rmeddis@30: function method=MAPparamsNormalIC ...
rmeddis@30:     (BFlist, sampleRate, showParams, paramChanges)
rmeddis@30: % MAPparams<> establishes a complete set of MAP parameters
rmeddis@30: % Parameter file names must be of the form <MAPparams> <name>
rmeddis@30: %
rmeddis@30: % input arguments
rmeddis@30: %  BFlist     (optional) specifies the desired list of channel BFs
rmeddis@30: %    otherwise defaults set below
rmeddis@30: %  sampleRate (optional), default is 50000.
rmeddis@30: %  showParams (optional) =1 prints out the complete set of parameters
rmeddis@30: % output argument
rmeddis@30: %  method passes a miscelleny of values
rmeddis@30: 
rmeddis@30: global inputStimulusParams OMEParams DRNLParams IHC_cilia_RPParams
rmeddis@30: global IHC_VResp_VivoParams IHCpreSynapseParams  AN_IHCsynapseParams
rmeddis@30: global MacGregorParams MacGregorMultiParams  filteredSACFParams
rmeddis@30: global experiment % used by calls from multiThreshold only
rmeddis@30: 
rmeddis@30: 
rmeddis@30: currentFile=mfilename;                      % i.e. the name of this mfile
rmeddis@30: method.parameterSource=currentFile(10:end); % for the record
rmeddis@30: 
rmeddis@30: efferentDelay=0.010;
rmeddis@30: method.segmentDuration=efferentDelay;
rmeddis@30: 
rmeddis@30: if nargin<3, showParams=0; end
rmeddis@30: if nargin<2, sampleRate=50000; end
rmeddis@30: if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default
rmeddis@30:     lowestBF=250; 	highestBF= 8000; 	numChannels=21;
rmeddis@30:     % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000
rmeddis@30:     BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));
rmeddis@30: end
rmeddis@30: % BFlist=1000;
rmeddis@30: 
rmeddis@30: % preserve for backward campatibility
rmeddis@30: method.nonlinCF=BFlist; 
rmeddis@30: method.dt=1/sampleRate; 
rmeddis@30: 
rmeddis@30: %%%%%%%%%%%%%%%%%%%%%%%%%%%%
rmeddis@30: % set  model parameters
rmeddis@30: %%%%%%%%%%%%%%%%%%%%%%%%%%%%
rmeddis@30: 
rmeddis@30: %%  #1 inputStimulus
rmeddis@30: inputStimulusParams=[];
rmeddis@30: inputStimulusParams.sampleRate= sampleRate; 
rmeddis@30: 
rmeddis@30: %%  #2 outerMiddleEar
rmeddis@30: OMEParams=[];  % clear the structure first
rmeddis@30: % outer ear resonances band pass filter  [gain lp order  hp]
rmeddis@30: OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];
rmeddis@30:                                        
rmeddis@30: % highpass stapes filter  
rmeddis@30: %  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)
rmeddis@30: OMEParams.OMEstapesLPcutoff= 1000;
rmeddis@30: OMEParams.stapesScalar=	     45e-9;
rmeddis@30: 
rmeddis@30: % Acoustic reflex: maximum attenuation should be around 25 dB Price (1966)
rmeddis@30: % i.e. a minimum ratio of 0.056.
