[Zooimage-commits] r91 - pkg/zooimage/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 21 09:57:28 CEST 2009
Author: romain
Date: 2009-04-21 09:57:25 +0200 (Tue, 21 Apr 2009)
New Revision: 91
Modified:
pkg/zooimage/R/ZIRes.r
pkg/zooimage/R/ZITrain.r
pkg/zooimage/R/utilities.r
pkg/zooimage/R/zid.r
pkg/zooimage/R/zie.r
pkg/zooimage/R/zim.r
pkg/zooimage/R/zip.r
Log:
using ClearProgress
Modified: pkg/zooimage/R/ZIRes.r
===================================================================
--- pkg/zooimage/R/ZIRes.r 2009-04-20 15:30:16 UTC (rev 90)
+++ pkg/zooimage/R/ZIRes.r 2009-04-21 07:57:25 UTC (rev 91)
@@ -123,7 +123,7 @@
class(restot) <- c("ZI1Res", "ZIRes", "data.frame")
}
}
- Progress (imax + 1, imax) # To dismiss the Progress() indication
+ ClearProgress()
# {{{ Final report
finish.loopfunction( ok = ok, show.log = show.log, bell = bell )
Modified: pkg/zooimage/R/ZITrain.r
===================================================================
--- pkg/zooimage/R/ZITrain.r 2009-04-20 15:30:16 UTC (rev 90)
+++ pkg/zooimage/R/ZITrain.r 2009-04-21 07:57:25 UTC (rev 91)
@@ -24,9 +24,8 @@
groups.template = c("[Basic]", "[Detailed]", "[Very detailed]"),
ident = NULL, show.log = TRUE, bell = FALSE, start.viewer = FALSE) {
- # {{{ Make sure unzip is available
+ # Make sure unzip is available
checkCapable( "unzip" )
- # }}}
# First, check that dir is valid
checkDirExists( dir )
@@ -37,12 +36,10 @@
checkEmptyDir( dir , message = "must be empty. Clean it first!" )
# Then, check that all zidfiles exist
- if(!all(file.exists(zidfiles)) || !all( hasExtension(zidfiles, "zid")) ) {
- stop( "One or more .zid files do not exist or is invalid!" )
- }
+ checkAllFileExist( zidfiles, "zid" )
# Finally, look for the groups.template
- groups.template <- groups.template[1]
+ groups.template <- match.arg( groups.template )
if (regexpr("^[[].+[]]$", groups.template) > 0) {
# This should be a template file in the default directory
groups.template <- paste(sub("^[[](.+)[]]$", "\\1", groups.template), ".zic", sep = "")
@@ -61,9 +58,8 @@
Progress(i, zmax)
unzip( zipfile = zidfiles[i] , path = dir, delete.source = FALSE )
}
- Progress(i + 1, zmax) # To dismiss the Progress() indication
+ ClearProgress()
-
# Create '_' subdir and unzip all vignettes there
dir_ <- file.path(dir, "_")
force.dir.create( dir_ )
@@ -79,7 +75,7 @@
unzip( zidfiles[i], path = dir_, delete.source = FALSE )
}
- Progress(i + 1, zmax) # To dismiss the Progress() indication
+ ClearProgress()
# Create the other directories
Lines <- scan(groups.template, character(), sep = "\n", skip = 2, quiet = TRUE)
@@ -207,9 +203,8 @@
mustbe(ZIRecode, "ZIRecode")
# Check that all levels in ZITrain$Class are represented in ZIRecode
- if (!all(sort(levels(ZITrain$Class)) == sort(ZIRecode[ , 1]))) {
- warnOrStop( "Not all levels of ZIRecode match levels of ZITrain" )
- }
+ mustmatch( levels(ZITrain$Class), ZIRecode[ , 1],
+ msg = "Not all levels of ZIRecode match levels of ZITrain" )
# Class column of ZITrain is transformed into a character vector
clas <- as.character(ZITrain$Class)
@@ -217,8 +212,9 @@
# It is then recoded
for (i in 1:nrow(ZIRecode)) {
- if (ZIRecode[i, 1] != ZIRecode[i, 2])
+ if (ZIRecode[i, 1] != ZIRecode[i, 2]){
recoded[clas == ZIRecode[i, 1]] <- ZIRecode[i, 2]
+ }
}
# ...and transformed back into a factor
@@ -228,7 +224,9 @@
# If a new path is given for these new groups, change it
path <- attr(ZIRecode, "path")
### TODO: check its validity here
- if(!is.null(path)) attr(res, "path") <- path
+ if(!is.null(path)){
+ attr(res, "path") <- path
+ }
return(res)
}
# }}}
Modified: pkg/zooimage/R/utilities.r
===================================================================
