The Virtual Brain Project

Source code for tvb.datatypes.tracts

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module docstring
.. moduleauthor:: Mihai Andrei <>

import numpy
from tvb.basic.logger.builder import get_logger
from tvb.basic.traits import core
from tvb.basic.traits.types_mapped import MappedType
from tvb.datatypes import arrays
from tvb.datatypes.region_mapping import RegionVolumeMapping

LOG = get_logger(__name__)

[docs]class Tracts(MappedType): """Datatype for results of diffusion imaging tractography.""" MAX_N_VERTICES = 2 ** 16 vertices = arrays.PositionArray( label="Vertex positions", file_storage=core.FILE_STORAGE_EXPAND, order=-1, doc="""An array specifying coordinates for the tracts vertices.""") tract_start_idx = arrays.IntegerArray( label="Tract starting indices", order=-1, doc="""Where is the first vertex of a tract in the vertex array""") tract_region = arrays.IntegerArray( label="Tract region index", required=False, order=-1, doc=""" An index used to find quickly all tract emerging from a region tract_region[i] is the region of the i'th tract. -1 represents the background """ ) region_volume_map = RegionVolumeMapping( label="Region volume Mapping used to create the tract_region index", required=False, order=-1 ) @property def tracts_count(self): return len(self.tract_start_idx) - 1 def get_tract(self, i): """ get a tract by index """ start, end = self.tract_start_idx[i:i + 2] return self.get_data('vertices', slice(start, end), close_file=False) def _get_tract_ids(self, region_id): tract_ids = numpy.where(self.tract_region == region_id)[0] return tract_ids def _get_track_ids_webgl_chunks(self, region_id): """ webgl can draw up to MAX_N_VERTICES vertices in a draw call. Assuming that no one track exceeds this limit we partition the tracts such that each track bundle has fewer than the max vertices :return: the id's of the tracts in a region chunked by the above criteria. """ # We have to split the int64 range in many uint16 ranges tract_ids = self._get_tract_ids(region_id) tract_id_chunks = [] chunk = [] count = 0 tidx = 0 tract_start_idx = self.tract_start_idx # traits make . expensive while tidx < len(tract_ids): # tidx always grows tid = tract_ids[tidx] start, end = tract_start_idx[tid:tid + 2] track_len = end - start if track_len >= self.MAX_N_VERTICES: raise ValueError('cannot yet handle very long tracts') count += track_len if count < self.MAX_N_VERTICES: # add this track to the current chunk and advance to next track chunk.append(tid) tidx += 1 else: # stay with the same track and start a new chunk tract_id_chunks.append(chunk) chunk = [] count = 0 if chunk: tract_id_chunks.append(chunk) # q = [] # for a in tract_id_chunks: # q.extend(a) # assert (numpy.array(q) == tract_ids).all() return tract_id_chunks def get_vertices(self, region_id, slice_number=0): """ Concatenates the vertices for all tracts starting in region_id. Returns a completely flat array as required by gl.bindBuffer apis """ region_id = int(region_id) slice_number = int(slice_number) chunks = self._get_track_ids_webgl_chunks(region_id) tract_ids = chunks[slice_number] tracts_vertices = [] for tid in tract_ids: tracts_vertices.append(self.get_tract(tid)) self.close_file() if tracts_vertices: tracts_vertices = numpy.concatenate(tracts_vertices) return tracts_vertices.ravel() else: return numpy.array([]) def get_line_starts(self, region_id): """ Returns a compact representation of the element buffers required to draw the streams via gl.drawElements A list of indices that describe where the first vertex for a tract is in the vertex array returned by get_tract_vertices_starting_in_region """ region_id = int(region_id) chunks = self._get_track_ids_webgl_chunks(region_id) chunk_line_starts = [] tract_start_idx = self.tract_start_idx # traits make the . expensive for tract_ids in chunks: offset = 0 tract_offsets = [0] for tid in tract_ids: start, end = tract_start_idx[tid:tid + 2] track_len = end - start offset += track_len tract_offsets.append(offset) chunk_line_starts.append(tract_offsets) return chunk_line_starts def get_urls_for_rendering(self): return ('/flow/read_datatype_attribute/' + self.gid + '/get_line_starts/False', '/flow/read_binary_datatype_attribute/' + self.gid + '/get_vertices')