[med-svn] [python-mne] 259/376: ENH : adding alpha version of script to remove EOG + ECG artifacts from data

[Yaroslav Halchenko]

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yoh pushed a commit to annotated tag v0.1
in repository python-mne.

commit c71e1602a9b97f2c2778909849392fcbaf800cb0
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Thu May 19 18:34:29 2011 -0400

    ENH : adding alpha version of script to remove EOG + ECG artifacts from data
---
 bin/mne_clean_eog_ecg.py | 139 +++++++++++++++++++++++++++++++++++++++++++++++
 setup.py                 |   1 +
 2 files changed, 140 insertions(+)

diff --git a/bin/mne_clean_eog_ecg.py b/bin/mne_clean_eog_ecg.py
new file mode 100755
index 0000000..e3fcc7c
--- /dev/null
+++ b/bin/mne_clean_eog_ecg.py
@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+"""Clean a raw file from EOG and ECG artifacts with PCA (ie SSP)
+"""
+
+# Authors : Dr Engr. Sheraz Khan,  P.Eng, Ph.D.
+#           Engr. Nandita Shetty,  MS.
+#           Alexandre Gramfort, Ph.D.
+
+
+import os
+import mne
+
+
+def clean_ecg_eog(in_fif_fname, out_fif_fname=None, eog=True, ecg=True,
+                  ecg_proj_fname=None, eog_proj_fname=None,
+                  ecg_event_fname=None, eog_event_fname=None, in_path='.'):
+    """Clean ECG from raw fif file
+
+    Parameters
+    ----------
+    in_fif_fname: string
+        Raw fif File
+    eog_event_fname: string
+        name of EOG event file required.
+    eog: bool
+        Reject or not EOG artifacts.
+    ecg: bool
+        Reject or not ECG artifacts.
+    ecg_event_fname: string
+        name of ECG event file required.
+    in_path:
+        Path where all the files are.
+    """
+    if not eog and not ecg:
+        raise Exception("EOG and ECG cannot be both disabled")
+
+    # Reading fif File
+    raw_in = mne.fiff.Raw(in_fif_fname)
+
+    if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
+        prefix = in_fif_fname[:-8]
+    else:
+        prefix = in_fif_fname[:-4]
+
+    if out_fif_fname is None:
+        out_fif_fname = prefix + '_clean_ecg_eog_raw.fif'
+    if ecg_proj_fname is None:
+        ecg_proj_fname = prefix + '_ecg_proj.fif'
+    if eog_proj_fname is None:
+        eog_proj_fname = prefix + '_eog_proj.fif'
+    if ecg_event_fname is None:
+        ecg_event_fname = prefix + '_ecg-eve.fif'
+    if eog_event_fname is None:
+        eog_event_fname = prefix + '_eog-eve.fif'
+
+    print 'Implementing ECG and EOG artifact rejection on data'
+
+    if ecg:
+        ecg_events = mne.artifacts.find_ecg_events(raw_in)
+        print "Writing ECG events in %s" % ecg_event_fname
+        mne.write_events(ecg_event_fname, ecg_events)
+
+        print 'Computing ECG projector'
+
+        command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '
+                   '--projtmin -0.08 --projtmax 0.08 --saveprojtag _ecg_proj '
+                   '--projnmag 2 --projngrad 1 --projevent 999 --highpass 5 '
+                   '--lowpass 35 --projmagrej 4000  --projgradrej 3000'
+                   % (in_path, in_fif_fname, ecg_event_fname))
+        st = os.system(command)
+
+        if st != 0:
+            print "Error while running : %s" % command
+
+    if eog:
+        eog_events = mne.artifacts.find_eog_events(raw_in)
+        print "Writing EOG events in %s" % eog_event_fname
+        mne.write_events(eog_event_fname, eog_events)
+
+        print 'Computing EOG projector'
+
+        command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '
+                   '--projtmin -0.15 --projtmax 0.15 --saveprojtag _eog_proj '
+                   '--projnmag 2 --projngrad 2 --projevent 998 --lowpass 35 '
+                   '--projmagrej 4000  --projgradrej 3000' % (in_path,
+                   in_fif_fname, eog_event_fname))
+
+        print 'Running : %s' % command
+
+        st = os.system(command)
+        if st != 0:
+            raise ValueError('Problem while running : %s' % command)
+
+    if out_fif_fname is not None:
+        # Applying the ECG EOG projector
+        print 'Applying ECG EOG projector'
+
+        command = ('mne_process_raw --cd %s --raw %s '
+                   '--proj %s --projoff --save %s --filteroff'
+                   % (in_path, in_fif_fname, in_fif_fname, out_fif_fname))
+        command += ' --proj %s --proj %s' % (ecg_proj_fname, eog_proj_fname)
+
+        print 'Command executed: %s' % command
+
+        st = os.system(command)
+
+        if st != 0:
+            raise ValueError('Pb while running : %s' % command)
+
+        print 'Done removing artifacts.'
+        print "Cleaned raw data saved in: %s" % out_fif_fname
+        print 'IMPORTANT : Please eye-ball the data !!'
+    else:
+        print 'Projection not applied to raw data.'
+
+
+if __name__ == '__main__':
+
+    from optparse import OptionParser
+
+    parser = OptionParser()
+    parser.add_option("-i", "--in", dest="raw_in",
+                    help="Input raw FIF file", metavar="FILE")
+    parser.add_option("-o", "--out", dest="raw_out",
+                    help="Output raw FIF file", metavar="FILE",
+                    default=None)
+    parser.add_option("-e", "--no-eog", dest="eog", action="store_false",
+                    help="Remove EOG", default=True)
+    parser.add_option("-c", "--no-ecg", dest="ecg", action="store_false",
+                    help="Remove ECG", default=True)
+
+    (options, args) = parser.parse_args()
+
+    raw_in = options.raw_in
+    raw_out = options.raw_out
+    eog = options.eog
+    ecg = options.ecg
+
+    clean_ecg_eog(raw_in, raw_out, eog=eog, ecg=ecg)
diff --git a/setup.py b/setup.py
index e407e97..17c511d 100755
--- a/setup.py
+++ b/setup.py
@@ -81,4 +81,5 @@ if __name__ == "__main__":
                    'mne.minimum_norm', 'mne.minimum_norm.tests',
                    'mne.layouts',
                    'mne.time_frequency', 'mne.time_frequency.tests'],
+         scripts=['bin/mne_clean_eog_ecg.py'],
          **extra_setuptools_args)

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