CLEANUP: remove unused definitions

eelbrain/_utils/__init__.py

@@ -1,4 +1,4 @@
 # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
-from .basic import (deprecated, IdDict, intervals, LazyProperty, keydefaultdict,
+from .basic import (deprecated, intervals, LazyProperty, keydefaultdict,
                     n_decimals, natsorted, log_level, set_log_level)
 from .system import caffeine

eelbrain/_utils/basic.py

@@ -106,29 +106,6 @@ def next(self):
         return self.seq[self.i - 1], self.seq[self.i]
 
 
-class IdDict(dict):
-    """
-    Dictionary to code a certain type of items to Ids; id_dict[item] returns
-    the Id for item if item has previously been added; otherwise it generates
-    a new Id (its length)
-    """
-    def __missing__(self, key):
-        new_id = len(self)
-        while new_id in self.values():
-            new_id += 1
-
-        super(IdDict, self).__setitem__(key, new_id)
-        return new_id
-
-    def __setitem__(self, key, value):
-        if value in self.values():
-            raise ValueError("Value already assigned: %r" % value)
-        elif key in self:
-            raise KeyError("Key already assigned: %r" % key)
-        else:
-            super(IdDict, self).__setitem__(key, value)
-
-
 class LazyProperty(object):
     "http://blog.pythonisito.com/2008/08/lazy-descriptors.html"
     def __init__(self, func):

eelbrain/_utils/subp.py

@@ -17,10 +17,7 @@
 import fnmatch
 import logging
 import os
-import re
-import shutil
 import subprocess
-import tempfile
 
 import mne
 from mne.utils import get_subjects_dir, run_subprocess
@@ -107,71 +104,6 @@ def command_exists(cmd):
                            stderr=subprocess.PIPE) == 0
 
 
-# classes for files ---
-
-class edf_file:
-    """
-    Converts an "eyelink data format" (.edf) file to a temporary directory
-    and parses its content.
-
-    """
-    def __init__(self, path):
-        # convert
-        if not os.path.exists(path):
-            err = "File does not exist: %r" % path
-            raise ValueError(err)
-
-        self.source_path = path
-        self.temp_dir = tempfile.mkdtemp()
-        cmd = [get_bin('edfapi', 'edf2asc'),  # options in Manual p. 106
-               '-t',  # use only tabs as delimiters
-               '-e',  # outputs event data only
-               '-nse',  # blocks output of start events
-               '-p', self.temp_dir,  # writes output with same name to <path> directory
-               path]
-
-        _run(cmd)
-
-        # find asc file
-        name, _ = os.path.splitext(os.path.basename(path))
-        ascname = os.path.extsep.join((name, 'asc'))
-        self.asc_path = os.path.join(self.temp_dir, ascname)
-        self.asc_file = open(self.asc_path)
-        self.asc_str = self.asc_file.read()
-
-        # find trigger events
-        #                           MSG   time    msg...      ID
-        re_trigger = re.compile(r'\bMSG\t(\d+)\tMEG Trigger: (\d+)')
-        self.triggers = re_trigger.findall(self.asc_str)
-
-        # find artifacts
-        #                            type                    start   end
-        re_artifact = re.compile(r'\b(ESACC|EBLINK)\t[LR]\t(\d+)\t(\d+)')
-        self.artifacts = re_artifact.findall(self.asc_str)
-
-    def __del__(self):
-        shutil.rmtree(self.temp_dir)
-
-    def __repr__(self):
-        return 'edf_file(%r)' % self.source_path
-
-
-def _format_path(path, fmt, is_new=False):
-    "helper function to format the path to mne files"
-    if not isinstance(path, basestring):
-        path = os.path.join(*path)
-
-    if fmt:
-        path = path.format(**fmt)
-
-    # test the path
-    path = os.path.expanduser(path)
-    if is_new or os.path.exists(path):
-        return path
-    else:
-        raise IOError("%r does not exist" % path)
-
-
 def open_in_finder(path):
     """Open ``path`` in the finder"""
     os.system('open %s' % path)
@@ -232,57 +164,6 @@ def fs_home_problem(fs_home):
                     "mri_surf2surf)" % fs_home)
 
