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Bug 670 - Batch processing of LSM files broken
Batch processing of LSM files broken
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-10-11 17:13 CDT by Pavol Bauer
Modified: 2014-06-16 15:01 CDT
3 users (show)

See Also:

Description Pavol Bauer 2013-10-11 17:13:29 CDT
In the current version of Fiji any type of Batch process / Macro applied on LSM (Carl Zeiss) files is aborted with the error message "IJ.openImage() returned null: file.lsm" where file.lsm is an arbitary filename in the input-dir.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Work\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\Work\Fiji.app

Information about the version of each plugin:

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  736bb192 20131010151654 plugins/Stack_Manipulation-2.0.0-SNAPSHOT.jar
  59f36299 20131010151654 plugins/Statistical_Region_Merging-2.0.0-SNAPSHOT.jar
  ca21e755 20131010151654 plugins/Stitching_-2.0.0-SNAPSHOT.jar
  30100de7 20131010151654 plugins/Sync_Win-1.7-fiji2-SNAPSHOT.jar
  685ca9dc 20131010151654 plugins/Thread_Killer-2.0.0-SNAPSHOT.jar
  2cee6c37 20131010151654 plugins/Threshold_Colour-2.0.1-SNAPSHOT.jar
  d822b123 20131010151654 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar
  584cb5b9 20131010151654 plugins/ToAST_-25.0.1-SNAPSHOT.jar
  4cf59217 20131010151654 plugins/TopoJ_-2.0.0-SNAPSHOT.jar
  369b6351 20131010151654 plugins/TrackMate_-2.1.1-SNAPSHOT.jar
  28a6b42a 20131010151654 plugins/Trainable_Segmentation-2.0.0-SNAPSHOT.jar
  59124982 20131010151654 plugins/TrakEM2_-1.0b-SNAPSHOT.jar
  8e7f3b79 20131010151654 plugins/TransformJ_-2.8.1-SNAPSHOT.jar
  c4e87a76 20131010151654 plugins/TurboReg_-2.0.0-SNAPSHOT.jar
  9558400d 20131010151654 plugins/UnwarpJ_.jar
  a32dfe46 20131010151654 plugins/Utilities/Close_All_Without_Saving.txt
  253c6df4 20131010151654 plugins/VIB_-2.0.0-SNAPSHOT.jar
  baa78901 20131010151654 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar
  81279d21 20131010151654 plugins/Video_Editing-2.0.0-SNAPSHOT.jar
  73396eef 20131010151654 plugins/View5D_-1.3.1-SNAPSHOT.jar
  980c0ed9 20131010151654 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar
  b9742297 20131010151654 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar
  2079ca32 20131010151654 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar
  0307564a 20131010151654 plugins/blockmatching_-2.0.0-SNAPSHOT.jar
  659ad6a3 20131010151654 plugins/ij-ImageIO_.jar
  82f900ac 20131010151654 plugins/level_sets-1.0.1-SNAPSHOT.jar
  89866b35 20131010151654 plugins/loci_plugins-4.4.9-SNAPSHOT.jar
  df2af815 20131010151654 plugins/mpicbg_-0.6.1-SNAPSHOT.jar
  5e32d936 20131010151654 plugins/panorama_.jar
  96b34801 20131010151654 plugins/readme.txt
  7e27d804 20131010151654 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar
  16012d5a 20131010151654 plugins/registration_3d-2.0.0-SNAPSHOT.jar
  34b7341d 20131010151658 retro/backport-util-concurrent-3.1.jar
  8759ba20 20131010151658 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b2 20131010151658 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38 20131010151658 scripts/InstallJava3D.m
  05a92a3c 20131010151658 scripts/IsJava3DInstalled.m
  ff34d026 20131010151658 scripts/Matlab3DViewerDemo_1.m
  25be149f 20131010151658 scripts/Matlab3DViewerDemo_2.m
  cb529b6c 20131010151658 scripts/Matlab3DViewerDemo_3.m
  53d2da73 20131010151658 scripts/Matlab3DViewerIntroduction.m
  4bb342fa 20131010151658 scripts/Miji.m
  868cd434 20131010151658 scripts/Miji_Test.m
  dc94c3a3 20131010151658 scripts/bfopen.m
  a77cab39 20131010151658 scripts/importTrackMateTracks.m
Comment 1 Wayne Rasband 2013-10-12 12:38:41 CDT
I can reproduce this problem in Fiji by deleting LSM_Reader.jar and LSM_Toolbox.jar from Fiji.app/plugins. I cannot reproduce the problem in ImageJ.
Comment 2 Wayne Rasband 2013-10-12 19:19:26 CDT
This bug in the Process>Batch>Macro command is fixed in the ImageJ 1.48e8 daily build, available at

   https://dl.dropboxusercontent.com/u/2810011/ij.jar

The daily build is not available via Help>Update ImageJ due to the U.S. Government partial shutdown.

The fix required adding

   if (imp==null) imp=Opener.openUsingBioFormats(path);

just after

   imp = IJ.openImage(path);

in the BatchProcessor.processFolder() method.