TVB-2359 New dual brain visualizer for time series

tvb/adapters/visualizers/__init__.py

@@ -35,6 +35,6 @@
 
 __all__ = ["annotations_viewer", "brain", "complex_imaginary_coherence", "connectivity", "connectivity_edge_bundle",
            "covariance", "cross_coherence", "cross_correlation", "eeg_monitor", "fourier_spectrum",
-           "histogram", "ica", "local_connectivity_view", "matrix_viewer", "pca", "pearson_cross_correlation",
+           "histogram", "ica", "local_connectivity_view", "matrix_viewer","new_dual_viewer","pca", "pearson_cross_correlation",
            "pearson_edge_bundle", "pse_discrete", "pse_isocline", "region_volume_mapping", "sensors", "surface_view",
            "time_series", "time_series_volume", "tract", "topographic", "wavelet_spectrogram"]

tvb/adapters/visualizers/new_dual_viewer.py

@@ -0,0 +1,127 @@
+# -*- 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 do download
+# TheVirtualBrain-Scientific Package (for simulators). See content of the
+# documentation-folder for more details. See also http://www.thevirtualbrain.org
+#
+# (c) 2012-2017, 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 follows:
+#
+#   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)
+#
+#
+
+
+from tvb.adapters.visualizers.brain import BrainViewer
+from tvb.adapters.visualizers.eeg_monitor import EegMonitor
+from tvb.adapters.visualizers.sensors import prepare_sensors_as_measure_points_params
+from tvb.adapters.visualizers.sensors import prepare_mapped_sensors_as_measure_points_params
+from tvb.basic.filters.chain import FilterChain
+from tvb.core.entities.storage import dao
+from tvb.datatypes.surfaces import EEGCap, CorticalSurface
+from tvb.datatypes.surfaces import Surface
+from tvb.datatypes.time_series import TimeSeries, TimeSeriesSEEG, TimeSeriesEEG, TimeSeriesRegion
+
+
+class NewDualViewer(BrainViewer):
+    """
+    New visualizer merging Brain 3D display and EEG lines display.
+    Same input as the DualBrainViewer
+    """
+    _ui_name = "(Work in progress)New Viewer for Time Series in 3D and 2D"
+    _ui_subsection = "new_brain_dual"
+
+    def get_input_tree(self):
+
+        return [{'name': 'time_series', 'label': 'Time Series', 'type': TimeSeries, 'required': True,
+                 'conditions': FilterChain(fields=[FilterChain.datatype + '.type',
+                                                   FilterChain.datatype + '._has_surface_mapping'],
+                                           operations=["in", "=="],
+                                           values=[['TimeSeriesEEG', 'TimeSeriesSEEG',
+                                                    'TimeSeriesMEG', 'TimeSeriesRegion'], True])},
+
+                {'name': 'projection_surface', 'label': 'Projection Surface', 'type': Surface, 'required': False,
+                 'description': 'A surface on which to project the results. When missing, the first EEGCap is taken'
+                                'This parameter is ignored when InternalSensors measures.'},
+
+                {'name': 'shell_surface', 'label': 'Shell Surface', 'type': Surface, 'required': False,
+                 'description': "Wrapping surface over the internal sensors, to be displayed "
+                                "semi-transparently, for visual purposes only."}]
+
+    def populate_surface_fields(self, time_series):
+        """
+        Prepares the urls from which the client may read the data needed for drawing the surface.
+        """
+
+        if isinstance(time_series, TimeSeriesRegion):
+            BrainViewer.populate_surface_fields(self, time_series)
+            return
+
+        self.one_to_one_map = False
+        self.region_map = None
+        self.connectivity = None
+
+        if self.surface is None:
+            eeg_cap = dao.get_generic_entity(EEGCap, "EEGCap", "type")
+            if len(eeg_cap) < 1:
+                raise Exception("No EEG Cap Surface found for display!")
+            self.surface = eeg_cap[0]
+
+    def retrieve_measure_points_prams(self, time_series):
+
+        if isinstance(time_series, TimeSeriesRegion):
+            return BrainViewer.retrieve_measure_points_prams(self, time_series)
+
+        self.measure_points_no = time_series.sensors.number_of_sensors
+
+        if isinstance(time_series, TimeSeriesEEG):
+            return prepare_mapped_sensors_as_measure_points_params(self.current_project_id,
+                                                                   time_series.sensors, self.surface)
+
+        return prepare_sensors_as_measure_points_params(time_series.sensors)
+
+    def launch(self, time_series, projection_surface=None, shell_surface=None):
+
+        self.surface = projection_surface
+
+        if isinstance(time_series, TimeSeriesSEEG) and shell_surface is None:
+            shell_surface = dao.try_load_last_entity_of_type(self.current_project_id, CorticalSurface)
+
+        params = BrainViewer.compute_parameters(self, time_series, shell_surface)
+        params.update(EegMonitor().compute_parameters(time_series, is_extended_view=True))
+
+        params['isOneToOneMapping'] = False
+        params['brainViewerTemplate'] = 'dual_brain_3d_view.html'
+
+        if isinstance(time_series, TimeSeriesSEEG):
+            params['brainViewerTemplate'] = "dual_brain_3d_internal_view.html"
+            # Mark as None since we only display shelf face and no point to load these as well
+            params['urlVertices'] = None
+            params['isSEEG'] = True
+
+        if isinstance(time_series, TimeSeriesRegion):
+            params['withTransparency'] = True
+        else:
+            params['withTransparency'] = False
+
+
+        return self.build_display_result("new_dual_brain/view", params,
+                                         pages=dict(controlPage="new_dual_brain/controls",
+                                                    channelsPage="commons/channel_selector.html"))