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	tshow or hide figures with the show_figures flag - cosmo - front and backend fo…
	git clone git://src.adamsgaard.dk/cosmo
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	---
	commit bb3d54aa230ee29a44e58f72a841b4638e3d09b8
	parent 2ca0c20467bfb639003cda0641fc73e35997d678
	Author: Anders Damsgaard <[email protected]>
	Date: Thu, 27 Aug 2015 16:06:18 +0200

	show or hide figures with the show_figures flag

	Diffstat:
	M matlab/file_scanner_mcmc_starter.m \| 6 +++++-
	M matlab/generate_plots.m \| 43 +++++++++++++++++++----------…

	2 files changed, 31 insertions(+), 18 deletions(-)
	---
	diff --git a/matlab/file_scanner_mcmc_starter.m b/matlab/file_scanner_mcmc_star…
	t@@ -30,6 +30,10 @@ debug = true; % show debugging output to matlab console
	% output graphics formats
	graphics_formats = {'fig', 'png', 'pdf'};

	+% show figures after they are generated in addition to saving them,
	+% values: 'on' or 'off'
	+show_figures = 'off';
	+
	% number of MCMC walkers
	n_walkers = 1;

	t@@ -84,7 +88,7 @@ while 1

	% generate plots
	%CompareWalks2(Ss, save_file)
	- generate_plots(Ss, save_file, graphics_formats)
	+ generate_plots(Ss, save_file, graphics_formats, show_figures);

	% delete or archive the file so it is not processed again
	%delete(infile)
	diff --git a/matlab/generate_plots.m b/matlab/generate_plots.m
	t@@ -1,4 +1,4 @@
	-function generate_plots(Ss, save_file, formats)
	+function generate_plots(Ss, save_file, formats, show_figures)

	%% Copied from m_pakke2014maj11/CompareWalks2.m
	% Generates and saves all relevant figures
	t@@ -9,7 +9,9 @@ Nwalkers = fixed_stuff.Nwalkers;
	M = size(fixed_stuff.mminmax,1);

	%Compare BurnIn
	-fh(1)=figure;
	+
	+fh(1) = figure('visible', show_figures);
	+
	for iwalk=1:min(4,Nwalkers) %only up to the first four walks
	QsBurnIns(:,iwalk)=Ss{iwalk}.QsBurnIn;
	Qss(:,iwalk) =Ss{iwalk}.Qs;
	t@@ -94,7 +96,7 @@ axis ij
	box on

	%Compare sampling cross-plots
	-fh = [fh;figure];
	+fh = [fh;figure('visible', show_figures)];
	Nbin = 50;

	mminmax = fixed_stuff.mminmax; %bounds of uniform prior intervals
	t@@ -137,7 +139,7 @@ for i1=1:M
	isub2 = iwalk; isub = isub2 + (isub1-1)*4;
	if isub>4*5
	isub1 = 1; isub=1;
	- fh = [fh;figure];
	+ fh = [fh;figure('visible', show_figures)];
	end
	subplot(5,4,isub)
	pcolor(xbins{i1},ybins,smoothgrid);
	t@@ -157,7 +159,7 @@ for i1=1:M
	end
	end

	-fh = [fh;figure];
	+fh = [fh;figure('visible', show_figures)];
	for i1 = 1:M
	for iwalk=1:min(4,Nwalkers)
	isub = (i1-1)*4 + iwalk;
	t@@ -174,26 +176,33 @@ for i1 = 1:M
	end
	end

	+
	+
	%Putting in titles over figure 2:4
	-figure(fh(2))
	+
	+figure(fh(2)); set(fh(2), 'Visible', show_figures)
	subplot(5,4,2)
	title(['Density cross-plots A. Result file =',save_file],'interp','none')
	-figure(fh(3))
	+
	+figure(fh(3)); set(fh(3), 'Visible', show_figures)
	subplot(5,4,2)
	title(['Density cross-plots B. Result file =',save_file],'interp','none')
	-figure(fh(4))
	+
	+figure(fh(4)); set(fh(4), 'Visible', show_figures)
	subplot(5,4,2)
	title(['Histograms. Result file =',save_file],'interp','none')

	-figpos1 = [6 474 1910 504];
	-figpos2 =[ 12 94 645 887];
	-figpos3 =[ 610 94 645 887];
	-figpos4 =[ 1207 94 740 887];
	-set(fh(2),'pos',figpos2)
	-set(fh(3),'pos',figpos3)
	-set(fh(4),'pos',figpos4)
	-set(fh(1),'pos',figpos1)
	-figure(fh(1))
	+if strcmp(show_figures, 'on')
	+ figpos1 = [6 474 1910 504];
	+ figpos2 =[ 12 94 645 887];
	+ figpos3 =[ 610 94 645 887];
	+ figpos4 =[ 1207 94 740 887];
	+ set(fh(2),'pos',figpos2)
	+ set(fh(3),'pos',figpos3)
	+ set(fh(4),'pos',figpos4)
	+ set(fh(1),'pos',figpos1)
	+ figure(fh(1))
	+end

	for i=1:4
	figure_save_multiformat(figure(fh(i)), ...