rmeddis@10: function method=MAPparamsStd ...
rmeddis@10:     (BFlist, sampleRate, showParams)
rmeddis@10: % MAPparams<> establishes a complete set of MAP parameters
rmeddis@10: % Parameter file names must be of the form <MAPparams> <name>
rmeddis@10: %
rmeddis@10: % input arguments
rmeddis@10: %  BFlist     (optional) specifies the desired list of channel BFs
rmeddis@10: %    otherwise defaults set below
rmeddis@10: %  sampleRate (optional), default is 50000.
rmeddis@10: %  showParams (optional) =1 prints out the complete set of parameters
rmeddis@10: % output argument
rmeddis@10: %  method passes a miscelleny of values
rmeddis@10: 
rmeddis@10: global inputStimulusParams OMEParams DRNLParams
rmeddis@10: global IHC_VResp_VivoParams IHCpreSynapseParams  AN_IHCsynapseParams
rmeddis@10: global MacGregorParams MacGregorMultiParams  filteredSACFParams
rmeddis@10: global experiment % used by calls from multiThreshold only
rmeddis@10: global IHC_cilia_RPParams
rmeddis@10: 
rmeddis@10: currentFile=mfilename;                      % i.e. the name of this mfile
rmeddis@10: method.parameterSource=currentFile(10:end); % for the record
rmeddis@10: 
rmeddis@10: switchOffEfferent=0;
rmeddis@10: efferentDelay=0.010;
rmeddis@10: method.segmentDuration=efferentDelay;
rmeddis@10: 
rmeddis@10: if nargin<3, showParams=0; end
rmeddis@10: if nargin<2, sampleRate=50000; end
rmeddis@10: if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default
rmeddis@10:     lowestBF=250; 	highestBF= 8000; 	numChannels=21;
rmeddis@10:     % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000
rmeddis@10:     BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));
rmeddis@10: end
rmeddis@10: % BFlist=1000;
rmeddis@10: 
rmeddis@10: % preserve for backward campatibility
rmeddis@10: method.nonlinCF=BFlist; 
rmeddis@10: method.dt=1/sampleRate; 
rmeddis@10: 
rmeddis@10: %%%%%%%%%%%%%%%%%%%%%%%%%%%%
rmeddis@10: % set  model parameters
rmeddis@10: %%%%%%%%%%%%%%%%%%%%%%%%%%%%
rmeddis@10: 
rmeddis@10: %%  #1 inputStimulus
rmeddis@10: inputStimulusParams=[];
rmeddis@10: inputStimulusParams.sampleRate= sampleRate; 
rmeddis@10: 
rmeddis@10: %%  #2 outerMiddleEar
rmeddis@10: OMEParams=[];  % clear the structure first
rmeddis@10: % outer ear resonances band pass filter  [gain lp order  hp]
rmeddis@10: OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];
rmeddis@10:                                        
rmeddis@10: % highpass stapes filter  
rmeddis@10: %  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)
rmeddis@10: OMEParams.OMEstapesLPcutoff= 1000;
rmeddis@10: OMEParams.stapesScalar=	     45e-9;
rmeddis@10: 
rmeddis@10: % Acoustic reflex: maximum attenuation should be around 25 dB Price (1966)
rmeddis@10: % i.e. a minimum ratio of 0.056.
