Mercurial > hg > map
diff parameterStore/MAPparamsOHCloss.m @ 38:c2204b18f4a2 tip
End nov big change
| author | Ray Meddis <rmeddis@essex.ac.uk> |
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| date | Mon, 28 Nov 2011 13:34:28 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parameterStore/MAPparamsOHCloss.m Mon Nov 28 13:34:28 2011 +0000 @@ -0,0 +1,328 @@ +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=[];