Revision 10:4ef8e0e63866

View differences:

parameterStore/MAPparamsEndo.m
1 
function method=MAPparamsEndo ...
2 
    (BFlist, sampleRate, showParams)
3 
% MAPparams<> establishes a complete set of MAP parameters
4 
% Parameter file names must be of the form <MAPparams> <name>
5 
%
6 
% input arguments
7 
%  BFlist     (optional) specifies the desired list of channel BFs
8 
%    otherwise defaults set below
9 
%  sampleRate (optional), default is 50000.
10 
%  showParams (optional) =1 prints out the complete set of parameters
11 
% output argument
12 
%  method passes a miscelleny of values
13 

  		




  
  14
  
    
global inputStimulusParams OMEParams DRNLParams


  		




  
  15
  
    
global IHC_VResp_VivoParams IHCpreSynapseParams  AN_IHCsynapseParams


  		




  
  16
  
    
global MacGregorParams MacGregorMultiParams  filteredSACFParams


  		




  
  17
  
    
global experiment % used by calls from multiThreshold only


  		




  
  18
  
    
global IHC_cilia_RPParams


  		




  
  19
  
    

  		




  
  20
  
    
currentFile=mfilename;                      % i.e. the name of this mfile


  		




  
  21
  
    
method.parameterSource=currentFile(10:end); % for the record


  		




  
  22
  
    

  		




  
  23
  
    
switchOffEfferent=0;


  		




  
  24
  
    
efferentDelay=0.010;


  		




  
  25
  
    
method.segmentDuration=efferentDelay;


  		




  
  26
  
    

  		




  
  27
  
    
if nargin<3, showParams=0; end


  		




  
  28
  
    
if nargin<2, sampleRate=50000; end


  		




  
  29
  
    
if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default


  		




  
  30
  
    
    lowestBF=250; 	highestBF= 8000; 	numChannels=21;


  		




  
  31
  
    
    % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000


  		




  
  32
  
    
    BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));


  		




  
  33
  
    
end


  		




  
  34
  
    
% BFlist=1000;


  		




  
  35
  
    

  		




  
  36
  
    
% preserve for backward campatibility


  		




  
  37
  
    
method.nonlinCF=BFlist; 


  		




  
  38
  
    
method.dt=1/sampleRate; 


  		




  
  39
  
    

  		




  
  40
  
    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%


  		




  
  41
  
    
% set  model parameters


  		




  
  42
  
    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%


  		




  
  43
  
    

  		




  
  44
  
    
%%  #1 inputStimulus


  		




  
  45
  
    
inputStimulusParams=[];


  		




  
  46
  
    
inputStimulusParams.sampleRate= sampleRate; 


  		




  
  47
  
    

  		




  
  48
  
    
%%  #2 outerMiddleEar


  		




  
  49
  
    
OMEParams=[];  % clear the structure first


  		




  
  50
  
    
% outer ear resonances band pass filter  [gain lp order  hp]


  		




  
  51
  
    
OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];


  		




  
  52
  
    
                                       


  		




  
  53
  
    
% highpass stapes filter  


  		




  
  54
  
    
%  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)


  		




  
  55
  
    
OMEParams.OMEstapesLPcutoff= 1000;


  		




  
  56
  
    
OMEParams.stapesScalar=	     45e-9;


  		




  
  57
  
    

  		




  
  58
  
    
% Acoustic reflex: maximum attenuation should be around 25 dB Price (1966)


  		




  
  59
  
    
% i.e. a minimum ratio of 0.056.


  		




  
  60
  
    
if ~switchOffEfferent


  		




  
  61
  
    
    % 'spikes' model: AR based on brainstem spiking activity (LSR)


  		




  
  62
  
    
    OMEParams.rateToAttenuationFactor=0.003;   % * N(all ICspikes)


  		




  
  63
  
    
%     OMEParams.rateToAttenuationFactor=0;   % * N(all ICspikes)


  		




  
  64
  
    
    % 'probability model': Ar based on An firing probabilities (LSR)


  		




  
  65
  
    
    OMEParams.rateToAttenuationFactorProb=0.005;% * N(all ANrates)


  		




  
  66
  
    
%     OMEParams.rateToAttenuationFactorProb=0;% * N(all ANrates)


  		




  
  67
  
    
else


  		




  
  68
  
    
    OMEParams.rateToAttenuationFactor=0;        % 0= off


  		




  
  69
  
    
    OMEParams.rateToAttenuationFactorProb=0;    % 0= off


  		




  
  70
  
    
end


  		




  
  71
  
    
% asymptote should be around 100-200 ms


  		




  
  72
  
    
OMEParams.ARtau=.05; % AR smoothing function


  		




  
  73
  
    
% delay must be longer than the segment length


  		




  
  74
  
    
OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency


  		




  
  75
  
    
OMEParams.ARrateThreshold=0;


  		




  
  76
  
    

  		




  
  77
  
    
%%  #3 DRNL


  		




  
  78
  
    
DRNLParams=[];  % clear the structure first


  		




  
  79
  
    
DRNLParams.BFlist=BFlist;


  		




  
  80
  
    

  		




  
  81
  
    
% DRNL nonlinear path


  		




  
  82
  
    
DRNLParams.a=3e4;     % nonlinear path gain (below compression threshold)


  		




  
  83
  
    
% DRNLParams.a=3e2;     % DRNL.a=0 means no OHCs (no nonlinear path)


  		




  
  84
  
    

  		




  
  85
  
    
DRNLParams.b=8e-6;    % *compression threshold raised compression


  		




  
  86
  
    
% DRNLParams.b=1;    % b=1 means no compression


  		




  
  87
  
    

  		




  
  88
  
    
DRNLParams.c=0.2;     % compression exponent


  		




  
  89
  
    
% nonlinear filters


  		




  
  90
  
    
DRNLParams.nonlinCFs=BFlist;


  		




  
  91
  
    
DRNLParams.nonlinOrder=	3;           % order of nonlinear gammatone filters


  		




  
  92
  
    
p=0.2895;   q=170;  % human  (% p=0.14;   q=366;  % cat)


  		




  
  93
  
    
DRNLParams.nlBWs=  p * BFlist + q;


  		




  
  94
  
    
DRNLParams.p=p;   DRNLParams.q=q;   % save p and q for printing only


  		




  
  95
  
    

  		




  
  96
  
    
% DRNL linear path:


  		




  
  97
  
    
DRNLParams.g=100;     % linear path gain factor


  		




  
  98
  
    
% linCF is not necessarily the same as nonlinCF


  		




  
  99
  
    
minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz


  		




  
  100
  
    
DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;


  		




  
  101
  
    
DRNLParams.linOrder=	3;           % order of linear gammatone filters


  		




  
  102
  
    
minLinBW=100; coeffLinBW=0.6531;


  		




  
  103
  
    
DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters


  		




  
  104
  
    

  		




  
  105
  
    
% DRNL MOC efferents


  		




  
  106
  
    
DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!


