import os
import sys
import numpy as np
import nibabel as nb
import nighresjava
from ..io 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}