Absorptions Code - Revision history

imported>Student2016 at 13:06, 16 December 2016

2016-12-16T13:06:54Z

imported>Student2016 at 12:59, 16 December 2016

2016-12-16T12:59:34Z

← Older revision		Revision as of 12:59, 16 December 2016
Line 33:		Line 33:
	% Change entries that are common to uniform and harmonic		% Change entries that are common to uniform and harmonic

	clear params		clear params

	for ii=2:-1:1		for ii=2:-1:1
	params(ii) = harmonicP;		params(ii) = harmonicP;
	params(ii).GaborFlag = 0.15;		params(ii).GaborFlag = 0.15;
	params(ii).freq = 30;		params(ii).freq = 30;
	end		end

	% params(1) is for the uniform field		% params(1) is for the uniform field

imported>Student2016 at 12:58, 16 December 2016

2016-12-16T12:58:51Z

← Older revision		Revision as of 12:58, 16 December 2016
Line 19:		Line 19:
	% Gaussian onset and offset of the grating		% Gaussian onset and offset of the grating

	tSeries = ieScale(fspecial('gaussian',[1,100],10),0,1);		tSeries = ieScale(fspecial('gaussian',[1,100],10),0,1);

	%		%

imported>Student2016 at 12:57, 16 December 2016

2016-12-16T12:57:40Z

← Older revision		Revision as of 12:57, 16 December 2016
Line 34:		Line 34:

	clear params		clear params

	for ii=2:-1:1		for ii=2:-1:1
	params(ii) = harmonicP;		params(ii) = harmonicP;

imported>Student2016 at 12:57, 16 December 2016

2016-12-16T12:57:20Z

Show changes

imported>Student2016 at 12:53, 16 December 2016

2016-12-16T12:53:37Z

← Older revision		Revision as of 12:53, 16 December 2016
Line 18:		Line 18:

	% Gaussian onset and offset of the grating		% Gaussian onset and offset of the grating

	tSeries = ieScale(fspecial('gaussian',[1,100],10),0,1);		tSeries = ieScale(fspecial('gaussian',[1,100],10),0,1);

	%		%
	% Have a look at the stimulus amplitude time series		% Have a look at the stimulus amplitude time series
Line 24:		Line 26:

	% This is the field of view of the scene.		% This is the field of view of the scene.

	sparams.fov = 0.5;		sparams.fov = 0.5;
	sparams.meanluminance = 200;		sparams.meanluminance = 200;
Line 29:		Line 32:
	% Initialize the harmonic parameters structure with default		% Initialize the harmonic parameters structure with default
	% Change entries that are common to uniform and harmonic		% Change entries that are common to uniform and harmonic

	clear params		clear params
	for ii=2:-1:1		for ii=2:-1:1
Line 37:		Line 41:

	% params(1) is for the uniform field		% params(1) is for the uniform field

	params(1).contrast = 0.5; % contrast of the two frequencies		params(1).contrast = 0.5; % contrast of the two frequencies

	% params(2) is matched and describes the grating		% params(2) is matched and describes the grating

	params(2).contrast = 0.4;		params(2).contrast = 0.4;

Line 45:		Line 51:

	% The call to create the optical image sequence		% The call to create the optical image sequence

	oisH = oisCreate('harmonic','blend',tSeries(len/2:len/2+1),'testParameters',params,'sceneParameters',sparams);		oisH = oisCreate('harmonic','blend',tSeries(len/2:len/2+1),'testParameters',params,'sceneParameters',sparams);

	% Have a look, though the code here is not that great yet so the look is		% Have a look, though the code here is not that great yet so the look is
	% only approximate.		% only approximate.

	oisH.visualize;		oisH.visualize;

imported>Student2016 at 12:52, 16 December 2016

2016-12-16T12:52:43Z

← Older revision		Revision as of 12:52, 16 December 2016
Line 8:		Line 8:

	%% Init Parameters		%% Init Parameters

	ieInit;		ieInit;

imported>Student2016: Created page with '%% Create harmonic sequences % % Make the images of harmonics % Compute the cone mosaic responses and photocurrent responses % Show how to control eye movements % % %% Init…'

2016-12-16T12:51:34Z

Created page with '%% Create harmonic sequences % % Make the images of harmonics % Compute the cone mosaic responses and photocurrent responses % Show how to control eye movements % % %% Init…'

New page

%% Create harmonic sequences
%
% Make the images of harmonics
% Compute the cone mosaic responses and photocurrent responses
% Show how to control eye movements
%
%

%% Init Parameters
ieInit;

%% Here is a new function: oisCreate

% We are going to mix a grating (harmonic) with a uniform background.
% These are the relative weights of the grating and background.
% Set up the timing

% Gaussian onset and offset of the grating
tSeries = ieScale(fspecial('gaussian',[1,100],10),0,1);
%
% Have a look at the stimulus amplitude time series
% vcNewGraphWin; plot(stimWeights);

% This is the field of view of the scene.
sparams.fov = 0.5;
sparams.meanluminance = 200;

