Updated colorbrewer build and paths in driver.

drive_allomtests.m

@@ -5,7 +5,9 @@
 clear all;
 close all;
 
-addpath('~/local/MATLAB/cbrewer/');
+addpath('functions/');
+addpath('tools/cbrewer/');
+
 %addpath('~/local/Matlab/cbrewer/');
 
 % Initialize the allometry library and the pointers

tools/cbrewer/cbrewer.m

@@ -0,0 +1,128 @@
+function [colormap]=cbrewer(ctype, cname, ncol, interp_method)
+%
+% CBREWER - This function produces a colorbrewer table (rgb data) for a 
+% given type, name and number of colors of the colorbrewer tables. 
+% For more information on 'colorbrewer', please visit
+% http://colorbrewer2.org/
+% 
+% The tables were generated from an MS-Excel file provided on the website
+% http://www.personal.psu.edu/cab38/ColorBrewer/ColorBrewer_updates.html
+%
+% 
+% [colormap]=cbrewer(ctype, cname, ncol, interp_method)
+%
+% INPUT:
+%   - ctype: type of color table 'seq' (sequential), 'div' (diverging), 'qual' (qualitative)
+%   - cname: name of colortable. It changes depending on ctype.
+%   - ncol:  number of color in the table. It changes according to ctype and
+%            cname
+%   - interp_method: interpolation method (see interp1.m). Default is "cubic" )
+% 
+% A note on the number of colors: Based on the original data, there is
+% only a certain number of colors available for each type and name of
+% colortable. When 'ncol' is larger then the maximum number of colors
+% originally given, an interpolation routine is called (interp1) to produce 
+% the "extended" colormaps.
+%
+% Example:  To produce a colortable CT of ncol X 3 entries (RGB) of 
+%           sequential type and named 'Blues' with 8 colors:
+%                   CT=cbrewer('seq', 'Blues', 8);
+%           To use this colortable as colormap, simply call:
+%                   colormap(CT)
+% 
+%           To see the various colormaps available according to their types and
+%           names, simply call: cbrewer()
+%
+%  This product includes color specifications and designs developed by
+%  Cynthia Brewer (http://colorbrewer.org/).
+%
+% Author: Charles Robert
+% email: [email protected]
+% Date: 06.12.2011
+% ------------------------------
+% 18.09.2015  Minor fixes, fixed a bug where the 'spectral' color table did not appear in the preview
+
+
+% load colorbrewer data
+load('colorbrewer.mat')
+% initialise the colormap is there are any problems
+colormap=[];
+if (~exist('interp_method', 'var'))
+    interp_method='cubic';
+end
+
+% If no arguments
+if (~exist('ctype', 'var') | ~exist('cname', 'var') | ~exist('ncol', 'var'))
+    disp(' ')
+    disp('[colormap] = cbrewer(ctype, cname, ncol [, interp_method])')
+    disp(' ')
+    disp('INPUT:')
+    disp('  - ctype: type of color table *seq* (sequential), *div* (divergent), *qual* (qualitative)')
+    disp('  - cname: name of colortable. It changes depending on ctype.')
+    disp('  - ncol:  number of color in the table. It changes according to ctype and cname')
+    disp('  - interp_method:  interpolation method  (see interp1.m). Default is "cubic" )')
+
+    disp(' ')
+    disp('Sequential tables:')
+    z={'Blues','BuGn','BuPu','GnBu','Greens','Greys','Oranges','OrRd','PuBu','PuBuGn','PuRd',...
+             'Purples','RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'Spectral'};
+    disp(z')     
+
+    disp('Divergent tables:')
+    z={'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn'};
+    disp(z')
+
+    disp(' ')
+    disp('Qualitative tables:')
+    %getfield(colorbrewer, 'qual')
+    z={'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3'};
+    disp(z')
+
+    plot_brewer_cmap
+    return
+end
+
+% Verify that the input is appropriate
+ctype_names={'div', 'seq', 'qual'};
+if (~ismember(ctype,ctype_names))
+    disp('ctype must be either: *div*, *seq* or *qual*')
+    colormap=[];
+    return
+end
+
+if (~isfield(colorbrewer.(ctype),cname))
+    disp(['The name of the colortable of type *' ctype '* must be one of the following:'])
+    getfield(colorbrewer, ctype)
+    colormap=[];
+    return
+end
+
+if (ncol>length(colorbrewer.(ctype).(cname)))
+%     disp(' ')
+%     disp('----------------------------------------------------------------------')
+%     disp(['The maximum number of colors for table *' cname '* is ' num2str(length(colorbrewer.(ctype).(cname)))])
+%     disp(['The new colormap will be extrapolated from these ' num2str(length(colorbrewer.(ctype).(cname))) ' values'])
+%     disp('----------------------------------------------------------------------')
+%     disp(' ')
+    cbrew_init=colorbrewer.(ctype).(cname){length(colorbrewer.(ctype).(cname))};
+    colormap=interpolate_cbrewer(cbrew_init, interp_method, ncol);
+    colormap=colormap./255;
+    return
+end
+
+if (isempty(colorbrewer.(ctype).(cname){ncol}))
+
+    while(isempty(colorbrewer.(ctype).(cname){ncol}))
+        ncol=ncol+1;
+    end        
+    disp(' ')
+    disp('----------------------------------------------------------------------')
+    disp(['The minimum number of colors for table *' cname '* is ' num2str(ncol)])
+    disp('This minimum value shall be defined as ncol instead')
+    disp('----------------------------------------------------------------------')
+    disp(' ')
+end
+
+colormap=(colorbrewer.(ctype).(cname){ncol})./255;
+
+end

