ScienceMode4 Python

Introduction

Pure Python implementation of HasomedScience ScienceMode 4 protocol for P24 (https://github.com/ScienceMode/ScienceMode4_P24) and I24 (https://github.com/ScienceMode/ScienceMode4_I24) devices. To use this library see section Installation. Library and examples are tested under Windows, Linux and MacOS.

See also Hints file for more information.

Requirements

Python 3.11 or higher

Library

Installation

• Install science_mode_4 library inclusive dependencies via pip
  • pip install science_mode_4
  • https://pypi.org/project/science-mode-4/

Dependencies

• PySerial
  • https://pypi.org/project/pyserial/
  • pip install pyserial
• PyUSB
  • https://pypi.org/project/pyusb/
  • pip install pyusb
  • On Windows
    • Install libusb-package to get libusb-XX.dll
      • https://pypi.org/project/libusb-package/
      • pip install libusb-package
    • Under Windows there may be driver issues
      • See https://github.com/libusb/libusb/wiki/Windows#How_to_use_libusb_on_Windows
      • Use Zadig to change driver for STM32 Virtual ComPort to libusb-XX.dll and reinstall driver

Build library

• Only necessary, if you made changes to the library or install a version from a branch
• Install build dependencies
  • python -m pip install --upgrade build
• Install other library dependencies
  • pip install -r src/science_mode_4/requirements.txt
• Optional run linter
  • pip install pylint
  • pylint .\src\science_mode_4\
• Build project
  • python -m build
• Install local library
  • pip install --force .\dist\science_mode_4-0.0.7-py3-none-any.whl (adjust filename accordingly)

Examples

Description

• Located in folder examples
• Run examples with python -m examples.<layer>.<example>
  • From root directory of this repository
  • Example: python -m examples.dyscom.example_dyscom_fastplotlib
  • All examples try to find the serial port that a science mode device is connected to automatically
  • If that fails, provide serial port name as parameter, e.g. python -m examples.<layer>.<example> COM3
• Good starting point for an simple stimulation is example example_mid_level
• Examples have own dependencies, see Dependencies for examples
• General layer
  • python -m examples.general.example_general
    • Demonstrates how to use general layer to initialize device, get serial number and firmware version
    • Does not call any stimulation functions
• Mid level layer
  • python -m examples.mid_level.example_mid_level_simple
    • Demonstrates how to use mid level layer, where a stimulation pattern is send to the stimulator and the device automatically executes the pattern by itself for 15s
  • python -m examples.mid_level.example_mid_level
    • Demonstrates how to use mid level layer, where a stimulation pattern is send to the stimulator and the device automatically executes the pattern by itself until user ends stimulation by keyboard
  • python -m examples.mid_level.example_mid_level_update
    • Demonstrates how to use mid level layer, to toggle stimulation channels by keyboard
• Low level layer
  • python -m examples.low_level.example_low_level
    • Demonstrates how to use low level layer, where host has to trigger stimulation manually, in this case by pressing a key
  • python -m examples.low_level.example_low_level_plot
    • Demonstrates how to use low level layer to stimulate, measure current and plot it in a graph using PyPlot
• Dyscom layer
  • python -m examples.dyscom.example_dyscom_get
    • Demonstrate how to use different get commands from dyscom layer
  • python -m examples.dyscom.example_dyscom_fastplotlib
    • Demonstrate how to use dyscom layer to measure data and plotting values using fastplotlib
  • python -m examples.dyscom.example_dyscom_pyplot
    • Demonstrate how to use dyscom layer to measure data and plotting values using PyPlot
  • python -m examples.dyscom.example_dyscom_write_csv
    • Demonstrate how to use dyscom layer to measure data and writing measurement data to a .csv-file
  • python -m examples.dyscom.example_dyscom_send_file
    • Demonstrate how to use dyscom layer to save measurement data on memory card and reading it afterwards

Dependencies for examples

• Install all dependencies
  • pip install -r examples/requirements.txt
• Py-Getch
  • https://pypi.org/project/py-getch/
  • pip install py-getch
• NumPy
  • https://pypi.org/project/numpy/
  • pip install numpy
• Matplotlib / PyPlot
  • https://pypi.org/project/matplotlib/
  • pip install matplotlib
• Fastplotlib with glfw backend
  • https://pypi.org/project/fastplotlib/
  • pip install -U fastplotlib
  • pip install -U glfw

Changes

0.0.11

• Implemented UsbConnection class
  • Alternative for SerialPortConnection, both share the same base class Connection
  • Added PyUSB and libusb-package as dependencies

0.0.12

• Dyscom init
  • Added channel settings register
• Some bugfixes

0.0.13

• Fixed error with example keyboard utils under Linux
• Enhanced example low level plot to show all channels

0.0.14

• Improved examples under Linux/MacOS

0.0.15

• Enhanced readme
• Changed current for ChannelPoint from int to float

0.0.16

• Fixed error with PacketLowLevelChannelConfigAck result

0.0.17

• Added sample that demonstrates how to read measurement data files from I24 devices

0.0.18

• Fixed error for mid level update when not using all channels

0.0.19

• Fixed error in ByteBuilder when printing object

0.0.20

• Changed return value of LayerMidLevel.get_current_data()
• Added locking to example_mid_level_update to synchronize call of async functions from different event loops
• Added error handling in SerialPortConnection._read_intern() to prevent ClearComErrors

0.0.21

• Added more error handling in SerialPortConnection._read_intern() to prevent ClearComErrors
• Added getter for underlying serial object in SerialPortConnection

0.0.22

• Library specific exception classes

0.0.23

• Added timeout parameters to SerialPortConnection constructor