Can I use plastimatch within python?

[lfra...@ucsc.edu]

...

[Paolo Zaffino]

Hi,
it is possible to execute registrations by using Plastimatch engine via the Python shell embedded in 3D Slicer.
You have to install the SlicerRT module (it's really easy, just to click "install" into the Slicer Extension Manager).
After that, assuming that you had successfully installed SlicerRT and that you loaded two images called "fixed_img.mha" and "mov_img.mha", you can try to execute this piece of code:

import vtkSlicerPlastimatchPyModuleLogicPython

reg=vtkSlicerPlastimatchPyModuleLogicPython.vtkPlmpyRegistration()

reg.SetMRMLScene(slicer.mrmlScene)

moving="mov_img"

fixed="fixed_img"

reg.SetFixedImageID(getNode(fixed).GetID())

reg.SetMovingImageID(getNode(moving).GetID())

output=slicer.vtkMRMLScalarVolumeNode()

slicer.mrmlScene.AddNode(output)

displayNode=slicer.vtkMRMLScalarVolumeDisplayNode()

slicer.mrmlScene.AddNode(displayNode)

reg.SetOutputVolumeID(output.GetID())

par="[STAGE]\nxform=bspline\noptim=lbfgsb\nimpl=plastimatch\nmetric=mse\nmax_its=100\nconvergence_tol=5\ngrad_tol=1.5\nres=22 1\ngrid_spac=40 40 40"

reg.SetRegistrationParameters(par)

reg.RunRegistration()

Obviously you must redefine the "par" string...it's just an example!
If Slicer freezes don't worry, it's busy to execute Plastimatch registration.

HTH.
Best.
Paolo


On 29/10/2015 21:24, lfra...@ucsc.edu wrote:

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[Sharp, Gregory C.]

Paolo, is this possible outside of 3D Slicer?

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[Paolo Zaffino]

Yes, it is possible.
Some time ago I wrote a very basic wrapper that offers the possibility to execute Plastimatch from Python.
The code is stored into the folder extra/python/pypla (http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=browse&path=%2Fplastimatch%2Ftrunk%2Fextra%2Fpython%2Fpypla%2F).
The main file is "plastimatch.py" that must be copied into a folder belonging to the python path.
In "pypla_test.py" there are some examples.

Note that in this case Plastimatch is not invoked as a library but only "hiddenly" executed as a shell command.

If some problem raises (also due to a changed way to call an executable) I am here to help to fix it.

Best.
Paolo