tools/cbrewer/change_jet.m

@@ -0,0 +1,64 @@
+% This script help produce a new 'jet'-like colormap based on other RGB reference colors
+
+% ------- I WAS ASKED ---------------
+% "is there a chance that you could add a diverging map going from blue to green to red as in jet, 
+% but using the red and blue from your RdBu map and the third darkest green from your RdYlGn map?""
+%
+% ANSWER:
+%   You should construct the new colormap based on the existing RGB values of 'jet'
+%   but projecting these RGB values on your new RGB basis. 
+% -----------------------------------
+
+% load colormaps
+jet=colormap('jet');
+RdBu=cbrewer('div', 'RdBu', 11);
+RdYlGn=cbrewer('div', 'RdYlGn', 11);
+
+% Define the new R, G, B references (p stands for prime)
+Rp=RdBu(1,:);
+Bp=RdBu(end, :);
+Gp=RdYlGn(end-2, :);
+RGBp=[Rp;Gp;Bp];
+
+% construct the new colormap based on the existing RGB values of jet
+% Project the RGB values on your new basis
+newjet = jet*RGBp;
+
+% store data in a strcuture, easier to handle
+cmap.jet=jet;
+cmap.newjet=newjet;
+cnames={'jet', 'newjet'};
+
+% plot the RGB values
+fh=figure();
+colors={'r', 'g', 'b'};
+for iname=1:length(cnames)
+   subplot(length(cnames),1,iname)
+   dat=cmap.(cnames{end-iname+1});
+   for icol=1:size(dat,2)
+      plot(dat(:,icol), 'color', colors{icol}, 'linewidth', 2);hold on;
+   end % icol
+   title([' "' cnames{end-iname+1} '" in RGB plot'])
+end
+
+% plot the colormaps
+fh=figure();
+for iname=1:length(cnames)
+   F=cmap.(cnames{iname});
+   ncol=length(F);
+   fg=1./ncol; % geometrical factor
+   X=fg.*[0 0 1 1];
+   Y=0.1.*[1 0 0 1]+(2*iname-1)*0.1;
+
+   for icol=1:ncol
+      X2=X+fg.*(icol-1);
+      fill(X2,Y,F(icol, :), 'linestyle', 'none')
+      hold all
+   end % icol
+   text(-0.1, mean(Y), cnames{iname}, 'HorizontalAlignment', 'right', 'FontWeight', 'bold', 'FontSize', 10, 'FontName' , 'AvantGarde')
+   xlim([-0.4, 1])
+   axis off
+   set(gcf, 'color', [1 1 1])
+   ylim([0.1 1.05.*max(Y)]);
+ end % iname
+

