text: #!/usr/bin/env python
  """Compute SSP/PCA projections for EOG artifacts
  
  You can do for example:
  
  $ mne compute_proj_eog -i sample_audvis_raw.fif --l-freq 1 --h-freq 35 --rej-grad 3000 --rej-mag 4000 --rej-eeg 100
  
  or
  
  $ mne compute_proj_eog -i sample_audvis_raw.fif --l-freq 1 --h-freq 35 --rej-grad 3000 --rej-mag 4000 --rej-eeg 100 --proj sample_audvis_ecg_proj.fif
  
  to exclude ECG artifacts from projection computation.
  """
  from __future__ import print_function
  
  # Authors : Alexandre Gramfort, Ph.D.
  #           Martin Luessi, Ph.D.
  
  from ..externals.six import string_types
  import os
  import sys
  import mne
  
  
  if __name__ == '__main__':
  
      from mne.commands.utils import get_optparser
  
      parser = get_optparser(__file__)
  
      parser.add_option("-i", "--in", dest="raw_in",
                        help="Input raw FIF file", metavar="FILE")
      parser.add_option("--tmin", dest="tmin", type="float",
                        help="Time before event in seconds",
                        default=-0.2)
      parser.add_option("--tmax", dest="tmax", type="float",
                        help="Time after event in seconds",
                        default=0.2)
      parser.add_option("-g", "--n-grad", dest="n_grad", type="int",
                        help="Number of SSP vectors for gradiometers",
                        default=2)
      parser.add_option("-m", "--n-mag", dest="n_mag", type="int",
                        help="Number of SSP vectors for magnetometers",
                        default=2)
      parser.add_option("-e", "--n-eeg", dest="n_eeg", type="int",
                        help="Number of SSP vectors for EEG",
                        default=2)
      parser.add_option("--l-freq", dest="l_freq", type="float",
                        help="Filter low cut-off frequency in Hz",
                        default=1)
      parser.add_option("--h-freq", dest="h_freq", type="float",
                        help="Filter high cut-off frequency in Hz",
                        default=35)
      parser.add_option("--eog-l-freq", dest="eog_l_freq", type="float",
                        help="Filter low cut-off frequency in Hz used for EOG event detection",
                        default=1)
      parser.add_option("--eog-h-freq", dest="eog_h_freq", type="float",
                        help="Filter high cut-off frequency in Hz used for EOG event detection",
                        default=10)
      parser.add_option("-p", "--preload", dest="preload",
                        help="Temporary file used during computation (to save memory)",
                        default=True)
      parser.add_option("-a", "--average", dest="average", action="store_true",
                        help="Compute SSP after averaging",
                        default=False)
      parser.add_option("--proj", dest="proj",
                        help="Use SSP projections from a fif file.",
                        default=None)
      parser.add_option("--filtersize", dest="filter_length", type="int",
                        help="Number of taps to use for filtering",
                        default=2048)
      parser.add_option("-j", "--n-jobs", dest="n_jobs", type="int",
                        help="Number of jobs to run in parallel",
                        default=1)
      parser.add_option("--rej-grad", dest="rej_grad", type="float",
                        help="Gradiometers rejection parameter in fT/cm (peak to peak amplitude)",
                        default=2000)
      parser.add_option("--rej-mag", dest="rej_mag", type="float",
                        help="Magnetometers rejection parameter in fT (peak to peak amplitude)",
                        default=3000)
      parser.add_option("--rej-eeg", dest="rej_eeg", type="float",
                        help="EEG rejection parameter in uV (peak to peak amplitude)",
                        default=50)
      parser.add_option("--rej-eog", dest="rej_eog", type="float",
                        help="EOG rejection parameter in uV (peak to peak amplitude)",
                        default=1e9)
      parser.add_option("--avg-ref", dest="avg_ref", action="store_true",
                        help="Add EEG average reference proj",
                        default=False)
      parser.add_option("--no-proj", dest="no_proj", action="store_true",
                        help="Exclude the SSP projectors currently in the fiff file",
                        default=False)
      parser.add_option("--bad", dest="bad_fname",
                        help="Text file containing bad channels list (one per line)",
                        default=None)
      parser.add_option("--event-id", dest="event_id", type="int",
                        help="ID to use for events", default=998)
      parser.add_option("--event-raw", dest="raw_event_fname",
                        help="raw file to use for event detection", default=None)
      parser.add_option("--tstart", dest="tstart", type="float",
                        help="Start artifact detection after tstart seconds", default=0.)
      parser.add_option("-c","--channel", dest="ch_name", type="string",
                        help="Custom EOG channel(s), comma separated",
                        default=None)
  
