def test_store_load_complete_region_mapping(tmph5factory, connectivity_factory, surface_factory, region_mapping_factory):
connectivity = connectivity_factory(2)
surface = surface_factory(5)
region_mapping = region_mapping_factory(surface, connectivity)
with ConnectivityH5(tmph5factory('Connectivity_{}.h5'.format(connectivity.gid))) as conn_h5:
conn_h5.store(connectivity)
conn_stored = Connectivity()
conn_h5.load_into(conn_stored)
with SurfaceH5(tmph5factory('Surface_{}.h5'.format(surface.gid))) as surf_h5:
surf_h5.store(surface)
surf_stored = Surface()
surf_h5.load_into(surf_stored)
with RegionMappingH5(tmph5factory('RegionMapping_{}.h5'.format(region_mapping.gid))) as rm_h5:
rm_h5.store(region_mapping)
rm_stored = RegionMapping()
rm_h5.load_into(rm_stored)
# load_into will not load dependent datatypes. connectivity and surface are undefined
with pytest.raises(TraitAttributeError):
rm_stored.connectivity
with pytest.raises(TraitAttributeError):
rm_stored.surface
rm_stored.connectivity = conn_stored
rm_stored.surface = surf_stored
assert rm_stored.connectivity is not None
assert rm_stored.surface is not None
def deserialize_simulator(simulator_gid, storage_path):
simulator_in_path = h5.path_for(storage_path, SimulatorH5,
simulator_gid)
simulator_in = Simulator()
with SimulatorH5(simulator_in_path) as simulator_in_h5:
simulator_in_h5.load_into(simulator_in)
connectivity_gid = simulator_in_h5.connectivity.load()
stimulus_gid = simulator_in_h5.stimulus.load()
simulation_state_gid = simulator_in_h5.simulation_state.load()
conn_index = dao.get_datatype_by_gid(connectivity_gid.hex)
conn = h5.load_from_index(conn_index)
simulator_in.connectivity = conn
if simulator_in.surface:
cortex_path = h5.path_for(storage_path, CortexH5,
simulator_in.surface.gid)
with CortexH5(cortex_path) as cortex_h5:
local_conn_gid = cortex_h5.local_connectivity.load()
region_mapping_gid = cortex_h5.region_mapping_data.load()
region_mapping_index = dao.get_datatype_by_gid(
region_mapping_gid.hex)
region_mapping_path = h5.path_for_stored_index(
region_mapping_index)
region_mapping = RegionMapping()
with RegionMappingH5(region_mapping_path) as region_mapping_h5:
region_mapping_h5.load_into(region_mapping)
region_mapping.gid = region_mapping_h5.gid.load()
surf_gid = region_mapping_h5.surface.load()
surf_index = dao.get_datatype_by_gid(surf_gid.hex)
surf_h5 = h5.h5_file_for_index(surf_index)
surf = CorticalSurface()
surf_h5.load_into(surf)
surf_h5.close()
region_mapping.surface = surf
simulator_in.surface.region_mapping_data = region_mapping
if local_conn_gid:
local_conn_index = dao.get_datatype_by_gid(local_conn_gid.hex)
local_conn = h5.load_from_index(local_conn_index)
simulator_in.surface.local_connectivity = local_conn
if stimulus_gid:
stimulus_index = dao.get_datatype_by_gid(stimulus_gid.hex)
stimulus = h5.load_from_index(stimulus_index)
simulator_in.stimulus = stimulus
return simulator_in, simulation_state_gid
def _store_related_region_mappings(self, original_conn_gid, new_connectivity_ht):
result = []
linked_region_mappings = dao.get_generic_entity(RegionMappingIndex, original_conn_gid, 'fk_connectivity_gid')
for mapping in linked_region_mappings:
original_rm = h5.load_from_index(mapping)
surface = self.load_traited_by_gid(mapping.fk_surface_gid)
new_rm = RegionMapping()
new_rm.connectivity = new_connectivity_ht
new_rm.surface = surface
new_rm.array_data = original_rm.array_data
result_rm_index = self.store_complete(new_rm)
result.append(result_rm_index)
return result
def _store_related_region_mappings(self, original_conn_gid,
new_connectivity_ht):
result = []
linked_region_mappings = dao.get_generic_entity(
RegionMappingIndex, original_conn_gid, 'connectivity_gid')
for mapping in linked_region_mappings:
original_rm = h5.load_from_index(mapping)
surface_idx = dao.get_generic_entity(SurfaceIndex,
mapping.surface_gid, 'gid')[0]
surface = h5.load_from_index(surface_idx)
new_rm = RegionMapping()
new_rm.connectivity = new_connectivity_ht
new_rm.surface = surface
new_rm.array_data = original_rm.array_data
result_rm_index = h5.store_complete(new_rm, self.storage_path)
result.append(result_rm_index)
return result
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]
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.set_operation_id(self.operation_id)
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]
