Added progress bar and some visualization

+AMF/+utils/defineCustomColormap.m

@@ -0,0 +1,28 @@
+function clist = define_custom_colormap(c_matrix,N)
+
+if length(c_matrix) == 3
+    clist(1,:) = c_matrix{1};           %start color
+    clist(ceil(N/2),:) = c_matrix{2};   %middle color
+    clist(N,:) = c_matrix{3};           %end color
+
+    dc1 = clist(ceil(N/2),:) - clist(1,:);
+    for i1 = 2:ceil(N/2)-1
+        clist(i1,:) = clist(i1-1,:) + dc1/(N-1);
+    end
+
+    dc2 = clist(N,:) - clist(ceil(N/2),:);
+    for i2 = ceil(N/2)+1:N-1
+        clist(i2,:) = clist(i2-1,:) + dc2/(N-1);
+    end
+
+
+elseif length(c_matrix) == 2
+    clist(1,:) = c_matrix{1}; %start color
+    clist(N,:) = c_matrix{2}; %end color    
+
+    dc = clist(N,:)-clist(1,:);
+
+    for i = 2:N-1
+        clist(i,:) = clist(i-1,:) + dc/(N-1);
+    end
+end

+AMF/+utils/getHist.m

@@ -0,0 +1,14 @@
+function [N,C] = getHist(t,v,r,ny)
+
+a = repmat(t,size(v,1),1);
+b = reshape(v.',numel(v),1);
+
+if numel(r) > 0
+    [N, C] = hist3([a,b],{t,[r(1) : (r(2)-r(1))/(ny-1) : r(2)]});
+else
+    [N, C] = hist3([a,b],[numel(t) ny]);
+end
+N = log10(N);
+N = N./max(max(N));
+
+N(N==-inf) = 0;

+AMF/+utils/mexify.m

@@ -0,0 +1,6 @@
+function outputStr = mexify(inputStr)
+
+outputStr = inputStr;
+
+% parsers
+outputStr = regexprep(outputStr, '([-+\w]+)\^([-+\w]+)', 'pow($1,$2)');

+AMF/+utils/mexify2.m

@@ -0,0 +1,8 @@
+function outputStr = mexify2(inputStr, compName)
+
+outputStr = inputStr;
+
+% parsers
+outputStr = regexprep(outputStr, '([-+\w]+)\^([-+\w]+)', 'pow($1,$2)');
+
+outputStr = regexprep(outputStr, 'if\((.*),(.*),(.*)\)', sprintf('0;\nif ($1)\n\t%s = $2;\nelse\n\t%s = $3;\nend', compName, compName));

+AMF/+utils/parfor_progress.m

@@ -0,0 +1,82 @@
+function percent = parfor_progress(N)
+%PARFOR_PROGRESS Progress monitor (progress bar) that works with parfor.
+%   PARFOR_PROGRESS works by creating a file called parfor_progress.txt in
+%   your working directory, and then keeping track of the parfor loop's
+%   progress within that file. This workaround is necessary because parfor
+%   workers cannot communicate with one another so there is no simple way
+%   to know which iterations have finished and which haven't.
+%
+%   PARFOR_PROGRESS(N) initializes the progress monitor for a set of N
+%   upcoming calculations.
+%
+%   PARFOR_PROGRESS updates the progress inside your parfor loop and
+%   displays an updated progress bar.
+%
+%   PARFOR_PROGRESS(0) deletes parfor_progress.txt and finalizes progress
+%   bar.
+%
+%   To suppress output from any of these functions, just ask for a return
+%   variable from the function calls, like PERCENT = PARFOR_PROGRESS which
+%   returns the percentage of completion.
+%
+%   Example:
+%
+%      N = 100;
+%      parfor_progress(N);
+%      parfor i=1:N
+%         pause(rand); % Replace with real code
+%         parfor_progress;
+%      end
+%      parfor_progress(0);
+%
+%   See also PARFOR.
+
+% By Jeremy Scheff - jdscheff@gmail.com - http://www.jeremyscheff.com/
+
+% error(nargchk(0, 1, nargin, 'struct'));
+
+if nargin < 1
+    N = -1;
+end
+
+percent = 0;
+w = 50; % Width of progress bar
+
+if N > 0
+    f = fopen('parfor_progress.txt', 'w');
+    if f<0
+        error('Do you have write permissions for %s?', pwd);
+    end
+    fprintf(f, '%d\n', N); % Save N at the top of progress.txt
+    fclose(f);
+
+    if nargout == 0
+        disp(['  0%[>', repmat(' ', 1, w), ']']);
+    end
+elseif N == 0
+    delete('parfor_progress.txt');
+    percent = 100;
+
+    if nargout == 0
+        disp([repmat(char(8), 1, (w+9)), char(10), '100%[', repmat('=', 1, w+1), ']']);
+    end
+else
+
+    if ~exist('parfor_progress.txt', 'file')
+        error('parfor_progress.txt not found. Run PARFOR_PROGRESS(N) before PARFOR_PROGRESS to initialize parfor_progress.txt.');
+    end
+
+    f = fopen('parfor_progress.txt', 'a');
+    fprintf(f, '1\n');
+    fclose(f);
+
+    f = fopen('parfor_progress.txt', 'r');
+    progress = fscanf(f, '%d');
+    fclose(f);
+    percent = (length(progress)-1)/progress(1)*100;
+
+    if nargout == 0
+        perc = sprintf('%3.0f%%', percent); % 4 characters wide, percentage
+        disp([repmat(char(8), 1, (w+9)), char(10), perc, '[', repmat('=', 1, round(percent*w/100)), '>', repmat(' ', 1, w - round(percent*w/100)), ']']);
+    end
+end

