MAP

if nargin<2, sampleRate=44100; end

OMEParams.OMEstapesHPcutoff= 1000;

OMEParams.rateToAttenuationFactor=0.05; % * N(all ICspikes)

OMEParams.rateToAttenuationFactorProb=0.02;    % * N(all ANrates)

DRNLParams.a=2e4;       % DRNL.a=0 means no OHCs (no nonlinear path)

DRNLParams.ctBMdB = 10; %Compression threshold dB re 10e-9 m displacement

DRNLParams.p=0.2895;   DRNLParams.q=250;   % save p and q for printing only

% p=0.2895;   q=250;      % human  (% p=0.14;   q=366;  % cat)

DRNLParams.nlBWs=  DRNLParams.p * BFlist + DRNLParams.q;

DRNLParams.g=100;       % linear path gain factor

DRNLParams.minMOCattenuationdB=-35;

DRNLParams.MOCtau =.0285;                         % smoothing for MOC

DRNLParams.rateToAttenuationFactor = .03;  % strength of MOC

DRNLParams.rateToAttenuationFactor = .0055;  % strength of MOC

% 'probability' model: MOC based on AN probability (HSR)

DRNLParams.rateToAttenuationFactorProb = 0.007;  % strength of MOC

DRNLParams.MOCrateThresholdProb =67;                % spikes/s probability only

IHC_cilia_RPParams.tc=	0.00012;   % 0.0003 Shamma

IHC_cilia_RPParams.C=	0.08;       % 0.1 scalar (C_cilia ) 

LSRtauCa=30e-6;            HSRtauCa=80e-6;            % seconds

% LSRtauCa=40e-6;            HSRtauCa=90e-6;            % seconds

AN_IHCsynapseParams.spikesTargetSampleRate=10000;

% AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes.

        MacGregorMultiParams.currentPerSpike=28e-9; % *per spike

% identify periodicities to be logged

    minPitch=	80; maxPitch=	500; numPitches=50;  

    maxLag=1/minPitch; minLag=1/maxPitch;

    lags= linspace(minLag, maxLag, numPitches);

    pitches=10.^ linspace(log10(minPitch), log10(maxPitch),numPitches);

    pitches=fliplr(pitches);

    % convert to lags for ACF

    filteredSACFParams.lags=lags;     % autocorrelation lags vector

    filteredSACFParams.acfTau=	.003;       % time constant of running ACF

    filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF

    % request plot of within-channel ACFs at fixed intervals in time

    filteredSACFParams.plotACFs=1;          

    filteredSACFParams.plotACFsInterval=0.002;

    filteredSACFParams.plotMoviePauses=.1;  

    filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags

    filteredSACFParams.lagsProcedure=  'useAllLags';

    %  'useAllLags' or 'omitShortLags'

    filteredSACFParams.criterionForOmittingLags=3;

        error('paramChanges error: paramChanges not a cell array')

function method=MAPparamsOHCloss ...

    (BFlist, sampleRate, showParams, paramChanges)

% MAPparamsOHCloss.m is a parameter file, similar in all respects to

% MAPparamsNormal except that the parameter 'DRNLParams.a' is set to zero.

%

% MAPparams<> establishes a complete set of MAP parameters

% Parameter file names must be of the form <MAPparams><name>

%

% Input arguments

%  BFlist     (optional) specifies the desired list of channel BFs

%    otherwise defaults set below

%  sampleRate (optional), default is 50000.

%  showParams (optional) =1 prints out the complete set of parameters

% Output argument

%  method passes a miscelleny of values

%  the use of 'method' is being phased out. use globals

global inputStimulusParams OMEParams DRNLParams IHC_cilia_RPParams

global IHCpreSynapseParams  AN_IHCsynapseParams

global MacGregorParams MacGregorMultiParams  filteredSACFParams

global experiment % used only by calls from multiThreshold

% global IHC_VResp_VivoParams

currentFile=mfilename;                      % i.e. the name of this mfile

method.parameterSource=currentFile(10:end); % for the record

efferentDelay=0.010;

method.segmentDuration=efferentDelay;

if nargin<3, showParams=0; end

if nargin<2, sampleRate=44100; end

if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default

    lowestBF=250; 	highestBF= 8000; 	numChannels=21;

    % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000

    BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));

end

% BFlist=1000;  % single channel option

% preserve for backward campatibility

method.nonlinCF=BFlist; 

method.dt=1/sampleRate; 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% set  model parameters

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%  #1 inputStimulus

inputStimulusParams=[];

inputStimulusParams.sampleRate= sampleRate; 

%%  #2 outerMiddleEar

OMEParams=[];  % clear the structure first

% outer ear resonances band pass filter  [gain lp order  hp]

OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];

% highpass stapes filter  

%  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)

OMEParams.OMEstapesHPcutoff= 1000;

OMEParams.stapesScalar=	     45e-9;

% Acoustic reflex: maximum attenuation should be around 25 dB (Price, 1966)

% i.e. a minimum ratio of 0.056.

