[ome-devel] Loci.formats missing

[Curtis Rueden]

Hi Romain,

The loci.formats.BF class is part of bio-formats_plugins:

  $ jar tf $FIJI_HOME/plugins/bio-formats_plugins-5.8.2.jar|grep BF
  loci/plugins/BF.class
  loci/plugins/util/BFVirtualStack.class

Do not use bioformats_package.jar with Fiji; doing so will create problems
with your classpath. See https://imagej.net/Uber-JAR.

How is your IntelliJ project set up? Are you using Maven or Gradle? If so,
which dependencies do you have declared? Have you read this guide:
https://imagej.net/IDEA ?

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, May 11, 2018 at 11:01 AM, Laine, Romain <r.laine at ucl.ac.uk> wrote:

> Hi David,
>
> Yes, using bioformats_package.jar file from the download link works fine !
>
> Many thanks. I am just not sure why the default bio-formats_plugins.jar in
> Fiji does not contain all the components.
>
>
>
> Thanks again !
>
>
>
> Romain
>
>
>
>
>
>
>
> *From: *ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk> on
> behalf of "David Gault (Staff)" <d.gault at dundee.ac.uk>
> *Reply-To: *OME External Developer List <ome-devel at lists.
> openmicroscopy.org.uk>
> *Date: *Friday, 11 May 2018 at 16:41
> *To: *OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
> *Subject: *Re: [ome-devel] Loci.formats missing
>
>
>
> Hi Romain,
>
>
>
> The simplest approach is likely to use the Bio-Formats package from
> https://www.openmicroscopy.org/bio-formats/downloads/ which contains all
> of the components and necessary dependencies to read images in ImageJ.
>
>
>
> Alternatively below you can find a list of the individual components (you
> will likely need the listed core components) along with a Maven example of
> how to add the components to your project:
>
> https://docs.openmicroscopy.org/bio-formats/5.8.2/
> developers/components.html
>
> https://github.com/ome/bio-formats-examples/blob/master/pom.xml
>
>
>
> With thanks,
>
> David Gault
>
>
>
> On 11 May 2018, at 15:58, Laine, Romain <r.laine at ucl.ac.uk> wrote:
>
>
>
> Dear list,
>
> I am developing an ImageJ java plugin using bio-format to load .sdt files
> using IntelliJ IDEA.
>
> I am trying to use the openImagePlus method as described in the
> Simple_Read.java example.
>
> However the loci.formats package seems to be missing from the
> bio-formats_plugins and therefore cannot be imported, so I cannot handle
> exceptions from openImagePlus.
>
> I am using the latest build bio-formats_plugins-5.9.0-
> 20180430.142015-2.jar
>
>
>
> Has anyone encountered/solved that problem?
>
>
>
> Many thanks !
>
>
>
> Romain
>
>
>
>
>
> ____________________________________
>
> *Dr Romain F. Laine*, PhD in Biophotonics
>
> PDRA at the Quantitative Imaging and Nanobiophysics group
>
> MRC Laboratory of Molecular Cell Biology (LMCB)
>
> University College London
>
> Gower Street, London, WC1E 6BT
>
> http://www.ucl.ac.uk/lmcb/users/romain-laine
>
>
>
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