The Virtual Brain Project

Source code for

# -*- 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
# (c) 2012-2017, 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 <>.
# 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)

Service layer, for storing/retrieving Resulting Figures in TVB.

.. moduleauthor:: Mihai Andrei <>
.. moduleauthor:: Ciprian Tomoiaga <>
.. moduleauthor:: Lia Domide <>

import os
from PIL import Image
import base64
import xml.dom.minidom
from StringIO import StringIO
from tvb.basic.logger.builder import get_logger
from tvb.core import utils
from tvb.core.entities import model
from import dao
from tvb.core.entities.file.files_helper import FilesHelper

[docs]class FigureService: """ Service layer for Figure entities. """ _TYPE_PNG = "png" _TYPE_SVG = "svg" _BRANDING_BAR_PNG = os.path.join(os.path.dirname(__file__), "resources", "branding_bar.png") _BRANDING_BAR_SVG = os.path.join(os.path.dirname(__file__), "resources", "branding_bar.svg") _DEFAULT_SESSION_NAME = "Default" _DEFAULT_IMAGE_FILE_NAME = "snapshot." def __init__(self): self.logger = get_logger(self.__class__.__module__) self.file_helper = FilesHelper() def _write_png(self, store_path, export_data): img_data = base64.b64decode(export_data) # decode the image final_image = # place it in a PIL stream branding_bar = # place the branding bar over final_image.paste(branding_bar, (0, final_image.size[1] - branding_bar.size[1]), branding_bar) # store to disk as PNG def _write_svg(self, store_path, export_data): dom = xml.dom.minidom.parseString(export_data) figureSvg = dom.getElementsByTagName('svg')[0] # get the original image dom = xml.dom.minidom.parse(FigureService._BRANDING_BAR_SVG) try: width = float(figureSvg.getAttribute('width').replace('px', '')) height = float(figureSvg.getAttribute('height').replace('px', '')) except ValueError: # defaults when dimensions are not given width = 1024 height = 768 figureSvg.setAttribute("width", str(width)) figureSvg.setAttribute("height", str(height)) finalSvg = dom.createElement('svg') # prepare the final svg brandingSvg = dom.getElementsByTagName('svg')[0] # get the branding bar brandingSvg.setAttribute("y", str(height)) # position it below the figure height += float(brandingSvg.getAttribute('height').replace('px', '')) # increase original height with branding bar's height finalSvg.setAttribute("width", str(width)) # same width as original figure finalSvg.setAttribute("height", str(height)) finalSvg.appendChild(figureSvg) # add the image finalSvg.appendChild(brandingSvg) # and the branding bar # Generate path where to store image with open(store_path, 'w') as dest: finalSvg.writexml(dest) # store to disk def _image_path(self, project_name, img_type): "Generate path where to store image" images_folder = self.file_helper.get_images_folder(project_name) file_name = FigureService._DEFAULT_IMAGE_FILE_NAME + img_type return utils.get_unique_file_name(images_folder, file_name) @staticmethod def _generate_image_name(project, user, operation, image_name): if not image_name: if operation is not None: # create a name based on the operation that created the image # e.g. TVB-Algo-Name-354 image_name = operation.algorithm.displayname.replace(' ', '-') else: # default to a generic name image_name = "figure" figure_count = dao.get_figure_count(, + 1 return 'TVB-%s-%s' % (image_name, figure_count)
[docs] def store_result_figure(self, project, user, img_type, export_data, image_name=None, operation_id=None): """ Store into a file, Result Image and reference in DB. """ store_path, file_name = self._image_path(, img_type) if img_type == FigureService._TYPE_PNG: # PNG file from canvas self._write_png(store_path, export_data) elif img_type == FigureService._TYPE_SVG: # SVG file from svg viewer self._write_svg(store_path, export_data) if operation_id: operation = dao.get_operation_by_id(operation_id) else: operation = None operation_id = None image_name = self._generate_image_name(project, user, operation, image_name) # Store entity into DB entity = model.ResultFigure(operation_id,,, FigureService._DEFAULT_SESSION_NAME, image_name, file_name, img_type) entity = dao.store_entity(entity) # Load instance from DB to have lazy fields loaded figure = dao.load_figure( # Write image meta data to disk self.file_helper.write_image_metadata(figure) if operation: # Force writing operation meta data on disk. # This is important later for operation import self.file_helper.write_operation_metadata(operation)
[docs] def retrieve_result_figures(self, project, user, selected_session_name='all_sessions'): """ Retrieve from DB all the stored Displayer previews that belongs to the specified session. The previews are for current user and project; grouped by session. """ result, previews_info = dao.get_previews(,, selected_session_name) for name in result: for figure in result[name]: figures_folder = self.file_helper.get_images_folder( figure_full_path = os.path.join(figures_folder, figure.file_path) # Compute the path figure.file_path = utils.path2url_part(figure_full_path) return result, previews_info
[docs] def load_figure(figure_id): """ Loads a stored figure by its id. """ return dao.load_figure(figure_id)
[docs] def edit_result_figure(self, figure_id, **data): """ Retrieve and edit a previously stored figure. """ figure = dao.load_figure(figure_id) figure.session_name = data['session_name'] = data['name'] dao.store_entity(figure) # Load instance from DB to have lazy fields loaded. figure = dao.load_figure(figure_id) # Store figure meta data in an XML attached to the image. self.file_helper.write_image_metadata(figure)
[docs] def remove_result_figure(self, figure_id): """ Remove figure from DB and file storage. """ figure = dao.load_figure(figure_id) # Delete all figure related files from disk. figures_folder = self.file_helper.get_images_folder( path2figure = os.path.join(figures_folder, figure.file_path) if os.path.exists(path2figure): os.remove(path2figure) self.file_helper.remove_image_metadata(figure) # Remove figure reference from DB. result = dao.remove_entity(model.ResultFigure, figure_id) return result