Source code for nighres.surface.surface_som_mapping

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_som_mapping(surface_mesh, mask_zeros=False, som_size=100, learning_time=100000, total_time=500000, save_data=False, overwrite=False, output_dir=None, file_name=None): """Surface SOM mapping Maps surface coordinates onto a self-organizing map. Parameters ---------- surface_mesh: mesh Mesh model of the surface mask_zeros: bool Whether to mask out zero values (default is False) som_size: int Size of the 2D SOM to generate learning_time: int Time for the learning stage iterations total_time: int Total number of iterations 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) * original (mesh): Surface mesh dictionary of "points", "faces" and "data" showing the SOM coordinates on the mesh * som (mesh): SOM mesh dictionary of "points", "faces" and "data" generated from the SOM grid itself Notes ---------- Original Java module by Pierre-Louis Bazin """ print("\nSurface som mapping") # make sure that saving related parameters are correct if save_data: output_dir = _output_dir_4saving(output_dir, surface_mesh) orig_file = os.path.join(output_dir, _fname_4saving(module=__name__,file_name=file_name, rootfile=surface_mesh, suffix='som-orig',ext='vtk')) som_file = os.path.join(output_dir, _fname_4saving(module=__name__,file_name=file_name, rootfile=surface_mesh, suffix='som-grid',ext='vtk')) if overwrite is False \ and os.path.isfile(orig_file) and os.path.isfile(som_file) : print("skip computation (use existing results)") output = {'original': orig_file, 'som': som_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.SomSurfaceCoordinates() # 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())) if orig_mesh['data'] is not None: algorithm.setSurfaceValues(nighresjava.JArray('float')( (orig_mesh['data'].flatten('C')).astype(float))) algorithm.setMaskZeroValues(mask_zeros) algorithm.setSomDimension(2) algorithm.setSomSize(som_size) algorithm.setLearningTime(learning_time) algorithm.setTotalTime(total_time) # 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.getMappedSurfacePoints(), dtype=np.float32).shape[0]/3) nfc = int(np.array(algorithm.getMappedSurfaceTriangles(), dtype=np.int32).shape[0]/3) print("surface...") orig_points = np.reshape(np.array(algorithm.getMappedSurfacePoints(), dtype=np.float32), (npt,3), 'C') orig_faces = np.reshape(np.array(algorithm.getMappedSurfaceTriangles(), dtype=np.int32), (nfc,3), 'C') orig_data = np.reshape(np.array(algorithm.getMappedSurfaceValues(), dtype=np.float32), (npt,2), 'F') # som_points = np.reshape(np.array(algorithm.getMappedSurfacePoints(), # dtype=np.float32), (npt,3), 'C') # som_faces = np.reshape(np.array(algorithm.getMappedSurfaceTriangles(), # dtype=np.int32), (nfc,3), 'C') # som_data = np.reshape(np.array(algorithm.getMappedSurfaceValues(), # dtype=np.float32), (npt,2), 'C') npt2 = int(np.array(algorithm.getMappedSomPoints(), dtype=np.float32).shape[0]/3) nfc2 = int(np.array(algorithm.getMappedSomTriangles(), dtype=np.int32).shape[0]/3) print("som... ("+str(npt2)+", "+str(nfc2)+")") som_points = np.reshape(np.array(algorithm.getMappedSomPoints(), dtype=np.float32), (npt2,3), 'C') som_faces = np.reshape(np.array(algorithm.getMappedSomTriangles(), dtype=np.int32), (nfc2,3), 'C') som_data = np.reshape(np.array(algorithm.getMappedSomValues(), dtype=np.float32), (npt2,2), 'F') # create the mesh dictionary mapped_orig_mesh = {"points": orig_points, "faces": orig_faces, "data": orig_data} mapped_som_mesh = {"points": som_points, "faces": som_faces, "data": som_data} if save_data: print("saving...") save_mesh(orig_file, mapped_orig_mesh) save_mesh(som_file, mapped_som_mesh) return {'original': orig_file, 'som': som_file} else: return {'original': mapped_orig_mesh, 'som': mapped_som_mesh}