[Zooimage-commits] r200 - in pkg: phytoimage phytoimage/R zooimage/R zooimage/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 11 15:36:02 CEST 2012
Author: phgrosjean
Date: 2012-06-11 15:36:02 +0200 (Mon, 11 Jun 2012)
New Revision: 200
Modified:
pkg/phytoimage/DESCRIPTION
pkg/phytoimage/NAMESPACE
pkg/phytoimage/R/zzz.r
pkg/zooimage/R/ZIRes.R
pkg/zooimage/R/gui.R
pkg/zooimage/R/zid.R
pkg/zooimage/man/RealTime.Rd
pkg/zooimage/man/utilities.Rd
pkg/zooimage/man/zid.Rd
pkg/zooimage/man/zie.Rd
Log:
Small changes (mainly in the documentation) for ZooImage
Modified: pkg/phytoimage/DESCRIPTION
===================================================================
--- pkg/phytoimage/DESCRIPTION 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/phytoimage/DESCRIPTION 2012-06-11 13:36:02 UTC (rev 200)
@@ -5,7 +5,7 @@
Date: 2012-05-07
Author: Ph. Grosjean & K. Denis
Maintainer: Ph. Grosjean <Philippe.Grosjean at umons.ac.be>
-Depends: R (>= 2.10.0), svMisc, svDialogs
+Depends: R (>= 2.10.0), svMisc, svDialogs, zooimage
Suggests: zooimage
Description: PhytoImage is a free (open source) solution for analyzing digital
images of phytoplankton. In combination with ImageJ, a free image analysis
Modified: pkg/phytoimage/NAMESPACE
===================================================================
--- pkg/phytoimage/NAMESPACE 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/phytoimage/NAMESPACE 2012-06-11 13:36:02 UTC (rev 200)
@@ -2,6 +2,7 @@
#import(tcltk2)
import(svMisc)
import(svDialogs)
+import(zooimage)
export(exitPgm)
export(closePhytoImage)
Modified: pkg/phytoimage/R/zzz.r
===================================================================
--- pkg/phytoimage/R/zzz.r 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/phytoimage/R/zzz.r 2012-06-11 13:36:02 UTC (rev 200)
@@ -41,7 +41,8 @@
options(ZIredefine = TRUE)
## Load the initial zooimage package now
- if (!require(zooimage)) stop("Package 'zooimage' is required!")
+ ## No, this is now done in NAMESPACE import!
+ #if (!require(zooimage)) stop("Package 'zooimage' is required!")
}
## Unloading PhytoImage
Modified: pkg/zooimage/R/ZIRes.R
===================================================================
--- pkg/zooimage/R/ZIRes.R 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/zooimage/R/ZIRes.R 2012-06-11 13:36:02 UTC (rev 200)
@@ -211,7 +211,7 @@
use.Dil = use.Dil)
}, zooImageError = function (e) return(NULL))
})
- list.add(lists)
+ listAdd(lists)
}
getSpectrum <- function (ZIDat, image, taxa = NULL, groups = NULL,
Modified: pkg/zooimage/R/gui.R
===================================================================
--- pkg/zooimage/R/gui.R 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/zooimage/R/gui.R 2012-06-11 13:36:02 UTC (rev 200)
@@ -1377,7 +1377,7 @@
byrow = TRUE))$res
if (!length(ctxFile)) return(invisible(NULL))
## Create the table
- createBatchFile(ctx = ctxFile, fil = FALSE, largest = FALSE,
+ createBatchFile(ctxfile = ctxFile, fil = FALSE, largest = FALSE,
vignettes = TRUE, scalebar = TRUE, enhance = FALSE, outline = FALSE,
masks = FALSE, verbose = TRUE, txt = FALSE,
import.name = "batchExampleParameters")
Modified: pkg/zooimage/R/zid.R
===================================================================
--- pkg/zooimage/R/zid.R 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/zooimage/R/zid.R 2012-06-11 13:36:02 UTC (rev 200)
