[med-svn] [python-mne] 02/05: Imported Upstream version 0.8.6+dfsg
Alexandre Gramfort
agramfort-guest at moszumanska.debian.org
Sat Oct 25 07:52:15 UTC 2014
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agramfort-guest pushed a commit to branch master
in repository python-mne.
commit 0630aa1c6c1d99400cead86b1a1a49f3806ba988
Author: Alexandre Gramfort <alexandre.gramfort at m4x.org>
Date: Mon Sep 22 16:05:35 2014 -0400
Imported Upstream version 0.8.6+dfsg
---
MANIFEST.in | 5 +++++
doc/source/python_reference.rst | 2 ++
doc/source/whats_new.rst | 2 +-
mne/__init__.py | 2 +-
mne/coreg.py | 3 ++-
mne/gui/_file_traits.py | 38 ++++++++++++++++++++------------------
mne/io/base.py | 8 ++++----
mne/io/edf/edf.py | 4 ++--
mne/report.py | 14 ++++++++------
9 files changed, 45 insertions(+), 33 deletions(-)
diff --git a/MANIFEST.in b/MANIFEST.in
index e2b071e..6e868f4 100644
--- a/MANIFEST.in
+++ b/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 *
diff --git a/doc/source/python_reference.rst b/doc/source/python_reference.rst
index 3704cc9..5c3f7fe 100644
--- a/doc/source/python_reference.rst
+++ b/doc/source/python_reference.rst
@@ -122,6 +122,8 @@ Functions:
File I/O
========
+.. currentmodule:: mne
+
Functions:
.. autosummary::
diff --git a/doc/source/whats_new.rst b/doc/source/whats_new.rst
index 0f31d17..23919c5 100644
--- a/doc/source/whats_new.rst
+++ b/doc/source/whats_new.rst
@@ -143,7 +143,7 @@ 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
diff --git a/mne/__init__.py b/mne/__init__.py
index a8c5268..2ae0043 100644
--- a/mne/__init__.py
+++ b/mne/__init__.py
@@ -1,7 +1,7 @@
"""MNE for MEG and EEG data analysis
"""
-__version__ = '0.8.3'
+__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,
diff --git a/mne/coreg.py b/mne/coreg.py
index ce634e1..2461380 100644
--- a/mne/coreg.py
+++ b/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)
diff --git a/mne/gui/_file_traits.py b/mne/gui/_file_traits.py
index 98a9425..6bc1b4a 100644
--- a/mne/gui/_file_traits.py
+++ b/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):
diff --git a/mne/io/base.py b/mne/io/base.py
index 98b2b31..a25f4cc 100644
--- a/mne/io/base.py
+++ b/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
diff --git a/mne/io/edf/edf.py b/mne/io/edf/edf.py
index 7282db6..ce755ed 100644
--- a/mne/io/edf/edf.py
+++ b/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
diff --git a/mne/report.py b/mne/report.py
index 980d08c..fedc78e 100644
--- a/mne/report.py
+++ b/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
--
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