Skip to content

Commit 8d85426

Browse files
EtienneCmbEtienneCmb
committed
Merge branch 'release/v0.3.4'
2 parents 3cc2f30 + 02a6a5e commit 8d85426

File tree

136 files changed

+10447
-10794
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

136 files changed

+10447
-10794
lines changed

‎.travis.yml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@ install:
3030
- conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib pip
3131
- source activate testenv
3232
- pip install mne
33+
- pip install nibabel
3334
- pip install setuptools
3435
- pip install nose
3536
- pip install PyOpenGL PyOpenGL_accelerate

‎README.rst‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ Visbrain
1616
:align: center
1717

1818

19-
**Visbrain** is an open-source python 3 package and provides hardware accelerated visualizations mainly for neuroscientific data. It is based on top of `VisPy <http://vispy.org/>`_ and PyQt and is distributed under the 3-Clause BSD license. We also provide an on line `documentation <http://visbrain.org>`_, `examples and datasets <http://visbrain.org/auto_examples/>`_ and can also be downloaded from `PyPi <https://pypi.python.org/pypi/visbrain/>`_.
19+
**Visbrain** is an open-source python 3 package dedicated to brain signals visualization. It is based on top of `VisPy <http://vispy.org/>`_ and PyQt and is distributed under the 3-Clause BSD license. We also provide an on line `documentation <http://visbrain.org>`_, `examples and datasets <http://visbrain.org/auto_examples/>`_ and can also be downloaded from `PyPi <https://pypi.python.org/pypi/visbrain/>`_.
2020

2121
Important links
2222
===============
@@ -70,8 +70,8 @@ Modules
7070

7171
* `Brain <http://visbrain.org/brain.html>`_ : visualize EEG/MEG/Intracranial data, connectivity in a standard MNI 3D brain (see `Brain examples <http://visbrain.org/auto_examples/index.html#brain-examples>`_).
7272
* `Sleep <http://visbrain.org/sleep.html>`_ : visualize polysomnographic data and hypnogram edition (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
73+
* `Signal <http://visbrain.org/signal.html>`_ : data-mining module for time-series inspection (see `Signal examples <http://visbrain.org/auto_examples/index.html#signal-examples>`_).
7374
* `Topo <http://visbrain.org/topo.html>`_ : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
74-
* `Ndviz <http://visbrain.org/ndviz.html>`_ : visualize multidimensional data and basic plotting forms (see `Ndviz examples <http://visbrain.org/auto_examples/index.html#ndviz-examples>`_).
7575
* `Figure <http://visbrain.org/figure.html>`_ : figure-layout for high-quality publication-like figures (see `Figure examples <http://visbrain.org/auto_examples/index.html#figure-examples>`_).
7676
* `Colorbar <http://visbrain.org/colorbar.html>`_ : colorbar editor (see `Colorbar examples <http://visbrain.org/auto_examples/index.html#colorbar-examples>`_).
7777

‎docs/Hypnogram_excerpt2_description.txt‎

Lines changed: 0 additions & 7 deletions
This file was deleted.

