maestapereira / convnwb

A module of helper code for converting data files to NWB.

convnwb

convnwb is a module of code to help with converting data to the NWB format.

Overview

This module contains general, task agnostic, utilities, for converting data to the NWB format.

Available sub-modules in convnwb include:

• io: includes save and load functions and utilities for working with files through the conversion process
• nsp: includes functionality that relating to managing recording files from neural signal processors
• objects: includes objects for storing relevant data, for example electrode or task related information
• paths: includes a Paths object and utilities for defining and using a consistent path structure
• plts: includes plot functions for examining data through the conversion process
• sorting: includes functionality relating to managing recording spike sorting
• timestamps: includes utilities for managing timestamps and aligning data streams
• utils: includes general utilities for working with data through the conversion process

For converting data, convnwb can be used together with the ConvertTEMPLATE.

Dependencies

convnwb is written in Python, and requires Python >= 3.6 to run.

It has the following required dependencies:

• numpy
• pyyaml

There are also optional dependencies, that offer extra functionality:

• pynwb is needed for validating NWB files
• matplotlib is needed for making plots to check conversions
• scikit-learn is needed to aligning sync pulses
• pandas is needed for utilities that load dataframes
• scipy is needed for some load and timestamp related functions
• h5py is needed for utilities that open HDF5 files
• neo is needed for loading & interacting with NSP files
• mat73 is needed for loading .mat files version >= 7.3
• pytest is needed to run the test suite locally

Installation

The current release version is the 0.3.X series.

Check the changelog for notes on updates and changes across versions.

This module should be installed from Github:

Install from a clone

First clone this repository, then move into the cloned repository, and install:

$ git clone https://github.com/HSUPipeline/convnwb
$ cd convnwb
$ pip install .

Contribute

This project welcomes and encourages contributions from the community!

To file bug reports and/or ask questions about this project, please use the Github issue tracker.

When interacting with this project, please follow the code of conduct.