bump version to 0.8.6

Conflicts:
	mne/report.py

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright © 2011, authors of MNE-Python
+Copyright © 2011-2014, authors of MNE-Python
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -9,7 +9,12 @@ recursive-include mne/data *.sel
 recursive-include mne/data *.fif.gz
 recursive-include mne/layouts *.lout
 recursive-include mne/layouts *.lay
+recursive-include mne/html *.js
+recursive-include mne/html *.css
 recursive-exclude examples/MNE-sample-data *
+recursive-exclude examples/MNE-testing-data *
+recursive-exclude examples/MNE-spm-face *
+recursive-exclude examples/MNE-somato-data *
 # recursive-include mne/fiff/tests/data *
 recursive-exclude mne/fiff/tests/data *
 recursive-exclude mne/fiff/bti/tests/data *

doc/source/index.rst

@@ -1,15 +1,3 @@
-==========================
-Google Summer of Code 2014
-==========================
-
-For the Google Summer of Code 2014 (GSOC) we are looking for two ambitious
-students with strong Python skills and a background and / or interest in brain
-imaging research. If you feel addressed or happen to know someone who might be
-interested please get in touch with us or forward this message to her / him.
-Here are our our `GSOC projects <http://goo.gl/4KkmRC>`_.
-`Registration <http://goo.gl/KMPQRf>`_ opens on March 10, 2014, 7 p.m. UTC.
-
-
 ========
 MNE Home
 ========

doc/source/python_reference.rst

@@ -122,6 +122,8 @@ Functions:
 File I/O
 ========
 
+.. currentmodule:: mne
+
 Functions:
 
 .. autosummary::
@@ -132,7 +134,7 @@ Functions:
    get_head_surf
    get_meg_helmet_surf
    parse_config
-   read_annot
+   read_labels_from_annot
    read_bem_solution
    read_bem_surfaces
    read_cov
@@ -151,7 +153,7 @@ Functions:
    read_surface
    read_trans
    save_stc_as_volume
-   write_annot
+   write_labels_to_annot
    write_bem_surface
    write_cov
    write_events
@@ -723,7 +725,19 @@ Decoding
 
 .. automodule:: mne.decoding
    :no-members:
+   :no-inherited-members:
 
+Classes:
+
+.. autosummary::
+   :toctree: generated/
+   :template: class.rst
+
+   Scaler
+   ConcatenateChannels
+   PSDEstimator
+   FilterEstimator
+   CSP
 
 Realtime
 ========
@@ -732,6 +746,20 @@ Realtime
 
 .. automodule:: mne.realtime
    :no-members:
+   :no-inherited-members:
+
+Classes:
+
+.. autosummary::
+   :toctree: generated/
+   :template: class.rst
+
+   RtEpochs
+   RtClient
+   MockRtClient
+   FieldTripClient
+   StimServer
+   StimClient
 
 MNE-Report
 ==========

doc/source/whats_new.rst

@@ -143,15 +143,13 @@ API
 
    - Deprecate Epochs.drop_picks in favor of a new method called drop_channels
 
-   - Deprecate `labels_from_parc` and `parc_from_labels` in favor of `read_annot` and `write_annot`
+   - Deprecate `labels_from_parc` and `parc_from_labels` in favor of `read_labels_from_annot` and `write_labels_to_annot`
 
    - The default of the new add_dist option of `setup_source_space` to add patch information will change from False to True in MNE-Python 0.9
 
-   - Deprecate `read_evoked` and `write_evoked` in favor of `read_evokeds` and `write_evokeds`.
-read_evokeds will return all Evoked instances in a file by default.
+   - Deprecate `read_evoked` and `write_evoked` in favor of `read_evokeds` and `write_evokeds`. read_evokeds will return all Evoked instances in a file by default.
 
-   - Deprecate `setno` in favor of `condition` in the initialization of an Evoked instance. This
-affects 'mne.fiff.Evoked' and 'read_evokeds', but not 'read_evoked'.
+   - Deprecate `setno` in favor of `condition` in the initialization of an Evoked instance. This affects 'mne.fiff.Evoked' and 'read_evokeds', but not 'read_evoked'.
 
