[Zooimage-commits] r198 - in pkg: phytoimage phytoimage/R phytoimage/inst/gui phytoimage/man zooimage zooimage/R zooimage/inst/gui zooimage/javasrc/src/org/sciviews/zooimage/tools zooimage/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jun 9 15:39:50 CEST 2012
Author: phgrosjean
Date: 2012-06-09 15:39:49 +0200 (Sat, 09 Jun 2012)
New Revision: 198
Added:
pkg/phytoimage/NAMESPACE
pkg/zooimage/inst/gui/ZooImage.icns
pkg/zooimage/inst/gui/ZooImage2_128.png
pkg/zooimage/inst/gui/ZooImage2_64.png
Removed:
pkg/phytoimage/ToDo.txt
pkg/zooimage/FunList.txt
Modified:
pkg/phytoimage/DESCRIPTION
pkg/phytoimage/R/gui.r
pkg/phytoimage/R/zzz.r
pkg/phytoimage/inst/gui/Menus.txt
pkg/phytoimage/inst/gui/MenusZIDlgWin.txt
pkg/phytoimage/inst/gui/ToolbarsZIDlgWin.txt
pkg/phytoimage/man/gui.Rd
pkg/phytoimage/man/phytoimage.package.Rd
pkg/zooimage/DESCRIPTION
pkg/zooimage/NAMESPACE
pkg/zooimage/R/RealTime.R
pkg/zooimage/R/ZIClass.R
pkg/zooimage/R/ZIConf.R
pkg/zooimage/R/ZIMan.R
pkg/zooimage/R/ZIRes.R
pkg/zooimage/R/ZITrain.R
pkg/zooimage/R/capabilities.R
pkg/zooimage/R/catcher.R
pkg/zooimage/R/errorHandling.R
pkg/zooimage/R/gui.R
pkg/zooimage/R/log.R
pkg/zooimage/R/misc.R
pkg/zooimage/R/programs.R
pkg/zooimage/R/utilities.R
pkg/zooimage/R/zic.R
pkg/zooimage/R/zid.R
pkg/zooimage/R/zie.R
pkg/zooimage/R/zim.R
pkg/zooimage/R/zip.R
pkg/zooimage/R/zis.R
pkg/zooimage/R/zzz.R
pkg/zooimage/inst/gui/Menus.txt
pkg/zooimage/inst/gui/MenusZIDlgWin.txt
pkg/zooimage/inst/gui/ToolbarsZIDlgWin.txt
pkg/zooimage/javasrc/src/org/sciviews/zooimage/tools/ZIJ.java
pkg/zooimage/man/RealTime.Rd
pkg/zooimage/man/ZIClass.Rd
pkg/zooimage/man/ZIMan.Rd
pkg/zooimage/man/ZIRes.Rd
pkg/zooimage/man/ZITrain.Rd
pkg/zooimage/man/gui.Rd
pkg/zooimage/man/utilities.Rd
pkg/zooimage/man/zid.Rd
pkg/zooimage/man/zie.Rd
pkg/zooimage/man/zim.Rd
pkg/zooimage/man/zip.Rd
pkg/zooimage/man/zis.Rd
pkg/zooimage/man/zooimage.package.Rd
Log:
Many changes towards version 3 of ZooImage and PhytoImage
Modified: pkg/phytoimage/DESCRIPTION
===================================================================
--- pkg/phytoimage/DESCRIPTION 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/DESCRIPTION 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,18 +1,16 @@
Package: phytoimage
Type: Package
Title: Analysis of numerical phytoplankton images
-Version: 1.2-1
-Date: 2007-05-29
+Version: 3.0-0
+Date: 2012-05-07
Author: Ph. Grosjean & K. Denis
-Maintainer: Ph. Grosjean <Philippe.Grosjean at umh.ac.be>
-Depends: R (>= 2.4.0), tcltk, tcltk2, svMisc
+Maintainer: Ph. Grosjean <Philippe.Grosjean at umons.ac.be>
+Depends: R (>= 2.10.0), svMisc, svDialogs
Suggests: zooimage
Description: PhytoImage is a free (open source) solution for analyzing digital
images of phytoplankton. In combination with ImageJ, a free image analysis
system, it processes digital images, measures individuals, trains for
automatic identification of taxa, and finally, measures phytoplankton samples
(abundances, total and partial size spectra or biomasses, etc.)
-License: GPL2 or above at your convenience. Send metadata and reprints to maintainer
- for every series you analyze and every paper you publish using PhytoImage (see the
- web site for further informations).
+License: GPL (>= 2)
URL: http://www.sciviews.org/zooimage
Added: pkg/phytoimage/NAMESPACE
===================================================================
--- pkg/phytoimage/NAMESPACE (rev 0)
+++ pkg/phytoimage/NAMESPACE 2012-06-09 13:39:49 UTC (rev 198)
@@ -0,0 +1,7 @@
+#import(tcltk)
+#import(tcltk2)
+import(svMisc)
+import(svDialogs)
+
+export(exitPgm)
+export(closePhytoImage)
Modified: pkg/phytoimage/R/gui.r
===================================================================
--- pkg/phytoimage/R/gui.r 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/R/gui.r 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,14 +1,14 @@
-"ExitPgm" <-
- function(){
- detach("package:phytoimage") # This is useful to allow updating the package!
