[med-svn] [python-mne] 08/15: New upstream version 0.13+git5-g028f2ee
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 18 22:17:30 UTC 2016
This is an automated email from the git hooks/post-receive script.
yoh pushed a commit to branch master
in repository python-mne.
commit 0d54c51ccf6e2b59222ccf85118aa9b32fd169fb
Author: Yaroslav Halchenko <debian at onerussian.com>
Date: Tue Oct 11 14:59:15 2016 -0400
New upstream version 0.13+git5-g028f2ee
---
circle.yml | 6 +++++-
examples/datasets/plot_megsim_data_single_trial.py | 4 ++--
examples/datasets/plot_spm_faces_dataset.py | 9 ++++-----
examples/decoding/plot_decoding_spatio_temporal_source.py | 2 +-
examples/inverse/plot_compute_mne_inverse_raw_in_label.py | 1 +
examples/realtime/ftclient_rt_average.py | 2 +-
examples/realtime/plot_compute_rt_average.py | 2 +-
mne/decoding/tests/test_time_gen.py | 6 +++---
mne/html/bootstrap.min.js | 7 +++++++
mne/html/d3.v3.min.js | 5 +++++
mne/html/jquery-1.10.2.min.js | 6 ++++++
mne/html/jquery-ui.min.js | 12 ++++++++++++
mne/html/mpld3.v0.2.min.js | 2 ++
mne/viz/evoked.py | 3 ++-
14 files changed, 52 insertions(+), 15 deletions(-)
diff --git a/circle.yml b/circle.yml
index 7092492..251b41f 100644
--- a/circle.yml
+++ b/circle.yml
@@ -80,6 +80,10 @@ dependencies:
if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_phantom_elekta.*" | wc -l) -gt 0 ]]; then
python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_elekta.data_path())" --accept-brainstorm-license;
fi;
+ if [[ $(cat $FNAME | grep -x ".*datasets.*megsim.*" | wc -l) -gt 0 ]]; then
+ python -c "import mne; print(mne.datasets.megsim.load_data(condition='visual', data_format='single-trial', data_type='simulation', update_path=True))";
+ python -c "import mne; print(mne.datasets.megsim.load_data(condition='visual', data_format='raw', data_type='experimental', update_path=True))";
+ fi;
fi;
done;
echo PATTERN="$PATTERN";
@@ -128,7 +132,7 @@ deployment:
- cd doc/_build/html && cp -rf * ~/mne-tools.github.io/dev
- cd ../mne-tools.github.io && git add -A && git commit -m 'Automated update of dev docs.' && git push origin master
stable:
- branch: maint/0.12
+ branch: maint/0.13
commands:
- git config --global user.email "circle at mne.com"
- git config --global user.name "Circle Ci"
diff --git a/examples/datasets/plot_megsim_data_single_trial.py b/examples/datasets/plot_megsim_data_single_trial.py
index 451e7e8..c337b51 100644
--- a/examples/datasets/plot_megsim_data_single_trial.py
+++ b/examples/datasets/plot_megsim_data_single_trial.py
@@ -15,7 +15,7 @@ Gilliam K, Donahue CH, Montano R, Bryant JE, Scott A, Stephen JM
Realistic Simulated and Empirical Data. Neuroinformatics 10:141-158
"""
-from mne import read_evokeds
+from mne import read_evokeds, combine_evoked
from mne.datasets.megsim import load_data
print(__doc__)
@@ -30,7 +30,7 @@ epochs_fnames = load_data(condition=condition, data_format='single-trial',
epochs_fnames = [f for f in epochs_fnames if 'sim6_trial_' in f][:10]
evokeds = [read_evokeds(f)[0] for f in epochs_fnames]
-mean_evoked = sum(evokeds[1:], evokeds[0])
+mean_evoked = combine_evoked(evokeds, weights='nave')
# Visualize the average
mean_evoked.plot()
diff --git a/examples/datasets/plot_spm_faces_dataset.py b/examples/datasets/plot_spm_faces_dataset.py
index 6277db2..c0a0943 100644
--- a/examples/datasets/plot_spm_faces_dataset.py
+++ b/examples/datasets/plot_spm_faces_dataset.py
@@ -25,7 +25,7 @@ import matplotlib.pyplot as plt
import mne
from mne.datasets import spm_face
from mne.preprocessing import ICA, create_eog_epochs
-from mne import io
+from mne import io, combine_evoked
from mne.minimum_norm import make_inverse_operator, apply_inverse