    - Deprecate `mne.fiff` module, use `mne.io` instead e.g. `mne.io.Raw` instead of `mne.fiff.Raw`.
 
@@ -166,38 +164,37 @@ affects 'mne.fiff.Evoked' and 'read_evokeds', but not 'read_evoked'.
 Authors
 ~~~~~~~~~
 
-The committer list for this release is the following (preceded by number
-of commits):
+The committer list for this release is the following (preceded by number of commits):
 
-   418  Denis A. Engemann
-   284  Alexandre Gramfort
-   242  Eric Larson
-   155  Christian Brodbeck
-   144  Mainak Jas
-    49  Martin Billinger
-    49  Andrew Dykstra
-    44  Tal Linzen
-    37  Dan G. Wakeman
-    36  Martin Luessi
-    26  Teon Brooks
-    20  Cathy Nangini
-    15  Hari Bharadwaj
-    15  Roman Goj
-    10  Ross Maddox
-     9  Marmaduke Woodman
-     8  Praveen Sripad
-     8  Tanay
-     8  Roan LaPlante
-     5  Saket Choudhary
-     4  Nick Ward
-     4  Mads Jensen
-     3  Olaf Hauk
-     3  Brad Buran
-     2  Daniel Strohmeier
-     2  Federico Raimondo
-     2  Alan Leggitt
-     1  Jean-Remi King
-     1  Matti Hamalainen
+   * 418  Denis A. Engemann
+   * 284  Alexandre Gramfort
+   * 242  Eric Larson
+   * 155  Christian Brodbeck
+   * 144  Mainak Jas
+   * 49  Martin Billinger
+   * 49  Andrew Dykstra
+   * 44  Tal Linzen
+   * 37  Dan G. Wakeman
+   * 36  Martin Luessi
+   * 26  Teon Brooks
+   * 20  Cathy Nangini
+   * 15  Hari Bharadwaj
+   * 15  Roman Goj
+   * 10  Ross Maddox
+   * 9  Marmaduke Woodman
+   * 8  Praveen Sripad
+   * 8  Tanay
+   * 8  Roan LaPlante
+   * 5  Saket Choudhary
+   * 4  Nick Ward
+   * 4  Mads Jensen
+   * 3  Olaf Hauk
+   * 3  Brad Buran
+   * 2  Daniel Strohmeier
+   * 2  Federico Raimondo
+   * 2  Alan Leggitt
+   * 1  Jean-Remi King
+   * 1  Matti Hamalainen
 
 
 .. _changes_0_7:

mne/__init__.py

@@ -1,7 +1,7 @@
 """MNE for MEG and EEG data analysis
 """
 
-__version__ = '0.8'
+__version__ = '0.8.6'
 
 # have to import verbose first since it's needed by many things
 from .utils import (set_log_level, set_log_file, verbose, set_config,

mne/channels.py

@@ -92,10 +92,11 @@ def equalize_channels(candidates, verbose=None):
     from .io.base import _BaseRaw
     from .epochs import Epochs
     from .evoked import Evoked
+    from .time_frequency import AverageTFR
 
-    if not all([isinstance(c, (_BaseRaw, Epochs, Evoked))
+    if not all([isinstance(c, (_BaseRaw, Epochs, Evoked, AverageTFR))
                 for c in candidates]):
-        valid = ['Raw', 'Epochs', 'Evoked']
+        valid = ['Raw', 'Epochs', 'Evoked', 'AverageTFR']
         raise ValueError('candidates must be ' + ' or '.join(valid))
 
     chan_max_idx = np.argmax([c.info['nchan'] for c in candidates])
@@ -175,6 +176,8 @@ class PickDropChannelsMixin(object):
         from .io.base import _BaseRaw
         from .epochs import Epochs
         from .evoked import Evoked
+        from .time_frequency import AverageTFR
+
         if isinstance(self, _BaseRaw):
             if not self.preload:
                 raise RuntimeError('Raw data must be preloaded to drop or pick'
@@ -197,6 +200,8 @@ class PickDropChannelsMixin(object):
             self._data = self._data[idx, :]
         elif isinstance(self, Epochs) and inst_has('_data'):
             self._data = self._data[:, idx, :]
+        elif isinstance(self, AverageTFR) and inst_has('data'):
+            self.data = self.data[idx, :, :]
         elif isinstance(self, Evoked):