rmeddis@10: if ~switchOffEfferent
rmeddis@10:     % 'spikes' model: AR based on brainstem spiking activity (LSR)
rmeddis@10:     OMEParams.rateToAttenuationFactor=0.003;   % * N(all ICspikes)
rmeddis@10: %     OMEParams.rateToAttenuationFactor=0;   % * N(all ICspikes)
rmeddis@10:     % 'probability model': Ar based on An firing probabilities (LSR)
rmeddis@10:     OMEParams.rateToAttenuationFactorProb=0.005;% * N(all ANrates)
rmeddis@10: %     OMEParams.rateToAttenuationFactorProb=0;% * N(all ANrates)
rmeddis@10: else
rmeddis@10:     OMEParams.rateToAttenuationFactor=0;        % 0= off
rmeddis@10:     OMEParams.rateToAttenuationFactorProb=0;    % 0= off
rmeddis@10: end
rmeddis@10: % asymptote should be around 100-200 ms
rmeddis@10: OMEParams.ARtau=.05; % AR smoothing function
rmeddis@10: % delay must be longer than the segment length
rmeddis@10: OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency
rmeddis@10: OMEParams.ARrateThreshold=0;
rmeddis@10: 
rmeddis@10: %%  #3 DRNL
rmeddis@10: DRNLParams=[];  % clear the structure first
rmeddis@10: DRNLParams.BFlist=BFlist;
rmeddis@10: 
rmeddis@10: % DRNL nonlinear path
rmeddis@10: DRNLParams.a=3e4;     % nonlinear path gain (below compression threshold)
rmeddis@10: % DRNLParams.a=3e2;     % DRNL.a=0 means no OHCs (no nonlinear path)
rmeddis@10: 
rmeddis@10: DRNLParams.b=8e-6;    % *compression threshold raised compression
rmeddis@10: % DRNLParams.b=1;    % b=1 means no compression
rmeddis@10: 
rmeddis@10: DRNLParams.c=0.2;     % compression exponent
rmeddis@10: % nonlinear filters
rmeddis@10: DRNLParams.nonlinCFs=BFlist;
rmeddis@10: DRNLParams.nonlinOrder=	3;           % order of nonlinear gammatone filters
rmeddis@10: p=0.2895;   q=170;  % human  (% p=0.14;   q=366;  % cat)
rmeddis@10: DRNLParams.nlBWs=  p * BFlist + q;
rmeddis@10: DRNLParams.p=p;   DRNLParams.q=q;   % save p and q for printing only
rmeddis@10: 
rmeddis@10: % DRNL linear path:
rmeddis@10: DRNLParams.g=100;     % linear path gain factor
rmeddis@10: % linCF is not necessarily the same as nonlinCF
rmeddis@10: minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz
rmeddis@10: DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;
rmeddis@10: DRNLParams.linOrder=	3;           % order of linear gammatone filters
rmeddis@10: minLinBW=100; coeffLinBW=0.6531;
rmeddis@10: DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters
rmeddis@10: 
rmeddis@10: % DRNL MOC efferents
rmeddis@10: DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!
rmeddis@10: if ~switchOffEfferent
rmeddis@10:     % 'spikes' model: MOC based on brainstem spiking activity (HSR)
rmeddis@10:     DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC
rmeddis@10:     DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC
rmeddis@10: %      DRNLParams.rateToAttenuationFactor = 0;  % strength of MOC
rmeddis@10: 
rmeddis@10:     % 'spikes' model: MOC based on brainstem spiking activity (HSR)
rmeddis@10:     DRNLParams.rateToAttenuationFactorProb = .002;  % strength of MOC
rmeddis@10: else
rmeddis@10:     DRNLParams.rateToAttenuationFactor = 0;     % 0 = MOC off (probability)
rmeddis@10:     DRNLParams.rateToAttenuationFactorProb = 0; % 0 = MOC off (spikes)
rmeddis@10: end
rmeddis@10: DRNLParams.MOCtau =.03;                         % smoothing for MOC
rmeddis@10: DRNLParams.MOCrateThreshold =50;                % set to AN rate threshold
rmeddis@10: 
rmeddis@10: 
rmeddis@10: %% #4 IHC_cilia_RPParams
rmeddis@10: 
rmeddis@10: IHC_cilia_RPParams.tc=	0.0003;   % 0.0003 filter time simulates viscocity
rmeddis@10: % IHC_cilia_RPParams.tc=	0.0005;   % 0.0003 filter time simulates viscocity
rmeddis@10: IHC_cilia_RPParams.C=	0.05;      % 0.1 scalar (C_cilia ) 
rmeddis@10: IHC_cilia_RPParams.u0=	5e-9;       
rmeddis@10: IHC_cilia_RPParams.s0=	30e-9;
rmeddis@10: IHC_cilia_RPParams.u1=	1e-9;
rmeddis@10: IHC_cilia_RPParams.s1=	1e-9;
rmeddis@10: 
