[ome-users] Can't open ND file of interupted sequance.

[Melissa Linkert]

Hi Dotan,

> Tested now with version 5.1.2 and the result is the same.
> Archive PexSeriesFtotal1_w2Brightfield_s2.zip was uploaded and contains ND and corresponding partial results.

Thank you for uploading the full dataset.  We have confirmed the error,
and are currently testing a fix:

https://github.com/openmicroscopy/bioformats/pull/1868

I would expect this fix to be included in the upcoming 5.1.3 release of
Bio-Formats.  In the meantime, you may be able to work around the problem by
deleting PexSeriesFtotal1_w1confmCherry_s5.tif, as this file does not
contain any image data.

Regards,
-Melissa

On Sun, Jul 05, 2015 at 07:05:46PM +0000, Dotan Kamber wrote:
> Hi Sebastian,
> 
> Thanks for the prompt reply.
> Tested now with version 5.1.2 and the result is the same.
> Archive PexSeriesFtotal1_w2Brightfield_s2.zip was uploaded and contains ND and corresponding partial results.
> 
> Best regards,
> Dotan
> 
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Sebastien Besson (Staff)
> Sent: Sunday, July 05, 2015 9:50 PM
> To: ome-users at lists.openmicroscopy.org.uk OME-users
> Subject: Re: [ome-users] Can't open ND file of interupted sequance.
> 
> Hi Dotan,
> 
> thank you very much for reporting your issue.
> 
> Could you please let us know which version of Bio-Formats you have
> installed?  "Help > About Plugins > Bio-Formats Plugins" (or
> "Help > About Plugins > LOCI Plugins” for old versions) should show the
> version number and date.
> 
> If you are using an older version than the latest release (5.1.2), could you
> try upgrading to the latest release and see if this solves the issue.
> If you are seeing this behavior with 5.1.2, it would be very helpful if you could
> send the dataset in question by uploading to:
> http://qa.openmicroscopy.org.uk/qa/upload.
> 
> Best regards,
> Sebastien
> 
> On 5 Jul 2015, at 09:24, Dotan Kamber <Dotan.Kamber at eb1.co.il<mailto:Dotan.Kamber at eb1.co.il>> wrote:
> 
> Dears,
> 
> When trying to open multi-position ND file where the experiment did not finish (not all positions were acquired) the file cannot be opened.
> 
> The error received -
> java.lang.ArithmeticException: / by zero
>                 at loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:883)
>                 at loci.formats.FormatReader.setId(FormatReader.java:1317)
>                 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)
> 
> The ND file can be opened if it is edited in a way that none-aquired positions are removed from the position list.
> 
> Example of ND file –
> "NDInfoFile", Version 1.0
> "Description", File recreated from images.
> "StartTime1", 20150527 14:39:03.085
> "DoTimelapse", FALSE
> "DoStage", TRUE
> "NStagePositions", 27
> "Stage1", "row:D,column:19,site:1"
> "Stage2", "row:D,column:19,site:2"
> "Stage3", "row:D,column:19,site:3"
> "Stage4", "row:D,column:20,site:1"
> "Stage5", "row:D,column:20,site:2"
> "Stage6", "row:D,column:20,site:3"
> "Stage7", "row:D,column:21,site:1"
> "Stage8", "row:D,column:21,site:2"
> "Stage9", "row:D,column:21,site:3"
> "Stage10", "row:E,column:21,site:1"
> "Stage11", "row:E,column:21,site:2"
> "Stage12", "row:E,column:21,site:3"
> "Stage13", "row:E,column:20,site:1"
> "Stage14", "row:E,column:20,site:2"
> "Stage15", "row:E,column:20,site:3"
> "Stage16", "row:E,column:19,site:1"
> "Stage17", "row:E,column:19,site:2"
> "Stage18", "row:E,column:19,site:3"
> "Stage19", "row:F,column:19,site:1"
> "Stage20", "row:F,column:19,site:2"
> "Stage21", "row:F,column:19,site:3"
> "Stage22", "row:F,column:20,site:1"
> "Stage23", "row:F,column:20,site:2"
> "Stage24", "row:F,column:20,site:3"
> "Stage25", "row:F,column:21,site:1"
> "Stage26", "row:F,column:21,site:2"
> "Stage27", "row:F,column:21,site:3"
> "DoWave", TRUE
> "NWavelengths", 2
> "WaveName1", "confmCherry"
> "WaveName2", "Brightfield"
> "DoZSeries", FALSE
> "WaveInFileName", TRUE
> "EndFile"
> 
> Best,
> 
> Dotan
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