- detach("package:zooimage")
+exitPgm <- function ()
+{
+ ## This is useful to allow updating the packages!
+ detach("package:phytoimage", unload = TRUE)
+ detach("package:zooimage", unload = TRUE)
cat("phytoimage package unloaded; To restart it, issue:\n> library(phytoimage)\n")
}
-"closePhytoImage" <-
- function() {
- require(zooimage)
- closeAssistant() # This is a ZooImage function!
- ExitPgm()
+closePhytoImage <- function ()
+{
+ #zooimage::closeAssistant()
+ exitPgm()
}
Modified: pkg/phytoimage/R/zzz.r
===================================================================
--- pkg/phytoimage/R/zzz.r 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/R/zzz.r 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,40 +1,56 @@
-".First.lib" <-
-function(libname, pkgname) {
- (require(svMisc) || stop("Package 'svMisc' from SciViews bundle is required!"))
- (require(svWidgets) || stop("Package 'svWidgets' from SciViews bundle is required!"))
- (require(tcltk2) || stop("Package 'tcltk2' is required!"))
+## Copyright (c) 2004-2012, Ph. Grosjean <phgrosjean at sciviews.org>
+##
+## This file is part of PhytoImage
+##
+## PhytoImage is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 2 of the License, or
+## (at your option) any later version.
+##
+## PhytoImage is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with PhytoImage. If not, see <http://www.gnu.org/licenses/>.
- # Define name and icon we want for the ZooImage application
- ZIname <- "PhytoImage1"
+## Loading and unloading PhytoImage
+
+.onLoad <- function (libname, pkgname)
+{
+ ## Define name and icon we want for the ZooImage application
+ ZIname <- "PhytoImage"
assignTemp("ZIname", ZIname)
- ZIetc <- file.path(.path.package(package = "phytoimage")[1], "etc")
+ ZIetc <- system.file("etc", package = "phytoimage")
assignTemp("ZIetc", ZIetc)
- ZIgui <- file.path(.path.package(package = "phytoimage")[1], "gui")
+ ZIgui <- system.file("gui", package = "phytoimage")
assignTemp("ZIgui", ZIgui)
- if (isWin())
- assignTemp("ZIico", tk2ico.create(file.path(getTemp("ZIgui"), "PhytoImage.ico")))
+ #if (isWin())
+ # assignTemp("ZIico", tk2ico.create(file.path(getTemp("ZIgui"), "PhytoImage.ico")))
- # Load the various image resources
- tkImgReadPackage("phytoimage")
- # Load the menus
- MenuReadPackage("phytoimage")
- # Indicate that other GUI resources should be loaded from the phytoimage package
+ ## Load the various image resources
+ #tkImgReadPackage("phytoimage")
+ ## Load the menus
+ #MenuReadPackage("phytoimage")
+ ## Indicate that other GUI resources should be loaded from the phytoimage package
ZIguiPackage <- "phytoimage"
assignTemp("ZIguiPackage", ZIguiPackage)
- # Make sure that ZooImage will not overwrite these entries
+ ## Make sure that ZooImage will not overwrite these entries
options(ZIredefine = TRUE)
- # Load the initial zooimage package now
- (require(zooimage) || stop("Package 'zooimage' is required!"))
+ ## Load the initial zooimage package now
+ if (!require(zooimage)) stop("Package 'zooimage' is required!")
}
-".Last.lib" <-
-function(libpath) {
- # Eliminate the PhytoImage menu entries
+## Unloading PhytoImage
+.onUnload <- function (libpath)
+{
+ ## Eliminate the PhytoImage menu entries
if (.Platform$GUI[1] == "Rgui") {
- require(svWidgets)
- try(MenuDel("$ConsoleMain/PhytoImage"), silent = TRUE)
- try(MenuDel("$ConsolePopup/PhytoImage"), silent = TRUE)
+ try(menuDel("$ConsoleMain/PhytoImage"), silent = TRUE)
+ try(menuDel("$ConsolePopup/PhytoImage"), silent = TRUE)
}
+ try(detach("package:zooimage", unload = TRUE), silent = TRUE)
}
Deleted: pkg/phytoimage/ToDo.txt
===================================================================
--- pkg/phytoimage/ToDo.txt 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/ToDo.txt 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,6 +0,0 @@
-PhytoImage - ToDo:
-------------------
-- A better PhytoImage.ico icon.