  		




  
  107
  
    
if ~switchOffEfferent


  		




  
  108
  
    
    % 'spikes' model: MOC based on brainstem spiking activity (HSR)


  		




  
  109
  
    
    DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC


  		




  
  110
  
    
    DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC


  		




  
  111
  
    
%      DRNLParams.rateToAttenuationFactor = 0;  % strength of MOC


  		




  
  112
  
    

  		




  
  113
  
    
    % 'spikes' model: MOC based on brainstem spiking activity (HSR)


  		




  
  114
  
    
    DRNLParams.rateToAttenuationFactorProb = .002;  % strength of MOC


  		




  
  115
  
    
else


  		




  
  116
  
    
    DRNLParams.rateToAttenuationFactor = 0;     % 0 = MOC off (probability)


  		




  
  117
  
    
    DRNLParams.rateToAttenuationFactorProb = 0; % 0 = MOC off (spikes)


  		




  
  118
  
    
end


  		




  
  119
  
    
DRNLParams.MOCtau =.03;                         % smoothing for MOC


  		




  
  120
  
    
DRNLParams.MOCrateThreshold =50;                % set to AN rate threshold


  		




  
  121
  
    

  		




  
  122
  
    

  		




  
  123
  
    
%% #4 IHC_cilia_RPParams


  		




  
  124
  
    

  		




  
  125
  
    
IHC_cilia_RPParams.tc=	0.0003;   % 0.0003 filter time simulates viscocity


  		




  
  126
  
    
% IHC_cilia_RPParams.tc=	0.0005;   % 0.0003 filter time simulates viscocity


  		




  
  127
  
    
IHC_cilia_RPParams.C=	0.05;      % 0.1 scalar (C_cilia ) 


  		




  
  128
  
    
IHC_cilia_RPParams.u0=	5e-9;       


  		




  
  129
  
    
IHC_cilia_RPParams.s0=	30e-9;


  		




  
  130
  
    
IHC_cilia_RPParams.u1=	1e-9;


  		




  
  131
  
    
IHC_cilia_RPParams.s1=	1e-9;


  		




  
  132
  
    

  		




  
  133
  
    
IHC_cilia_RPParams.Gmax= 5e-9;    % 2.5e-9 maximum conductance (Siemens)


  		




  
  134
  
    
IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance


  		




  
  135
  
    

  		




  
  136
  
    
%  #5 IHC_RP


  		




  
  137
  
    
IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)


  		




  
  138
  
    
IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)


  		




  
  139
  
    
% IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)


  		




  
  140
  
    
IHC_cilia_RPParams.Et=	0.07;          % endocochlear potential (V)


  		




  
  141
  
    

  		




  
  142
  
    
IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)


  		




  
  143
  
    
IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential


  		




  
  144
  
    
IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances


  		




  
  145
  
    

  		




  
  146
  
    

  		




  
  147
  
    
%%  #5 IHCpreSynapse


  		




  
  148
  
    
IHCpreSynapseParams=[];


  		




  
  149
  
    
IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance


  		




  
  150
  
    
IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance


  		




  
  151
  
    
IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential


  		




  
  152
  
    
IHCpreSynapseParams.beta=	400;	% determine Ca channel opening


  		




  
  153
  
    
IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening


  		




  
  154
  
    
IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms


  		




  
  155
  
    
IHCpreSynapseParams.power=	3;


  		




  
  156
  
    
% reminder: changing z has a strong effect on HF thresholds (like Et)


  		




  
  157
  
    
IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate


  		




  
  158
  
    

  		




  
  159
  
    
LSRtauCa=50e-6;            HSRtauCa=85e-6;            % seconds


  		




  
  160
  
    
% LSRtauCa=35e-6;            HSRtauCa=70e-6;            % seconds


  		




  
  161
  
    
IHCpreSynapseParams.tauCa= [LSRtauCa HSRtauCa]; %LSR and HSR fiber


  		




  
  162
  
    

  		




  
  163
  
    
%%  #6 AN_IHCsynapse


  		




  
  164
  
    
% c=kym/(y(l+r)+kl)	(spontaneous rate)


  		




  
  165
  
    
% c=(approx)  ym/l  (saturated rate)


  		




  
  166
  
    
AN_IHCsynapseParams=[];             % clear the structure first


  		




  
  167
  
    
AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse


  		




  
  168
  
    
AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate


  		




  
  169
  
    
AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate


  		




  
  170
  
    

  		




  
  171
  
    
AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store


  		




  
  172
  
    
AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store


  		




  
  173
  
    

  		




  
  174
  
    
% reduce l to increase saturated rate


  		




  
  175
  
    
AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft


  		




  
  176
  
    
AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft


  		




  
  177
  
    

  		




  
  178
  
    
AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell


  		




  
  179
  
    
% AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell


  		




  
  180
  
    

  		




  
  181
  
    
AN_IHCsynapseParams.refractory_period=	0.00075;


  		




  
  182
  
    
% number of AN fibers at each BF (used only for spike generation)


  		




  
  183
  
    
AN_IHCsynapseParams.numFibers=	100; 


  		




  
  184
  
    
AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike


  		




  
  185
  
    

  		




  
  186
  
    
%%  #7 MacGregorMulti (first order brainstem neurons)


  		




  
  187
  
    
MacGregorMultiParams=[];


  		




  
  188
  
    
MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose


  		




  
  189
  
    
switch MacGregorMultiType


  		




  
  190
  
    
    case 'primary-like'


  		




  
  191
  
    
        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF


  		




  
  192
  
    
        MacGregorMultiParams.type = 'primary-like cell';


  		




  
  193
  
    
        MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers


  		




  
  194
  
    
        MacGregorMultiParams.dendriteLPfreq=200;  % dendritic filter


  		




  
  195
  
    
        MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike


  		




  
  196
  
    
        MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)


  		




  
  197
  
    
        MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)


  		




  
  198
  
    
        MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)


  		




  
  199
  
    
        MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S


  		




  
  200
  
    
        MacGregorMultiParams.tauGk=	0.0012; % K+ conductance tau (s)


  		




  
  201
  
    
        MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)


  		




  
  202
  
    
        MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)


  		




  
  203
  
    
        MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau


  		




  
  204
  
    
        MacGregorMultiParams.Er=-0.06;      % resting potential (V)


  		




  
  205
  
    
        MacGregorMultiParams.Eb=0.06;       % spike height (V)


  		




  
  206
  
    

  		




  
  207
  
    
    case 'chopper'


  		




  
  208
  
    
        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF


  		




  
  209
  
    
        MacGregorMultiParams.type = 'chopper cell';


  		




  
  210
  
    
        MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers


  		




  
  211
  
    
%         MacGregorMultiParams.fibersPerNeuron=6;  % N input fibers


  		




  
  212
  
    

  		




  
  213
  
    
        MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter


  		




