progress bar

AMF/+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/+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/+AMF/@ModelResult/plotAll.m

@@ -1,6 +1,14 @@
-function this = plotAll(this, type, mode)
+function this = plotAll(this, type, varargin)
 
-if nargin < 3, mode = 'TRAJ'; end
+if nargin < 3, mode = 'TRAJ'; 
+else mode = varargin{1};
+end
+
+if length(varargin)>1
+    split = varargin{2};
+else
+    split = 9;
+end
 
 import AMF.utils.defineCustomColormap
 
@@ -9,15 +17,20 @@
     comps = comps(logical([this.parameters.fit]));
 end
 
+
 n = length(comps);
-ns = sqrt(n);
+ns = sqrt(split);
+% ns = sqrt(n);
 
 numIter = this.options.numIter;
 
 figure('Name', upper(type));
 
 for i = 1:n
-    subplot(ceil(ns),ceil(ns),i); hold on;
+    figure(ceil(i/split));
+    counter = ceil(i/split);
+    subplot(ceil(ns),ceil(ns),i-(counter-1)*split); hold on;
+%     subplot(ceil(ns),ceil(ns),i); hold on;
 
     comp = comps(i);
 
@@ -31,9 +44,10 @@
             plotHist(this, comp, colorMap);
 
         case 'HIST_LOG'
-
-            % TODO: plot logarithmic histograms
-
+          % TODO: plot logarithmic histograms
+        case 'MAD' % median absolute deviation
+            plotMad(this, comp, 'g');
+
         otherwise
             error('Unknown plot mode %s', mode);
     end

AMF/+AMF/@ModelResult/plotMad.m

@@ -0,0 +1,22 @@
+function [hp1, hp2] = plotMad(this, comp, color)
+% plot median absolute deviation
+time_steps = this.options.numTimeSteps;
+meta = zeros(time_steps,4);
+for dt = 1:time_steps
+    y = quantile(comp.val(dt,:),[0.05 0.16 0.25 0.5 0.75 0.84 0.95], 2);
+    meta(dt,1) = y(4);
+    meta(dt,2) = median(abs(comp.val(dt,:)- meta(dt,1)));
+    meta(dt,3) = meta(dt,1)+meta(dt,2);
+    meta(dt,4) = meta(dt,1)-meta(dt,2);    
+end
+time = 1:time_steps;
+time = time*this.time(end)/time_steps;
+X = [time fliplr(time)];
+Yupp = meta(:,3)';
+Ylwr = meta(:,4)';
+Y = [Ylwr fliplr(Yupp)];
+hp1 = fill(X, Y, color);
+hp2 = plot(time, meta(:,1), '-k', 'LineWidth', 2);  
+
+end
+

AMF/+AMF/@ModelResult/plot.m → AMF/+AMF/@ModelResult/plots.m

@@ -1,4 +1,4 @@
-function this = plot(this, names, mode)
+function this = plots(this, names, mode)
 
 if nargin < 3, mode = 'TRAJ'; end
 
@@ -31,6 +31,24 @@
         case 'HIST_LOG'
 
             % TODO: plot logarithmic histograms
+        case 'MAD' % median absolute deviation
+            time_steps = this.options.numTimeSteps;
+            meta = zeros(time_steps,4);
+            for dt = 1:time_steps
+                y = quantile(comp.val(dt,:),[0.05 0.16 0.25 0.5 0.75 0.84 0.95], 2);
+                meta(dt,1) = y(4);
+                meta(dt,2) = median(abs(comp.val(dt,:)- meta(dt,1)));
+                meta(dt,3) = meta(dt,1)+meta(dt,2);
+                meta(dt,4) = meta(dt,1)-meta(dt,2);    
+            end
+            time = 1:time_steps;
+            time = time*this.time(end)/time_steps;
+            X = [time fliplr(time)];
+            Yupp = meta(:,3)';
+            Ylwr = meta(:,4)';
+            Y = [Ylwr fliplr(Yupp)];
+            hp = fill(X, Y, 'g');
+            plot(time, meta(:,1), '-k', 'LineWidth', 2);         
 
         otherwise
             error('Unknown plot mode %s', mode);

AMF/+AMF/runADAPT.m

@@ -27,6 +27,7 @@
 result = model.result;
 
 tic
+utils.parfor_progress(numIter);
 parfor it = 1:numIter
     model2 = model; % parfor fix
     elt = 0;
@@ -47,14 +48,17 @@
 
             success = 1;
         catch err
-            %
+            disp(err.message);
+            utils.parfor_progress2;
         end
     end
+    utils.parfor_progress;
 
-    fprintf('Computed trajectory %d [%d] - %.2fs\n', it, max(model2.result.sse), elt);
+%     fprintf('Computed trajectory %d [%d] - %.2fs\n', it, max(model2.result.sse), elt);
 
     result(it) = model2.result;
 end
+parfor_progress(0);
 toc
 
 result = AMF.ModelResult(model, result);

AMF/models/dietModel/Hall/Hall.m

@@ -0,0 +1,9 @@
+function EE = Hall(t, dEI )
+%Energy Expenditure in mice according to Hall
+LM = 25;
+FM = -0.0649.*t.^2 + 2.0961.*t + 2.5263;
+
+EE = 2.1 + 0.331.*LM + 0.202.*FM + 0.4.*dEI;
+
+end
+

AMF/models/dietModel/Hall/bw_fit.m

@@ -0,0 +1,21 @@
+% Fit body weight data
+
+time = diets.t3/(24*7); % weeks HFD
+TG = diets.perTG_m*853/1e6; % g TG
+
+% fit to polynomial
+p = polyfit(time, TG, 2); % -0.0649*x^2 + 2.0961*x + 2.5263
+
+% plot polynomial and data
+x1 = linspace(0, 12, 100);
+y1 = polyval(p,x1);
+
+figure(1);hold on;
+plot(time, TG, 'ok', x1, y1, '-k', 'LineWidth', 2);
+xlabel('Time on HFD  (weeks)');
+ylabel('Body TG  (g)');
+saveas(1, 'BW.emf');
+
+% slope at t= 3 = 1.7067 g TG/week
+% slope at t=10 = 0.7981 g TG/week
+

AMF/models/dietModel/Hall/hall_plot.m

@@ -0,0 +1,11 @@
+% Hall
+t = linspace(0,16,100);
+t1 = [3 10];
+x1 = [11.3+1.35 12.9+1.35];
+ee3 = Hall(t, 3);
+ee2 = Hall(t, 2);
+ee4 = Hall(t, 4);
+ee909 = Hall(t, 0.909);
+plot(t,ee2, '--k', t, ee3, '-k', t, ee4, '--k',t, ee909, '--b', t1, x1, 'or', 'LineWidth', 2);
+xlabel('Time on HFD (weeks)')
+ylabel('Energy Expenditure (kcal/day)')