# -*- 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:: Ionel Ortelecan <ionel.ortelecan@codemart.ro>
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
.. moduleauthor:: Bogdan Neacsa <bogdan.neacsa@codemart.ro>
"""
import numpy
from tvb.adapters.datatypes.db.time_series import *
from tvb.adapters.datatypes.h5.surface_h5 import SurfaceH5
from tvb.adapters.datatypes.h5.time_series_h5 import TimeSeriesH5, TimeSeriesSurfaceH5
from tvb.adapters.visualizers.eeg_monitor import EegMonitor
from tvb.adapters.visualizers.sensors import prepare_mapped_sensors_as_measure_points_params
from tvb.adapters.visualizers.sensors import prepare_sensors_as_measure_points_params, function_sensors_to_surface
from tvb.adapters.visualizers.surface_view import ensure_shell_surface, SurfaceURLGenerator, ABCSurfaceDisplayer
from tvb.core.adapters.abcadapter import ABCAdapterForm
from tvb.core.adapters.abcdisplayer import URLGenerator
from tvb.core.entities.storage import dao
from tvb.core.neocom import h5
from tvb.core.neotraits.forms import TraitDataTypeSelectField
from tvb.core.neotraits.view_model import DataTypeGidAttr, ViewModel
from tvb.datatypes.surfaces import Surface, SurfaceTypesEnum
MAX_MEASURE_POINTS_LENGTH = 600
[docs]class BrainViewerModel(ViewModel):
time_series = DataTypeGidAttr(
linked_datatype=TimeSeries,
label='Time Series (Region or Surface)'
)
shell_surface = DataTypeGidAttr(
linked_datatype=Surface,
required=False,
label='Shell Surface',
doc='Surface to be displayed semi-transparently as overlay, for visual navigation purposes only.'
)
[docs]class BrainViewer(ABCSurfaceDisplayer):
"""
Interface between the 3D view of the Brain Cortical Surface and TVB framework.
This viewer will build the required parameter dictionary that will be sent to the HTML / JS for further processing,
having as end result a brain surface plus activity that will be displayed in 3D.
"""
_ui_name = "Brain Activity Visualizer"
PAGE_SIZE = 500
[docs] def get_required_memory_size(self, view_model):
# type: (BrainViewerModel) -> numpy.ndarray
"""
Assume one page doesn't get 'dumped' in time and it is highly probably that
two consecutive pages will be in the same time in memory.
"""
time_series = self.load_entity_by_gid(view_model.time_series)
overall_shape = time_series.get_data_shape()
used_shape = (overall_shape[0] / (self.PAGE_SIZE * 2.0), overall_shape[1], overall_shape[2], overall_shape[3])
return numpy.prod(used_shape) * 8.0
[docs] def launch(self, view_model):
# type: (BrainViewerModel) -> dict
"""
Build visualizer's page.
"""
time_series_index = self.load_entity_by_gid(view_model.time_series)
shell_surface_index = None
if view_model.shell_surface:
shell_surface_index = self.load_entity_by_gid(view_model.shell_surface)
params = self.compute_parameters(time_series_index, shell_surface_index)
return self.build_display_result("brain/view", params, pages=dict(controlPage="brain/controls"))
[docs] def populate_surface_fields(self, time_series_index):
"""
To be overwritten for populating fields: one_to_one_map/connectivity/region_map/surface fields
"""
self.one_to_one_map = isinstance(time_series_index, TimeSeriesSurfaceIndex)
if self.one_to_one_map:
self.PAGE_SIZE /= 10
surface_gid = time_series_index.fk_surface_gid
surface_index = dao.get_datatype_by_gid(surface_gid)
region_map_indexes = dao.get_generic_entity(RegionMappingIndex, surface_gid, 'fk_surface_gid')
if len(region_map_indexes) < 1:
region_map_index = None
connectivity_index = None
else:
region_map_index = region_map_indexes[0]
connectivity_index = dao.get_datatype_by_gid(region_map_index.fk_connectivity_gid)
else:
connectivity_index = dao.get_datatype_by_gid(time_series_index.fk_connectivity_gid)
if time_series_index.fk_region_mapping_gid:
region_map_index = dao.get_datatype_by_gid(time_series_index.fk_region_mapping_gid)
else:
region_map_indexes = dao.get_generic_entity(RegionMappingIndex, connectivity_index.gid,
'fk_connectivity_gid')
region_map_index = region_map_indexes[0]
surface_index = dao.get_datatype_by_gid(region_map_index.fk_surface_gid)
self.connectivity_index = connectivity_index
self.region_map_gid = None if region_map_index is None else region_map_index.gid
self.surface_gid = None if surface_index is None else surface_index.gid
self.surface_h5 = None if surface_index is None else h5.h5_file_for_index(surface_index)
[docs] def retrieve_measure_points_params(self, time_series):
"""
To be overwritten method, for retrieving the measurement points (region centers, EEG sensors).
