Autoselecting files instead of using uigetfile GUI

I want to be able to run the simple_diagnostics.m without having to select a file and instead have it run and select continuously on a bunch of files.So my question is what do i have to do to this script to have it automatically select files from the path /home/matlab/Desktop/test/.

%%simple_diagnostics

% this script inputs a mat file containing trajectories, and histograms
% various simple properties. 

%%set up path, if necessary

setuppath;

%%set all defaults

matname = '';
matpath = '';

% load settings

pathtocomputeperframestats = which('simple_diagnostics');
savedsettingsfile = strrep(pathtocomputeperframestats,'simple_diagnostics.m','.simplediagnosticssrc.mat');
if exist(savedsettingsfile,'file')
  load(savedsettingsfile);
end

%%choose a mat file to analyze
helpmsg = 'Choose mat file for which to compute and plot a few simple statistics.';
matname = [matpath,matname];
[matname,matpath] = uigetfilehelp('*.mat','Choose mat file to analyze',matname,'helpmsg',helpmsg);
if isnumeric(matname) && matname == 0,
  return;
end
fprintf('Matfile: %s%s\n\n',matpath,matname);

if exist(savedsettingsfile,'file'),
  save('-append',savedsettingsfile,'matname','matpath');
else
  save(savedsettingsfile,'matname','matpath');
end
matnameonly = matname;

%%get conversion to mm, seconds

[convertunits_succeeded,matname] = convert_units_f('isautomatic',true,'matname',matnameonly,'matpath',matpath);

%%load in the data

[trx,matname,loadsucceeded] = load_tracks(matname);
if ~loadsucceeded,
  msgbox('Could not load trx from file %s\n',matname);
  return;
end

% remove flies with less than 2 frames of data
minnframes = 2;
trx = prune_short_trajectories(trx,minnframes);

%%plot all the trajectories

figure(1);

nflies = length(trx);

% put all the flies on one figure
n1 = round(sqrt(nflies));
n2 = ceil(nflies/n1);
hax = createsubplots(n1,n2,[[.05,.01];[.05,.05]]);
hax = reshape(hax,[n1,n2])'; % column major
hax = hax(:)';
if n1*n2 > nflies,
  delete(hax(nflies+1:end));
  hax = hax(1:nflies);
end

% get bounds for all flies
x_mm = [trx.x_mm];
x_mm = x_mm(~isnan( x_mm ) & ~isinf( x_mm ));
y_mm = [trx.y_mm];
y_mm = y_mm(~isnan( y_mm ) & ~isinf( y_mm ));
minx = min( x_mm );
maxx = max( x_mm );
miny = min( y_mm );
maxy = max( y_mm );
dx = maxx - minx;
dy = maxy - miny;

for fly = 1:nflies,

    % plot just the trajectory
    axes(hax(fly));
    plot(trx(fly).x_mm,trx(fly).y_mm,'k.-','markersize',3,'linewidth',.5);
    title(sprintf('Fly %d, frames %d to %d',fly,trx(fly).firstframe,trx(fly).endframe));
    axis equal;
    axis([minx-.025*dx,maxx+.025*dx,miny-.025*dy,maxy+.025*dy]);

    % onlt put an x-axis on the lowest plots
    [c,r] = ind2sub([n2,n1],fly);
    if r ~= n1 && r*n2+c <= nflies,
      set(hax(fly),'xticklabel',{});
    end
    if c ~= 1,
      set(hax(fly),'yticklabel',{});
    end
  end

linkaxes(hax);

%%histogram position in the arena for all flies

figure(2); 
clf;

nbinsx = 100;
nbinsy = max(1,round(nbinsx*dy/dx));
edgesx = linspace(minx,maxx,nbinsx+1);
edgesy = linspace(miny,maxy,nbinsy+1);
centersx = (edgesx(1:end-1)+edgesx(2:end))/2;
centersy = (edgesy(1:end-1)+edgesy(2:end))/2;
counts = hist3([[trx.x_mm];[trx.y_mm]]',{centersx,centersy});
freq_position = counts / sum(counts(:));

hax = createsubplots(1,2,.05);
axes(hax(1));
imagesc([centersx(1),centersx(end)],[centersy(1),centersy(end)],freq_position');
axis image;
axis xy;
title('Position heat map, frequency');
colorbar;
axes(hax(2));
imagesc([centersx(1),centersx(end)],[centersy(1),centersy(end)],log(freq_position'));
title('Position heat map, log frequency');
axis image;
axis xy
colorbar;