% 'spikes' model: AR based on brainstem spiking activity (LSR)

OMEParams.rateToAttenuationFactor=0.05; % * N(all ICspikes)

% 'probability model': Ar based on AN firing probabilities (LSR)

OMEParams.rateToAttenuationFactorProb=0.02;    % * N(all ANrates)

% asymptote should be around 100-200 ms

OMEParams.ARtau=.250; % AR smoothing function 250 ms fits Hung and Dallos

% delay must be longer than the segment length

OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency

OMEParams.ARrateThreshold=40;

%%  #3 DRNL

DRNLParams=[];  % clear the structure first

% DRNLParams.BFlist=BFlist;

%   *** DRNL nonlinear path

% broken stick compression

% DRNLParams.a=2e4;     % normal value (commented out)

DRNLParams.a=0;         % DRNL.a=0 means no OHCs (no nonlinear path)

DRNLParams.c=.2;        % compression exponent

DRNLParams.ctBMdB = 10; %Compression threshold dB re 10e-9 m displacement

% filters

DRNLParams.nonlinOrder=	3;  % order of nonlinear gammatone filters

DRNLParams.nonlinCFs=BFlist;

DRNLParams.p=0.2895;   DRNLParams.q=250;   % save p and q for printing only

% p=0.2895;   q=250;      % human  (% p=0.14;   q=366;  % cat)

DRNLParams.nlBWs=  DRNLParams.p * BFlist + DRNLParams.q;

%   *** DRNL linear path:

DRNLParams.g=100;       % linear path gain factor

DRNLParams.linOrder=3;  % order of linear gammatone filters

% linCF is not necessarily the same as nonlinCF

minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz

DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;

% bandwidths (linear)

minLinBW=100; coeffLinBW=0.6531;

DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters

%   *** DRNL MOC efferents

DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!

DRNLParams.minMOCattenuationdB=-35;

% 'spikes' model: MOC based on brainstem spiking activity (HSR)

DRNLParams.MOCtau =.0285;                         % smoothing for MOC

DRNLParams.rateToAttenuationFactor = .03;  % strength of MOC

DRNLParams.rateToAttenuationFactor = .0055;  % strength of MOC

% 'probability' model: MOC based on AN probability (HSR)

DRNLParams.MOCtauProb =.285;                         % smoothing for MOC

DRNLParams.rateToAttenuationFactorProb = 0.007;  % strength of MOC

DRNLParams.MOCrateThresholdProb =67;                % spikes/s probability only

%% #4 IHC_cilia_RPParams

IHC_cilia_RPParams.tc=	0.00012;   % 0.0003 Shamma

IHC_cilia_RPParams.C=	0.08;       % 0.1 scalar (C_cilia ) 

IHC_cilia_RPParams.u0=	5e-9;       

IHC_cilia_RPParams.s0=	30e-9;

IHC_cilia_RPParams.u1=	1e-9;

IHC_cilia_RPParams.s1=	1e-9;

IHC_cilia_RPParams.Gmax= 6e-9;    % 2.5e-9 maximum conductance (Siemens)

IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance

IHC_cilia_RPParams.Ga=	.8e-9;  % 4.3e-9 fixed apical membrane conductance

%  #5 IHC_RP

IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)

% IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)

IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)

IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)

IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential

IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances

%%  #5 IHCpreSynapse

IHCpreSynapseParams=[];

IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance

% IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance

IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential

IHCpreSynapseParams.beta=	400;	% determine Ca channel opening

IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening

IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms

IHCpreSynapseParams.power=	3;

% reminder: changing z has a strong effect on HF thresholds (like Et)

IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate

LSRtauCa=30e-6;            HSRtauCa=80e-6;            % seconds

% LSRtauCa=40e-6;            HSRtauCa=90e-6;            % seconds

% IHCpreSynapseParams.tauCa= [15e-6 80e-6]; %LSR and HSR fiber

IHCpreSynapseParams.tauCa= [LSRtauCa HSRtauCa]; %LSR and HSR fiber

%%  #6 AN_IHCsynapse

AN_IHCsynapseParams=[];             % clear the structure first

% number of AN fibers at each BF (used only for spike generation)

AN_IHCsynapseParams.numFibers=	100; 

% absolute refractory period. Relative refractory period is the same. 

