Exporting NWB files¶
You can use the export feature of PyNWB to create a modified version of an existing NWB file, while preserving the original file.
To do so, first open the NWB file using
NWBHDF5IO. Then, read the NWB file into an
NWBFile object or its child objects, and export the modified
NWBFile object to a new file path.
The modifications will appear in the exported file and not the original file.
These modifications can consist of removals of containers, additions of containers, and changes to container attributes.
If container attributes are changed, then
NWBFile.set_modified() must be called
NWBFile before exporting.
with NWBHDF5IO(self.read_path, mode='r') as read_io: nwbfile = read_io.read() # ... # modify nwbfile nwbfile.set_modified() # this may be necessary if the modifications are changes to attributes with NWBHDF5IO(self.export_path, mode='w') as export_io: export_io.export(src_io=read_io, nwbfile=nwbfile)
h5py.Dataset objects act directly on the read file on disk.
Changes are applied immediately and do not require exporting or writing the file. If you want to modify a dataset
only in the new file, than you should replace the whole object with a new array holding the modified data. To
prevent unintentional changes to the source file, the source file should be opened with
Moving containers within the same file is currently not supported directly via export. See the following discussion on the NWB Help Desk for details.
After exporting an
NWBFile, the object IDs of the
NWBFile and its child containers will be identical to the
object IDs of the read
NWBFile and its child containers. The object ID of a container uniquely identifies the
container within a file, but should not be used to distinguish between two different files.
The tutorial Adding/Removing Containers from an NWB File provides additional examples of adding and removing containers from an NWB file.
How do I create a copy of an NWB file with different data layouts (e.g., applying compression)?¶
How do I generate new object IDs for a newly exported NWB file?¶
export, call the method
generate_new_id on the
NWBFile to generate
a new set of object IDs for the
NWBFile and all of its children, recursively. Then export the
The original NWB file is preserved.
with NWBHDF5IO(self.read_path, manager=manager, mode='r') as read_io: nwbfile = read_io.read() # ... # modify nwbfile if desired nwbfile.generate_new_id() with NWBHDF5IO(self.export_path, mode='w') as export_io: export_io.export(src_io=read_io, nwbfile=nwbfile)
How do I write a newly instantiated
NWBFile to two different file paths?¶
PyNWB does not support writing an
NWBFile that was not read from a file to two different files.
For example, if you instantiate
NWBFile A and write it to file path 1, you cannot also write it to file path 2.
However, you can first write the
NWBFile to file path 1, read the
NWBFile from file path 1, and
then export it to file path 2.
with NWBHDF5IO(self.filepath1, manager=manager, mode='w') as write_io: write_io.write(nwbfile) with NWBHDF5IO(self.filepath1, manager=manager, mode='r') as read_io: read_nwbfile = read_io.read() with NWBHDF5IO(self.filepath2, mode='w') as export_io: export_io.export(src_io=read_io, nwbfile=nwbfile)