def _params_meg_sensors(self,
meg_sensors,
projection_surface=None,
shell_surface=None):
params = prepare_sensors_as_measure_points_params(meg_sensors)
params.update({
'shelfObject':
prepare_shell_surface_urls(self.current_project_id, shell_surface),
'urlVertices':
'',
'urlTriangles':
'',
'urlLines':
'[]',
'urlNormals':
'',
'boundaryURL':
'',
'urlRegionMap':
''
})
if projection_surface is not None:
params.update(self._compute_surface_params(projection_surface))
return self.build_display_result(
"sensors/sensors_eeg",
params,
pages={"controlPage": "sensors/sensors_controls"})
def launch(self, view_model):
# type: (TractViewerModel) -> dict
from tvb.adapters.visualizers.surface_view import prepare_shell_surface_urls
url_track_starts, url_track_vertices = view_model.tracts.get_urls_for_rendering(
)
if view_model.tracts.region_volume_map is None:
raise Exception(
'only tracts with an associated region volume map are supported at this moment'
)
connectivity = view_model.tracts.region_volume_map.connectivity
params = dict(title="Tract Visualizer",
shelfObject=prepare_shell_surface_urls(
self.current_project_id,
view_model.shell_surface,
preferred_type=CorticalSurface),
urlTrackStarts=url_track_starts,
urlTrackVertices=url_track_vertices)
params.update(
self.build_params_for_selectable_connectivity(connectivity))
return self.build_display_result(
"tract/tract_view",
params,
pages={"controlPage": "tract/tract_viewer_controls"})
def _params_eeg_sensors(self,
eeg_sensors,
eeg_cap=None,
shell_surface=None):
params = prepare_mapped_sensors_as_measure_points_params(
self.current_project_id, eeg_sensors, eeg_cap)
params.update({
'shelfObject':
prepare_shell_surface_urls(self.current_project_id, shell_surface),
'urlVertices':
'',
'urlTriangles':
'',
'urlLines':
'[]',
'urlNormals':
''
})
if eeg_cap is not None:
params.update(self._compute_surface_params(eeg_cap))
return self.build_display_result(
"sensors/sensors_eeg",
params,
pages={"controlPage": "sensors/sensors_controls"})
def launch(self, tracts, shell_surface=None):
url_track_starts, url_track_vertices = tracts.get_urls_for_rendering()
if tracts.region_volume_map is None:
raise Exception(
'only tracts with an associated region volume map are supported at this moment'
)
connectivity = tracts.region_volume_map.connectivity
params = dict(title="Tract Visualizer",
shelfObject=prepare_shell_surface_urls(
self.current_project_id,
shell_surface,
preferred_type=CorticalSurface),
urlTrackStarts=url_track_starts,
urlTrackVertices=url_track_vertices)
params.update(
self.build_template_params_for_subselectable_datatype(
connectivity))
return self.build_display_result(
"tract/tract_view",
params,
pages={"controlPage": "tract/tract_viewer_controls"})
def _params_internal_sensors(self, internal_sensors, shell_surface=None):
params = prepare_sensors_as_measure_points_params(internal_sensors)
params['shelfObject'] = prepare_shell_surface_urls(self.current_project_id, shell_surface)
return self.build_display_result('sensors/sensors_internal', params,
pages={'controlPage': 'sensors/sensors_controls'})
def _params_internal_sensors(self, internal_sensors, shell_surface=None):
params = prepare_sensors_as_measure_points_params(internal_sensors)
params['shelfObject'] = prepare_shell_surface_urls(
self.current_project_id, shell_surface)
return self.build_display_result(
'sensors/sensors_internal',
params,
pages={'controlPage': 'sensors/sensors_controls'})
def _params_internal_sensors(self, internal_sensors, shell_surface=None):
params = prepare_sensors_as_measure_points_params(internal_sensors)
if shell_surface is None:
shell_surface = dao.try_load_last_entity_of_type(self.current_project_id, CorticalSurface)
params['shelfObject'] = prepare_shell_surface_urls(self.current_project_id, shell_surface)
return self.build_display_result('sensors/sensors_internal', params,
