[ome-users] bio-formats error on tf8 file import

[Melissa Linkert]

Hi Kai,

> We have a user acquiring rather large datasets on it (multichannel + z-stack + time laps, about 7 GB per image), which worked fine in the past.
> 
> However, opening the tf8-files from his last acquisition fails with an error (see below).
> 
> The acquisition itself finished without error, but it is likely that the C drive of the acquisition machine was low on space at the end of the experiment.
> 
> Due to restrictions in the acquisition software (FEI Live Acquisition software) the data has to be recorded to the C drive.
> 
> Is there still something that could be done in order to save the data?

Thank you for reporting this problem.  Would you be willing to upload
the file that doesn't open?  That would greatly help us to either fix
this in Bio-Formats (if it's a bug) or find a way to recover the data
(if the file is corrupt).

I have sent FTP server credentials privately, as it sounds like the file is too large
to be uploaded via our QA system.

Regards,
-Melissa

On Mon, Feb 01, 2016 at 12:56:39PM +0000, Kai Schleicher wrote:
> Hi,
> 
> The output on one of our microscopes is a tf8.
> 
> We have a user acquiring rather large datasets on it (multichannel + z-stack + time laps, about 7 GB per image), which worked fine in the past.
> 
> However, opening the tf8-files from his last acquisition fails with an error (see below).
> 
> The acquisition itself finished without error, but it is likely that the C drive of the acquisition machine was low on space at the end of the experiment.
> 
> Due to restrictions in the acquisition software (FEI Live Acquisition software) the data has to be recorded to the C drive.
> 
> Is there still something that could be done in order to save the data?
> 
> Thanks and cheers,
> Kai
> 
> loci.formats.FormatException: loci.common.ReflectException: Cannot execute method: getNumPages
>                at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:149)
>                at loci.formats.FormatReader.setId(FormatReader.java:1426)
>                at loci.formats.DelegateReader.setId(DelegateReader.java:298)
>                at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
>                at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
>                at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>                at loci.plugins.in.Importer.run(Importer.java:76)
>                at loci.plugins.LociImporter.run(LociImporter.java:78)
>                at ij.IJ.runUserPlugIn(IJ.java:212)
>                at ij.IJ.runPlugIn(IJ.java:176)
>                at ij.Executer.runCommand(Executer.java:136)
>                at ij.Executer.run(Executer.java:65)
>                at ij.IJ.run(IJ.java:292)
>                at ij.IJ.run(IJ.java:267)
>                at ij.macro.Functions.doRun(Functions.java:603)
>                at ij.macro.Functions.doFunction(Functions.java:96)
>                at ij.macro.Interpreter.doStatement(Interpreter.java:230)
>                at ij.macro.Interpreter.doStatements(Interpreter.java:218)
>                at ij.macro.Interpreter.run(Interpreter.java:115)
>                at ij.macro.Interpreter.run(Interpreter.java:85)
>                at ij.macro.MacroRunner.run(MacroRunner.java:139)
>                at java.lang.Thread.run(Thread.java:662)
> Caused by: loci.common.ReflectException: Cannot execute method: getNumPages
>                at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:316)
>                at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:146)
>                ... 21 more
> Caused by: java.lang.reflect.InvocationTargetException
>                at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>                at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>                at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>                at java.lang.reflect.Method.invoke(Method.java:597)
>                at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:311)
>                ... 22 more
> Caused by: java.io.IOException: Bad magic number, should be 42.
>                at com.sun.media.jai.codecimpl.CodecUtils.toIOException(CodecUtils.java:76)
>                at com.sun.media.jai.codecimpl.TIFFImageDecoder.getNumPages(TIFFImageDecoder.java:98)
>                ... 27 more
> Caused by: java.lang.IllegalArgumentException: Bad magic number, should be 42.
>                at com.sun.media.jai.codec.TIFFDirectory.getNumDirectories(TIFFDirectory.java:601)
>                at com.sun.media.jai.codecimpl.TIFFImageDecoder.getNumPages(TIFFImageDecoder.java:96)
>                ... 27 more
> 
> 
> 
> 
> --
> Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
> Phone: +41 61 267 22 50 | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>
> 

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