TheVirtualBrain:

TheDocumentationwebsite.

Source code for tvb.core.adapters.abcdisplayer

# -*- 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,
# 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 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)
#
#
"""
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""
import importlib
import json
import os
from abc import ABCMeta
from threading import Lock
from uuid import UUID

from six import add_metaclass
from tvb.core.adapters.abcadapter import AdapterLaunchModeEnum, ABCAdapter
from tvb.core.adapters.exceptions import LaunchException
from tvb.core.neocom import h5
from tvb.core.neotraits.view_model import ViewModel

LOCK_CREATE_FIGURE = Lock()


[docs]class URLGenerator(object): FLOW = 'flow' INVOKE_ADAPTER = 'invoke_adapter' H5_FILE = 'read_from_h5_file' DATATYPE_ATTRIBUTE = 'read_datatype_attribute' BINARY_DATATYPE_ATTRIBUTE = 'read_binary_datatype_attribute' @staticmethod
[docs] def build_base_h5_url(entity_gid): url_regex = '/{}/{}/{}' return url_regex.format(URLGenerator.FLOW, URLGenerator.H5_FILE, entity_gid)
@staticmethod
[docs] def build_url(adapter_id, method_name, entity_gid, parameter=None): if isinstance(entity_gid, UUID): entity_gid = entity_gid.hex url_regex = '/{}/{}/{}/{}/{}' url = url_regex.format(URLGenerator.FLOW, URLGenerator.INVOKE_ADAPTER, adapter_id, method_name, entity_gid) if parameter is not None: url += "?" + str(parameter) return url
@staticmethod
[docs] def build_h5_url(entity_gid, method_name, flatten=False, datatype_kwargs=None, parameter=None): json_kwargs = json.dumps(datatype_kwargs) if isinstance(entity_gid, UUID): entity_gid = entity_gid.hex url_regex = '/{}/{}/{}/{}/{}/{}' url = url_regex.format(URLGenerator.FLOW, URLGenerator.H5_FILE, entity_gid, method_name, flatten, json_kwargs) if parameter is not None: url += "?" + str(parameter) return url
@staticmethod
[docs] def paths2url(datatype_gid, attribute_name, flatten=False, parameter=None): """ Prepare a File System Path for passing into an URL. """ if isinstance(datatype_gid, UUID): datatype_gid = datatype_gid.hex url_regex = '/{}/{}/{}/{}/{}' url = url_regex.format(URLGenerator.FLOW, URLGenerator.DATATYPE_ATTRIBUTE, datatype_gid, attribute_name, flatten) if parameter is not None: url += "?" + str(parameter) return url
@staticmethod
[docs] def build_binary_datatype_attribute_url(datatype_gid, attribute_name, parameter=None): if isinstance(datatype_gid, UUID): datatype_gid = datatype_gid.hex url_regex = '/{}/{}/{}/{}' url = url_regex.format(URLGenerator.FLOW, URLGenerator.BINARY_DATATYPE_ATTRIBUTE, datatype_gid, attribute_name) if parameter is not None: url += "?" + str(parameter) return url
@add_metaclass(ABCMeta)
[docs]class ABCDisplayer(ABCAdapter, metaclass=ABCMeta): """ Abstract class, for marking Adapters used for UI display only. """ KEY_CONTENT = "mainContent" KEY_IS_ADAPTER = "isAdapter" VISUALIZERS_ROOT = '' launch_mode = AdapterLaunchModeEnum.SYNC_SAME_MEM
[docs] def get_output(self): return []
def _prelaunch(self, operation, view_model, available_disk_space=0): """ Shortcut in case of visualization calls. """ self.current_project_id = operation.project.id self.user_id = operation.fk_launched_by self.storage_path = self.storage_interface.get_project_folder(operation.project.name, str(operation.id)) return self.launch(view_model=view_model), 0
[docs] def get_required_disk_size(self, view_model): """ Visualizers should no occupy any additional disk space. """ return 0
[docs] def build_display_result(self, template, parameters, pages=None): """ Helper method for building the result of the ABCDisplayer. :param template : relative path towards the HTML template to display :param parameters : dictionary with parameters for "template" :param pages : dictionary of pages to be used with <xi:include> """ module_ref = importlib.import_module(self.VISUALIZERS_ROOT) relative_path = os.path.basename(os.path.dirname(module_ref.__file__)) jinja_separator = '/' template = relative_path + jinja_separator + template if pages: for key, value in pages.items(): if value is not None: value = relative_path + jinja_separator + value parameters[key] = value parameters[self.KEY_CONTENT] = template parameters[self.KEY_IS_ADAPTER] = True return parameters
@staticmethod
[docs] def get_one_dimensional_list(list_of_elements, expected_size, error_msg): """ Used for obtaining a list of 'expected_size' number of elements from the list 'list_of_elements'. If the list 'list_of_elements' doesn't have sufficient elements then an exception will be thrown. list_of_elements - a list of one or two dimensions expected_size - the number of elements that should have the returned list error_msg - the message that will be used for the thrown exception. """ if len(list_of_elements) > 0 and isinstance(list_of_elements[0], list): if len(list_of_elements[0]) < expected_size: raise LaunchException(error_msg) return list_of_elements[0][:expected_size] else: if len(list_of_elements) < expected_size: raise LaunchException(error_msg) return list_of_elements[:expected_size]
@staticmethod
[docs] def dump_with_precision(xs, precision=3): """ Dump a list of numbers into a string, each at the specified precision. """ format_str = "%0." + str(precision) + "g" return "[" + ",".join(format_str % s for s in xs) + "]"
@staticmethod
[docs] def prepare_shell_surface_params(shell_surface, surface_url_generator): """ Prepares urls that are necessary for a shell surface. """ if shell_surface: shell_h5 = h5.h5_file_for_index(shell_surface) shell_vertices, shell_normals, _, shell_triangles, _ = surface_url_generator.get_urls_for_rendering(shell_h5) shellObject = json.dumps([shell_vertices, shell_normals, shell_triangles]) shell_h5.close() return shellObject return None