% Initialize the harmonic parameters structure with default
% Change entries that are common to uniform and harmonic
clear params
for ii=2:-1:1
params(ii) = harmonicP;
params(ii).GaborFlag = 0.15;
params(ii).freq = 30;
end

% params(1) is for the uniform field
params(1).contrast = 0.5; % contrast of the two frequencies

% params(2) is matched and describes the grating
params(2).contrast = 0.4;

len = length(tSeries);

% The call to create the optical image sequence
oisH = oisCreate('harmonic','blend',tSeries(len/2:len/2+1),'testParameters',params,'sceneParameters',sparams);

% Have a look, though the code here is not that great yet so the look is
% only approximate.
oisH.visualize;

% oisH.timeStep

%% Now, make the cone mosaic and compute absorptions and current

fov = oiGet(oisH.oiFixed,'fov');
emSamples = oisH.length;

cMosaic = coneMosaic;
% cMosaic.noiseFlag = true;
cMosaic.integrationTime = 0.001;
cMosaic.setSizeToFOV(0.5*fov);

% The number of eye movement samples should extend as long as the oisH
% So these should be equal
%
% tSamples * cMosaic.integrationTime = oisH.length*oisH.timeStep
%
%
tSamples = floor(oisH.length*oisH.timeStep/cMosaic.integrationTime);
cMosaic.emGenSequence(tSamples);

% Compute and then look
cMosaic.compute(oisH);
cMosaic.window;

fprintf('Spatial frequency %.1f cpd\n',params(ii).freq/sparams.fov);

%% Create the current with and without noise

% cMosaic.os.noiseFlag = true;
cMosaic.computeCurrent;
cMosaic.window;

%% Compute and look at the current
% cMosaic.os.noiseFlag = false;
cMosaic.computeCurrent;
cMosaic.window;

%% How to adjust the eye movement parameters
% create simple sinusoidal eye movement
emF = 3; emA = 3;
x = round(emA*sin(2*pi*emF*(1:tSamples)/tSamples));
y = zeros(size(x(:)));
cMosaic.emPositions = [x(:),y(:)];
[abs_move, curr_move] = cMosaic.compute(oisH,'currentFlag',true);
abs_move = squeeze(abs_move);
curr_move = squeeze(curr_move);
movement_pos = cMosaic.emPositions;

cMosaic.plot('eye movement path'); % How did we do?
set(gca,'xlim',[-15 15],'ylim',[-15 15]);

% no tremor
em_noMove = emCreate; % Create an eye movement object
em_noMove.emFlag = [0 0 0]; % Make sure tremor, draft and saccade are all on
em_noMove.tremor.amplitude = 0.02; % Set the big amplitude
cMosaic.emGenSequence(tSamples,'em',em_noMove); % Generate the sequence
[abs_noMove, curr_noMove] = cMosaic.compute(oisH,'currentFlag',true);
abs_noMove = squeeze(abs_noMove);
curr_noMove = squeeze(curr_noMove);
noMove_pos = cMosaic.emPositions;

cMosaic.plot('eye movement path'); % How did we do?
set(gca,'xlim',[-15 15],'ylim',[-15 15]);
%% plot movement
figure;
hold on;
plot(1:length(movement_pos),movement_pos,'b');
plot(1:length(noMove_pos),noMove_pos,'r');
hold off;
title('eye movement over time');
xlabel('time (ms)');
ylabel('distance (cone width)');

%% check to see if absorptions were actually computed differently
% t = 1:size(abs_move,3);
% plot(t,squeeze(abs_noMove(45,45,:)),t,squeeze(abs_move(45,45,:)));

%% absorption level comparison
H = sum(abs_move,3)./sum(abs_noMove,3);
figure();
imagesc(H);
colorbar;
title('Ratio of total absorptions (with mvmnt / without mvmnt)');
% figure();
% imagesc(sum(abs_noMove,3));
avg_ratio = sum(sum(H))/numel(H)

%% Separate cone types
% calculate absorption sums for R,G,B cones
red_indices = find(cMosaic.pattern == 2);
green_indices = find(cMosaic.pattern == 3);
blue_indices = find(cMosaic.pattern == 4);

avg_ratio_red = sum(sum(H(red_indices)))/numel(H(red_indices));
avg_ratio_blue = sum(sum(H(blue_indices)))/numel(H(blue_indices));
avg_ratio_green = sum(sum(H(green_indices)))/numel(H(green_indices));

ratios = [avg_ratio_red avg_ratio_green avg_ratio_blue];
figure();
C = categorical(ratios,ratios,{'L','M','S'});
h = histogram(C,'BarWidth',0.5);
set(gca,'ylim',[0 1.2]);
title('Ratio of absorption total absorptions by cone type');

% figure();
% subplot(3,1,1);
% plot(1:length(red_indices),H(red_indices));
% subplot(3,1,2);
% plot(1:length(green_indices),H(green_indices));
% subplot(3,1,3);
% plot(1:length(blue_indices),H(blue_indices));