Mouse over triggers an exception while saving virtual stack (Metamorph)

[bruvellu]

Hello,

I ran into an intriguing error while saving a virtual Metamorph stack to TIFF. If I pass the mouse over another window (also a virtual stack), the saving fails with an exception Current file should not be null (see below).

It appears to be specific to the Metamorph format; it doesn't happen while saving a regular TIFF virtual stack to file. The dataset is a timelapse with multiple positions and slices. I can provide a subset if needed for debugging.

Steps:

1. Import the Metamorph (.nd) file using Bio-Formats
2. Mark the checkbox to open as a virtual stack
3. Select all series to be opened (stacks for different positions)
4. Click on the window of a virtual stack and press CTRL+S to save as TIFF
5. While the stack is being saved, mouse over the window of another stack
6. An exception window pops-up and the saving halts

Screencast:

Screencast from 31-07-23 15:52:36.webm

Exception:

(Fiji Is Just) ImageJ 2.14.0/1.54f; Java 1.8.0_172 [64-bit]; Linux 3.10.0-1062.4.3.el7.x86_64; 1193MB of 120000MB (<1%)

java.lang.IllegalStateException: FormatReader.getImageCount: Current file should not be null; call setId(String) first
    at loci.formats.FormatTools.assertId(FormatTools.java:988)
    at loci.formats.FormatReader.getImageCount(FormatReader.java:685)
    at loci.formats.in.MetamorphReader.openBytes(MetamorphReader.java:329)
    at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:167)
    at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
    at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
    at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:83)
    at loci.plugins.util.BFVirtualStack.getProcessor(BFVirtualStack.java:185)
    at ij.io.ImageWriter.write16BitVirtualStack(ImageWriter.java:103)
    at ij.io.ImageWriter.write(ImageWriter.java:292)
    at ij.io.TiffEncoder.write(TiffEncoder.java:129)
    at ij.io.TiffEncoder.write(TiffEncoder.java:150)
    at ij.io.FileSaver.saveAsTiffStack(FileSaver.java:218)
    at ij.io.FileSaver.saveAsTiff(FileSaver.java:91)
    at ij.io.FileSaver.save(FileSaver.java:68)
    at ij.plugin.Commands.save(Commands.java:63)
    at ij.plugin.Commands.run(Commands.java:33)
    at ij.IJ.runPlugIn(IJ.java:216)
    at ij.Executer.runCommand(Executer.java:152)
    at ij.Executer.run(Executer.java:70)
    at java.lang.Thread.run(Thread.java:748)

Cheers, Bruno

[ctrueden]

@bruvellu That error is intriguing indeed!

CC @sbesson @dgault @melissalinkert @joshmoore to loop them in, since it is not clear whether the bug-fix will need to be on the Bio-Formats side or the ImageJ side.

[melissalinkert]

@bruvellu : that error suggests that one of the underlying .tiff or .stk files could not be read. Are you able to open all of the planes in the dataset without a virtual stack, using the Specify range for each series option to open a subset of planes at a time?

[bruvellu]

Hi @ctrueden and @melissalinkert,

Yes, I'm able to open the datasets without a virtual stack. I also managed to save every individual series from virtual to TIFF, so it looks like all the .stk files are readable (as long as I don't pass the mouse over another window during the saving). Could it be that the mouse hovering confuses ImageJ as to which virtual slice it should be loading/writing?

Cheers

[joshmoore]

The only additional thought that occurs to me is if this isn't a concurrency issue. If the call to save has a reader instance and the mouse over event attempts some setting on the same reader, the call to openBytes might catch the reader with its pants down.

[dgault]

I have managed to reproduce the same issue, though I have not yet found the root cause of the problem. Iw ill try and test some more to see if I can locate the issue. I suspect it is going to be specific to the Bio-Formats virtual stack.

[dgault]

I have copied the issue to the Bio-Formats repo as I have been unable to reproduce with a standard Tiff Virtual Stack, so it indeed appears to be related specifically to Bio-Formats. You can close this ImageJ Issue in favour of the new Bio-Formats Issue.

[bruvellu]

Great, thanks @dgault!