             self.data = self.data[idx, :]
 

mne/coreg.py

@@ -1150,6 +1150,7 @@ def scale_source_space(subject_to, src_name, subject_from=None, scale=None,
 
     if add_dist:
         logger.info("Recomputing distances, this might take a while")
-        add_source_space_distances(sss, sss[0]['dist_limit'], n_jobs)
+        dist_limit = np.asscalar(sss[0]['dist_limit'])
+        add_source_space_distances(sss, dist_limit, n_jobs)
 
     write_source_spaces(dst, sss)

mne/gui/_file_traits.py

@@ -118,18 +118,19 @@ def set_fs_home():
         return True
 
 def _fs_home_problem(fs_home):
-    "Check FREESURFER_HOME path"
-    test_dir = os.path.join(fs_home, 'subjects', 'fsaverage')
+    """Check FREESURFER_HOME path
+
+    Return str describing problem or None if the path is okay.
+    """
     if fs_home is None:
-        problem = "FREESURFER_HOME is not set."
+        return "FREESURFER_HOME is not set."
     elif not os.path.exists(fs_home):
-        problem = "FREESURFER_HOME (%s) does not exist." % fs_home
-    elif not os.path.exists(test_dir):
-        problem = ("FREESURFER_HOME (%s) does not contain the fsaverage "
-                   "subject." % fs_home)
+        return "FREESURFER_HOME (%s) does not exist." % fs_home
     else:
-        problem = None
-    return problem
+        test_dir = os.path.join(fs_home, 'subjects', 'fsaverage')
+        if not os.path.exists(test_dir):
+            return ("FREESURFER_HOME (%s) does not contain the fsaverage "
+                    "subject." % fs_home)
 
 
 def get_mne_root():
@@ -197,18 +198,19 @@ def set_mne_root(set_mne_bin=False):
         return True
 
 def _mne_root_problem(mne_root):
-    "Check MNE_ROOT path"
-    test_dir = os.path.join(mne_root, 'share', 'mne', 'mne_analyze')
+    """Check MNE_ROOT path
+
+    Return str describing problem or None if the path is okay.
+    """
     if mne_root is None:
-        problem = "MNE_ROOT is not set."
+        return "MNE_ROOT is not set."
     elif not os.path.exists(mne_root):
-        problem = "MNE_ROOT (%s) does not exist." % mne_root
-    elif not os.path.exists(test_dir):
-        problem = ("MNE_ROOT (%s) is missing files. If this is your MNE "
-                   "installation, consider reinstalling." % mne_root)
+        return "MNE_ROOT (%s) does not exist." % mne_root
     else:
-        problem = None
-    return problem
+        test_dir = os.path.join(mne_root, 'share', 'mne', 'mne_analyze')
+        if not os.path.exists(test_dir):
+            return ("MNE_ROOT (%s) is missing files. If this is your MNE "
+                    "installation, consider reinstalling." % mne_root)
 
 
 class BemSource(HasTraits):

mne/io/base.py

@@ -1445,8 +1445,6 @@ def _write_raw(fname, raw, info, picks, format, data_type, reset_range, start,
     logger.info('Writing %s' % use_fname)
 
     meas_id = info['meas_id']
-    if meas_id is None:
-        meas_id = 0
 
     fid, cals = _start_writing_raw(use_fname, info, picks, data_type,
                                    reset_range)
@@ -1460,7 +1458,8 @@ def _write_raw(fname, raw, info, picks, format, data_type, reset_range, start,
         start_block(fid, FIFF.FIFFB_REF)
         write_int(fid, FIFF.FIFF_REF_ROLE, FIFF.FIFFV_ROLE_PREV_FILE)
         write_string(fid, FIFF.FIFF_REF_FILE_NAME, prev_fname)
-        write_id(fid, FIFF.FIFF_REF_FILE_ID, meas_id)
+        if meas_id is not None:
