export_rename_weight_tables.py

# Author: Denis A. Engemann <d.engemann@fz-juelich.de>

""" Export Magnes3600WH weight tables for your study

If you want to include reference channels (might be a good idea),
currently, the way to go is to use the following mne command
to create the compensation data:

$ mne_create_comp_data
usage: mne_create_comp_data [options]
This program takes a text format compensation data matrix and converts it into fif.
    --in name         The input file.
    --kind value      Then compensation kind to assign (default = 101)
    --out name        The output file.
    --help            print this info.
    --version         print version info.

mne_create_comp_data -in my_weigths.txt -out my_weigths.fif


And this mne command to add it to the exported fiff:

$ mne_add_to_meas_info
usage: mne_add_to_meas_info [options]
Add new data to meas info.
    --add name        The file to add.
    --dest name       The destination file.
    --help            print this info.
    --version         print version info.

This example demonstrates how to get the weight tables out of the Solaris DAW.
You can edit + save this example and run it using python which is installed
on megsun02. Alternatively you can past it into the python interpreter,
block by block. This will allow you to play with this stuff.

CAVE:
This script assumes you've already exported you data to the path bound to the
variable destination and that you organized it in a 'path/subject_name' style.

"""

import os.path as op
from commands import getstatusoutput

study_name = 'SOMO'  # adjust this accordingly
find = 'find . | grep %s' % study_name

destination = '/export/raid_meg1/exp'  # set your path here

res, hits = getstatusoutput(find)  # system command find

if res > 0:  # break if sth goes wrong.
    raise RuntimeError(hits)

# get the top level study folders for each subject
targets = [h for h in hits.split() if 'config' in h.split('/')[-1]]

# prepare Eberhard's command and insert open string formatting slots
print_tables = 'print_table -P %s -S %s -s %r -r %s -WP DC:supine:both'

exclude = '203511', '203373', '204652'  # my subjects to be excluded

"""
The following renaming operation addresses 2 issues.
The current mne-python exporter renames the ref channels because I wrote it so.
Integrating the weights however requires all ref channels can be linked to
MEG channels. For this reason, on printing the tables I've got to
rename them such that they match the names in the exported fiff.
"""

REF_CH = ['GxxA', 'GyxA', 'GyyA', 'GzxA', 'GzyA', 'MCxA', 'MCxaA', 'MCyA',
          'MCyaA', 'MCzA', 'MCzaA', 'MLxA', 'MLxaA', 'MLyA', 'MLyaA', 'MLzA',
          'MLzaA', 'MRxA', 'MRxaA', 'MRyA', 'MRyaA', 'MRzA', 'MRzaA']

NEW_CH = ['RFG%03d' % ii for ii, ch in enumerate(REF_CH[:5], 1)]
NEW_CH += ['RFM%03d' % ii for ii, ch in enumerate(REF_CH[5:], 1)]

CH_SEP = '\t    '  # channel names are separated like this.

ch_map = dict(zip(REF_CH, NEW_CH))  # create a mapping between old : new


def rename(line):
    """ This will be fed with one line from the weight tables
    """
    # this is mandatory, the C routine expects integers.
    if any(k in line for k in ('NumSignalChans', 'NumReferenceChans')):
        line = ''.join(ch for ch in line if ch.isdigit())
    # this is a fix, related to the renaming. For future vesions
    # of the exporter this block might be dropped.
    elif any(k in line for k in REF_CH):
        line = CH_SEP.join(ch_map.get(k, '') for k in line.split(CH_SEP))
    # also this is mandatory
    elif line.startswith('A'):
        line = line.split('\t')
        line.insert(0, 'MEG%03d' % int(line[0].strip('A')))
        line.pop(1)
        line = '\t'.join(line)
    return line


def match(line):
    """ This is used to drop lines that aren't expected by the C routine"""
    matches = []
    if line.startswith('A'):
        matches += [1]
    elif any(k in line for k in REF_CH):
        matches += [1]
    elif any(k in line for k in ('NumSignalChans', 'NumReferenceChans')):
        matches += [1]
    return any(matches)


def rename_weights(weights):
    """This is the renaming function, this will stay for a while"""
    return '\n'.join(rename(li) for li in weights.split('\n') if match(li))


# let's get our hands dirty and do what we need to do..
for conf in targets:
    P, S, scan, run = conf.split('/')[1:-1]  # get -P -S -s -r
    scan = scan.replace('@', ' ')  # required to make Eberhard's program happy.
    if P not in exclude:  # only process subjects to be included
        fname = 'weigths_%s_%s_run%s.txt' % (P, scan, run)  # compile file name
        cmd = print_tables % (P, S, scan, run)  # compile command
        res, output = getstatusoutput(cmd)  # run command
        if res == 0:
            weights = rename_weights(output)
            with open(op.join(destination, S, P, fname), 'w') as fi:
                fi.write(weights)
        else:
            print res
            break