plugin dev in elcipse

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plugin dev in elcipse

Daniel White
Hi All,

I'm setting up my plugin dev environment (win7 x64), by reading the docs on the fiji.sc pages. 
I got eclipse installed, new JDK installed and seen by eclipse, 
Colocalization_Analysis plugin cloned from github using github for windows
I imported the plugin as described with the import maven project gadget in eclipse,
and it got the dependencies as jars apparently.

So i can run imageJ from there by highlighting the ij jar and doing run as java application, 
but the coloc_2 plugin doesnt appear in the Analyze menu??????

The Fiji.sc docs describe how to do a plugin in the script editor, 
or how to develop imageJ itself in eclipse, 
but not how to get one of the external Fiji plugins, like coloc analysis, 
and then run Fiji with my hacked plugin code running from eclipse????

Can I help fix the docs so noobs like me can get started easier, 
and in the process get myself up and running with a little help from on of you folks please?

cheers

Dan White

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Re: plugin dev in elcipse

Mark Hiner
Hi Daniel,

>The Fiji.sc docs describe how to do a plugin in the script editor, 
>or how to develop imageJ itself in eclipse, 
>but not how to get one of the external Fiji plugins, like coloc analysis, 
>and then run Fiji with my hacked plugin code running from eclipse????

This process is described in the Developing Fiji in Eclipse tutorial[1] - which I just updated with a bit more information.

>i can run imageJ from there by highlighting the ij jar and doing run as java application

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.

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.

On Thu, Jun 25, 2015 at 7:32 AM, Daniel White <[hidden email]> wrote:
Hi All,

I'm setting up my plugin dev environment (win7 x64), by reading the docs on the fiji.sc pages. 
I got eclipse installed, new JDK installed and seen by eclipse, 
Colocalization_Analysis plugin cloned from github using github for windows
I imported the plugin as described with the import maven project gadget in eclipse,
and it got the dependencies as jars apparently.

So i can run imageJ from there by highlighting the ij jar and doing run as java application, 
but the coloc_2 plugin doesnt appear in the Analyze menu??????

The Fiji.sc docs describe how to do a plugin in the script editor, 
or how to develop imageJ itself in eclipse, 
but not how to get one of the external Fiji plugins, like coloc analysis, 
and then run Fiji with my hacked plugin code running from eclipse????

Can I help fix the docs so noobs like me can get started easier, 
and in the process get myself up and running with a little help from on of you folks please?

cheers

Dan White

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ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel



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Re: plugin dev in elcipse

Daniel White
Hi Mark, Hi Tom
I seem to be having trouble getting the colocalization analysis plugins top build, this is in Eclipse mars. 

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?

what would a main class look like for running the coloc plugin straight from ellipse, without having to copy a .jar into another fiji ?

its not obvious for an elclipse noob like me. 

cheers

D



On 25 June 2015 at 19:39, Mark Hiner <[hidden email]> wrote:
Hi Daniel,

>The Fiji.sc docs describe how to do a plugin in the script editor, 
>or how to develop imageJ itself in eclipse, 
>but not how to get one of the external Fiji plugins, like coloc analysis, 
>and then run Fiji with my hacked plugin code running from eclipse????

This process is described in the Developing Fiji in Eclipse tutorial[1] - which I just updated with a bit more information.

>i can run imageJ from there by highlighting the ij jar and doing run as java application

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.

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.

On Thu, Jun 25, 2015 at 7:32 AM, Daniel White <[hidden email]> wrote:
Hi All,

I'm setting up my plugin dev environment (win7 x64), by reading the docs on the fiji.sc pages. 
I got eclipse installed, new JDK installed and seen by eclipse, 
Colocalization_Analysis plugin cloned from github using github for windows
I imported the plugin as described with the import maven project gadget in eclipse,
and it got the dependencies as jars apparently.

So i can run imageJ from there by highlighting the ij jar and doing run as java application, 
but the coloc_2 plugin doesnt appear in the Analyze menu??????

The Fiji.sc docs describe how to do a plugin in the script editor, 
or how to develop imageJ itself in eclipse, 
but not how to get one of the external Fiji plugins, like coloc analysis, 
and then run Fiji with my hacked plugin code running from eclipse????

Can I help fix the docs so noobs like me can get started easier, 
and in the process get myself up and running with a little help from on of you folks please?

cheers

Dan White

_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel




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Re: plugin dev in elcipse

Mark Hiner
Hi Dan,

>its not obvious for an elclipse noob like me.

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).

>what would a main class look like for running the coloc plugin straight from ellipse

Coloc 2 already has a dependency on fiji-lib, so you just need a class with two things:

1. import fiji.Debug;

2. a main method like this:
    public static void main(String[] args) {
        Debug.run(null, null);
    } 

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.

>i dont see any place where the coloc .jar is biult and saved? Where should the built .jar be located by default?

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.

Let us know if you run into any more problems or if any of this is unclear!

Best,
Mark

On Thu, Jul 9, 2015 at 3:40 AM, Daniel White <[hidden email]> wrote:
Hi Mark, Hi Tom
I seem to be having trouble getting the colocalization analysis plugins top build, this is in Eclipse mars. 

