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

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

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

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

from pypulsepal.write_tests import write_default_settings

write_default_settings(serial_port="/dev/ttyACM0")

Write (funky) test params to all channels

from pypulsepal.write_tests import write_test_settings_for_manual_check

write_test_settings_for_manual_check(serial_port="/dev/ttyACM0")

Installation

pip

pip install pypulsepal

git

git clone https://github.com/larsrollik/pypulsepal.git
cd pypulsepal/
pip install -e .

pip + git

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

Problems & issues

Please open issues or pull-requests 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.

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.

This work is derived from the Sanworks PulsePal Python API (commit: 5bb189f).

The architecture of the API is imported and inspired by the pybpodapi.com.arcom module from the pybpod-api.

For changes from the original implementation, see the git history since commit 972bc1e.

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