print(__doc__)
@@ -74,7 +74,7 @@ ica.apply(epochs) # clean data, default in place
evoked = [epochs[k].average() for k in event_ids]
-contrast = evoked[1] - evoked[0]
+contrast = combine_evoked(evoked, weights=[-1, 1]) # Faces - scrambled
evoked.append(contrast)
@@ -128,7 +128,6 @@ stc = apply_inverse(contrast, inverse_operator, lambda2, method, pick_ori=None)
# stc.save('spm_%s_dSPM_inverse' % constrast.comment)
# Plot contrast in 3D with PySurfer if available
-brain = stc.plot(hemi='both', subjects_dir=subjects_dir)
-brain.set_time(170.0) # milliseconds
-brain.show_view('ventral')
+brain = stc.plot(hemi='both', subjects_dir=subjects_dir, initial_time=0.170,
+ views=['ven'])
# brain.save_image('dSPM_map.png')
diff --git a/examples/decoding/plot_decoding_spatio_temporal_source.py b/examples/decoding/plot_decoding_spatio_temporal_source.py
index bb62fda..28cd1a7 100644
--- a/examples/decoding/plot_decoding_spatio_temporal_source.py
+++ b/examples/decoding/plot_decoding_spatio_temporal_source.py
@@ -148,5 +148,5 @@ stc_feat = mne.SourceEstimate(feature_weights, vertices=vertices,
tmin=stc.tmin, tstep=stc.tstep,
subject='sample')
-brain = stc_feat.plot(hemi='split', views=['lat', 'med'], transparent=True,
+brain = stc_feat.plot(views=['lat'], transparent=True,
initial_time=0.1, time_unit='s')
diff --git a/examples/inverse/plot_compute_mne_inverse_raw_in_label.py b/examples/inverse/plot_compute_mne_inverse_raw_in_label.py
index f59bb29..550d29b 100644
--- a/examples/inverse/plot_compute_mne_inverse_raw_in_label.py
+++ b/examples/inverse/plot_compute_mne_inverse_raw_in_label.py
@@ -35,6 +35,7 @@ raw = mne.io.read_raw_fif(fname_raw)
inverse_operator = read_inverse_operator(fname_inv)
label = mne.read_label(fname_label)
+raw.set_eeg_reference() # set average reference.
start, stop = raw.time_as_index([0, 15]) # read the first 15s of data
# Compute inverse solution
diff --git a/examples/realtime/ftclient_rt_average.py b/examples/realtime/ftclient_rt_average.py
index 486ae12..10b89cf 100644
--- a/examples/realtime/ftclient_rt_average.py
+++ b/examples/realtime/ftclient_rt_average.py
@@ -74,7 +74,7 @@ with FieldTripClient(host='localhost', port=1972,
if ii == 0:
evoked = ev
else:
- evoked += ev
+ evoked = mne.combine_evoked([evoked, ev], weights='nave')
ax[0].cla()
ax[1].cla() # clear axis
diff --git a/examples/realtime/plot_compute_rt_average.py b/examples/realtime/plot_compute_rt_average.py
index 107d169..fd3b171 100644
--- a/examples/realtime/plot_compute_rt_average.py
+++ b/examples/realtime/plot_compute_rt_average.py
@@ -55,7 +55,7 @@ for ii, ev in enumerate(rt_epochs.iter_evoked()):
if ii == 0:
evoked = ev
else:
- evoked += ev
+ evoked = mne.combine_evoked([evoked, ev], weights='nave')
plt.clf() # clear canvas
evoked.plot(axes=plt.gca()) # plot on current figure
plt.pause(0.05)
diff --git a/mne/decoding/tests/test_time_gen.py b/mne/decoding/tests/test_time_gen.py
index 0a5bd13..5c72648 100644
--- a/mne/decoding/tests/test_time_gen.py
+++ b/mne/decoding/tests/test_time_gen.py
@@ -60,13 +60,13 @@ def test_generalization_across_time():
y_4classes = np.hstack((epochs.events[:7, 2], epochs.events[7:, 2] + 1))
if check_version('sklearn', '0.18'):
from sklearn.model_selection import (KFold, StratifiedKFold,
- ShuffleSplit, LeaveOneLabelOut)
+ ShuffleSplit, LeaveOneGroupOut)
cv_shuffle = ShuffleSplit()
- cv = LeaveOneLabelOut()
+ cv = LeaveOneGroupOut()
# XXX we cannot pass any other parameters than X and y to cv.split
# so we have to build it before hand
cv_lolo = [(train, test) for train, test in cv.split(
- X=y_4classes, y=y_4classes, labels=y_4classes)]
+ y_4classes, y_4classes, y_4classes)]
