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Bug 968 - Relative paths in command like broken.
Relative paths in command like broken.
Status: CONFIRMED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-12-05 08:12 CST by Alexey Zaytsev
Modified: 2014-12-18 13:23 CST
2 users (show)

See Also:

Description Alexey Zaytsev 2014-12-05 08:12:41 CST
It seems that the command line no longer understands relative paths. When passing a 'file', fiji gives an error not being able to open '/file'.

Emample:
~/work/fiji/Fiji.app/ImageJ-linux64 IM000702.Tif

Pops an error: "/IM000702.Tif" (No such file or directory).

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.13.0-37-generic
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/xl0/work/fiji/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/xl0/work/fiji/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141126221327)
Fiji: http://fiji.sc/update/ (last check:20141125171145)
Comment 1 Curtis Rueden 2014-12-18 13:23:52 CST
It might be a TIFF-specific bug, since I don't see it when testing with a PNG. It seems you can avoid the issue by writing "./IM000702.Tif" instead of just "IM000702.Tif".

However, you'll then stumble over another bug: when passing files for ImageJ1 to open in this manner, they never appear in the UI, due to how ImageJ2 handles command line arguments. See https://github.com/imagej/imagej-legacy/issues/89

Until these bugs are fixed, one workaround is to pass the "--open" flag before the filename; e.g.:

    ~/work/fiji/Fiji.app/ImageJ-linux64 --open IM000702.Tif