/usr/share/psychtoolbox-3/PsychDemos/IsomerizationsInDishDemo.m is in psychtoolbox-3-common 3.0.11.20140816.dfsg1-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 | % IsomerizationsInDishDemo
%
% Shows how to compute photoreceptor isomerizations using toolbox
% routines. These calculations are for a retinal preparation
% that consists of a retina in a dish and thus do not include
% any preretinal absorption. Parameters are set up for a
% Guinea Pig retina. The file spd_apparatusrel.mat contains
% the relative spectrum of the light with respect to which
% the computation is accomplished.
%
% NOTE, DHB, 7/19/13. This demo routine and its associated data routines
% (DefaultPhotoreceptors, FillInPhotoreceptors, PrintPhotoreceptors)
% should be better integrated with the more recent code that
% implements the CIE physiological cone fundamentals, and the
% whole set of stuff should be better documented. See also
% IsomerizationsInDishDemo
% CIEConeFundamentalsTest
% ComputeCIEConeFundamentals
% ComputeRawConeFundamentals
% DefaultPhotoreceptors
% FillInPhotoreceptors
% PrintPhotoreceptors
% RetIrradianceToIsoRecSec
% In particular, there should be some default for the
% photoreceptors structure that gives one the CIE cone
% fundamentals in all their parametric glory, plus additional
% parameters that yield real energy/quantal sensitivites so
% that the resulting coordinates are isomerization rates in
% real units. I think that we're close to having that, but
% better documentation and tidying is needed.
%
% 05/06/03 lyin Wrote it.
% 06/26/03 dhb Rewrote to be self-contained, plus new calling conventions.
% 07/10/03 dhb Various tuning.
% 07/11/03 dhb Grab data through subroutines. Get rid of integration time.
% 04/2/13 dhb Change clear all to clear, and close figs.
% 04/27/13 dhb Improve comments.
% 7/19/13 dhb Print out photoreceptors structure using PrintPhotoreceptors.
% 8/11/13 dhb Protect against case when absorbance is provided directly.
%% clear
clear; close all;
%% Set photoreceptor properties.
%
% The photoreceptors structure gets filled with
% key parameters values (pupil size, eye length,
% pre-retinal absorbance, etc.)
%
% The routine DefaultPhotoreceptors is a high level
% call. It fills in the 'source' fields and some
% values according to high-level descriptor (e.g.,
% ('GuineaPig'). See help for that routine
% for available options.
%
% The routine FillInPhotoreceptors fetches the actual
% values for various fields, depending on the source.
%
% To get a feel for this, check what is in the photoreceptors
% structure after the first call, and then after the second.
photoreceptors = DefaultPhotoreceptors('GuineaPig');
photoreceptors = FillInPhotoreceptors(photoreceptors);
%% Define common wavelength sampling for this script.
%
% S is [start delta nsamples] for the wavelengths in nm.
% This is standard PTB convention.
S = photoreceptors.nomogram.S;
%% Computation of light spectrum. This is based on how Lu Yin
% calibrates the irradiance in his apparatus, but the code
% following just needs the incident irradiance in quanta/[sec-um2-wlinterval].
%
% First the relative spectrum of the light is measured using the CVI
% spectral radiometer. Then the absolute power of the light is measured
% using a broadband radiometer that measures total power in watts. The
% radiometer receives the light through a pinhole of known size. With this
% information, we can get incident power in watts/um^2-wlinterval.
% Routine WattsToRetIrradiance does the conversion, taking into account
% instrument calibration information as well as the relative spectrum,
% which here we just load.
load spd_apparatusrel % Relative spectrum measured in apparatus
readingInWatts = 0.0128e-6 ; % Watts (0.0128 uWatts)
[irradianceWatts,irradianceS] = WattsToRetIrradiance( ...
spd_apparatusrel,S_apparatusrel,readingInWatts);
irradianceQuanta = EnergyToQuanta(irradianceS,irradianceWatts);
figure(1); clf; set(gcf,'Position',[100 400 700 300]);
subplot(1,2,1); hold on
set(plot(SToWls(irradianceS),irradianceQuanta,'r'),'LineWidth',2);
set(title('Light Spectrum'),'FontSize',14);
set(xlabel('Wavelength (nm)'),'FontSize',12);
set(ylabel('Quanta/sec-um^2-wlinterval'),'FontSize',12);
%% Do the work in toolbox function. See help text there
% for details.
[isoPerConeSec,absPerConeSec,photoreceptors] = ...
RetIrradianceToIsoRecSec(irradianceWatts,S,photoreceptors);
%% Make a plot showing the effective photoreceptor sensitivities in quantal
% units, expressed as probability of absorption.
subplot(1,2,2); hold on
set(plot(SToWls(S),photoreceptors.effectiveAbsorptance(1,:),'g'),'LineWidth',2);
set(plot(SToWls(S),photoreceptors.effectiveAbsorptance(2,:),'b'),'LineWidth',2);
set(plot(SToWls(S),photoreceptors.effectiveAbsorptance(3,:),'k'),'LineWidth',2);
set(title('Effective Absorptance'),'FontSize',14);
set(xlabel('Wavelength (nm)'),'FontSize',12);
set(ylabel('Probability'),'FontSize',12);
axis([300 800 0 1]);
%% Print out photoreceptors structure
fprintf('\n');
PrintPhotoreceptors(photoreceptors);
fprintf('\n');
%% Print out a table summarizing the calculation.
fprintf('***********************************************\n');
fprintf('Isomerization calculations for retina in a dish\n');
fprintf('\n');
fprintf('Photoreceptor Type |\t M\t S\t Rod\n');
fprintf('______________________________________________________________________________________\n');
fprintf('\n');
if (isfield(photoreceptors.nomogram,'lambdaMax'))
fprintf('Lambda max |\t%8.1f\t%8.1f\t%8.1f\t nm\n',photoreceptors.nomogram.lambdaMax);
end
fprintf('Outer Segment Length |\t%8.1f\t%8.1f\t%8.1f\t um\n',photoreceptors.OSlength.value);
fprintf('Outer Segment Diameter |\t%8.1f\t%8.1f\t%8.1f\t um\n',photoreceptors.OSdiameter.value);
fprintf('Inner Segment Diameter |\t%8.1f\t%8.1f\t%8.1f\t um\n',photoreceptors.ISdiameter.value);
fprintf('\n');
fprintf('Axial Specific Density |\t%8.3f\t%8.3f\t%8.3f\t /um\n',photoreceptors.specificDensity.value);
fprintf('Axial Optical Density |\t%8.3f\t%8.3f\t%8.3f\n',photoreceptors.axialDensity.value);
fprintf('Peak isomerization prob. |\t%8.3f\t%8.3f\t%8.3f\n',max(photoreceptors.isomerizationAbsorptance,[],2));
fprintf('______________________________________________________________________________________\n');
fprintf('\n');
fprintf('Absorption Rate |\t%4.2e\t%4.2e\t%4.2e\t quanta/photoreceptor-sec\n',...
absPerConeSec);
fprintf('Isomerization Efficiency |\t%8.3f\t%8.3f\t%8.3f\n',...
photoreceptors.quantalEfficiency.value);
fprintf('Isomerization Rate |\t%4.2e\t%4.2e\t%4.2e\t iso/photoreceptor-sec\n',...
isoPerConeSec);
fprintf('In log10 units |\t%8.2f\t%8.2f\t%8.2f\t log10(iso)/photoreceptor-sec\n',...
log10(isoPerConeSec));
fprintf('______________________________________________________________________________________\n');
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