUI operations, and only Modified: pkg/zooimage/man/zooimage.package.Rd =================================================================== --- pkg/zooimage/man/zooimage.package.Rd 2013-02-06 09:23:47 UTC (rev 239) +++ pkg/zooimage/man/zooimage.package.Rd 2013-02-11 19:53:51 UTC (rev 240) @@ -16,8 +16,8 @@ \tabular{ll}{ Package: \tab zooimage\cr Type: \tab Package\cr - Version: \tab 3.0-2\cr - Date: \tab 2013-02-06\cr + Version: \tab 3.0-3\cr + Date: \tab 2013-02-11\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 Tue Feb 12 20:57:00 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 12 Feb 2013 20:57:00 +0100 (CET) Subject: [Zooimage-commits] r241 - in pkg/zooimage: . R man Message-ID: <20130212195700.71153183CA0@r-forge.r-project.org> Author: phgrosjean Date: 2013-02-12 20:57:00 +0100 (Tue, 12 Feb 2013) New Revision: 241 Modified: pkg/zooimage/DESCRIPTION pkg/zooimage/NEWS pkg/zooimage/R/utilities.R pkg/zooimage/man/zooimage.package.Rd Log: Added new items in dropVars() Modified: pkg/zooimage/DESCRIPTION =================================================================== --- pkg/zooimage/DESCRIPTION 2013-02-11 19:53:51 UTC (rev 240) +++ pkg/zooimage/DESCRIPTION 2013-02-12 19:57:00 UTC (rev 241) @@ -1,8 +1,8 @@ Package: zooimage Type: Package Title: Analysis of numerical zooplankton images -Version: 3.0-3 -Date: 2013-02-11 +Version: 3.0-4 +Date: 2013-02-12 Author: Ph. Grosjean, K. Denis & R. Francois Maintainer: Philippe Grosjean Depends: R (>= 2.14.0), svMisc (>= 0.9-67), svDialogs (>= 0.9-53), mlearning Modified: pkg/zooimage/NEWS =================================================================== --- pkg/zooimage/NEWS 2013-02-11 19:53:51 UTC (rev 240) +++ pkg/zooimage/NEWS 2013-02-12 19:57:00 UTC (rev 241) @@ -1,5 +1,11 @@ = zooimage News +== Changes in zooimage 3.0-4 + +* Default dropVars(): adding a few items, including 'Skew', 'Kurt' and + 'Solidity' that produce NAs in ImageJ for multiple ROIs objects. + + == Changes in zooimage 3.0-3 * Minor adaptations to DESCRIPTION file. Modified: pkg/zooimage/R/utilities.R =================================================================== --- pkg/zooimage/R/utilities.R 2013-02-11 19:53:51 UTC (rev 240) +++ pkg/zooimage/R/utilities.R 2013-02-12 19:57:00 UTC (rev 241) @@ -114,7 +114,9 @@ "FIT_Ch2_Ch1_Ratio", "FIT_Ch4_Peak", "FIT_Ch4_TOF", "FIT_Timestamp1", "FIT_Timestamp2", "FIT_Camera", "FIT_FringSize", "FIT_CircleFit", "FIT_Ch1_Area", "FIT_Ch2_Area", "FIT_Ch3_Area", - "FIT_TimeStamp1", "FIT_Source_Image.1")) + "FIT_TimeStamp1", "FIT_Source_Image.1", + "X.Item.1", "FeretAngle", "Count", + "Skew", "Kurt", "Solidity")) # Last 3: NAs with multiple ROIs as.character(res) } Modified: pkg/zooimage/man/zooimage.package.Rd =================================================================== --- pkg/zooimage/man/zooimage.package.Rd 2013-02-11 19:53:51 UTC (rev 240) +++ pkg/zooimage/man/zooimage.package.Rd 2013-02-12 19:57:00 UTC (rev 241) @@ -16,8 +16,8 @@ \tabular{ll}{ Package: \tab zooimage\cr Type: \tab Package\cr - Version: \tab 3.0-3\cr - Date: \tab 2013-02-11\cr + Version: \tab 3.0-4\cr + Date: \tab 2013-02-12\cr License: \tab GPL 2 or above at your convenience.\cr } Everytime you publish results that use ZooImage, you must place a reference