# With sklearn >= 0.17, `clf` can be identified as a regressor, and
# the scoring metrics can therefore be automatically assigned.
diff --git a/mne/html/bootstrap.min.js b/mne/html/bootstrap.min.js
new file mode 100644
index 0000000..1a6258e
--- /dev/null
+++ b/mne/html/bootstrap.min.js
@@ -0,0 +1,7 @@
+/*!
+ * Bootstrap v3.0.3 (http://getbootstrap.com)
+ * Copyright 2013 Twitter, Inc.
+ * Licensed under http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+if("undefined"==typeof jQuery)throw new Error("Bootstrap requires jQuery");+function(a){"use strict";function b(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in b)if(void 0!==a.style[c])return{end:b[c]}}a.fn.emulateTransitionEnd=function(b){var c=!1,d=this;a(this).one(a.support.transition.end,function(){c=!0});var e=function(){c||a(d).tri [...]
\ No newline at end of file
diff --git a/mne/html/d3.v3.min.js b/mne/html/d3.v3.min.js
new file mode 100644
index 0000000..eed58e6
--- /dev/null
+++ b/mne/html/d3.v3.min.js
@@ -0,0 +1,5 @@
+!function(){function n(n){return null!=n&&!isNaN(n)}function t(n){return n.length}function e(n){for(var t=1;n*t%1;)t*=10;return t}function r(n,t){try{for(var e in t)Object.defineProperty(n.prototype,e,{value:t[e],enumerable:!1})}catch(r){n.prototype=t}}function u(){}function i(n){return aa+n in this}function o(n){return n=aa+n,n in this&&delete this[n]}function a(){var n=[];return this.forEach(function(t){n.push(t)}),n}function c(){var n=0;for(var t in this)t.charCodeAt(0)===ca&&++n;retu [...]
+},t.clipExtent=function(n){return arguments.length?(w=n,_=n?Pe(n[0][0],n[0][1],n[1][0],n[1][1]):bt,u()):w},t.scale=function(n){return arguments.length?(h=+n,r()):h},t.translate=function(n){return arguments.length?(g=+n[0],p=+n[1],r()):[g,p]},t.center=function(n){return arguments.length?(v=n[0]%360*Na,d=n[1]%360*Na,r()):[v*La,d*La]},t.rotate=function(n){return arguments.length?(m=n[0]%360*Na,y=n[1]%360*Na,x=n.length>2?n[2]%360*Na:0,r()):[m*La,y*La,x*La]},Xo.rebind(t,f,"precision"),functio [...]
+}return r.invert=function(t){return Io(n.invert(t))},r.domain=function(t){return arguments.length?(n.domain(t),r):n.domain().map(Io)},r.nice=function(n,t){function e(e){return!isNaN(e)&&!n.range(e,Io(+e+1),t).length}var i=r.domain(),o=Ti(i),a=null==n?u(o,10):"number"==typeof n&&u(o,n);return a&&(n=a[0],t=a[1]),r.domain(Pi(i,t>1?{floor:function(t){for(;e(t=n.floor(t));)t=Io(t-1);return t},ceil:function(t){for(;e(t=n.ceil(t));)t=Io(+t+1);return t}}:n))},r.ticks=function(n,t){var e=Ti(r.dom [...]