rmeddis@30: % 'spikes' model: AR based on brainstem spiking activity (LSR)
rmeddis@30: OMEParams.rateToAttenuationFactor=0.006;   % * N(all ICspikes)
rmeddis@30: % OMEParams.rateToAttenuationFactor=0;   % * N(all ICspikes)
rmeddis@30: 
rmeddis@30: % 'probability model': Ar based on AN firing probabilities (LSR)
rmeddis@30: OMEParams.rateToAttenuationFactorProb=0.01;% * N(all ANrates)
rmeddis@30: % OMEParams.rateToAttenuationFactorProb=0;% * N(all ANrates)
rmeddis@30: 
rmeddis@30: % asymptote should be around 100-200 ms
rmeddis@30: OMEParams.ARtau=.05; % AR smoothing function
rmeddis@30: % delay must be longer than the segment length
rmeddis@30: OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency
rmeddis@30: OMEParams.ARrateThreshold=0;
rmeddis@30: 
rmeddis@30: %%  #3 DRNL
rmeddis@30: DRNLParams=[];  % clear the structure first
rmeddis@30: DRNLParams.BFlist=BFlist;
rmeddis@30: 
rmeddis@30: % DRNL nonlinear path
rmeddis@30: DRNLParams.a=5e4;     % DRNL.a=0 means no OHCs (no nonlinear path)
rmeddis@30: DRNLParams.a=2e4;     % DRNL.a=0 means no OHCs (no nonlinear path)
rmeddis@30: 
rmeddis@30: DRNLParams.b=8e-6;    % *compression threshold raised compression
rmeddis@30: % DRNLParams.b=1;    % b=1 means no compression
rmeddis@30: 
rmeddis@30: DRNLParams.c=0.2;     % compression exponent
rmeddis@30: % nonlinear filters
rmeddis@30: DRNLParams.nonlinCFs=BFlist;
rmeddis@30: DRNLParams.nonlinOrder=	3;           % order of nonlinear gammatone filters
rmeddis@30: p=0.2895;   q=170;  % human  (% p=0.14;   q=366;  % cat)
rmeddis@30: DRNLParams.nlBWs=  p * BFlist + q;
rmeddis@30: DRNLParams.p=p;   DRNLParams.q=q;   % save p and q for printing only
rmeddis@30: 
rmeddis@30: % DRNL linear path:
rmeddis@30: DRNLParams.g=100;     % linear path gain factor
rmeddis@30: % linCF is not necessarily the same as nonlinCF
rmeddis@30: minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz
rmeddis@30: DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;
rmeddis@30: DRNLParams.linOrder=	3;           % order of linear gammatone filters
rmeddis@30: minLinBW=100; coeffLinBW=0.6531;
rmeddis@30: DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters
rmeddis@30: 
rmeddis@30: % DRNL MOC efferents
rmeddis@30: DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!
rmeddis@30: 
rmeddis@30: % 'spikes' model: MOC based on brainstem spiking activity (HSR)
rmeddis@30: DRNLParams.rateToAttenuationFactor = .01;  % strength of MOC
rmeddis@30: %      DRNLParams.rateToAttenuationFactor = 0;  % strength of MOC
rmeddis@30: % 'probability' model: MOC based on AN spiking activity (HSR)
rmeddis@30: DRNLParams.rateToAttenuationFactorProb = .0055;  % strength of MOC
rmeddis@30: % DRNLParams.rateToAttenuationFactorProb = .0;  % strength of MOC
rmeddis@30: DRNLParams.MOCrateThresholdProb =70;                % spikes/s probability only
rmeddis@30: 
rmeddis@30: DRNLParams.MOCtau =.1;                         % smoothing for MOC
rmeddis@30: 
rmeddis@30: 
rmeddis@30: %% #4 IHC_cilia_RPParams
rmeddis@30: 
rmeddis@30: IHC_cilia_RPParams.tc=	0.0003;   % 0.0003 filter time simulates viscocity
rmeddis@30: % IHC_cilia_RPParams.tc=	0.0005;   % 0.0003 filter time simulates viscocity
rmeddis@30: IHC_cilia_RPParams.C=	0.03;      % 0.1 scalar (C_cilia ) 
rmeddis@30: IHC_cilia_RPParams.u0=	5e-9;       
rmeddis@30: IHC_cilia_RPParams.s0=	30e-9;
rmeddis@30: IHC_cilia_RPParams.u1=	1e-9;
rmeddis@30: IHC_cilia_RPParams.s1=	1e-9;
rmeddis@30: 
rmeddis@30: IHC_cilia_RPParams.Gmax= 6e-9;    % 2.5e-9 maximum conductance (Siemens)
rmeddis@30: IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance
rmeddis@30: IHC_cilia_RPParams.Ga=	.8e-9;  % 4.3e-9 fixed apical membrane conductance
rmeddis@30: 
rmeddis@30: %  #5 IHC_RP
rmeddis@30: IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)
rmeddis@30: % IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)
rmeddis@30: IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)
rmeddis@30: 
rmeddis@30: IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)
rmeddis@30: IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential
rmeddis@30: IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances
rmeddis@30: 
rmeddis@30: 
rmeddis@30: %%  #5 IHCpreSynapse
rmeddis@30: IHCpreSynapseParams=[];
rmeddis@30: IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance
rmeddis@30: IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance
rmeddis@30: IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential
