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Source code for tvb.config.init.introspector_registry

# -*- 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) 2012-2022, 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,
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# 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/>.
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#   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)
#
#

import inspect
from importlib import import_module

import tvb.adapters.uploaders
import tvb.adapters.visualizers
import tvb.adapters.datatypes.db
from tvb.adapters.analyzers import ALL_ANALYZERS
from tvb.adapters.creators import ALL_CREATORS
from tvb.adapters.simulator import ALL_SIMULATORS
from tvb.adapters.uploaders import ALL_UPLOADERS
from tvb.adapters.visualizers import ALL_VISUALIZERS
from tvb.adapters.datatypes.db import ALL_DATATYPES
from tvb.config.algorithm_categories import *
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.entities.model.model_datatype import DataType
from tvb.adapters.analyzers.metrics_group_timeseries import TimeseriesMetricsAdapter
from tvb.adapters.creators.allen_creator import AllenConnectomeBuilder
from tvb.adapters.simulator.simulator_adapter import SimulatorAdapter
from tvb.adapters.visualizers.connectivity import ConnectivityViewer
from tvb.adapters.visualizers.pse_discrete import DiscretePSEAdapter
from tvb.adapters.visualizers.pse_isocline import IsoclinePSEAdapter

LOGGER = get_logger(__name__)


[docs]def import_adapters(adapters_top_module, all_adapter_files): """ @:param adapters_top_module: top module under which the ABCAdapter instances are searched for @:param all_adapter_files: list of strings representing python submodules. We will import these, relative to 'adapters_top_module' and introspect ass concrete subclasses of ABCAdapter defined inside @:returns: list of ABCAdapter subclasses """ result = [] for adapters_file in all_adapter_files: try: adapters_module = import_module("." + adapters_file, adapters_top_module.__name__) for ad_class in dir(adapters_module): ad_class = adapters_module.__dict__[ad_class] if inspect.isclass(ad_class) and not inspect.isabstract(ad_class) and issubclass(ad_class, ABCAdapter): if ad_class.can_be_active(): result.append(ad_class) else: LOGGER.warning("Skipped Adapter(probably because MATLAB not found):" + str(ad_class)) except ImportError: LOGGER.exception("Could not introspect Adapters file:" + adapters_file) return result
[docs]def import_dt_index(dt_top_module, all_dt_files): """ @:param dt_top_module: top module under which the DataType instances are searched for @:param all_dt_files: list of strings representing python submodules. We will import these, relative to 'dt_top_module' and introspect ass concrete subclasses of DataType defined inside @:returns: list of Dt Index subclasses """ result = [] for adapters_file in all_dt_files: try: adapters_module = import_module("." + adapters_file, dt_top_module.__name__) for ad_class in dir(adapters_module): ad_class = adapters_module.__dict__[ad_class] if inspect.isclass(ad_class) and not inspect.isabstract(ad_class) and issubclass(ad_class, DataType): result.append(ad_class) except ImportError: LOGGER.exception("Could not introspect Adapters file:" + adapters_file) return result
[docs]class IntrospectionRegistry(object): """ This registry gathers classes that have a role in generating DB tables and rows. It is used at introspection time, for the following operations: - fill-in all rows in the ALGORITHM_CATEGORIES table - fill-in all rows in the ALGORITHMS table. Will add BCT algorithms only if Matlab/Octave path is set - generate DB tables for all datatype indexes - keep an evidence of the datatype index removers All classes that subclass AlgorithmCategoryConfig, ABCAdapter, ABCRemover, HasTraitsIndex should be imported here and added to the proper dictionary/list. e.g. Each new class of type HasTraitsIndex should be imported here and added to the DATATYPES list. """ ADAPTERS = { AnalyzeAlgorithmCategoryConfig: import_adapters(tvb.adapters.analyzers, ALL_ANALYZERS), SimulateAlgorithmCategoryConfig: import_adapters(tvb.adapters.simulator, ALL_SIMULATORS), UploadAlgorithmCategoryConfig: import_adapters(tvb.adapters.uploaders, ALL_UPLOADERS), ViewAlgorithmCategoryConfig: import_adapters(tvb.adapters.visualizers, ALL_VISUALIZERS), CreateAlgorithmCategoryConfig: import_adapters(tvb.adapters.creators, ALL_CREATORS), } DATATYPES = import_dt_index(tvb.adapters.datatypes.db, ALL_DATATYPES) SIMULATOR_MODULE = SimulatorAdapter.__module__ SIMULATOR_CLASS = SimulatorAdapter.__name__ CONNECTIVITY_MODULE = ConnectivityViewer.__module__ CONNECTIVITY_CLASS = ConnectivityViewer.__name__ ALLEN_CREATOR_MODULE = AllenConnectomeBuilder.__module__ ALLEN_CREATOR_CLASS = AllenConnectomeBuilder.__name__ MEASURE_METRICS_MODULE = TimeseriesMetricsAdapter.__module__ MEASURE_METRICS_CLASS = TimeseriesMetricsAdapter.__name__ DISCRETE_PSE_ADAPTER_MODULE = DiscretePSEAdapter.__module__ DISCRETE_PSE_ADAPTER_CLASS = DiscretePSEAdapter.__name__ ISOCLINE_PSE_ADAPTER_MODULE = IsoclinePSEAdapter.__module__ ISOCLINE_PSE_ADAPTER_CLASS = IsoclinePSEAdapter.__name__