Passing full path to a NWB file

[gviejo]

Hello I would like to know if it is possible to give the full path of an object within a NWB file.
For example, I create two objects within the field acquisition

    from pynwb.testing.mock.base import mock_TimeSeries
    from pynwb.testing.mock.file import mock_NWBFile

    # Tsd
    nwbfile = mock_NWBFile()
    tsd1 = mock_TimeSeries("tsd1")
    nwbfile.add_acquisition(tsd1)
    tsd2 = mock_TimeSeries("tsd2")
    nwbfile.add_acquisition(tsd2)

I know I can access with nwbfile.acquisition['tsd1']. Is there something closer to nwb['/acquisition/tsd1'] ?
Thank you for your help.
Guillaume

[rly]

@gviejo Accessing an object by HDF5 path is not supported by PyNWB right now, but perhaps it should. PyNWB was designed to be an API where objects are accessed in a more convenient way for average users than using the raw HDF5 representation under the hood. Some groups are hidden, like the "general" group, and objects are generally accessed as values of dictionaries and attributes of other objects. This is especially convenient where some low-level implementations are best hidden to the user, like how ragged arrays work in a DynamicTable.

What are you trying to do using this way of accessing objects? How do you know what the objects are named? We could add this feature into PyNWB.

Right now though, if you want to access an object by its known HDF5 path, you can use h5py.

[gviejo]

Hi Ryan, I am trying to solve this pull request .
For solving it, I would need to write a test that basically give the same name for 2 objects but within different subfield. For example
object 1 in /acquisition/timeseries and object 2 in /processing/timeseries. It is not clear to me if it is possible in NWB or if every object has a unique name?
Thanks

[oruebel]

object 1 in /acquisition/timeseries and object 2 in /processing/timeseries. It is not clear to me if it is possible in NWB or if every object has a unique name?

Every object must have a unique path in the file, but you can certainly have two objects with the same name in two different locations of the file, i.e., having /acquisition/timeseries and /processing/my_module/timeseries is fine. I believe, for /processing you may also need to create a processing module. I.e,. something like this should work:

from datetime import datetime
import numpy as np
from pynwb import NWBFile, NWBHDF5IO
from pynwb.base import TimeSeries
from pynwb.processing import ProcessingModule

# Create an NWB file
nwbfile = NWBFile(session_description='test session',
                  identifier='NWB123',
                  session_start_time=datetime.now().astimezone())

# Create sample data for the TimeSeries
data = np.random.randn(100)  # 100 random data points
timestamps = np.arange(100)  # 100 time points

# Create a TimeSeries object with the same name for acquisition
timeseries_acq = TimeSeries(name='timeseries',
                            data=data,
                            unit='mV',
                            timestamps=timestamps)

# Add the TimeSeries to the acquisition group
nwbfile.add_acquisition(timeseries_acq)

# Create a TimeSeries object with the same name for processing
timeseries_proc = TimeSeries(name='timeseries',
                             data=data,
                             unit='mV',
                             timestamps=timestamps)

# Create a ProcessingModule and add the TimeSeries to it
processing_module = ProcessingModule(name='processed', description='processed data')
processing_module.add(timeseries_proc)

# Add the ProcessingModule to the NWB file
nwbfile.add_processing_module(processing_module)

# Write the NWB file
with NWBHDF5IO('example_file.nwb', 'w') as io:
    io.write(nwbfile)

# Read the NWB file and verify the contents
with NWBHDF5IO('example_file.nwb', 'r') as io:
    nwbfile = io.read()
    print(nwbfile.acquisition['timeseries'])
    print(nwbfile.processing['processed'].get('timeseries'))

[gviejo]

Thank you Oliver. I think the line from pynwb.processing import ProcessingModule is incorrect for pynwb 2.8.1. It works with from pynwb import ProcessingModule.