rmeddis@0: function method=MAPparamsNormal ...
rmeddis@26:     (BFlist, sampleRate, showParams, paramChanges)
rmeddis@0: % MAPparams<> establishes a complete set of MAP parameters
rmeddis@35: % Parameter file names must be of the form <MAPparams><name>
rmeddis@0: %
rmeddis@35: % Input arguments
rmeddis@0: %  BFlist     (optional) specifies the desired list of channel BFs
rmeddis@0: %    otherwise defaults set below
rmeddis@0: %  sampleRate (optional), default is 50000.
rmeddis@0: %  showParams (optional) =1 prints out the complete set of parameters
rmeddis@35: % Output argument
rmeddis@0: %  method passes a miscelleny of values
rmeddis@35: %  the use of 'method' is being phased out. use globals
rmeddis@0: 
rmeddis@26: global inputStimulusParams OMEParams DRNLParams IHC_cilia_RPParams
rmeddis@35: global IHCpreSynapseParams  AN_IHCsynapseParams
rmeddis@0: global MacGregorParams MacGregorMultiParams  filteredSACFParams
rmeddis@35: global experiment % used only by calls from multiThreshold
rmeddis@35: % global IHC_VResp_VivoParams
rmeddis@0: 
rmeddis@0: currentFile=mfilename;                      % i.e. the name of this mfile
rmeddis@0: method.parameterSource=currentFile(10:end); % for the record
rmeddis@0: 
rmeddis@0: efferentDelay=0.010;
rmeddis@0: method.segmentDuration=efferentDelay;
rmeddis@0: 
rmeddis@0: if nargin<3, showParams=0; end
rmeddis@38: if nargin<2, sampleRate=44100; end
rmeddis@0: if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default
rmeddis@0:     lowestBF=250; 	highestBF= 8000; 	numChannels=21;
rmeddis@0:     % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000
rmeddis@0:     BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));
rmeddis@0: end
rmeddis@35: % BFlist=1000;  % single channel option
rmeddis@0: 
rmeddis@0: % preserve for backward campatibility
rmeddis@0: method.nonlinCF=BFlist; 
rmeddis@0: method.dt=1/sampleRate; 
rmeddis@0: 
rmeddis@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%
rmeddis@0: % set  model parameters
rmeddis@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%
rmeddis@0: 
rmeddis@0: %%  #1 inputStimulus
rmeddis@0: inputStimulusParams=[];
rmeddis@0: inputStimulusParams.sampleRate= sampleRate; 
rmeddis@0: 
rmeddis@0: %%  #2 outerMiddleEar
rmeddis@0: OMEParams=[];  % clear the structure first
rmeddis@0: % outer ear resonances band pass filter  [gain lp order  hp]
rmeddis@0: OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];
rmeddis@0:                                        
rmeddis@0: % highpass stapes filter  
rmeddis@0: %  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)
rmeddis@38: OMEParams.OMEstapesHPcutoff= 1000;
rmeddis@0: OMEParams.stapesScalar=	     45e-9;
rmeddis@0: 
rmeddis@35: % Acoustic reflex: maximum attenuation should be around 25 dB (Price, 1966)
rmeddis@0: % i.e. a minimum ratio of 0.056.
rmeddis@16: % 'spikes' model: AR based on brainstem spiking activity (LSR)
rmeddis@38: OMEParams.rateToAttenuationFactor=0.05; % * N(all ICspikes)
rmeddis@16: % 'probability model': Ar based on AN firing probabilities (LSR)
rmeddis@38: OMEParams.rateToAttenuationFactorProb=0.02;    % * N(all ANrates)
rmeddis@16: 
rmeddis@0: % asymptote should be around 100-200 ms
rmeddis@35: OMEParams.ARtau=.250; % AR smoothing function 250 ms fits Hung and Dallos
rmeddis@0: % delay must be longer than the segment length
rmeddis@0: OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency
rmeddis@34: OMEParams.ARrateThreshold=40;
rmeddis@0: 
rmeddis@0: %%  #3 DRNL
rmeddis@0: DRNLParams=[];  % clear the structure first
rmeddis@35: % DRNLParams.BFlist=BFlist;
rmeddis@0: 
rmeddis@35: %   *** DRNL nonlinear path
rmeddis@35: % broken stick compression
rmeddis@38: DRNLParams.a=2e4;       % DRNL.a=0 means no OHCs (no nonlinear path)
rmeddis@35: DRNLParams.c=.2;        % compression exponent
rmeddis@38: DRNLParams.ctBMdB = 10; %Compression threshold dB re 10e-9 m displacement
rmeddis@0: 
rmeddis@35: % filters
rmeddis@35: DRNLParams.nonlinOrder=	3;  % order of nonlinear gammatone filters
rmeddis@0: DRNLParams.nonlinCFs=BFlist;
rmeddis@38: DRNLParams.p=0.2895;   DRNLParams.q=250;   % save p and q for printing only
rmeddis@38: % p=0.2895;   q=250;      % human  (% p=0.14;   q=366;  % cat)
rmeddis@38: DRNLParams.nlBWs=  DRNLParams.p * BFlist + DRNLParams.q;
rmeddis@0: 
rmeddis@35: %   *** DRNL linear path:
rmeddis@38: DRNLParams.g=100;       % linear path gain factor
rmeddis@35: DRNLParams.linOrder=3;  % order of linear gammatone filters
rmeddis@0: % linCF is not necessarily the same as nonlinCF
rmeddis@0: minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz
rmeddis@0: DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;
rmeddis@35: % bandwidths (linear)
rmeddis@0: minLinBW=100; coeffLinBW=0.6531;
rmeddis@0: DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters
rmeddis@0: 
rmeddis@35: %   *** DRNL MOC efferents
rmeddis@0: DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!
