Source code for sekupy.io.configuration

import os

import logging
logger = logging.getLogger(__name__)




def read_configuration(filename, section):
    """Read the data configuration file.

    It gets alle the information for data loading.
    the configuration file must be composed in this way

    .. configuration.conf

    [path]
    data_path=/media/robbis/DATA/fmri/carlo_ofp/
    subjects=/media/robbis/DATA/fmri/carlo_ofp/subjects.csv
    experiment=ofp
    types=OFP,RESIDUALS,OFP_NORES
    TR=1.7

    [OFP]
    sub_dir=analysis_SEP/DE_ASS_noHP/SINGLE_TRIAL_MAGS_voxelwise
    event_file=eventfile_beta_plus
    event_header=True
    img_pattern=residuals_sorted.nii.gz
    runs=1
    mask_dir=/media/robbis/DATA/fmri/carlo_ofp/1_single_ROIs
    brain_mask=glm_atlas_mask_333.nii.gz

    [roi_labels]
    lateral_ips=/media/robbis/DATA/fmri/carlo_ofp/1_single_ROIs

    For bids layout keywords use bids_{keyword}.


    Parameters
    ----------
    filename : str
        The pathname of the configuration file.

        The configuration file must specify

    section : str
        The subsection of the configuration file to be

    Returns
    -------
    cfg : dictionary
        A dictionary with all the information to load data
    """
    import configparser
    config = configparser.ConfigParser()
    config.read(filename)

    logger.info('Reading config file %s' %(filename))

    types = config.get('path', 'types').split(',')

    if types.count(section) > 0:
        types.remove(section)

    for typ in types:
        config.remove_section(typ)

    configuration = []

    for sec in config.sections():

        if sec == 'roi_labels':
            roi_labels = dict()
            for k, v in config.items(sec):
                roi_labels[k] = v

            configuration.append(('roi_labels', roi_labels))

        for item in config.items(sec):
            configuration.append(item)
            logger.debug(item)

    cfg = dict(configuration)
    check_configuration(cfg)

    return cfg






def check_configuration(cfg):

    mandatory_keys = ["subjects", "data_path", "event_file", "img_pattern", "brain_mask"]

    for key in mandatory_keys:
        if key not in cfg.keys():
            logger.debug("No %s field in configuration" % (key))







def conf_to_json(config_file):

    import configparser
    config = configparser.ConfigParser()
    config.read(config_file)

    json_ = dict()

    for sec in config.sections():
        json_[sec] = dict()
        for item in config.items(sec):
            json_[sec][item[0]] = item[1]

    import json

    conf_fname = config_file[:config_file.find('.')]

    json_fname = open('%s.json' %(conf_fname), 'w')
    json.dump(json_, json_fname, indent=0)

    return json_






def read_json_configuration(path, json_fname, experiment):

    import json
    json_file = os.path.join(path, json_fname)

    conf = json.load(open(json_file, 'r'))

    experiments = conf['path']['types'].split(',')
    _ = [conf.pop(exp) for exp in experiments if exp != experiment]  

    logger.info(conf)

    return conf






def save_configuration(path, dictionary, filename="configuration.json"):

    import json

    fname = os.path.join(path, filename)

    json_dict = {k: str(v) for k, v in dictionary.items()}

    with open(fname, "w") as f:
        f.write(json.dumps(json_dict, indent=0))