wip py3k

mne/beamformer/_dics.py

@@ -18,6 +18,7 @@
 from ..source_estimate import SourceEstimate
 from ..time_frequency import CrossSpectralDensity, compute_epochs_csd
 from ._lcmv import _prepare_beamformer_input
+import six
 
 
 @verbose
@@ -77,7 +78,7 @@ def _apply_dics(data, info, tmin, forward, noise_csd, data_csd, reg,
     n_orient = 3 if is_free_ori else 1
     n_sources = G.shape[1] // n_orient
 
-    for k in xrange(n_sources):
+    for k in range(n_sources):
         Wk = W[n_orient * k: n_orient * k + n_orient]
         Gk = G[:, n_orient * k: n_orient * k + n_orient]
         Ck = np.dot(Wk, Gk)
@@ -191,7 +192,7 @@ def dics(evoked, forward, noise_csd, data_csd, reg=0.01, label=None,
 
     stc = _apply_dics(data, info, tmin, forward, noise_csd, data_csd, reg=reg,
                       label=label, pick_ori=pick_ori)
-    return stc.next()
+    return six.advance_iterator(stc)
 
 
 @verbose
@@ -372,7 +373,7 @@ def dics_source_power(info, forward, noise_csds, data_csds, reg=0.01,
 
         # Compute spatial filters
         W = np.dot(G.T, Cm_inv)
-        for k in xrange(n_sources):
+        for k in range(n_sources):
             Wk = W[n_orient * k: n_orient * k + n_orient]
             Gk = G[:, n_orient * k: n_orient * k + n_orient]
             Ck = np.dot(Wk, Gk)

mne/beamformer/_lcmv.py

@@ -21,6 +21,7 @@
 from ..source_space import label_src_vertno_sel
 from ..utils import logger, verbose
 from .. import Epochs
+import six
 
 
 @verbose
@@ -289,8 +290,8 @@ def lcmv(evoked, forward, noise_cov, data_cov, reg=0.01, label=None,
     data = evoked.data
     tmin = evoked.times[0]
 
-    stc = _apply_lcmv(data, info, tmin, forward, noise_cov, data_cov, reg,
-                      label, pick_ori=pick_ori).next()
+    stc = six.advance_iterator(_apply_lcmv(data, info, tmin, forward, noise_cov, data_cov, reg,
+                      label, pick_ori=pick_ori))
 
     return stc
 
@@ -431,8 +432,8 @@ def lcmv_raw(raw, forward, noise_cov, data_cov, reg=0.01, label=None,
     data, times = raw[picks, start:stop]
     tmin = times[0]
 
-    stc = _apply_lcmv(data, info, tmin, forward, noise_cov, data_cov, reg,
-                      label, picks, pick_ori).next()
+    stc = six.advance_iterator(_apply_lcmv(data, info, tmin, forward, noise_cov, data_cov, reg,
+                      label, picks, pick_ori))
 
     return stc
 

mne/beamformer/tests/test_dics.py

@@ -1,3 +1,4 @@
+from __future__ import print_function
 import warnings
 import os.path as op
 import copy as cp
@@ -206,7 +207,7 @@ def test_dics_source_power():
     for freq, data_csd in zip(frequencies, data_csds):
         data_csd.frequencies = [freq]
     noise_csds = data_csds
-    with warnings.catch_warnings(True) as w:
+    with warnings.catch_warnings(record=True) as w:
         dics_source_power(epochs.info, forward, noise_csds, data_csds)
     assert len(w) == 1
 
@@ -235,7 +236,7 @@ def test_tf_dics():
                    freq_bins, reg=reg, label=label)
 
     assert_true(len(stcs) == len(freq_bins))
-    print stcs[0].shape
+    print(stcs[0].shape)
     assert_true(stcs[0].shape[1] == 4)
 