"""
if self.connectivity_index is None:
self.measure_points_no = 0
return {'urlMeasurePoints': [],
'urlMeasurePointsLabels': [],
'noOfMeasurePoints': 0}
connectivity_gid = self.connectivity_index.gid
measure_points = SurfaceURLGenerator.build_h5_url(connectivity_gid, 'get_centres')
measure_points_labels = SurfaceURLGenerator.build_h5_url(connectivity_gid, 'get_region_labels')
self.measure_points_no = self.connectivity_index.number_of_regions
return {'urlMeasurePoints': measure_points,
'urlMeasurePointsLabels': measure_points_labels,
'noOfMeasurePoints': self.measure_points_no}
[docs] def compute_parameters(self, time_series, shell_surface=None):
"""
Create the required parameter dictionary for the HTML/JS viewer.
:rtype: `dict`
:raises Exception: when
* number of measure points exceeds the maximum allowed
* a Face object cannot be found in database
"""
self.populate_surface_fields(time_series)
url_vertices, url_normals, url_lines, url_triangles, url_region_map = SurfaceURLGenerator.get_urls_for_rendering(
self.surface_h5, self.region_map_gid)
hemisphere_chunk_mask = self.surface_h5.get_slices_to_hemisphere_mask()
params = self.retrieve_measure_points_params(time_series)
if not self.one_to_one_map and self.measure_points_no > MAX_MEASURE_POINTS_LENGTH:
raise Exception("Max number of measure points " + str(MAX_MEASURE_POINTS_LENGTH) + " exceeded.")
time_series_h5 = h5.h5_file_for_index(time_series)
assert isinstance(time_series_h5, TimeSeriesH5)
base_adapter_url, time_urls = self._prepare_data_slices(time_series)
min_val, max_val = time_series_h5.get_min_max_values()
legend_labels = self._compute_legend_labels(min_val, max_val)
state_variables = time_series.get_labels_for_dimension(1)
if self.surface_gid and self.region_map_gid:
boundary_url = SurfaceURLGenerator.get_url_for_region_boundaries(self.surface_gid, self.region_map_gid,
self.stored_adapter.id)
else:
boundary_url = ''
shell_surface = ensure_shell_surface(self.current_project_id, shell_surface)
params.update(dict(title="Cerebral Activity: " + time_series.title, isOneToOneMapping=self.one_to_one_map,
urlVertices=json.dumps(url_vertices), urlTriangles=json.dumps(url_triangles),
urlLines=json.dumps(url_lines), urlNormals=json.dumps(url_normals),
urlRegionMap=json.dumps(url_region_map), base_adapter_url=base_adapter_url,
time=json.dumps(time_urls), minActivity=min_val, maxActivity=max_val,
legendLabels=legend_labels, labelsStateVar=state_variables,
labelsModes=list(range(time_series.data_length_4d)), extended_view=False,
shellObject=self.prepare_shell_surface_params(shell_surface, SurfaceURLGenerator),
biHemispheric=self.surface_h5.bi_hemispheric.load(),
hemisphereChunkMask=json.dumps(hemisphere_chunk_mask),
pageSize=self.PAGE_SIZE, urlRegionBoundaries=boundary_url,
measurePointsLabels=self.get_space_labels(time_series_h5),
measurePointsTitle=time_series.title))
params.update(self.build_params_for_subselectable_ts(time_series_h5))
time_series_h5.close()
if self.surface_h5:
self.surface_h5.close()
return params
@staticmethod
def _prepare_mappings(mappings_dict):
"""
Get full mapping dictionary between the original vertices and multiple slices (for WebGL compatibility).
