diff parameterStore/MAPparamsNormalIC.m @ 30:1a502830d462

MT update

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parameterStore/MAPparamsNormalIC.m	Mon Jul 11 14:31:29 2011 +0100
@@ -0,0 +1,302 @@
+function method=MAPparamsNormalIC ...
+    (BFlist, sampleRate, showParams, paramChanges)
+% 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
+
+global inputStimulusParams OMEParams DRNLParams IHC_cilia_RPParams
+global IHC_VResp_VivoParams IHCpreSynapseParams  AN_IHCsynapseParams
+global MacGregorParams MacGregorMultiParams  filteredSACFParams
+global experiment % used by calls from multiThreshold only
+
+
+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;
+
+% 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.OMEstapesLPcutoff= 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=0.006;   % * N(all ICspikes)
+% OMEParams.rateToAttenuationFactor=0;   % * N(all ICspikes)
+
+% 'probability model': Ar based on AN firing probabilities (LSR)
+OMEParams.rateToAttenuationFactorProb=0.01;% * N(all ANrates)
+% OMEParams.rateToAttenuationFactorProb=0;% * N(all ANrates)
+
+% asymptote should be around 100-200 ms
+OMEParams.ARtau=.05; % AR smoothing function
+% delay must be longer than the segment length
+OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency
+OMEParams.ARrateThreshold=0;
+
+%%  #3 DRNL
+DRNLParams=[];  % clear the structure first
+DRNLParams.BFlist=BFlist;
+
+% DRNL nonlinear path
+DRNLParams.a=5e4;     % DRNL.a=0 means no OHCs (no nonlinear path)
+DRNLParams.a=2e4;     % DRNL.a=0 means no OHCs (no nonlinear path)
+
+DRNLParams.b=8e-6;    % *compression threshold raised compression
+% DRNLParams.b=1;    % b=1 means no compression
+
+DRNLParams.c=0.2;     % compression exponent
+% nonlinear filters
+DRNLParams.nonlinCFs=BFlist;
+DRNLParams.nonlinOrder=	3;           % order of nonlinear gammatone filters
+p=0.2895;   q=170;  % human  (% p=0.14;   q=366;  % cat)
+DRNLParams.nlBWs=  p * BFlist + q;
+DRNLParams.p=p;   DRNLParams.q=q;   % save p and q for printing only
+
+% DRNL linear path:
+DRNLParams.g=100;     % linear path gain factor
+% 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;
+DRNLParams.linOrder=	3;           % order of linear gammatone filters
+minLinBW=100; coeffLinBW=0.6531;
+DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters
+
+% DRNL MOC efferents
+DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!
+
+% 'spikes' model: MOC based on brainstem spiking activity (HSR)
+DRNLParams.rateToAttenuationFactor = .01;  % strength of MOC
+%      DRNLParams.rateToAttenuationFactor = 0;  % strength of MOC
+% 'probability' model: MOC based on AN spiking activity (HSR)
+DRNLParams.rateToAttenuationFactorProb = .0055;  % strength of MOC
+% DRNLParams.rateToAttenuationFactorProb = .0;  % strength of MOC
+DRNLParams.MOCrateThresholdProb =70;                % spikes/s probability only
+
+DRNLParams.MOCtau =.1;                         % smoothing for MOC
+
+
+%% #4 IHC_cilia_RPParams
+
+IHC_cilia_RPParams.tc=	0.0003;   % 0.0003 filter time simulates viscocity
+% IHC_cilia_RPParams.tc=	0.0005;   % 0.0003 filter time simulates viscocity
+IHC_cilia_RPParams.C=	0.03;      % 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=35e-6;            HSRtauCa=85e-6;            % seconds
+% LSRtauCa=35e-6;            HSRtauCa=70e-6;            % seconds
+IHCpreSynapseParams.tauCa= [ HSRtauCa]; %LSR and HSR fiber
+
+%%  #6 AN_IHCsynapse
+% c=kym/(y(l+r)+kl)	(spontaneous rate)
+% c=(approx)  ym/l  (saturated rate)
+AN_IHCsynapseParams=[];             % clear the structure first
+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
+
+AN_IHCsynapseParams.refractory_period=	0.00075;
+% number of AN fibers at each BF (used only for spike generation)
+AN_IHCsynapseParams.numFibers=	100; 
+AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike
+
+AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes.
+
+%%  #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.fibersPerNeuron=6;  % N input fibers
+
+        MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter
+        MacGregorMultiParams.currentPerSpike=35e-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=	[0.001 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=120e-9;% *(A) per spike
+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=	0.0005;     % 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=  'useBernsteinLagWeights';
+% 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)
+    nChanges=length(paramChanges);
+    for idx=1:nChanges
+        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=[];