Source code for nighres.surface.surface_inflation

import os
import sys
import numpy as np
import nibabel as nb
import nighresjava
from import load_mesh, save_mesh
from ..utils import _output_dir_4saving, _fname_4saving,_check_available_memory

[docs]def surface_inflation(surface_mesh, step_size=0.75, max_iter=2000, max_curv=10.0, save_data=False, overwrite=False, output_dir=None, file_name=None): """Surface inflation Inflate a surface with the method of Tosun et al _[1]. Parameters ---------- surface_mesh: mesh Mesh model of the surface step_size: float Relaxation rate in [0, 1]: values closer to 1 are more stable but slower (default is 0.75) max_iter: int Maximum number of iterations (default is 2000) max_curv: float Desired maximum curvature (default is 10.0) save_data: bool Save output data to file (default is False) overwrite: bool 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", "faces" and "data" showing the SOM coordinates on the mesh Notes ---------- Original Java module by Pierre-Louis Bazin """ print("\nSurface inflation") # make sure that saving related parameters are correct if save_data: output_dir = _output_dir_4saving(output_dir, surface_mesh) infl_file = os.path.join(output_dir, _fname_4saving(module=__name__,file_name=file_name, rootfile=surface_mesh, suffix='infl-mesh',ext='vtk')) if overwrite is False \ and os.path.isfile(infl_file) : print("skip computation (use existing results)") output = {'result': infl_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.SurfaceInflation() # load the data orig_mesh = load_mesh(surface_mesh) algorithm.setSurfacePoints(nighresjava.JArray('float')( (orig_mesh['points'].flatten('C')).astype(float))) algorithm.setSurfaceTriangles(nighresjava.JArray('int')( (orig_mesh['faces'].flatten('C')).astype(int).tolist())) algorithm.setStepSize(step_size) algorithm.setMaxIter(max_iter) algorithm.setMaxCurv(max_curv) # 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 print("collect outputs") npt = int(np.array(algorithm.getInflatedSurfacePoints(), dtype=np.float32).shape[0]/3) nfc = int(np.array(algorithm.getInflatedSurfaceTriangles(), dtype=np.int32).shape[0]/3) print("surface...") orig_points = np.reshape(np.array(algorithm.getInflatedSurfacePoints(), dtype=np.float32), (npt,3), 'C') orig_faces = np.reshape(np.array(algorithm.getInflatedSurfaceTriangles(), dtype=np.int32), (nfc,3), 'C') orig_data = np.reshape(np.array(algorithm.getInflatedSurfaceValues(), dtype=np.float32), (npt), 'F') # create the mesh dictionary inflated_orig_mesh = {"points": orig_points, "faces": orig_faces, "data": orig_data} if save_data: print("saving...") save_mesh(infl_file, inflated_orig_mesh) return {'result': infl_file} else: return {'result': inflated_orig_mesh}