‎docs/brainAPI.rst‎

Lines changed: 46 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,52 @@
44
Main *Brain* class inputs
55
~~~~~~~~~~~~~~~~~~~~~~~~~
66

7-
.. autoclass:: visbrain.brain.brain.Brain
7+
.. currentmodule:: visbrain.brain.brain
8+
9+
.. autoclass:: Brain
10+
11+
.. rubric:: Methods
12+
13+
.. autosummary::
14+
~Brain.show
15+
~visbrain.brain.user.BrainUserMethods.quit
16+
~visbrain.brain.user.BrainUserMethods.rotate
17+
~visbrain.brain.user.BrainUserMethods.background_color
18+
~visbrain.brain.user.BrainUserMethods.screenshot
19+
~visbrain.brain.user.BrainUserMethods.load_config
20+
~visbrain.brain.user.BrainUserMethods.save_config
21+
~visbrain.brain.user.BrainUserMethods.brain_control
22+
~visbrain.brain.user.BrainUserMethods.brain_list
23+
~visbrain.brain.user.BrainUserMethods.add_mesh
24+
~visbrain.brain.user.BrainUserMethods.volume_control
25+
~visbrain.brain.user.BrainUserMethods.add_volume
26+
~visbrain.brain.user.BrainUserMethods.volume_list
27+
~visbrain.brain.user.BrainUserMethods.cross_sections_control
28+
~visbrain.brain.user.BrainUserMethods.sources_control
29+
~visbrain.brain.user.BrainUserMethods.sources_opacity
30+
~visbrain.brain.user.BrainUserMethods.sources_display
31+
~visbrain.brain.user.BrainUserMethods.add_sources
32+
~visbrain.brain.user.BrainUserMethods.sources_fit
33+
~visbrain.brain.user.BrainUserMethods.sources_to_convex_hull
34+
~visbrain.brain.user.BrainUserMethods.cortical_projection
35+
~visbrain.brain.user.BrainUserMethods.cortical_repartition
36+
~visbrain.brain.user.BrainUserMethods.sources_colormap
37+
~visbrain.brain.user.BrainUserMethods.time_series_control
38+
~visbrain.brain.user.BrainUserMethods.add_time_series
39+
~visbrain.brain.user.BrainUserMethods.pictures_control
40+
~visbrain.brain.user.BrainUserMethods.add_pictures
41+
~visbrain.brain.user.BrainUserMethods.connect_control
42+
~visbrain.brain.user.BrainUserMethods.add_connect
43+
~visbrain.brain.user.BrainUserMethods.roi_control
44+
~visbrain.brain.user.BrainUserMethods.roi_list
45+
~visbrain.brain.user.BrainUserMethods.roi_opacity
46+
~visbrain.brain.user.BrainUserMethods.roi_light_reflection
47+
~visbrain.brain.user.BrainUserMethods.cbar_control
48+
~visbrain.brain.user.BrainUserMethods.cbar_select
49+
~visbrain.brain.user.BrainUserMethods.cbar_list
50+
~visbrain.brain.user.BrainUserMethods.cbar_export
51+
~visbrain.brain.user.BrainUserMethods.cbar_autoscale
52+
853

954
.. ##########################################################################
1055
.. GUI

‎docs/changelog_futur.rst‎

Lines changed: 9 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -6,34 +6,21 @@ Changelog and future directions
66
Changelog
77
---------
88

9-
v0.3.2
9+
v0.3.4
1010
^^^^^^
1111

1212
Visbrain
1313
~~~~~~~~
1414

15-
* New topoplot module
16-
* Screenshots improvements (new screenshot window from the GUI)
15+
* *Ndviz* has been replaced by *Signal*
1716

