Avoid solid

[mkn]

Hi,

I am modeling some neural pathways and portions of it go along the muscle layer in the human body model. Is it possible to avoid solid intersection?

I came across something like this in the IMSafe toolbox:

So I'm wondering if it is possible to do this using Python.

Thanks!

[bryn]

The algorithm/evaluator is called:

s4l_v1.analysis.em_evaluators.ImplantSafety

[bryn]

Here is a script I found. Not sure it still runs, but I guess it should help you get started:

import tempfile
import os

import s4l_v1.model as model
from s4l_v1.model import Vec3, Unit

import s4l_v1.simulation as simulators
import s4l_v1.simulation.emfdtd as emfdtd

# Preamble ---------------
import s4l_v1.document as doc

sim = doc.AllSimulations[0]

# assumptions
sphere = model.AllEntities()["Sphere 1"]
assert sphere
assert isinstance(sim, emfdtd.Simulation)

sim_xtor = sim.Results()  # pin this variable, otherwise wrapped members are deleted
efield_port = sim_xtor["Overall Field"]["EM E(x,y,z,f0)"]
hfield_port = sim_xtor["Overall Field"]["EM H(x,y,z,f0)"]

# Demo ---------------------------------------------------
from s4l_v1.analysis.em_evaluators import ImplantSafety
from s4l_v1.analysis import RegisterAlgorithm


# Creates ImSafe algorithm
imsafe = ImplantSafety() # 0. create algorithm and connect to e-field port
imsafe.SetInputConnection(0, hfield_port)

# Disks options
base_line = model.CreateSpline([Vec3(52.0, 0.0, 0.0), Vec3(0, 32, 0), Vec3(-9, 70, 0)])
imsafe.SetBaseLine(base_line)  # 1. define baseline
total_len = imsafe.EvalBaseLineLength()

imsafe.ModelUnits = Unit.MilliMeter
imsafe.SetDisks(
    position=[0, 0.1, 1], radii=[10.0] * 3
)  # 2. define disks along baseline
centers, normals, radii = imsafe.GetDisks()
print("centers", centers, imsafe.ModelUnits)
print("normals", normals, imsafe.ModelUnits)
print("radii", radii, imsafe.ModelUnits)

# Line generation options #3. setup line options
imsafe.NumberOfLinesProp.Value = 5
imsafe.LengthDeviationProp.Value = 10  # %
imsafe.NormalToEndDisksProp.Value = True
imsafe.MinSplineResolutionProp.Value = 0.01 * total_len  # or
# imsafe.MinSplineResolutionProp.SetValueAs(0.05, Unit.Meter)

imsafe.EnableConstraintsProp.Value = False  # 4. setup obstacles
imsafe.SetAsObstacles([sphere])

RegisterAlgorithm(imsafe)
assert imsafe.UpdateAttributes(), "Guarantees output ports are updated"

imsafe.ClearOutputLines()
assert imsafe.Update(0)

filepath = os.path.join(tempfile.mkdtemp(), "line.txt")
print("Exporting to", filepath)
imsafe.ExportLines(filepath, snapshot_index=0)

imsafe.ClearOutputLines()
imsafe.ImportLines(filepath)


# Creates viewer
import s4l_v1.analysis.viewers as viewers

dv = viewers.SurfaceViewer()
dv.SetInputConnection(0, imsafe.GetOutputPort(2))

RegisterAlgorithm(dv)

[bryn]

• it simply takes the first simulation. Note, the evaluator needs an existing simulation because it tests if the splines pass through voxels of the "Entities to Avoid" list
• the entities to avoid are set via SetAsObstacles(entity_list). the script assumes this entity is called "Sphere `"
• the script creates a spline as baseline, but you could also create the baseline in the GUI, and get it via base_line = model.AllEntities()["My Baseline"]

[mkn]

Thanks for the scrip @bryn. I am actually curious if it is possible to set an obstacle to avoid in the modelling window when drawing an object, outside of IMSafe.

[bryn]

Only by snapping to objects. One strategy can be to use planar cuts to snap inside solids/surfaces