<div dir="ltr">Hi Heinrich,<div><br></div><div>> I got confused with the introduction of bio-formats 5.0<br></div><div><br></div><div>The new dependency for the Bio-Formats ImageJ plugins is:</div><div><br></div><div> <dependency></div>
<div> <groupId>ome</groupId></div><div> <artifactId>bio-formats_plugins</artifactId></div><div> <version>5.0.0</version></div><div> </dependency></div><div><br></div><div>
> Fiji reported issues about duplicate commands </div><div><br></div><div>That is not supposed to be the case. Is your Fiji fully up to date?</div><div><br></div><div><div>> The bio-formats API tells me that the loci.plugins.util.LibraryChecker</div>
<div>> exists, but not in which jar it is.</div></div><div><br></div><div>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.</div>
<div><br></div><div><div>> I figured that maybe a few classes may have been transferred from</div><div>> loci_plugins to bio-formats, so the issue may be resolved by using</div><div>> loci_plugins 5.0.</div></div>
<div><br></div><div>Actually, there is no longer an artifact called "loci_plugins" nor one called "bio-formats". And the groupId changed from loci to ome.</div><div><br></div><div>You can browse the full list of such artifacts for the 5.0.0 release at:</div>
<div><a href="http://maven.imagej.net/index.html#nexus-search;gav~ome~~5.0.0~~">http://maven.imagej.net/index.html#nexus-search;gav~ome~~5.0.0~~</a><br></div><div><br></div><div><div>> I am afraid I missed a crucial starting point on how to know how to</div>
<div>> find stuff.</div></div><div><br></div><div>To find artifacts, you can search at:</div><div><a href="http://maven.imagej.net/">http://maven.imagej.net/</a></div><div><div><br></div></div><div>Or, if you find the source repository on GitHub, you can look inside the pom.xml there.</div>
<div><br></div><div>So to find the LibraryChecker, you can:</div><div><br></div><div>* browse to the Bio-Formats source code:</div><div> <a href="https://github.com/openmicroscopy/bioformats">https://github.com/openmicroscopy/bioformats</a></div>
<div>* switch to the 5.0.0 release tag:</div><div> <a href="https://github.com/openmicroscopy/bioformats/tree/v5.0.0">https://github.com/openmicroscopy/bioformats/tree/v5.0.0</a><br></div><div>* press T to search for a file</div>
<div>* type in LibraryChecker</div><div>* press Enter to jump to that file</div><div>* note that it is inside of "components/bio-formats-plugins"</div><div>* click on the "bio-formats-plugins" part of the path</div>
<div>* click on the pom.xml in that same directory</div><div>* see that it has an artifactId of "bio-formats_plugins"</div><div>* note that the groupId (inherited from the parent) is "ome"</div><div><br>
</div><div>HTH,</div><div>Curtis</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Mar 7, 2014 at 3:22 AM, Grabmayr, Heinrich <span dir="ltr"><<a href="mailto:Heinrich.Grabmayr@ph.tum.de" target="_blank">Heinrich.Grabmayr@ph.tum.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Hi there,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-US">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.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">up to now, I had used loci-plugins4.4 as a dependency<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <dependency><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <groupId>loci</groupId><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <artifactId>loci_plugins</artifactId><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <version>4.4-SNAPSHOT</version><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> </dependency><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">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<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <dependency><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <groupId>loci</groupId><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <artifactId>bio-formats</artifactId><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> <version>5.0-SNAPSHOT</version><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> </dependency><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">but compiling fails because then, the package loci.plugins does not exist.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">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.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">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 <a href="http://maven.imagej.net/content/groups/public" target="_blank">
http://maven.imagej.net/content/groups/public</a>” (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??<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">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..<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> Heinrich<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">[1] <a href="http://maven.imagej.net:8081/index.html#nexus-search;quick~bio-formats" target="_blank">
http://maven.imagej.net:8081/index.html#nexus-search;quick~bio-formats</a><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">[2] <a href="http://downloads.openmicroscopy.org/bio-formats/5.0.0/#api" target="_blank">
http://downloads.openmicroscopy.org/bio-formats/5.0.0/#api</a><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">Heinrich Grabmayr<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">Technische Universität München<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">E27 cellular biophysics<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt">James-Franck-Str.1<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt">85748 Garching<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt">Tel: <a href="tel:%2B49%2089%20289%2012487" value="+498928912487" target="_blank">+49 89 289 12487</a></span><span lang="EN-US"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
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