def import_region_mapping(user, project, import_file_path, surface_gid, connectivity_gid, same_process=True):
view_model = RegionMappingImporterModel()
view_model.mapping_file = import_file_path
view_model.surface = surface_gid
view_model.connectivity = connectivity_gid
TestFactory.launch_importer(RegionMappingImporter, view_model, user, project, same_process)
return TestFactory._assert_one_more_datatype(project, RegionMappingIndex)
def import_surface_rm(project_id, conn_gid):
# Import surface and region mapping from tvb_data berlin subjects (68 regions)
rm_file = try_get_absolute_path("tvb_data", "berlinSubjects/DH_20120806/DH_20120806_RegionMapping.txt")
surface_zip_file = try_get_absolute_path("tvb_data", "berlinSubjects/DH_20120806/DH_20120806_Surface_Cortex.zip")
surface_importer = ABCAdapter.build_adapter_from_class(ZIPSurfaceImporter)
surface_imp_model = ZIPSurfaceImporterModel()
surface_imp_model.uploaded = surface_zip_file
surface_imp_operation = fire_operation(project_id, surface_importer, surface_imp_model)
surface_imp_operation = wait_to_finish(surface_imp_operation)
surface_gid = dao.get_results_for_operation(surface_imp_operation.id)[0].gid
rm_importer = ABCAdapter.build_adapter_from_class(RegionMappingImporter)
rm_imp_model = RegionMappingImporterModel()
rm_imp_model.mapping_file = rm_file
rm_imp_model.surface = surface_gid
rm_imp_model.connectivity = conn_gid
rm_import_operation = fire_operation(project_id, rm_importer, rm_imp_model)
wait_to_finish(rm_import_operation)
def launch_operation_examples(tvb_client_instance):
logger.info("Requesting projects for logged user")
projects_of_user = tvb_client_instance.get_project_list()
assert len(projects_of_user) > 0
logger.info("TVB has {} projects for this user".format(len(projects_of_user)))
project_gid = projects_of_user[0].gid
# --- Launch operations to import a Connectivity, a Surface and a RegionMapping ---
logger.info("Importing a connectivity from ZIP...")
zip_connectivity_importer_model = ZIPConnectivityImporterModel()
zip_connectivity_importer_model.uploaded = compute_tvb_data_path('connectivity', 'connectivity_96.zip')
zip_connectivity_importer_model.normalization = 'region'
operation_gid = tvb_client_instance.launch_operation(project_gid, ZIPConnectivityImporter,
zip_connectivity_importer_model)
monitor_operation(tvb_client_instance, operation_gid)
logger.info("Get the result of connectivity import...")
connectivity_dto = tvb_client_instance.get_operation_results(operation_gid)[0]
logger.info("Importing a surface from ZIP...")
zip_surface_importer_model = ZIPSurfaceImporterModel()
zip_surface_importer_model.uploaded = compute_tvb_data_path('surfaceData', 'cortex_16384.zip')
zip_surface_importer_model.surface_type = CORTICAL
zip_surface_importer_model.should_center = False
operation_gid = tvb_client_instance.launch_operation(project_gid, ZIPSurfaceImporter, zip_surface_importer_model)
monitor_operation(tvb_client_instance, operation_gid)
logger.info("Get the result of surface import...")
surface_dto = tvb_client_instance.get_operation_results(operation_gid)[0]
logger.info("Importing a region mapping...")
rm_importer_model = RegionMappingImporterModel()
rm_importer_model.mapping_file = compute_tvb_data_path('regionMapping', 'regionMapping_16k_76.txt')
rm_importer_model.connectivity = connectivity_dto.gid
rm_importer_model.surface = surface_dto.gid
operation_gid = tvb_client_instance.launch_operation(project_gid, RegionMappingImporter, rm_importer_model)
monitor_operation(tvb_client_instance, operation_gid)
logger.info("Get the result of region mapping import...")
region_mapping_dto = tvb_client_instance.get_operation_results(operation_gid)[0]
# --- Load the region mapping together with references information in 3 different ways ---
logger.info("1.Download and load the region mapping with all its references...")
region_mapping_complete = tvb_client_instance.load_datatype_with_full_references(region_mapping_dto.gid,
tvb_client_instance.temp_folder)
logger.info("1.This region mapping is linked to a connectivity with GID={} and number_of_regions={}".format(
region_mapping_complete.connectivity.gid, region_mapping_complete.connectivity.number_of_regions))
logger.info("2.Download and load the region mapping with only GIDs for its references...")
