Merge branch 'trunk' of https://github.com/the-virtual-brain/scientific_library into trunk

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5668 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1246
Fix Sphinx errors. Include equations in api documentation for all models.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5669 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Some minor refactoring

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5699 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Added a get_default_selection on a timeseries. By default all measure points are selected and the viewers should display all time lines. A TimeSeriesRegion with an edited connectivity will show only the active nodes after the edit.  
Added a method on timeseries which returns a gid that should be used to obtain the valid selections for this timeseries
Replaced Timeseries<Sensor>Framework classes with a single class

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5705 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Renamed connectivityGid to filteGid

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5708 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Added attribute to connectivty: number of connections, which is the number of nonzero entries in the weights matrix. 

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5750 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Expand connectivity summary info: 
+ (non-zero) It gives the basic descriptive measure computed over non-zero entries
+ (connections) Only relevant for tract lengths. It is the same as above, but only for valid connections -- non-zero entries in the weights matrix.



git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5751 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Added assertion line for number of connections

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5752 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
As a quick and dirty fix I duplicated the get_summary info related methods.
They now compute the statistics only for non-zero entries in the input array.
There is a usemask flag with which we can use another array (**mask_array**) 
to retrieve/index the elements of interest in **array**. 
It remains very specific to the Connectivity datatype. It is not always the case
that we want to ignore non zero values. TODO: make sure that array and mask array 
have the same shape.



git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5753 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Corrected range of tau_K in LarterBreakspear model

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5757 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Corrected ranges in Zetterberg Jansen model

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5758 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Undo last commit do this script

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5759 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Update LB model demo

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5760 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fix Sigmoidal coupling.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5761 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Add an import error for the plot tri matrix. It needs matplotlib >= 1.3.1, current version in thedistribution packages is 1.2.1

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5762 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Small fix for failing test

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5763 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Added import for mpl toolkits in matplotlib 1.2.1 

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5765 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1276
Implement a generic method to compute non-zero min/max/var/mean values for Array traited attributes.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5767 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1274
MPLH5 Adapter for Person Correlation Coefficient datatype.
(adapts the existing viewer from scientific tools)
Update manuals and add screen-shots with the new visualizers.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5769 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Update mpl_toolkit import and error message

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5773 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1