rmeddis@10: IHC_cilia_RPParams.Gmax= 5e-9;    % 2.5e-9 maximum conductance (Siemens)
rmeddis@10: IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance
rmeddis@10: 
rmeddis@10: %  #5 IHC_RP
rmeddis@10: IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)
rmeddis@10: IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)
rmeddis@10: IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)
rmeddis@10: % IHC_cilia_RPParams.Et=	0.07;          % endocochlear potential (V)
rmeddis@10: 
rmeddis@10: IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)
rmeddis@10: IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential
rmeddis@10: IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances
rmeddis@10: 
rmeddis@10: 
rmeddis@10: %%  #5 IHCpreSynapse
rmeddis@10: IHCpreSynapseParams=[];
rmeddis@10: IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance
rmeddis@10: IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance
rmeddis@10: IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential
rmeddis@10: IHCpreSynapseParams.beta=	400;	% determine Ca channel opening
rmeddis@10: IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening
rmeddis@10: IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms
rmeddis@10: IHCpreSynapseParams.power=	3;
rmeddis@10: % reminder: changing z has a strong effect on HF thresholds (like Et)
rmeddis@10: IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate
rmeddis@10: 
rmeddis@10: LSRtauCa=50e-6;            HSRtauCa=85e-6;            % seconds
rmeddis@10: % LSRtauCa=35e-6;            HSRtauCa=70e-6;            % seconds
rmeddis@10: IHCpreSynapseParams.tauCa= [LSRtauCa HSRtauCa]; %LSR and HSR fiber
rmeddis@10: 
rmeddis@10: %%  #6 AN_IHCsynapse
rmeddis@10: % c=kym/(y(l+r)+kl)	(spontaneous rate)
rmeddis@10: % c=(approx)  ym/l  (saturated rate)
rmeddis@10: AN_IHCsynapseParams=[];             % clear the structure first
rmeddis@10: AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse
rmeddis@10: AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate
rmeddis@10: AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate
rmeddis@10: 
rmeddis@10: AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store
rmeddis@10: AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store
rmeddis@10: 
rmeddis@10: % reduce l to increase saturated rate
rmeddis@10: AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft
rmeddis@10: AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft
rmeddis@10: 
rmeddis@10: AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell
rmeddis@10: % AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell
rmeddis@10: 
rmeddis@10: AN_IHCsynapseParams.refractory_period=	0.00075;
rmeddis@10: % number of AN fibers at each BF (used only for spike generation)
rmeddis@10: AN_IHCsynapseParams.numFibers=	100; 
rmeddis@10: AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike
rmeddis@10: 
rmeddis@10: %%  #7 MacGregorMulti (first order brainstem neurons)
rmeddis@10: MacGregorMultiParams=[];
rmeddis@10: MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose
rmeddis@10: switch MacGregorMultiType
rmeddis@10:     case 'primary-like'
rmeddis@10:         MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF
rmeddis@10:         MacGregorMultiParams.type = 'primary-like cell';
rmeddis@10:         MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers
rmeddis@10:         MacGregorMultiParams.dendriteLPfreq=200;  % dendritic filter
rmeddis@10:         MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike
rmeddis@10:         MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)
rmeddis@10:         MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)
rmeddis@10:         MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)
rmeddis@10:         MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S
rmeddis@10:         MacGregorMultiParams.tauGk=	0.0012; % K+ conductance tau (s)