-- Redefine .\etc\Basic.zic / Detailed.zic / Very_detailed.zic with plausible phytoplankton taxa
-- Idem for conversion.txt
-- Create the web site http://www.sciviews.org/phytoimage
\ No newline at end of file
Modified: pkg/phytoimage/inst/gui/Menus.txt
===================================================================
--- pkg/phytoimage/inst/gui/Menus.txt 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/inst/gui/Menus.txt 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,13 +1,13 @@
-# PhytoImage1 menu
-# by Ph. Grosjean, 2006 <phgrosjean at sciviews.org>
+# PhytoImage menu
+# by Ph. Grosjean, 2006-2012 <phgrosjean at sciviews.org>
# Add menus to the RGui console (Windows only)
$ConsoleMain
|$PhytoImage
||Assistant... ~~ ZIDlg()
||-
-||Exit PhytoImage ~~ ExitPgm()
-||About ... ~~ AboutZI()
+||Exit PhytoImage ~~ exitPgm()
+||About ... ~~ aboutZI()
# Add menu to the RGui console popup (Windows only)
$ConsolePopup
Modified: pkg/phytoimage/inst/gui/MenusZIDlgWin.txt
===================================================================
--- pkg/phytoimage/inst/gui/MenusZIDlgWin.txt 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/inst/gui/MenusZIDlgWin.txt 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,5 +1,5 @@
-# PhytoImage1 Tk menu
-# by Ph. Grosjean, 2006-2010 <phgrosjean at sciviews.org>
+# PhytoImage Tk menu
+# by Ph. Grosjean, 2006-2012 <phgrosjean at sciviews.org>
# Create a Tk menu (intended for a window called 'ZIDlgWin')
$Tk.ZIDlgWin
@@ -10,9 +10,11 @@
||Make .&zid files... Ctrl+Z ~~ makeZid()
||-
||&Make training set... Ctrl+M ~~ makeTrain()
+||Add vignettes to training set ~~ increaseTrain()
||&Read training set.. Ctrl+T ~~ readTrain()
||Make &classifier... Ctrl+C ~~ makeClass()
||A&nalyze classifier... Ctrl+N ~~ analyzeClass()
+||Automatic classification of vignettes ~~ vignettesClass()
||--
||Edit samples &description... Ctrl+D ~~ editDescription()
||Process &samples... Ctrl+S ~~ processSamples()
@@ -23,7 +25,7 @@
|||From the &assistant Ctrl+X ~~ closeAssistant()
|||From &PhytoImage ~~ closePhytoImage()
|$Real-time
-||&Start process... ~~ realtimeRun()
+||&Start process... ~~ realtimeStart()
||&Stop process... ~~ realtimeStop()
||&Export results... ~~ realtimeSave()
||&Remove data... ~~ realtimeReset()
@@ -44,38 +46,38 @@
||Simple acquisition (&VueScan) ~~ startPgm("VueScan", switchdir = TRUE)
|$Functions
||$PhytoImage &Metadata (zim)
-|||create.zim() ~~ guiDlgFunction("create.zim")
-|||edit.zim() ~~ guiDlgFunction("edit.zim")
+|||zimCreate() ~~ guiDlgFunction("zimCreate")
+|||zimEdit() ~~ guiDlgFunction("zimEdit")
|||-
-|||make.zim() ~~ guiDlgFunction("make.zim")
-|||verify.zim() ~~ guiDlgFunction("verify.zim")
+|||zimMake() ~~ guiDlgFunction("zimMake")
+|||zimVerify() ~~ guiDlgFunction("zimVerify")
|||--
-|||e&xtract.zims() ~~ guiDlgFunction("extract.zims")
-|||refresh.zims() ~~ guiDlgFunction("refresh.zims")
+|||zimE&xtractAll() ~~ guiDlgFunction("zimExtractAll")
+|||zimRefreshAll() ~~ guiDlgFunction("zimRefreshAll")
||$PhytoImage &Picture (zip)
-|||zip.img() ~~ guiDlgFunction("zip.img")
-|||zip.img.&all() ~~ guiDlgFunction("zip.img.all")
+|||zipImg() ~~ guiDlgFunction("zipImg")
+|||zipImg&All() ~~ guiDlgFunction("zipImgAll")
|||-
-|||unzip.img() ~~ guiDlgFunction("unzip.img")
-|||u&nzip.img.all() ~~ guiDlgFunction("unzip.img.all")
+|||unzipImg() ~~ guiDlgFunction("unzipImg")
+|||u&nzipImgAll() ~~ guiDlgFunction("unzipImgAll")
||$PhytoImage &Data (zid)
-|||make.RData() ~~ guiDlgFunction("make.RData")
-|||read.zid() ~~ guiDlgFunction("read.zid")
-|||zid.extract() ~~ guiDlgFunction("zid.extract")
+|||makeRData() ~~ guiDlgFunction("makeRData")
+|||zidRead() ~~ guiDlgFunction("zidRead")
+|||zidExtract() ~~ guiDlgFunction("zidExtract")
|||-
-|||verify.zid() ~~ guiDlgFunction("verify.zid")
-|||verify.zid.&all() ~~ guiDlgFunction("verify.zid.all")
+|||zidVerify() ~~ guiDlgFunction("zidVerify")
+|||zidVerify&All() ~~ guiDlgFunction("zidVerifyAll")
|||--
-|||compress.zid() ~~ guiDlgFunction("compress.zid")
-|||c&ompress.zid.all() ~~ guiDlgFunction("compress.zid.all")
