Micromed IO library

A library to read, emulate, and forward Micromed data in standard formats. See online doc.

Main features:

simulate online data from a trc file
push online tcp data to LSL server
convert trc to mne format
rename trc files to include the recording datetime

Install

$ pip install micromed-io

Convert a Micromed (.trc) file to MNE (.fif) format

from micromed_io.to_mne import create_mne_from_micromed_recording
mne_raw = create_mne_from_micromed_recording("path/to/file.TRC")

Emulate TRC to TCP & read/forward to LSL server

See details in next sections

Emulate Online Micromed TCP from .trc file

$ mmio_emulate_trc --file=../data/sample.TRC --address=localhost --port=5123

Emulate the online data stream of Micromed to test your real-time platform. See all the arguments and adapt them:

$ mmio_emulate_trc --help # to see all arguments

Read TCP and push to LSL Stream

$ mmio_tcp_to_lsl --address=localhost --port=5123

While receiving online data throug tcp, this command forward the data to 3 LSL stream outlets:

Micromed_EEG: the eeg data in float32 format [n_channels, n_samples]
Micromed_Markers: markers if any in int32 format [sample, marker] (2 channels)
Micromed_Notes: notes if any in string format [sample, note] (2 channels)

You can easily change the LSL parameters:

$ mmio_tcp_to_lsl --help # to see all arguments

Read TRC file

from micromed_io.trc import MicromedTRC
mmtrc = MicromedTRC("sample.TRC")

Then you have access to the trc data:

mmtrc.get_header()
mmtrc.get_markers()
mmtrc.get_data()
mmtrc.get_notes()

Read and parse Micromed TCP live data

Download tcp_to_lsl.py from the github repo in scripts/

$ python tcp_to_lsl.py --address=localhost --port=5123

Note: Micromed TCP behaves as a client. If you want to try the emulate/read TCP script, launch the reader first that acts as server, then the emulator.

Read online Micromed TCP in a sliding window buffer

If you plan to use the Micromed data as input of a decoder, you probably want epochs of format (n_channels, n_samples). Then the MicromedBuffer class is for you. The script tcp_to_epoch.py shows you how to use it (see the PROCESS HERE comment). It uses a buffer that mimics the sliding window and triggers each time it is filled.

from micromed_io.buffer import MicromedBuffer
micromed_buffer = MicromedBuffer(epoch_duration=5, epoch_overlap=2.5)

To run the example, you can download and run the tcp_to_epoch.py script in extern/ folder:

$ python tcp_to_epoch.py --epoch-size=5 --overlap=2.5

Rename TRC files with recording datetime

$ mmio_rename_trc --dirpath=./ --format=%Y%m%d-%H%M%S

Rename the TRC files of the given folder to include the recording date in the filename. Output is : <filename>__<recording_date>.TRC. The format must be compliant with python strftime format codes

mmio_rename_trc --help # to see help

Local install

Download the repo and:

$ conda env create -f environment.yml
$ conda activate mmio
$ poetry install

Please feel free to reach me if you want to contribute.

Metadata

Release files for micromed-io 0.3.9

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for micromed-io 0.3.9
File	Size	Uploaded
micromed_io-0.3.9.tar.gz	20.2 kB	Dec 22, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for micromed-io 0.3.9
File	Interpreter	ABI	Platform	Reset
micromed_io-0.3.9-py3-none-any.whl 26.0 kB Dec 22, 2023	Python 3	none	any	Details

Total release size: 46.2 kB

Release files / micromed_io-0.3.9.tar.gz

Download URL	micromed_io-0.3.9.tar.gz
Size	20.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`3d0c32e593ea8383b58bbc6853452b3b4f774f57fdaf10548bf60324022b7409`
BLAKE2b-256 checksum How to use checksums	`31b784c809ecbbcfd26cbf0b5eb504952fc0606aa0ac1cbbaa94f803633442ca`
Upload date	Dec 22, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`poetry/1.7.1 CPython/3.9.12 Windows/10`

Release files / micromed_io-0.3.9-py3-none-any.whl

Download URL	micromed_io-0.3.9-py3-none-any.whl
Size	26.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`8abe4a7d15b93251dc02fc1eb62e748f98254a023d6a4096a40d0928f37fc0ba`
BLAKE2b-256 checksum How to use checksums	`75ee0e30e73f3d34c6e5e79d94f87f7a72c85bd6df7f5c681125c8f741b39054`
Upload date	Dec 22, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`poetry/1.7.1 CPython/3.9.12 Windows/10`