Demonstration of the loading of NWB namespaces in different contexts

print_namespaces.py

import pynwb
from pynwb.spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace

from hdmf.spec import NamespaceCatalog
from hdmf.build import TypeMap


def print_namespace_versions(type_map):
    """Print the namespace name and version of all namespaces in the given type map."""
    for ns_name in type_map.namespace_catalog.namespaces:
        print("%s: %s" % (ns_name, type_map.namespace_catalog.get_namespace(ns_name)["version"]))


path = r"C:\Users\Ryan\Documents\NWB_Data\AIBS_ecephys_dandiset21\sub-699733573_ses-715093703_probe-810755797_ecephys.nwb"

# pynwb contains the latest versions of certain namespaces (pynwb, hdmf-common, and hdmf-experimental)
# that are available at the time of release of this version of pynwb.
# these namespaces are automatically loaded into all NWBHDF5IO objects subsequently created
print("Namespaces loaded in global scope:")
print_namespace_versions(pynwb.get_manager().type_map)
print()

# NWB files contain cached namespaces which may have different versions that the
# namespaces with the same name loaded in the global scope
catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)
pynwb.NWBHDF5IO.load_namespaces(catalog, path)
tm = TypeMap(catalog)
print("Namespaces cached in the NWB file '%s':" % path)
print_namespace_versions(tm)
print()

# the global scope namespaces are loaded into the NWBHDF5IO object when it is created
# when load_namespaces=True, all namespaces cached within the NWB file that are not
# already in the namespaces within the NWBHDF5IO object (ignoring the version of the namespace)
# are then loaded into the NWBHDF5IO object
io = pynwb.NWBHDF5IO(path, "r", load_namespaces=True)
print("Namespaces loaded in the build manager for the NWB file '%s':" % path)
print_namespace_versions(io.manager.type_map)
print()

# loading cached namespaces into an NWBHDF5IO object does not affect the namespaces
# loaded in the global scope
print("Namespaces loaded in global scope:")
print_namespace_versions(pynwb.get_manager().type_map)
print()

# load a namespace into the global scope, which will be loaded into all NWBHDF5IO objects
# subsequently created
namespace_filepath = "ndx-ecog.namespace.yaml"
pynwb.load_namespaces(namespace_filepath)

# note that the new namespace is present in the global scope
print("Namespaces loaded in global scope:")
print_namespace_versions(pynwb.get_manager().type_map)
print()

# note that the new namespace is present in the namespaces for this NWBHDF5IO object
io = pynwb.NWBHDF5IO(path, "r", load_namespaces=True)
print("Namespaces loaded in the build manager for the NWB file '%s':" % path)
print_namespace_versions(io.manager.type_map)
print()