help > On scripting for V3D
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Oct 21, 2010  02:10 PM | Xinghua Lou
On scripting for V3D
Dear Dr. Peng,

My name is Xinghua Lou and I am using your wonderful V3D for visualizing my work. By far V3D works perfectly for visualizing a single volume of my data but I am having problems when dealing with a series of volumetric data. In particular, I wish to load and visualize the volumes in my 3D+T data subsequently and meanwhile rotate the view. The basic functionality of V3D is in fact sufficient for such task but it will be great if I can somehow script to control this animated process.

I wonder if it is possible to do scripting in your current V3D or if it is possible to control the data and the view via the plugin system.

Thanks a lot for your attention and consideration. I am looking forward to hearing from you.

Best regards,
Xinghua Lou.
Oct 21, 2010  04:10 PM | Hanchuan Peng
RE: On scripting for V3D
xinghua,

thanks for the interest.

Your question may be addressed in a few different ways.

(1) If you just want to batch processing the images and take advantage of the 3d viewer, it is very easy to write a plugin that use the new V3D "push" technique that can continuous feed data to 3d viewers (both glocal and/or local 3d viewers) and the tri-view window. There is a plugin demo program for that. If you don't know how to start, we can also show you how to do that.

In this way, you can indeed have almost full control of the V3D system, w/o even touching its main codebase.

(2) We are still working on a command-line based scripting method to let V3D be able to accept image(s) and do the processing. There was an issue with the event control of the Qt-based system for that, but we do plan to do that soon.

best,
-hanchuan

Originally posted by Xinghua Lou:
Dear Dr. Peng,

My name is Xinghua Lou and I am using your wonderful V3D for visualizing my work. By far V3D works perfectly for visualizing a single volume of my data but I am having problems when dealing with a series of volumetric data. In particular, I wish to load and visualize the volumes in my 3D+T data subsequently and meanwhile rotate the view. The basic functionality of V3D is in fact sufficient for such task but it will be great if I can somehow script to control this animated process.

I wonder if it is possible to do scripting in your current V3D or if it is possible to control the data and the view via the plugin system.

Thanks a lot for your attention and consideration. I am looking forward to hearing from you.

Best regards,
Xinghua Lou. [/userquote]
Nov 18, 2010  10:11 PM | Hanchuan Peng
RE: On scripting for V3D

as of now (v2.540) V3D accepts command line file (even web address) to open files (image, surface objects, neurons, point cloud, linker files, atlas files, etc)!

Try it and let us know any problems.

V3D website: http://penglab.janelia.org/proj/v3d/



Originally posted by Hanchuan Peng:
xinghua,

thanks for the interest.

Your question may be addressed in a few different ways.

(1) If you just want to batch processing the images and take advantage of the 3d viewer, it is very easy to write a plugin that use the new V3D "push" technique that can continuous feed data to 3d viewers (both glocal and/or local 3d viewers) and the tri-view window. There is a plugin demo program for that. If you don't know how to start, we can also show you how to do that.

In this way, you can indeed have almost full control of the V3D system, w/o even touching its main codebase.

(2) We are still working on a command-line based scripting method to let V3D be able to accept image(s) and do the processing. There was an issue with the event control of the Qt-based system for that, but we do plan to do that soon.

best,
-hanchuan

Originally posted by Xinghua Lou:
Dear Dr. Peng,

My name is Xinghua Lou and I am using your wonderful V3D for visualizing my work. By far V3D works perfectly for visualizing a single volume of my data but I am having problems when dealing with a series of volumetric data. In particular, I wish to load and visualize the volumes in my 3D+T data subsequently and meanwhile rotate the view. The basic functionality of V3D is in fact sufficient for such task but it will be great if I can somehow script to control this animated process.

I wonder if it is possible to do scripting in your current V3D or if it is possible to control the data and the view via the plugin system.

Thanks a lot for your attention and consideration. I am looking forward to hearing from you.

Best regards,
Xinghua Lou. [/userquote][/userquote]
Nov 19, 2010  12:11 PM | Hanchuan Peng
RE: On scripting for V3D
As of 2010-10-19, this function has been re-tested on all different file types ( http://penglab.janelia.org/proj/v3d/V3D/... ) on MacBook Pro OS 10.5.8 32bit successfully.

As of 2010-10-18, the function was tested successfully on another Mac Pro workstation.

As of 2010-10-18, Yang reported opening the http://penglab.janelia.org/proj/v3d/L1DS... on Windows 7 workstation failed. Need to probe the cause.


V3D website: http://penglab.janelia.org/proj/v3d