[ome-users] czi multi-file images

[Maier, Lorenz]

Hi Melissa,

> I would expect that to work now if you select the desired file and check the "Open files individually" option in the "Bio-Formats Import Options"
window.  If that doesn't work with your datasets, please let us know.

This is so much better now, thanks a lot!


It isn't working 100% reliably, however:
- If I open file 300 with the "open files individually" option, it's working as expected.

- For file 3, three series are shown, with the first two being all white in the preview. That resembles the behavior of a much older version of bioformats, when there were n-1 black series prepended.

- With file 4, I get an Exception:

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:1140)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:723)
	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.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)


Best regards,
Lorenz

-----Ursprüngliche Nachricht-----
Von: Melissa Linkert [mailto:melissa.linkert at gmail.com] Im Auftrag von Melissa Linkert
Gesendet: Donnerstag, 8. Mai 2014 13:53
An: Maier, Lorenz
Cc: ome-users at lists.openmicroscopy.org.uk
Betreff: Re: [ome-users] czi multi-file images

Hi Lorenz,

> I've compiled the changes that you proposed for the CZI reader a few days ago from your git repository and replaced the jars/bioformats/formats-*.jar files of Fiji with the new ones.
> 
> The changes look quite promising! By now, the setId() of the 300gb multi-file czi dataset I've sent you takes only 2.5h instead of 5h when they are loaded directly from our network folder. 

I'm glad to hear that it's looking better!

> How much effort would it be to allow loading the individual 1gb files of the dataset?
> 
> I assume that you have implemented reading the headers from all of the files because the CZI specs do not specify which data is stored where. The actual implementation in Zen blue, however, only has the option to split the dataset by the series.
> 
> So I know that the images I would like to load are stored e.g. in file 123, but Fiji spends 2.5h reading headers from all 300 files before even asking me which series I want to display.

I would expect that to work now if you select the desired file and check the "Open files individually" option in the "Bio-Formats Import Options"
window.  If that doesn't work with your datasets, please let us know.

Regards,
-Melissa

On Thu, May 08, 2014 at 09:58:59AM +0200, Maier, Lorenz wrote:
> Hi Melissa,
> 
> I've compiled the changes that you proposed for the CZI reader a few days ago from your git repository and replaced the jars/bioformats/formats-*.jar files of Fiji with the new ones.
> 
> The changes look quite promising! By now, the setId() of the 300gb multi-file czi dataset I've sent you takes only 2.5h instead of 5h when they are loaded directly from our network folder. 
> 
> How much effort would it be to allow loading the individual 1gb files of the dataset?
> 
> I assume that you have implemented reading the headers from all of the files because the CZI specs do not specify which data is stored where. The actual implementation in Zen blue, however, only has the option to split the dataset by the series.
> 
> So I know that the images I would like to load are stored e.g. in file 123, but Fiji spends 2.5h reading headers from all 300 files before even asking me which series I want to display.
> 
> 
> Best regards,
> Lorenz
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