Photocurrent Code - Revision history

imported>Student2016 at 11:31, 16 December 2016

2016-12-16T11:31:03Z

← Older revision		Revision as of 11:31, 16 December 2016
Line 90:		Line 90:
	coneSpectrum_withMovements = Spectra_withMovements(row,col,:);		coneSpectrum_withMovements = Spectra_withMovements(row,col,:);
	avgredConesAmp = avgredConesAmp + squeeze(coneSpectrum_withMovements./coneSpectrum_noMovements);		avgredConesAmp = avgredConesAmp + squeeze(coneSpectrum_withMovements./coneSpectrum_noMovements);
	~~avgredConesAmp = avgredConesAmp./length(redCones);~~
	end		end
			avgredConesAmp = avgredConesAmp./length(redCones);
	plot((0:tSamples/2-1)./0.128,squeeze(avgredConesAmp(1:64)));		plot((0:tSamples/2-1)./0.128,squeeze(avgredConesAmp(1:64)));
	end;		end;

imported>Student2016 at 11:13, 16 December 2016

2016-12-16T11:13:20Z

← Older revision		Revision as of 11:13, 16 December 2016
Line 90:		Line 90:
	coneSpectrum_withMovements = Spectra_withMovements(row,col,:);		coneSpectrum_withMovements = Spectra_withMovements(row,col,:);
	avgredConesAmp = avgredConesAmp + squeeze(coneSpectrum_withMovements./coneSpectrum_noMovements);		avgredConesAmp = avgredConesAmp + squeeze(coneSpectrum_withMovements./coneSpectrum_noMovements);
			avgredConesAmp = avgredConesAmp./length(redCones);
	end		end
	plot((0:tSamples/2-1)./0.128,squeeze(avgredConesAmp(1:64)));		plot((0:tSamples/2-1)./0.128,squeeze(avgredConesAmp(1:64)));

imported>Student2016 at 11:03, 16 December 2016

2016-12-16T11:03:09Z

← Older revision		Revision as of 11:03, 16 December 2016
Line 4:		Line 4:
	% changed to test different factors for eye movements.		% changed to test different factors for eye movements.

	%
	ieInit;		ieInit;

Line 23:		Line 22:
	fft_bin2_vals = zeros(10,1);		fft_bin2_vals = zeros(10,1);

	figure		figure;
	hold on		hold on;
	for a = 1:length(freq)		for a = 1:length(freq)

Line 92:		Line 91:
	avgredConesAmp = avgredConesAmp + squeeze(coneSpectrum_withMovements./coneSpectrum_noMovements);		avgredConesAmp = avgredConesAmp + squeeze(coneSpectrum_withMovements./coneSpectrum_noMovements);
	end		end
	plot((0:tSamples/2-1)./0.128,squeeze(avgredConesAmp(1:64)))		plot((0:tSamples/2-1)./0.128,squeeze(avgredConesAmp(1:64)));
	end		end;
	hold off		hold off;
	xlabel('Temporal Frequency (Hz)');		xlabel('Temporal Frequency (Hz)');
	ylabel('Ratio (EM to no EM)');		ylabel('Ratio (EM to no EM)');
	title('Ratios for Red Cones');		title('Ratios for Red Cones');
	legend('1 cpd','13.25 cpd','25.5 cpd','37.75 cpd','50 cpd');		legend('1 cpd','13.25 cpd','25.5 cpd','37.75 cpd','50 cpd');

imported>Student2016 at 11:02, 16 December 2016

2016-12-16T11:02:08Z

← Older revision		Revision as of 11:02, 16 December 2016
Line 71:		Line 71:
	cMosaic.emPositions = [x(:),y(:)];		cMosaic.emPositions = [x(:),y(:)];
	cMosaic.name = 'Horizontal em';		cMosaic.name = 'Horizontal em';
	~~% cMosaic.plot('eye movement path');~~
	cMosaic.compute(oisH);		cMosaic.compute(oisH);
	cMosaic.computeCurrent;		cMosaic.computeCurrent;
	~~% vcNewGraphWin;~~
	~~% cMosaic.window;~~

	deMeanedMosaic = bsxfun(@minus,cMosaic.current,mean(cMosaic.current,3));		deMeanedMosaic = bsxfun(@minus,cMosaic.current,mean(cMosaic.current,3));

imported>Student2016 at 11:01, 16 December 2016

2016-12-16T11:01:22Z

← Older revision		Revision as of 11:01, 16 December 2016
Line 44:		Line 44:
	% The call to create the retinal image sequence		% The call to create the retinal image sequence
	oisH = oisCreate('harmonic','blend',weights,'testParameters',params,'sceneParameters',sparams);		oisH = oisCreate('harmonic','blend',weights,'testParameters',params,'sceneParameters',sparams);
	~~% oisH.visualize;~~
	fov = oiGet(oisH.oiFixed,'fov');		fov = oiGet(oisH.oiFixed,'fov');
	~~% tSamples = oisH.length;~~
	tSamples = 128;		tSamples = 128;

imported>Student2016 at 11:00, 16 December 2016

2016-12-16T11:00:56Z

← Older revision		Revision as of 11:00, 16 December 2016
Line 4:		Line 4:
	% changed to test different factors for eye movements.		% changed to test different factors for eye movements.

