Source code for tvb.adapters.visualizers.ica

# -*- coding: utf-8 -*-
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"""
A matrix visualizer for the Independent Component Analysis.
It displays the mixing matrix of size n_features x n_components

.. moduleauthor:: Paula Popa <paula.popa@codemart.ro>
.. moduleauthor:: Paula Sanz Leon <Paula@tvb.invalid>
"""

from tvb.adapters.datatypes.db.mode_decompositions import IndependentComponentsIndex
from tvb.adapters.visualizers.matrix_viewer import ABCMappedArraySVGVisualizer
from tvb.basic.neotraits.api import Attr
from tvb.core.adapters.abcadapter import ABCAdapterForm
from tvb.core.adapters.arguments_serialisation import slice_str
from tvb.core.neocom import h5
from tvb.core.neotraits.forms import TraitDataTypeSelectField, IntField
from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr
from tvb.datatypes.mode_decompositions import IndependentComponents



[docs]
class ICAModel(ViewModel):
    datatype = DataTypeGidAttr(
        linked_datatype=IndependentComponents,
        label='Independent component analysis:'
    )

    i_svar = Attr(
        field_type=int,
        default=0,
        label='Index of state variable (defaults to first state variable)'
    )

    i_mode = Attr(
        field_type=int,
        default=0,
        label='Index of mode (defaults to first mode)'
    )




[docs]
class ICAForm(ABCAdapterForm):

    def __init__(self):
        super(ICAForm, self).__init__()
        self.datatype = TraitDataTypeSelectField(ICAModel.datatype, name='datatype', conditions=self.get_filters())
        self.i_svar = IntField(ICAModel.i_svar, name='i_svar')
        self.i_mode = IntField(ICAModel.i_mode, name='i_mode')


[docs]
    @staticmethod
    def get_view_model():
        return ICAModel



[docs]
    @staticmethod
    def get_required_datatype():
        return IndependentComponentsIndex



[docs]
    @staticmethod
    def get_filters():
        return None



[docs]
    @staticmethod
    def get_input_name():
        return 'datatype'





[docs]
class ICA(ABCMappedArraySVGVisualizer):
    _ui_name = "Independent Components Analysis Visualizer"
    _ui_subsection = "ica"


[docs]
    def get_form_class(self):
        return ICAForm



[docs]
    def launch(self, view_model):
        # type: (ICAModel) -> dict
        """Construct data for visualization and launch it."""
        ica_gid = view_model.datatype
        ica_index = self.load_entity_by_gid(ica_gid)

        slice_given = slice_str((slice(None), slice(None), slice(view_model.i_svar), slice(view_model.i_mode)))
        if view_model.i_svar < 0 or view_model.i_svar >= ica_index.parsed_shape[2]:
            view_model.i_svar = 0
        if view_model.i_mode < 0 or view_model.i_mode >= ica_index.parsed_shape[3]:
            view_model.i_mode = 0
        slice_used = slice_str((slice(None), slice(None), slice(view_model.i_svar), slice(view_model.i_mode)))

        with h5.h5_file_for_index(ica_index) as h5_file:
            unmixing_matrix = h5_file.unmixing_matrix[..., view_model.i_svar, view_model.i_mode]
            prewhitening_matrix = h5_file.prewhitening_matrix[..., view_model.i_svar, view_model.i_mode]
        Cinv = unmixing_matrix.dot(prewhitening_matrix)

        title = 'ICA region contribution -- (Ellipsis, %d, 0)' % (view_model.i_svar)
        labels = self.extract_source_labels(ica_index)
        pars = self.compute_params(ica_index, Cinv, title, [labels, labels],
                                   slice_given, slice_used, slice_given != slice_used)
        return self.build_display_result("matrix/svg_view", pars)