"""
prepared_mappings = []
for key in mappings_dict:
this_mappings = []
vert_map_dict = mappings_dict[key]
vertices_indexes = vert_map_dict['indices']
this_mappings.append(vertices_indexes[0].tolist())
for i in range(1, len(vertices_indexes)):
if vertices_indexes[i][0] == vertices_indexes[i][1]:
this_mappings.append(vertices_indexes[i][0])
else:
for index in range(vertices_indexes[i][0], vertices_indexes[i][1] + 1):
this_mappings.append(index)
prepared_mappings.append(this_mappings)
return prepared_mappings
@staticmethod
def _compute_legend_labels(min_val, max_val, nr_labels=5, min_nr_dec=3):
"""
Compute rounded labels for MIN and MAX values such that decimals will show a difference between them.
"""
if len(str(min_val).split('.')) == 2:
min_integer, min_decimals = str(min_val).split('.')
else:
min_integer, min_decimals = [str(int(min_val)), ""]
if len(str(max_val).split('.')) == 2:
max_integer, max_decimals = str(max_val).split('.')
else:
max_integer, max_decimals = [str(int(max_val)), ""]
idx = min_nr_dec
if len(min_decimals) < min_nr_dec or len(max_decimals) < min_nr_dec:
processed_min_val = float(min_val)
processed_max_val = float(max_val)
elif min_integer != max_integer:
processed_min_val = float(min_integer + '.' + min_decimals[:min_nr_dec])
processed_max_val = float(max_integer + '.' + max_decimals[:min_nr_dec])
else:
for idx, val in enumerate(min_decimals):
if idx < len(max_decimals) or val != max_decimals[idx]:
break
processed_min_val = float(min_integer + '.' + min_decimals[:idx])
processed_max_val = float(max_integer + '.' + max_decimals[:idx])
value_diff = (processed_max_val - processed_min_val) / (nr_labels + 1)
inter_values = [round(processed_min_val + value_diff * i, idx) for i in range(nr_labels, 0, -1)]
return [processed_max_val] + inter_values + [processed_min_val]
def _prepare_data_slices(self, time_series_index):
"""
Prepare data URL for retrieval with slices of timeSeries activity and Time-Line.
:returns: [activity_urls], [timeline_urls]
Currently timeline_urls has just one value, as on client is loaded entirely anyway.
"""
time_series_gid = time_series_index.gid
activity_base_url = URLGenerator.build_url(self.stored_adapter.id, 'read_data_page_split', time_series_gid, "")
time_urls = [SurfaceURLGenerator.build_h5_url(time_series_gid, 'read_time_page',
parameter="current_page=0;page_size=" +
str(time_series_index.data_length_1d))]
return activity_base_url, time_urls
[docs] def read_data_page_split(self, time_series_gid, from_idx, to_idx, step=None, specific_slices=None):
with h5.h5_file_for_gid(time_series_gid) as time_series_h5:
assert isinstance(time_series_h5, TimeSeriesH5)
basic_result = time_series_h5.read_data_page(from_idx, to_idx, step, specific_slices)
if not isinstance(time_series_h5, TimeSeriesSurfaceH5):
return basic_result.tolist()
surface_gid = time_series_h5.surface.load()
result = []
with h5.h5_file_for_gid(surface_gid) as surface_h5:
assert isinstance(surface_h5, SurfaceH5)
number_of_split_slices = surface_h5.number_of_split_slices.load()
if number_of_split_slices <= 1:
result.append(basic_result.tolist())
else:
for slice_number in range(surface_h5.number_of_split_slices):
start_idx, end_idx = surface_h5.get_slice_vertex_boundaries(slice_number)
result.append(basic_result[:, start_idx:end_idx].tolist())
return result
[docs]class DualBrainViewerModel(ViewModel):
time_series = DataTypeGidAttr(
linked_datatype=TimeSeries,
label='Time Series'
)
projection_surface = DataTypeGidAttr(
linked_datatype=Surface,
required=False,
label='Projection Surface',
doc='A surface on which to project the results. When missing, the first EEGCap is taken. '
'This parameter is ignored when InternalSensors measures.'
