Source code for tvb.core.adapters.abcdisplayer

# -*- coding: utf-8 -*-
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.. moduleauthor:: Lia Domide <>
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


[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 = 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