Created new ndx-photostim extension

ndx-photostim/README.md

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+# ndx-photostim Extension for NWB
+
+<div style="display:inline">
+<img src="https://github.com/histedlab/ndx-photostim/blob/main/docs/images/ext.png?raw=True" height="50em" style="margin: 0em 0em 0em 0em;" align="right">
+<img src="https://github.com/histedlab/ndx-photostim/blob/main/docs/images/nwb.png?raw=True" height="50em" style="margin: 0em 0em 0em 0em; " align="right">
+This is a <a href="https://www.nwb.org/">NeuroData Without Borders (NWB)</a> extension for storing data and metadata from <a href="https://www.nature.com/articles/nmeth.3217">holographic photostimulation</a>
+methods. It includes containers for storing photostimulation-specific device parameters, holographic patterns 
+(either 2D or 3D), and time series data related to photostimulation.
+</div>
+
+<br>We release six <a href="https://pynwb.readthedocs.io/en/stable/">PyNWB</a> containers as part of this extension (we currently only have a Python implementation, rather than both Python and a MATLAB ones -- this is why the `matnwb` directory is empty):
+
+* The `SpatialLightModulator` and `Laser` containers store metadata about the spatial light modulator and laser used in the photostimulation, respectively. These containers are then stored within the `PhotostimulationMethod` parent container, which stores the remaining photostimulation method-specifici metadata.
+* `HolographicPattern` stores the **holographic pattern** used in stimulation.
+* `PhotostimulationSeries` contains the **time series data** corresponding to the presentation of a given stimulus (where the stimulus is represented by a `HolographicPattern` container linked to the `PhotostimulationSeries`).
+* We group **all time series & patterns for a given experiment** together using the `PhotostimulationTable` container. This object is a dynamic table, where each row in the table corresponds to a single `PhotostimulationSeries`. Additionally, the table links to the `StimulationDevice` used in the experiment.
+
+
+## Background
+
+<img src="https://github.com/histedlab/ndx-photostim/blob/main/docs/images/Cap1.PNG?raw=True" width="225em" align="left" style=" margin:0.5em 0.5em 0.5em 0.5em;">
+State-of-the-art <a href="https://www.nature.com/articles/s41467-017-01031-3">holographic photostimulation methods</a>, used in concert with <a href="https://www.nature.com/articles/nmeth818">two-photon imaging</a>, 
+allow unprecedented 
+control and measurement of cell activity in the living brain. Methods for managing data for two-photon imaging 
+experiments are improving, but there is little to no standardization of data for holographic stimulation methods. 
+Stimulation in vivo depends on fine-tuning many experimental variables, which poses a challenge for reproducibility 
+and data sharing between researchers. To improve <a href="https://www.sciencedirect.com/science/article/pii/S0896627321009557">standardization</a> of photostimulation data storage and processing, 
+we release this extension as a generic data format for simultaneous holographic stimulation experiments, 
+using the NWB format to store experimental details and data relating to both acquisition 
+and photostimulation.
+
+## Installation
+
+To install the extension, first clone the `ndx_photostim` repository to the desired folder using the command
+```angular2svg
+git clone https://github.com/histedlab/ndx-photostim.git
+```
+Then, to install the requisite python packages and extension, run:
+```angular2svg
+python -m pip install -r requirements.txt -r requirements-dev.txt
+python setup.py install
+```
+The extension can then be imported into python scripts via `import ndx_photostim`.
+
+## Usage
+
+**For full example usage, see [tutorial.ipynb](https://github.com/histedlab/ndx-photostim/blob/main/tutorial.ipynb)**
+
+Below is example code to:
+1. Create a device used in photostimulation
+2. Simulate and store photostimulation ROIs
+3. Store the time series corresponding to each stimulation
+4. Record all time series and patterns used in an experiment in a table
+5. Write the above to an NWB file and read it back
+
+
+```python
+import numpy as np
+from dateutil.tz import tzlocal
+from datetime import datetime
+from pynwb import NWBFile, NWBHDF5IO
+from ndx_photostim import SpatialLightModulator, Laser, PhotostimulationMethod, HolographicPattern, \
+    PhotostimulationSeries, PhotostimulationTable
+
+# create an example NWB file
+nwbfile = NWBFile('ndx-photostim_example', 'EXAMPLE_ID', datetime.now(tzlocal()))
