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function T_quantal = ComputeRawConeFundamentals(params,staticParams)
b'% T_quantal = ComputeRawConeFundamentals(params,staticParams)'
b'% Function to compute normalized cone quantal sensitivities'
b'% from underlying pieces and parameters.'
b'% In the passed params structure, you can either pass'
b'% the lambdaMax values for the photopigment, in which'
b'% case the absorbance is computed from the specified'
b'% nomogram, or you can pass the absorbance values'
b'% directly in T_xxx format. A typical choice in this'
b'% case would be 10.^T_lgo10coneabsorbance_ss for the'
b'% Stockman-Sharpe/CIE estimates.'
b"% It's not clear that it is necessary to normalize; eventually"
b'% this should probably be changed to provide fundamentals that'
b'% give actual quantal efficiency.'
b'% The typical use of this function is to be called by '
b'% ComputeCIEConeFundamentals, which sets up the'
b'% passed structures acording to the CIE standard. '
b'% This routine, however, could in principle be used'
b'% with a wide variety of choices of the component pieces.'
b'% 8/12/11 dhb Starting to make this actually work.'
b'% 8/14/11 dhb Change name, expand comment.'
b'index = find(params.axialDensity <= 0.0001);'
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params.axialDensity(index) = 0.0001;
b'% Handle optional values'
b"if (~isfield(params,'extraLens'))"
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params.extraLens = 0;
b"if (~isfield(params,'extraMac'))"
b'% Prereceptor transmittance. Sometimes adjustments of peak density'
b'% recommended by various standards push the density less than'
b'% zero at some wavelengths, so we need to make sure we never have'
b'% transmittance greater than 1.'
b'lens = 10.^-(-log10(staticParams.lensTransmittance)+params.extraLens);'
b'mac = 10.^-(-log10(staticParams.macularTransmittance)+params.extraMac);'
b"% Compute nomogram if absorbance wasn't passed directly. We detect"
b'% a direct pass by the existance of params.absorbance.'
b"if (isfield(params,'absorbance'))"
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absorbance = params.absorbance;
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absorbance = PhotopigmentNomogram(staticParams.S,params.lambdaMax,staticParams.whichNomogram);
b'% Handle special case where we deal with ser/ala polymorphism for L cone'
b'if (size(absorbance,1) == 4)'
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absorbtance = AbsorbanceToAbsorbtance(absorbance,staticParams.S,...
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[params.axialDensity(1) ; params.axialDensity(1) ; ...
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params.axialDensity(2) ; params.axialDensity(3)]);
b'elseif (size(absorbance,1) == 3)'
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absorbtance = AbsorbanceToAbsorbtance(absorbance,staticParams.S,...
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[params.axialDensity(1) ; params.axialDensity(2) ; ...
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params.axialDensity(3)]);
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error('Unexpected number of photopigment lambda max values passed');
b'%% Put together pre-receptor and receptor parts'
b'for i = 1:size(absorbtance,1)'
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absorbtance(i,:) = absorbtance(i,:) .* lens .* mac;
b'% Put it into the right form'
b'T_quantal = zeros(3,staticParams.S(3));'
b'if (size(absorbtance,1) == 4)'
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T_quantal(1,:) = staticParams.LserWeight*absorbtance(1,:) + ...
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(1-staticParams.LserWeight)*absorbtance(2,:);
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T_quantal(2,:) = absorbtance(3,:);
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T_quantal(3,:) = absorbtance(4,:);
b'elseif (size(absorbtance,1) == 3)'
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T_quantal(1,:) = absorbtance(1,:);
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T_quantal(2,:) = absorbtance(2,:);
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T_quantal(3,:) = absorbtance(3,:);
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error('Unexpected number of photopigment lambda max values passed');
b'% Normalize to max of one for each receptor'
b'for i = 1:size(T_quantal,1)'
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T_quantal(i,:) = T_quantal(i,:)/max(T_quantal(i,:));
b'\\ No newline at end of file'
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function [T_quantalAbsorptionsNormalized,T_quantalAbsorptions,T_quantalIsomerizations] = ComputeRawConeFundamentals(params,staticParams)
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% [T_quantalAbsorptionsNormalized,T_quantalAbsorptions,T_quantalIsomerizations] = ComputeRawConeFundamentals(params,staticParams)
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% Function to compute normalized cone quantal sensitivities
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% from underlying pieces and parameters.
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% Note that this routine returns quantal sensitivities. You
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% may want energy sensitivities. In that case, use EnergyToQuanta to convert
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% T_energy = EnergyToQuanta(S,T_quantal')'
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% and then renormalize. (You call EnergyToQuanta because you're converting
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% sensitivities, which go the opposite directoin from spectra.)
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% The routine also returns two quantal sensitivity functions. The first gives
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% the probability that a photon will be absorbed. The second is the probability
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% that the photon will cause a photopigment isomerization. It is the latter
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% that is what you want to compute isomerization rates from retinal illuminance.
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% See note at the end of function FillInPhotoreceptors for some information about
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% convention. In particular, this routine takes pre-retinal absorption into
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% account in its computation of probability of absorptions and isomerizations,
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% so that the relevant retinal illuminant is one computed without accounting for
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% those factors. This routine does not account for light attenuation due to
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% the pupil, however. The only use of pupil size here is becuase of its
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% slight effect on lens density as accounted for in the CIE standard.
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% In the passed params structure, you can either pass
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% the lambdaMax values for the photopigment, in which
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% case the absorbance is computed from the specified
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% nomogram, or you can pass the absorbance values
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% directly in T_xxx format. A typical choice in this
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% case would be 10.^T_lgo10coneabsorbance_ss for the
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% Stockman-Sharpe/CIE estimates.
