meshing

navis.conversion.meshing.get_surface_voxels

Return surface voxels.

Source code in navis/conversion/meshing.py

def get_surface_voxels(voxels):
    """Return surface voxels."""
    # Use bounding boxes to keep matrix small
    bb_min = voxels.min(axis=0)
    #bb_max = voxels.max(axis=0)
    #dim = bb_max - bb_min

    # Voxel offset
    voxel_off = voxels - bb_min

    # Generate empty array
    mat = _voxels_to_matrix(voxel_off)

    # Erode
    mat_erode = binary_erosion(mat)

    # Substract
    mat_surface = np.bitwise_and(mat, np.invert(mat_erode))

    # Turn back into voxels
    voxels_surface = _matrix_to_voxels(mat_surface) + bb_min

    return voxels_surface

navis.conversion.meshing.parse_obj

Parse .obj string and return vertices and faces.

Source code in navis/conversion/meshing.py

def parse_obj(obj):
    """Parse .obj string and return vertices and faces."""
    lines = obj.split('\n')
    verts = []
    faces = []
    for l in lines:
        if l.startswith('v '):
            verts.append([float(v) for v in l[2:].split(' ')])
        elif l.startswith('f '):
            f = [v.split('//')[0] for v in l[2:].split(' ')]
            faces.append([int(v) for v in f])

    # `.obj` faces start with vertex indices of 1 -> set to 0
    return np.array(verts), np.array(faces) - 1

navis.conversion.meshing.remove_surface_voxels

Removes surface voxels.

Source code in navis/conversion/meshing.py

def remove_surface_voxels(voxels, **kwargs):
    """Removes surface voxels."""
    # Use bounding boxes to keep matrix small
    bb_min = voxels.min(axis=0)
    #bb_max = voxels.max(axis=0)
    #dim = bb_max - bb_min

    # Voxel offset
    voxel_off = voxels - bb_min

    # Generate empty array
    mat = _voxels_to_matrix(voxel_off)

    # Erode
    mat_erode = binary_erosion(mat, **kwargs)

    # Turn back into voxels
    voxels_erode = _matrix_to_voxels(mat_erode) + bb_min

    return voxels_erode