[ome-users] GatanReader bug

[Jean-Marie Burel (Staff)]

Hi Martin
I forgot to mention in my previous e-mail.
Could you submit one of the files that currently failed to import?

Thanks
Jmarie

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Martin Jones <Martin.Jones at crick.ac.uk<mailto:Martin.Jones at crick.ac.uk>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Monday, 14 September 2015 14:42
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] GatanReader bug

Thanks, I've downloaded the latest versions of bioformats (via Fiji updater) and bftools.zip (from http://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/ today) but I'm still unable to open my .dm4 files.

Importing with Fiji results in a popup message that I don't think I got before saying "Sorry, there was a problem during import."

Here are the results of ./showinf:

G12-Laptop02:bftools jones58$ ./showinf ~/Desktop/Example_Gatan_File.dm4
Checking file format [Gatan Digital Micrograph]
Initializing reader
GatanReader initializing /Users/jones58/Desktop/Example_Gatan_File.dm4
Verifying Gatan format
Reading tags
Exception in thread "main" loci.formats.FormatException: Unable to parse metadata tag
at loci.formats.in.GatanReader.initFile(GatanReader.java:202)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1028)
at loci.formats.tools.ImageInfo.main(ImageInfo.java:1117)
Caused by: java.lang.NumberFormatException: For input string: "50"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.<init>(Double.java:608)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:487)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)
at loci.formats.in.GatanReader.initFile(GatanReader.java:200)
... 5 more


Any help or advice is much appreciated!

Cheers,
Martin


On 4 Sep 2015, at 11:17, Jean-Marie Burel (Staff) <j.burel at dundee.ac.uk<mailto:j.burel at dundee.ac.uk>> wrote:

Hi Martin

Thanks for reporting the issue. The problem has already been solved see https://github.com/openmicroscopy/bioformats/pull/1928

The fix will be included in the 5.1.4 version of Bio-Formats, version that we are planning to release early next week.

Cheers

Jmarie

The University of Dundee is a registered Scottish Charity, No: SC015096
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Dr. Martin Jones

Electron Microscopy STP
The Francis Crick Institute
Lincoln's Inn Fields Laboratory
44 Lincoln's Inn Fields
London WC2A 3LY

T: +44 (0)20 7269 3346 (Room 1B16)
E: Martin.Jones at crick.ac.uk<mailto:Martin.Jones at crick.ac.uk>
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The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.

The University of Dundee is a registered Scottish Charity, No: SC015096
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