cp_walk_parameters.py

# -*- coding: utf-8 -*-
"""
CP project:
read time / distance vars from c3d files

@author: Jussi (jnu@iki.fi)
"""

from __future__ import print_function
import gaitutils
import numpy as np
import logging

from gaitutils import timedist, c3d
from cp_common import get_files, params


logger = logging.getLogger(__name__)

# analysis vars of interest
vars = gaitutils.report.text._timedist_vars

def _read_data(subject, vars, cond):
    """ Returns a dict of parameters for each trial """
    Cfiles = get_files(subject, cond)
    # 'unknown' is the default condition name
    datas = {f: c3d.get_analysis(f)['unknown'] for f in Cfiles}
    datas_ok = {
        f: data for f, data in datas.items() if all([var in data for var in vars])
    }
    logger.debug(
        '%s/%s: %d files read, %d files contained data'
        % (subject, cond, len(datas), len(datas_ok))
    )
    not_ok = set(datas.keys()) - set(datas_ok.keys())
    if not_ok:
        logger.debug('following files not ok:')
        for fn in not_ok:
            logger.debug(fn)
    if datas_ok:
        logger.debug('including files:')
        for fn in datas_ok:
            logger.debug(fn)
    return datas_ok


def _process_data(datas, vars, cond):
    """Yields lists for each variable"""

    if not datas:
        logger.debug('no data, terminating')
        raise ValueError('No data')

    # for picking units
    data0 = datas.values()[0]

    # collect into dict
    results = dict()
    for var in vars:
        results[var] = dict()
        results[var]['unit'] = data0[var]['unit']
        for context in ['Right', 'Left']:
            results[var][context] = list()
            for f, data in datas.items():
                if context not in data[var]:
                    logger.debug(
                        'missing data for %s: %s in file %s' % (var, context, f)
                    )
                else:
                    thisdata = data[var][context]
                    if thisdata is not None:
                        results[var][context].append(thisdata)
                    else:
                        logger.debug(
                            'data is None for %s: %s in file %s' % (var, context, f)
                        )
    # these are common to all vars
    range_ = ''
    type_ = 1
    for var in vars:
        unit_ = results[var]['unit']
        for context in ['Right', 'Left']:
            data = np.array(results[var][context])
            mean_ = data.mean()
            std_ = data.std()
            yield [
                '%s mean, %s %s' % (var, context.lower(), cond),
                unit_,
                range_,
                type_,
                mean_,
            ]
            yield [
                '%s stddev, %s %s' % (var, context.lower(), cond),
                unit_,
                range_,
                type_,
                std_,
            ]


def get_results(subjects):
    if not isinstance(subjects, list):
        subjects = [subjects]
    logger.debug('starting time-distance analysis')
    results = dict()
    for j, subject in enumerate(subjects):
        logger.debug('processing subject %s' % subject)
        for cond in params['analysis_types']:
            datas = _read_data(subject, vars, cond)
            for r in _process_data(datas, vars, cond):
                var = r[0]
                if var not in results:
                    results[var] = r
                else:
                    results[var].append(r[-1])
    logger.debug('time-distance analysis finished')
    return results


def get_timedist_values(subjects):
    """Get timedist vals for subjects (normal trials only).
    Returns tuple of timedist (mean, std)"""
    if not isinstance(subjects, list):
        subjects = [subjects]
    logger.debug('starting time-distance analysis')
    ans = list()
    filenames = list()
    for subject in subjects:
        logger.info('processing subject %s' % subject)
        Nfiles = get_files(subject, 'normal')
        filenames.extend(Nfiles)
        ans.extend([c3d.get_analysis(c3dfile) for c3dfile in Nfiles])
    return ans, filenames