Merge branch 'release/v0.3.4'

Author: EtienneCmb

.travis.yml

@@ -30,6 +30,7 @@ install:
   - conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib pip
   - source activate testenv
   - pip install mne
+  - pip install nibabel
   - pip install setuptools
   - pip install nose
   - pip install PyOpenGL PyOpenGL_accelerate

README.rst

@@ -16,7 +16,7 @@ Visbrain
    :align:   center
 
 
-**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/>`_.
+**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/>`_.
 
 Important links
 ===============
@@ -70,8 +70,8 @@ Modules
 
 * `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>`_).
 * `Sleep <http://visbrain.org/sleep.html>`_ : visualize polysomnographic data and hypnogram edition (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
+* `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>`_).
 * `Topo <http://visbrain.org/topo.html>`_ : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
-* `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>`_).
 * `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>`_).
 * `Colorbar <http://visbrain.org/colorbar.html>`_ : colorbar editor (see `Colorbar examples <http://visbrain.org/auto_examples/index.html#colorbar-examples>`_).
 

docs/Hypnogram_excerpt2_description.txt

@@ -4,7 +4,52 @@
 Main *Brain* class inputs
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. autoclass:: visbrain.brain.brain.Brain
+.. currentmodule:: visbrain.brain.brain
+
+.. autoclass:: Brain
+
+    .. rubric:: Methods
+
+    .. autosummary::
+        ~Brain.show
+        ~visbrain.brain.user.BrainUserMethods.quit
+        ~visbrain.brain.user.BrainUserMethods.rotate
+        ~visbrain.brain.user.BrainUserMethods.background_color
+        ~visbrain.brain.user.BrainUserMethods.screenshot
+        ~visbrain.brain.user.BrainUserMethods.load_config
+        ~visbrain.brain.user.BrainUserMethods.save_config
+        ~visbrain.brain.user.BrainUserMethods.brain_control
+        ~visbrain.brain.user.BrainUserMethods.brain_list
+        ~visbrain.brain.user.BrainUserMethods.add_mesh
+        ~visbrain.brain.user.BrainUserMethods.volume_control
+        ~visbrain.brain.user.BrainUserMethods.add_volume
+        ~visbrain.brain.user.BrainUserMethods.volume_list
+        ~visbrain.brain.user.BrainUserMethods.cross_sections_control
+        ~visbrain.brain.user.BrainUserMethods.sources_control
+        ~visbrain.brain.user.BrainUserMethods.sources_opacity
+        ~visbrain.brain.user.BrainUserMethods.sources_display
+        ~visbrain.brain.user.BrainUserMethods.add_sources
+        ~visbrain.brain.user.BrainUserMethods.sources_fit
+        ~visbrain.brain.user.BrainUserMethods.sources_to_convex_hull
+        ~visbrain.brain.user.BrainUserMethods.cortical_projection
+        ~visbrain.brain.user.BrainUserMethods.cortical_repartition
+        ~visbrain.brain.user.BrainUserMethods.sources_colormap
+        ~visbrain.brain.user.BrainUserMethods.time_series_control
+        ~visbrain.brain.user.BrainUserMethods.add_time_series
+        ~visbrain.brain.user.BrainUserMethods.pictures_control
+        ~visbrain.brain.user.BrainUserMethods.add_pictures
+        ~visbrain.brain.user.BrainUserMethods.connect_control
+        ~visbrain.brain.user.BrainUserMethods.add_connect
+        ~visbrain.brain.user.BrainUserMethods.roi_control
+        ~visbrain.brain.user.BrainUserMethods.roi_list
+        ~visbrain.brain.user.BrainUserMethods.roi_opacity
+        ~visbrain.brain.user.BrainUserMethods.roi_light_reflection
+        ~visbrain.brain.user.BrainUserMethods.cbar_control
+        ~visbrain.brain.user.BrainUserMethods.cbar_select
+        ~visbrain.brain.user.BrainUserMethods.cbar_list
+        ~visbrain.brain.user.BrainUserMethods.cbar_export
+        ~visbrain.brain.user.BrainUserMethods.cbar_autoscale
+
 