%%histogram speed

figure(3);
clf;
hax = createsubplots(1,3,[.05,.1]);

% compute speed for all flies
speed = [];
for fly = 1:nflies,
  speedcurr = sqrt(diff(trx(fly).x_mm).^2 + diff(trx(fly).y_mm).^2)*trx(fly).fps;
  speed = [speed,speedcurr];
end

% choose bins
nbins = max(1,min(100,round(length(speed)/20)));
prctlastbin = 1;
edges = [linspace(0,prctile(speed,100-prctlastbin),nbins),max(speed)];
centers = (edges(1:end-1)+edges(2:end))/2;

% histogram for all flies
counts = histc(speed,edges);
counts(end-1) = counts(end-1) + counts(end);
counts = counts(1:end-1);
freq_speed_allflies = counts / sum(counts);

% do each fly individually
freq_speed_perfly = zeros(nflies,nbins);
for fly = 1:nflies,
  speedcurr = sqrt(diff(trx(fly).x_mm).^2 + diff(trx(fly).y_mm).^2)*trx(fly).fps;
  counts = histc(speedcurr,edges);
  counts(end-1) = counts(end-1) + counts(end);
  counts = counts(1:end-1);
  freq_speed_perfly(fly,:) = counts / sum(counts);
end

axes(hax(1));
xplot = centers;
nskip = nbins/10;
xplot(end) = (1+nskip)*centers(end-1)-nskip*centers(end-2);
plot(xplot,freq_speed_perfly,'-','linewidth',.25);
hold on;
plot(xplot,freq_speed_allflies,'k.-','linewidth',5);
dx = xplot(end)-xplot(1);
dy = max(freq_speed_allflies);
ax = [-dx/20,xplot(end)+dx/20,0,dy+dy/20];
axis(ax);

% reset xticks
xtick = get(gca,'xtick');
xticklabel = cellstr(get(gca,'xticklabel'));
xticklabel(xtick > xplot(end-1)) = [];
xtick(xtick > xplot(end-1)) = [];
xtick(end+1) = xplot(end);
xticklabel{end+1} = sprintf('> %.1f',edges(end-1));
set(gca,'xtick',xtick,'xticklabel',xticklabel);
xlabel('speed (mm/s)');
ylabel('frequency');
title('histogram of speed for all flies');

axes(hax(2));
semilogy(xplot,freq_speed_perfly,'-','linewidth',.25);
hold on;
h2 = semilogy(xplot,freq_speed_allflies,'k.-','linewidth',5);
% reset xticks
xtick = get(gca,'xtick');
xticklabel = cellstr(get(gca,'xticklabel'));
xticklabel(xtick > xplot(end-1)) = [];
xtick(xtick > xplot(end-1)) = [];
xtick(end+1) = xplot(end);
xticklabel{end+1} = sprintf('> %.1f',edges(end-1));
set(gca,'xtick',xtick,'xticklabel',xticklabel);
ax = [-dx/20,xplot(end)+dx/20,min(freq_speed_perfly(:)),dy+dy/20];
axis(ax);
title('log frequency plot');
xlabel('speed (mm/s)');
legend(h2,'All flies');

axes(hax(3));
loglog(xplot,freq_speed_perfly,'-','linewidth',.25);
hold on;
loglog(xplot,freq_speed_allflies,'k.-','linewidth',5);
% reset xticks
xtick = get(gca,'xtick');
xticklabel = cellstr(get(gca,'xticklabel'));
xticklabel(xtick > xplot(end-1)) = [];
xtick(xtick > xplot(end-1)) = [];
xtick(end+1) = xplot(end);
xticklabel{end+1} = sprintf('> %.1f',edges(end-1));
set(gca,'xtick',xtick,'xticklabel',xticklabel);
ax = [centers(1),xplot(end)+dx/20,min(freq_speed_perfly(:)),dy+dy/20];
axis(ax);
title('log-log frequency plot');
xlabel('speed (mm/s)');