+|||zidCompress() ~~ guiDlgFunction("zidCompress")
+|||zidC&ompressAll() ~~ guiDlgFunction("zidCompressAll")
|||---
-|||uncompress.zid() ~~ guiDlgFunction("uncompress.zid")
-|||u&ncompress.zid.all() ~~ guiDlgFunction("uncompress.zid.all")
+|||zidUncompress() ~~ guiDlgFunction("zidUncompress")
+|||zidU&ncompressAll() ~~ guiDlgFunction("zidUncompressAll")
||$PhytoImage &Samples Metadata (zis)
-|||createZis() ~~ guiDlgFunction("createZis")
-|||editZis() ~~ guiDlgFunction("editZis")
+|||zisCreate() ~~ guiDlgFunction("zisCreate")
+|||zisEdit() ~~ guiDlgFunction("zisEdit")
|||-
-|||read.description() ~~ guiDlgFunction("read.description")
+|||readDescription() ~~ guiDlgFunction("readDescription")
||--
||$PhytoImage &Training set
|||prepare.ZITrain() ~~ guiDlgFunction("prepare.ZITrain")
@@ -88,20 +90,20 @@
|||unzip.ZITrain() ~~ guiDlgFunction("unzip.ZITrain")
|||---
|||re&code.ZITrain() ~~ guiDlgFunction("recode.ZITrain")
-|||make.ZIRecode.level() ~~ guiDlgFunction("make.ZIRecode.level()")
+|||ZIRecodeLevels() ~~ guiDlgFunction("ZIRecodeLevels")
||$PhytoImage &Classifier
|||ZIClass() ~~ guiDlgFunction("ZIClass")
|||predict() ~~ guiDlgFunction("predict.ZIClass")
|||-
|||confu() ~~ guiDlgFunction("confu")
-|||confu.&map() ~~ guiDlgFunction("confu.map")
+|||confusion&Map() ~~ guiDlgFunction("confusionMap")
||$PhytoImage &Results
-|||process.sample() ~~ guiDlgFunction("process.sample")
-|||p&rocess.samples() ~~ guiDlgFunction("process.samples")
+|||sampleProcess() ~~ guiDlgFunction("sampleProcess")
+|||sampleP&rocessAll() ~~ guiDlgFunction("sampleProcessAll")
|||-
-|||Abd.sample() ~~ guiDlgFunction("Abd.sample")
-|||Bio.sample() ~~ guiDlgFunction("Bio.sample")
-|||Spectrum.sample() ~~ guiDlgFunction("Spectrum.sample")
+|||sampleAbd() ~~ guiDlgFunction("sampleAbd")
+|||sampleBio() ~~ guiDlgFunction("sampleBio")
+|||sampleSpectrum() ~~ guiDlgFunction("sampleSpectrum")
|$Utilities
||Calibrate grayscale (16bit) ~~ calib()
||Biomass conversion specification ~~ startPgm("ZIEditor", cmdline = file.path(getTemp("ZIetc"), "Conversion.txt"))
@@ -111,10 +113,9 @@
|||&Activate next ~~ {dev.set(); if (isRgui()) bringToTop()}
|||&Close all ~~ graphics.off()
|$Options
-||Change &active dir... ~~ Setwd(paste(tkchooseDirectory(), collapse = " "))
+||Change &active dir... ~~ setwd(dlgDir()$res)
||-
||Define decimal separator... ~~ optInOutDecimalSep()
-
|$Help
||&Online help ~~ help("phytoimage")
||&Manual Ctrl+H ~~ viewManual()
Modified: pkg/phytoimage/inst/gui/ToolbarsZIDlgWin.txt
===================================================================
--- pkg/phytoimage/inst/gui/ToolbarsZIDlgWin.txt 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/inst/gui/ToolbarsZIDlgWin.txt 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,5 +1,5 @@
-# PhytoImage1 Tk toolbar
-# by Ph. Grosjean, 2006 <phgrosjean at sciviews.org>
+# PhytoImage Tk toolbar
+# by Ph. Grosjean, 2002012 <phgrosjean at sciviews.org>
# Create a Tk toolbar (intended for a window called 'ZIDlgWin')
$Tk.ZIDlgWin
@@ -19,5 +19,5 @@
||[butGlasses]View results... ~~ viewResults()
||[butExport]Export results... ~~ exportResults()
||-
-||[butBlueBook]Help ~~ browseURL(findhtmlhelp("phytoimage"))
+#||[butBlueBook]Help ~~ browseURL(findhtmlhelp("phytoimage"))
||[butBuoy]Manual ~~ viewManual()
Modified: pkg/phytoimage/man/gui.Rd
===================================================================
--- pkg/phytoimage/man/gui.Rd 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/man/gui.Rd 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,5 +1,5 @@
\name{gui}
-\alias{ExitPgm}
+\alias{exitPgm}
\alias{closePhytoImage}
\title{ The PhytoImage GUI (Graphical User Interface) }
@@ -7,15 +7,15 @@
These function manage GUI parts, in addition to the GUI functions in the ZooImage package.
}
\usage{
-ExitPgm()
+exitPgm()
closePhytoImage()
}
\value{
- \code{ExitPgm()} and \code{closePhytoImage()} unload the phytoimage/zooimage packages
+ \code{exitPgm()} and \code{closePhytoImage()} unload the phytoimage/zooimage packages
(for instance, to allow updating them).
