[med-svn] [python-mne] 38/376: better example of reading evoked data

[Yaroslav Halchenko]

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

commit ce9c4284d88947b045f6f2a822051c6fd2c9beb1
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Wed Jan 19 16:58:05 2011 -0500

    better example of reading evoked data
---
 examples/plot_read_epochs.py | 75 ++++++++++++++++++++++++++++++++++++++++++++
 examples/read_epochs.py      | 45 --------------------------
 mne/epochs.py                |  4 +--
 3 files changed, 77 insertions(+), 47 deletions(-)

diff --git a/examples/plot_read_epochs.py b/examples/plot_read_epochs.py
new file mode 100644
index 0000000..cbf28b9
--- /dev/null
+++ b/examples/plot_read_epochs.py
@@ -0,0 +1,75 @@
+"""
+==================================
+Reading epochs from a raw FIF file
+==================================
+
+This script shows how to read the epochs from a raw file given
+a list of events. For illustration, we compute the evoked responses
+for both MEG and EEG data by averaging all the epochs.
+
+"""
+# Authors: Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
+#          Matti Hamalainen <msh at nmr.mgh.harvard.edu>
+#
+# License: Simplified BSD
+
+print __doc__
+
+import os
+import numpy as np
+
+import mne
+from mne import fiff
+
+###############################################################################
+# Set parameters
+raw_fname = os.environ['MNE_SAMPLE_DATASET_PATH']
+raw_fname += '/MEG/sample/sample_audvis_raw.fif'
+event_fname = os.environ['MNE_SAMPLE_DATASET_PATH']
+event_fname += '/MEG/sample/sample_audvis_raw-eve.fif'
+event_id = 1
+tmin = -0.2
+tmax = 0.5
+
+#   Setup for reading the raw data
+raw = fiff.setup_read_raw(raw_fname)
+events = mne.read_events(event_fname)
+
+#   Set up pick list: MEG + STI 014 - bad channels (modify to your needs)
+include = [] # or stim channel ['STI 014']
+exclude = raw['info']['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
+
+# MEG
+meg_picks = fiff.pick_types(raw['info'], meg=True, eeg=False, stim=False,
+                                            include=include, exclude=exclude)
+meg_data, times, channel_names = mne.read_epochs(raw, events, event_id,
+                                                tmin, tmax, picks=meg_picks)
+meg_epochs = np.array([d['epoch'] for d in meg_data]) # build 3D matrix
+meg_evoked_data = np.mean(meg_epochs, axis=0) # compute evoked fields
+
+# EEG
+eeg_picks = fiff.pick_types(raw['info'], meg=False, eeg=True, stim=False,
+                                            include=include, exclude=exclude)
+eeg_data, times, channel_names = mne.read_epochs(raw, events, event_id,
+                                                tmin, tmax, picks=eeg_picks)
+eeg_epochs = np.array([d['epoch'] for d in eeg_data]) # build 3D matrix
+eeg_evoked_data = np.mean(eeg_epochs, axis=0) # compute evoked potentials
+
+###############################################################################
+# View evoked response
+import pylab as pl
+pl.clf()
+pl.subplot(2, 1, 1)
+pl.plot(times, meg_evoked_data.T)
+pl.xlim([times[0], times[-1]])
+pl.xlabel('time (ms)')
+pl.ylabel('Magnetic Field (T)')
+pl.title('MEG evoked field')
+pl.subplot(2, 1, 2)
+pl.plot(times, eeg_evoked_data.T)
+pl.xlim([times[0], times[-1]])
+pl.xlabel('time (ms)')
+pl.ylabel('Potential (V)')
+pl.title('EEG evoked potential')
+pl.subplots_adjust(0.175, 0.04, 0.94, 0.94, 0.2, 0.33)
+pl.show()
diff --git a/examples/read_epochs.py b/examples/read_epochs.py
deleted file mode 100644
index a06a675..0000000
--- a/examples/read_epochs.py
+++ /dev/null
@@ -1,45 +0,0 @@
-"""
-==================================
-Reading epochs from a raw FIF file
-==================================
-"""
-# Authors: Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
-#          Matti Hamalainen <msh at nmr.mgh.harvard.edu>
-#
-# License: Simplified BSD
-
-print __doc__
-
-import mne
-from mne import fiff
-
-###############################################################################
-# Set parameters
-raw_fname = 'MNE-sample-data/MEG/sample/sample_audvis_raw.fif'
-event_name = 'MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif'
-event_id = 1
-tmin = -0.2
-tmax = 0.5
-pick_all = True
-
-#   Setup for reading the raw data
-raw = fiff.setup_read_raw(raw_fname)
-events = mne.read_events(event_name)
-
-if pick_all:
-   # Pick all
-   picks = range(raw['info']['nchan'])
-else:
-   #   Set up pick list: MEG + STI 014 - bad channels (modify to your needs)
-   include = ['STI 014'];
-   want_meg = True
-   want_eeg = False
-   want_stim = False
-   picks = fiff.pick_types(raw['info'], want_meg, want_eeg, want_stim,
-                                include, raw['info']['bads'])
-
-data, times, channel_names = mne.read_epochs(raw, events, event_id,
-                                                    tmin, tmax, picks=picks)
-
-# for epoch in data:
-    
\ No newline at end of file
diff --git a/mne/epochs.py b/mne/epochs.py
index 4a99c94..ca3b9ac 100644
--- a/mne/epochs.py
+++ b/mne/epochs.py
@@ -158,7 +158,7 @@ def read_epochs(raw, events, event_id, tmin, tmax, picks=None,
                                                 data[0]['epoch'].shape[1])
 
     #   Remember to close the file descriptor
-    raw['fid'].close()
-    print 'File closed.'
+    # raw['fid'].close()
+    # print 'File closed.'
 
     return data, times, ch_names

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