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help > RE: Vaa3D within a workflow
Dec 18, 2014 10:12 PM | Hanchuan Peng
RE: Vaa3D within a workflow
For question 1.
Yes it is pretty easy to create a workflow both inside Vaa3D and using command line scripting to wrap up Vaa3D modules (plugins).
Inside Vaa3D, you can create a superplugin which will call other plugins using the do_func() calls (see the Vaa3D plugin interface for details) (then most information will be passed in-memory), or simply use system-calls (then most information will be passed at the file level).
Outside Vaa3D at the command line level, you can simply run Vaa3D using sth like "vaa3d -h" to see how many, and what are the currently available plugins, and how to run them. Then you pile up all necessary such command line calls. Then you have a nice workflow. This is how we run big batch jobs on cluster machines.
For question 2, you need to be specific about what sophisticated functions you want. Vaa3D has many many functions, but we still to know what is exactly you want.
For question 3, Vaa3D can be executed in both GUI mode or in command line mode. We use both extensively. In addition, you could also use MPI inside your own plugin. Some people do that and got a lot of success (e.g. boost the speed 10 times by using 10 cores at the same time).
-Hanchuan
Originally posted by Chris Snyder:
Yes it is pretty easy to create a workflow both inside Vaa3D and using command line scripting to wrap up Vaa3D modules (plugins).
Inside Vaa3D, you can create a superplugin which will call other plugins using the do_func() calls (see the Vaa3D plugin interface for details) (then most information will be passed in-memory), or simply use system-calls (then most information will be passed at the file level).
Outside Vaa3D at the command line level, you can simply run Vaa3D using sth like "vaa3d -h" to see how many, and what are the currently available plugins, and how to run them. Then you pile up all necessary such command line calls. Then you have a nice workflow. This is how we run big batch jobs on cluster machines.
For question 2, you need to be specific about what sophisticated functions you want. Vaa3D has many many functions, but we still to know what is exactly you want.
For question 3, Vaa3D can be executed in both GUI mode or in command line mode. We use both extensively. In addition, you could also use MPI inside your own plugin. Some people do that and got a lot of success (e.g. boost the speed 10 times by using 10 cores at the same time).
-Hanchuan
Originally posted by Chris Snyder:
Apologies if some questions have already been
answered. Please feel free to just answer the ones you feel have
not been answered.
1) I would like to segment c elegans neurons. I was planning on writing it in opencv (python or C++), but in terms of visualizing whether a given segmentation algorithm is actually working, I think your program is the best. Would it be easy to create a work flow from a python or C program into Vaa3D?
2) Do you think that Vaa3D has enough built in capability that a very sophisticated image processing algorithm could be built with minor tweaks on top of existing plugins?
3) What support does Vaa3D offer for parallelism? In C a simple openmp line or two will do. I would eventually like to run my program on a cluster through a command line. Is very much functionality of Vaa3D lost when moving from the graphical inter phase to the command line?
1) I would like to segment c elegans neurons. I was planning on writing it in opencv (python or C++), but in terms of visualizing whether a given segmentation algorithm is actually working, I think your program is the best. Would it be easy to create a work flow from a python or C program into Vaa3D?
2) Do you think that Vaa3D has enough built in capability that a very sophisticated image processing algorithm could be built with minor tweaks on top of existing plugins?
3) What support does Vaa3D offer for parallelism? In C a simple openmp line or two will do. I would eventually like to run my program on a cluster through a command line. Is very much functionality of Vaa3D lost when moving from the graphical inter phase to the command line?
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| Title | Author | Date |
|---|---|---|
| Chris Snyder | Dec 18, 2014 | |
| Hanchuan Peng | Dec 18, 2014 | |