The Virtual Brain Project

Source code for tvb.adapters.uploaders.obj_importer

# -*- 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
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# (c) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others
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# This program is free software: you can redistribute it and/or modify it under the
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#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
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#   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:: Mihai Andrei <mihai.andrei@codemart.ro>
"""

from tvb.adapters.uploaders.abcuploader import ABCUploader
from tvb.adapters.uploaders.obj.surface import ObjSurface
from tvb.core.adapters.exceptions import ParseException, LaunchException
from tvb.core.entities.storage import transactional, dao
from tvb.datatypes.surfaces import ALL_SURFACES_SELECTION, FACE, Surface, make_surface, center_vertices


[docs]class ObjSurfaceImporter(ABCUploader): """ This imports geometry data stored in wavefront obj format """ _ui_name = "Surface OBJ" _ui_subsection = "obj_importer" _ui_description = "Import geometry data stored in wavefront obj format"
[docs] def get_upload_input_tree(self): """ Take as input an obj file """ return [{'name': 'surface_type', 'type': 'select', 'label': 'Specify file type : ', 'required': True, 'options': ALL_SURFACES_SELECTION, 'default': FACE}, {'name': 'data_file', 'type': 'upload', 'required_type': '.obj', 'label': 'Please select file to import', 'required': True}, {'name': 'should_center', 'type': 'bool', 'default': False, 'label': 'Center surface using vertex means along axes'}]
[docs] def get_output(self): return [Surface]
@transactional
[docs] def launch(self, surface_type, data_file, should_center=False): """ Execute import operations: """ try: surface = make_surface(surface_type) if surface is None: raise ParseException("Could not determine surface type! %s" % surface_type) surface.storage_path = self.storage_path surface.zero_based_triangles = True with open(data_file) as f: obj = ObjSurface(f) if should_center: vertices = center_vertices(obj.vertices) else: vertices = obj.vertices surface.vertices = vertices surface.triangles = obj.triangles if obj.have_normals: self.log.debug("OBJ came with normals included") surface.vertex_normals = obj.normals else: self.log.warning("OBJ came without normals. We will try to compute them...") validation_result = surface.validate() if validation_result.warnings: self.add_operation_additional_info(validation_result.summary()) return [surface] except ParseException as excep: self.log.exception(excep) raise LaunchException(excep)