The Virtual Brain Project

Source code for tvb.adapters.uploaders.zip_surface.parser

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#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
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"""
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""
import os
import re
import numpy
from tvb.core.entities.file.files_helper import TvbZip


[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 with TvbZip(path) as self._zipf: self._read() def _read(self): vertices, normals, triangles = self._group_by_type(sorted(self._zipf.namelist())) 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) vertices_in_lh = self._read_vertices self._read_files(vertices_rh, normals_rh, triangles_rh) 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) 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): """ 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._zipf.open(vertices_file) triangles_file = self._zipf.open(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._zipf.open(normals_file) current_normals = numpy.loadtxt(normals_file, dtype=numpy.float32) self.normals.append(current_normals) normals_file .close()