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_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}