  
  214
  
    
        MacGregorMultiParams.currentPerSpike=35e-9; % *per spike


  		




  
  215
  
    
%         MacGregorMultiParams.currentPerSpike=45e-9; % *per spike


  		




  
  216
  
    
        


  		




  
  217
  
    
        MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)


  		




  
  218
  
    
        MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)


  		




  
  219
  
    
        MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)


  		




  
  220
  
    
        MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S


  		




  
  221
  
    
        MacGregorMultiParams.tauGk=	0.0001;% K+ conductance tau (s)


  		




  
  222
  
    
        MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)


  		




  
  223
  
    
        MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)


  		




  
  224
  
    
        MacGregorMultiParams.tauTh=	0.02; % variable threshold tau


  		




  
  225
  
    
        MacGregorMultiParams.Er=-0.06;    % resting potential (V)


  		




  
  226
  
    
        MacGregorMultiParams.Eb=0.06;     % spike height (V)


  		




  
  227
  
    
        MacGregorMultiParams.PSTHbinWidth=	1e-4;


  		




  
  228
  
    
end


  		




  
  229
  
    

  		




  
  230
  
    
%%  #8 MacGregor (second-order neuron). Only one per channel


  		




  
  231
  
    
MacGregorParams=[];                 % clear the structure first


  		




  
  232
  
    
MacGregorParams.type = 'chopper cell';


  		




  
  233
  
    
MacGregorParams.fibersPerNeuron=10; % N input fibers


  		




  
  234
  
    
MacGregorParams.dendriteLPfreq=100; % dendritic filter


  		




  
  235
  
    
MacGregorParams.currentPerSpike=120e-9;% *(A) per spike


  		




  
  236
  
    

  		




  
  237
  
    
MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)


  		




  
  238
  
    
MacGregorParams.tauM=0.002;         % membrane time constant (s)


  		




  
  239
  
    
MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)


  		




  
  240
  
    
MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S


  		




  
  241
  
    
MacGregorParams.tauGk=	0.0003;     % K+ conductance tau (s)


  		




  
  242
  
    
MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)


  		




  
  243
  
    
MacGregorParams.c=	0;              % threshold shift on spike, (V)


  		




  
  244
  
    
MacGregorParams.tauTh=	0.02;       % variable threshold tau


  		




  
  245
  
    
MacGregorParams.Er=-0.06;           % resting potential (V)


  		




  
  246
  
    
MacGregorParams.Eb=0.06;            % spike height (V)


  		




  
  247
  
    
MacGregorParams.debugging=0;        % (special)


  		




  
  248
  
    
% wideband accepts input from all channels (of same fiber type)


  		




  
  249
  
    
% use wideband to create inhibitory units


  		




  
  250
  
    
MacGregorParams.wideband=0;         % special for wideband units


  		




  
  251
  
    
% MacGregorParams.saveAllData=0;


  		




  
  252
  
    

  		




  
  253
  
    
%%  #9 filteredSACF


  		




  
  254
  
    
minPitch=	300; maxPitch=	3000; numPitches=60;    % specify lags


  		




  
  255
  
    
pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));


  		




  
  256
  
    
filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector


  		




  
  257
  
    
filteredSACFParams.acfTau=	.003;       % time constant of running ACF


  		




  
  258
  
    
filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF


  		




  
  259
  
    
filteredSACFParams.plotFilteredSACF=1;  % 0 plots unfiltered ACFs


  		




  
  260
  
    
filteredSACFParams.plotACFs=0;          % special plot (see code)


  		




  
  261
  
    
%  filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags


  		




  
  262
  
    
filteredSACFParams.lagsProcedure=  'useAllLags';


  		




  
  263
  
    
% filteredSACFParams.lagsProcedure=  'useBernsteinLagWeights';


  		




  
  264
  
    
% filteredSACFParams.lagsProcedure=  'omitShortLags';


  		




  
  265
  
    
filteredSACFParams.criterionForOmittingLags=3;


  		




  
  266
  
    

  		




  
  267
  
    
% checks


  		




  
  268
  
    
if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron


  		




  
  269
  
    
    error('MacGregorMulti: too few input fibers for input to MacG unit')


  		




  
  270
  
    
end


  		




  
  271
  
    

  		




  
  272
  
    

  		




  
  273
  
    
%% write all parameters to the command window


  		




  
  274
  
    
% showParams is currently set at the top of htis function


  		




  
  275
  
    
if showParams


  		




  
  276
  
    
    fprintf('\n %%%%%%%%\n')


  		




  
  277
  
    
    fprintf('\n%s\n', method.parameterSource)


  		




  
  278
  
    
    fprintf('\n')


  		




  
  279
  
    
    nm=UTIL_paramsList(whos);


  		




  
  280
  
    
    for i=1:length(nm)


  		




  
  281
  
    
        %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])


  		




  
  282
  
    
        if ~strcmp(nm(i), 'method')


  		




  
  283
  
    
            eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])


  		




  
  284
  
    
        end


  		




  
  285
  
    
    end


  		




  
  286
  
    
end


  		




  
  287
  
    

  		




  
  288
  
    

  		




  
  289
  
    

  		




  
  290
  
    
% **********************************************************************  comparison data


  		




  
  291
  
    
% store individual data here for display on the multiThreshold GUI (if used)


  		




  
  292
  
    
% the final value in each vector is an identifier (BF or duration))


  		




  
  293
  
    
if isstruct(experiment)


  		




  
  294
  
    
    switch experiment.paradigm


  		




  
  295
  
    
        case {'IFMC','IFMC_8ms'}


  		




  
  296
  
    
            % based on MPa


  		




  
  297
  
    
            comparisonData=[


  		




  
  298
  
    
                66	51	49	48	46	45	54	250;


  		




  
  299
  
    
                60	54	46	42	39	49	65	500;


  		




  
  300
  
    
                64	51	38	32	33	59	75	1000;


  		




  
  301
  
    
                59	51	36	30	41	81	93	2000;


  		




  
  302
  
    
                71	63	53	44	36	76	95	4000;


  		




  
  303
  
    
                70	64	43	35	35	66	88	6000;


  		




  
  304
  
    
                110	110	110	110	110	110	110	8000;


  		




  
  305
  
    
                ];


  		




  
  306
  
    
            if length(BFlist)==1 && ~isempty(comparisonData)


  		




  
  307
  
    
                availableFrequencies=comparisonData(:,end)';


  		




  
  308
  
    
                findRow= find(BFlist==availableFrequencies);


  		




  
  309
  
    
                if ~isempty (findRow)


  		




  
  310
  
    
                    experiment.comparisonData=comparisonData(findRow,:);


  		




  
  311
  
    
                end


  		




  
  312
  
    
            end


  		




  
  313
  
    

  		




  
  314
  
    
        case {'TMC','TMC_8ms'}


  		




  
  315
  
    
            % based on MPa


  		




  
  316
  
    
            comparisonData=[


  		




