Source code for nighres.surface.levelset_to_mesh

import os
import sys
import numpy as np
import nibabel as nb
import nighresjava
from import load_volume, save_volume, load_mesh_geometry, save_mesh_geometry
from ..utils import _output_dir_4saving, _fname_4saving,_check_available_memory

[docs]def levelset_to_mesh(levelset_image, connectivity="18/6", level=0.0, inclusive=True, save_data=False, overwrite=False, output_dir=None, file_name=None): """Levelset to mesh Creates a triangulated mesh from the distance to a levelset surface representation using a connectivity-consistent marching cube algorithm. Parameters ---------- levelset_image: niimg Levelset image to be turned into a mesh connectivity: {"6/18","6/26","18/6","26/6"}, optional Choice of digital connectivity to build the mesh (default is 18/6) level: float, optional Value of the levelset function to use as isosurface (default is 0) inclusive: bool, optional Whether voxels at the exact 'level' value are inside the isosurface (default is True) save_data: bool, optional Save output data to file (default is False) overwrite: bool, optional Overwrite existing results (default is False) output_dir: str, optional Path to desired output directory, will be created if it doesn't exist file_name: str, optional Desired base name for output files with file extension (suffixes will be added) Returns ---------- dict Dictionary collecting outputs under the following keys (suffix of output files in brackets) * result (mesh): Surface mesh dictionary of "points" and "faces" (_l2m-mesh) Notes ---------- Ported from original Java module by Pierre-Louis Bazin. Original algorithm from [1]_ and adapted from [2]_. References ---------- .. [1] Han et al (2003). A Topology Preserving Level Set Method for Geometric Deformable Models doi: .. [2] Lucas et al (2010). The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software doi: """ print("\nLevelset to Mesh") # make sure that saving related parameters are correct if save_data: output_dir = _output_dir_4saving(output_dir, levelset_image) mesh_file = os.path.join(output_dir, _fname_4saving(module=__name__,file_name=file_name, rootfile=levelset_image, suffix='l2m-mesh',ext="vtk")) if overwrite is False \ and os.path.isfile(mesh_file) : print("skip computation (use existing results)") output = {'result': mesh_file} return output # start virtual machine if not running try: mem = _check_available_memory() nighresjava.initVM(initialheap=mem['init'], maxheap=mem['max']) except ValueError: pass # initiate class algorithm = nighresjava.SurfaceLevelsetToMesh() # load the data lvl_img = load_volume(levelset_image) lvl_data = lvl_img.get_data() hdr = lvl_img.header aff = lvl_img.affine resolution = [x.item() for x in hdr.get_zooms()] dimensions = lvl_data.shape algorithm.setResolutions(resolution[0], resolution[1], resolution[2]) algorithm.setDimensions(dimensions[0], dimensions[1], dimensions[2]) algorithm.setLevelsetImage(nighresjava.JArray('float')( (lvl_data.flatten('F')).astype(float))) algorithm.setConnectivity(connectivity) algorithm.setZeroLevel(level) algorithm.setInclusive(inclusive) # execute class try: algorithm.execute() except: # if the Java module fails, reraise the error it throws print("\n The underlying Java code did not execute cleanly: ") print(sys.exc_info()[0]) raise return # collect outputs npt = int(np.array(algorithm.getPointList(), dtype=np.float32).shape[0]/3) mesh_points = np.reshape(np.array(algorithm.getPointList(), dtype=np.float32), (npt,3), 'C') nfc = int(np.array(algorithm.getTriangleList(), dtype=np.int32).shape[0]/3) mesh_faces = np.reshape(np.array(algorithm.getTriangleList(), dtype=np.int32), (nfc,3), 'C') # create the mesh dictionary mesh = {"points": mesh_points, "faces": mesh_faces} if save_data: save_mesh_geometry(mesh_file, mesh) return {'result': mesh_file} else: return {'result': mesh}