rmeddis@38: DRNLParams.minMOCattenuationdB=-35;
rmeddis@23: 
rmeddis@16: % 'spikes' model: MOC based on brainstem spiking activity (HSR)
rmeddis@38: DRNLParams.MOCtau =.0285;                         % smoothing for MOC
rmeddis@38: DRNLParams.rateToAttenuationFactor = .03;  % strength of MOC
rmeddis@38: DRNLParams.rateToAttenuationFactor = .0055;  % strength of MOC
rmeddis@35: 
rmeddis@38: % 'probability' model: MOC based on AN probability (HSR)
rmeddis@35: DRNLParams.MOCtauProb =.285;                         % smoothing for MOC
rmeddis@38: DRNLParams.rateToAttenuationFactorProb = 0.007;  % strength of MOC
rmeddis@38: DRNLParams.MOCrateThresholdProb =67;                % spikes/s probability only
rmeddis@0: 
rmeddis@0: 
rmeddis@0: %% #4 IHC_cilia_RPParams
rmeddis@38: IHC_cilia_RPParams.tc=	0.00012;   % 0.0003 Shamma
rmeddis@38: IHC_cilia_RPParams.C=	0.08;       % 0.1 scalar (C_cilia ) 
rmeddis@0: IHC_cilia_RPParams.u0=	5e-9;       
rmeddis@0: IHC_cilia_RPParams.s0=	30e-9;
rmeddis@0: IHC_cilia_RPParams.u1=	1e-9;
rmeddis@0: IHC_cilia_RPParams.s1=	1e-9;
rmeddis@0: 
rmeddis@28: IHC_cilia_RPParams.Gmax= 6e-9;    % 2.5e-9 maximum conductance (Siemens)
rmeddis@8: IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance
rmeddis@28: IHC_cilia_RPParams.Ga=	.8e-9;  % 4.3e-9 fixed apical membrane conductance
rmeddis@0: 
rmeddis@0: %  #5 IHC_RP
rmeddis@0: IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)
rmeddis@28: % IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)
rmeddis@0: IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)
rmeddis@0: 
rmeddis@0: IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)
rmeddis@0: IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential
rmeddis@0: IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances
rmeddis@0: 
rmeddis@0: 
rmeddis@0: %%  #5 IHCpreSynapse
rmeddis@0: IHCpreSynapseParams=[];
rmeddis@0: IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance
rmeddis@35: % IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance
rmeddis@0: IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential
rmeddis@0: IHCpreSynapseParams.beta=	400;	% determine Ca channel opening
rmeddis@0: IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening
rmeddis@0: IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms
rmeddis@0: IHCpreSynapseParams.power=	3;
rmeddis@0: % reminder: changing z has a strong effect on HF thresholds (like Et)
rmeddis@0: IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate
rmeddis@0: 
rmeddis@38: LSRtauCa=30e-6;            HSRtauCa=80e-6;            % seconds
rmeddis@38: % LSRtauCa=40e-6;            HSRtauCa=90e-6;            % seconds
rmeddis@35: % IHCpreSynapseParams.tauCa= [15e-6 80e-6]; %LSR and HSR fiber
rmeddis@0: IHCpreSynapseParams.tauCa= [LSRtauCa HSRtauCa]; %LSR and HSR fiber
rmeddis@0: 
rmeddis@0: %%  #6 AN_IHCsynapse
rmeddis@35: AN_IHCsynapseParams=[];             % clear the structure first
rmeddis@35: % number of AN fibers at each BF (used only for spike generation)
rmeddis@35: AN_IHCsynapseParams.numFibers=	100; 
rmeddis@35: % absolute refractory period. Relative refractory period is the same. 