}
-\author{ Philippe Grosjean <Philippe.Grosjean at umh.ac.be> }
+\author{ Philippe Grosjean <Philippe.Grosjean at umons.ac.be> }
\keyword{ utilities }
Modified: pkg/phytoimage/man/phytoimage.package.Rd
===================================================================
--- pkg/phytoimage/man/phytoimage.package.Rd 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/phytoimage/man/phytoimage.package.Rd 2012-06-09 13:39:49 UTC (rev 198)
@@ -19,24 +19,20 @@
\tabular{ll}{
Package: \tab phytoimage\cr
Type: \tab Package\cr
-Version: \tab 1.2-0\cr
-Date: \tab 2007-05-24\cr
+Version: \tab 3.0-0\cr
+Date: \tab 2012-05-07\cr
License: \tab GPL 2 or above at your convenience.\cr
}
-For any series that you analyses with PhytoImage, the only constraints are:
-- To send main metadata and a short description of your series, and the way it
- is analyzed to Philippe.Grosjean at umh.ac.be (this will be included to the
- PhytoImage web site (in order to keep track of its use).
-- Everytime you publish results that use PhytoImage, you must place a reference
- to the PhytoImage web site (http://www.sciviews.org/phytoimage) in your publication.
- For papers, send also a reprint to Philippe.Grosjean at umh.ac.be, preferrably
- as a PDF file.
+Everytime you publish results that use PhytoImage, you must place a reference
+to the Zoo/PhytoImage web site (http://www.sciviews.org/zooimage) in your publication.
+For papers, send also a reprint to Philippe.Grosjean at umh.ac.be, preferrably
+as a PDF file.
}
\author{
Philippe Grosjean & Kevin Denis, Numerical Ecology of Aquatic Systems,
-Mons-Hainaut University, Belgium.
+Mons University, Belgium.
-Maintainer: Philippe Grosjean <Philippe.Grosjean at umh.ac.be>
+Maintainer: Philippe Grosjean <Philippe.Grosjean at umons.ac.be>
}
\references{
Not yet!
Modified: pkg/zooimage/DESCRIPTION
===================================================================
--- pkg/zooimage/DESCRIPTION 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/zooimage/DESCRIPTION 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,12 +1,12 @@
Package: zooimage
Type: Package
Title: Analysis of numerical zooplankton images
-Version: 2.0-0
-Date: 2010-04-06
+Version: 3.0-0
+Date: 2012-05-05
Author: Ph. Grosjean, K. Denis & R. Francois
-Maintainer: Ph. Grosjean <Philippe.Grosjean at umh.ac.be>
-Depends: R (>= 2.10.0), utils, tcltk, tcltk2, svMisc, svWidgets, svDialogs, grDevices, MASS, randomForest, ipred, rpart, e1071, nnet, class, tree, RColorBrewer, gplots
-Suggests: rJava, RWeka
+Maintainer: Ph. Grosjean <Philippe.Grosjean at umons.ac.be>
+Depends: R (>= 2.10.0), utils, svMisc, svDialogs, grDevices, MASS, randomForest, ipred, rpart, e1071, nnet, class, tree, RColorBrewer, gplots
+Suggests: rJava, RWeka, RWekajars
Description: ZooImage is a free (open source) solution for analyzing digital
images of zooplankton. In combination with ImageJ, a free image analysis
system, it processes digital images, measures individuals, trains for
Deleted: pkg/zooimage/FunList.txt
===================================================================
--- pkg/zooimage/FunList.txt 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/zooimage/FunList.txt 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,105 +0,0 @@
-= ZooImage internal functions and objects
-
-== capabilities.R
-
-ZOOIMAGEENV = environment
-checkCapable(cap)
-capabilities = list
-checkZipAvailable()
-checkUnzipAvailable()
-checkZipnoteAvailable()
-checkIdentifyAvailable()
-checkConvertAvailable()
-checkPpmtopgmAvailable()
-checkDcRawAvailable()
-checkAvailable_pnm2biff()
-checkAvailable_divide()
-checkAvailable_statistics()
-checkAvailable_biff2tiff()
-checkAvailable_java()
-checkCapabilityAvailable(cap, cmd, msg)
-getZooImageCapability(cap = "zip")
-zooImageCapabilities(...)
-
-
-== catcher.R
-
-catch.env = environment
-catch(call)
-recallWithCatcher(call, debug = FALSE)
-getCatcher()
-setCatcher(catcher)
-dummyCatcher(call)
-resetCatcher()
-
-
-== errorHandling.R
-
-stop(..., call. = TRUE, domain = NULL)
-warning(..., call. = TRUE, immediate. = FALSE, domain = NULL)
-zooImageError(msg = "error", env = parent.frame(),
- errorClass = NULL, context = NULL, verbose = getOption("verbose"))
-zooImageWarning(msg = "warning", env = parent.frame())
-zooImageErrorDrivers = list
-zooImageWarningDrivers = list
-zooImageErrorContext(fun, context)
-zooImageWarningContext(fun, context)
-getZooImageConditionFunction(calls, drivers, default, context.fun)
-getZooImageErrorFunction(calls)
-getZooImagheWarningFunction(calls)
-[[.zooImageError(x, ...)
-[[.zooImageWarning(x, ...)
