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Bug 901 - Fiji cannot open stacks
Fiji cannot open stacks
Status: CONFIRMED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-13 20:56 CDT by Saumya Saurabh
Modified: 2014-08-25 15:03 CDT
3 users (show)

See Also:
Description Saumya Saurabh 2014-08-13 20:56:18 CDT 
When I try to open an image sequence that consists of 60 files in one fiolder, I get this error:


(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 76MB of 6103MB (1%)
 
java.lang.NullPointerException
	at io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:781)
	at io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:740)
	at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
	at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
	at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
	at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:297)
	at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:208)
	at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
	at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
	at io.scif.img.ImgOpener.read(ImgOpener.java:808)
	at io.scif.img.ImgOpener.read(ImgOpener.java:793)
	at io.scif.img.ImgOpener.read(ImgOpener.java:793)
	at io.scif.img.ImgOpener.read(ImgOpener.java:793)
	at io.scif.img.ImgOpener.read(ImgOpener.java:775)
	at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:761)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:362)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
	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.interceptOpenImage(DefaultLegacyHooks.java:430)
	at ij.plugin.FolderOpener.run(FolderOpener.java:115)
	at ij.IJ.runPlugIn(IJ.java:172)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)

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:\Users\saumyas2\DOWNLO~1\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\saumyas2\DOWNLO~1\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140711150647)
Fiji: http://fiji.sc/update/ (last check:20140714170940)

Files not up-to-date:
  3abf4e77 (MODIFIED) 20140813185222 jars/ij-1.49d.jar
Comment 1 Mark Hiner 2014-08-14 07:23:04 CDT 
Hello,

 As a temporary workaround you can run "Edit > Options > ImageJ2" and uncheck "Use SCIFIO when opening files"

Image sequences in general are not well-tested in SCIFIO right now, but it looks like there is also a bug in the Micromanager file support.

Would you mind using "Help > Upload sample image" to share one of the Micromanager image files that is failing, so we can reproduce and fix this bug?

Thank you very much for the report!
Comment 2 Curtis Rueden 2014-08-25 15:03:24 CDT 
No need to upload sample data; we already have MM datasets demonstrating this issue, which I just confirmed still occurs with the most recent version of Fiji with SCIFIO enabled.

Relevant stack trace is:

java.lang.ArrayIndexOutOfBoundsException: 2
	at io.scif.formats.MicromanagerFormat$Position.getFile(MicromanagerFormat.java:870)
	at io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:757)
	at io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:721)
	at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
	at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
	at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
	at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:297)
	at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:208)
	at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
	at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
	at io.scif.img.ImgOpener.read(ImgOpener.java:808)
	at io.scif.img.ImgOpener.read(ImgOpener.java:793)
	at io.scif.img.ImgOpener.read(ImgOpener.java:793)
	at io.scif.img.ImgOpener.read(ImgOpener.java:775)
	at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:761)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:362)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
	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:136)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)

Using the dataset in our data repository's micromanager/colin folder.