@@ -517,7 +517,7 @@
rdata <- file.path(zidfile, RdataFile)
if (!file.exists(rdata)) {
# Try to create it
- makeRData(zidfile, show.log = FALSE)
+ zidDatMake(zidfile, show.log = FALSE)
checkFileExists(rdata,
message = "Error creating the .RData file")
}
Modified: pkg/zooimage/man/RealTime.Rd
===================================================================
--- pkg/zooimage/man/RealTime.Rd 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/zooimage/man/RealTime.Rd 2012-06-11 13:36:02 UTC (rev 200)
@@ -11,7 +11,7 @@
}
\usage{
-lstRead(x, skip = 2)
+lstRead(lstfile, skip = 2)
realtimeOptions(lstdir = ".", ZIClass, type = "b", size.threshold = NULL,
breaks = seq(0.05, 3, by = 0.1), conv.dir = ".", images.per.sec = 7,
flow.cell = 600, concentration = "p/mL", collage = NULL, size = 5, lag = 2,
@@ -23,7 +23,7 @@
}
\arguments{
- \item{x}{ a connection or a character string giving the name of the FlowCAM
+ \item{lstfile}{ a connection or a character string giving the name of the FlowCAM
'list' file to read }
\item{skip}{ number of row to skip in the 'list' file }
\item{lstdir}{ The directory where the FlowCAM .lst file is located }
Modified: pkg/zooimage/man/utilities.Rd
===================================================================
--- pkg/zooimage/man/utilities.Rd 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/zooimage/man/utilities.Rd 2012-06-11 13:36:02 UTC (rev 200)
@@ -8,18 +8,18 @@
\alias{gettextZI}
\alias{getVar}
\alias{getDec}
-\alias{list.add}
-\alias{list.merge}
-\alias{list.reduce}
+\alias{listAdd}
+\alias{listMerge}
+\alias{listReduce}
\alias{listSamples}
\alias{makeId}
-\alias{noext}
+\alias{noExt}
\alias{parseIni}
\alias{Progress}
\alias{selectFile}
\alias{setKey}
-\alias{trimstring}
-\alias{underscore2space}
+\alias{trimString}
+\alias{underscoreToSpace}
\alias{ZIpgm}
\alias{ZIpgmHelp}
@@ -30,9 +30,9 @@
}
\usage{
-list.merge(x, y)
-list.add(\dots, .list = list(\dots))
-list.reduce(\dots, .list = list(\dots), FUN = "+")
+listMerge(x, y)
+listAdd(\dots, .list = list(\dots))
+listReduce(\dots, .list = list(\dots), FUN = "+")
calcVars(x)
ecd(area)
@@ -51,9 +51,9 @@
getDec()
-noext(file)
-trimstring(char)
-underscore2space(char)
+noExt(file)
+trimString(char)
+underscoreToSpace(char)
parseIni(data, label = "1")
Progress(value, max.value = NULL)
@@ -180,9 +180,9 @@
\examples{
# Character strings and filenames manipulation functions
-underscore2space("Some_string_to_convert")
-trimstring(" \tString with\textra spaces \t")
-noext(paste(tempfile(), ".ext", sep = ""))
+underscoreToSpace("Some_string_to_convert")
+trimString(" \tString with\textra spaces \t")
+noExt(paste(tempfile(), ".ext", sep = ""))
# Given a correct ZooImage name for a sample, return parts of it
smp__ <- "MTLG.2010-03-15.H1+A1.03_dat1.zim"
Modified: pkg/zooimage/man/zid.Rd
===================================================================
--- pkg/zooimage/man/zid.Rd 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/zooimage/man/zid.Rd 2012-06-11 13:36:02 UTC (rev 200)
@@ -1,9 +1,9 @@
\name{zid}
-\alias{makeRData}
\alias{zidClean}
\alias{zidCompress}
\alias{zidCompressAll}
-\alias{zidRead}
+\alias{zidDatMake}
+\alias{zidDatRead}
\alias{zidUncompress}
\alias{zidUncompressAll}
\alias{zidVerify}
@@ -16,28 +16,31 @@
Compress, uncompress and verify ZooImage Data files.
