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Bug 163 - Stitching routine see invisible files in Mac OSX version
Stitching routine see invisible files in Mac OSX version
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2010-04-14 22:48 CDT by Graham Thomas
Modified: 2011-04-13 19:35 CDT
1 user (show)

See Also:
Description Graham Thomas 2010-04-14 22:48:01 CDT 
Using the 'stitch directory with images' plug in in the Mac OSX version (Image JA 1.43s) it sees an extra file in the log:

/Users/grahamthomas/Desktop/ORR stitching grid 1/.DS_Store
/Users/grahamthomas/Desktop/ORR stitching grid 1/ORR_004.tif
/Users/grahamthomas/Desktop/ORR stitching grid 1/ORR_005.tif
/Users/grahamthomas/Desktop/ORR stitching grid 1/ORR_006.tif
/Users/grahamthomas/Desktop/ORR stitching grid 1/ORR_007.tif
/Users/grahamthomas/Desktop/ORR stitching grid 1/ORR_008.tif
/Users/grahamthomas/Desktop/ORR stitching grid 1/ORR_009.tif
Found 7 files.


One of these .DS_Store is an invisible system file of some kind. When I hit OK to start the routine it abandons ship with the following exception:

java.lang.NullPointerException
	at loci.plugins.importer.ImporterOptions.showDialogs(ImporterOptions.java:242)
	at loci.plugins.importer.Importer.run(Importer.java:149)
	at loci.plugins.LociImporter.run(LociImporter.java:77)
	at ij.IJ.runUserPlugIn(IJ.java:188)
	at ij.IJ.runPlugIn(IJ.java:155)
	at ij.IJ.runPlugIn(IJ.java:144)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:302)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:38)
	at ij.IJ.runUserPlugIn(IJ.java:188)
	at ij.IJ.runPlugIn(IJ.java:155)
	at ij.IJ.runPlugIn(IJ.java:144)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:412)
	at ij.io.Opener.openImage(Opener.java:289)
	at ij.io.Opener.openImage(Opener.java:308)
	at stitching.CommonFunctions.loadImage(CommonFunctions.java:73)
	at Stitch_Image_Directory.run(Stitch_Image_Directory.java:168)
	at ij.IJ.runUserPlugIn(IJ.java:188)
	at ij.IJ.runPlugIn(IJ.java:155)
	at ij.Executer.runCommand(Executer.java:147)
	at ij.Executer.run(Executer.java:78)
	at java.lang.Thread.run(Thread.java:637)

Other notes:
When I browse for the image directory I have only an 'all files' choice in the dropdown menu so I can't pick out just the tifs that way. Also in the bioformats import options checking the similar files or individual files makes no difference.

I am guessing that the extra non-image file is upseting things and should not be seen.





Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.5.8
  java.version => 1.6.0_17
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_17-b04-248-9M3125
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 14.3-b01-101
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /
Comment 1 Curtis Rueden 2010-04-22 00:07:11 CDT 
Steffi, perhaps this bug could be fixed by using loci.formats.FilePattern as we discussed during the hackathon. You'll find this class in the bio-formats submodule, at components/bio-formats/src/loci/formats/FilePattern.java.

If you want to try it out, you can use the main method for testing:

  java -cp $FIJI_HOME/plugins/loci_tools.jar:$FIJI_HOME/bio-formats/jar/log4j.properties loci.formats.FilePattern "/Users/grahamthomas/Desktop/ORR stitching grid 1/ORR_004.tif"

This command will require the bio-formats submodule to be checked out, and updated to the latest trunk, in order to work. Sorry about the log4j.properties junk but all of our output uses SLF4J/log4j and adding a simple config file was the fastest way I could find to make the main method output properly.

Anyway, it's not vital that you be able to execute the main method; it's just an illustration. Probably most useful will be the Javadoc:

  http://hudson.openmicroscopy.org.uk/job/LOCI/javadoc/loci/formats/FilePattern.html

Let me know if you have any questions about it.
Comment 2 Johannes Schindelin 2011-03-23 15:15:57 CDT 
Thomas, you can use a better pattern, no?
Comment 3 Johannes Schindelin 2011-04-13 18:28:35 CDT 
Using a more strict file pattern works for me.
Comment 4 Johannes Schindelin 2011-04-13 19:35:49 CDT 
After I closed this bug, I got a nice private reply. It pointed out that 'Stitch directory with images' does not ask for a file pattern.

So now I fixed this in http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=commit;h=eb77158dfd2406acb230d3958facba0a21a774c7 and uploaded it, and hope for more effective communication with the next bug report.