Merge all Odin config stuff into one module

bptools/odin/cli.py

@@ -3,7 +3,7 @@
 from argparse import ArgumentParser
 import os.path as osp
 
-from .configgen import make_config_name, make_odin_config
+from .config import make_config_name, make_odin_config
 
 
 def _read_good_leads(filename):

bptools/odin/config.py

@@ -1,17 +1,147 @@
 import os.path as osp
 from io import StringIO
+from datetime import datetime
 from contextlib import contextmanager
+
 try:
     from typing import List
 except ImportError:  # pragma: no cover
     pass
+
 import pandas as pd
 
 from bptools.util import FromSeriesMixin
 from bptools.jacksheet import read_jacksheet
 from bptools.pairs import create_pairs, create_monopolar_pairs
 
 
+def _num_to_bank_label(num):
+    """Convert a channel number to a more human-friendly ENS bank label (e.g.,
+    1 -> A-CH01).
+
+    """
+    banks = {
+        0: 'A',
+        1: 'B',
+        2: 'C',
+        3: 'D'
+    }
+    bank = banks[num // 64]
+    return "{}-CH{:02d}".format(bank, num % 64)
+
+
+def make_config_name(subject, localization, montage, stim):
+    """Create the configuration filename using the standard naming convetion.
+
+    .. todo:: Merge into ElectrodeConfig?
+
+    Parameters
+    ----------
+    subject : str
+    localization : int
+    montage : int
+    stim : bool
+
+    """
+    now = datetime.now()
+    name_tmpl = "{subject:s}_{day:02d}{month:s}{year:04d}L{localization:d}M{montage:d}{stim:s}"
+    name = name_tmpl.format(**{
+        'subject': subject,
+        'day': now.day,
+        'month': now.strftime('%b'),
+        'year': now.year,
+        'localization': localization,
+        'montage': montage,
+        'stim': 'STIM' if stim else 'NOSTIM'
+    })
+    return name.upper()
+
+
+def make_odin_config(jacksheet_filename, config_name, default_surface_area,
+                     path=None, good_leads=None, scheme='bipolar'):
+    """Create an Odin ENS electrode configuration CSV file.
+
+    .. todo:: Merge into ElectrodeConfig class as a method.
+
+    Parameters
+    ----------
+    jacksheet_filename : str
+        Input jacksheet filename.
+    config_name : str
+        Configuration file name.
+    default_surface_area : float
+        Default surface area for electrodes.
+    path : str
+        Directory to write file to. If None, return as a string.
+    good_leads : list or None
+        Jackbox numbers to use when configuring sense channels. This is usually
+        determined from the ``good_leads.txt`` file. When None, use all.
+    scheme : str
+        Referencing scheme to use (``bipolar`` or ``monopolar``).
+
+    Notes
+    -----
+    In the future, jacksheets should optionally include extra annotations such
+    as type of electrode (depth, grid, strip) and surface areas.
+
+    """
+    assert isinstance(default_surface_area, float)
+    assert scheme in ['bipolar', 'monopolar'], "invalid referencing scheme"
+
+    js = read_jacksheet(jacksheet_filename)
+
+    if scheme == 'bipolar':
+        pairs = create_pairs(jacksheet_filename)
+    elif scheme == 'monopolar':
+        pairs = create_monopolar_pairs(jacksheet_filename)
+
+    subject, name = config_name.split('_')
+
+    # Header
+    config = [
+        "ODINConfigurationVersion:,#1.2#",
+        "ConfigurationName:," + name,
+        "SubjectID:," + subject,
+        "Contacts:",
+    ]
+
+    # Channel definitions
+    for n, row in js.iterrows():
+        jbox_num = n
+        chan = _num_to_bank_label(jbox_num)
+        data = [row.label, str(jbox_num), str(jbox_num), "{:.03f}".format(default_surface_area),
+                "#Electrode {} jack box {}#".format(chan, jbox_num)]
+        config.append(','.join(data))
+
+    # Sense definitions
+    config.append("SenseChannelSubclasses:")
+    config.append("SenseChannels:")
+    for _, row in pairs.iterrows():
+        if good_leads is not None:
+            if row.contact1 not in good_leads:
+                continue
+            if row.contact2 not in good_leads and scheme != "monopolar":
+                continue
+        data = [row.label1, row.pair.replace('-', ''),
+                str(row.contact1), str(row.contact2), 'x',
+                "#{}#".format(row.pair)]
+        config.append(','.join(data))
+
+    # Stim definitions
+    config.append("StimulationChannelSubclasses:")
+    config.append("StimulationChannels:")
+    config.append("REF:,0,Common")
+    config.append('EOF')
+
+    if path is not None:
+        outfile = osp.join(path, config_name + '.csv')
+        with open(outfile, 'w') as f:
+            f.write('\n'.join(config))
+            f.write('\n')
+    else:
+        return "\n".join(config)
+
+
 class _SlotsMixin(object):
     def __eq__(self, other):
         return all([

bptools/test/test_odin.py

@@ -5,8 +5,7 @@
 import pytest
 import pandas as pd
 
-from bptools.odin.configgen import make_odin_config, make_config_name
-from bptools.odin.config import ElectrodeConfig
+from bptools.odin.config import ElectrodeConfig, make_odin_config, make_config_name
 from bptools.odin import cli
 from bptools.test import datafile, tempdir, HERE