Source code for tvb.datatypes.projections

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"""
The ProjectionMatrices DataTypes.

.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""

from tvb.basic.readers import try_get_absolute_path, FileReader
from tvb.datatypes import surfaces, sensors
from tvb.basic.neotraits.api import HasTraits, TVBEnum, Attr, NArray, Final


[docs] class ProjectionsTypeEnum(TVBEnum): EEG = "projEEG" MEG = "projMEG" SEEG = "projSEEG"
[docs] class ProjectionMatrix(HasTraits): """ Base DataType for representing a ProjectionMatrix. The projection is between a source of type CorticalSurface and a set of Sensors. """ projection_type = Final(field_type=str) brain_skull = Attr( field_type=surfaces.BrainSkull, label="Brain Skull", default=None, required=False, doc="""Boundary between skull and cortex domains.""") skull_skin = Attr( field_type=surfaces.SkullSkin, label="Skull Skin", default=None, required=False, doc="""Boundary between skull and skin domains.""") skin_air = Attr( field_type=surfaces.SkinAir, label="Skin Air", default=None, required=False, doc="""Boundary between skin and air domains.""") conductances = Attr( field_type=dict, label="Domain conductances", required=False, default={'air': 0.0, 'skin': 1.0, 'skull': 0.01, 'brain': 1.0}, doc=""" A dictionary representing the conductances of ... """) sources = Attr( field_type=surfaces.CorticalSurface, label="surface or region", default=None) sensors = Attr( field_type=sensors.Sensors, label="Sensors", default=None, required=False, doc=""" A set of sensors to compute projection matrix for them. """) projection_data = NArray(label="Projection Matrix Data", default=None, required=True) @property def shape(self): return self.projection_data.shape
[docs] @classmethod def from_file(cls, source_file, matlab_data_name=None, is_brainstorm=False): proj = cls() source_full_path = try_get_absolute_path("tvb_data.projectionMatrix", source_file) reader = FileReader(source_full_path) if is_brainstorm: proj.projection_data = reader.read_gain_from_brainstorm() else: proj.projection_data = reader.read_array(matlab_data_name=matlab_data_name) return proj
[docs] class ProjectionSurfaceEEG(ProjectionMatrix): """ Specific projection, from a CorticalSurface to EEG sensors. """ projection_type = Final(field_type=str, default=ProjectionsTypeEnum.EEG.value) sensors = Attr(field_type=sensors.SensorsEEG)
[docs] @classmethod def from_file(cls, source_file='projection_eeg_65_surface_16k.npy', matlab_data_name="ProjectionMatrix", is_brainstorm=False): return ProjectionMatrix.from_file.__func__(cls, source_file, matlab_data_name, is_brainstorm)
[docs] class ProjectionSurfaceMEG(ProjectionMatrix): """ Specific projection, from a CorticalSurface to MEG sensors. """ projection_type = Final(field_type=str, default=ProjectionsTypeEnum.MEG.value) sensors = Attr(field_type=sensors.SensorsMEG)
[docs] @classmethod def from_file(cls, source_file='projection_meg_276_surface_16k.npy', matlab_data_name=None, is_brainstorm=False): return ProjectionMatrix.from_file.__func__(cls, source_file, matlab_data_name, is_brainstorm)
[docs] class ProjectionSurfaceSEEG(ProjectionMatrix): """ Specific projection, from a CorticalSurface to SEEG sensors. """ projection_type = Final(field_type=str, default=ProjectionsTypeEnum.SEEG.value) sensors = Attr(field_type=sensors.SensorsInternal)
[docs] @classmethod def from_file(cls, source_file='projection_seeg_588_surface_16k.npy', matlab_data_name=None, is_brainstorm=False): return ProjectionMatrix.from_file.__func__(cls, source_file, matlab_data_name, is_brainstorm)
[docs] def make_proj_matrix(proj_type): """ Build a ProjectionMatrix instance, based on an input type :param proj_type: one of the supported subtypes :return: Instance of the corresponding projectiion matrix class, or None """ if proj_type == ProjectionsTypeEnum.EEG.value: return ProjectionSurfaceEEG() elif proj_type == ProjectionsTypeEnum.MEG.value: return ProjectionSurfaceMEG() elif proj_type == ProjectionsTypeEnum.SEEG.value: return ProjectionSurfaceSEEG() return None