ndx-survey-data Extension for NWB

Structure for storing the survey data in a NWB file.

Installation

$ pip install git+https://github.com/catalystneuro/ndx-survey-data.git

Usage

from pynwb import NWBHDF5IO, NWBFile
import datetime
from ndx_survey_data.survey_definitions import nrs_survey_table


nrs_survey_table.add_row(
    pain_intensity_rating=1,
    pain_relief_rating=5,
    relative_pain_intensity_rating=2,
    pain_unpleasantness=3,
    unix_timestamp=1588217283
)

nrs_survey_table.add_row(
    pain_intensity_rating=3,
    pain_relief_rating=1,
    relative_pain_intensity_rating=6,
    pain_unpleasantness=2,
    unix_timestamp=1588217283
)

nrs_survey_table.add_row(
    pain_intensity_rating=5,
    pain_relief_rating=2,
    relative_pain_intensity_rating=0,
    pain_unpleasantness=2,
    unix_timestamp=1588217283
)

nrs_survey_table.add_row(
    pain_intensity_rating=3,
    pain_relief_rating=1,
    relative_pain_intensity_rating=6,
    pain_unpleasantness=2,
    unix_timestamp=1588217283
)
nwbfile = NWBFile('description', 'id', datetime.now().astimezone())

nwbfile.create_processing_module(name='behavior', description='survey/behavioral data')

nwbfile.processing['behavior'].add(nrs_survey_table)

with NWBHDF5IO('test_nwb.nwb', 'w') as io:
    io.write(nwbfile)

with NWBHDF5IO('test_nwb.nwb', 'r', load_namespaces=True) as io:
    nwbfile = io.read()
    print(nwbfile.processing['behavior'].data_interfaces['nrs_survey_table'].to_dataframe().to_html())

To add a custom survey:

from ndx_survey_data import QuestionResponse, SurveyTable

q1 = QuestionResponse(name='question1',
                      description='desc',
                      options=['option 1', 'option 2', 'option 3'])

q2 = QuestionResponse(name='question2', 
                      description='desc',
                      options=['option 1', 'option 2', 'option 3'])

q3 = QuestionResponse(name='question3', 
                      description='desc',
                      options=['option 1', 'option 2', 'option 3'])


custom_survey_table = SurveyTable(name='custom_survey_table',
                               description='desc', 
                               columns=[q1, q2, q3])

custom_survey_table.add_row(question1=1, question2=3, question3=0, unix_timestamp=1588217283)
custom_survey_table.add_row(question1=3, question2=1, question3=0, unix_timestamp=1588217283)
custom_survey_table.add_row(question1=2, question2=2, question3=2, unix_timestamp=1588217283)