How to get spatial coordinate information of an anatomical structure?

[yiyang]

Hello,

I am using a script to place electric dipoles within specific structures in an anatomical model, such as the gastrointestinal (GI) tract (including the stomach, small intestine, etc.). The question is, how can I get the coordinates of the space occupied by the model of the GI tract, or in other words, how can I verify that the electric dipoles I place are inside the tissue of the GI tract? Thanks for your help!

[bryn]

To get the bounding box of some tissues, say

• Large_intestine_lumen
• Large_intestine_wall

and test if some points are inside these tissues you can use the GetEntityPointDistance API, e.g., something like this:

import numpy as np
import s4l_v1.model as s4l_model

Vec3 = s4l_model.Vec3

def sample_box(p1: Vec3, p2: Vec3) -> list[Vec3]:
    xs = np.linspace(p1[0], p2[0], 10)
    ys = np.linspace(p1[1], p2[1], 10)
    zs = np.linspace(p1[2], p2[2], 10)

    X, Y, Z = np.meshgrid(xs, ys, zs, indexing="ij")
    points = np.vstack([X.ravel(), Y.ravel(), Z.ravel()]).T
    return [Vec3(p) for p in points]

    
def find_entities(root_group: s4l_model.EntityGroup, names: list[str]):
    entities = s4l_model.CollectEntities([root_group])
    entities = [e for e in entities if e.Name in names]
    return entities
    
    
if __name__ == "__main__":
    model_group = s4l_model.AllEntities()["Thelonious_6y_m_v3.1b02_posable"]
    entities = find_entities(model_group, ["Large_intestine_lumen", "Large_intestine_wall"])
    p1, p2 = s4l_model.GetBoundingBox(entities)
    points = sample_box(p1, p2)
    
    inside_gi_tract = np.zeros(len(points), dtype=np.uint8)
    for entity in entities:
        distance = s4l_model.GetEntityPointDistance(entity, points)
        
        for idx, dist in enumerate(distance):
            # note: negative distance means inside the closed surface
            if dist.Distance <= 0.0:
                inside_gi_tract[idx] = True