 
-def process_raw(raw, save='{raw}_filt', args=['projoff'], rm_eve=True, **kwargs):
-    """
-    Calls ``mne_process_raw`` to process raw fiff files. All
-    options can be submitted in ``args`` or as kwargs (for a description of
-    the options, see mne manual 2.7.3, ch. 4 / p. 41)
-
-    raw : str(path)
-        Source file.
-    save : str(path)
-        Destination file. ``'{raw}'`` will be replaced with the raw file path
-        without the extension.
-    args : list of str
-        Options that do not require a value (e.g., to specify ``--filteroff``,
-        use ``args=['filteroff']``).
-    rm_eve : bool
-        Remove the event file automatically generated by ``mne_process_raw``
-    **kwargs:**
-        ``mne_process_raw`` options that require values (see example).
-
-    Example::
-
-        >>> process_raw('/some/file_raw.fif', highpass=8, lowpass=12)
-
-    """
-    raw_name, _ = os.path.splitext(raw)
-    eve_file = '%s-eve.fif' % raw_name
-    if raw_name.endswith('_raw'):
-        raw_name = raw_name[:-4]
-
-    save = save.format(raw=raw_name)
-
-    cmd = [get_bin('mne', 'mne_process_raw'),
-           '--raw', raw,
-           '--save', save]
-
-    for arg in args:
-        cmd.append('--%s' % arg)
-
-    for key, value in kwargs.iteritems():
-        cmd.append('--%s' % key)
-        cmd.append(value)
-
-    _run(cmd)
-    if rm_eve:
-        try:
-            os.remove(eve_file)
-        except Exception as err:
-            print("Could not remove %r" % eve_file)
-            print(err)
-
-
 def _run(cmd, v=None, cwd=None, block=True):
     """Run a command
 
@@ -501,102 +382,6 @@ def run_mne_browse_raw(fif_dir, subject=None, subjects_dir=None, modal=False):
     _run_mne_gui('mne_browse_raw', fif_dir, modal, subject, subjects_dir)
 
 
-def do_forward_solution(paths=dict(rawfif=None,
-                                   mri_sdir=None,
-                                   fwd='{fif}-fwd.fif',
-                                   bem=None,
-                                   src=None,
-                                   trans=None),
-                        overwrite=False, v=1):
-    """
-    MNE Handbook 3.13
-
-    """
-    fif_file = paths.get('rawfif')
-    mri_sdir = paths.get('mri_sdir')
-    fwd_file = paths.get('fwd')
-    bem_file = paths.get('bem')
-    src_file = paths.get('src')
-    trans_file = paths.get('trans')
-
-    mri_dir, mri_subject = os.path.split(mri_sdir)
-
-    fif_name, _ = os.path.splitext(fif_file)
-    fwd_file = fwd_file.format(fif=fif_name)
-
-    os.environ['SUBJECTS_DIR'] = mri_dir
-    cmd = [get_bin('mne', "mne_do_forward_solution"),
-           '--subject', mri_subject,
-           '--src', src_file,
-           '--bem', bem_file,
-#           '--mri', mri_cor_file, # MRI description file containing the MEG/MRI coordinate transformation.
-           '--mri', trans_file,  # MRI description file containing the MEG/MRI coordinate transformation.
-#           '--trans', trans_file, #  head->MRI coordinate transformation (obviates --mri).
-           '--meas', fif_file,  # provides sensor locations and coordinate transformation between the MEG device coordinates and MEG head-based coordinates.
-           '--fwd', fwd_file,  # '--destdir', target_file_dir, # optional
-           '--megonly']
-
-    if overwrite:
-        cmd.append('--overwrite')
-    elif os.path.exists(fwd_file):
-        raise IOError("fwd file at %r already exists" % fwd_file)
-
-    out, err = _run(cmd, v=v)
-    if os.path.exists(fwd_file):
-        return fwd_file
-    else:
-        err = "fwd-file not created"
-        err = '\n'.join([err, "command out:", out])
-        raise RuntimeError(err)
-
-
-def do_inverse_operator(fwd_file, cov_file, inv_file='{cov}inv.fif',
-                        loose=False, fixed=False):
-    cov, _ = os.path.splitext(cov_file)
-    if cov.endswith('cov'):
-        cov = cov[:-3]
-
-    inv_file = inv_file.format(cov=cov)
-
-    cmd = [get_bin('mne', "mne_do_inverse_operator"),
-           '--fwd', fwd_file,
-           '--meg',  # Employ MEG data in the inverse calculation. If neither --meg nor --eeg is set only MEG channels are included.
-           '--depth',
-           '--megreg', 0.1,
-           '--noisecov', cov_file,
-           '--inv', inv_file,  # Save the inverse operator decomposition here.
-           ]
-
-    if loose:
-        cmd.extend(['--loose', loose])
-    elif fixed:
-        cmd.append('--fixed')
-
-    _, err = _run(cmd)
-    if not os.path.exists(inv_file):
-        raise RuntimeError('\n'.join(["inv-file not created", err]))
-
-
-def mne_make_morph_maps(s_to='fsaverage', s_from=None, redo=False, subjects_dir=None):
-    """
-    s_to, s_from : str | None
-        None -> all subejcts
-
-    """
-    cmd = [get_bin('mne', "mne_make_morph_maps")]
-    if not s_to or not s_from:
-        cmd.append('--all')
-    if s_to:
-        cmd.extend(('--to', s_to))
-    if s_from:
-        cmd.extend(('--from', s_from))
-    if redo:
-        cmd.appen('--redo')
-    if subjects_dir:
-        os.environ['SUBJECTS_DIR'] = subjects_dir
-    _run(cmd)
-
-
 # freesurfer---