The Virtual Brain Project

Source code for tvb.adapters.uploaders.region_mapping_importer

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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.
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"""
.. moduleauthor:: Calin Pavel
"""

import os
import numpy
import shutil
import zipfile
import tempfile
from tvb.adapters.uploaders.abcuploader import ABCUploader
from tvb.basic.logger.builder import get_logger
from tvb.basic.profile import TvbProfile
from tvb.core.adapters.exceptions import LaunchException
from tvb.core.entities.file.files_helper import FilesHelper
from tvb.datatypes.surfaces import CorticalSurface
from tvb.datatypes.region_mapping import RegionMapping
from tvb.datatypes.connectivity import Connectivity



[docs]class RegionMapping_Importer(ABCUploader): """ Upload RegionMapping from a TXT, ZIP or BZ2 file. """ _ui_name = "RegionMapping" _ui_subsection = "region_mapping_importer" _ui_description = "Import a Region Mapping (Surface - Connectivity) from TXT/ZIP/BZ2" logger = get_logger(__name__)
[docs] def get_upload_input_tree(self): """ Define input parameters for this importer. """ return [{'name': 'mapping_file', 'type': 'upload', 'required_type': '.txt, .zip, .bz2', 'label': 'Please upload region mapping file (txt, zip or bz2 format)', 'required': True, 'description': 'Expected a text/zip/bz2 file containing region mapping values.'}, {'name': 'surface', 'label': 'Brain Surface', 'type': CorticalSurface, 'required': True, 'datatype': True, 'description': 'The Brain Surface used by uploaded region mapping.'}, {'name': 'connectivity', 'label': 'Connectivity', 'type': Connectivity, 'required': True, 'datatype': True, 'description': 'The Connectivity used by uploaded region mapping.'} ]
[docs] def get_output(self): return [RegionMapping]
[docs] def launch(self, mapping_file, surface, connectivity): """ Creates region mapping from uploaded data. :param mapping_file: an archive containing data for mapping surface to connectivity :raises LaunchException: when * a parameter is None or missing * archive has more than one file * uploaded files are empty * number of vertices in imported file is different to the number of surface vertices * imported file has negative values * imported file has regions which are not in connectivity """ if mapping_file is None: raise LaunchException("Please select mappings file which contains data to import") if surface is None: raise LaunchException("No surface selected. Please initiate upload again and select a brain surface.") if connectivity is None: raise LaunchException("No connectivity selected. Please initiate upload again and select one.") self.logger.debug("Reading mappings from uploaded file") if zipfile.is_zipfile(mapping_file): tmp_folder = tempfile.mkdtemp(prefix='region_mapping_zip_', dir=TvbProfile.current.TVB_TEMP_FOLDER) try: files = FilesHelper().unpack_zip(mapping_file, tmp_folder) if len(files) > 1: raise LaunchException("Please upload a ZIP file containing only one file.") array_data = self.read_list_data(files[0], dtype=numpy.int32) finally: if os.path.exists(tmp_folder): shutil.rmtree(tmp_folder) else: array_data = self.read_list_data(mapping_file, dtype=numpy.int32) # Now we do some checks before building final RegionMapping if array_data is None or len(array_data) == 0: raise LaunchException("Uploaded file does not contains any data. Please initiate upload with another file.") # Check if we have a mapping for each surface vertex. if len(array_data) != surface.number_of_vertices: msg = "Imported file contains a different number of values than the number of surface vertices. " \ "Imported: %d values while surface has: %d vertices." % (len(array_data), surface.number_of_vertices) raise LaunchException(msg) # Now check if the values from imported file correspond to connectivity regions if array_data.min() < 0: raise LaunchException("Imported file contains negative values. Please fix problem and re-import file") if array_data.max() >= connectivity.number_of_regions: msg = "Imported file contains invalid regions. Found region: %d while selected connectivity has: %d " \ "regions defined (0 based)." % (array_data.max(), connectivity.number_of_regions) raise LaunchException(msg) self.logger.debug("Creating RegionMapping instance") region_mapping_inst = RegionMapping() region_mapping_inst.storage_path = self.storage_path region_mapping_inst.surface = surface region_mapping_inst.connectivity = connectivity if array_data is not None: region_mapping_inst.array_data = array_data return [region_mapping_inst]