# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need to download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2023, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program. If not, see <http://www.gnu.org/licenses/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
#
#
"""
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""
import os
import re
import numpy
from tvb.storage.storage_interface import StorageInterface
[docs]class ZipSurfaceParser(object):
"""
Parser for a surface zip.
Hemispheres are detected if the file name prefixes are the same
and the suffixes start with: left, right or l, r or lh, rh.
For example : verticesl.txt and verticesr.txt their uncommon suffixes are l, r
"""
VERTICES_TOKEN = "vertices"
NORMALS_TOKEN = "normals"
TRIANGLES_TOKEN = "triangles"
LEFT_SUFFIX_RE = re.compile('^(left|lh|l).*')
"If a vertex file has a suffix matching this it is considered left hemispheric"
RIGHT_SUFFIX_RE = re.compile('^(right|rh|r).*')
def __init__(self, path):
self.bi_hemispheric = False
self.vertices, self.normals, self.triangles = [], [], []
self.hemisphere_mask = []
self._read_vertices = 0
self.storage_interface = StorageInterface()
self._read(path)
def _read(self, path):
vertices, normals, triangles = self._group_by_type(sorted(self.storage_interface.get_filenames_in_zip(path)))
if len(vertices) == 0:
raise Exception("Cannot find vertices file.")
if len(vertices) != len(triangles):
raise Exception("The number of vertices files should be equal to the number of triangles files.")
if len(normals) != 0 and len(normals) != len(triangles):
raise Exception("The number of normals files should either be 0 or equal to the numer of triangles files")
vertices_lh, vertices_rh = self._group_by_hemisph(vertices)
normals_lh, normals_rh = self._group_by_hemisph(normals)
triangles_lh, triangles_rh = self._group_by_hemisph(triangles)
self.bi_hemispheric = (
len(vertices_lh) == len(vertices_rh) and
len(normals_lh) == len(normals_rh) and
len(triangles_lh) == len(triangles_rh)
)
if self.bi_hemispheric:
self._read_files(vertices_lh, normals_lh, triangles_lh, path)
vertices_in_lh = self._read_vertices
self._read_files(vertices_rh, normals_rh, triangles_rh, path)
self._stack_arrays()
self.hemisphere_mask = numpy.ones(len(self.vertices), dtype=numpy.bool_)
self.hemisphere_mask[0:vertices_in_lh] = 0
else:
self._read_files(vertices, normals, triangles, path)
self._stack_arrays()
self.hemisphere_mask = numpy.zeros(len(self.vertices), dtype=numpy.bool_)
def _stack_arrays(self):
self.vertices = numpy.vstack(self.vertices)
self.triangles = numpy.vstack(self.triangles)
if self.normals:
self.normals = numpy.vstack(self.normals)
def _group_by_type(self, names):
vertices, normals, triangles = [], [], []
for name in names:
if self.VERTICES_TOKEN in name:
vertices.append(name)
elif self.NORMALS_TOKEN in name:
normals.append(name)
elif self.TRIANGLES_TOKEN in name:
triangles.append(name)
return vertices, normals, triangles
def _group_by_hemisph(self, names):
""" groups by hemisphere """
lefts, rights, rest = [], [], []
prefix_pos = len(os.path.commonprefix(names))
for name in names:
suffix = name[prefix_pos:]
if self.LEFT_SUFFIX_RE.match(suffix):
lefts.append(name)
elif self.RIGHT_SUFFIX_RE.match(suffix):
rights.append(name)
else:
rest.append(name)
if len(rest) != 0 or len(lefts) != len(rights):
return lefts + rights + rest, []
else:
return lefts, rights
def _read_files(self, vertices_files, normals_files, triangles_files, path):
"""
Read vertices, normals and triangles from files.
All files of a type are concatenated.
"""
# we need to process vertices in parallel with triangles, so that we can offset triangle indices
for vertices_file, triangles_file in zip(vertices_files, triangles_files):
vertices_file = self.storage_interface.open_tvb_zip(path, vertices_file)
triangles_file = self.storage_interface.open_tvb_zip(path, triangles_file)
current_vertices = numpy.loadtxt(vertices_file, dtype=numpy.float32)
self.vertices.append(current_vertices)
current_triangles = numpy.loadtxt(triangles_file, dtype=numpy.int32)
# offset triangles by amount of previously read vertices
current_triangles += self._read_vertices
self.triangles.append(current_triangles)
self._read_vertices += len(current_vertices)
vertices_file.close()
triangles_file.close()
for normals_file in normals_files:
normals_file = self.storage_interface.open_tvb_zip(path, normals_file)
current_normals = numpy.loadtxt(normals_file, dtype=numpy.float32)
self.normals.append(current_normals)
normals_file.close()