rmeddis@10:         MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)
rmeddis@10:         MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)
rmeddis@10:         MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau
rmeddis@10:         MacGregorMultiParams.Er=-0.06;      % resting potential (V)
rmeddis@10:         MacGregorMultiParams.Eb=0.06;       % spike height (V)
rmeddis@10: 
rmeddis@10:     case 'chopper'
rmeddis@10:         MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF
rmeddis@10:         MacGregorMultiParams.type = 'chopper cell';
rmeddis@10:         MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers
rmeddis@10: %         MacGregorMultiParams.fibersPerNeuron=6;  % N input fibers
rmeddis@10: 
rmeddis@10:         MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter
rmeddis@10:         MacGregorMultiParams.currentPerSpike=35e-9; % *per spike
rmeddis@10: %         MacGregorMultiParams.currentPerSpike=45e-9; % *per spike
rmeddis@10:         
rmeddis@10:         MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)
rmeddis@10:         MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)
rmeddis@10:         MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)
rmeddis@10:         MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S
rmeddis@10:         MacGregorMultiParams.tauGk=	0.0001;% K+ conductance tau (s)
rmeddis@10:         MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)
rmeddis@10:         MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)
rmeddis@10:         MacGregorMultiParams.tauTh=	0.02; % variable threshold tau
rmeddis@10:         MacGregorMultiParams.Er=-0.06;    % resting potential (V)
rmeddis@10:         MacGregorMultiParams.Eb=0.06;     % spike height (V)
rmeddis@10:         MacGregorMultiParams.PSTHbinWidth=	1e-4;
rmeddis@10: end
rmeddis@10: 
rmeddis@10: %%  #8 MacGregor (second-order neuron). Only one per channel
rmeddis@10: MacGregorParams=[];                 % clear the structure first
rmeddis@10: MacGregorParams.type = 'chopper cell';
rmeddis@10: MacGregorParams.fibersPerNeuron=10; % N input fibers
rmeddis@10: MacGregorParams.dendriteLPfreq=100; % dendritic filter
rmeddis@10: MacGregorParams.currentPerSpike=120e-9;% *(A) per spike
rmeddis@10: 
rmeddis@10: MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)
rmeddis@10: MacGregorParams.tauM=0.002;         % membrane time constant (s)
rmeddis@10: MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)
rmeddis@10: MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S
rmeddis@10: MacGregorParams.tauGk=	0.0003;     % K+ conductance tau (s)
rmeddis@10: MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)
rmeddis@10: MacGregorParams.c=	0;              % threshold shift on spike, (V)
rmeddis@10: MacGregorParams.tauTh=	0.02;       % variable threshold tau
rmeddis@10: MacGregorParams.Er=-0.06;           % resting potential (V)
rmeddis@10: MacGregorParams.Eb=0.06;            % spike height (V)
rmeddis@10: MacGregorParams.debugging=0;        % (special)
rmeddis@10: % wideband accepts input from all channels (of same fiber type)
rmeddis@10: % use wideband to create inhibitory units
rmeddis@10: MacGregorParams.wideband=0;         % special for wideband units
rmeddis@10: % MacGregorParams.saveAllData=0;
rmeddis@10: 
rmeddis@10: %%  #9 filteredSACF
rmeddis@10: minPitch=	300; maxPitch=	3000; numPitches=60;    % specify lags
rmeddis@10: pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));
rmeddis@10: filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector
rmeddis@10: filteredSACFParams.acfTau=	.003;       % time constant of running ACF
rmeddis@10: filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF
rmeddis@10: filteredSACFParams.plotFilteredSACF=1;  % 0 plots unfiltered ACFs
rmeddis@10: filteredSACFParams.plotACFs=0;          % special plot (see code)
rmeddis@10: %  filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags
rmeddis@10: filteredSACFParams.lagsProcedure=  'useAllLags';
rmeddis@10: % filteredSACFParams.lagsProcedure=  'useBernsteinLagWeights';
rmeddis@10: % filteredSACFParams.lagsProcedure=  'omitShortLags';
rmeddis@10: filteredSACFParams.criterionForOmittingLags=3;
rmeddis@10: 
rmeddis@10: % checks
rmeddis@10: if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron
rmeddis@10:     error('MacGregorMulti: too few input fibers for input to MacG unit')
rmeddis@10: end
rmeddis@10: 
rmeddis@10: 
rmeddis@10: %% write all parameters to the command window
rmeddis@10: % showParams is currently set at the top of htis function
rmeddis@10: if showParams
rmeddis@10:     fprintf('\n %%%%%%%%\n')
rmeddis@10:     fprintf('\n%s\n', method.parameterSource)
rmeddis@10:     fprintf('\n')
rmeddis@10:     nm=UTIL_paramsList(whos);
rmeddis@10:     for i=1:length(nm)
rmeddis@10:         %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])
rmeddis@10:         if ~strcmp(nm(i), 'method')
rmeddis@10:             eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])
rmeddis@10:         end
rmeddis@10:     end
rmeddis@10: end
rmeddis@10: 
rmeddis@10: 
rmeddis@10: 
rmeddis@10: % **********************************************************************  comparison data
rmeddis@10: % store individual data here for display on the multiThreshold GUI (if used)
rmeddis@10: % the final value in each vector is an identifier (BF or duration))
rmeddis@10: if isstruct(experiment)
rmeddis@10:     switch experiment.paradigm
rmeddis@10:         case {'IFMC','IFMC_8ms'}
rmeddis@10:             % based on MPa
rmeddis@10:             comparisonData=[
rmeddis@10:                 66	51	49	48	46	45	54	250;
rmeddis@10:                 60	54	46	42	39	49	65	500;
rmeddis@10:                 64	51	38	32	33	59	75	1000;
rmeddis@10:                 59	51	36	30	41	81	93	2000;
rmeddis@10:                 71	63	53	44	36	76	95	4000;
rmeddis@10:                 70	64	43	35	35	66	88	6000;
rmeddis@10:                 110	110	110	110	110	110	110	8000;
rmeddis@10:                 ];
rmeddis@10:             if length(BFlist)==1 && ~isempty(comparisonData)
rmeddis@10:                 availableFrequencies=comparisonData(:,end)';
rmeddis@10:                 findRow= find(BFlist==availableFrequencies);
rmeddis@10:                 if ~isempty (findRow)
rmeddis@10:                     experiment.comparisonData=comparisonData(findRow,:);
rmeddis@10:                 end
rmeddis@10:             end
rmeddis@10: 
rmeddis@10:         case {'TMC','TMC_8ms'}
rmeddis@10:             % based on MPa
rmeddis@10:             comparisonData=[
rmeddis@10:                 48	58	63	68	75	80	85	92	99	250;
rmeddis@10:                 33	39	40	49	52	61	64	77	79	500;
rmeddis@10:                 39	42	50	81	83	92	96	97	110	1000;
rmeddis@10:                 24	26	32	37	46	51	59	71	78	2000;
rmeddis@10:                 65	68	77	85	91	93	110	110	110	4000;
rmeddis@10:                 20	19	26	44	80	95	96	110	110	6000;
rmeddis@10:                 ];
rmeddis@10:             if length(BFlist)==1 && ~isempty(comparisonData)
rmeddis@10:                 availableFrequencies=comparisonData(:,end)';
rmeddis@10:                 findRow= find(BFlist==availableFrequencies);
rmeddis@10:                 if ~isempty (findRow)
rmeddis@10:                     experiment.comparisonData=comparisonData(findRow,:);
rmeddis@10:                 end
rmeddis@10:             end
rmeddis@10: 
rmeddis@10:         case { 'absThreshold',  'absThreshold_8'}
rmeddis@10:             % MPa thresholds
rmeddis@10:             experiment.comparisonData=[
rmeddis@10:                 32	26	16	18	22	22 0.008;
rmeddis@10:                 16	13	6	9	15	11 0.500
rmeddis@10:                 ];
rmeddis@10: 
rmeddis@10: 
rmeddis@10:         otherwise
rmeddis@10:             experiment.comparisonData=[];
rmeddis@10:     end
rmeddis@10: end
rmeddis@10: 
rmeddis@10: