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    filename: README.m
    path of file: ./repos/CanlabCore/CanlabCore/External/boundedline
    
    the code of the file until where you have to start completion: %% |boundedline.m|: line with shaded error/confidence bounds
% Author: Kelly Kearney
%
% This repository includes the code for the |boundedline.m| Matlab function
% and the accompanying |outlinebounds.m| function, along with all dependent
% functions required to run them.
%
% The |boundedline| function allows a user to easily plot and line with a
% shaded patch around it.  Ths sort of plot is often used to indicate
% uncertainty intervals or error bounds around a line.
%
%% Getting started
%
% *Prerequisites*
%
% This function requires Matlab R14 or later.
%
% *Downloading and installation*
%
% This code can be downloaded from <https://github.com/kakearney/boundedline-pkg/ Github>
% or the
% <http://www.mathworks.com/matlabcentral/fileexchange/27485-boundedline-m
% MatlabCentral File Exchange>.  The File Exchange entry is updated daily
% from the GitHub repository.   
%
% *Matlab Search Path*
%
% The following folders need to be added to your Matlab Search path (via
% |addpath|, |pathtool|, etc.):
%
%   boundedline-pkg/Inpaint_nans
%   boundedline-pkg/boundedline
%   boundedline-pkg/catuneven
%   boundedline-pkg/singlepatch

%% Syntax
%
% |boundedline(x, y, b)| plots a line with coordinates given by
% |x| and |y|, surrounded by a patch extending a certain distance |b|
% above/below that line.  The dimensions of the |x|, |y|, and |b| arrays
% can vary to allow for multiple lines to be plotted at once, and for
% patch bounds to be either constant or varying along the length of the
% line.  See function header help for full details of these variations.
%  
% |boundedline(..., 'alpha')| renders the bounded area patch using a
% partially-transparent patch the same color as the corresponding line(s).
% If not included, the bounded area will use a fully-opaque patch in a
% lighter shade of the corresponding line color.
%
% |boundedline(..., 'transparency', transp)| indicates the
% tranparency or intensity of the bounds patch, using a scalar between 0
% and 1.  Default is 0.2.
%
% |boundedline(..., 'orientation', orient)| indicates the orientation of
% the bounds.  Orientation can be either |'vert'| for vertical (y-direction)
% bounds, or |'horiz'| for horizontal (x-direction) bounds.  Default is
% |'vert'|.
%
% |boundedline(..., 'nan', nanflag)| indicates how the bounds patch should
% handle NaNs in the line coordinates or bounds values.  Options are
% |'fill'|, to smooth over the gap using neighboring values, |'gap'| to
% leave a blank space in the patch at those points, or |'remove'| to drop
% the NaN-points entirely, leading to linear interpolation of the gap in
% the patch.  See examples below for more details on these options.
%
% |boundedline(..., 'cmap', cmap)| colors the lines (in order of plotting)
% acording to the colors in this n x 3 colormap array, overriding any
% linespec or default colors.
%
% |boundedline(..., ax)| plots the bounded line to the axis indicated by
% handle |ax|.  If not included, the current axis is used.
%
% |[hl, hp] = boundedline(...)| returns the handles the resulting line
% and patch object(s).
%
% |hout = outlinebounds(hl, hp)| adds an outline to the bounds patch
% generated by |boundedline|, returning the handle of the resulting line
% object in |hout|.
%
% Full details of all input and output variables for both functions can be
% accessed via the |help| function.

%% Example 1: Plotting lines using various syntax opti
    
function
% and the accompanying |outlinebounds.m| function, along with all dependent
% functions required to run them.
%
% The |boundedline| function allows a user to easily plot and line with a
% shaded patch around it.  Ths sort of plot is often used to indicate
% uncertainty intervals or error bounds around a line.
%
%% Getting started
%
% *Prerequisites*
%
% This function requires Matlab R14 or later.
%
% *Downloading and installation*
%
% This code can be downloaded from <https://github.com/kakearney/boundedline-pkg/ Github>
% or the
% <http://www.mathworks.com/matlabcentral/fileexchange/27485-boundedline-m
% MatlabCentral File Exchange>.  The File Exchange entry is updated daily
% from the GitHub repository.   
%
% *Matlab Search Path*
%
% The following folders need to be added to your Matlab Search path (via
% |addpath|, |pathtool|, etc.):
%
%   boundedline-pkg/Inpaint_nans
%   boundedline-pkg/boundedline
%   boundedline-pkg/catuneven
%   boundedline-pkg/singlepatch

%% Syntax
%
% |boundedline(x, y, b)| plots a line with coordinates given by
% |x| and |y|, surrounded by a patch extending a certain distance |b|
% above/below that line.  The dimensions of the |x|, |y|, and |b| arrays
% can vary to allow for multiple lines to be plotted at once, and for
% patch bounds to be either constant or varying along the length of the
% line.  See function header help for full details of these variations.
%  
% |boundedline(..., 'alpha')| renders the bounded area patch using a
% partially-transparent patch the same color as the corresponding line(s).
% If not included, the bounded area will use a fully-opaque patch in a
% lighter shade of the corresponding line color.
%
% |boundedline(..., 'transparency', transp)| indicates the
% tranparency or intensity of the bounds patch, using a scalar between 0
% and 1.  Default is 0.2.
%
% |boundedline(..., 'orientation', orient)| indicates the orientation of
% the bounds.  Orientation can be either |'vert'| for vertical (y-direction)
% bounds, or |'horiz'| for horizontal (x-direction) bounds.  Default is
% |'vert'|.
%
% |boundedline(..., 'nan', nanflag)| indicates how the bounds patch should
% handle NaNs in the line coordinates or bounds values.  Options are
% |'fill'|, to smooth over the gap using neighboring values, |'gap'| to
% leave a blank space in the patch at those points, or |'remove'| to drop
% the NaN-points entirely, leading to linear interpolation of the gap in
% the patch.  See examples below for more details on these options.
%
% |boundedline(..., 'cmap', cmap)| colors the lines (in order of plotting)
% acording to the colors in this n x 3 colormap array, overriding any
% linespec or default colors.
%
% |boundedline(..., ax)| plots the bounded line to the axis indicated by
% handle |ax|.  If not included, the current axis is used.
%
% |[hl, hp] = boundedline(...)| returns the handles the resulting line
% and patch object(s).
%
% |hout = outlinebounds(hl, hp)| adds an outline to the bounds patch
% generated by |boundedline|, returning the handle of the resulting line
% object in |hout|.
%
% Full details of all input and output variables for both functions can be
% accessed via the |help| function.

%% Example 1: Plotting lines using various syntax options
%
% This example builds the 4-panel example image used on the MatlabCentral
% File Exchange, which shows several different methods for supplying line
% coordinates, bounds coordinates, and shading options.
%
% The first axis plots two lines using the LineSpec option for input, which
% allows yoy to set line color, line color, and marker type for each line.
% The bounds on the first line vary over x, while the bounds on the second
% line are constant for all x. An outline is added to the bounds so the
% overlapping region can be seen more clearly. 

x = linspace(0, 2*pi, 50);
y1 = sin(x);
y2 = cos(x);
e1 = rand(size(y1))*.5+.5;
e2 = [.25 .5];

ax(1) = subplot(2,2,1);
[l,p] = boundedline(x, y1, e1, '-b*', x, y2, e2, '--ro');
outlinebounds(l,p);
title('Opaque bounds, with outline');
axis tight;

%%
% For our second axis, we use the same 2 lines, and this time assign
% x-varying bounds to both lines.  Rather than using the LineSpec syntax,
% this  example uses the default color order to assign the colors of the
% lines and patches.  I also turn on the |'alpha'| option, which rend