tools/cbrewer/interpolate_cbrewer.m

@@ -0,0 +1,36 @@
+function [interp_cmap]=interpolate_cbrewer(cbrew_init, interp_method, ncolors)
+% 
+% INTERPOLATE_CBREWER - interpolate a colorbrewer map to ncolors levels
+%
+% INPUT:
+%   - cbrew_init: the initial colormap with format N*3
+%   - interp_method: interpolation method, which can be the following:
+%               'nearest' - nearest neighbor interpolation
+%               'linear'  - bilinear interpolation
+%               'spline'  - spline interpolation
+%               'cubic'   - bicubic interpolation as long as the data is
+%                           uniformly spaced, otherwise the same as 'spline'
+%   - ncolors=desired number of colors 
+%
+% Author: Charles Robert
+% email: [email protected]
+% Date: 14.10.2011
+
+
+% just to make sure, in case someone puts in a decimal
+ncolors=round(ncolors);
+
+% How many data points of the colormap available
+nmax=size(cbrew_init,1);
+
+% create the associated X axis (using round to get rid of decimals)
+a=(ncolors-1)./(nmax-1);
+X=round([0 a:a:(ncolors-1)]);
+X2=0:ncolors-1;
+
+z=interp1(X,cbrew_init(:,1),X2,interp_method);
+z2=interp1(X,cbrew_init(:,2),X2,interp_method);
+z3=interp1(X,cbrew_init(:,3),X2, interp_method);
+interp_cmap=round([z' z2' z3']);
+
+end

tools/cbrewer/license.txt

@@ -0,0 +1,24 @@
+Copyright (c) 2015, Charles Robert
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the distribution
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

tools/cbrewer/plot_brewer_cmap.m

@@ -0,0 +1,50 @@
+% Plots and identifies the various colorbrewer tables available.
+% Is called by cbrewer.m when no arguments are given.
+%
+% Author: Charles Robert
+% email: [email protected]
+% Date: 14.10.2011
+
+
+
+load('colorbrewer.mat')
+
+ctypes={'div', 'seq', 'qual'};
+ctypes_title={'Diverging', 'Sequential', 'Qualitative'};
+cnames{1,:}={'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral'};
+cnames{2,:}={'Blues','BuGn','BuPu','GnBu','Greens','Greys','Oranges','OrRd','PuBu','PuBuGn','PuRd',...
+             'Purples','RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd'};
+cnames{3,:}={'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3'};
+
+figure('position', [314 327 807 420])
+for itype=1:3
+
+    %fh(itype)=figure();
+    subplot(1,3,itype)
+
+    for iname=1:length(cnames{itype,:})
+
+        ncol=length(colorbrewer.(ctypes{itype}).(cnames{itype}{iname}));
+        fg=1./ncol; % geometrical factor
+
+        X=fg.*[0 0 1 1];
+        Y=0.1.*[1 0 0 1]+(2*iname-1)*0.1;
+        F=cbrewer(ctypes{itype}, cnames{itype}{iname}, ncol);
+
+        for icol=1:ncol
+            X2=X+fg.*(icol-1);
+            fill(X2,Y,F(icol, :), 'linestyle', 'none')
+            text(-0.1, mean(Y), cnames{itype}{iname}, 'HorizontalAlignment', 'right', 'FontWeight', 'bold', 'FontSize', 10, 'FontName' , 'AvantGarde')
+            xlim([-0.4, 1])
+            hold all
+        end % icol
+        %set(gca, 'box', 'off')
+        title(ctypes_title{itype}, 'FontWeight', 'bold', 'FontSize', 16, 'FontName' , 'AvantGarde')
+        axis off
+        set(gcf, 'color', [1 1 1])
+    end % iname
+    ylim([0.1 1.05.*max(Y)]);
+end %itype
+
+set(gcf, 'MenuBar', 'none')
+set(gcf, 'Name', 'ColorBrewer Color maps')