Source code for tvb.adapters.visualizers.complex_imaginary_coherence

# -*- 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) 2012-2024, 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:: Dan Pop <dan.pop@codemart.ro>
.. moduleauthor:: Paula Sanz Leon <Paula@tvb.invalid>
.. moduleauthor:: Stuart A. Knock <Stuart@tvb.invalid>

"""
import json

import numpy
from tvb.adapters.datatypes.db.spectral import ComplexCoherenceSpectrumIndex
from tvb.core.adapters.abcadapter import ABCAdapterForm
from tvb.core.adapters.abcdisplayer import ABCDisplayer, 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.datatypes.spectral import ComplexCoherenceSpectrum


[docs] class ImaginaryCoherenceDisplayModel(ViewModel): input_data = DataTypeGidAttr( linked_datatype=ComplexCoherenceSpectrum, label='Complex Coherence Result', doc='Imaginary Coherence Analysis to display' )
[docs] class ImaginaryCoherenceDisplayForm(ABCAdapterForm): def __init__(self): super(ImaginaryCoherenceDisplayForm, self).__init__() self.input_data = TraitDataTypeSelectField(ImaginaryCoherenceDisplayModel.input_data, 'input_data', conditions=self.get_filters())
[docs] @staticmethod def get_view_model(): return ImaginaryCoherenceDisplayModel
[docs] @staticmethod def get_required_datatype(): return ComplexCoherenceSpectrumIndex
[docs] @staticmethod def get_input_name(): return 'input_data'
[docs] @staticmethod def get_filters(): return None
[docs] class ImaginaryCoherenceDisplay(ABCDisplayer): """ This viewer takes as inputs a result from complex coherence analysis, and returns required parameters for a MatplotLib representation. """ _ui_name = "Complex (Imaginary) Coherence Visualizer" _ui_subsection = "complex_coherence"
[docs] def get_form_class(self): return ImaginaryCoherenceDisplayForm
[docs] def get_required_memory_size(self, view_model): # type: (ImaginaryCoherenceDisplayModel) -> numpy.ndarray """ Return the required memory to run this algorithm. """ with h5.h5_file_for_gid(view_model.input_data) as input_data_h5: required_memory = numpy.prod(input_data_h5.read_data_shape()) * 8 return required_memory
[docs] def launch(self, view_model): # type: (ImaginaryCoherenceDisplayModel) -> dict """ Draw interactive display. """ self.log.debug("Plot started...") with h5.h5_file_for_gid(view_model.input_data) as input_data_h5: source_gid = input_data_h5.source.load() source_index = self.load_entity_by_gid(source_gid) params = dict(plotName=source_index.type, xAxisName="Frequency [kHz]", yAxisName="CohSpec", available_xScale=["Linear", "Logarithmic"], available_spectrum=json.dumps(input_data_h5.spectrum_types), spectrum_list=input_data_h5.spectrum_types, xscale="Linear", spectrum=input_data_h5.spectrum_types[0], url_base=URLGenerator.build_h5_url(view_model.input_data, 'get_spectrum_data', parameter=""), # TODO investigate the static xmin and xmax values xmin=0.02, xmax=0.8) return self.build_display_result("complex_coherence/view", params)