Source code for tvb.adapters.uploaders.zip_surface_importer

# -*- coding: utf-8 -*-
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.. moduleauthor:: Calin Pavel <>
.. moduleauthor:: Bogdan Neacsa <>

import numpy

from tvb.adapters.uploaders.zip_surface.parser import ZipSurfaceParser
from tvb.basic.logger.builder import get_logger
from tvb.basic.neotraits.api import Attr, EnumAttr
from tvb.core.adapters.exceptions import LaunchException
from tvb.core.adapters.abcuploader import ABCUploader, ABCUploaderForm
from tvb.adapters.datatypes.db.surface import SurfaceIndex
from tvb.core.neotraits.forms import TraitUploadField, SelectField, BoolField
from tvb.core.neotraits.uploader_view_model import UploaderViewModel
from tvb.core.neotraits.view_model import Str
from tvb.datatypes.surfaces import make_surface, center_vertices, SurfaceTypesEnum

[docs] class ZIPSurfaceImporterModel(UploaderViewModel): uploaded = Str( label='Surface file (zip)' ) surface_type = EnumAttr( default=SurfaceTypesEnum.CORTICAL_SURFACE, label='Surface type' ) zero_based_triangles = Attr( field_type=bool, required=False, default=True, label='Zero based triangles' ) should_center = Attr( field_type=bool, required=False, label='Center surface using vertex means along axes' )
[docs] class ZIPSurfaceImporterForm(ABCUploaderForm): def __init__(self): super(ZIPSurfaceImporterForm, self).__init__() self.uploaded = TraitUploadField(ZIPSurfaceImporterModel.uploaded, '.zip', 'uploaded') self.surface_type = SelectField(ZIPSurfaceImporterModel.surface_type, 'surface_type') self.zero_based_triangles = BoolField(ZIPSurfaceImporterModel.zero_based_triangles, name='zero_based_triangles') self.should_center = BoolField(ZIPSurfaceImporterModel.should_center, name='should_center') del self.surface_type.choices[-1]
[docs] @staticmethod def get_view_model(): return ZIPSurfaceImporterModel
[docs] @staticmethod def get_upload_information(): return { 'uploaded': '.zip' }
[docs] class ZIPSurfaceImporter(ABCUploader): """ Handler for uploading a Surface Data archive, with files holding vertices, normals and triangles to represent a surface data. """ _ui_name = "Surface ZIP" _ui_subsection = "zip_surface_importer" _ui_description = "Import a Surface from ZIP" logger = get_logger(__name__)
[docs] def get_form_class(self): return ZIPSurfaceImporterForm
[docs] def get_output(self): return [SurfaceIndex]
@staticmethod def _make_surface(surface_type): result = make_surface(surface_type) if result is not None: return result exception_str = "Could not determine surface type (selected option %s)" % surface_type raise LaunchException(exception_str)
[docs] def launch(self, view_model): # type: (ZIPSurfaceImporterModel) -> [SurfaceIndex] """ Execute import operations: unpack ZIP and build Surface object as result :raises LaunchException: when * `uploaded` is missing * `surface_type` is invalid :raises RuntimeError: when triangles contain an invalid vertex index """ if view_model.uploaded is None: raise LaunchException("Please select ZIP file which contains data to import") self.logger.debug( "Start to import surface: '%s' from file: %s" % (view_model.surface_type, view_model.uploaded)) try: zip_surface = ZipSurfaceParser(view_model.uploaded) except IOError: exception_str = "Did not find the specified ZIP at %s" % view_model.uploaded raise LaunchException(exception_str) # Detect and instantiate correct surface type self.logger.debug("Create surface instance") surface = self._make_surface(view_model.surface_type.value) surface.zero_based_triangles = view_model.zero_based_triangles if view_model.should_center: vertices = center_vertices(zip_surface.vertices) else: vertices = zip_surface.vertices surface.vertices = vertices if len(zip_surface.normals) != 0: surface.vertex_normals = zip_surface.normals if view_model.zero_based_triangles: surface.triangles = zip_surface.triangles else: surface.triangles = zip_surface.triangles - 1 if zip_surface.bi_hemispheric:"Hemispheres detected") surface.hemisphere_mask = zip_surface.hemisphere_mask surface.compute_triangle_normals() # Now check if the triangles of the surface are valid triangles_min_vertex = numpy.amin(surface.triangles) if triangles_min_vertex < 0: if triangles_min_vertex == -1 and not view_model.zero_based_triangles: raise LaunchException("Triangles contain a negative vertex index. Maybe you have a ZERO based surface.") else: raise LaunchException("Your triangles contain a negative vertex index: %d" % triangles_min_vertex) no_of_vertices = len(surface.vertices) triangles_max_vertex = numpy.amax(surface.triangles) if triangles_max_vertex >= no_of_vertices: if triangles_max_vertex == no_of_vertices and view_model.zero_based_triangles: raise LaunchException("Your triangles contain an invalid vertex index: %d. " "Maybe your surface is NOT ZERO Based." % triangles_max_vertex) else: raise LaunchException("Your triangles contain an invalid vertex index: %d." % triangles_max_vertex) validation_result = surface.validate() if validation_result.warnings: self.add_operation_additional_info(validation_result.summary()) surface.configure() self.logger.debug("Surface ready to be stored") return self.store_complete(surface)