-extractMessage(err)
-
-
-== misc.R
-
-getSample(x, unique = FALSE, must.have, msg)
-backspaces(n = getOption("width"))
-callStack()
-hasExtension(file, extension = "zip", pattern = extensionPattern(extension))
-list.files.ext(dir, extension = "zip", pattern = extensionPattern(extension), ...)
-list.zim(zidir, ...)
-list.dat1.zim(zidir, ...)
-list.zip(zidir, ...)
-list.zid(zidir, ...)
-extensionPattern(extension = "tif", add.dot = !grepl("[.]", extension))
-checkFileExists(file, extension, message = "file not found: %s", force.file = FALSE)
-checkAllFileExist(files, extension)
-checkDirExists(dir, message = 'Path "%s" does not exist or is not a directory')
-checkEmptyDir(dir, message = "not empty")
-force.dir.create(path, ...)
-checkFirstLine(file, expected = "ZI1", message = 'file "%s" is not a valid ZooImage version 1 file', stop = FALSE)
-list.dir(dir, ...)
-mustbe(x, class, msg)
-mustallbe(..., .list = list(...), class, msg)
-mustmatch(x, y, msg)
-mustallmatch(..., .list = list(...), msg = "all must match")
-mustcontain(container, element, msg)
-mustbeString(x, length)
-template(file = "default.zim", dir = getOption("ZITemplates"))
-finish.loopfunction(ok = TRUE, ok.console.msg = "-- Done! --\n", ok.log.msg = "\n-- OK, no error found. --", nok.console.msg = " -- Done! [ERROR(S) FOUND] --\n", nok.log.msg = "-- Error(s)! --", bell = TRUE, show.log = FALSE, show.console = TRUE)
-zip(zipfile , directory, delete.source = FALSE, comment.file = NULL, delete.zipfile.first = TRUE)
-zip_addcomments(zip, comment.file, on.failure = stop(sprintf(on.failure.msg , comment.file, zip)), on.failure.msg = "problem adding comment from '%s' to file '%s' ", on.success)
-unzip(zipfile, path, delete.source = FALSE)
-zipnote(zipfile, outfile = NULL)
-
-= programs.R
-
-program(prog, args, ..., dir)
-xite(prog, args, ...)
-xite_pnm2biff(input, output)
-xite_statistics(file)
-xite_divide(meangray, image, bf, cor)
-xite_biff2tiff(cor, tif)
-imagemagick(prog, args, ...)
-imagemagick_identify(file)
-imagemagick_convert(file, size1, size2)
-misc(prog, args, ...)
-misc_dcraw(file, arguments, output)
-netpbm(prog, args, ...)
-netpbm_tifftopnm(input, output)
-netpbm_pgmhist(file, delete = TRUE)
-netpbm_ppmtopgm(ppm, pgm)
-editor(file, editor = getOption("ZIEditor"))
-imageViewer(dir = getwd())
Modified: pkg/zooimage/NAMESPACE
===================================================================
--- pkg/zooimage/NAMESPACE 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/zooimage/NAMESPACE 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,145 +1,145 @@
- import(utils)
- import(tcltk)
- import(tcltk2)
- import(svMisc)
- import(svWidgets)
- import(svDialogs)
- import(grDevices)
- import(ipred)
- import(MASS)
- import(randomForest)
- import(class)
- import(rpart)
- import(e1071)
- import(nnet)
- import(tree)
- import(gplots)
- import(RColorBrewer)
+import(utils)
+#import(tcltk)
+#import(tcltk2)
+import(svMisc)
+#import(svWidgets)
+import(svDialogs)
+import(grDevices)
+import(ipred)
+import(MASS)
+import(randomForest)
+import(class)
+import(rpart)
+import(e1071)
+import(nnet)
+import(tree)
+import(gplots)
+import(RColorBrewer)
-export(Abd.sample)
-export(AboutZI)
+export(aboutZI)
export(acquireImg)
-export(AddVignToTrain)
export(analyzeClass)
export(BFcorrection)
-export(Bio.sample)
- export(calc.vars)
+export(calcVars)
export(calib)
export(calibrate)
export(checkBF)
-export(ClassifVigns)
-export(clean.after.zid)
- export(ClearProgress)
+export(clearProgress)
export(closeAssistant)
export(closeZooImage)
export(compareExif)
-export(compile.zie)
-export(compress.zid)
-export(compress.zid.all)
-export(create.zim)
-export(createZis)
- export(ecd)
+export(ecd)
export(editDescription)
-export(edit.zim)
-export(editZis)
-export(ExitZI)
+export(exitZI)
export(expand.ZITrain)
export(exportResults)
-export(extract.zims)
export(focusGraph)
export(focusR)
-export(FormVarsSelect)
- export(getDec)
+export(formulaVarSel)
+export(getDec)
export(getKey)
- export(getList)
- export(get.sampleinfo)
- export(gettextZI)
- export(getVar)
+export(getList)
+export(gettextZI)
+export(getSpectrum)
+export(getVar)
export(get.ZITrain)
export(histSpectrum)
export(importImg)