18-
Brain module
19-
~~~~~~~~~~~~
20-
21-
* Bug fixing
22-
23-
v0.3.0
24-
^^^^^^
25-
26-
Brain module
27-
~~~~~~~~~~~~
17+
Sleep
18+
~~~~~
2819

29-
* Add time-series and pictures attached to sources
30-
* Colorbar integration improvements
31-
* Add volume and cross-sections
32-
* Enable to import new brain template and nifti volumes
33-
* Add XYZ source's tab to find where source's are localized
34-
* Improve ROI selection
35-
* New user methods
36-
* GUI and Doc improvements
20+
* List of supported files has been extended + better integration of MNE
21+
* Start lazy loading for huge files
22+
* Improve down-sampling
23+
* Command-line control
3724

3825
Future directions
3926
-----------------
@@ -44,9 +31,7 @@ Visbrain
4431
* conda installation
4532
* Independent of the VisPy developer version for better installation (ST)
4633
* Code style improvements (flake8 and numpydoc) (ST)
47-
* Improve coverage (right now, PyQt tests failed) (ST)
48-
* Improve doc with sphinx-gallery (ST)
49-
* New modules are planned (*Connect*, *Signal*, *Image*, *ERP*, *Topo*) (LT)
34+
* New modules are planned (*Connect*, *Pictures*, *ERP*) (LT)
5035

5136
Brain
5237
^^^^^
@@ -59,8 +44,6 @@ Brain
5944
Sleep
6045
^^^^^
6146

62-
* Better integration of non-supported files (compatibility with MNE) (ST)
63-
* Command-line control (LT)
6447
* De-noising (LT)
6548
* Zero re-referencing (LT)
6649
* Automatic-scoring (LT)

‎docs/conf.py‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -39,8 +39,11 @@
3939
'sphinx.ext.viewcode',
4040
'sphinx.ext.todo',
4141
'numpydoc',
42+
'sphinx.ext.autosummary',
4243
'sphinx_gallery.gen_gallery',
44+
'sphinx_click.ext',
4345
]
46+
# , 'sphinx.ext.napoleon'
4447
# 'sphinx.ext.githubpages',
4548

4649
sphinx_gallery_conf = {
@@ -79,9 +82,9 @@
7982
# built documents.
8083
#
8184
# The short X.Y version.
82-
version = '0.3.3'
85+
version = '0.3.4'
8386
# The full version, including alpha/beta/rc tags.
84-
release = '0.3.3'
87+
release = '0.3.4'
8588

8689
# The language for content autogenerated by Sphinx. Refer to documentation
8790
# for a list of supported languages.
@@ -106,7 +109,7 @@
106109
#default_role = None
107110

108111
# If true, '()' will be appended to :func: etc. cross-reference text.
109-
#add_function_parentheses = True
112+
add_function_parentheses = False
110113

111114
# If true, the current module name will be prepended to all description
112115
# unit titles (such as .. function::).

‎docs/documentation.rst‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,10 +9,9 @@ Documentation
99

1010
brain
1111
sleep
12+
signal
1213
topo
13-
ndviz
1414
colorbar
1515
figure
1616
utils
1717
io
18-
vbexport

‎docs/ico/sleep.png‎

-35.9 KB
Binary file not shown.

‎docs/index.rst‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,15 +19,17 @@
1919
Visbrain documentation
2020
######################
2121

22-
Visbrain is a python 3 package dedicated to multi-purpose neuroscience visualization tools. Here is the list of the current modules :
22+
Visbrain is an open-source python 3 package dedicated to brain signals visualization. It is based on top of VisPy and PyQt and is distributed under the 3-Clause BSD license.
2323

2424
.. figure:: /picture/visbrain_readme.png
2525
:align: center
2626

27+
Visbrain includes six visualization modules :
28+
2729
* :ref:`Brain` : visualize EEG/MEG/Intracranial data, connectivity in a standard MNI 3D brain (see `Brain examples <http://visbrain.org/auto_examples/index.html#brain-examples>`_).
2830
* :ref:`Sleep` : visualize polysomnographic data and hypnogram edition (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
29-
* :ref:`topo` : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
30-
* :ref:`Ndviz` : visualize multidimensional data and basic plotting forms (see `Ndviz examples <http://visbrain.org/auto_examples/index.html#ndviz-examples>`_).
31+
* :ref:`Signal` : data-mining module for time-series inspection (see `Signal examples <http://visbrain.org/auto_examples/index.html#signal-examples>`_).
32+
* :ref:`Topo` : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
3133
* :ref:`Figure` : figure-layout for high-quality publication-like figures (see `Figure examples <http://visbrain.org/auto_examples/index.html#figure-examples>`_).
3234
* :ref:`colorbar` : colorbar editor (see `Colorbar examples <http://visbrain.org/auto_examples/index.html#colorbar-examples>`_).
3335

‎docs/io.rst‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ MNE
1717

1818
.. autofunction:: visbrain.io.dependencies.is_nibabel_installed
1919

20-
.. autofunction:: visbrain.io.mneio.mne_read_sleep
20+
.. autofunction:: visbrain.io.mneio.mne_switch
2121

2222
Configuration file
2323
------------------

0 commit comments

Comments
 (0)