AN_IHCsynapseParams.refractory_period=	0.00075;

AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike

AN_IHCsynapseParams.spikesTargetSampleRate=10000;

% AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes.

% c=kym/(y(l+r)+kl)	(spontaneous rate)

% c=(approx)  ym/l  (saturated rate)

AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse

AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate

AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate

AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store

AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store

% reduce l to increase saturated rate

AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft

AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft

AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell

% AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell

%%  #7 MacGregorMulti (first order brainstem neurons)

MacGregorMultiParams=[];

MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose

switch MacGregorMultiType

    case 'primary-like'

        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF

        MacGregorMultiParams.type = 'primary-like cell';

        MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers

        MacGregorMultiParams.dendriteLPfreq=200;  % dendritic filter

        MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike

        MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)

        MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)

        MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)

        MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S

        MacGregorMultiParams.tauGk=	0.0012; % K+ conductance tau (s)

        MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)

        MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)

        MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau

        MacGregorMultiParams.Er=-0.06;      % resting potential (V)

        MacGregorMultiParams.Eb=0.06;       % spike height (V)

    case 'chopper'

        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF

        MacGregorMultiParams.type = 'chopper cell';

        MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers

        MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter

        MacGregorMultiParams.currentPerSpike=28e-9; % *per spike

%         MacGregorMultiParams.currentPerSpike=30e-9; % *per spike

        MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)

        MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)

        MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)

        MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S

        MacGregorMultiParams.tauGk=	0.0005;% K+ conductance tau (s)

        MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)

        MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)

        MacGregorMultiParams.tauTh=	0.02; % variable threshold tau

        MacGregorMultiParams.Er=-0.06;    % resting potential (V)

        MacGregorMultiParams.Eb=0.06;     % spike height (V)

        MacGregorMultiParams.PSTHbinWidth=	1e-4;

end

%%  #8 MacGregor (second-order neuron). Only one per channel

MacGregorParams=[];                 % clear the structure first

MacGregorParams.type = 'chopper cell';

MacGregorParams.fibersPerNeuron=10; % N input fibers

MacGregorParams.dendriteLPfreq=100; % dendritic filter

MacGregorParams.currentPerSpike=40e-9;% *(A) per spike

MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)

MacGregorParams.tauM=0.002;         % membrane time constant (s)

MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)

MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S

MacGregorParams.tauGk=	0.0012;     % K+ conductance tau (s)

MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)

MacGregorParams.c=	0;              % threshold shift on spike, (V)

MacGregorParams.tauTh=	0.02;       % variable threshold tau

MacGregorParams.Er=-0.06;           % resting potential (V)

MacGregorParams.Eb=0.06;            % spike height (V)

MacGregorParams.debugging=0;        % (special)

% wideband accepts input from all channels (of same fiber type)

% use wideband to create inhibitory units

MacGregorParams.wideband=0;         % special for wideband units

% MacGregorParams.saveAllData=0;

%%  #9 filteredSACF

minPitch=	300; maxPitch=	3000; numPitches=60;    % specify lags

pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));

filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector

filteredSACFParams.acfTau=	.003;       % time constant of running ACF

filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF

filteredSACFParams.plotFilteredSACF=1;  % 0 plots unfiltered ACFs

filteredSACFParams.plotACFs=0;          % special plot (see code)

%  filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags

filteredSACFParams.lagsProcedure=  'useAllLags';

% filteredSACFParams.lagsProcedure=  'omitShortLags';

filteredSACFParams.criterionForOmittingLags=3;

