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Bug 896 - Fiji cannot open PGMs after the recent updates
Fiji cannot open PGMs after the recent updates
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-12 01:14 CDT by Mason
Modified: 2014-08-27 13:35 CDT
3 users (show)

See Also:

Attachments
Sample PGM image that won't import (254 bytes, image/x-portable-graymap)
2014-08-12 01:18 CDT, Mason

Description Mason 2014-08-12 01:14:03 CDT 
I've been using FIJI for a project of mine for the past year, and since the past month, it's been failing to import any sort of PGM that my program outputs. This is the output of the exception it gives me:

(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 12MB of 6131MB (<1%)
 
java.lang.NumberFormatException: For input string: "2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2"

	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)

	at java.lang.Integer.parseInt(Integer.java:458)

	at java.lang.Integer.parseInt(Integer.java:499)

	at io.scif.formats.PGMFormat$Parser.typedParse(PGMFormat.java:183)

	at io.scif.formats.PGMFormat$Parser.typedParse(PGMFormat.java:161)

	at io.scif.AbstractParser.parse(AbstractParser.java:252)

	at io.scif.AbstractParser.parse(AbstractParser.java:335)

	at io.scif.AbstractParser.parse(AbstractParser.java:52)

	at io.scif.AbstractReader.setSource(AbstractReader.java:270)

	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)

	at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)

	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)

	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)

	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)

	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)

	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)

	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)

	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:421)

	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:154)

	at ij.IJ.runPlugIn(IJ.java)

	at ij.Executer.runCommand(Executer.java:131)

	at ij.Executer.run(Executer.java:64)

	at java.lang.Thread.run(Thread.java:662)

Thanks.

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140802105300)
Fiji: http://fiji.sc/update/ (last check:20140730140634)
Comment 1 Mason 2014-08-12 01:18:37 CDT 
Created attachment 195
Sample PGM image that won't import
Comment 2 Mark Hiner 2014-08-12 13:40:34 CDT 
Thanks for the report!

It looks like this is a bug in the SCIFIO PGM reader. You can disable SCIFIO for now via the Edit > Options > ImageJ2 dialog, which should allow you to continue to analyze your PGM data until this issue is resolved.
Comment 3 Mark Hiner 2014-08-12 13:43:05 CDT 
See also: https://github.com/scifio/scifio/issues/217
Comment 4 Curtis Rueden 2014-08-25 14:57:24 CDT 
Bug has been fixed. Will close this issue once a new version of SCIFIO has been released and uploaded.
Comment 5 Mark Hiner 2014-08-27 13:35:02 CDT 
Fixed in the SCIFIO 0.16.2 release. Now live on Fiji.