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% The typical use of this function is to be called by
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% ComputeCIEConeFundamentals, which sets up the
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% passed structures acording to the CIE standard.
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% This routine, however, could in principle be used
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% with a wide variety of choices of the component pieces.
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% The other place this function is used is in attempts to
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% fit a set of cone fundamentals by doing parameter search
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% over the pieces. It is this second use that led to the
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% parameters being split over two separate structures, one
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% that is held static during the fit and the other which
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% contains the parameters that could be searched over by a calling
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% routine. For examples, see:
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% FitConeFundamentalsWithNomogram, FitConeFundamentalsTest.
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% Looking around today (8/10/13), I (DHB) don't see any examples where
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% this routine is called directly. Rather, it is a subfunction
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% called by ComputeCIEConeFundamentals. The search routines above
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% use ComputeCIEConeFundamentals, and only search over lambdaMax
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% values. I think I wrote this with the thought that I might one
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% day search over more parameters, but lost motivation to carry it
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% The computations done here are very similar to those done in
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% routine FillInPhotoreceptors. I (DHB) think that I forgot about
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% what FillInPhotoreceptors could do when I wrote this, which has
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% led to some redundancy. FillInPhotoreceptors returns a field
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% called effectiveAbsorbtance, which are the actual quantal efficiencies
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% (not normalized) referred to the cornea. FillInPhotoceptors also
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% computes a field isomerizationAbsorbtance, which takes the quantal
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% efficiency of isomerizations (probability of an isomerization given
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% an absorption into acount. This routine does not do that.
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% It would probably be clever to unify the two sets of routines a
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% little more, but we may never get to it. The routine ComputeCIEConeFundamentals
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% does contain a check that this routine and what is returned by FillInPhotoreceptors
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% agree with each other, for cases where the parameters match.
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% See also: ComputeCIEConeFundamentals, CIEConeFundamentalsTest, FitConeFundamentalsWithNomogram,
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% FitConeFundamentalsTest, DefaultPhotoreceptors, FillInPhotoreceptors.
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% 8/12/11 dhb Starting to make this actually work.
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% 8/14/11 dhb Change name, expand comments.
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% 8/10/13 dhb Expand comments. Return unscaled quantal efficiencies too.
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index = find(params.axialDensity <= 0.0001);
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params.axialDensity(index) = 0.0001;
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% Handle optional values
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if (~isfield(params,'extraLens'))
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params.extraLens = 0;
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if (~isfield(params,'extraMac'))
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% Prereceptor transmittance. Sometimes adjustments of peak density
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% recommended by various standards push the density less than
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% zero at some wavelengths, so we need to make sure we never have
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% transmittance greater than 1.
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lens = 10.^-(-log10(staticParams.lensTransmittance)+params.extraLens);
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mac = 10.^-(-log10(staticParams.macularTransmittance)+params.extraMac);
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% Compute nomogram if absorbance wasn't passed directly. We detect
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% a direct pass by the existance of params.absorbance.
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if (isfield(params,'absorbance'))
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absorbance = params.absorbance;
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absorbance = PhotopigmentNomogram(staticParams.S,params.lambdaMax,staticParams.whichNomogram);
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% Compute absorbtance
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% Handle special case where we deal with ser/ala polymorphism for L cone
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if (size(absorbance,1) == 4)
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absorbtance = AbsorbanceToAbsorbtance(absorbance,staticParams.S,...
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[params.axialDensity(1) ; params.axialDensity(1) ; ...
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params.axialDensity(2) ; params.axialDensity(3)]);
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elseif (size(absorbance,1) == 3)
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absorbtance = AbsorbanceToAbsorbtance(absorbance,staticParams.S,...
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[params.axialDensity(1) ; params.axialDensity(2) ; ...
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params.axialDensity(3)]);
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elseif (size(absorbance,1) == 1 && params.DORODS)
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absorbtance = AbsorbanceToAbsorbtance(absorbance,staticParams.S,...
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params.axialDensity(1));
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error('Unexpected number of photopigment lambda max values passed');
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%% Put together pre-receptor and receptor parts
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for i = 1:size(absorbtance,1)
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absorbtance(i,:) = absorbtance(i,:) .* lens .* mac;
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%% Put it into the right form
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if (size(absorbtance,1) == 4)
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T_quantalAbsorptions = zeros(3,staticParams.S(3));
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T_quantalAbsorptions(1,:) = staticParams.LserWeight*absorbtance(1,:) + ...
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(1-staticParams.LserWeight)*absorbtance(2,:);
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T_quantalAbsorptions(2,:) = absorbtance(3,:);
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T_quantalAbsorptions(3,:) = absorbtance(4,:);
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elseif (size(absorbtance,1) == 3)
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T_quantalAbsorptions = zeros(3,staticParams.S(3));
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T_quantalAbsorptions(1,:) = absorbtance(1,:);
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T_quantalAbsorptions(2,:) = absorbtance(2,:);
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T_quantalAbsorptions(3,:) = absorbtance(3,:);
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elseif (size(absorbtance,1) == 1 && params.DORODS)
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T_quantalAbsorptions = zeros(1,staticParams.S(3));
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T_quantalAbsorptions(1,:) = absorbtance(1,:);
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error('Unexpected number of photopigment lambda max values passed');
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%% Normalize to max of one for each receptor, and also compute isomerization quantal efficiency.
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for i = 1:size(T_quantalAbsorptions,1)
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T_quantalIsomerizations = T_quantalAbsorptions*staticParams.quantalEfficiency(i);
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T_quantalAbsorptionsNormalized(i,:) = T_quantalAbsorptions(i,:)/max(T_quantalAbsorptions(i,:));
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Psychtoolbox/PsychColorimetricData/ComputeRawConeFundamentals.m
