Source code for tvb.adapters.visualizers.pca

# -*- 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
#
#

"""
A displayer for the principal component analysis.

.. moduleauthor:: Marmaduke Woodman <marmaduke.woodman@univ-amu.fr>

"""
import json
from tvb.adapters.datatypes.db.mode_decompositions import PrincipalComponentsIndex
from tvb.adapters.visualizers.time_series import ABCSpaceDisplayer
from tvb.core.adapters.abcadapter import ABCAdapterForm
from tvb.core.adapters.abcdisplayer import URLGenerator
from tvb.core.neocom import h5
from tvb.core.neotraits.forms import TraitDataTypeSelectField
from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr
from tvb.core.utils import TVBJSONEncoder
from tvb.datatypes.mode_decompositions import PrincipalComponents


[docs] class PCAModel(ViewModel): pca = DataTypeGidAttr( linked_datatype=PrincipalComponents, label='Principal component analysis:' )
[docs] class PCAForm(ABCAdapterForm): def __init__(self): super(PCAForm, self).__init__() self.pca = TraitDataTypeSelectField(PCAModel.pca, name='pca', conditions=self.get_filters())
[docs] @staticmethod def get_view_model(): return PCAModel
[docs] @staticmethod def get_input_name(): return 'pca'
[docs] @staticmethod def get_filters(): return None
[docs] @staticmethod def get_required_datatype(): return PrincipalComponentsIndex
[docs] class PCA(ABCSpaceDisplayer): _ui_name = "Principal Components Analysis Visualizer"
[docs] def get_form_class(self): return PCAForm
[docs] def get_required_memory_size(self, view_model): # type: (PCAModel) -> int """Return required memory. Here, it's unknown/insignificant.""" return -1
[docs] def launch(self, view_model): # type: (PCAModel) -> dict """Construct data for visualization and launch it.""" with h5.h5_file_for_gid(view_model.pca) as ts_h5: source_gid = ts_h5.source.load() with h5.h5_file_for_gid(source_gid) as source_h5: labels_data = self.get_space_labels(source_h5) fractions_update_url = URLGenerator.build_h5_url(view_model.pca, 'read_fractions_data') weights_update_url = URLGenerator.build_h5_url(view_model.pca, 'read_weights_data') return self.build_display_result("pca/view", dict(labels_data=json.dumps(labels_data, cls=TVBJSONEncoder), fractions_update_url=fractions_update_url, weights_update_url=weights_update_url))