[ome-devel] loci-plugins vs bio-formats

[Curtis Rueden]

Hi Heinrich,

> I got confused with the introduction of bio-formats 5.0

The new dependency for the Bio-Formats ImageJ plugins is:

  <dependency>
    <groupId>ome</groupId>
    <artifactId>bio-formats_plugins</artifactId>
    <version>5.0.0</version>
  </dependency>

> Fiji reported issues about duplicate commands

That is not supposed to be the case. Is your Fiji fully up to date?

> The bio-formats API tells me that the loci.plugins.util.LibraryChecker
> exists, but not in which jar it is.

In Fiji, press L and type "Find Jar for Class", then type
"loci.plugins.util.LibraryChecker" as the argument. It will tell you that
the class lives in bio-formats_plugins-5.0.0.jar now.

> I figured that maybe a few classes may have been transferred from
> loci_plugins to bio-formats, so the issue may be resolved by using
> loci_plugins 5.0.

Actually, there is no longer an artifact called "loci_plugins" nor one
called "bio-formats". And the groupId changed from loci to ome.

You can browse the full list of such artifacts for the 5.0.0 release at:
http://maven.imagej.net/index.html#nexus-search;gav~ome~~5.0.0~~

> I am afraid I missed a crucial starting point on how to know how to
> find stuff.

To find artifacts, you can search at:
http://maven.imagej.net/

Or, if you find the source repository on GitHub, you can look inside the
pom.xml there.

So to find the LibraryChecker, you can:

* browse to the Bio-Formats source code:
     https://github.com/openmicroscopy/bioformats
* switch to the 5.0.0 release tag:
     https://github.com/openmicroscopy/bioformats/tree/v5.0.0
* press T to search for a file
* type in LibraryChecker
* press Enter to jump to that file
* note that it is inside of "components/bio-formats-plugins"
* click on the "bio-formats-plugins" part of the path
* click on the pom.xml in that same directory
* see that it has an artifactId of "bio-formats_plugins"
* note that the groupId (inherited from the parent) is "ome"

HTH,
Curtis


On Fri, Mar 7, 2014 at 3:22 AM, Grabmayr, Heinrich <
Heinrich.Grabmayr at ph.tum.de> wrote:

>  Hi there,
>
>
>
> I have written a few ImageJ plugins that use bio-formats. They used to
> work until I got confused with the introduction of bio-formats 5.0, so I
> would be grateful for help on that.
>
>
>
> up to now, I had used loci-plugins4.4 as a dependency
>
>                                <dependency>
>
>                                                <groupId>loci</groupId>
>
>
> <artifactId>loci_plugins</artifactId>
>
>
> <version>4.4-SNAPSHOT</version>
>
>                                </dependency>
>
>
>
> after updating Fiji to include new bio-formats jars (as suggested by
> Curtis in "Re: [ome-users] Bioformats gone!"), Fiji reported issues about
> duplicate commands which led me to believe that loci_plugins.jar has been
> replaced by bio-formats.jar (the imagej-maven index [1] tells me that there
> is such a jar), so I replaced the dependency to
>
>                                <dependency>
>
>                                                <groupId>loci</groupId>
>
>
> <artifactId>bio-formats</artifactId>
>
>
> <version>5.0-SNAPSHOT</version>
>
>                                </dependency>
>
>
>
> but compiling fails because then, the package loci.plugins does not exist.
>
>
>
> I checked on the bio-formats download website [2], and found various jars,
> but neither loci_plugins, nor bio-formats. The bio-formats API tells me
> that the loci.plugins.util.LibraryChecker exists, but not in which jar it
> is.
>
>
>
> Then I figured that maybe a few classes may have been transferred from
> loci_plugins to bio-formats, so the issue may be resolved by using
> loci_plugins 5.0. With this dependency, however, my plugin does not
> compile, telling me "Failure to find imagej:ij:jar:1.43u in
> http://maven.imagej.net/content/groups/public" (I am using the latest
> imagej version ${imagej1.version} as a dependency). This error reproducibly
> happens with loci_plugins 5.0 and not with 4.4. That totally confuses me
> because whether or not maven can find an imagej version should not depend
> on the version of loci_plugins, should it??
>
>
>
> Can anyone help me with this specific issue? And more generally, I am
> afraid I missed a crucial starting point on how to know how to find stuff.
> Usually, I google for the API and then get clues by the package names..
>
>
>
> Thanks
>
>     Heinrich
>
>
>
> [1] http://maven.imagej.net:8081/index.html#nexus-search;quick~bio-formats
>
> [2] http://downloads.openmicroscopy.org/bio-formats/5.0.0/#api
>
>
>
>
>
> Heinrich Grabmayr
>
>
>
> Technische Universität München
>
> E27 cellular biophysics
>
> James-Franck-Str.1
>
> 85748 Garching
>
> Tel: +49 89 289 12487
>
>
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
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