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diff --git a/mne/html/jquery-1.10.2.min.js b/mne/html/jquery-1.10.2.min.js
new file mode 100644
index 0000000..da41706
--- /dev/null
+++ b/mne/html/jquery-1.10.2.min.js
@@ -0,0 +1,6 @@
+/*! jQuery v1.10.2 | (c) 2005, 2013 jQuery Foundation, Inc. | jquery.org/license
+//@ sourceMappingURL=jquery-1.10.2.min.map
+*/
+(function(e,t){var n,r,i=typeof t,o=e.location,a=e.document,s=a.documentElement,l=e.jQuery,u=e.$,c={},p=[],f="1.10.2",d=p.concat,h=p.push,g=p.slice,m=p.indexOf,y=c.toString,v=c.hasOwnProperty,b=f.trim,x=function(e,t){return new x.fn.init(e,t,r)},w=/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/.source,T=/\S+/g,C=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,N=/^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,k=/^<(\w+)\s*\/?>(?:<\/\1>|)$/,E=/^[\],:{}\s]*$/,S=/(?:^|:|,)(?:\s*\[)+/g,A=/\\(?:["\\\/bfnrt]|u[\da-fA-F]{4})/ [...]
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diff --git a/mne/html/jquery-ui.min.js b/mne/html/jquery-ui.min.js
new file mode 100644
index 0000000..82bbb67
--- /dev/null
+++ b/mne/html/jquery-ui.min.js
@@ -0,0 +1,12 @@
+/*! jQuery UI - v1.10.3 - 2013-05-03
+* http://jqueryui.com
+* Includes: jquery.ui.core.js, jquery.ui.widget.js, jquery.ui.mouse.js, jquery.ui.draggable.js, jquery.ui.droppable.js, jquery.ui.resizable.js, jquery.ui.selectable.js, jquery.ui.sortable.js, jquery.ui.effect.js, jquery.ui.accordion.js, jquery.ui.autocomplete.js, jquery.ui.button.js, jquery.ui.datepicker.js, jquery.ui.dialog.js, jquery.ui.effect-blind.js, jquery.ui.effect-bounce.js, jquery.ui.effect-clip.js, jquery.ui.effect-drop.js, jquery.ui.effect-explode.js, jquery.ui.effect-fade.js, [...]
+* Copyright 2013 jQuery Foundation and other contributors; Licensed MIT */
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+if(n){if(a=this._find(s),a.length)return a.find(".ui-tooltip-content").html(n),void 0;s.is("[title]")&&(i&&"mouseover"===i.type?s.attr("title",""):s.removeAttr("title")),a=this._tooltip(s),e(s,a.attr("id")),a.find(".ui-tooltip-content").html(n),this.options.track&&i&&/^mouse/.test(i.type)?(this._on(this.document,{mousemove:o}),o(i)):a.position(t.extend({of:s},this.options.position)),a.hide(),this._show(a,this.options.show),this.options.show&&this.options.show.delay&&(h=this.delayedShow=s [...]
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diff --git a/mne/html/mpld3.v0.2.min.js b/mne/html/mpld3.v0.2.min.js
new file mode 100644
index 0000000..adefb15
--- /dev/null
+++ b/mne/html/mpld3.v0.2.min.js
@@ -0,0 +1,2 @@
+!function(t){function s(t){var s={};for(var o in t)s[o]=t[o];return s}function o(t,s){t="undefined"!=typeof t?t:10,s="undefined"!=typeof s?s:"abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";for(var o=s.charAt(Math.round(Math.random()*(s.length-11))),e=1;t>e;e++)o+=s.charAt(Math.round(Math.random()*(s.length-1)));return o}function e(s,o){var e=t.interpolate([s[0].valueOf(),s[1].valueOf()],[o[0].valueOf(),o[1].valueOf()]);return function(t){var s=e(t);return[new Date(s[0]), [...]
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diff --git a/mne/viz/evoked.py b/mne/viz/evoked.py
index 37a5c32..42abbe8 100644
--- a/mne/viz/evoked.py
+++ b/mne/viz/evoked.py
@@ -200,7 +200,8 @@ def _plot_evoked(evoked, picks, exclude, unit, show,
units = _handle_default('units', units)
# Valid data types ordered for consistency
valid_channel_types = ['eeg', 'grad', 'mag', 'seeg', 'eog', 'ecg', 'emg',
- 'dipole', 'gof', 'bio', 'ecog', 'hbo', 'hbr']
+ 'dipole', 'gof', 'bio', 'ecog', 'hbo', 'hbr',
+ 'misc']
if picks is None:
picks = list(range(info['nchan']))
--
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