+export(increaseTrain)
export(isTestFile)
export(is.zim)
export(list.add)
-export(list.dat1.zim)
- export(list.merge)
+export(list.merge)
export(listObjects)
-export(list.samples)
-export(list.zim)
+export(listSamples)
export(loadObjects)
- export(logClear)
- export(logError)
- export(logProcess)
- export(logView)
- export(logWarning)
+export(logClear)
+export(logError)
+export(logProcess)
+export(logView)
+export(logWarning)
export(lvq)
export(makeClass)
- export(make.Id)
-export(make.RData)
+export(makeId)
+export(makeRData)
export(makeTrain)
export(makeZid)
-export(make.zie)
-export(make.zim)
-export(make.ZIRecode.level)
export(modalAssistant)
export(nnet2)
export(noext)
export(optInOutDecimalSep)
- export(parse.ini)
+export(parseIni)
export(plotAbdBio)
export(prepare.ZITrain)
export(processImg)
-export(process.sample)
-export(process.samples)
+export(processSample)
+export(processSampleAll)
export(processSamples)
- export(Progress)
-export(RawConvert)
-export(read.description)
+export(Progress)
+export(rawConvert)
+export(readDescription)
export(readExifRaw)
export(readTrain)
-export(read.zid)
export(read.ZITrain)
export(realtimeReset)
-export(realtimeRun)
export(realtimeSave)
+export(realtimeStart)
export(realtimeStop)
export(recode.ZITrain)
-export(refresh.zims)
export(removeObjects)
+export(sampleAbd)
+export(sampleBio)
+export(sampleInfo)
+export(sampleSpectrum)
export(saveObjects)
- export(selectFile)
+export(selectFile)
export(setKey)
- export(setwd)
-export(Spectrum)
-export(Spectrum.sample)
export(startPgm)
export(trimstring)
-export(uncompress.zid)
-export(uncompress.zid.all)
export(underscore2space)
-export(unzip.img)
-export(unzip.img.all)
+export(unzipImg)
+export(unzipImgAll)
export(unzip.ZITrain)
-export(verify.zid)
-export(verify.zid.all)
-export(verify.zim)
export(viewManual)
export(viewResults)
+export(vignettesClass)
export(write.ZITrain)
export(ZIClass)
export(ZIConf)
-export(zid.extract)
+export(zicCheck)
+export(zidClean)
+export(zidCompress)
+export(zidCompressAll)
+export(zidExtract)
+export(zidRead)
+export(zidUncompress)
+export(zidUncompressAll)
+export(zidVerify)
+export(zidVerifyAll)
export(ZIDlg)
export(ZIE)
export(ZIEimportJpg)
export(ZIEimportTable)
export(ZIEimportTif)
export(ZIEimportZie)
- export(ZIpgm)
- export(ZIpgmhelp)
-export(zip.img)
-export(zip.img.all)
+export(zieCompile)
+export(zieMake)
+export(zimCreate)
+export(zimDatList)
+export(zimEdit)
+export(zimExtractAll)
+export(zimList)
+export(zimMake)
+export(zimRefreshAll)
+export(zimVerify)
+export(ZIpgm)
+export(ZIpgmHelp)
+export(zipImg)
+export(zipImgAll)
export(zip.ZITrain)
+export(ZIRecodeLevels)
+export(zisCreate)
+export(zisEdit)
S3method(predict, nnet2)
S3method(predict, lvq)
@@ -152,82 +152,81 @@
S3method(merge, ZITable)
# The following objects are NOT exported
- # ZOOIMAGEENV (environment holding ZooImage data)
- # backspaces
- # callstack
- # catch
- # catch.env
- # chekcAllFileExist
- # checkAvailable_java
- # checkAvailable_biff2tiff # Eliminate Xite programs
- # checkAvailable_divide # Eliminate Xite programs
- # checkAvailable_pnm2biff # Eliminate Xite programs
- # checkAvailable_statistics # Eliminate Xite programs
- # checkCapabilityAvailable
- # checkCapable
- # checkCapabilityAvailable
- # checkConvertAvailable # Eliminate?
- # checkDcRawAvailable # Eliminate?
- # checkDirExists
- # checkEmptyDir
- # checkFileExists
- # checkFirstLine
- # checkIdentifyAvailable # Eliminate?
- # checkPpmtopgmAvailable # Eliminate?
- # checkUnzipAvailable
- # checkZipAvailable
- # checkZipnoteAvailable
- # dummyCatcher
- # editor(file, editor = getOption("ZIEditor"))
- # extensionPattern
- # extractMessage
- # finish.loopfunction
- # force.dir.create
- # getCatcher
- # getSample
- # getZooImageCapability
- # getZooImageConditionFunction
- # getZooImageErrorFunction
- # getZooImageWarningFunction
- # hasExtension
- # imagemagick(prog, args, ...)
- # imagemagick_convert(file, size1, size2)
- # imagemagick_identify(file)
- # imageViewer(dir = getwd())
- # list.files.ext
- # list.dat1.zim
- # list.dir
- # list.zim
- # list.zid
- # list.zip
- # misc(prog, args, ...)
- # misc_dcraw(file, arguments, output)
- # netpbm(prog, args, ...)