+AMF/+utils/parfor_progress2.m

@@ -0,0 +1,82 @@
+function percent = parfor_progress2(N)
+%PARFOR_PROGRESS Progress monitor (progress bar) that works with parfor.
+%   PARFOR_PROGRESS works by creating a file called parfor_progress.txt in
+%   your working directory, and then keeping track of the parfor loop's
+%   progress within that file. This workaround is necessary because parfor
+%   workers cannot communicate with one another so there is no simple way
+%   to know which iterations have finished and which haven't.
+%
+%   PARFOR_PROGRESS(N) initializes the progress monitor for a set of N
+%   upcoming calculations.
+%
+%   PARFOR_PROGRESS updates the progress inside your parfor loop and
+%   displays an updated progress bar.
+%
+%   PARFOR_PROGRESS(0) deletes parfor_progress.txt and finalizes progress
+%   bar.
+%
+%   To suppress output from any of these functions, just ask for a return
+%   variable from the function calls, like PERCENT = PARFOR_PROGRESS which
+%   returns the percentage of completion.
+%
+%   Example:
+%
+%      N = 100;
+%      parfor_progress(N);
+%      parfor i=1:N
+%         pause(rand); % Replace with real code
+%         parfor_progress;
+%      end
+%      parfor_progress(0);
+%
+%   See also PARFOR.
+
+% By Jeremy Scheff - jdscheff@gmail.com - http://www.jeremyscheff.com/
+
+% error(nargchk(0, 1, nargin, 'struct'));
+
+if nargin < 1
+    N = -1;
+end
+
+percent = 0;
+w = 50; % Width of progress bar
+
+if N > 0
+    f = fopen('parfor_progress.txt', 'w');
+    if f<0
+        error('Do you have write permissions for %s?', pwd);
+    end
+    fprintf(f, '%d\n', N); % Save N at the top of progress.txt
+    fclose(f);
+
+    if nargout == 0
+        disp(['  0%[>', repmat(' ', 1, w), ']']);
+    end
+elseif N == 0
+    delete('parfor_progress.txt');
+    percent = 100;
+
+    if nargout == 0
+        disp([repmat(char(8), 1, (w+9)), char(10), '100%[', repmat('=', 1, w+1), ']']);
+    end
+else
+
+    if ~exist('parfor_progress.txt', 'file')
+        error('parfor_progress.txt not found. Run PARFOR_PROGRESS(N) before PARFOR_PROGRESS to initialize parfor_progress.txt.');
+    end
+
+%     f = fopen('parfor_progress.txt', 'a');
+%     fprintf(f, '1\n');
+%     fclose(f);
+
+    f = fopen('parfor_progress.txt', 'r');
+    progress = fscanf(f, '%d');
+    fclose(f);
+    percent = (length(progress)-1)/progress(1)*100;
+
+    if nargout == 0
+        perc = sprintf('%3.0f%%', percent); % 4 characters wide, percentage
+        disp([perc, '[', repmat('=', 1, round(percent*w/100)), '>', repmat(' ', 1, w - round(percent*w/100)), ']']);
+    end
+end

+AMF/+utils/writeFile.m

@@ -0,0 +1,5 @@
+function writeFile(fn, content)
+
+fid = fopen(fn, 'w');
+fprintf(fid, content);
+fclose(fid);

+AMF/+visualisation/define_custom_colormap.m

@@ -0,0 +1,28 @@
+function clist = define_custom_colormap(c_matrix,N)
+
+if length(c_matrix) == 3
+    clist(1,:) = c_matrix{1};           %start color
+    clist(ceil(N/2),:) = c_matrix{2};   %middle color
+    clist(N,:) = c_matrix{3};           %end color
+
+    dc1 = clist(ceil(N/2),:) - clist(1,:);
+    for i1 = 2:ceil(N/2)-1
+        clist(i1,:) = clist(i1-1,:) + dc1/(N-1);
+    end
+
+    dc2 = clist(N,:) - clist(ceil(N/2),:);
+    for i2 = ceil(N/2)+1:N-1
+        clist(i2,:) = clist(i2-1,:) + dc2/(N-1);
+    end
+
+
+elseif length(c_matrix) == 2
+    clist(1,:) = c_matrix{1}; %start color
+    clist(N,:) = c_matrix{2}; %end color    
+
+    dc = clist(N,:)-clist(1,:);
+
+    for i = 2:N-1
+        clist(i,:) = clist(i-1,:) + dc/(N-1);
+    end
+end