+            write_id(fid, FIFF.FIFF_REF_FILE_ID, meas_id)
         write_int(fid, FIFF.FIFF_REF_FILE_NUM, part_idx - 1)
         end_block(fid, FIFF.FIFFB_REF)
 
@@ -1509,7 +1508,8 @@ def _write_raw(fname, raw, info, picks, format, data_type, reset_range, start,
             start_block(fid, FIFF.FIFFB_REF)
             write_int(fid, FIFF.FIFF_REF_ROLE, FIFF.FIFFV_ROLE_NEXT_FILE)
             write_string(fid, FIFF.FIFF_REF_FILE_NAME, op.basename(next_fname))
-            write_id(fid, FIFF.FIFF_REF_FILE_ID, meas_id)
+            if meas_id is not None:
+                write_id(fid, FIFF.FIFF_REF_FILE_ID, meas_id)
             write_int(fid, FIFF.FIFF_REF_FILE_NUM, next_idx)
             end_block(fid, FIFF.FIFFB_REF)
             break

mne/io/edf/edf.py

@@ -590,8 +590,8 @@ def _get_edf_info(fname, n_eeg, stim_channel, annot, annotmap, tal_channel,
         chan_info['cal'] = cal
         chan_info['logno'] = idx
         chan_info['scanno'] = idx
-        chan_info['range'] = physical_range
-        chan_info['unit_mul'] = unit_mul
+        chan_info['range'] = physical_range * (10 ** unit_mul)
+        chan_info['unit_mul'] = 0.
         chan_info['ch_name'] = ch_name
         chan_info['unit'] = FIFF.FIFF_UNIT_V
         chan_info['coord_frame'] = FIFF.FIFFV_COORD_HEAD

mne/report.py

@@ -10,12 +10,14 @@ import os
 import os.path as op
 import fnmatch
 import re
-import numpy as np
+import codecs
 import time
 from glob import glob
 import warnings
 import base64
 
+import numpy as np
+
 from . import read_evokeds, read_events, Covariance
 from .io import Raw, read_info
 from .utils import _TempDir, logger, verbose, get_subjects_dir
@@ -108,7 +110,7 @@ def _fig_to_mrislice(function, orig_size, sl, **kwargs):
                                                   format='png')
     output = BytesIO()
     Image.open(temp_sl_fname).save(output, format='png')
-    return output.getvalue().encode('base64')
+    return base64.b64encode(output.getvalue()).decode('ascii')
 
 
 @_check_report_mode
@@ -291,7 +293,7 @@ def _build_image(data, cmap='gray'):
     fig.figimage(data, cmap=cmap)
     output = BytesIO()
     fig.savefig(output, dpi=1.0, format='png')
-    return output.getvalue().encode('base64')
+    return base64.b64encode(output.getvalue()).decode('ascii')
 
 
 def _iterate_sagittal_slices(array, limits=None):
@@ -404,7 +406,7 @@ slider_template = HTMLTemplate(u"""
 def _build_html_slider(slices_range, slides_klass, slider_id):
     """Build an html slider for a given slices range and a slices klass.
     """
-    startvalue = (slices_range[0] + slices_range[-1]) / 2 + 1
+    startvalue = (slices_range[0] + slices_range[-1]) // 2 + 1
     return slider_template.substitute(slider_id=slider_id,
                                       klass=slides_klass,
                                       minvalue=slices_range[0],
@@ -831,8 +833,8 @@ class Report(object):
 
         if overwrite or not op.isfile(fname):
             logger.info('Saving report to location %s' % fname)
-            fobj = open(fname, 'w')
-            fobj.write(_fix_global_ids(''.join(self.html)))
+            fobj = codecs.open(fname, 'w', 'utf-8')
+            fobj.write(_fix_global_ids(u''.join(self.html)))
             fobj.close()
 
             # remove header, TOC and footer to allow more saves

mne/tests/test_utils.py

@@ -263,7 +263,7 @@ def test_fetch_file():
