How to get geometry from existing mesh

Question

Hi,

I have read a mesh file (opencarp format) using

meshname = "myMeshPath"

But when I want to define an electrode for a stimulation, the code was something like

electrode = mesh.block_region(geom,'stimulus', 0, E1_lower_bound, E1_upper_bound, False)

geom should be the geometry of the mesh, but how could I get the geometry from the mesh model I just read?

Thanks

Answer 1

The method you are using only works on block meshes. Details are given in the documentation: 

https://opencarp.org/doxygen-carputils/master/namespacecarputils_1_1mesh_1_1block.html#a1bafbdc8549aba16a40c0f0184fc458e 

https://opencarp.org/documentation/carputils-documentation#master/classcarputils_1_1mesh_1_1block_1_1Block.html

For more complex methods, the stimulus class provides more flexibility:

https://opencarp.org/documentation/carputils-documentation#master/classcarputils_1_1model_1_1stimulus_1_1Stimulus.html

Comments

If possible, could you provide an example on how to use it?

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Manual stimuli are for example set in the reentry induction example:
https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/02_EP_tissue/21_reentry_induction/run.py

With the code defining the stimuli being here:
https://git.opencarp.org/openCARP/carputils/-/blob/master/carputils/model/induceReentry.py#L602

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But in the reentry induction example, isn't the sinus node still defined by this block_boundary_condition function that only works with block meshes? How could I set the electrode or the sinus node on non-block meshes?

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Yes, it is.
You can set almost arbitrary stimuli by directly using openCARP's Stim parameter group as done on the part of the reentry example referred to above:
https://git.opencarp.org/openCARP/carputils/-/blob/master/carputils/model/induceReentry.py#L602

Stim is described in Section 23.3 of the openCARP manual:
https://opencarp.org/documentation/user-manual

PS: Our terms of service require the use of your full name on all openCARP infrastructure (Q&A, GitLab...)

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I tied to use the Stim parameter group parameters yet I still received the error L5 : error: Empty stimulus[0] electrode def! Aborting!

stim = ['-num_stim', 1,
            '-stimulus[0].stimtype', 0,
            '-stimulus[0].strength', 120.0,
            '-stimulus[0].duration', 2.0,
            '-stimulus[0].start', 0,
            '-stimulus[0].x0', 2100,
            '-stimulus[0].xd', 32000,
            '-stimulus[0].y0', 2100,
            '-stimulus[0].yd', 310,
            '-stimulus[0].z0', 2100,
            '-stimulus[0].zd', 4200,
            '-stimulus[0].npls', 1,
            '-stimulus[0].ctr_def',1,
            '-stim[0].elec.dump_vtx_file',0,
            '-stim[0].elec.geom_type',5,
            '-stim[0].elec.geomID', 0,
            '-stim[0].elec.p0[0]', 1,
            '-stim[0].elec.p0[1]', 1,
            '-stim[0].elec.p0[2]', 1,
            '-floating_ground', 1]

Would you mind letting me know where this error message was defined so I could check what exactly is wrong with it? Or perhaps if you have any suggestions on how to fix such problem?

I saw on another q&a posts that this error message could have something to do with ExtraTags and IntraTags, but not sure how it was relevant, could you help me clear that up? Thanks