  
  317
  
    
                48	58	63	68	75	80	85	92	99	250;


  		




  
  318
  
    
                33	39	40	49	52	61	64	77	79	500;


  		




  
  319
  
    
                39	42	50	81	83	92	96	97	110	1000;


  		




  
  320
  
    
                24	26	32	37	46	51	59	71	78	2000;


  		




  
  321
  
    
                65	68	77	85	91	93	110	110	110	4000;


  		




  
  322
  
    
                20	19	26	44	80	95	96	110	110	6000;


  		




  
  323
  
    
                ];


  		




  
  324
  
    
            if length(BFlist)==1 && ~isempty(comparisonData)


  		




  
  325
  
    
                availableFrequencies=comparisonData(:,end)';


  		




  
  326
  
    
                findRow= find(BFlist==availableFrequencies);


  		




  
  327
  
    
                if ~isempty (findRow)


  		




  
  328
  
    
                    experiment.comparisonData=comparisonData(findRow,:);


  		




  
  329
  
    
                end


  		




  
  330
  
    
            end


  		




  
  331
  
    

  		




  
  332
  
    
        case { 'absThreshold',  'absThreshold_8'}


  		




  
  333
  
    
            % MPa thresholds


  		




  
  334
  
    
            experiment.comparisonData=[


  		




  
  335
  
    
                32	26	16	18	22	22 0.008;


  		




  
  336
  
    
                16	13	6	9	15	11 0.500


  		




  
  337
  
    
                ];


  		




  
  338
  
    

  		




  
  339
  
    

  		




  
  340
  
    
        otherwise


  		




  
  341
  
    
            experiment.comparisonData=[];


  		




  
  342
  
    
    end


  		




  
  343
  
    
end


  		




  
  344
  
    

  		




  
  345
  
    

  		












  

    
      parameterStore/MAPparamsOHC.m
    
  





  
  1
  
    
function method=MAPparamsOHC ...


  		




  
  2
  
    
    (BFlist, sampleRate, showParams)


  		




  
  3
  
    
% MAPparams<> establishes a complete set of MAP parameters


  		




  
  4
  
    
% Parameter file names must be of the form <MAPparams> <name>


  		




  
  5
  
    
%


  		




  
  6
  
    
% input arguments


  		




  
  7
  
    
%  BFlist     (optional) specifies the desired list of channel BFs


  		




  
  8
  
    
%    otherwise defaults set below


  		




  
  9
  
    
%  sampleRate (optional), default is 50000.


  		




  
  10
  
    
%  showParams (optional) =1 prints out the complete set of parameters


  		




  
  11
  
    
% output argument


  		




  
  12
  
    
%  method passes a miscelleny of values


  		




  
  13
  
    

  		




  
  14
  
    
global inputStimulusParams OMEParams DRNLParams


  		




  
  15
  
    
global IHC_VResp_VivoParams IHCpreSynapseParams  AN_IHCsynapseParams


  		




  
  16
  
    
global MacGregorParams MacGregorMultiParams  filteredSACFParams


  		




  
  17
  
    
global experiment % used by calls from multiThreshold only


  		




  
  18
  
    
global IHC_cilia_RPParams


  		




  
  19
  
    

  		




  
  20
  
    
currentFile=mfilename;                      % i.e. the name of this mfile


  		




  
  21
  
    
method.parameterSource=currentFile(10:end); % for the record


  		




  
  22
  
    

  		




  
  23
  
    
switchOffEfferent=0;


  		




  
  24
  
    
efferentDelay=0.010;


  		




  
  25
  
    
method.segmentDuration=efferentDelay;


  		




  
  26
  
    

  		




  
  27
  
    
if nargin<3, showParams=0; end


  		




  
  28
  
    
if nargin<2, sampleRate=50000; end


  		




  
  29
  
    
if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default


  		




  
  30
  
    
    lowestBF=250; 	highestBF= 8000; 	numChannels=21;


  		




  
  31
  
    
    % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000


  		




  
  32
  
    
    BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));


  		




  
  33
  
    
end


  		




  
  34
  
    
% BFlist=1000;


  		




  
  35
  
    

  		




  
  36
  
    
% preserve for backward campatibility


  		




  
  37
  
    
method.nonlinCF=BFlist; 


  		




  
  38
  
    
method.dt=1/sampleRate; 


  		




  
  39
  
    

  		




  
  40
  
    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%


  		




  
  41
  
    
% set  model parameters


  		




  
  42
  
    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%


  		




  
  43
  
    

  		




  
  44
  
    
%%  #1 inputStimulus


  		




  
  45
  
    
inputStimulusParams=[];


  		




  
  46
  
    
inputStimulusParams.sampleRate= sampleRate; 


  		




  
  47
  
    

  		




  
  48
  
    
%%  #2 outerMiddleEar


  		




  
  49
  
    
OMEParams=[];  % clear the structure first


  		




  
  50
  
    
% outer ear resonances band pass filter  [gain lp order  hp]


  		




  
  51
  
    
OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];


  		




  
  52
  
    
                                       


  		




  
  53
  
    
% highpass stapes filter  


  		




  
  54
  
    
%  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)


  		




  
  55
  
    
OMEParams.OMEstapesLPcutoff= 1000;


  		




  
  56
  
    
OMEParams.stapesScalar=	     45e-9;


  		




  
  57
  
    

  		




  
  58
  
    
% Acoustic reflex: maximum attenuation should be around 25 dB Price (1966)


  		




  
  59
  
    
% i.e. a minimum ratio of 0.056.


  		




  
  60
  
    
if ~switchOffEfferent


  		




  
  61
  
    
    % 'spikes' model: AR based on brainstem spiking activity (LSR)


  		




  
  62
  
    
    OMEParams.rateToAttenuationFactor=0.003;   % * N(all ICspikes)


  		




  
  63
  
    
%     OMEParams.rateToAttenuationFactor=0;   % * N(all ICspikes)


  		




  
  64
  
    
    % 'probability model': Ar based on An firing probabilities (LSR)


  		




  
  65
  
    
    OMEParams.rateToAttenuationFactorProb=0.005;% * N(all ANrates)


  		




  
  66
  
    
%     OMEParams.rateToAttenuationFactorProb=0;% * N(all ANrates)


  		




  
  67
  
    
else


  		




  
  68
  
    
    OMEParams.rateToAttenuationFactor=0;        % 0= off


  		




  
  69
  
    
    OMEParams.rateToAttenuationFactorProb=0;    % 0= off


  		




  
  70
  
    
end


  		




  
  71
  
    
% asymptote should be around 100-200 ms


  		




  
  72
  
    
OMEParams.ARtau=.05; % AR smoothing function


  		




  
  73
  
    
% delay must be longer than the segment length


  		




  
  74
  
    
OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency


  		




  
  75
  
    
OMEParams.ARrateThreshold=0;


  		




  
  76
  
    

  		




  
  77
  
    
%%  #3 DRNL


  		