     # Skipping test if no internet connection available
     try:
         urllib.request.urlopen("http://github.com", timeout=2)
-    except urllib.request.URLError:
+    except:
         from nose.plugins.skip import SkipTest
         raise SkipTest('No internet connection, skipping download test.')
 

mne/time_frequency/__init__.py

@@ -2,6 +2,7 @@
 """
 
 from .tfr import induced_power, single_trial_power, morlet, tfr_morlet
+from .tfr import AverageTFR
 from .psd import compute_raw_psd, compute_epochs_psd
 from .csd import CrossSpectralDensity, compute_epochs_csd
 from .ar import yule_walker, ar_raw, iir_filter_raw

mne/time_frequency/tests/test_tfr.py

@@ -3,6 +3,7 @@ import os.path as op
 from numpy.testing import assert_array_almost_equal
 from nose.tools import assert_true, assert_false, assert_equal
 
+import mne
 from mne import io, Epochs, read_events, pick_types
 from mne.time_frequency import single_trial_power
 from mne.time_frequency.tfr import cwt_morlet, morlet, tfr_morlet
@@ -51,6 +52,10 @@ def test_time_frequency():
     freqs = np.arange(6, 20, 5)  # define frequencies of interest
     n_cycles = freqs / 4.
 
+    # Test first with a single epoch
+    power, itc = tfr_morlet(epochs[0], freqs=freqs, n_cycles=n_cycles,
+                            use_fft=True, return_itc=True)
+
     power, itc = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles,
                             use_fft=True, return_itc=True)
 
@@ -91,3 +96,14 @@ def test_time_frequency():
                                       n_cycles=2)
 
     assert_array_almost_equal(np.mean(single_power), power.data)
+
+    power_pick = power.pick_channels(power.ch_names[:10:2])
+    assert_equal(len(power_pick.ch_names), len(power.ch_names[:10:2]))
+    assert_equal(power_pick.data.shape[0], len(power.ch_names[:10:2]))
+    power_drop = power.drop_channels(power.ch_names[1:10:2])
+    assert_equal(power_drop.ch_names, power_pick.ch_names)
+    assert_equal(power_pick.data.shape[0], len(power_drop.ch_names))
+
+    mne.equalize_channels([power_pick, power_drop])
+    assert_equal(power_pick.ch_names, power_drop.ch_names)
+    assert_equal(power_pick.data.shape, power_drop.data.shape)

mne/time_frequency/tfr.py

@@ -386,7 +386,7 @@ def _induced_power(data, Fs, frequencies, use_fft=True, n_cycles=7,
         plf = np.empty((n_channels, n_frequencies, n_times), dtype=np.complex)
 
         for c in range(n_channels):
-            X = np.squeeze(data[:, c, :])
+            X = data[:, c, :]
             this_psd, this_plf = _time_frequency(X, Ws, use_fft)
             psd[c], plf[c] = this_psd[:, ::decim], this_plf[:, ::decim]
     else:
@@ -476,6 +476,9 @@ def _preproc_tfr(data, times, freqs, tmin, tmax, fmin, fmax, mode,
 
     freqs = freqs[ifmin:ifmax]
 
+    # crop data
+    data = data[:, ifmin:ifmax, itmin:itmax]
+
     times *= 1e3
     if dB:
         data = 20 * np.log10(data)

mne/viz/raw.py

@@ -365,7 +365,7 @@ def plot_raw(raw, events=None, duration=10.0, start=0.0, n_channels=None,
     for t in ['grad', 'mag']:
         inds += [pick_types(info, meg=t, ref_meg=False, exclude=[])]
         types += [t] * len(inds[-1])
-    pick_kwargs = dict(meg=False, exclude=[])
+    pick_kwargs = dict(meg=False, ref_meg=False, exclude=[])
     for t in ['eeg', 'eog', 'ecg', 'emg', 'ref_meg', 'stim', 'resp',
               'misc', 'chpi', 'syst', 'ias', 'exci']:
         pick_kwargs[t] = True