}
\usage{
-zidCompress(zidir, type = "ZI1", check = TRUE, check.vignettes = TRUE,
- replace = FALSE, delete.source = replace, check.zip = TRUE, show.log = TRUE)
-zidCompressAll(path = ".", samples = NULL, type = "ZI1", check = TRUE,
+zidCompress(zidir, type = c("ZI1", "ZI2", "ZI3"), check = TRUE,
check.vignettes = TRUE, replace = FALSE, delete.source = replace,
- show.log = TRUE, bell = FALSE)
-makeRData(zidir, type = "ZI1", replace = FALSE, show.log = TRUE)
+ check.zip = TRUE, show.log = TRUE)
+zidCompressAll(path = ".", samples = NULL, type = c("ZI1", "ZI2", "ZI3"),
+ check = TRUE, check.vignettes = TRUE, replace = FALSE,
+ delete.source = replace, show.log = TRUE, bell = FALSE)
zidClean(path = ".", samples = NULL)
-zidRead(zidfile)
+zidDatMake(zidir, type = "ZI3", replace = FALSE, show.log = TRUE)
+zidDatRead(zidfile)
zidUncompress(zidfile, path = dirname(zidfile), delete.source = FALSE,
show.log = TRUE)
zidUncompressAll(path = ".", zidfiles = zidList(path), path.extract = path,
skip.existing.dirs = TRUE, delete.source = FALSE, show.log = TRUE,
bell = FALSE)
-zidVerify(zidir, type = "ZI1", check.vignettes = TRUE, show.log = TRUE)
-zidVerifyAll(path = ".", samples = NULL, type = "ZI1", check.vignettes = TRUE,
- show.log = TRUE, bell = FALSE)
+zidVerify(zidir, type = c("ZI1", "ZI2", "ZI3"), check.vignettes = TRUE,
+ show.log = TRUE)
+zidVerifyAll(path = ".", samples = NULL, type = c("ZI1", "ZI2", "ZI3"),
+ check.vignettes = TRUE, show.log = TRUE, bell = FALSE)
zidExtract(file, zidfile)
}
\arguments{
\item{zidir}{ A directory containing data to put in a .zid files }
- \item{type}{ Currently, only 'ZI1' type is supported (ZooImage1) }
+ \item{type}{ The ZI file format, currently 'ZI1', 'ZI2' or 'ZI3' types are
+ supported (ZooImage1-3) }
\item{check}{ Do we check the files in this directory before/after compression? }
\item{check.vignettes}{ Do we check if the future .zid file contains all vignettes? }
\item{replace}{ Do we replace existingfiles? }
Modified: pkg/zooimage/man/zie.Rd
===================================================================
--- pkg/zooimage/man/zie.Rd 2012-06-11 08:44:30 UTC (rev 199)
+++ pkg/zooimage/man/zie.Rd 2012-06-11 13:36:02 UTC (rev 200)
@@ -18,7 +18,7 @@
move.to.raw = TRUE, zip.images = "[.][tT][iI][fF]$",show.log = TRUE,
bell = FALSE)
zieCompile(path = ".", Tablefile = "Table.txt", Template = "ImportTemplate.zie",
- Filemap = paste("Import_", noext(Tablefile), ".zie", sep = ""),
+ Filemap = paste("Import_", noExt(Tablefile), ".zie", sep = ""),
Nrange = c(1, 1000), replace = TRUE, make.it = FALSE, show.log = make.it)
ZIE(title, filter, description, pattern, command, author, version, date,
license, url, depends = "R (>= 2.4.0), zooimage (>= 1.0-0)",
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