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Bug 744 - problem opening .czi files
problem opening .czi files
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
: 747
Depends on:
Blocks:
 
Reported: 2014-05-08 12:11 CDT by tomancak
Modified: 2015-04-21 11:20 CDT
5 users (show)

See Also:

Description tomancak 2014-05-08 12:11:51 CDT
This is probably a bioformats issue, but perhaps you have some insight.

We have problems opening some .czi files produced by Zeiss Lightsheet Z1. The data are saved as one .czi file per angle. Some open normally while others produce the error pasted below.

We suspect a software problem since these files were openable before (2-3 weeks ago).

I uploaded two example files through the Fiji wiki

spim_TL003_Angle4.czi WORKS

and

spim_TL002_Angle1.czi DOES NOT OPEN

Thanks very much for your help

PAvel



(Fiji Is Just) ImageJ 1.48v; Java 1.6.0_24 [64-bit]; Linux 2.6.32-279.22.1.el6.x86_64; 9711MB of 94804MB (10%)
 
java.lang.IllegalArgumentException: Invalid T index: 1/1
	at loci.formats.FormatTools.getIndex(FormatTools.java:372)
	at loci.formats.FormatTools.getIndex(FormatTools.java:317)
	at loci.formats.FormatReader.getIndex(FormatReader.java:1051)
	at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1020)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:615)
	at loci.formats.FormatReader.setId(FormatReader.java:1315)
	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:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
	at ij.io.Opener.openImage(Opener.java:311)
	at ij.io.Opener.openImage(Opener.java:334)
	at ij.io.Opener.open(Opener.java:144)
	at ij.io.Opener.openAndAddToRecent(Opener.java:247)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.32-279.22.1.el6.x86_64
  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 => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/pavlopou/Desktop/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  ij.dir => /home/pavlopou/Desktop/Fiji.app

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Comment 1 Curtis Rueden 2014-05-08 13:27:12 CDT
Did you try with the Bio-Formats update site enabled?

If so, and the problem still occurs, then we'll need to forward the bug on to the Bio-Formats developers.
Comment 2 tomancak 2014-05-08 13:45:22 CDT
Hi Curtis,

I am quite sure that the Bioformats update site is enabled. I explicitly looked in the advanced mode of the updater and the site was clicked.

I would turn to Bioformats right away, but I couldn't find a place on their site to upload the large files. Also its difficult to transfer the state of my Fiji to that mailing list. Or?

Thanks a lot for looking into this.

PAvel
Comment 3 Curtis Rueden 2014-05-08 17:04:18 CDT
Melissa says: "That's a known issue that we're fixing for 5.0.2."
Comment 4 tomancak 2014-05-09 01:50:44 CDT
Ok, thanks.

As with everything concerning bioformats this quite a show stopper. No image open, no science.

Any chance, in Fiji, to revert to a previous version of bioformats where this was working? That's what biologists do, 'save' an old version of Fiji without update.

All the best

PAvel
Comment 5 Curtis Rueden 2014-05-09 10:55:42 CDT
Does the Life-Line version of Fiji (linked from http://fiji.sc/Downloads) work the way you need?

I am concerned that reverting to an old Bio-Formats will revert other bug-fixes that other users might need.

Best would be if the bug could be fixed ASAP and merged to the Bio-Formats dev_5_0 integration branch, so that the fix automatically becomes available from the Bio-Formats update site. But that will depend on what Melissa and the other Bio-Formats developers currently have on their plates. Alternately, if there are any programmers in your lab who can try their hand at fixing it, they could submit the patch upstream and get the issue resolved sooner.
Comment 6 Curtis Rueden 2014-05-09 11:16:26 CDT
I also want to take the opportunity to rant a little here: Zeiss's CZI format is yet another complicated new format that requires lots of time from the Bio-Formats  developers. If you require support for this format within ImageJ to be really robust, shouldn't that be a requirement that users demand from Zeiss before purchasing their equipment?
Comment 7 tomancak 2014-05-10 07:42:16 CDT
Yes, that is what we are constantly doing, talking to Zeiss about the need to work with Bioformats to settle this new format in. And I think all involved, Zeiss, Bioformats and Fiji/ImageJ team are doing their best to make that format stable. Unfortunately, everybody is busy and has many other priorities. In an ideal case, someone would pay money to bioformats to move it up their priority cue. Finding that funding proves difficult, but we are working on it.

In my lab only Tobias would have any chance to contribute to this and frankly, I don't think it is particularly easy to get into the Bioformats source code for an outsiders (my impression).

What is mysterious to me is that functionality that was there for a long time disappears. The czi didn't change, something in Bioformats got corrupted.

