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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Curtis,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Great, thank you – that is amazing (and my plugin now compiles)!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> Heinrich<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ctrueden.wisc@gmail.com [mailto:ctrueden.wisc@gmail.com]
<b>Im Auftrag von </b>Curtis Rueden<br>
<b>Gesendet:</b> Freitag, 7. März 2014 11:13<br>
<b>An:</b> Grabmayr, Heinrich<br>
<b>Cc:</b> ome-devel@lists.openmicroscopy.org.uk<br>
<b>Betreff:</b> Re: [ome-devel] loci-plugins vs bio-formats<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Heinrich,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">> I got confused with the introduction of bio-formats 5.0<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The new dependency for the Bio-Formats ImageJ plugins is:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> <dependency><o:p></o:p></p>
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<p class="MsoNormal"> <groupId>ome</groupId><o:p></o:p></p>
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<p class="MsoNormal"> <artifactId>bio-formats_plugins</artifactId><o:p></o:p></p>
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<p class="MsoNormal"> <version>5.0.0</version><o:p></o:p></p>
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<p class="MsoNormal"> </dependency><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">> Fiji reported issues about duplicate commands <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">That is not supposed to be the case. Is your Fiji fully up to date?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">> The bio-formats API tells me that the loci.plugins.util.LibraryChecker<o:p></o:p></p>
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<p class="MsoNormal">> exists, but not in which jar it is.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">> I figured that maybe a few classes may have been transferred from<o:p></o:p></p>
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<p class="MsoNormal">> loci_plugins to bio-formats, so the issue may be resolved by using<o:p></o:p></p>
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<p class="MsoNormal">> loci_plugins 5.0.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Actually, there is no longer an artifact called "loci_plugins" nor one called "bio-formats". And the groupId changed from loci to ome.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You can browse the full list of such artifacts for the 5.0.0 release at:<o:p></o:p></p>
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<p class="MsoNormal"><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><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">> I am afraid I missed a crucial starting point on how to know how to<o:p></o:p></p>
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<p class="MsoNormal">> find stuff.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">To find artifacts, you can search at:<o:p></o:p></p>
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<p class="MsoNormal"><a href="http://maven.imagej.net/">http://maven.imagej.net/</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Or, if you find the source repository on GitHub, you can look inside the pom.xml there.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">So to find the LibraryChecker, you can:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">* browse to the Bio-Formats source code:<o:p></o:p></p>
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<p class="MsoNormal"> <a href="https://github.com/openmicroscopy/bioformats">https://github.com/openmicroscopy/bioformats</a><o:p></o:p></p>
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<p class="MsoNormal">* switch to the 5.0.0 release tag:<o:p></o:p></p>
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<p class="MsoNormal"> <a href="https://github.com/openmicroscopy/bioformats/tree/v5.0.0">https://github.com/openmicroscopy/bioformats/tree/v5.0.0</a><o:p></o:p></p>
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<p class="MsoNormal">* press T to search for a file<o:p></o:p></p>
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<p class="MsoNormal">* type in LibraryChecker<o:p></o:p></p>
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<p class="MsoNormal">* press Enter to jump to that file<o:p></o:p></p>
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<p class="MsoNormal">* note that it is inside of "components/bio-formats-plugins"<o:p></o:p></p>
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<p class="MsoNormal">* click on the "bio-formats-plugins" part of the path<o:p></o:p></p>
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<p class="MsoNormal">* click on the pom.xml in that same directory<o:p></o:p></p>
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<p class="MsoNormal">* see that it has an artifactId of "bio-formats_plugins"<o:p></o:p></p>
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<p class="MsoNormal">* note that the groupId (inherited from the parent) is "ome"<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">HTH,<o:p></o:p></p>
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<p class="MsoNormal">Curtis<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, Mar 7, 2014 at 3:22 AM, Grabmayr, Heinrich <<a href="mailto:Heinrich.Grabmayr@ph.tum.de" target="_blank">Heinrich.Grabmayr@ph.tum.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi there,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">up to now, I had used loci-plugins4.4 as a dependency</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <dependency></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <groupId>loci</groupId></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <artifactId>loci_plugins</artifactId></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <version>4.4-SNAPSHOT</version></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </dependency></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <dependency></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <groupId>loci</groupId></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <artifactId>bio-formats</artifactId></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <version>5.0-SNAPSHOT</version></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </dependency></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">but compiling fails because then, the package loci.plugins does not exist.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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??</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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..</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Thanks</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> Heinrich</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt">Heinrich Grabmayr</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt">Technische Universität München</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt">E27 cellular biophysics</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:9.0pt">James-Franck-Str.1</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:9.0pt">85748 Garching</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:9.0pt">Tel:
<a href="tel:%2B49%2089%20289%2012487" target="_blank">+49 89 289 12487</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><o:p></o:p></p>
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