pages={'controlPage': 'sensors/sensors_controls'})
def _params_internal_sensors(self, internal_sensors, shell_surface=None):
params = prepare_sensors_as_measure_points_params(internal_sensors)
if shell_surface is None:
shell_surface = dao.try_load_last_entity_of_type(
self.current_project_id, CorticalSurface)
params['shelfObject'] = prepare_shell_surface_urls(
self.current_project_id, shell_surface)
return self.build_display_result(
'sensors/sensors_internal',
params,
pages={'controlPage': 'sensors/sensors_controls'})
def _params_meg_sensors(self, meg_sensors, projection_surface=None, shell_surface=None):
params = prepare_sensors_as_measure_points_params(meg_sensors)
params.update({
'shelfObject': prepare_shell_surface_urls(self.current_project_id, shell_surface),
'urlVertices': '', 'urlTriangles': '', 'urlLines': '[]', 'urlNormals': '',
'boundaryURL': '', 'urlRegionMap': ''})
if projection_surface is not None:
params.update(self._compute_surface_params(projection_surface))
return self.build_display_result("sensors/sensors_eeg", params,
pages={"controlPage": "sensors/sensors_controls"})
def _params_eeg_sensors(self, eeg_sensors, eeg_cap=None, shell_surface=None):
params = prepare_mapped_sensors_as_measure_points_params(self.current_project_id, eeg_sensors, eeg_cap)
params.update({
'shelfObject': prepare_shell_surface_urls(self.current_project_id, shell_surface),
'urlVertices': '', 'urlTriangles': '', 'urlLines': '[]', 'urlNormals': ''
})
if eeg_cap is not None:
params.update(self._compute_surface_params(eeg_cap))
return self.build_display_result("sensors/sensors_eeg", params,
pages={"controlPage": "sensors/sensors_controls"})
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 = self.surface.get_urls_for_rendering(True, self.region_map)
hemisphere_chunk_mask = self.surface.get_slices_to_hemisphere_mask()
params = self.retrieve_measure_points_prams(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.")
base_activity_url, time_urls = self._prepare_data_slices(time_series)
min_val, max_val = time_series.get_min_max_values()
legend_labels = self._compute_legend_labels(min_val, max_val)
data_shape = time_series.read_data_shape()
state_variables = time_series.labels_dimensions.get(time_series.labels_ordering[1], [])
if self.surface and self.region_map:
boundary_url = self.surface.get_url_for_region_boundaries(self.region_map)
else:
boundary_url = ''
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_activity_url=base_activity_url,
time=json.dumps(time_urls), minActivity=min_val, maxActivity=max_val,
legendLabels=legend_labels, labelsStateVar=state_variables,
labelsModes=range(data_shape[3]), extended_view=False,
shelfObject=prepare_shell_surface_urls(self.current_project_id, shell_surface),
biHemispheric=self.surface.bi_hemispheric,
hemisphereChunkMask=json.dumps(hemisphere_chunk_mask),
time_series=time_series, pageSize=self.PAGE_SIZE, urlRegionBoundaries=boundary_url,
measurePointsLabels=time_series.get_space_labels(),
measurePointsTitle=time_series.title))
params.update(self.build_template_params_for_subselectable_datatype(time_series))
return params
def launch(self, tracts, shell_surface=None):
url_track_starts, url_track_vertices = tracts.get_urls_for_rendering()
if tracts.region_volume_map is None:
raise Exception('only tracts with an associated region volume map are supported at this moment')
connectivity = tracts.region_volume_map.connectivity
params = dict(title="Tract Visualizer",
shelfObject=prepare_shell_surface_urls(self.current_project_id, shell_surface, preferred_type=CorticalSurface),
urlTrackStarts=url_track_starts,
urlTrackVertices=url_track_vertices)
params.update(self.build_template_params_for_subselectable_datatype(connectivity))
return self.build_display_result("tract/tract_view", params,
pages={"controlPage": "tract/tract_viewer_controls"})