%%histogram change in orientation

figure(4);
clf;
hax = createsubplots(1,3,[.05,.1]);

% compute speed for all flies
speed = [];
for fly = 1:nflies,
  speedcurr = sqrt(modrange(diff(trx(fly).theta),-pi,pi).^2 + ...
    modrange(diff(trx(fly).y_mm),-pi,pi).^2)*trx(fly).fps*180/pi;
  speed = [speed,speedcurr];
end

% choose bins
nbins = max(1,min(100,round(length(speed)/20)));
prctlastbin = 1;
edges = [linspace(0,prctile(speed,100-prctlastbin),nbins),max(speed)];
centers = (edges(1:end-1)+edges(2:end))/2;

% histogram for all flies
counts = histc(speed,edges);
counts(end-1) = counts(end-1) + counts(end);
counts = counts(1:end-1);
freq_angularspeed_allflies = counts / sum(counts);

% do each fly individually
freq_angularspeed_perfly = zeros(nflies,nbins);
for fly = 1:nflies,
  speedcurr = sqrt(modrange(diff(trx(fly).theta),-pi,pi).^2 + ...
    modrange(diff(trx(fly).y_mm),-pi,pi).^2)*trx(fly).fps*180/pi;
  counts = histc(speedcurr,edges);
  counts(end-1) = counts(end-1) + counts(end);
  counts = counts(1:end-1);
  freq_angularspeed_perfly(fly,:) = counts / sum(counts);
end

axes(hax(1));
xplot = centers;
nskip = nbins/10;
xplot(end) = (1+nskip)*centers(end-1)-nskip*centers(end-2);
plot(xplot,freq_angularspeed_perfly,'-','linewidth',.25);
hold on;
plot(xplot,freq_angularspeed_allflies,'k.-','linewidth',5);
dx = xplot(end)-xplot(1);
dy = max(freq_speed_allflies);
ax = [-dx/20,xplot(end)+dx/20,0,dy+dy/20];
axis(ax);

% reset xticks
xtick = get(gca,'xtick');
xticklabel = cellstr(get(gca,'xticklabel'));
xticklabel(xtick > xplot(end-1)) = [];
xtick(xtick > xplot(end-1)) = [];
xtick(end+1) = xplot(end);
xticklabel{end+1} = sprintf('> %.1f',edges(end-1));
set(gca,'xtick',xtick,'xticklabel',xticklabel);
xlabel('angular speed (deg/s)');
ylabel('frequency');
title('histogram of angular speed for all flies');

axes(hax(2));
semilogy(xplot,freq_angularspeed_perfly,'-','linewidth',.25);
hold on;
h2 = semilogy(xplot,freq_angularspeed_allflies,'k.-','linewidth',5);
% reset xticks
xtick = get(gca,'xtick');
xticklabel = cellstr(get(gca,'xticklabel'));
xticklabel(xtick > xplot(end-1)) = [];
xtick(xtick > xplot(end-1)) = [];
xtick(end+1) = xplot(end);
xticklabel{end+1} = sprintf('> %.1f',edges(end-1));
set(gca,'xtick',xtick,'xticklabel',xticklabel);
ax = [-dx/20,xplot(end)+dx/20,min(freq_angularspeed_perfly(:)),dy+dy/20];
axis(ax);
title('log frequency plot');
xlabel('angular speed (deg/s)');
legend(h2,'All flies');

axes(hax(3));
loglog(xplot,freq_angularspeed_perfly,'-','linewidth',.25);
hold on;
loglog(xplot,freq_angularspeed_allflies,'k.-','linewidth',5);
% reset xticks
xtick = get(gca,'xtick');
xticklabel = cellstr(get(gca,'xticklabel'));
xticklabel(xtick > xplot(end-1)) = [];
xtick(xtick > xplot(end-1)) = [];
xtick(end+1) = xplot(end);
xticklabel{end+1} = sprintf('> %.1f',edges(end-1));
set(gca,'xtick',xtick,'xticklabel',xticklabel);
ax = [centers(1),xplot(end)+dx/20,min(freq_angularspeed_perfly(:)),dy+dy/20];
axis(ax);
title('log-log frequency plot');
xlabel('angular speed (deg/s)');

Answer 1

[Walter Roberson]

http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F