     # Manually calculating source power in several time windows to compare

mne/beamformer/tests/test_lcmv.py

@@ -299,7 +299,7 @@ def test_tf_lcmv():
         raw_band.filter(l_freq, h_freq, method='iir', n_jobs=1, picks=picks)
         epochs_band = mne.Epochs(raw_band, epochs.events, epochs.event_id,
                                  tmin=tmin, tmax=tmax, proj=True)
-        with warnings.catch_warnings(True):  # not enough samples
+        with warnings.catch_warnings(record=True):  # not enough samples
             noise_cov = compute_covariance(epochs_band, tmin=tmin, tmax=tmin +
                                            win_length)
         noise_cov = mne.cov.regularize(noise_cov, epochs_band.info, mag=reg,
@@ -311,7 +311,7 @@ def test_tf_lcmv():
         # time windows to compare to tf_lcmv results and test overlapping
         if (l_freq, h_freq) == freq_bins[0]:
             for time_window in time_windows:
-                with warnings.catch_warnings(True):
+                with warnings.catch_warnings(record=True):
                     data_cov = compute_covariance(epochs_band,
                                                   tmin=time_window[0],
                                                   tmax=time_window[1])
@@ -360,7 +360,7 @@ def test_tf_lcmv():
     assert_raises(ValueError, tf_lcmv, epochs_preloaded, forward, noise_covs,
                   tmin, tmax, tstep, win_lengths, freq_bins)
 
-    with warnings.catch_warnings(True):  # not enough samples
+    with warnings.catch_warnings(record=True):  # not enough samples
         # Pass only one epoch to test if subtracting evoked
         # responses yields zeros
         stcs = tf_lcmv(epochs[0], forward, noise_covs, tmin, tmax, tstep,

mne/commands/mne_clean_eog_ecg.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 """Clean a raw file from EOG and ECG artifacts with PCA (ie SSP)
 """
+from __future__ import print_function
 
 # Authors : Dr Engr. Sheraz Khan,  P.Eng, Ph.D.
 #           Engr. Nandita Shetty,  MS.
@@ -55,14 +56,14 @@ def clean_ecg_eog(in_fif_fname, out_fif_fname=None, eog=True, ecg=True,
     if eog_event_fname is None:
         eog_event_fname = prefix + '_eog-eve.fif'
 
-    print 'Implementing ECG and EOG artifact rejection on data'
+    print('Implementing ECG and EOG artifact rejection on data')
 
     if ecg:
         ecg_events, _, _  = mne.preprocessing.find_ecg_events(raw_in)
-        print "Writing ECG events in %s" % ecg_event_fname
+        print("Writing ECG events in %s" % ecg_event_fname)
         mne.write_events(ecg_event_fname, ecg_events)
 
-        print 'Computing ECG projector'
+        print('Computing ECG projector')
 
         command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '
                    '--projtmin -0.08 --projtmax 0.08 --saveprojtag _ecg_proj '
@@ -72,48 +73,48 @@ def clean_ecg_eog(in_fif_fname, out_fif_fname=None, eog=True, ecg=True,
         st = os.system(command)
 
         if st != 0:
-            print "Error while running : %s" % command
+            print("Error while running : %s" % command)
 
     if eog:
         eog_events = mne.preprocessing.find_eog_events(raw_in)
-        print "Writing EOG events in %s" % eog_event_fname
+        print("Writing EOG events in %s" % eog_event_fname)
         mne.write_events(eog_event_fname, eog_events)
 
-        print 'Computing EOG projector'
+        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
+        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'
+        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
+        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 !!'
+        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.'
+        print('Projection not applied to raw data.')
 
 
 if __name__ == '__main__':

mne/commands/mne_compute_proj_ecg.py

@@ -5,10 +5,12 @@
 
 $ mne compute_proj_ecg -i sample_audvis_raw.fif -c "MEG 1531" --l-freq 1 --h-freq 100 --rej-grad 3000 --rej-mag 4000 --rej-eeg 100
 """
+from __future__ import print_function
 
