Simulation outputs

andrea_h

Hello everyone!

I'm currently running an electrical simulation using Sim4Life. So far, I've been using the analysis options provided by S4L, but I'm curious if there's a way to directly access and manipulate the output.

The electric field generated is of type <class 's4l_v1._api.analysiswrappers.AlgorithmOutput'>. According to the API, this represents "the output port of an algorithm, which is passed to the input connection of another algorithm. This class is the intermediate object used in a connection between two algorithms."

Is there a way to access the field matrix without exporting it to MATLAB?

Thanks in advance for your help!

Sylvain

You can directly access the data of any algorithm. Here is an example to get you started:

import numpy as np

simulation = document.AllSimulations[0]
simulation_extractor = simulation.Results()

em_sensor_extractor = simulation_extractor["Overall Field"]

efield_sensor = em_sensor_extractor['EM E(x,y,z,f0)']
efield_sensor.Update()   # THIS IS NECESSARY, otherwise the algorithm output will not contain any data and there will be an allocation error when trying to access it...

field_data= efield_sensor.Data

grid = field_data.Grid
print(grid.XAxis) # for example...

e_field = field_data.Field(0)   # 0 is the first "snapshot", typically this is the recorded frequency

print(e_field.shape)  # should be the dimensions of the numpy array

num_components = e_field.shape[1]  # 3 for vectors

nx, ny, nz = grid.XAxis.size, grid.YAxis.size, grid.ZAxis.size
    
if field_data.ValueLocation == s4l.analysis.core.eValueLocation.kCellCenter:
        nx, ny, nz = nx - 1, ny - 1, nz - 1

 e_field_reshaped= np.reshape(e_field, (nz, ny, nx, -1))

andrea_h

This post is deleted!

andrea_h

@Sylvain Hello!
Thank you so much!
So as far as I understand the coordinates are located on the grid. Which I guess depends on the meshes for the simulation.

On the other hand, the e_field is store in .Field(0) which holds a vector for each point.

And the reshape np.reshape(e_field, (nz, ny, nx, -1)). Its because the first coordinate with respect to the e_field is in the z axis?

bryn

it is because the data is ordered using x-fastest indexing. This means (for a scalar field)

if you increase the index by 1, you move one position in x direction (unless you are at the boundary).
if you move by nx, you move by one position in y direction (the stride is nx)
if you move by nx * nz, you move by one position in z direction (the stride is nx * ny)

andrea_h

Great! Goit it, thank you so much.
One last question regarding where the simulation outputs are located and saved. The coordinates of the voxelized entities where can be found?

Thank you so much for your time

ZMT zurich med tech

Simulation outputs