# -*- 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) 2012-2023, 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:: Lia Domide <lia.domide@codemart.ro>
"""
import importlib
import json
import os
import numpy
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
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'
[docs] @staticmethod
def build_base_h5_url(entity_gid):
url_regex = '/{}/{}/{}'
return url_regex.format(URLGenerator.FLOW, URLGenerator.H5_FILE, entity_gid)
[docs] @staticmethod
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
[docs] @staticmethod
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
[docs] @staticmethod
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
[docs] @staticmethod
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
[docs]@add_metaclass(ABCMeta)
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
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
[docs] @staticmethod
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]
[docs] @staticmethod
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) + "]"
[docs] @staticmethod
def handle_infinite_values(data):
"""
Replace positive infinite values with the biggest float number available in numpy, and negative infinite
values with the smallest float number available in numpy.
"""
float_max = numpy.finfo(numpy.float64).max
data[data == numpy.PINF] = float_max
float_min = numpy.finfo(numpy.float64).min
data[data == numpy.NINF] = float_min
return data
[docs] @staticmethod
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)
vertices, normals, lines, triangles, _ = surface_url_generator.get_urls_for_rendering(shell_h5)
shell_object = json.dumps([vertices, normals, triangles, lines])
shell_h5.close()
return shell_object
return None
