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

[Dotan Kamber]

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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