)
shell_surface = DataTypeGidAttr(
linked_datatype=Surface,
required=False,
label='Shell Surface',
doc='Wrapping surface over the internal sensors, to be displayed '
'semi-transparently, for visual purposes only.'
)
[docs]class DualBrainViewer(BrainViewer):
"""
Visualizer merging Brain 3D display and EEG lines display.
"""
_ui_name = "Brain Activity Viewer in 3D and 2D"
_ui_subsection = "brain_dual"
[docs] def populate_surface_fields(self, time_series_index):
"""
Prepares the urls from which the client may read the data needed for drawing the surface.
"""
if isinstance(time_series_index, TimeSeriesRegionIndex):
BrainViewer.populate_surface_fields(self, time_series_index)
return
self.one_to_one_map = False
self.region_map_gid = None
self.connectivity_index = None
if self.surface_index is None:
eeg_cap = dao.get_generic_entity(SurfaceIndex, SurfaceTypesEnum.EEG_CAP_SURFACE.value, "surface_type")
if len(eeg_cap) < 1:
raise Exception("No EEG Cap Surface found for display!")
self.surface_index = eeg_cap[0]
self.surface_gid = self.surface_index.gid
self.surface_h5 = h5.h5_file_for_index(self.surface_index)
[docs] def retrieve_measure_points_params(self, time_series):
if isinstance(time_series, TimeSeriesRegionIndex):
return BrainViewer.retrieve_measure_points_params(self, time_series)
sensors_index = dao.get_datatype_by_gid(time_series.fk_sensors_gid)
self.measure_points_no = sensors_index.number_of_sensors
if isinstance(time_series, TimeSeriesEEGIndex):
return prepare_mapped_sensors_as_measure_points_params(sensors_index, self.surface_index,
self.stored_adapter.id)
return prepare_sensors_as_measure_points_params(sensors_index)
[docs] def sensors_to_surface(self, sensors_gid, surface_to_map_gid):
# Method needs to be defined on the adapter, to be called from JS
return function_sensors_to_surface(sensors_gid, surface_to_map_gid)
[docs] def launch(self, view_model):
# type: (DualBrainViewerModel) -> dict
time_series_index = self.load_entity_by_gid(view_model.time_series)
self.surface_index = None
shell_surface_index = None
if view_model.projection_surface:
self.surface_index = self.load_entity_by_gid(view_model.projection_surface)
if view_model.shell_surface:
shell_surface_index = self.load_entity_by_gid(view_model.shell_surface)
if isinstance(time_series_index, TimeSeriesSEEGIndex):
shell_surface_index = ensure_shell_surface(self.current_project_id, shell_surface_index,
SurfaceTypesEnum.CORTICAL_SURFACE)
params = BrainViewer.compute_parameters(self, time_series_index, shell_surface_index)
eeg_monitor = EegMonitor()
params.update(eeg_monitor.compute_parameters(time_series_index, is_extended_view=True))
params['isOneToOneMapping'] = False
params['brainViewerTemplate'] = 'view.html'
if isinstance(time_series_index, TimeSeriesSEEGIndex):
params['brainViewerTemplate'] = "internal_view.html"
# Mark as None since we only display shell face and no point to load these as well
params['urlVertices'] = None
params['isSEEG'] = True
return self.build_display_result("brain/extendedview", params,
pages=dict(controlPage="brain/extendedcontrols",
channelsPage="commons/channel_selector.html"))