 # Authors : Alexandre Gramfort, Ph.D.
 #           Martin Luessi, Ph.D.
 
+from six import string_types
 import os
 import sys
 import mne
@@ -154,7 +156,7 @@
 
     if bad_fname is not None:
         bads = [w.rstrip().split()[0] for w in open(bad_fname).readlines()]
-        print 'Bad channels read : %s' % bads
+        print('Bad channels read : %s' % bads)
     else:
         bads = []
 
@@ -191,15 +193,15 @@
         raw_event.close()
 
     if proj_fname is not None:
-        print 'Including SSP projections from : %s' % proj_fname
+        print('Including SSP projections from : %s' % proj_fname)
         # append the ecg projs, so they are last in the list
         projs = mne.read_proj(proj_fname) + projs
 
-    if isinstance(preload, basestring) and os.path.exists(preload):
+    if isinstance(preload, string_types) and os.path.exists(preload):
         os.remove(preload)
 
-    print "Writing ECG projections in %s" % ecg_proj_fname
+    print("Writing ECG projections in %s" % ecg_proj_fname)
     mne.write_proj(ecg_proj_fname, projs)
 
-    print "Writing ECG events in %s" % ecg_event_fname
+    print("Writing ECG events in %s" % ecg_event_fname)
     mne.write_events(ecg_event_fname, events)

mne/commands/mne_compute_proj_eog.py

@@ -11,10 +11,12 @@
 
 to exclude ECG artifacts from projection computation.
 """
+from __future__ import print_function
 
 # Authors : Alexandre Gramfort, Ph.D.
 #           Martin Luessi, Ph.D.
 
+from six import string_types
 import os
 import sys
 import mne
@@ -137,7 +139,7 @@
 
     if bad_fname is not None:
         bads = [w.rstrip().split()[0] for w in open(bad_fname).readlines()]
-        print 'Bad channels read : %s' % bads
+        print('Bad channels read : %s' % bads)
     else:
         bads = []
 
@@ -176,15 +178,15 @@
         raw_event.close()
 
     if proj_fname is not None:
-        print 'Including SSP projections from : %s' % proj_fname
+        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, basestring) and os.path.exists(preload):
+    if isinstance(preload, string_types) and os.path.exists(preload):
         os.remove(preload)
 
-    print "Writing EOG projections in %s" % eog_proj_fname
+    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
+    print("Writing EOG events in %s" % eog_event_fname)
     mne.write_events(eog_event_fname, events)

mne/commands/mne_flash_bem_model.py

@@ -13,6 +13,7 @@
 directory.
 
 """
+from __future__ import print_function
 
 # Authors:  Rey Rene Ramirez, Ph.D.   e-mail: rrramir at uw.edu
 #           Alexandre Gramfort, Ph.D.
@@ -71,19 +72,19 @@ def make_flash_bem(subject, subjects_dir, flash05, flash30, show=False):
     # flash_dir = os.getcwd()
     if not os.path.exists('parameter_maps'):
         os.mkdir("parameter_maps")
-    print "--- Converting Flash 5"
+    print("--- Converting Flash 5")
     os.system('mri_convert -flip_angle %s -tr 25 %s mef05.mgz' %
                                             (5 * math.pi / 180, flash05))
-    print "--- Converting Flash 30"
+    print("--- Converting Flash 30")
     os.system('mri_convert -flip_angle %s -tr 25 %s mef30.mgz' %
                                             (30 * math.pi / 180, flash30))
-    print "--- Running mne_flash_bem"
+    print("--- Running mne_flash_bem")
     os.system('mne_flash_bem --noconvert')
     os.chdir(os.path.join(subjects_dir, subject, 'bem'))
     if not os.path.exists('flash'):
         os.mkdir("flash")
     os.chdir("flash")
-    print "[done]"
+    print("[done]")
 
     if show:
         fnames = ['outer_skin.surf', 'outer_skull.surf', 'inner_skull.surf']