<div dir="ltr"><div><div><div><div><div><div><div>Hi Dan,<br><br>>its not obvious for an elclipse noob like me. <br><br></div><div>No worries. I definitely found the instructions confusing as well (which is why for a long time I'd just build and copy the jars).<br></div><div><br>>what would a main class look like for running the coloc plugin straight from ellipse<br><br></div>Coloc 2 already has a dependency on fiji-lib, so you just need a class with two things:<br><br>1. import fiji.Debug;<br><br></div>2. a main method like this:<br> public static void main(String[] args) {<br> Debug.run(null, null);<br> } <br><br></div>You can just put that method in Coloc_2.java, for example, and run it in Eclipse. It should start up an ImageJ instance with Coloc_2 installed properly.<br><br>>i dont see any place where the coloc .jar is biult and saved? Where should the built .jar be located by default?<br><br></div>If you build it as a Maven project Eclipse should create the .jars[1]. Also all ImageJ/Fiji projects can be built from the command line[2] by using mvn. In either case the output jar is in the /target subdirectory, per Maven convention.<br><br></div>Let us know if you run into any more problems or if any of this is unclear!<br><br></div>Best,<br></div>Mark<br><div><div><div><br>[1] <a href="http://stackoverflow.com/questions/12993504/my-maven-java-project-in-eclipse-doesnt-generate-jar-file">http://stackoverflow.com/questions/12993504/my-maven-java-project-in-eclipse-doesnt-generate-jar-file</a><br>[2] <a href="http://imagej.net/Developing_ImageJ_on_the_command_line#Build_the_source">http://imagej.net/Developing_ImageJ_on_the_command_line#Build_the_source</a><br></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 9, 2015 at 3:40 AM, Daniel White <span dir="ltr"><<a href="mailto:dan@chalkie.org.uk" target="_blank">dan@chalkie.org.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Mark, Hi Tom<div>I seem to be having trouble getting the colocalization analysis plugins top build, this is in Eclipse mars. </div><div><br></div><div>I imported the maven project, and imageJ runs fine from eclipse, but i dont see any place where the coloc .jar is biult and saved? Where should the built .jar be located by default?</div><div><br></div><div>what would a main class look like for running the coloc plugin straight from ellipse, without having to copy a .jar into another fiji ?</div><div><br></div><div>maybe i am missing something at <a href="http://imagej.net/Developing_Fiji_in_Eclipse#Running_and_Debugging" style="font-size:12.8000001907349px" target="_blank">http://imagej.net/Developing_Fiji_in_Eclipse#Running_and_Debugging</a></div><div>its not obvious for an elclipse noob like me. </div><div><br></div><div>cheers</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>D</div><div><br></div><div><br></div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 25 June 2015 at 19:39, Mark Hiner <span dir="ltr"><<a href="mailto:hiner@wisc.edu" target="_blank">hiner@wisc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Daniel,<span><br><div><br></div><div>>The Fiji.sc docs describe how to do a plugin in the script editor, </div><div>>or how to develop imageJ itself in eclipse, </div><div>>but not how to get one of the external Fiji plugins, like coloc analysis, </div><div>>and then run Fiji with my hacked plugin code running from eclipse????</div><br></span></div>This process is described in the Developing Fiji in Eclipse tutorial[1] - which I just updated with a bit more information.<span><br><br>>i can run imageJ from there by highlighting the ij jar and doing run as java application<br><br></span></div>If you are running ij.jar from the Maven dependencies of Colocalisation_Analysis, then Eclipse is likely just literally executing the jar without anything else on the classpath. Using Debug.run will give you an ImageJ with your plugin loaded properly.<br><br></div>Also, if you don't want to make a temporary main method, you can always build the .jar for your plugin and put it into an existing Fiji installation.<br><div><div><br></div><div>Hope that helps.<br><br></div><div>Best,<br></div><div>Mark<br></div><div><br>[1] <a href="http://imagej.net/Developing_Fiji_in_Eclipse#Running_and_Debugging" target="_blank">http://imagej.net/Developing_Fiji_in_Eclipse#Running_and_Debugging</a><br><div><br></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Thu, Jun 25, 2015 at 7:32 AM, Daniel White <span dir="ltr"><<a href="mailto:dan@chalkie.org.uk" target="_blank">dan@chalkie.org.uk</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hi All,<div><br></div><div>I'm setting up my plugin dev environment (win7 x64), by reading the docs on the <a href="http://fiji.sc" target="_blank">fiji.sc</a> pages. </div><div>I got eclipse installed, new JDK installed and seen by eclipse, </div><div>Colocalization_Analysis plugin cloned from github using github for windows</div><div>I imported the plugin as described with the import maven project gadget in eclipse,</div><div>and it got the dependencies as jars apparently.</div><div><br></div><div>So i can run imageJ from there by highlighting the ij jar and doing run as java application, </div><div>but the coloc_2 plugin doesnt appear in the Analyze menu??????</div><div><br></div><div>The Fiji.sc docs describe how to do a plugin in the script editor, </div><div>or how to develop imageJ itself in eclipse, </div><div>but not how to get one of the external Fiji plugins, like coloc analysis, </div><div>and then run Fiji with my hacked plugin code running from eclipse????</div><div><br></div><div>Can I help fix the docs so noobs like me can get started easier, </div><div>and in the process get myself up and running with a little help from on of you folks please?</div><div><br></div><div>cheers</div><div><br></div><div>Dan White</div></div>
<br></div></div>_______________________________________________<br>
ImageJ-devel mailing list<br>
<a href="mailto:ImageJ-devel@imagej.net" target="_blank">ImageJ-devel@imagej.net</a><br>
<a href="http://imagej.net/mailman/listinfo/imagej-devel" rel="noreferrer" target="_blank">http://imagej.net/mailman/listinfo/imagej-devel</a><br>
<br></blockquote></div><br></div>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>