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https://github.com/larsrollik/pypulsepal

Python API to interact with PulsePal
https://github.com/larsrollik/pypulsepal

api arduino-due hardware-api pulse-generator pulsepal python stimulation

Last synced: 5 days ago
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Python API to interact with PulsePal

Host: GitHub
URL: https://github.com/larsrollik/pypulsepal
Owner: larsrollik
License: gpl-3.0
Created: 2022-03-22T09:15:04.000Z (almost 3 years ago)
Default Branch: main
Last Pushed: 2023-01-17T07:09:54.000Z (almost 2 years ago)
Last Synced: 2024-11-19T19:56:24.794Z (about 1 month ago)
Topics: api, arduino-due, hardware-api, pulse-generator, pulsepal, python, stimulation
Language: Python
Homepage:
Size: 72.3 KB
Stars: 1
Watchers: 1
Forks: 1
Open Issues: 3
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE

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README

        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6379627.svg)](https://doi.org/10.5281/zenodo.6379627)

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# PyPulsePal

Python API for the PulsePal open-source pulse train generator

---

Version: "0.0.2.dev0"

This package provides an API to the [PulsePal] hardware.

This API is a re-implementation of the original [PulsePal Python 3 API] that draws from the `pybpod-api` communication protoool.

## Example usage

#### script/function

```python

import time

from pypulsepal import PulsePal

serial_port = "/dev/ttyACM0"  # for unix or "COM"-style port names for Windows

# Create PulsePal object

pp = PulsePal(serial_port=serial_port)

# Set parameters

## Manually

pp.program_one_param(channel=2, param_name="phase1Duration", param_value=.002)

## Via convencience functions

pp.set_resting_voltage(channel=2, voltage=4.2)

# Upload parameters

pp.upload_all()

# Trigger selected channels

pp.trigger_selected_channels(channel_2=True, channel_4=True)

time.sleep(1)

# Stop outputs

pp.stop_all_outputs()

time.sleep(1)

# Save settings (also done automatically on disconnect)

pp.save_settings()

```

##### Channels can also be triggered all at once

```python

import time

from pypulsepal import PulsePal

serial_port = "/dev/ttyACM0"  # for unix or "COM"-style port names for Windows

# Create PulsePal object

pp = PulsePal(serial_port=serial_port)

# Trigger all channels

pp.trigger_all_channels()

time.sleep(1)

# Stop outputs

pp.stop_all_outputs()

```

#### as context manager

```python

import time

from pypulsepal import PulsePal

with PulsePal(serial_port="/dev/ttyACM0") as pp:

    # set params

    pp.upload_all()

    # do something

    time.sleep(2)

```

#### Write `default` params to all channels

```python

from pypulsepal.write_tests import write_default_settings

write_default_settings(serial_port="/dev/ttyACM0")

```

#### Write (funky) `test` params to all channels

```python

from pypulsepal.write_tests import write_test_settings_for_manual_check

write_test_settings_for_manual_check(serial_port="/dev/ttyACM0")

```

## Installation

#### pip

```shell

pip install pypulsepal

```

#### git

```shell

git clone https://github.com/larsrollik/pypulsepal.git

cd pypulsepal/

pip install -e .

```

#### pip + git

```shell

pip install git+https://github.com/larsrollik/pypulsepal.git

```

## Problems & issues

Please open [issues](https://github.com/larsrollik/pypulsepal/issues) or [pull-requests](https://github.com/larsrollik/pypulsepal/pulls) in this repository.

## Citation

Please cite the original [PulsePal] and [PyBpod] code and publications that this package is based on.

To cite `PyPulsePal` with a reference to the current version (as publicly documented on Zenodo), please use:

> Rollik, Lars B. (2021). PyPulsePal: Python API for the PulsePal open-source pulse train generator. doi: [10.5281/zenodo.6379627](https://doi.org/10.5281/zenodo.6379627).

**BibTeX**

```BibTeX

@misc{rollik2022pypulsepal,

    author       = {Lars B. Rollik},

    title        = {{PyPulsePal: Python API for the PulsePal open-source pulse train generator}},

    year         = {2022},

    month        = mar,

    publisher    = {Zenodo},

    url          = {https://doi.org/10.5281/zenodo.6379627},

    doi          = {10.5281/zenodo.6379627},

  }

```

## License & sources

This software is released under the **[GNU GPL v3.0](https://github.com/larsrollik/pypulsepal/blob/main/LICENSE)**.

This work is derived from the [Sanworks PulsePal Python API](https://github.com/sanworks/PulsePal/tree/develop) ([commit: 5bb189f](https://github.com/sanworks/PulsePal/commit/5bb189fec8d7435433b8c23f7bae520f92e271af)).

The architecture of the API is imported and inspired by the `pybpodapi.com.arcom` module from the [pybpod-api](https://github.com/pybpod/pybpod-api).

For changes from the original implementation, see the git history since [commit 972bc1e](https://github.com/larsrollik/pypulsepal/commit/972bc1ed3d07b6809e6cbcd05373be3b76ae5b5b).

## Useful code references

- [PyBpod com ArCOM]

- [PyBpod com protocol]

- [PyBpod message headers]

- [PulsePal Python 3 API]

- [PulsePal .ino file]

- [PulsePal param definitions]

## TODO

- [ ] Simplify parameter dicts in `definitions`: into nested dict with first level for name, then standard sub-dict (default value, dtype, dtype legacy(model 1), scaling, )

- [ ] Complete API functions with all PulsePal opcodes, e.g. for Arduino logic levels (see [PulsePal USB v2 opcode list])

- [ ] Move PulsePal hardware settings to init and remove defaults for easier upgrade in future

- [ ] API function to accept list of dicts (from json settings file)

  - to make overwrites on channels to get from value-based logic to channel parameter sets

  - add write function to save all settings to json for documentation

[//]: # (links)

[Pulsepal]: https://github.com/sanworks/PulsePal

[PyBpod]: https://github.com/pybpod/pybpod

[PyBpod com ArCOM]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/com/arcom.py

[PyBpod com protocol]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/bpod/bpod_com_protocol.py

[PyBpod message headers]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/com/protocol/send_msg_headers.py

[PulsePal Python 3 API]: https://github.com/sanworks/PulsePal/blob/develop/Python/Python3/PulsePal.py

[PulsePal .ino file]: https://github.com/sanworks/PulsePal/blob/develop/Firmware/PulsePal_2_0_1/PulsePal_2_0_1.ino

[PulsePal param definitions]: https://sites.google.com/site/pulsepalwiki/matlab-gnu-octave/functions/programpulsepalparam

[PulsePal USB v2 opcode list]: https://sites.google.com/site/pulsepalwiki/usb-serial-interface/usb-interface-v2-x