 .. ##########################################################################
 ..                                    GUI

docs/brainAPI.rst

@@ -6,34 +6,21 @@ Changelog and future directions
 Changelog
 ---------
 
-v0.3.2
+v0.3.4
 ^^^^^^
 
 Visbrain
 ~~~~~~~~
 
-* New topoplot module
-* Screenshots improvements (new screenshot window from the GUI)
+* *Ndviz* has been replaced by *Signal*
 
-Brain module
-~~~~~~~~~~~~
-
-* Bug fixing
-
-v0.3.0
-^^^^^^
-
-Brain module
-~~~~~~~~~~~~
+Sleep
+~~~~~
 
-* Add time-series and pictures attached to sources
-* Colorbar integration improvements
-* Add volume and cross-sections
-* Enable to import new brain template and nifti volumes
-* Add XYZ source's tab to find where source's are localized
-* Improve ROI selection
-* New user methods
-* GUI and Doc improvements
+* List of supported files has been extended + better integration of MNE
+* Start lazy loading for huge files
+* Improve down-sampling
+* Command-line control
 
 Future directions
 -----------------
@@ -44,9 +31,7 @@ Visbrain
 * conda installation
 * Independent of the VisPy developer version for better installation (ST)
 * Code style improvements (flake8 and numpydoc) (ST)
-* Improve coverage (right now, PyQt tests failed) (ST)
-* Improve doc with sphinx-gallery (ST)
-* New modules are planned (*Connect*, *Signal*, *Image*, *ERP*, *Topo*) (LT)
+* New modules are planned (*Connect*, *Pictures*, *ERP*) (LT)
 
 Brain
 ^^^^^
@@ -59,8 +44,6 @@ Brain
 Sleep
 ^^^^^
 
-* Better integration of non-supported files (compatibility with MNE)  (ST)
-* Command-line control (LT)
 * De-noising (LT)
 * Zero re-referencing (LT)
 * Automatic-scoring (LT)

docs/changelog_futur.rst

@@ -39,8 +39,11 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.todo',
     'numpydoc',
+    'sphinx.ext.autosummary',
     'sphinx_gallery.gen_gallery',
+    'sphinx_click.ext',
 ]
+    # , 'sphinx.ext.napoleon'
 #     'sphinx.ext.githubpages',
 
 sphinx_gallery_conf = {
@@ -79,9 +82,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.3.3'
+version = '0.3.4'
 # The full version, including alpha/beta/rc tags.
-release = '0.3.3'
+release = '0.3.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -106,7 +109,7 @@
 #default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+add_function_parentheses = False
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).

docs/conf.py

@@ -9,10 +9,9 @@ Documentation
 
     brain
     sleep
+    signal
     topo
-    ndviz
     colorbar
     figure
     utils
     io
-    vbexport

docs/documentation.rst

@@ -19,15 +19,17 @@
 Visbrain documentation
 ######################
 
-Visbrain is a python 3 package dedicated to multi-purpose neuroscience visualization tools. Here is the list of the current modules :
+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.
 
 .. figure::  /picture/visbrain_readme.png
    :align:   center
 
+Visbrain includes six visualization modules :
+
 * :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>`_).
 * :ref:`Sleep` : visualize polysomnographic data and hypnogram edition (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
-* :ref:`topo` : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
-* :ref:`Ndviz` : visualize multidimensional data and basic plotting forms (see `Ndviz examples <http://visbrain.org/auto_examples/index.html#ndviz-examples>`_).
+* :ref:`Signal` : data-mining module for time-series inspection (see `Signal examples <http://visbrain.org/auto_examples/index.html#signal-examples>`_).
+* :ref:`Topo` : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
 * :ref:`Figure` : figure-layout for high-quality publication-like figures (see `Figure examples <http://visbrain.org/auto_examples/index.html#figure-examples>`_).
 * :ref:`colorbar` : colorbar editor (see `Colorbar examples <http://visbrain.org/auto_examples/index.html#colorbar-examples>`_).
 

docs/ico/sleep.png

@@ -17,7 +17,7 @@ MNE
 
 .. autofunction:: visbrain.io.dependencies.is_nibabel_installed
 
-.. autofunction:: visbrain.io.mneio.mne_read_sleep
+.. autofunction:: visbrain.io.mneio.mne_switch
 
 Configuration file
 ------------------