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

ZMT zurich med tech

Avoid solid