  
  78
  
    
DRNLParams=[];  % clear the structure first


  		




  
  79
  
    
DRNLParams.BFlist=BFlist;


  		




  
  80
  
    

  		




  
  81
  
    
% DRNL nonlinear path


  		




  
  82
  
    
DRNLParams.a=3e4;     % nonlinear path gain (below compression threshold)


  		




  
  83
  
    
DRNLParams.a=0;     % DRNL.a=0 means no OHCs (no nonlinear path)


  		




  
  84
  
    

  		




  
  85
  
    
DRNLParams.b=8e-6;    % *compression threshold raised compression


  		




  
  86
  
    
% DRNLParams.b=1;    % b=1 means no compression


  		




  
  87
  
    

  		




  
  88
  
    
DRNLParams.c=0.2;     % compression exponent


  		




  
  89
  
    
% nonlinear filters


  		




  
  90
  
    
DRNLParams.nonlinCFs=BFlist;


  		




  
  91
  
    
DRNLParams.nonlinOrder=	3;           % order of nonlinear gammatone filters


  		




  
  92
  
    
p=0.2895;   q=170;  % human  (% p=0.14;   q=366;  % cat)


  		




  
  93
  
    
DRNLParams.nlBWs=  p * BFlist + q;


  		




  
  94
  
    
DRNLParams.p=p;   DRNLParams.q=q;   % save p and q for printing only


  		




  
  95
  
    

  		




  
  96
  
    
% DRNL linear path:


  		




  
  97
  
    
DRNLParams.g=100;     % linear path gain factor


  		




  
  98
  
    
% linCF is not necessarily the same as nonlinCF


  		




  
  99
  
    
minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz


  		




  
  100
  
    
DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;


  		




  
  101
  
    
DRNLParams.linOrder=	3;           % order of linear gammatone filters


  		




  
  102
  
    
minLinBW=100; coeffLinBW=0.6531;


  		




  
  103
  
    
DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters


  		




  
  104
  
    

  		




  
  105
  
    
% DRNL MOC efferents


  		




  
  106
  
    
DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!


  		




  
  107
  
    
if ~switchOffEfferent


  		




  
  108
  
    
    % 'spikes' model: MOC based on brainstem spiking activity (HSR)


  		




  
  109
  
    
    DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC


  		




  
  110
  
    
    DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC


  		




  
  111
  
    
%      DRNLParams.rateToAttenuationFactor = 0;  % strength of MOC


  		




  
  112
  
    

  		




  
  113
  
    
    % 'spikes' model: MOC based on brainstem spiking activity (HSR)


  		




  
  114
  
    
    DRNLParams.rateToAttenuationFactorProb = .002;  % strength of MOC


  		




  
  115
  
    
else


  		




  
  116
  
    
    DRNLParams.rateToAttenuationFactor = 0;     % 0 = MOC off (probability)


  		




  
  117
  
    
    DRNLParams.rateToAttenuationFactorProb = 0; % 0 = MOC off (spikes)


  		




  
  118
  
    
end


  		




  
  119
  
    
DRNLParams.MOCtau =.03;                         % smoothing for MOC


  		




  
  120
  
    
DRNLParams.MOCrateThreshold =50;                % set to AN rate threshold


  		




  
  121
  
    

  		




  
  122
  
    

  		




  
  123
  
    
%% #4 IHC_cilia_RPParams


  		




  
  124
  
    

  		




  
  125
  
    
IHC_cilia_RPParams.tc=	0.0003;   % 0.0003 filter time simulates viscocity


  		




  
  126
  
    
% IHC_cilia_RPParams.tc=	0.0005;   % 0.0003 filter time simulates viscocity


  		




  
  127
  
    
IHC_cilia_RPParams.C=	0.05;      % 0.1 scalar (C_cilia ) 


  		




  
  128
  
    
IHC_cilia_RPParams.u0=	5e-9;       


  		




  
  129
  
    
IHC_cilia_RPParams.s0=	30e-9;


  		




  
  130
  
    
IHC_cilia_RPParams.u1=	1e-9;


  		




  
  131
  
    
IHC_cilia_RPParams.s1=	1e-9;


  		




  
  132
  
    

  		




  
  133
  
    
IHC_cilia_RPParams.Gmax= 5e-9;    % 2.5e-9 maximum conductance (Siemens)


  		




  
  134
  
    
IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance


  		




  
  135
  
    

  		




  
  136
  
    
%  #5 IHC_RP


  		




  
  137
  
    
IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)


  		




  
  138
  
    
IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)


  		




  
  139
  
    
IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)


  		




  
  140
  
    
% IHC_cilia_RPParams.Et=	0.07;          % endocochlear potential (V)


  		




  
  141
  
    

  		




  
  142
  
    
IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)


  		




  
  143
  
    
IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential


  		




  
  144
  
    
IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances


  		




  
  145
  
    

  		




  
  146
  
    

  		




  
  147
  
    
%%  #5 IHCpreSynapse


  		




  
  148
  
    
IHCpreSynapseParams=[];


  		




  
  149
  
    
IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance


  		




  
  150
  
    
IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance


  		




  
  151
  
    
IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential


  		




  
  152
  
    
IHCpreSynapseParams.beta=	400;	% determine Ca channel opening


  		




  
  153
  
    
IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening


  		




  
  154
  
    
IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms


  		




  
  155
  
    
IHCpreSynapseParams.power=	3;


  		




  
  156
  
    
% reminder: changing z has a strong effect on HF thresholds (like Et)


  		




  
  157
  
    
IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate


  		




  
  158
  
    

  		




  
  159
  
    
LSRtauCa=50e-6;            HSRtauCa=85e-6;            % seconds


  		




  
  160
  
    
% LSRtauCa=35e-6;            HSRtauCa=70e-6;            % seconds


  		




  
  161
  
    
IHCpreSynapseParams.tauCa= [LSRtauCa HSRtauCa]; %LSR and HSR fiber


  		




  
  162
  
    

  		




  
  163
  
    
%%  #6 AN_IHCsynapse


  		




  
  164
  
    
% c=kym/(y(l+r)+kl)	(spontaneous rate)


  		




  
  165
  
    
% c=(approx)  ym/l  (saturated rate)


  		




  
  166
  
    
AN_IHCsynapseParams=[];             % clear the structure first


  		




  
  167
  
    
AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse


  		




  
  168
  
    
AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate


  		




  
  169
  
    
AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate


  		




  
  170
  
    

  		




  
  171
  
    
AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store


  		




  
  172
  
    
AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store


  		




  
  173
  
    

  		




  
  174
  
    
% reduce l to increase saturated rate


  		




  
  175
  
    
AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft


  		




  
  176
  
    
AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft


  		




  
  177
  
    

  		




  
  178
  
    
AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell


  		




  
  179
  
    
% AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell


  		




  
  180
  
    

  		




