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Bug 702 - ffmpeg video fails in vitual stack mode
ffmpeg video fails in vitual stack mode
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-02-11 12:04 CST by Pedro Camello
Modified: 2014-08-24 13:23 CDT
3 users (show)

See Also:
Description Pedro Camello 2014-02-11 12:04:32 CST 
I open a relatively big file (around 1000 slices) with the File>Import>Movie(FFMPEG) plugin, using the virtual stack option.
Then I need to crop the area of interest of the stack to make the file lighter and the posterior processing faster. When I made this in last december 2013 I did not get any problem. However, I get now this message error:

>(Fiji Is Just) ImageJ 1.48q; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 21MB of 2791MB (<1%)
 >
>java.lang.IllegalArgumentException: Argument out of range: 1
>	at ij.VirtualStack.deleteSlice(VirtualStack.java:63)
>	at ij.process.StackProcessor.resize(StackProcessor.java:120)
>	at ij.plugin.Resizer.run(Resizer.java:136)
>	at ij.IJ.runPlugIn(IJ.java:169)
>	at ij.Executer.runCommand(Executer.java:131)
>	at ij.Executer.run(Executer.java:64)
>	at java.lang.Thread.run(Thread.java:662)

In addition, when I use the Duplicate command I also get an error:

>(Fiji Is Just) ImageJ 1.48q; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 117MB of 2791MB (4%)
> 
>java.lang.NullPointerException
>	at ij.plugin.Duplicator.run(Duplicator.java:86)
>	at ij.plugin.Duplicator.run(Duplicator.java:51)
>	at ij.IJ.runPlugIn(IJ.java:169)
>	at ij.Executer.runCommand(Executer.java:131)
>	at ij.Executer.run(Executer.java:64)
>	at java.lang.Thread.run(Thread.java:662)

Wayne Rasband replied this:

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: D:\INSTAL~1\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => D:\INSTAL~1\Fiji\Fiji.app

Information about the version of each plugin:

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  b9742297 20131222110548 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar
  2079ca32 20131222110554 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar
  0307564a 20131222110530 plugins/blockmatching_-2.0.0-SNAPSHOT.jar
  e9f8f392 20131224163338 plugins/cookbook_.jar
  659ad6a3 20110307142230 plugins/ij-ImageIO_.jar
  82f900ac 20131222110602 plugins/level_sets-1.0.1-SNAPSHOT.jar
  bb271925 20140211182129 plugins/loci_plugins.jar
  527312b2 20131224163334 plugins/mcib3d-suite/mcib3d-core.jar
  cef74c40 20131224163336 plugins/mcib3d-suite/mcib3d_plugins.jar
  7f0caa5d 20131224163311 plugins/miglayout-3.7.3.1-swing.jar
  25fe65a6 20120223151004 plugins/mm_nd_and_roi_pack.jar
  69795d1f 20120807195145 plugins/mosaic_plugins.jar
  df2af815 20131222110506 plugins/mpicbg_-0.6.1-SNAPSHOT.jar
  5e32d936 20110307142230 plugins/panorama_.jar
  27c6f58b 20131222110631 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar
  16012d5a 20131222110630 plugins/registration_3d-2.0.0-SNAPSHOT.jar
  41cae167 20131224163329 plugins/slim_plugin-1.0.0-SNAPSHOT.jar
  14eaf670 20131224163317 plugins/visad-lite-2.0.20070828.jar
  574cdfce 20131224163318 plugins/visbio_plugins-1.0-SNAPSHOT.jar
  e6e0879f 20110307142240 retro/backport-util-concurrent-3.1.jar
  8759ba20 20130514233319 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b2 20130514233320 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38 20110928104553 scripts/InstallJava3D.m
  05a92a3c 20110928104553 scripts/IsJava3DInstalled.m
  ff34d026 20120811012333 scripts/Matlab3DViewerDemo_1.m
  25be149f 20110928104553 scripts/Matlab3DViewerDemo_2.m
  cb529b6c 20120811012334 scripts/Matlab3DViewerDemo_3.m
  53d2da73 20120811012333 scripts/Matlab3DViewerIntroduction.m
  4bb342fa 20120811012333 scripts/Miji.m
  868cd434 20110928104551 scripts/Miji_Test.m
  d3260180 20110307142230 scripts/Record_Desktop.py
  0ea7f8fc 20110307142230 scripts/Record_Window.py
  dc94c3a3 20110928104551 scripts/bfopen.m
  a77cab39 20131222110642 scripts/importTrackMateTracks.m
Comment 1 Johannes Schindelin 2014-03-05 15:47:03 CST 
Please note that the FFMPEG plugin is unmaintained for the momen. Also, the problem you describe seems to be triggered by a recent change in ImageJ 1.x' VirtualStack; downgrading might work around the problem.