NWB tutorial

docs/source/HedAnnotationInNWB.md

@@ -0,0 +1,121 @@
+# HED annotation in NWB (draft)
+
+[**Neurodata Without Borders (NWB)**](https://www.nwb.org/) is a data standard for organizing neurophysiology data.
+NWB is used extensively as the data representation for single cell and animal recordings as well as
+human neuroimaging modalities such as IEEG. HED (Hierarchical Event Descriptors) is a system of
+standardized vocabularies and supporting tools that allows fine-grained annotation of data.
+
+Each NWB file (extension `.nwb`) is a self-contained (and hopefully complete) representation of
+experimental data for a single experiment.
+The file should contain all experimental stimuli, acquired data, and metadata synchronized to a global
+timeline for the experiment.
+See [**Intro to NWB**](https://nwb-overview.readthedocs.io/en/latest/intro_to_nwb/1_intro_to_nwb.html)
+for a basic introduction to NWB.
+
+## The ndx-hed NWB extension
+The [**ndx-hed**](https://github.com/hed-standard/ndx-hed) extension allows HED annotations to be added as a column to any NWB
+[**DynamicTable**](https://hdmf-common-schema.readthedocs.io/en/stable/format.html#sec-dynamictable).
+extends the NWB [**VectorData**](https://hdmf-common-schema.readthedocs.io/en/stable/format.html#sec-dynamictable) 
+class, allowing HED data to be added as a column to any NWB
+[**DynamicTable**](https://hdmf-common-schema.readthedocs.io/en/stable/format.html#sec-dynamictable).
+The `DynamicTable` class is the underlying base class for many data structures within NWB files,
+and this extension allows HED annotations to be easily added to NWB.
+See [**DynamicTable Tutorial**](https://hdmf.readthedocs.io/en/stable/tutorials/plot_dynamictable_tutorial.html#sphx-glr-tutorials-plot-dynamictable-tutorial-py)
+for a basic guide for usage in Python and
+[**DynamicTable Tutorial (MATLAB)**](https://neurodatawithoutborders.github.io/matnwb/tutorials/html/dynamic_tables.html)
+for introductory usage in MATLAB.
+
+The class that implements the ndx-hed extension is called `HedTags`.
+This class represents a column vector (`VectorData`) of HED tags and the version
+of the HedSchema needed to validate the tags. 
+Valid
+which 
+
+## Example HED usage in NWB
+
+### HED as a standalone vector
+
+The `HedTags` class has two required argument (the `hed_version` and the `data`) and two optional arguments
+(`name` and `description`).
+
+````{admonition} Create a HedTags object.
+:class: tip
+
+```python
+tags = HedTags(hed_version='8.3.0', data=["Correct-action", "Incorrect-action"])
+```
+````
+The result is a `VectorData` object whose data vector includes 2 elements.
+Notice that data is a list with 2 values representing two distinct HED strings.
+The values of these elements are validated using HED schema version 8.3.0 when `tags` is created. 
+If any of the tags had been invalid, the constructor would raise a `ValueError`.
+
+````{admonition} Add a row to an existing HED VectorData
+:class: tip
+
+```python
+tags.add_row("Sensory-event, Visual-presentation")
+```
+After this `add_row` operation, `tags` has 3 elements. Notice that "Sensory-event, Visual-presentation"
+is a single HED string, not two HED strings.
+
+````
+
+### HED in a table
+
+The following color table uses HED tags to define the meanings of integer codes:
+| color_code | HED |
+|----- | --- |
+| 1 | `Red` |
+| 2 | `Green` |
+| 3 | `Blue` |
+
+````{admonition} Create an NWB DynamicTable to represent the color table.
+:class: tip
+
+```python
+
+color_nums = VectorData(name="color_code", description="Internal color codes", data=[1,2,3])
+color_tags = HedTags(name="HED", hed_version="8.2.0", data=["Red", "Green", "Blue"])
+color_table = DynamicTable(
+ name="colors", description="Experimental colors", columns=[color_num, color_tags])
+```
+````
+The example sets up a table with columns named `color_code` and `HED`.
+Here are some common operations that you might want to perform on such a table:
+````{admonition}
+Get row 0 of `color_table` as a Pandas DataFrame:
+```python
+df = color_table[0]
+```
+Append a row to `color_table`:
+```python
+color_table.add_row(color_code=4, HED="Black")
+```
+````
+The `HED`
+color_table = DynamicTable(name="colors", description="Color table for the experiment",
+ columns=[{"name"="code", "description"="Internal color codes", data=[1, 2, 3]},
+ HedTags(name="HED", hed_version="8.3.0", data=["Red", "Green", "Blue"])]
+
+```
+
+
+
+```
+## Installation
+
+## Implementation
+The implementation is based around
+### The HedTags class
+
+
+
+### In TrialTable
+
+### in EventTable
+
+file including the `TimeIntervals`, `Units`, `PlaneSegmentation`, and many of the
+the `icephys` tables (`ExperimentalConditionsTable`, `IntracellularElectrodesTable`,
+`IntracellularResponsesTable, `IntracellularStimuliTable`, `RepetitionsTable`, SequentialRecordingsTable`,
+`SimultaneousRecordingsTable` and the `SweepTable`)(`TrialTable`, Epch

docs/source/index.rst

@@ -116,6 +116,7 @@ Visit the `HED project homepage <https://github.com/hed-standard>`_ for links to
 
  BidsAnnotationQuickstart.md
  HedAnnotationQuickstart.md
+ HedAnnotationInNWB.md
  HedValidationGuide.md
  HedSearchGuide.md
  HedSummaryGuide.md