I will try the lifeline Fiji, thanks for the suggestion.

All the best

PAvel
Comment 8 Curtis Rueden 2014-05-10 11:26:42 CDT
I have a potential fix. Can you please try replacing your Fiji's jars/bio-formats/formats-gpl.jar with this one:

http://curtis.imagej.net/fiji-bug-744/formats-gpl.jar

It was a ostensibly a trivial bug to fix.

Here is exactly what I did to fix this bug:

1) Clone bioformats.git from https://github.com/openmicroscopy/bioformats.

2) Switch to the "dev_5_0" branch.

3) Import the code into Eclipse using File > Import > Existing Maven Project. This is the same procedure we use for ImgLib2.

4) Open ZeissCZIReader by pressing Cmd+Shift+T and typing in "ZeissCZIReader"

5) Add a main method to the class as follows:

  public static void main(String... args) throws Exception {
    ZeissCZIReader r = new ZeissCZIReader();
    r.setId("/Users/curtis/Desktop/spim_TL002_Angle1.czi");
    r.openBytes(0);
  }

6) Press Shift+F5 to verify that the ArrayIndexOutOfBounds bug occurs.

7) Looked at the line numbers of the stack trace, and jumped to the relevant part of the "assignPlaneIndices" method.

8) Added System.out.println statements check the values of t, getSizeT, and related variables. (You could alternately use the Eclipse debugger to do this.)

9) Noticed that the value of t is set to 1, which is out of bounds when getSizeT() return 1 (with a 0-based indexing scheme).

10) Searched for where the t variable is defined by selecting a place where "t" is used and pressing Cmd+Shift+G to look it up. Jumped to the first usage of t, which is on line 942.

11) Saw that t is first assigned on line 965, with the following code:

            t = dimension.start;
            if (t > getSizeT()) {
              t = getSizeT() - 1;
            }

12) The check "t > getSizeT()" will not catch when t is equal to getSizeT(). So I changed it to ">=" instead. I was more confident this is a good solution because just above that block, the analogous case for Z looks like:

            z = dimension.start;
            if (z >= getSizeZ()) {
              z = getSizeZ() - 1;
            }

13) Pressed Shift+F11 to run the code again. This time it read the plane successfully.

14) On the command line, ran "ant jar" to build a new formats-gpl.jar file. (Alternately, "mvn package" works too, which is how we do it in ImgLib2.)

15) Copied the new formats-gpl.jar into my Fiji and verified that I could open your first angle sample file.

16) Double checked, using "git blame" on ZeissCZIReader.java, that there was no other rationale written in previous commit messages for why the check might have been written as "t > getSizeT()". I found that that code was part of the initial version of ZeissCZIReader, so very likely to be less well tested.

17) Wrote up this explanation.

> frankly, I don't think it is particularly easy to get into the Bioformats source code for an outsiders (my impression).

I honestly don't know how to make it any easier for people like Tobias to fix bugs in Bio-Formats. Things like creating a new file format reader are more daunting, yes, but just fixing a bug like this is not supposed to be off-putting.

So: What can the OME team do to make Bio-Formats development more approachable, from your perspective as well as that of developers such as Tobias, so that some of the maintenance burden can be shared by the community instead of all on the OME team's shoulders?
Comment 9 Curtis Rueden 2014-05-13 10:59:35 CDT
*** Bug 747 has been marked as a duplicate of this bug. ***
Comment 10 Josh Moore 2014-05-15 04:29:15 CDT
Thanks for the debugging and the detailed explanation, Curtis. Perhaps it would be better to move the conversation off the issue tracker, though? I've added mailto:ome-devel@lists.openmicroscopy.org.uk to the CC list. Anyone who'd like to follow-up there (or one of the other resources at https://www.openmicroscopy.org/site/community/ ) is certainly encouraged to make suggestions for improvement. We know it's not impossible to get involved -- https://www.openmicroscopy.org/site/about/ome-contributors -- but would certainly like to remove blockers where we can. Cheers, ~Josh
Comment 11 tomancak 2014-05-15 08:37:48 CDT
Thanks Curtis, your fix jars/bio-formats/formats-gpl.jar helped solves the problem with .czi files.

I discovered several other problems with the metadata interpretation. I will take it to the appropriate mailing list.

All the best

PAvel
Comment 12 Curtis Rueden 2014-06-26 22:25:40 CDT
PAvel, could you please close this bug if the problems with CZI have been resolved now? Or if not, make sure that the OME team has sample non-working data? Thanks!
Comment 13 Curtis Rueden 2015-04-21 11:20:08 CDT
Presumed fixed. If there is still an issue, please report it to the Bio-Formats team:

http://openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html