  
  181
  
    
AN_IHCsynapseParams.refractory_period=	0.00075;


  		




  
  182
  
    
% number of AN fibers at each BF (used only for spike generation)


  		




  
  183
  
    
AN_IHCsynapseParams.numFibers=	100; 


  		




  
  184
  
    
AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike


  		




  
  185
  
    

  		




  
  186
  
    
%%  #7 MacGregorMulti (first order brainstem neurons)


  		




  
  187
  
    
MacGregorMultiParams=[];


  		




  
  188
  
    
MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose


  		




  
  189
  
    
switch MacGregorMultiType


  		




  
  190
  
    
    case 'primary-like'


  		




  
  191
  
    
        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF


  		




  
  192
  
    
        MacGregorMultiParams.type = 'primary-like cell';


  		




  
  193
  
    
        MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers


  		




  
  194
  
    
        MacGregorMultiParams.dendriteLPfreq=200;  % dendritic filter


  		




  
  195
  
    
        MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike


  		




  
  196
  
    
        MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)


  		




  
  197
  
    
        MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)


  		




  
  198
  
    
        MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)


  		




  
  199
  
    
        MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S


  		




  
  200
  
    
        MacGregorMultiParams.tauGk=	0.0012; % K+ conductance tau (s)


  		




  
  201
  
    
        MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)


  		




  
  202
  
    
        MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)


  		




  
  203
  
    
        MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau


  		




  
  204
  
    
        MacGregorMultiParams.Er=-0.06;      % resting potential (V)


  		




  
  205
  
    
        MacGregorMultiParams.Eb=0.06;       % spike height (V)


  		




  
  206
  
    

  		




  
  207
  
    
    case 'chopper'


  		




  
  208
  
    
        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF


  		




  
  209
  
    
        MacGregorMultiParams.type = 'chopper cell';


  		




  
  210
  
    
        MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers


  		




  
  211
  
    
%         MacGregorMultiParams.fibersPerNeuron=6;  % N input fibers


  		




  
  212
  
    

  		




  
  213
  
    
        MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter


  		




  
  214
  
    
        MacGregorMultiParams.currentPerSpike=35e-9; % *per spike


  		




  
  215
  
    
%         MacGregorMultiParams.currentPerSpike=45e-9; % *per spike


  		




  
  216
  
    
        


  		




  
  217
  
    
        MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)


  		




  
  218
  
    
        MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)


  		




  
  219
  
    
        MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)


  		




  
  220
  
    
        MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S


  		




  
  221
  
    
        MacGregorMultiParams.tauGk=	0.0001;% K+ conductance tau (s)


  		




  
  222
  
    
        MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)


  		




  
  223
  
    
        MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)


  		




  
  224
  
    
        MacGregorMultiParams.tauTh=	0.02; % variable threshold tau


  		




  
  225
  
    
        MacGregorMultiParams.Er=-0.06;    % resting potential (V)


  		




  
  226
  
    
        MacGregorMultiParams.Eb=0.06;     % spike height (V)


  		




  
  227
  
    
        MacGregorMultiParams.PSTHbinWidth=	1e-4;


  		




  
  228
  
    
end


  		




  
  229
  
    

  		




  
  230
  
    
%%  #8 MacGregor (second-order neuron). Only one per channel


  		




  
  231
  
    
MacGregorParams=[];                 % clear the structure first


  		




  
  232
  
    
MacGregorParams.type = 'chopper cell';


  		




  
  233
  
    
MacGregorParams.fibersPerNeuron=10; % N input fibers


  		




  
  234
  
    
MacGregorParams.dendriteLPfreq=100; % dendritic filter


  		




  
  235
  
    
MacGregorParams.currentPerSpike=120e-9;% *(A) per spike


  		




  
  236
  
    

  		




  
  237
  
    
MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)


  		




  
  238
  
    
MacGregorParams.tauM=0.002;         % membrane time constant (s)


  		




  
  239
  
    
MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)


  		




  
  240
  
    
MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S


  		




  
  241
  
    
MacGregorParams.tauGk=	0.0003;     % K+ conductance tau (s)


  		




  
  242
  
    
MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)


  		




  
  243
  
    
MacGregorParams.c=	0;              % threshold shift on spike, (V)


  		




  
  244
  
    
MacGregorParams.tauTh=	0.02;       % variable threshold tau


  		




  
  245
  
    
MacGregorParams.Er=-0.06;           % resting potential (V)


  		




  
  246
  
    
MacGregorParams.Eb=0.06;            % spike height (V)


  		




  
  247
  
    
MacGregorParams.debugging=0;        % (special)


  		




  
  248
  
    
% wideband accepts input from all channels (of same fiber type)


  		




  
  249
  
    
% use wideband to create inhibitory units


  		




  
  250
  
    
MacGregorParams.wideband=0;         % special for wideband units


  		




  
  251
  
    
% MacGregorParams.saveAllData=0;


  		




  
  252
  
    

  		




  
  253
  
    
%%  #9 filteredSACF


  		




  
  254
  
    
minPitch=	300; maxPitch=	3000; numPitches=60;    % specify lags


  		




  
  255
  
    
pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));


  		




  
  256
  
    
filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector


  		




  
  257
  
    
filteredSACFParams.acfTau=	.003;       % time constant of running ACF


  		




  
  258
  
    
filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF


  		




  
  259
  
    
filteredSACFParams.plotFilteredSACF=1;  % 0 plots unfiltered ACFs


  		




  
  260
  
    
filteredSACFParams.plotACFs=0;          % special plot (see code)


  		




  
  261
  
    
%  filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags


  		




  
  262
  
    
filteredSACFParams.lagsProcedure=  'useAllLags';


  		




  
  263
  
    
% filteredSACFParams.lagsProcedure=  'useBernsteinLagWeights';


  		




  
  264
  
    
% filteredSACFParams.lagsProcedure=  'omitShortLags';


  		




  
  265
  
    
filteredSACFParams.criterionForOmittingLags=3;


  		




  
  266
  
    

  		




  
  267
  
    
% checks


  		




  
  268
  
    
if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron


  		




  
  269
  
    
    error('MacGregorMulti: too few input fibers for input to MacG unit')


  		




  
  270
  
    
end


  		




  
  271
  
    

  		




  
  272
  
    

  		




  
  273
  
    
%% write all parameters to the command window


  		




  
  274
  
    
% showParams is currently set at the top of htis function


  		




  
  275
  
    
if showParams


  		




  
  276
  
    
    fprintf('\n %%%%%%%%\n')


  		




  
  277
  
    
    fprintf('\n%s\n', method.parameterSource)


  		




  
  278
  
    
    fprintf('\n')


  		




  
  279
  
    
    nm=UTIL_paramsList(whos);


  		




  
  280
  
    
    for i=1:length(nm)


  		




  
  281
  
    
        %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])


  		




  
  282
  
    
        if ~strcmp(nm(i), 'method')


  		




