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Debug the use of relative links (#46)
* Change zarr extension for NWB conversion * Add external link support for sphinx * Add tutorial to show how to create and NWB file with NWBZarrIO directly * Make source path for links relative to the current Zarr file and add function to resolve relative paths on read * Fix requirement definition in setup.py * Update requirements-dev.txt * Update run_tests.yml * Update test.py * Update tox.ini * Updated ToDo and Limitations list in docs Co-authored-by: mavaylon1 <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| """ | ||
| .. _nwbzarrio_tutorial: | ||
| Creating NWB files using ``NWBZarrIO`` | ||
| ====================================== | ||
| Similar to :py:class:`pynwb.NWBHDF5IO`, the :py:class:`~hdmf_zarr.nwb.NWBZarrIO` extends the basic | ||
| :py:class:`~hdmf_zarr.backend.ZarrIO` to perform default setup for BuildManager, loading or namespaces etc., | ||
| in the context of the NWB format, to simplify using hdmf-zarr with the NWB data standard. With this we | ||
| can use :py:class:`~hdmf_zarr.nwb.NWBZarrIO` directly with the PyNWB API to read/write NWB files to/from Zarr. | ||
| I.e., we can follow the standard PyNWB tutorials for using NWB files, and only need to replace | ||
| :py:class:`pynwb.NWBHDF5IO` with :py:class:`~hdmf_zarr.nwb.NWBZarrIO` for read/write (and replace the | ||
| use of py:class:`H5DataIO` with :py:class:`~hdmf_zarr.utils.ZarrDataIO`). | ||
| Creating and NWB extracellular electrophysiology file | ||
| ----------------------------------------------------- | ||
| As an example, we here create an extracellular electrophysiology NWB file. | ||
| This example is derived from :pynwb-docs:`Extracellular Electrophysiology <tutorials/domain/ecephys.html>` | ||
| tutorial. | ||
| """ | ||
| # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnail_plot_nwbzarrio.png' | ||
| # Ignore warnings about the development of the ZarrIO backend | ||
| import warnings | ||
| warnings.filterwarnings('ignore', '.*The ZarrIO backend is experimental*', ) | ||
|
|
||
| from datetime import datetime | ||
| from dateutil.tz import tzlocal | ||
|
|
||
| import numpy as np | ||
| from pynwb import NWBFile | ||
| from pynwb.ecephys import ElectricalSeries, LFP | ||
|
|
||
| # Create the NWBFile | ||
| nwbfile = NWBFile( | ||
| session_description="my first synthetic recording", | ||
| identifier="EXAMPLE_ID", | ||
| session_start_time=datetime.now(tzlocal()), | ||
| experimenter="Dr. Bilbo Baggins", | ||
| lab="Bag End Laboratory", | ||
| institution="University of Middle Earth at the Shire", | ||
| experiment_description="I went on an adventure with thirteen dwarves " | ||
| "to reclaim vast treasures.", | ||
| session_id="LONELYMTN", | ||
| ) | ||
|
|
||
| # Create a device | ||
| device = nwbfile.create_device( | ||
| name="array", description="the best array", manufacturer="Probe Company 9000" | ||
| ) | ||
|
|
||
| # Add electrodes and electrode groups to the NWB file | ||
| nwbfile.add_electrode_column(name="label", description="label of electrode") | ||
|
|
||
| nshanks = 4 | ||
| nchannels_per_shank = 3 | ||
| electrode_counter = 0 | ||
|
|
||
| for ishank in range(nshanks): | ||
| # create an electrode group for this shank | ||
| electrode_group = nwbfile.create_electrode_group( | ||
| name="shank{}".format(ishank), | ||
| description="electrode group for shank {}".format(ishank), | ||
| device=device, | ||
| location="brain area", | ||
| ) | ||
| # add electrodes to the electrode table | ||
| for ielec in range(nchannels_per_shank): | ||
| nwbfile.add_electrode( | ||
| x=5.3, y=1.5, z=8.5, imp=np.nan, | ||
| filtering='unknown', | ||
| group=electrode_group, | ||
| label="shank{}elec{}".format(ishank, ielec), | ||
| location="brain area", | ||
| ) | ||
| electrode_counter += 1 | ||
|
|
||
| # Create a table region to select the electrodes to record from | ||
| all_table_region = nwbfile.create_electrode_table_region( | ||
| region=list(range(electrode_counter)), # reference row indices 0 to N-1 | ||
| description="all electrodes", | ||
| ) | ||
|
|
||
| # Add a mock electrical recording acquisition to the NWBFile | ||
| raw_data = np.random.randn(50, 4) | ||
| raw_electrical_series = ElectricalSeries( | ||
| name="ElectricalSeries", | ||
| data=raw_data, | ||
| electrodes=all_table_region, | ||
| starting_time=0.0, # timestamp of the first sample in seconds relative to the session start time | ||
| rate=20000.0, # in Hz | ||
| ) | ||
| nwbfile.add_acquisition(raw_electrical_series) | ||
|
|
||
| # Add a mock LFP processing result to the NWBFile | ||
| lfp_data = np.random.randn(50, 4) | ||
| lfp_electrical_series = ElectricalSeries( | ||
| name="ElectricalSeries", | ||
| data=lfp_data, | ||
| electrodes=all_table_region, | ||
| starting_time=0.0, | ||
| rate=200.0, | ||
| ) | ||
| lfp = LFP(electrical_series=lfp_electrical_series) | ||
| ecephys_module = nwbfile.create_processing_module( | ||
| name="ecephys", description="processed extracellular electrophysiology data" | ||
| ) | ||
| ecephys_module.add(lfp) | ||
|
|
||
| # Add mock spike times and units to the NWBFile | ||
| nwbfile.add_unit_column(name="quality", description="sorting quality") | ||
|
|
||
| poisson_lambda = 20 | ||
| firing_rate = 20 | ||
| n_units = 10 | ||
| for n_units_per_shank in range(n_units): | ||
| n_spikes = np.random.poisson(lam=poisson_lambda) | ||
| spike_times = np.round( | ||
| np.cumsum(np.random.exponential(1 / firing_rate, n_spikes)), 5 | ||
| ) | ||
| nwbfile.add_unit( | ||
| spike_times=spike_times, quality="good", waveform_mean=[1.0, 2.0, 3.0, 4.0, 5.0] | ||
| ) | ||
|
|
||
| ############################################################################### | ||
| # Writing the NWB file to Zarr | ||
| # ----------------------------- | ||
| from hdmf_zarr.nwb import NWBZarrIO | ||
| import os | ||
|
|
||
| path = "ecephys_tutorial.nwb.zarr" | ||
| absolute_path = os.path.abspath(path) | ||
| with NWBZarrIO(path=path, mode="w") as io: | ||
| io.write(nwbfile) | ||
|
|
||
| ############################################################################### | ||
| # Test opening the file | ||
| # --------------------- | ||
| with NWBZarrIO(path=path, mode="r") as io: | ||
| infile = io.read() | ||
|
|
||
| ############################################################################### | ||
| # Test opening with the absolute path instead | ||
| # ------------------------------------------- | ||
| with NWBZarrIO(path=absolute_path, mode="r") as io: | ||
| infile = io.read() | ||
|
|
||
| ############################################################################### | ||
| # Test changing the current directory | ||
| # ------------------------------------ | ||
|
|
||
| import os | ||
| os.chdir(os.path.abspath(os.path.join(os.getcwd(), "../"))) | ||
|
|
||
| with NWBZarrIO(path=absolute_path, mode="r") as io: | ||
| infile = io.read() |
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