      options, args = parser.parse_args()
  
      raw_in = options.raw_in
  
      if raw_in is None:
          parser.print_help()
          sys.exit(1)
  
      tmin = options.tmin
      tmax = options.tmax
      n_grad = options.n_grad
      n_mag = options.n_mag
      n_eeg = options.n_eeg
      l_freq = options.l_freq
      h_freq = options.h_freq
      eog_l_freq = options.eog_l_freq
      eog_h_freq = options.eog_h_freq
      average = options.average
      preload = options.preload
      filter_length = options.filter_length
      n_jobs = options.n_jobs
      reject = dict(grad=1e-13 * float(options.rej_grad),
                    mag=1e-15 * float(options.rej_mag),
                    eeg=1e-6 * float(options.rej_eeg),
                    eog=1e-6 * float(options.rej_eog))
      avg_ref = options.avg_ref
      no_proj = options.no_proj
      bad_fname = options.bad_fname
      event_id = options.event_id
      proj_fname = options.proj
      raw_event_fname = options.raw_event_fname
      tstart = options.tstart
      ch_name = options.ch_name
  
      if bad_fname is not None:
          bads = [w.rstrip().split()[0] for w in open(bad_fname).readlines()]
          print('Bad channels read : %s' % bads)
      else:
          bads = []
  
      if raw_in.endswith('_raw.fif') or raw_in.endswith('-raw.fif'):
          prefix = raw_in[:-8]
      else:
          prefix = raw_in[:-4]
  
      eog_event_fname = prefix + '_eog-eve.fif'
  
      if average:
          eog_proj_fname = prefix + '_eog_avg_proj.fif'
      else:
          eog_proj_fname = prefix + '_eog_proj.fif'
  
      raw = mne.fiff.Raw(raw_in, preload=preload)
  
      if raw_event_fname is not None:
          raw_event = mne.fiff.Raw(raw_event_fname)
      else:
          raw_event = raw
  
      flat = None  # XXX : not exposed to the user
      projs, events = mne.preprocessing.compute_proj_eog(raw=raw,
                      raw_event=raw_event, tmin=tmin, tmax=tmax, n_grad=n_grad,
                      n_mag=n_mag, n_eeg=n_eeg, l_freq=l_freq, h_freq=h_freq,
                      average=average, filter_length=filter_length,
                      n_jobs=n_jobs, reject=reject, flat=flat, bads=bads,
                      avg_ref=avg_ref, no_proj=no_proj, event_id=event_id,
                      eog_l_freq=eog_l_freq, eog_h_freq=eog_h_freq, 
                      tstart=tstart, ch_name=ch_name, copy=False)
  
      raw.close()
  
      if raw_event_fname is not None:
          raw_event.close()
  
      if proj_fname is not None:
          print('Including SSP projections from : %s' % proj_fname)
          # append the eog projs, so they are last in the list
          projs = mne.read_proj(proj_fname) + projs
  
      if isinstance(preload, string_types) and os.path.exists(preload):
          os.remove(preload)
  
      print("Writing EOG projections in %s" % eog_proj_fname)
      mne.write_proj(eog_proj_fname, projs)
  
      print("Writing EOG events in %s" % eog_event_fname)
      mne.write_events(eog_event_fname, events)
  