+
+# store the spatial light modulator used
+slm = SpatialLightModulator(name='slm',
+                            model='Meadowlark',
+                            size=np.array([512, 512]))
+
+# store the laser used
+laser = Laser(name='laser',
+              model='Coherent Monaco',
+              wavelength=1030,
+              power=8,
+              peak_pulse_energy=20,
+              pulse_rate=500)
+
+# create a container for the method used for photostimulation, and link the SLM and laser to it
+ps_method = PhotostimulationMethod(name="methodA",
+                                   stimulus_method="scanless",
+                                   sweep_pattern="none",
+                                   sweep_size=0,
+                                   time_per_sweep=0,
+                                   num_sweeps=0)
+ps_method.add_slm(slm)
+ps_method.add_laser(laser)
+
+# define holographic pattern
+hp = HolographicPattern(name='pattern1',
+                        image_mask_roi=np.round(np.random.rand(5, 5)),
+                        stim_duration=0.300,
+                        power_per_target=8)
+
+# show the mask
+hp.show_mask()
+
+# define stimulation time series using holographic pattern
+ps_series = PhotostimulationSeries(name="series_1",
+                            format='interval',
+                            data=[1, -1, 1, -1],
+                            timestamps=[0.5, 1, 2, 4],
+                            pattern=hp,
+                            method=ps_method)
+
+# add the stimulus to the NWB file
+nwbfile.add_stimulus(ps_series)
+
+# create a table to store the time series/patterns for all stimuli together, along with experiment-specific
+# parameters
+stim_table = PhotostimulationTable(name='test', description='...')
+stim_table.add_series(ps_series)
+
+# plot the timestamps when the stimulus was presented
+stim_table.plot_presentation_times()
+
+# create a processing module and add the PresentationTable to it
+module = nwbfile.create_processing_module(name="photostimulation", description="example photostimulation table")
+module.add(stim_table)
+
+# write to an NWB file and read it back
+with NWBHDF5IO("example_file.nwb", "w") as io:
+    io.write(nwbfile)
+
+with NWBHDF5IO("example_file.nwb", "r", load_namespaces=True) as io:
+    read_nwbfile = io.read()
+
+    # Check the file & processing module
+    print(read_nwbfile)
+    print(read_nwbfile.processing['photostimulation'])
+
+if os.path.exists("example_file.nwb"):
+    os.remove("example_file.nwb")
+```
+## Running tests
+
+<a href="https://pynwb.readthedocs.io/en/stable/software_process.html#continuous-integration">Unit and integration
+tests</a> are implemented using <a href="https://docs.pytest.org/en/7.2.x/">pytest</a>, and can be run via the command 
+`pytest` from the root of the extension directory (i.e., inside `ndx-photostim/src`). In addition, the
+`pytest` command will also run a test of the example code above.
+
+## Documentation
+
+### Specification
+
+
+Documentation for the extension's <a href="https://schema-language.readthedocs.io/en/latest/">specification</a>, which is based on the YAML files, is generated and stored in
+the `./docs` folder. To create it, run the following from the home directory:
+```angular2svg
+cd docs
+make fulldoc
+```
+This will save documentation to the `./docs/build` folder, and can be accessed via the 
+`./docs/build/html/index.html` file.
+
+### API
+
+To generate documentation for the Python API (stores in `./api_docs`), we use <a href="https://www.sphinx-doc.org/en/master/">Sphinx</a> 
+and a template from <a href="https://readthedocs.org/">ReadTheDocs</a>. API documentation can
+be created by running 
+```angular2svg
+sphinx-build -b html api_docs/source/ api_docs/build/
+```
+from the home folder. Similar to the specification docs, API documentation is stored in `./api_docs/build`. Select 
+`./api_docs/build/index.html` to access the API documentation in a website format.
+
+
+## Credit
+
+Code by Carl Harris and Paul LaFosse (equal contribution). Collaboration between the NIMH's [Data Science and Sharing Team](https://cmn.nimh.nih.gov/dsst) and [Histed Lab](https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/ncb).
+
+
+This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
+

ndx-photostim/ndx-meta.yaml

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+name: ndx-photostim
+version: 0.0.3
+src: https://github.com/histedlab/ndx-photostim
+pip: https://pypi.org/project/ndx-photostim
+license: BSD3
+maintainers:
+  - lafosse
+  - histed