Ryan Ly rly
rly
/ xarray_reading_nwb_hdf5_via_zarr_rfs.ipynb
Last active
March 28, 2024 07:37
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rly
/ fix_dandiset_000776.py
Last active
February 8, 2024 02:01
Script to fix invalid "order_optical_channels" group in NWB files in dandiset 000776
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| # In dandiset 000776, the data is invalid against the spec. See https://github.com/dandi/helpdesk/issues/126 | |
| # To fix the files in dandiset 000776, run this script on dandihub. This script performs the following data surgery | |
| # steps: | |
| # | |
| # 1. Replace the "order_optical_channels" link from all `ImagingVolume` objects with a subgroup | |
| # that is the link target (at /processing/NeuroPAL/OpticalChannelRefs) | |
| # 2. Add the "ndx-multichannel-volume" version 0.1.12 schema | |
| # 3. Remove the "ndx-multichannel-volume" version 0.1.9 schema | |
| # 4. Remove the "order_optical_channels" group from all "MultiChannelVolume" objects | |
| # 5. Remove the "OpticalChannelRefs" group within "/processing" |
rly
/ remove_units_table.ipynb
Created
January 16, 2024 19:28
Demonstration of how to remove the Units table from an NWB file
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rly
/ measure_hdf5_group_overhead.ipynb
Created
January 5, 2024 22:10
Measure the space overhead of creating many HDF5 groups
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rly
/ pynwb_1798.ipynb
Last active
December 14, 2023 06:10
Example code for https://github.com/NeurodataWithoutBorders/pynwb/issues/1798
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rly
/ fix_dandiset_000114.py
Last active
November 21, 2023 02:46
Script to fix incorrect namespace attributes in NWB files in dandiset 000114
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| import glob | |
| import h5py | |
| import argparse | |
| from typing import Union | |
| def replace_namespace(_: str, h5obj: Union[h5py.Dataset, h5py.Group]): | |
| # change the attribute "namespace" from value "hdmf-experimental" to "hdmf-common" | |
| # for all DynamicTableRegion and VectorData neurodata types from ndx-photometry. | |
| if h5obj.attrs.get("namespace") == "hdmf-experimental": |
rly
/ test_modify_nwb.ipynb
Created
October 9, 2023 21:44
Tests on what is currently possible for modifying an NWB file using PyNWB and h5py
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rly
/ get_namespace_versions.ipynb
Last active
August 16, 2023 17:56
Get the versions of the namespaces/extensions cached in an NWB file or used by PyNWB
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rly
/ spec_non_string_value.ipynb
Created
June 17, 2023 12:29
Test behavior of PyNWB/HDMF with an attribute spec that has a non-text or non-scalar default value.
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rly
/ test_column_of_containers.ipynb
Last active
May 30, 2023 20:07
Create an NWB DynamicTable with a column of object references
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