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Bug 946 - can't open .ids file with IFiji/ImageJ2 Bio-formats Importer
can't open .ids file with IFiji/ImageJ2 Bio-formats Importer
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-10-16 22:06 CDT by Laura Serbus
Modified: 2014-10-30 13:25 CDT
2 users (show)

See Also:
Description Laura Serbus 2014-10-16 22:06:14 CDT 
I had a .ids file here to open, and at first it looks like this is going fine.  But then it says, "Sorry, there was a problem during import" and the text window (log) that pops up says this:

loci.formats.FormatException: ICS file not found.
	at loci.formats.in.ICSReader.initFile(ICSReader.java:775)
	at loci.formats.FormatReader.setId(FormatReader.java:1317)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:202)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)

Can you help?
I've heard that Image J used to be able to open the .ids type of files, hoping we can still do that.

  best regards,
    Laura

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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 => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141015131008)
Fiji: http://fiji.sc/update/ (last check:20141014055500)

Files not up-to-date:
  9f4f8151 (OBSOLETE_UNINSTALLED) 20140707074617 jars/jython-2.5.2.jar
Comment 1 Curtis Rueden 2014-10-30 13:25:46 CDT 
Presuming your file is an Image Cytometry Format file...
https://en.wikipedia.org/wiki/Image_Cytometry_Standard

Then there are two ways data can be stored:
* Version 2.0 of the format: a single ICS file containing both pixels and metadata
* Version 1.0 of the format: a split set of files: ICS file containing the metadata and IDS containing pixels.

If you have an IDS file but no ICS file, you are unfortunately out of luck -- the ICS file is necessary to interpret the data.