rmeddis@35: AN_IHCsynapseParams.refractory_period=	0.00075;
rmeddis@35: AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike
rmeddis@38: AN_IHCsynapseParams.spikesTargetSampleRate=10000;
rmeddis@38: % AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes.
rmeddis@35: 
rmeddis@0: % c=kym/(y(l+r)+kl)	(spontaneous rate)
rmeddis@0: % c=(approx)  ym/l  (saturated rate)
rmeddis@0: AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse
rmeddis@0: AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate
rmeddis@0: AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate
rmeddis@0: 
rmeddis@0: AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store
rmeddis@0: AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store
rmeddis@0: 
rmeddis@0: % reduce l to increase saturated rate
rmeddis@0: AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft
rmeddis@0: AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft
rmeddis@0: 
rmeddis@0: AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell
rmeddis@0: % AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell
rmeddis@0: 
rmeddis@15: 
rmeddis@0: %%  #7 MacGregorMulti (first order brainstem neurons)
rmeddis@0: MacGregorMultiParams=[];
rmeddis@0: MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose
rmeddis@0: switch MacGregorMultiType
rmeddis@0:     case 'primary-like'
rmeddis@0:         MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF
rmeddis@0:         MacGregorMultiParams.type = 'primary-like cell';
rmeddis@0:         MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers
rmeddis@0:         MacGregorMultiParams.dendriteLPfreq=200;  % dendritic filter
rmeddis@0:         MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike
rmeddis@0:         MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)
rmeddis@0:         MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)
rmeddis@0:         MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)
rmeddis@0:         MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S
rmeddis@0:         MacGregorMultiParams.tauGk=	0.0012; % K+ conductance tau (s)
rmeddis@0:         MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)
rmeddis@0:         MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)
rmeddis@0:         MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau
rmeddis@0:         MacGregorMultiParams.Er=-0.06;      % resting potential (V)
rmeddis@0:         MacGregorMultiParams.Eb=0.06;       % spike height (V)
rmeddis@0: 
rmeddis@0:     case 'chopper'
rmeddis@0:         MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF
rmeddis@0:         MacGregorMultiParams.type = 'chopper cell';
rmeddis@0:         MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers
rmeddis@0: 
rmeddis@0:         MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter
rmeddis@38:         MacGregorMultiParams.currentPerSpike=28e-9; % *per spike
rmeddis@28: %         MacGregorMultiParams.currentPerSpike=30e-9; % *per spike
rmeddis@0:         
rmeddis@0:         MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)
rmeddis@0:         MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)
rmeddis@0:         MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)
rmeddis@0:         MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S
rmeddis@15:         MacGregorMultiParams.tauGk=	0.0005;% K+ conductance tau (s)
rmeddis@0:         MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)
rmeddis@0:         MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)
rmeddis@0:         MacGregorMultiParams.tauTh=	0.02; % variable threshold tau
rmeddis@0:         MacGregorMultiParams.Er=-0.06;    % resting potential (V)
rmeddis@0:         MacGregorMultiParams.Eb=0.06;     % spike height (V)
rmeddis@0:         MacGregorMultiParams.PSTHbinWidth=	1e-4;
rmeddis@0: end
rmeddis@0: 
rmeddis@0: %%  #8 MacGregor (second-order neuron). Only one per channel
rmeddis@0: MacGregorParams=[];                 % clear the structure first
rmeddis@0: MacGregorParams.type = 'chopper cell';
rmeddis@0: MacGregorParams.fibersPerNeuron=10; % N input fibers
rmeddis@0: MacGregorParams.dendriteLPfreq=100; % dendritic filter
rmeddis@28: MacGregorParams.currentPerSpike=40e-9;% *(A) per spike
rmeddis@0: 
rmeddis@0: MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)
rmeddis@0: MacGregorParams.tauM=0.002;         % membrane time constant (s)
rmeddis@0: MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)
rmeddis@0: MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S
rmeddis@35: MacGregorParams.tauGk=	0.0012;     % K+ conductance tau (s)
