[Zooimage-commits] r125 - in pkg/zooimage: R inst/imagej/plugins src/src/org/sciviews/zooimage

[noreply at r-forge.r-project.org]

Author: romain
Date: 2009-05-04 14:55:09 +0200 (Mon, 04 May 2009)
New Revision: 125

Modified:
   pkg/zooimage/R/gui.r
   pkg/zooimage/R/zie.r
   pkg/zooimage/inst/imagej/plugins/_zooimage.jar
   pkg/zooimage/src/src/org/sciviews/zooimage/ImageFileProcessor.java
Log:
working around java problem by providing full path name in ijplugin

Modified: pkg/zooimage/R/gui.r
===================================================================
--- pkg/zooimage/R/gui.r	2009-05-04 11:51:05 UTC (rev 124)
+++ pkg/zooimage/R/gui.r	2009-05-04 12:55:09 UTC (rev 125)
@@ -1080,13 +1080,13 @@
 ijplugin <- function( zimfile, 
 	ij.plugin = c("Scanner_Gray16", "MacroPhoto_Gray16", "Scanner_Color", "Microscope_Color" ) ){
 	
+	ij.plugin <- match.arg( ij.plugin )
 	cmd <- sprintf( 'java -Xmx900m -cp .:"%s":"%s" org.sciviews.zooimage.ZooImage %s "%s"', 
 		system.file( "imagej", "ij.jar", package = "zooimage" ), 
 		system.file( "imagej", "plugins", "_zooimage.jar", package = "zooimage" ), 
-		ij.plugin, 
-		zimfile )
-	# system( cmd, intern = TRUE )
-	cmd
+		ij.plugin,
+		tools:::file_path_as_absolute(zimfile) )
+	system( cmd )
 }
 # }}}
 

Modified: pkg/zooimage/R/zie.r
===================================================================
--- pkg/zooimage/R/zie.r	2009-05-04 11:51:05 UTC (rev 124)
+++ pkg/zooimage/R/zie.r	2009-05-04 12:55:09 UTC (rev 125)
@@ -293,6 +293,7 @@
 	### TODO: allow restarting from a given point!
 	cat("Checking all lines in the .zie file for raw images...\n")
 	allImages <- character(0)
+	nLines <- length(Lines)
 	for (i in 1:nLines) {
 		### TODO: allow restarting from a given point and eliminate previous 
 		###       lines for which there are no images (considered as already processed!)

Modified: pkg/zooimage/inst/imagej/plugins/_zooimage.jar
===================================================================
(Binary files differ)

Modified: pkg/zooimage/src/src/org/sciviews/zooimage/ImageFileProcessor.java
===================================================================
--- pkg/zooimage/src/src/org/sciviews/zooimage/ImageFileProcessor.java	2009-05-04 11:51:05 UTC (rev 124)
+++ pkg/zooimage/src/src/org/sciviews/zooimage/ImageFileProcessor.java	2009-05-04 12:55:09 UTC (rev 125)
@@ -21,7 +21,6 @@
 import org.sciviews.zooimage.files.ZimFile;
 import org.sciviews.zooimage.log.Log;
 import org.sciviews.zooimage.tools.FileExtensions;
-import org.sciviews.zooimage.tools.FileUtilities;
 import org.sciviews.zooimage.tools.IJUtilities;
 import org.sciviews.zooimage.tools.Images;
 import org.sciviews.zooimage.tools.ZIJ;