Source code for tvb.adapters.uploaders.region_mapping_importer

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.. moduleauthor:: Calin Pavel

import tempfile
import zipfile

import numpy
from tvb.adapters.datatypes.db.region_mapping import RegionMappingIndex
from tvb.basic.logger.builder import get_logger
from tvb.basic.profile import TvbProfile
from tvb.core.adapters.abcuploader import ABCUploader, ABCUploaderForm
from tvb.core.adapters.exceptions import LaunchException
from tvb.core.entities.filters.chain import FilterChain
from tvb.core.neocom import h5
from tvb.core.neotraits.forms import TraitUploadField, TraitDataTypeSelectField
from tvb.core.neotraits.uploader_view_model import UploaderViewModel
from tvb.core.neotraits.view_model import Str, DataTypeGidAttr
from tvb.datatypes.connectivity import Connectivity
from tvb.datatypes.region_mapping import RegionMapping
from tvb.datatypes.surfaces import Surface, SurfaceTypesEnum

[docs]class RegionMappingImporterModel(UploaderViewModel): mapping_file = Str( label='Please upload region mapping file (txt, zip or bz2 format)', doc='Expected a text/zip/bz2 file containing region mapping values.' ) surface = DataTypeGidAttr( linked_datatype=Surface, label='Brain Surface', doc='The Brain Surface used by uploaded region mapping.' ) connectivity = DataTypeGidAttr( linked_datatype=Connectivity, label='Connectivity', required=True, doc='The Connectivity used by uploaded region mapping.' )
[docs]class RegionMappingImporterForm(ABCUploaderForm): def __init__(self): super(RegionMappingImporterForm, self).__init__() self.mapping_file = TraitUploadField(RegionMappingImporterModel.mapping_file, ('.txt', '.zip', '.bz2'), 'mapping_file') surface_conditions = FilterChain(fields=[FilterChain.datatype + '.surface_type'], operations=['=='], values=[SurfaceTypesEnum.CORTICAL_SURFACE.value]) self.surface = TraitDataTypeSelectField(RegionMappingImporterModel.surface, name='surface', conditions=surface_conditions) self.connectivity = TraitDataTypeSelectField(RegionMappingImporterModel.connectivity, name='connectivity')
[docs] @staticmethod def get_view_model(): return RegionMappingImporterModel
[docs] @staticmethod def get_upload_information(): return { 'mapping_file': ('.txt', '.zip', '.bz2') }
[docs]class RegionMappingImporter(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_form_class(self): return RegionMappingImporterForm
[docs] def get_output(self): return [RegionMappingIndex]
[docs] def launch(self, view_model): # type: (RegionMappingImporterModel) -> [RegionMappingIndex] """ Creates region mapping from uploaded data. :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 view_model.mapping_file is None: raise LaunchException("Please select mappings file which contains data to import") if view_model.surface is None: raise LaunchException("No surface selected. Please initiate upload again and select a brain surface.") if view_model.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(view_model.mapping_file): tmp_folder = tempfile.mkdtemp(prefix='region_mapping_zip_', dir=TvbProfile.current.TVB_TEMP_FOLDER) try: files = self.storage_interface.unpack_zip(view_model.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: self.storage_interface.remove_folder(tmp_folder, True) else: array_data = self.read_list_data(view_model.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. surface_idx = self.load_entity_by_gid(view_model.surface) if len(array_data) != surface_idx.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_idx.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") conn_idx = self.load_entity_by_gid(view_model.connectivity) if array_data.max() >= conn_idx.number_of_regions: msg = "Imported file contains invalid regions. Found region: %d while selected connectivity has: %d " \ "regions defined (0 based)." % (array_data.max(), conn_idx.number_of_regions) raise LaunchException(msg) self.logger.debug("Creating RegionMapping instance") surface_ht = h5.load_from_index(surface_idx) connectivity_ht = h5.load_from_index(conn_idx) region_mapping = RegionMapping(surface=surface_ht, connectivity=connectivity_ht, array_data=array_data) return self.store_complete(region_mapping)