rmeddis@0: MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)
rmeddis@0: MacGregorParams.c=	0;              % threshold shift on spike, (V)
rmeddis@0: MacGregorParams.tauTh=	0.02;       % variable threshold tau
rmeddis@0: MacGregorParams.Er=-0.06;           % resting potential (V)
rmeddis@0: MacGregorParams.Eb=0.06;            % spike height (V)
rmeddis@0: MacGregorParams.debugging=0;        % (special)
rmeddis@0: % wideband accepts input from all channels (of same fiber type)
rmeddis@0: % use wideband to create inhibitory units
rmeddis@0: MacGregorParams.wideband=0;         % special for wideband units
rmeddis@0: % MacGregorParams.saveAllData=0;
rmeddis@0: 
rmeddis@0: %%  #9 filteredSACF
rmeddis@38: % identify periodicities to be logged
rmeddis@38:     minPitch=	80; maxPitch=	500; numPitches=50;  
rmeddis@38:     maxLag=1/minPitch; minLag=1/maxPitch;
rmeddis@38:     lags= linspace(minLag, maxLag, numPitches);
rmeddis@38:     pitches=10.^ linspace(log10(minPitch), log10(maxPitch),numPitches);
rmeddis@38:     pitches=fliplr(pitches);
rmeddis@38:     % convert to lags for ACF
rmeddis@38:     filteredSACFParams.lags=lags;     % autocorrelation lags vector
rmeddis@38:     filteredSACFParams.acfTau=	.003;       % time constant of running ACF
rmeddis@38:     filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF
rmeddis@38:     % request plot of within-channel ACFs at fixed intervals in time
rmeddis@38:     filteredSACFParams.plotACFs=1;          
rmeddis@38:     filteredSACFParams.plotACFsInterval=0.002;
rmeddis@38:     filteredSACFParams.plotMoviePauses=.1;  
rmeddis@38: 
rmeddis@38:     filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags
rmeddis@38:     filteredSACFParams.lagsProcedure=  'useAllLags';
rmeddis@38:     %  'useAllLags' or 'omitShortLags'
rmeddis@38:     filteredSACFParams.criterionForOmittingLags=3;
rmeddis@38: 
rmeddis@0: 
rmeddis@0: % checks
rmeddis@0: if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron
rmeddis@0:     error('MacGregorMulti: too few input fibers for input to MacG unit')
rmeddis@0: end
rmeddis@0: 
rmeddis@0: 
rmeddis@26: %% now accept last minute parameter changes required by the calling program
rmeddis@26: % paramChanges
rmeddis@26: if nargin>3 && ~isempty(paramChanges)
rmeddis@35:     if ~iscellstr(paramChanges)
rmeddis@38:         error('paramChanges error: paramChanges not a cell array')
rmeddis@35:     end
rmeddis@35:     
rmeddis@26:     nChanges=length(paramChanges);
rmeddis@26:     for idx=1:nChanges
rmeddis@35:         x=paramChanges{idx};
rmeddis@35:         x=deblank(x);
rmeddis@35:         if ~isempty(x)
rmeddis@35:             if ~strcmp(x(end),';')
rmeddis@35:                 error(['paramChanges error (terminate with semicolon) ' x])
rmeddis@35:             end
rmeddis@35:             st=strtrim(x(1:strfind(x,'.')-1));
rmeddis@35:             fld=strtrim(x(strfind(x,'.')+1:strfind(x,'=')-1));
rmeddis@35:             value=x(strfind(x,'=')+1:end);
rmeddis@35:             if isempty(st) || isempty(fld) || isempty(value)
rmeddis@35:                 error(['paramChanges error:' x])
rmeddis@35:             end
rmeddis@35:             
rmeddis@35:             x1=eval(['isstruct(' st ')']);
rmeddis@35:             cmd=['isfield(' st ',''' fld ''')'];
rmeddis@35:             x2=eval(cmd);
rmeddis@35:             if ~(x1*x2)
rmeddis@35:                 error(['paramChanges error:' x])
rmeddis@35:             end
rmeddis@35:         end
rmeddis@35:         
rmeddis@35:         % no problems so go ahead
rmeddis@26:         eval(paramChanges{idx})
rmeddis@26:     end
rmeddis@26: end
rmeddis@26: 
rmeddis@26: 
rmeddis@0: %% write all parameters to the command window
rmeddis@0: % showParams is currently set at the top of htis function
rmeddis@0: if showParams
rmeddis@0:     fprintf('\n %%%%%%%%\n')
rmeddis@0:     fprintf('\n%s\n', method.parameterSource)
rmeddis@0:     fprintf('\n')
rmeddis@0:     nm=UTIL_paramsList(whos);
rmeddis@0:     for i=1:length(nm)
rmeddis@0:         %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])
rmeddis@0:         if ~strcmp(nm(i), 'method')
rmeddis@0:             eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])
rmeddis@0:         end
rmeddis@0:     end
rmeddis@0: 
rmeddis@26:     % highlight parameter changes made locally
rmeddis@26:     if nargin>3 && ~isempty(paramChanges)
rmeddis@26:         fprintf('\n Local parameter changes:\n')
rmeddis@26:         for i=1:length(paramChanges)
rmeddis@26:             disp(paramChanges{i})
rmeddis@26:         end
rmeddis@0:     end
rmeddis@0: end
rmeddis@0: 
rmeddis@26: % for backward compatibility
rmeddis@26: experiment.comparisonData=[];