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?

what would a main class look like for running the coloc plugin straight from ellipse, without having to copy a .jar into another fiji ?

its not obvious for an elclipse noob like me. 

cheers

D



On 25 June 2015 at 19:39, Mark Hiner <[hidden email]> wrote:
Hi Daniel,

>The Fiji.sc docs describe how to do a plugin in the script editor, 
>or how to develop imageJ itself in eclipse, 
>but not how to get one of the external Fiji plugins, like coloc analysis, 
>and then run Fiji with my hacked plugin code running from eclipse????

This process is described in the Developing Fiji in Eclipse tutorial[1] - which I just updated with a bit more information.

>i can run imageJ from there by highlighting the ij jar and doing run as java application

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.

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.

On Thu, Jun 25, 2015 at 7:32 AM, Daniel White <[hidden email]> wrote:
Hi All,

I'm setting up my plugin dev environment (win7 x64), by reading the docs on the fiji.sc pages. 
I got eclipse installed, new JDK installed and seen by eclipse, 
Colocalization_Analysis plugin cloned from github using github for windows
I imported the plugin as described with the import maven project gadget in eclipse,
and it got the dependencies as jars apparently.

So i can run imageJ from there by highlighting the ij jar and doing run as java application, 
but the coloc_2 plugin doesnt appear in the Analyze menu??????

The Fiji.sc docs describe how to do a plugin in the script editor, 
or how to develop imageJ itself in eclipse, 
but not how to get one of the external Fiji plugins, like coloc analysis, 
and then run Fiji with my hacked plugin code running from eclipse????

Can I help fix the docs so noobs like me can get started easier, 
and in the process get myself up and running with a little help from on of you folks please?

cheers

Dan White

_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel





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Re: plugin dev in elcipse

Daniel White
Thanks Mark!

I found the jar!
Hiding in plain sight in the correct place.i just expected to see it also from eclipse.... But you don't. Noob error

I will try the main method way too to see if it's easier or more comfortable. 

I can also update the wiki so this makes sense to a clueless noob like myself. 

Cheers

D

On Thursday, July 9, 2015, Mark Hiner <[hidden email]> wrote:
Hi Dan,

>its not obvious for an elclipse noob like me.

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).

>what would a main class look like for running the coloc plugin straight from ellipse

Coloc 2 already has a dependency on fiji-lib, so you just need a class with two things:

1. import fiji.Debug;

2. a main method like this:
    public static void main(String[] args) {
        Debug.run(null, null);
    } 

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.

>i dont see any place where the coloc .jar is biult and saved? Where should the built .jar be located by default?

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.

Let us know if you run into any more problems or if any of this is unclear!

Best,
Mark

On Thu, Jul 9, 2015 at 3:40 AM, Daniel White <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;dan@chalkie.org.uk&#39;);" target="_blank">dan@...> wrote:
Hi Mark, Hi Tom
I seem to be having trouble getting the colocalization analysis plugins top build, this is in Eclipse mars. 

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?

what would a main class look like for running the coloc plugin straight from ellipse, without having to copy a .jar into another fiji ?

its not obvious for an elclipse noob like me. 

cheers

D



On 25 June 2015 at 19:39, Mark Hiner <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;hiner@wisc.edu&#39;);" target="_blank">hiner@...> wrote:
Hi Daniel,

>The Fiji.sc docs describe how to do a plugin in the script editor, 
>or how to develop imageJ itself in eclipse, 
>but not how to get one of the external Fiji plugins, like coloc analysis, 
>and then run Fiji with my hacked plugin code running from eclipse????

This process is described in the Developing Fiji in Eclipse tutorial[1] - which I just updated with a bit more information.

>i can run imageJ from there by highlighting the ij jar and doing run as java application

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.

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.

On Thu, Jun 25, 2015 at 7:32 AM, Daniel White <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;dan@chalkie.org.uk&#39;);" target="_blank">dan@...> wrote:
Hi All,

I'm setting up my plugin dev environment (win7 x64), by reading the docs on the fiji.sc pages. 
I got eclipse installed, new JDK installed and seen by eclipse, 
Colocalization_Analysis plugin cloned from github using github for windows
I imported the plugin as described with the import maven project gadget in eclipse,
and it got the dependencies as jars apparently.

So i can run imageJ from there by highlighting the ij jar and doing run as java application, 
but the coloc_2 plugin doesnt appear in the Analyze menu??????

The Fiji.sc docs describe how to do a plugin in the script editor, 
or how to develop imageJ itself in eclipse, 
but not how to get one of the external Fiji plugins, like coloc analysis, 
and then run Fiji with my hacked plugin code running from eclipse????

Can I help fix the docs so noobs like me can get started easier, 
and in the process get myself up and running with a little help from on of you folks please?

cheers

Dan White

_______________________________________________
ImageJ-devel mailing list
<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;ImageJ-devel@imagej.net&#39;);" target="_blank">ImageJ-devel@...
http://imagej.net/mailman/listinfo/imagej-devel





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