Modular Data Storage using External Files

PyNWB supports linking between files using external links.

Example Use Case: Integrating data from multiple files

NBWContainer classes (e.g., TimeSeries) support the integration of data stored in external HDF5 files with NWB data files via external links. To make things more concrete, let’s look at the following use case. We want to simultaneously record multiple data streams during data acquisition. Using the concept of external links allows us to save each data stream to an external HDF5 files during data acquisition and to afterwards link the data into a single NWB:N file. In this case, each recording becomes represented by a separate file-system object that can be set as read-only once the experiment is done. In the following we are using TimeSeries as an example, but the same approach works for other NWBContainers as well.

Tip

The same strategies we use here for creating External Links also apply to Soft Links. The main difference between soft and external links is that soft links point to other objects within the same file while external links point to objects in external files.

Tip

In the case of TimeSeries, the uncorrected timestamps generated by the acquisition system can be stored (or linked) in the sync group. In the NWB:N format, hardware-recorded time data must then be corrected to a common time base (e.g., timestamps from all hardware sources aligned) before it can be included in the timestamps of the TimeSeries. This means, in the case of TimeSeries we need to be careful that we are not including data with incompatible timestamps in the same file when using external links.

Warning

External links can become stale/break. Since external links are pointing to data in other files external links may become invalid any time files are modified on the file system, e.g., renamed, moved or access permissions are changed.

Creating test data

In the following we are creating two TimeSeries each written to a separate file. We then show how we can integrate these files into a single NWBFile.

from datetime import datetime
from dateutil.tz import tzlocal
from pynwb import NWBFile
from pynwb import TimeSeries
from pynwb import NWBHDF5IO
import numpy as np

# Create the base data
start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
create_date = datetime(2017, 4, 15, 12, tzinfo=tzlocal())
data = np.arange(1000).reshape((100, 10))
timestamps = np.arange(100)
filename1 = 'external1_example.nwb'
filename2 = 'external2_example.nwb'
filename3 = 'external_linkcontainer_example.nwb'
filename4 = 'external_linkdataset_example.nwb'

# Create the first file
nwbfile1 = NWBFile(session_description='demonstrate external files',
                   identifier='NWBE1',
                   session_start_time=start_time,
                   file_create_date=create_date)
# Create the second file
test_ts1 = TimeSeries(name='test_timeseries1',
                      data=data,
                      unit='SIunit',
                      timestamps=timestamps)
nwbfile1.add_acquisition(test_ts1)
# Write the first file
io = NWBHDF5IO(filename1, 'w')
io.write(nwbfile1)
io.close()

# Create the second file
nwbfile2 = NWBFile(session_description='demonstrate external files',
                   identifier='NWBE2',
                   session_start_time=start_time,
                   file_create_date=create_date)
# Create the second file
test_ts2 = TimeSeries(name='test_timeseries2',
                      data=data,
                      unit='SIunit',
                      timestamps=timestamps)
nwbfile2.add_acquisition(test_ts2)
# Write the second file
io = NWBHDF5IO(filename2, 'w')
io.write(nwbfile2)
io.close()

Linking to select datasets

Step 1: Create the new NWBFile

# Create the first file
nwbfile4 = NWBFile(session_description='demonstrate external files',
                   identifier='NWBE4',
                   session_start_time=start_time,
                   file_create_date=create_date)

Step 4: Write the data

from pynwb import NWBHDF5IO

io4 = NWBHDF5IO(filename4, 'w')
io4.write(nwbfile4,
          link_data=True)     # <-------- Specify default behavior to link rather than copy data
io4.close()

Note

In the case of TimeSeries one advantage of linking to just the main dataset is that we can now use our own timestamps in case the timestamps in the original file are not aligned with the clock of the NWBFile we are creating. In this way we can use the linking to “re-align” different TimeSeries without having to copy the main data.

Linking to whole Containers

Appending to files and linking is made possible by passing around the same BuildManager. You can get a manager to pass around using the get_manager function.

from pynwb import get_manager

manager = get_manager()

Tip

You can pass in extensions to get_manager using the extensions argument.

Step 2: Add the container to another NWBFile

To intergrate both TimeSeries into a single file we simply create a new NWBFile and our existing TimeSeries to it. PyNWB’s NWBHDF5IO backend then automatically detects that the TimeSeries have already been written to another file and will create external links for us.

# Create a new NWBFile that links to the external timeseries
nwbfile3 = NWBFile(session_description='demonstrate external files',
                   identifier='NWBE3',
                   session_start_time=start_time,
                   file_create_date=create_date)
nwbfile3.add_acquisition(timeseries_1)             # <--------
nwbfile3.add_acquisition(timeseries_2)             # <--------

# Write our third file that includes our two timeseries as external links
io3 = NWBHDF5IO(filename3, 'w', manager=manager)
io3.write(nwbfile3)
io3.close()

Copying an NWBFile for linking

Using the copy method allows us to easily create a shallow copy of a whole NWB:N file with links to all data in the original file. For example, we may want to store processed data in a new file separate from the raw data, while still being able to access the raw data. See the Exploratory data analysis with NWB tutorial for a detailed example.

Creating a single file for sharing

External links are convenient but to share data we may want to hand a single file with all the data to our collaborator rather than having to collect all relevant files. To do this, HDF5IO (and in turn NWBHDF5IO) provide the convenience function copy_file, which copies an HDF5 file and resolves all external links.

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