[OpenSPIM] Fwd: OpenSPIM Digest, Vol 23, Issue 2

[G.D. Marquart]

---------- Forwarded message ----------
From: "G.D. Marquart" <gmarquart at gmail.com>
To: rk685 at york.ac.uk,
Cc:
Date: Tue, 3 Mar 2015 13:37:09 -0500
Subject: Re: OpenSPIM Digest, Vol 23, Issue 2
Hey Rob,

Someone more knowledgeable feel free to correct me, but...

I believe the SPIMAcq won't work with any laser but those specifically
defined in the code (or with variables identical to those in
src/main/java/spim/setup/Laser.java).  So in order to get your laser
working in the plugin, I believe you'll have to download the source
for the SPIMAcq
plugin <https://github.com/openspim/SPIMAcquisition>, make a java profile
similar to this
<https://github.com/openspim/SPIMAcquisition/blob/master/src/main/java/spim/setup/Cobolt.java>
for your OBIS using variable names you can find here
<https://github.com/hadim/micromanager/blob/96f12e31227b2173b98093036c735a6f42b5516e/DeviceAdapters/CoherentOBIS/CoherentOBIS.cpp>,
place that new file in the appropriate folder (src/main/java/setup/) and
then compile it yourself (using maven).  Because it's still a Coherent
laser and they appear to use the same variable names to address the laser,
I think you can just copy the CoherentCube.java file, rename where you see
CoherentCube to OBIS, and rename the file to OBIS.java.

To compile, you'll need Maven which you can get here
<http://maven.apache.org/download.cgi> (need to setup a number of user
variables to get it to run, see installation instructions).  once maven is
installed, copy the SPIMAcq source from the git repository into
Fiji.app/plugins/Micro-Manager and run the following commands (in cmd.exe)
from that directory to compile.

mvn install:install-file -DgroupId=org.micromanager
-Dversion=1.4.20-SNAPSHOT -Dpackaging=jar -DartifactId=MMJ_ -Dfile=MMJ_.jar

mvn install:install-file -DgroupId=org.micromanager
-Dversion=1.4.20-SNAPSHOT -Dpackaging=jar -DartifactId=MMCoreJ
-Dfile=MMCoreJ.jar

mvn -Dscijava.enforce.skip


This should create a SPIMAcq that now supports your laser that you can copy
into the appropriate folder in Fiji.


Hope this helps,


Graham

On Tue, Mar 3, 2015 at 1:00 PM, openspim-request at openspim.org <
openspim-request at openspim.org> wrote:

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> Today's Topics:
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>    1. OpenSPIM plugin does not allow to control laser
>       (Robert Konstandelos)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Mar 2015 13:52:48 +0000
> From: Robert Konstandelos <rk685 at york.ac.uk>
> To: openspim at openspim.org
> Subject: [OpenSPIM] OpenSPIM plugin does not allow to control laser
> Message-ID:
>         <
> CALKrRTGuUBTOvhVfbNS8QP9pEfB2pMUnJYb5dn2gVkZOsiRmdQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> I am having an issue with the OpenSPIM plugin as it does not allow me to
> control my coherent obis laser through this application. The app constantly
> says my power is zero and whenever I try to change the setting it returns
> to zero even when it is on!
>
> I am just wondering whether there is a way that this can be fixed. I have
> the correct settings specified on the micromanager page for the coherent
> obis so I am wondering whether there maybe something I have missed.
>
> Any help would be much appreciated.
>
> Thanks
>
> Rob
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