% checks

if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron

    error('MacGregorMulti: too few input fibers for input to MacG unit')

end

%% now accept last minute parameter changes required by the calling program

% paramChanges

if nargin>3 && ~isempty(paramChanges)

    if ~iscellstr(paramChanges)

        error('paramChanges error: paramChanges not a cell array')

    end

    nChanges=length(paramChanges);

    for idx=1:nChanges

        x=paramChanges{idx};

        x=deblank(x);

        if ~isempty(x)

            if ~strcmp(x(end),';')

                error(['paramChanges error (terminate with semicolon) ' x])

            end

            st=strtrim(x(1:strfind(x,'.')-1));

            fld=strtrim(x(strfind(x,'.')+1:strfind(x,'=')-1));

            value=x(strfind(x,'=')+1:end);

            if isempty(st) || isempty(fld) || isempty(value)

                error(['paramChanges error:' x])

            end

            x1=eval(['isstruct(' st ')']);

            cmd=['isfield(' st ',''' fld ''')'];

            x2=eval(cmd);

            if ~(x1*x2)

                error(['paramChanges error:' x])

            end

        end

        % no problems so go ahead

        eval(paramChanges{idx})

    end

end

%% write all parameters to the command window

% showParams is currently set at the top of htis function

if showParams

    fprintf('\n %%%%%%%%\n')

    fprintf('\n%s\n', method.parameterSource)

    fprintf('\n')

    nm=UTIL_paramsList(whos);

    for i=1:length(nm)

        %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])

        if ~strcmp(nm(i), 'method')

            eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])

        end

    end

    % highlight parameter changes made locally

    if nargin>3 && ~isempty(paramChanges)

        fprintf('\n Local parameter changes:\n')

        for i=1:length(paramChanges)

            disp(paramChanges{i})

        end

    end

end

% for backward compatibility

experiment.comparisonData=[];

function method=MAPparamsPL ...

    (BFlist, sampleRate, showParams, paramChanges)

% MAPparamsPL.m is a parameter file, similar in all respects to

%  MAPparamsNormal except that a primary-like' neuron is used at the 

%  level of the cochlear nuclues (rather than a chopper cell).

%

% MAPparams<> establishes a complete set of MAP parameters

% Parameter file names must be of the form <MAPparams><name>

%

% Input arguments

%  BFlist     (optional) specifies the desired list of channel BFs

%    otherwise defaults set below

%  sampleRate (optional), default is 50000.

%  showParams (optional) =1 prints out the complete set of parameters

% Output argument

%  method passes a miscelleny of values

%  the use of 'method' is being phased out. use globals

global inputStimulusParams OMEParams DRNLParams IHC_cilia_RPParams

global IHCpreSynapseParams  AN_IHCsynapseParams

global MacGregorParams MacGregorMultiParams  filteredSACFParams

global experiment % used only by calls from multiThreshold

% global IHC_VResp_VivoParams

currentFile=mfilename;                      % i.e. the name of this mfile

method.parameterSource=currentFile(10:end); % for the record

efferentDelay=0.010;

method.segmentDuration=efferentDelay;

if nargin<3, showParams=0; end

if nargin<2, sampleRate=50000; end

if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default

    lowestBF=250; 	highestBF= 8000; 	numChannels=21;

    % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000

    BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));

end

% BFlist=1000;  % single channel option

% preserve for backward campatibility

method.nonlinCF=BFlist; 

method.dt=1/sampleRate; 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% set  model parameters

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%  #1 inputStimulus

inputStimulusParams=[];

inputStimulusParams.sampleRate= sampleRate; 

%%  #2 outerMiddleEar

OMEParams=[];  % clear the structure first

% outer ear resonances band pass filter  [gain lp order  hp]

OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];

% highpass stapes filter  

%  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)

OMEParams.OMEstapesHPcutoff= 1000;

OMEParams.stapesScalar=	     45e-9;

% Acoustic reflex: maximum attenuation should be around 25 dB (Price, 1966)

% i.e. a minimum ratio of 0.056.

% 'spikes' model: AR based on brainstem spiking activity (LSR)

OMEParams.rateToAttenuationFactor=0.05; % * N(all ICspikes)

% 'probability model': Ar based on AN firing probabilities (LSR)

OMEParams.rateToAttenuationFactorProb=0.02;    % * N(all ANrates)

% asymptote should be around 100-200 ms

OMEParams.ARtau=.250; % AR smoothing function 250 ms fits Hung and Dallos

% delay must be longer than the segment length

OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency

OMEParams.ARrateThreshold=40;

%%  #3 DRNL

DRNLParams=[];  % clear the structure first

% DRNLParams.BFlist=BFlist;

%   *** DRNL nonlinear path

% broken stick compression

DRNLParams.a=2e4;       % DRNL.a=0 means no OHCs (no nonlinear path)