rmeddis@30: IHCpreSynapseParams.beta=	400;	% determine Ca channel opening
rmeddis@30: IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening
rmeddis@30: IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms
rmeddis@30: IHCpreSynapseParams.power=	3;
rmeddis@30: % reminder: changing z has a strong effect on HF thresholds (like Et)
rmeddis@30: IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate
rmeddis@30: 
rmeddis@30: LSRtauCa=35e-6;            HSRtauCa=85e-6;            % seconds
rmeddis@30: % LSRtauCa=35e-6;            HSRtauCa=70e-6;            % seconds
rmeddis@30: IHCpreSynapseParams.tauCa= [ HSRtauCa]; %LSR and HSR fiber
rmeddis@30: 
rmeddis@30: %%  #6 AN_IHCsynapse
rmeddis@30: % c=kym/(y(l+r)+kl)	(spontaneous rate)
rmeddis@30: % c=(approx)  ym/l  (saturated rate)
rmeddis@30: AN_IHCsynapseParams=[];             % clear the structure first
rmeddis@30: AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse
rmeddis@30: AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate
rmeddis@30: AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate
rmeddis@30: 
rmeddis@30: AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store
rmeddis@30: AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store
rmeddis@30: 
rmeddis@30: % reduce l to increase saturated rate
rmeddis@30: AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft
rmeddis@30: AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft
rmeddis@30: 
rmeddis@30: AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell
rmeddis@30: % AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell
rmeddis@30: 
rmeddis@30: AN_IHCsynapseParams.refractory_period=	0.00075;
rmeddis@30: % number of AN fibers at each BF (used only for spike generation)
rmeddis@30: AN_IHCsynapseParams.numFibers=	100; 
rmeddis@30: AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike
rmeddis@30: 
rmeddis@30: AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes.
rmeddis@30: 
rmeddis@30: %%  #7 MacGregorMulti (first order brainstem neurons)
rmeddis@30: MacGregorMultiParams=[];
rmeddis@30: MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose
rmeddis@30: switch MacGregorMultiType
rmeddis@30:     case 'primary-like'
rmeddis@30:         MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF
rmeddis@30:         MacGregorMultiParams.type = 'primary-like cell';
rmeddis@30:         MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers
rmeddis@30:         MacGregorMultiParams.dendriteLPfreq=200;  % dendritic filter
rmeddis@30:         MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike
rmeddis@30:         MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)
rmeddis@30:         MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)
rmeddis@30:         MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)
rmeddis@30:         MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S
rmeddis@30:         MacGregorMultiParams.tauGk=	0.0012; % K+ conductance tau (s)
rmeddis@30:         MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)
rmeddis@30:         MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)
rmeddis@30:         MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau
rmeddis@30:         MacGregorMultiParams.Er=-0.06;      % resting potential (V)
rmeddis@30:         MacGregorMultiParams.Eb=0.06;       % spike height (V)
rmeddis@30: 
rmeddis@30:     case 'chopper'
rmeddis@30:         MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF
rmeddis@30:         MacGregorMultiParams.type = 'chopper cell';
rmeddis@30:         MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers
rmeddis@30: %         MacGregorMultiParams.fibersPerNeuron=6;  % N input fibers
rmeddis@30: 
rmeddis@30:         MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter
rmeddis@30:         MacGregorMultiParams.currentPerSpike=35e-9; % *per spike
rmeddis@30: %         MacGregorMultiParams.currentPerSpike=30e-9; % *per spike
rmeddis@30:         
rmeddis@30:         MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)
rmeddis@30:         MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)
rmeddis@30:         MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)
rmeddis@30:         MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S
rmeddis@30:         MacGregorMultiParams.tauGk=	[0.001 0.0005];% K+ conductance tau (s)
rmeddis@30:         MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)