  
  283
  
    
            eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])


  		




  
  284
  
    
        end


  		




  
  285
  
    
    end


  		




  
  286
  
    
end


  		




  
  287
  
    

  		




  
  288
  
    

  		




  
  289
  
    

  		




  
  290
  
    
% **********************************************************************  comparison data


  		




  
  291
  
    
% store individual data here for display on the multiThreshold GUI (if used)


  		




  
  292
  
    
% the final value in each vector is an identifier (BF or duration))


  		




  
  293
  
    
if isstruct(experiment)


  		




  
  294
  
    
    switch experiment.paradigm


  		




  
  295
  
    
        case {'IFMC','IFMC_8ms'}


  		




  
  296
  
    
            % based on MPa


  		




  
  297
  
    
            comparisonData=[


  		




  
  298
  
    
                66	51	49	48	46	45	54	250;


  		




  
  299
  
    
                60	54	46	42	39	49	65	500;


  		




  
  300
  
    
                64	51	38	32	33	59	75	1000;


  		




  
  301
  
    
                59	51	36	30	41	81	93	2000;


  		




  
  302
  
    
                71	63	53	44	36	76	95	4000;


  		




  
  303
  
    
                70	64	43	35	35	66	88	6000;


  		




  
  304
  
    
                110	110	110	110	110	110	110	8000;


  		




  
  305
  
    
                ];


  		




  
  306
  
    
            if length(BFlist)==1 && ~isempty(comparisonData)


  		




  
  307
  
    
                availableFrequencies=comparisonData(:,end)';


  		




  
  308
  
    
                findRow= find(BFlist==availableFrequencies);


  		




  
  309
  
    
                if ~isempty (findRow)


  		




  
  310
  
    
                    experiment.comparisonData=comparisonData(findRow,:);


  		




  
  311
  
    
                end


  		




  
  312
  
    
            end


  		




  
  313
  
    

  		




  
  314
  
    
        case {'TMC','TMC_8ms'}


  		




  
  315
  
    
            % based on MPa


  		




  
  316
  
    
            comparisonData=[


  		




  
  317
  
    
                48	58	63	68	75	80	85	92	99	250;


  		




  
  318
  
    
                33	39	40	49	52	61	64	77	79	500;


  		




  
  319
  
    
                39	42	50	81	83	92	96	97	110	1000;


  		




  
  320
  
    
                24	26	32	37	46	51	59	71	78	2000;


  		




  
  321
  
    
                65	68	77	85	91	93	110	110	110	4000;


  		




  
  322
  
    
                20	19	26	44	80	95	96	110	110	6000;


  		




  
  323
  
    
                ];


  		




  
  324
  
    
            if length(BFlist)==1 && ~isempty(comparisonData)


  		




  
  325
  
    
                availableFrequencies=comparisonData(:,end)';


  		




  
  326
  
    
                findRow= find(BFlist==availableFrequencies);


  		




  
  327
  
    
                if ~isempty (findRow)


  		




  
  328
  
    
                    experiment.comparisonData=comparisonData(findRow,:);


  		




  
  329
  
    
                end


  		




  
  330
  
    
            end


  		




  
  331
  
    

  		




  
  332
  
    
        case { 'absThreshold',  'absThreshold_8'}


  		




  
  333
  
    
            % MPa thresholds


  		




  
  334
  
    
            experiment.comparisonData=[


  		




  
  335
  
    
                32	26	16	18	22	22 0.008;


  		




  
  336
  
    
                16	13	6	9	15	11 0.500


  		




  
  337
  
    
                ];


  		




  
  338
  
    

  		




  
  339
  
    

  		




  
  340
  
    
        otherwise


  		




  
  341
  
    
            experiment.comparisonData=[];


  		




  
  342
  
    
    end


  		




  
  343
  
    
end


  		




  
  344
  
    

  		




  
  345
  
    

  		












  

    
      parameterStore/MAPparamsStd.m
    
  





  
  1
  
    
function method=MAPparamsStd ...


  		




  
  2
  
    
    (BFlist, sampleRate, showParams)


  		




  
  3
  
    
% MAPparams<> establishes a complete set of MAP parameters


  		




  
  4
  
    
% Parameter file names must be of the form <MAPparams> <name>


  		




  
  5
  
    
%


  		




  
  6
  
    
% input arguments


  		




  
  7
  
    
%  BFlist     (optional) specifies the desired list of channel BFs


  		




  
  8
  
    
%    otherwise defaults set below


  		




  
  9
  
    
%  sampleRate (optional), default is 50000.


  		




  
  10
  
    
%  showParams (optional) =1 prints out the complete set of parameters


  		




  
  11
  
    
% output argument


  		




  
  12
  
    
%  method passes a miscelleny of values


  		




  
  13
  
    

  		




  
  14
  
    
global inputStimulusParams OMEParams DRNLParams


  		




  
  15
  
    
global IHC_VResp_VivoParams IHCpreSynapseParams  AN_IHCsynapseParams


  		




  
  16
  
    
global MacGregorParams MacGregorMultiParams  filteredSACFParams


  		




  
  17
  
    
global experiment % used by calls from multiThreshold only


  		




  
  18
  
    
global IHC_cilia_RPParams


  		




  
  19
  
    

  		




  
  20
  
    
currentFile=mfilename;                      % i.e. the name of this mfile


  		




  
  21
  
    
method.parameterSource=currentFile(10:end); % for the record


  		




  
  22
  
    

  		




  
  23
  
    
switchOffEfferent=0;


  		




  
  24
  
    
efferentDelay=0.010;


  		




  
  25
  
    
method.segmentDuration=efferentDelay;


  		




  
  26
  
    

  		




  
  27
  
    
if nargin<3, showParams=0; end


  		




  
  28
  
    
if nargin<2, sampleRate=50000; end


  		




  
  29
  
    
if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default


  		




  
  30
  
    
    lowestBF=250; 	highestBF= 8000; 	numChannels=21;


  		




  
  31
  
    
    % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000


  		




  
  32
  
    
    BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));


  		




  
  33
  
    
end


  		




  
  34
  
    
% BFlist=1000;


  		




  
  35
  
    

  		




  
  36
  
    
% preserve for backward campatibility


  		




  
  37
  
    
method.nonlinCF=BFlist; 


  		




  
  38
  
    
method.dt=1/sampleRate; 


  		




  
  39
  
    

  		




  
  40
  
    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%


  		




  
  41
  
    
% set  model parameters


  		




  
  42
  
    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%


  		




  
  43
  
    

  		




  
  44
  
    
%%  #1 inputStimulus


  		




  
  45
  
    
inputStimulusParams=[];


  		




  
  46
  
    
inputStimulusParams.sampleRate= sampleRate; 


  		




  
  47
  
    

  		




  
  48
  
    
%%  #2 outerMiddleEar


  		




  
  49
  
    
OMEParams=[];  % clear the structure first


  		




  
  50
  
    
% outer ear resonances band pass filter  [gain lp order  hp]


  		




  
  51
  
    
OMEParams.externalResonanceFilters=      [ 10 1 1000 4000];


  		




  
  52
  
    
                                       


  		




  
  53
  
    
% highpass stapes filter  


  		




  
  54
  
    
%  Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)


  		




  
  55
  
    
OMEParams.OMEstapesLPcutoff= 1000;


  		




  
  56
  
    
OMEParams.stapesScalar=	     45e-9;


  		




  
  57
  
    

  		




  
  58
  
    
% Acoustic reflex: maximum attenuation should be around 25 dB Price (1966)


  		




  
  59
  
    
% i.e. a minimum ratio of 0.056.


