ecogdata: data loading for Viventi lab recordings

This library provides data preprocessing and packaging for recording systems used by the Viventi lab for micro-electrocorticography.

• Data wrangling from numerous data acquisition systems:

  • Open-ephys (.continuous files)
  • National instruments (.tdms files)
  • Intan (.rhd files, but needs HDF5 conversion: https://github.com/miketrumpis/rhd-to-hdf5)

• Parallelized array signal processing with shared memory

• HDF5-based memory mapping and dataset storage

• Array read/write abstraction spanning multiple mapped input files

• Trial/stimulus event alignment

Install

Preliminary: set up your virtualenv or conda env. With conda, you can use the provided YAML file to create a working environment.

$ conda env create --file conda_env.yml --name <your-env-name>
$ conda activate <your-env-name>

Then clone ecogdata:

$ git clone https://github.com/miketrumpis/ecogdata.git

Last, use pip to install ecogdata in any way you choose. I use "editable" mode to avoid re-installing after git pulls: pip install -e

$ python -m pip install -e ./ecogdata

Note that pip needs to differentiate installing from a path versus from PyPI, hence the contrived "./" path syntax. If this is not working in a non-unix command terminal, then do this instead (and likewise for the following instructions):

$ cd ecogdata
$ python -m pip install -e .

To run tests on the source code, install a variation package and run pytest. (If using conda, you may want to install pytest through conda.)

$ python -m pip install -e ./ecogdata[test]
$ python -m pytest ecogdata/ecogdata

Docs & demo notebooks

To build API documentation and usage demos, first install docs requirements ([docs] package variation) and run sphinx. (If using conda, you may want to install the docs requirements in setup.cfg through conda.)

$ python -m pip install -e ./ecogdata[docs]
$ cd ecogdata/docs
$ make all

Alternatively, install jupyter and run the notebooks in docs/source/usage_demos interactively.