DRNLParams.c=.2;        % compression exponent

DRNLParams.ctBMdB = 10; %Compression threshold dB re 10e-9 m displacement

% filters

DRNLParams.nonlinOrder=	3;  % order of nonlinear gammatone filters

DRNLParams.nonlinCFs=BFlist;

DRNLParams.p=0.2895;   DRNLParams.q=250;   % save p and q for printing only

% p=0.2895;   q=250;      % human  (% p=0.14;   q=366;  % cat)

DRNLParams.nlBWs=  DRNLParams.p * BFlist + DRNLParams.q;

%   *** DRNL linear path:

DRNLParams.g=100;       % linear path gain factor

DRNLParams.linOrder=3;  % order of linear gammatone filters

% linCF is not necessarily the same as nonlinCF

minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz

DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;

% bandwidths (linear)

minLinBW=100; coeffLinBW=0.6531;

DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters

%   *** DRNL MOC efferents

DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!

DRNLParams.minMOCattenuationdB=-35;

% 'spikes' model: MOC based on brainstem spiking activity (HSR)

DRNLParams.MOCtau =.0285;                         % smoothing for MOC

DRNLParams.rateToAttenuationFactor = .03;  % strength of MOC

DRNLParams.rateToAttenuationFactor = .0055;  % strength of MOC

% 'probability' model: MOC based on AN probability (HSR)

DRNLParams.MOCtauProb =.285;                         % smoothing for MOC

DRNLParams.rateToAttenuationFactorProb = 0.007;  % strength of MOC

DRNLParams.MOCrateThresholdProb =67;                % spikes/s probability only

%% #4 IHC_cilia_RPParams

IHC_cilia_RPParams.tc=	0.00012;   % 0.0003 Shamma

IHC_cilia_RPParams.C=	0.08;       % 0.1 scalar (C_cilia ) 

IHC_cilia_RPParams.u0=	5e-9;       

IHC_cilia_RPParams.s0=	30e-9;

IHC_cilia_RPParams.u1=	1e-9;

IHC_cilia_RPParams.s1=	1e-9;

IHC_cilia_RPParams.Gmax= 6e-9;    % 2.5e-9 maximum conductance (Siemens)

IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance

IHC_cilia_RPParams.Ga=	.8e-9;  % 4.3e-9 fixed apical membrane conductance

%  #5 IHC_RP

IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)

% IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)

IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)

IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)

IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential

IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances

%%  #5 IHCpreSynapse

IHCpreSynapseParams=[];

IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance

% IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance

IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential

IHCpreSynapseParams.beta=	400;	% determine Ca channel opening

IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening

IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms

IHCpreSynapseParams.power=	3;

% reminder: changing z has a strong effect on HF thresholds (like Et)

IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate

LSRtauCa=30e-6;            HSRtauCa=80e-6;            % seconds

% LSRtauCa=40e-6;            HSRtauCa=90e-6;            % seconds

% IHCpreSynapseParams.tauCa= [15e-6 80e-6]; %LSR and HSR fiber

IHCpreSynapseParams.tauCa= [LSRtauCa HSRtauCa]; %LSR and HSR fiber

%%  #6 AN_IHCsynapse

AN_IHCsynapseParams=[];             % clear the structure first

% number of AN fibers at each BF (used only for spike generation)

AN_IHCsynapseParams.numFibers=	100; 

% absolute refractory period. Relative refractory period is the same. 

AN_IHCsynapseParams.refractory_period=	0.00075;

AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike

AN_IHCsynapseParams.spikesTargetSampleRate=sampleRate;

% AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes.

% c=kym/(y(l+r)+kl)	(spontaneous rate)

% c=(approx)  ym/l  (saturated rate)

AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse

AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate

AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate

AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store

AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store

% reduce l to increase saturated rate

AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft

AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft

AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell

% AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell

%%  #7 MacGregorMulti (first order brainstem neurons)

MacGregorMultiParams=[];

% MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose

MacGregorMultiType='primary-like'; % MacGregorMultiType='primary-like'; %choose

switch MacGregorMultiType

    case 'primary-like'

        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF

        MacGregorMultiParams.type = 'primary-like cell';

        MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers

        MacGregorMultiParams.dendriteLPfreq=500;  % dendritic filter

        MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike

        MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)

        MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)

        MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)

        MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S

        MacGregorMultiParams.tauGk=	0.0005; % K+ conductance tau (s)

        MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)

        MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)

        MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau

        MacGregorMultiParams.Er=-0.06;      % resting potential (V)

        MacGregorMultiParams.Eb=0.06;       % spike height (V)

    case 'chopper'

        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF

        MacGregorMultiParams.type = 'chopper cell';

        MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers

        MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter

        MacGregorMultiParams.currentPerSpike=28e-9; % *per spike

%         MacGregorMultiParams.currentPerSpike=30e-9; % *per spike

        MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)

        MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)

        MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)

        MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S

        MacGregorMultiParams.tauGk=	0.0005;% K+ conductance tau (s)

        MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)

        MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)

        MacGregorMultiParams.tauTh=	0.02; % variable threshold tau

        MacGregorMultiParams.Er=-0.06;    % resting potential (V)

        MacGregorMultiParams.Eb=0.06;     % spike height (V)

        MacGregorMultiParams.PSTHbinWidth=	1e-4;

end

%%  #8 MacGregor (second-order neuron). Only one per channel

MacGregorParams=[];                 % clear the structure first

MacGregorParams.type = 'chopper cell';

MacGregorParams.fibersPerNeuron=10; % N input fibers

MacGregorParams.dendriteLPfreq=100; % dendritic filter

MacGregorParams.currentPerSpike=40e-9;% *(A) per spike

MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)

MacGregorParams.tauM=0.002;         % membrane time constant (s)

MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)

MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S

MacGregorParams.tauGk=	0.0012;     % K+ conductance tau (s)

MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)

MacGregorParams.c=	0;              % threshold shift on spike, (V)

MacGregorParams.tauTh=	0.02;       % variable threshold tau

MacGregorParams.Er=-0.06;           % resting potential (V)

MacGregorParams.Eb=0.06;            % spike height (V)

MacGregorParams.debugging=0;        % (special)

% wideband accepts input from all channels (of same fiber type)

% use wideband to create inhibitory units

MacGregorParams.wideband=0;         % special for wideband units

% MacGregorParams.saveAllData=0;

%%  #9 filteredSACF

minPitch=	300; maxPitch=	3000; numPitches=60;    % specify lags

pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));

filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector

filteredSACFParams.acfTau=	.003;       % time constant of running ACF

filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF

filteredSACFParams.plotFilteredSACF=1;  % 0 plots unfiltered ACFs

filteredSACFParams.plotACFs=0;          % special plot (see code)

%  filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags

filteredSACFParams.lagsProcedure=  'useAllLags';

% filteredSACFParams.lagsProcedure=  'omitShortLags';

filteredSACFParams.criterionForOmittingLags=3;

% checks

if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron

    error('MacGregorMulti: too few input fibers for input to MacG unit')

end

%% now accept last minute parameter changes required by the calling program

% paramChanges

if nargin>3 && ~isempty(paramChanges)

    if ~iscellstr(paramChanges)

        error('paramChanges error: paramChanges not a cell array')

    end

    nChanges=length(paramChanges);

    for idx=1:nChanges

        x=paramChanges{idx};

        x=deblank(x);

        if ~isempty(x)

            if ~strcmp(x(end),';')

                error(['paramChanges error (terminate with semicolon) ' x])

            end

            st=strtrim(x(1:strfind(x,'.')-1));

            fld=strtrim(x(strfind(x,'.')+1:strfind(x,'=')-1));

            value=x(strfind(x,'=')+1:end);

            if isempty(st) || isempty(fld) || isempty(value)

                error(['paramChanges error:' x])

            end

            x1=eval(['isstruct(' st ')']);

            cmd=['isfield(' st ',''' fld ''')'];

            x2=eval(cmd);

            if ~(x1*x2)

                error(['paramChanges error:' x])

            end

        end

        % no problems so go ahead

        eval(paramChanges{idx})

    end

end

%% write all parameters to the command window

% showParams is currently set at the top of htis function

if showParams

    fprintf('\n %%%%%%%%\n')

    fprintf('\n%s\n', method.parameterSource)

    fprintf('\n')

    nm=UTIL_paramsList(whos);

    for i=1:length(nm)

        %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])

        if ~strcmp(nm(i), 'method')

            eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])

        end

    end

    % highlight parameter changes made locally

    if nargin>3 && ~isempty(paramChanges)

        fprintf('\n Local parameter changes:\n')

        for i=1:length(paramChanges)

            disp(paramChanges{i})

        end

    end

end

% for backward compatibility

experiment.comparisonData=[];