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

[Grabmayr, Heinrich]

Hi Curtis,

Great, thank you - that is amazing (and my plugin now compiles)!

Best
  Heinrich

Von: ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] Im Auftrag von Curtis Rueden
Gesendet: Freitag, 7. März 2014 11:13
An: Grabmayr, Heinrich
Cc: ome-devel at lists.openmicroscopy.org.uk
Betreff: Re: [ome-devel] loci-plugins vs bio-formats

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<mailto: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<tel:%2B49%2089%20289%2012487>


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