+AMF/+visualisation/define_figure_details.m

@@ -0,0 +1,59 @@
+function plotinfo = define_figure_details(varargin)
+
+    if ~isempty(varargin)
+        plotinfo = varargin{1};
+    else
+        plotinfo = struct();
+    end
+    % figure size
+    dx = 10;
+    dy = 50;
+    ss = get(0,'ScreenSize');
+    xmax = ss(3)-dx-10;
+    ymax = ss(4)-dy-80;
+    set(0,'DefaultFigurePosition',[dx dy xmax ymax]);
+
+
+    % font size
+    if ~isfield(plotinfo,'FS')
+        plotinfo.FS = 24; %40;
+    end
+
+    % line width of axes
+    if ~isfield(plotinfo,'LW_axes')
+        plotinfo.LW_axes = 2; %3;
+    end
+
+    % line width & marker size of (raw) data points
+    if ~isfield(plotinfo,'LW_data')
+        plotinfo.LW_data = 2;
+    end
+    if ~isfield(plotinfo,'MS_data')
+        plotinfo.MS_data = 14;
+    end
+
+    % line width of spline data
+    if ~isfield(plotinfo,'LW_spline')
+        plotinfo.LW_spline = 3;
+    end
+
+    % line width of model simulations / trajectories
+    if ~isfield(plotinfo,'LW_sim')
+        plotinfo.LW_sim = 4;
+    end
+
+
+    % text properties
+    set(0,'DefaultTextFontName','Myriad')
+    set(0,'DefaultTextFontSize',plotinfo.FS);
+    set(0,'DefaultTextInterpreter','tex');    
+
+    % line and marker properties
+    set(0,'DefaultLineLineWidth',plotinfo.LW_data);
+    set(0,'DefaultLineMarkerSize',plotinfo.MS_data);
+
+    % axes properties
+    set(0,'DefaultAxesFontName','Myriad')
+    set(0,'DefaultAxesFontSize',plotinfo.FS);
+    set(0,'DefaultAxesLineWidth',plotinfo.LW_axes);    
+end

+AMF/+visualisation/errorbar_tick.m

@@ -0,0 +1,70 @@
+function errorbar_tick(h,w,xtype)
+%ERRORBAR_TICK Adjust the width of errorbars
+%   ERRORBAR_TICK(H) adjust the width of error bars with handle H.
+%      Error bars width is given as a ratio of X axis length (1/80).
+%   ERRORBAR_TICK(H,W) adjust the width of error bars with handle H.
+%      The input W is given as a ratio of X axis length (1/W). The result 
+%      is independent of the x-axis units. A ratio between 20 and 80 is usually fine.
+%   ERRORBAR_TICK(H,W,'UNITS') adjust the width of error bars with handle H.
+%      The input W is given in the units of the current x-axis.
+%
+%   See also ERRORBAR
+%
+
+% Author: Arnaud Laurent
+% Creation : Jan 29th 2009
+% MATLAB version: R2007a
+%
+% Notes: This function was created from a post on the french forum :
+% http://www.developpez.net/forums/f148/environnements-developpement/matlab/
+% Author : Jerome Briot (Dut) 
+%   http://www.mathworks.com/matlabcentral/newsreader/author/94805
+%   http://www.developpez.net/forums/u125006/dut/
+% It was further modified by Arnaud Laurent and Jerome Briot.
+
+% Check numbers of arguments
+error(nargchk(1,3,nargin))
+
+% Check for the use of V6 flag ( even if it is depreciated ;) )
+flagtype = get(h,'type');
+
+% Check number of arguments and provide missing values
+if nargin==1
+	w = 80;
+end
+
+if nargin<3
+   xtype = 'ratio';
+end
+
+% Calculate width of error bars
+if ~strcmpi(xtype,'units')
+    dx = diff(get(gca,'XLim'));	% Retrieve x limits from current axis
+    w = dx/w;                   % Errorbar width
+end
+
+% Plot error bars
+if strcmpi(flagtype,'hggroup') % ERRORBAR(...)
+
+    hh=get(h,'children');		% Retrieve info from errorbar plot
+    x = get(hh(2),'xdata');		% Get xdata from errorbar plot
+
+    x(4:9:end) = x(1:9:end)-w/2;	% Change xdata with respect to ratio
+    x(7:9:end) = x(1:9:end)-w/2;
+    x(5:9:end) = x(1:9:end)+w/2;
+    x(8:9:end) = x(1:9:end)+w/2;
+
+    set(hh(2),'xdata',x(:))	% Change error bars on the figure
+
+else  % ERRORBAR('V6',...)
+
+    x = get(h(1),'xdata');		% Get xdata from errorbar plot
+
+    x(4:9:end) = x(1:9:end)-w/2;	% Change xdata with respect to the chosen ratio
+    x(7:9:end) = x(1:9:end)-w/2;
+    x(5:9:end) = x(1:9:end)+w/2;
+    x(8:9:end) = x(1:9:end)+w/2;
+
+    set(h(1),'xdata',x(:))	% Change error bars on the figure
+
+end