rmeddis@30:         MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)
rmeddis@30:         MacGregorMultiParams.tauTh=	0.02; % variable threshold tau
rmeddis@30:         MacGregorMultiParams.Er=-0.06;    % resting potential (V)
rmeddis@30:         MacGregorMultiParams.Eb=0.06;     % spike height (V)
rmeddis@30:         MacGregorMultiParams.PSTHbinWidth=	1e-4;
rmeddis@30: end
rmeddis@30: 
rmeddis@30: %%  #8 MacGregor (second-order neuron). Only one per channel
rmeddis@30: MacGregorParams=[];                 % clear the structure first
rmeddis@30: MacGregorParams.type = 'chopper cell';
rmeddis@30: MacGregorParams.fibersPerNeuron=10; % N input fibers
rmeddis@30: MacGregorParams.dendriteLPfreq=100; % dendritic filter
rmeddis@30: MacGregorParams.currentPerSpike=120e-9;% *(A) per spike
rmeddis@30: MacGregorParams.currentPerSpike=40e-9;% *(A) per spike
rmeddis@30: 
rmeddis@30: MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)
rmeddis@30: MacGregorParams.tauM=0.002;         % membrane time constant (s)
rmeddis@30: MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)
rmeddis@30: MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S
rmeddis@30: MacGregorParams.tauGk=	0.0005;     % K+ conductance tau (s)
rmeddis@30: MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)
rmeddis@30: MacGregorParams.c=	0;              % threshold shift on spike, (V)
rmeddis@30: MacGregorParams.tauTh=	0.02;       % variable threshold tau
rmeddis@30: MacGregorParams.Er=-0.06;           % resting potential (V)
rmeddis@30: MacGregorParams.Eb=0.06;            % spike height (V)
rmeddis@30: MacGregorParams.debugging=0;        % (special)
rmeddis@30: % wideband accepts input from all channels (of same fiber type)
rmeddis@30: % use wideband to create inhibitory units
rmeddis@30: MacGregorParams.wideband=0;         % special for wideband units
rmeddis@30: % MacGregorParams.saveAllData=0;
rmeddis@30: 
rmeddis@30: %%  #9 filteredSACF
rmeddis@30: minPitch=	300; maxPitch=	3000; numPitches=60;    % specify lags
rmeddis@30: pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));
rmeddis@30: filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector
rmeddis@30: filteredSACFParams.acfTau=	.003;       % time constant of running ACF
rmeddis@30: filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF
rmeddis@30: filteredSACFParams.plotFilteredSACF=1;  % 0 plots unfiltered ACFs
rmeddis@30: filteredSACFParams.plotACFs=0;          % special plot (see code)
rmeddis@30: %  filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags
rmeddis@30: filteredSACFParams.lagsProcedure=  'useAllLags';
rmeddis@30: % filteredSACFParams.lagsProcedure=  'useBernsteinLagWeights';
rmeddis@30: % filteredSACFParams.lagsProcedure=  'omitShortLags';
rmeddis@30: filteredSACFParams.criterionForOmittingLags=3;
rmeddis@30: 
rmeddis@30: % checks
rmeddis@30: if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron
rmeddis@30:     error('MacGregorMulti: too few input fibers for input to MacG unit')
rmeddis@30: end
rmeddis@30: 
rmeddis@30: 
rmeddis@30: %% now accept last minute parameter changes required by the calling program
rmeddis@30: % paramChanges
rmeddis@30: if nargin>3 && ~isempty(paramChanges)
rmeddis@30:     nChanges=length(paramChanges);
rmeddis@30:     for idx=1:nChanges
rmeddis@30:         eval(paramChanges{idx})
rmeddis@30:     end
rmeddis@30: end
rmeddis@30: 
rmeddis@30: 
rmeddis@30: %% write all parameters to the command window
rmeddis@30: % showParams is currently set at the top of htis function
rmeddis@30: if showParams
rmeddis@30:     fprintf('\n %%%%%%%%\n')
rmeddis@30:     fprintf('\n%s\n', method.parameterSource)
rmeddis@30:     fprintf('\n')
rmeddis@30:     nm=UTIL_paramsList(whos);
rmeddis@30:     for i=1:length(nm)
rmeddis@30:         %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])
rmeddis@30:         if ~strcmp(nm(i), 'method')
rmeddis@30:             eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])
rmeddis@30:         end
rmeddis@30:     end
rmeddis@30: 
rmeddis@30:     % highlight parameter changes made locally
rmeddis@30:     if nargin>3 && ~isempty(paramChanges)
rmeddis@30:         fprintf('\n Local parameter changes:\n')
rmeddis@30:         for i=1:length(paramChanges)
rmeddis@30:             disp(paramChanges{i})
rmeddis@30:         end
rmeddis@30:     end
rmeddis@30: end
rmeddis@30: 
rmeddis@30: % for backward compatibility
rmeddis@30: experiment.comparisonData=[];