Source code for tvb.adapters.uploaders.region_mapping_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 to download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2023, 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 <http://www.gnu.org/licenses/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
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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 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_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)
