[ome-users] czi multi-file images

Melissa Linkert melissa at glencoesoftware.com
Thu May 15 02:11:29 BST 2014 

Hi Lorenz,

> in the meantime I ran a macro which tests if the number of series is not equal to 1 with the "open files individually" option set.
> The failing files are 3,6,12,69,138,276, each with as many "series" as their index.

Thank you for the additional investigation.

There is now one more commit on the previously-mentioned pull request which should address
this - each of the files when opened separately should have a single
series.  Note that files #41, #117, #165, #182, #196, #223 in the
dataset I have from you are all smaller than the rest of the files in
the dataset, so if the T sizes are different it is because there are
planes actually missing.

Regards,
-Melissa

On Tue, May 13, 2014 at 09:48:14AM +0200, Maier, Lorenz wrote:
> Hi,
> 
> in the meantime I ran a macro which tests if the number of series is not equal to 1 with the "open files individually" option set.
> The failing files are 3,6,12,69,138,276, each with as many "series" as their index.
> 
> Best,
> Lorenz
> 
> -----Ursprüngliche Nachricht-----
> Von: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] Im Auftrag von Maier, Lorenz
> Gesendet: Montag, 12. Mai 2014 22:59
> An: ome-users at lists.openmicroscopy.org.uk
> Betreff: Re: [ome-users] czi multi-file images
> 
> Hi Melissa,
> 
> with the latest version of the 'czi-part-2' branch, the error of file 4 is gone, thanks!
> 
> The bug of file "..(3).czi" remains, however: there seem to be 2 prepended series with white preview and all black content of the same dimensions as the correct third series.
> So far, I tested only a few files manually. The bug seems to be the same for files 3, 6, and 12, but not for 9.
> 
> Best regards,
> Lorenz
> 
> 
> 
> 
> -----Ursprüngliche Nachricht-----
> Von: Melissa Linkert [mailto:melissa.linkert at gmail.com] Im Auftrag von Melissa Linkert
> Gesendet: Sonntag, 11. Mai 2014 05:09
> An: Maier, Lorenz
> Cc: ome-users at lists.openmicroscopy.org.uk
> Betreff: Re: [ome-users] czi multi-file images
> 
> Hi Lorenz,
> 
> > 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:
> 
> I would expect both problems to be resolved with the last two commits on the 'czi-part-2' branch corresponding to pull request #1078:
> 
> https://github.com/melissalinkert/bioformats/commit/a59e2e301482144fa3e278f9aeea98c35a8a8e1e
> https://github.com/melissalinkert/bioformats/commit/41efc34c62998e2e78a3fc8273973afebcf982f6
> 
> If you see the same problems after recompiling and updating, then please let us know.
> 
> Regards,
> -Melissa
> 
> On Thu, May 08, 2014 at 03:01:01PM +0200, Maier, Lorenz wrote:
> > 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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