--- pkg/zooimage/R/utilities.r 2009-04-20 15:30:16 UTC (rev 90)
+++ pkg/zooimage/R/utilities.r 2009-04-21 07:57:25 UTC (rev 91)
@@ -502,7 +502,7 @@
}
invisible(NULL)
}
-EraseProgress <- function( ){
+ClearProgress <- function( ){
Progress( 2, 1 )
}
# }}}
@@ -667,6 +667,16 @@
invisible( NULL )
}
+
+checkAllFileExist <- function( files, extension){
+ if( !all( file.exists( files ) ) ){
+ stop( "one or more file does not exist" )
+ }
+ if( !missing(extension) && ! all( hasExtension( files, extension ) ) ){
+ stop( "one or more files have wrong extension" )
+ }
+}
+
#' checks if a directory exists
#'
#' @param dir the directory to check
@@ -755,7 +765,7 @@
}
mustmatch <- function( x, y, msg ){
- if( !all( x == y ) ){
+ if( !all( sort( x ) == sort( y ) ) ){
if( missing(msg) ) msg <- sprintf( "'%s' and '%s' must match", deparse(substitute(x)), deparse(substitute(y)) )
stop( msg )
}
Modified: pkg/zooimage/R/zid.r
===================================================================
--- pkg/zooimage/R/zid.r 2009-04-20 15:30:16 UTC (rev 90)
+++ pkg/zooimage/R/zid.r 2009-04-21 07:57:25 UTC (rev 91)
@@ -426,7 +426,7 @@
})
}
- Progress (smax + 1, smax) # To dismiss the Progress() indication
+ ClearProgress()
# }}}
# {{{ Possibly clean the whole directory (move .zim files to \_raw
@@ -578,8 +578,7 @@
# TODO: set the calling handlers in a way that ok is created
ok <- TRUE
- Progress (smax + 1, smax) # To dismiss the Progress() indication
-
+ ClearProgress()
finish.loopfunction( ok, bell = bell, show.log = show.log )
}
# }}}
Modified: pkg/zooimage/R/zie.r
===================================================================
--- pkg/zooimage/R/zie.r 2009-04-20 15:30:16 UTC (rev 90)
+++ pkg/zooimage/R/zie.r 2009-04-21 07:57:25 UTC (rev 91)
@@ -301,7 +301,7 @@
allImages <- c(allImages, File)
}
}
- Progress (nLines + 1, nLines) # To dismiss the Progress() indication
+ ClearProgress()
logProcess("Checking all lines in the .zie file for raw images... OK!")
cat("...OK!\n")
# }}}
@@ -661,7 +661,7 @@
# }}}
# {{{ cleans up
- Progress (nLines + 1, nLines) # To dismiss the Progress() indication
+ ClearProgress()
# Possibly remove latest blank-field from root directory (not needed any more!)
if (!is.null(BlankField)) {
# Delete blank-field images (.pgm and .img) in the root directory
Modified: pkg/zooimage/R/zim.r
===================================================================
--- pkg/zooimage/R/zim.r 2009-04-20 15:30:16 UTC (rev 90)
+++ pkg/zooimage/R/zim.r 2009-04-21 07:57:25 UTC (rev 91)
@@ -64,9 +64,8 @@
}
# }}}
- Progress (zmax + 1, zmax) # To dismiss the Progress() indication
-
# {{{ cleans up
+ ClearProgress()
finish.loopfunction( ok, bell = bell, show.log = show.log )
# }}}
}
@@ -440,7 +439,7 @@
ok <<- FALSE
} )
}
- Progress (zmax + 1, zmax) # To dismiss the Progress() indication
+ ClearProgress()
}
if (ok) {
@@ -464,7 +463,7 @@
on.success = logProcess( "OK", zipfiles[i] ) )
}
- Progress (imax + 1, imax) # To dismiss the Progress() indication
+ ClearProgress()
# }}}
# {{{ cleans up
Modified: pkg/zooimage/R/zip.r
===================================================================
--- pkg/zooimage/R/zip.r 2009-04-20 15:30:16 UTC (rev 90)
+++ pkg/zooimage/R/zip.r 2009-04-21 07:57:25 UTC (rev 91)
@@ -147,7 +147,7 @@
ok <- FALSE
}
}
- Progress (zmax + 1, zmax) # To dismiss the progress() indication
+ ClearProgress()
}
if (ok) {
logProcess("\n-- OK, no error found. --")
@@ -180,7 +180,7 @@
}
#}}}
- Progress (imax + 1, imax) # To dismiss the Progress() indication
+ ClearProgress()
#{{{ Final report
finish.loopfunction( ok, bell = bell, show.log = show.log )
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