- # netpbm_pgmhist(file, delete = TRUE)
- # netpbm_ppmtopgm(ppm, pgm)
- # netpbm_tifftopnm(input, output)
- # program(prog, args, ..., dir)
- # recallWithCatcher
- # resetCatcher
- # setCatcher
- # stop
- # template
- # unzip
- # warning
- # xite(prog, args, ...)
- # xite_biff2tiff(cor, tif)
- # xite_divide(meangray, image, bf, cor)
- # xite_pnm2biff(input, output)
- # xite_statistics(file)
- # zip
- # zip_addcomments(
- # zipnote
- # zooImageCapabilities
- # zooImageError
- # [[.zooImageError
- # zooImageErrorContext
- # zooImageErrorDrivers
- # zooImageWarning
- # [[.zooImageWarning
- # zooImageWarningContext
- # zooImageWarningDrivers
+# ZOOIMAGEENV (environment holding ZooImage data)
+# backspaces
+# callstack
+# catch
+# catch.env
+# checkFileExistAll
+# checkJavaAvailable
+# checkBiff2tiffAvailable # Eliminate Xite programs
+# checkDivideAvailable # Eliminate Xite programs
+# checkPnm2biffAvailable # Eliminate Xite programs
+# checkStatisticsAvailable # Eliminate Xite programs
+# checkCapabilityAvailable
+# checkCapable
+# checkCapabilityAvailable
+# checkConvertAvailable # Eliminate?
+# checkDcRawAvailable # Eliminate?
+# checkDirExists
+# checkEmptyDir
+# checkFileExists
+# checkFirstLine
+# checkIdentifyAvailable # Eliminate?
+# checkPpmtopgmAvailable # Eliminate?
+# checkUnzipAvailable
+# checkZipAvailable
+# checkZipnoteAvailable
+# dummyCatcher
+# editor
+# extensionPattern
+# extractMessage
+# finishLoop
+# forceDirCreate
+# getCatcher
+# getSample
+# getZooImageCapability
+# getZooImageConditionFunction
+# getZooImageErrorFunction
+# getZooImageWarningFunction
+# hasExtension
+# imagemagick
+# imagemagick_convert
+# imagemagick_identify
+# imageViewer
+# jpgList
+# listFilesExt
+# list.dir
+# misc
+# misc_dcraw
+# netpbm
+# netpbm_pgmhist
+# netpbm_ppmtopgm
+# netpbm_tifftopnm
+# program
+# recallWithCatcher
+# resetCatcher
+# setCatcher
+# stop
+# template
+# unzip
+# warning
+# xite
+# xite_biff2tiff
+# xite_divide
+# xite_pnm2biff
+# xite_statistics
+# zidList
+# zipList
+# zip
+# zipNoteAdd
+# zipNote
+# zooImageCapabilities
+# zooImageError
+# [[.zooImageError
+# zooImageErrorContext
+# zooImageErrorDrivers
+# zooImageWarning
+# [[.zooImageWarning
+# zooImageWarningContext
+# zooImageWarningDrivers
Modified: pkg/zooimage/R/RealTime.R
===================================================================
--- pkg/zooimage/R/RealTime.R 2011-08-02 12:22:08 UTC (rev 197)
+++ pkg/zooimage/R/RealTime.R 2012-06-09 13:39:49 UTC (rev 198)
@@ -1,109 +1,137 @@
-# Copyright (c) 2008-2010, Ph. Grosjean <phgrosjean at sciviews.org>
-#
-# This file is part of ZooImage
-#
-# ZooImage is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 2 of the License, or
-# (at your option) any later version.
-#
-# ZooImage is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with ZooImage. If not, see <http://www.gnu.org/licenses/>.
+## Copyright (c) 2008-2012, Ph. Grosjean <phgrosjean at sciviews.org>
+##
+## This file is part of ZooImage
+##
+## ZooImage is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 2 of the License, or
+## (at your option) any later version.
+##
+## ZooImage is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with ZooImage. If not, see <http://www.gnu.org/licenses/>.
-# TODO: rework all this!!!
-# Functions and dialog box created for the real time recogntion
-"realtimeRun" <- function ()
+## Functions and dialog box created for the real time recogntion
+realtimeStart <- function ()
{
- # Process real time recognition during a FlowCAM experiment
- # First remove existing file from the global environment before read a new sample
+ ## Process real time recognition during a FlowCAM experiment
+ ## First remove existing file from the global environment before
+ ## we read a new sample
realtimeReset()
- # Ask for an algorithm and one or several sample to compare
+ ## Ask for an algorithm and one or several samples to compare with
defval <- "Only One Sample"
opts <- c("Only One Sample",
"Comparison with One Other Sample",
"Comparison with Several Other Samples")
- # Then, show the dialog box
- res <- modalAssistant(paste(getTemp("ZIname"),
- "Real-Time recognition for FlowCAM"),
- c("This is a beta version of the real time recognition",
- "of FlowCAM samples developed for the AMORE III project.",
- "Warning! This method is only developed for FlowCAM data,",
- "and with a classifier made with FlowCAM parameters only.",
- "", "Select an option:", ""), init = defval,
- options = opts, help.topic = "makeClass")
- if (res == "ID_CANCEL") return(invisible())
- # Only one sample
+ ## Then, show the dialog box
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/zooimage -r 198
More information about the Zooimage-commits
mailing list