	%%		%
	ieInit;		ieInit;

	%% Initialize parameters		% Initialize parameters

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

imported>Student2016: Created page with '%% This script sets up a gaussian grating that is constant over the simulation, % then loops over an array of spatial frequencies to find various results % such as photocurrent…'

2016-12-16T10:59:51Z

Created page with '%% This script sets up a gaussian grating that is constant over the simulation, % then loops over an array of spatial frequencies to find various results % such as photocurrent…'

New page

%% This script sets up a gaussian grating that is constant over the simulation,
% then loops over an array of spatial frequencies to find various results
% such as photocurrent spectra and amplification. Parameters can be
% changed to test different factors for eye movements.

%%
ieInit;

%% Initialize parameters

% Gaussian onset and offset of the grating
stimWeights = ieScale(fspecial('gaussian',[1,50],15),0,1);
% Padded by zeroes
weights = [zeros(1, 30), stimWeights, zeros(1, 30)];

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

% Initialize the harmonic parameters structure with default
% Change entries that are common to uniform and harmonic
freq = linspace(1,50,5);
ratios = zeros(3,1);
fft_bin2_vals = zeros(10,1);

figure
hold on
for a = 1:length(freq)

clear params
for ii=2:-1:1
params(ii) = harmonicP;
params(ii).GaborFlag = 0.2;
params(ii).freq = freq(a);
params(ii).row = 256;
params(ii).col = 256;
end

% params(1) is for the uniform field
params(1).contrast = 1.0; % contrast of the two frequencies

% params(2) is matched and describes the grating
params(2).contrast = 1.0;

% The call to create the retinal image sequence
oisH = oisCreate('harmonic','blend',weights,'testParameters',params,'sceneParameters',sparams);
% oisH.visualize;
fov = oiGet(oisH.oiFixed,'fov');
% tSamples = oisH.length;
tSamples = 128;

cMosaic = coneMosaic;
cMosaic.integrationTime = 0.001;
cMosaic.setSizeToFOV(fov);
cMosaic.os.noiseFlag = 'none';

% create em object without movement
em_noMovement = emCreate; % Create an eye movement object
em_noMovement.emFlag = [0 0 0]; % Make sure tremor, draft and saccade are all off
cMosaic.emGenSequence(tSamples,'em',em_noMovement); % Generate the sequence

cMosaic.compute(oisH);
cMosaic.computeCurrent;

deMeanedMosaic = bsxfun(@minus,cMosaic.current,mean(cMosaic.current,3));

Spectra_noMovements = abs(fft(deMeanedMosaic,128,3));
avgSpectrum_noMovements = squeeze(sum(sum(Spectra_noMovements)))./93^2;

% create em object with movement
emF = 1; emA = 93/30;
x = round(emA*sin(2*pi*emF*(1:tSamples)/tSamples));
y = zeros(size(x(:)));
cMosaic.emPositions = [x(:),y(:)];
cMosaic.name = 'Horizontal em';
% cMosaic.plot('eye movement path');
cMosaic.compute(oisH);
cMosaic.computeCurrent;
% vcNewGraphWin;
% cMosaic.window;

deMeanedMosaic = bsxfun(@minus,cMosaic.current,mean(cMosaic.current,3));
Spectra_withMovements = abs(fft(deMeanedMosaic,128,3));
avgSpectrum_withMovements = squeeze(sum(sum(Spectra_withMovements)))./93^2;

avgSpectraAmp = sum(sum(Spectra_withMovements./Spectra_noMovements))./93^2;
redCones = find(cMosaic.pattern == 3);
avgredConesAmp = zeros(128,1);
for i = 1:length(redCones)
col = ceil(redCones(i)/93);
row = mod(redCones(i),93);
if row == 0
row = 93;
end
coneSpectrum_noMovements = Spectra_noMovements(row,col,:);
coneSpectrum_withMovements = Spectra_withMovements(row,col,:);
avgredConesAmp = avgredConesAmp + squeeze(coneSpectrum_withMovements./coneSpectrum_noMovements);
end
plot((0:tSamples/2-1)./0.128,squeeze(avgredConesAmp(1:64)))
end
hold off
xlabel('Temporal Frequency (Hz)');
ylabel('Ratio (EM to no EM)');
title('Ratios for Red Cones');
legend('1 cpd','13.25 cpd','25.5 cpd','37.75 cpd','50 cpd');