region_mapping_with_links = tvb_client_instance.load_datatype_with_links(region_mapping_dto.gid,
tvb_client_instance.temp_folder)
logger.info("2.This region mapping is linked to a connectivity with GID={}".format(
region_mapping_with_links.connectivity.gid))
logger.info("3.Only download the region mapping on client machine...")
region_mapping_path = tvb_client_instance.retrieve_datatype(region_mapping_dto.gid, tvb_client_instance.temp_folder)
logger.info("3.Load the region mapping that was already downloaded on client machine...")
local_region_mapping_with_links = tvb_client_instance.load_datatype_from_file(region_mapping_path)
logger.info("3.This region mapping is linked to a connectivity with GID={}".format(
local_region_mapping_with_links.connectivity.gid))
# --- Launch operation to run a Degree Analyzer over the Connectivity ---
bct_model = BaseBCTModel()
bct_model.connectivity = connectivity_dto.gid
operation_gid = tvb_client_instance.launch_operation(project_gid, Degree, bct_model)
monitor_operation(tvb_client_instance, operation_gid)
logger.info("Get the result of BCT...")
bct_dto = tvb_client_instance.get_operation_results(operation_gid)[0]
logger.info("The resulted BCT has GID={}".format(bct_dto.gid))
surface_result = tvb_client.get_operation_results(operation_gid)[0]
logger.info("Downloading the connectivity from server...")
connectivity_path = tvb_client.retrieve_datatype(connectivity_result.gid, TvbProfile.current.TVB_TEMP_FOLDER)
logger.info("Downloading the surface from server...")
surface_path = tvb_client.retrieve_datatype(surface_result.gid, TvbProfile.current.TVB_TEMP_FOLDER)
logger.info("Preparing a region mapping H5 file using the downloaded connectivity and surface...")
rm_view_model = RegionMappingImporterModel()
rm_text_path = os.path.join(os.path.dirname(tvb_data.__file__), 'regionMapping', 'regionMapping_16k_76.txt')
rm_view_model.mapping_file = rm_text_path
conn_db = dao.get_datatype_by_gid(connectivity_result.gid).gid
rm_view_model.connectivity = UUID(conn_db)
surface_db = dao.get_datatype_by_gid(surface_result.gid).gid
rm_view_model.surface = UUID(surface_db)
logger.info("Launching region mapping upload operation...")
operation_gid = tvb_client.launch_operation(project_gid, RegionMappingImporter, rm_view_model)
while True:
status = tvb_client.get_operation_status(operation_gid)
if status in [STATUS_FINISHED, STATUS_CANCELED, STATUS_ERROR]:
break
time.sleep(5)
logger.info("The region mapping uploading has finished with status: {}".format(status))
os.remove(connectivity_path)
os.remove(surface_path)
logger.info("Preparing a connectivity csv H5 file (this one requires two datatype files: one containing weights and the other one containing tracts)...")
csv_view_model = CSVConnectivityImporterModel()
zip_surface_importer_model.surface_type = CORTICAL
zip_surface_importer_model.should_center = False
operation_gid = tvb_client.launch_operation(project_gid,
ZIPSurfaceImporter,
zip_surface_importer_model)
monitor_operation(tvb_client, operation_gid)
logger.info("Get the result of surface import...")
surface_dto = tvb_client.get_operation_results(operation_gid)[0]
logger.info("Importing a region mapping...")
rm_importer_model = RegionMappingImporterModel()
rm_importer_model.mapping_file = compute_tvb_data_path(
'regionMapping', 'regionMapping_16k_76.txt')
rm_importer_model.connectivity = connectivity_dto.gid
rm_importer_model.surface = surface_dto.gid
operation_gid = tvb_client.launch_operation(project_gid,
RegionMappingImporter,
rm_importer_model)
monitor_operation(tvb_client, operation_gid)
logger.info("Get the result of region mapping import...")
region_mapping_dto = tvb_client.get_operation_results(operation_gid)[0]
# --- Load the region mapping together with references information in 3 different ways ---
logger.info(
"1.Download and load the region mapping with all its references...")
region_mapping_complete = tvb_client.load_datatype_with_full_references(
region_mapping_dto.gid, tvb_client.temp_folder)
logger.info(