LAMP-cortex 2021.5.21

The Cortex data analysis toolkit for the LAMP Platform.

Cortex data analysis pipeline for the LAMP Platform.

Overview

This API client is used to process and featurize data collected in LAMP. Visit our documentation for more information about the LAMP Platform.

Installation

Prerequisites

Python 3.4+ and pip.

• You may need root permissions, using sudo.
• Alternatively, to install locally, use pip --user.
• If pip is not recognized as a command, use python3 -m pip.

Installation

pip install git+https://github.com/BIDMCDigitalPsychiatry/LAMP-cortex.git@master

Alternatively, instead of pip install, you may need to use python3 -m pip install --user.

Configuration

Ensure your server_address is set correctly. If using the default server, it will be api.lamp.digital. Keep your access_key (sometimes an email address) and secret_key (sometimes a password) private and do not share them with others. While you are able to set these parameters as arguments to the cortex executable, it is preferred to set them as session-wide environment variables. You can also run the script from the command line:

LAMP_SERVER_ADDRESS=api.lamp.digital LAMP_ACCESS_KEY=XXX LAMP_SECRET_KEY=XXX python3 -m \
  cortex significant_locations \
    --id=U26468383 \
    --start=1583532346000 \
    --end=1583618746000 \
    --k_max=9

Or another example using the CLI arguments instead of environment variables (and outputting to a file):

python3 -m \
  cortex --format=csv --server-address=api.lamp.digital --access-key=XXX --secret-key=XXX \
    survey --id=U26468383 --start=1583532346000 --end=1583618746000 \
    2>/dev/null 1>./my_cortex_output.csv

Example

# environment variables must already contain LAMP configuration info
from pprint import pprint
from cortex import all_features, significant_locations, trips
pprint(all_features())
for i in range(1583532346000, 1585363115000, 86400000):
    pprint(significant_locations(id="U26468383", start=i, end=i + 86400000))