diff --git a/docs/gallery/advanced_io/plot_editing.py b/docs/gallery/advanced_io/plot_editing.py index d555c4a9b..b7dff1bd0 100644 --- a/docs/gallery/advanced_io/plot_editing.py +++ b/docs/gallery/advanced_io/plot_editing.py @@ -14,14 +14,11 @@ file after editing it. See :ref:`validating`. -In-place editing with h5py ---------------------------- -The :py:mod:`h5py` package allows for in-place editing of HDF5 files. Where possible, -this is the recommended way to edit HDF5 files. - -Editing values of datasets and attributes -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -You can change the value(s) of a dataset using :py:mod:`h5py`. +Editing datasets in place +-------------------------- +When reading an HDF5 NWB file, PyNWB exposes :py:class:`h5py.Dataset` objects, which can +be edited in place. For this to work, you must open the file in read/write mode +(``"r+"`` or ``"a"``). First, let's create an NWB file with data: """ @@ -50,23 +47,29 @@ with NWBHDF5IO("test_edit.nwb", "w") as io: io.write(nwbfile) - ############################################## -# Now, let's try to edit the values of the dataset: -import h5py +# Editing values of datasets +# ~~~~~~~~~~~~~~~~~~~~~~~~~~ +# +# Now, let's edit the values of the dataset + +with NWBHDF5IO("test_edit.nwb", "r+") as io: + nwbfile = io.read() + nwbfile.acquisition["synthetic_timeseries"].data[:10] = 0.0 -with h5py.File("test_edit.nwb", "r+") as f: - f["acquisition"]["synthetic_timeseries"]["data"][:10] = 0.0 ############################################## -# This will edit the dataset in-place, and should work for all datasets. You can also -# edit attributes in-place: +# You can also edit the attributes of that dataset through the ``attrs`` attribute: -with h5py.File("test_edit.nwb", "r+") as f: - f["acquisition"]["synthetic_timeseries"]["data"].attrs["unit"] = "volts" +with NWBHDF5IO("test_edit.nwb", "r+") as io: + nwbfile = io.read() + nwbfile.acquisition["synthetic_timeseries"].data.attrs["unit"] = "volts" ############################################## -# This also works for attributes of groups: +# If you want to edit the attributes of a group, you will need to open the file and edit +# it using :py:mod:`h5py`: + +import h5py with h5py.File("test_edit.nwb", "r+") as f: f["acquisition"]["synthetic_timeseries"].attrs["description"] = "Random values in volts" @@ -135,17 +138,17 @@ # ``maxshape``, then the dataset will have a fixed shape. You can change the shape of # this dataset. -import h5py -with h5py.File("test_edit2.nwb", "r+") as f: - f["acquisition"]["synthetic_timeseries"]["data"].resize((200, 100)) +with NWBHDF5IO("test_edit2.nwb", "r+") as io: + nwbfile = io.read() + nwbfile.acquisition["synthetic_timeseries"].resize((200, 100)) ############################################## # This will change the shape of the dataset in-place. If you try to change the shape of # a dataset with a fixed shape, you will get an error. # -# Replacing a dataset in h5py -# ---------------------------- +# Replacing a dataset using h5py +# ------------------------------ # There are several types of dataset edits that cannot be done in-place: # # * Changing the shape of a dataset with a fixed shape