LoganJF/cmlreaders

CML data reading made easy

CML Data Readers

This repository contains a collection of utility classes for reading lab-specific file formats. Many of these readers have previously existed in other repositories, but are being migrated to a single repository since they are logically related.

More information and usage examples are provided in the documentation.

Installation

The following assumes you have already installed Anaconda or Miniconda.

conda create -y -n environment_name python=3
source activate environment_name
conda install -c pennmem cmlreaders

Note

In some installations using Anaconda (as opposed to miniconda), it may be necessary to also install the bottleneck package:

conda install -y bottleneck

Usage examples

What follows are some basic usage examples. See the documentation for a more complete guide to getting started.

Get the index of all RAM data:

>>> from cmlreaders import CMLReader, get_data_index
>>> df = get_data_index("r1")

Find unique experiments performed by R1111M:

>>> df[df["subject"] == "R1111M"]["experiment"].unique()
array(['FR1', 'FR2', 'PAL1', 'PAL2', 'PS2', 'catFR1'], dtype=object)

Load montage pair data from FR1 session 0:

>>> reader = CMLReader("R1111M", "FR1", 0)
>>> pairs = reader.load("pairs")
>>> pairs.columns()
Index(['contact_1', 'contact_2', 'label', 'is_stim_only', 'type_1', 'type_2',
       'avg.dural.region', 'avg.dural.x', 'avg.dural.y', 'avg.dural.z',
       'avg.region', 'avg.x', 'avg.y', 'avg.z', 'dk.region', 'dk.x', 'dk.y',
       'dk.z', 'id', 'ind.dural.region', 'ind.dural.x', 'ind.dural.y',
       'ind.dural.z', 'ind.region', 'ind.x', 'ind.y', 'ind.z', 'is_explicit',
       'stein.region', 'stein.x', 'stein.y', 'stein.z', 'tal.region', 'tal.x',
       'tal.y', 'tal.z', 'wb.region', 'wb.x', 'wb.y', 'wb.z'],
      dtype='object')

Select word onset events:

>>> events = reader.load("events")
>>> words = events[events["type"] == "WORD"]
>>> len(words)
288

Load EEG 100 ms before and after word onset using the bipolar referencing scheme:

>>> eeg = reader.load_eeg(events=words, rel_start=-100, rel_stop=100, scheme=pairs)
>>> eeg.data.shape
(288, 141, 100)

Testing

Since this repository is specific to the data formats of the lab, almost all tests require RHINO access. To run the test suite from a computer with RHINO mounted:

pytest cmlreaders/ --rhino-root [path_to_mount_point] --cov=html

Upon completion, the coverage report will be saved into htmlcov/ in the top level directory of the project.