  		




  
  60
  
    
if ~switchOffEfferent


  		




  
  61
  
    
    % 'spikes' model: AR based on brainstem spiking activity (LSR)


  		




  
  62
  
    
    OMEParams.rateToAttenuationFactor=0.003;   % * N(all ICspikes)


  		




  
  63
  
    
%     OMEParams.rateToAttenuationFactor=0;   % * N(all ICspikes)


  		




  
  64
  
    
    % 'probability model': Ar based on An firing probabilities (LSR)


  		




  
  65
  
    
    OMEParams.rateToAttenuationFactorProb=0.005;% * N(all ANrates)


  		




  
  66
  
    
%     OMEParams.rateToAttenuationFactorProb=0;% * N(all ANrates)


  		




  
  67
  
    
else


  		




  
  68
  
    
    OMEParams.rateToAttenuationFactor=0;        % 0= off


  		




  
  69
  
    
    OMEParams.rateToAttenuationFactorProb=0;    % 0= off


  		




  
  70
  
    
end


  		




  
  71
  
    
% asymptote should be around 100-200 ms


  		




  
  72
  
    
OMEParams.ARtau=.05; % AR smoothing function


  		




  
  73
  
    
% delay must be longer than the segment length


  		




  
  74
  
    
OMEParams.ARdelay=efferentDelay;  %Moss gives 8.5 ms latency


  		




  
  75
  
    
OMEParams.ARrateThreshold=0;


  		




  
  76
  
    

  		




  
  77
  
    
%%  #3 DRNL


  		




  
  78
  
    
DRNLParams=[];  % clear the structure first


  		




  
  79
  
    
DRNLParams.BFlist=BFlist;


  		




  
  80
  
    

  		




  
  81
  
    
% DRNL nonlinear path


  		




  
  82
  
    
DRNLParams.a=3e4;     % nonlinear path gain (below compression threshold)


  		




  
  83
  
    
% DRNLParams.a=3e2;     % DRNL.a=0 means no OHCs (no nonlinear path)


  		




  
  84
  
    

  		




  
  85
  
    
DRNLParams.b=8e-6;    % *compression threshold raised compression


  		




  
  86
  
    
% DRNLParams.b=1;    % b=1 means no compression


  		




  
  87
  
    

  		




  
  88
  
    
DRNLParams.c=0.2;     % compression exponent


  		




  
  89
  
    
% nonlinear filters


  		




  
  90
  
    
DRNLParams.nonlinCFs=BFlist;


  		




  
  91
  
    
DRNLParams.nonlinOrder=	3;           % order of nonlinear gammatone filters


  		




  
  92
  
    
p=0.2895;   q=170;  % human  (% p=0.14;   q=366;  % cat)


  		




  
  93
  
    
DRNLParams.nlBWs=  p * BFlist + q;


  		




  
  94
  
    
DRNLParams.p=p;   DRNLParams.q=q;   % save p and q for printing only


  		




  
  95
  
    

  		




  
  96
  
    
% DRNL linear path:


  		




  
  97
  
    
DRNLParams.g=100;     % linear path gain factor


  		




  
  98
  
    
% linCF is not necessarily the same as nonlinCF


  		




  
  99
  
    
minLinCF=153.13; coeffLinCF=0.7341;   % linCF>nonlinBF for BF < 1 kHz


  		




  
  100
  
    
DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;


  		




  
  101
  
    
DRNLParams.linOrder=	3;           % order of linear gammatone filters


  		




  
  102
  
    
minLinBW=100; coeffLinBW=0.6531;


  		




  
  103
  
    
DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear  filters


  		




  
  104
  
    

  		




  
  105
  
    
% DRNL MOC efferents


  		




  
  106
  
    
DRNLParams.MOCdelay = efferentDelay;            % must be < segment length!


  		




  
  107
  
    
if ~switchOffEfferent


  		




  
  108
  
    
    % 'spikes' model: MOC based on brainstem spiking activity (HSR)


  		




  
  109
  
    
    DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC


  		




  
  110
  
    
    DRNLParams.rateToAttenuationFactor = .009;  % strength of MOC


  		




  
  111
  
    
%      DRNLParams.rateToAttenuationFactor = 0;  % strength of MOC


  		




  
  112
  
    

  		




  
  113
  
    
    % 'spikes' model: MOC based on brainstem spiking activity (HSR)


  		




  
  114
  
    
    DRNLParams.rateToAttenuationFactorProb = .002;  % strength of MOC


  		




  
  115
  
    
else


  		




  
  116
  
    
    DRNLParams.rateToAttenuationFactor = 0;     % 0 = MOC off (probability)


  		




  
  117
  
    
    DRNLParams.rateToAttenuationFactorProb = 0; % 0 = MOC off (spikes)


  		




  
  118
  
    
end


  		




  
  119
  
    
DRNLParams.MOCtau =.03;                         % smoothing for MOC


  		




  
  120
  
    
DRNLParams.MOCrateThreshold =50;                % set to AN rate threshold


  		




  
  121
  
    

  		




  
  122
  
    

  		




  
  123
  
    
%% #4 IHC_cilia_RPParams


  		




  
  124
  
    

  		




  
  125
  
    
IHC_cilia_RPParams.tc=	0.0003;   % 0.0003 filter time simulates viscocity


  		




  
  126
  
    
% IHC_cilia_RPParams.tc=	0.0005;   % 0.0003 filter time simulates viscocity


  		




  
  127
  
    
IHC_cilia_RPParams.C=	0.05;      % 0.1 scalar (C_cilia ) 


  		




  
  128
  
    
IHC_cilia_RPParams.u0=	5e-9;       


  		




  
  129
  
    
IHC_cilia_RPParams.s0=	30e-9;


  		




  
  130
  
    
IHC_cilia_RPParams.u1=	1e-9;


  		




  
  131
  
    
IHC_cilia_RPParams.s1=	1e-9;


  		




  
  132
  
    

  		




  
  133
  
    
IHC_cilia_RPParams.Gmax= 5e-9;    % 2.5e-9 maximum conductance (Siemens)


  		




  
  134
  
    
IHC_cilia_RPParams.Ga=	1e-9;  % 4.3e-9 fixed apical membrane conductance


  		




  
  135
  
    

  		




  
  136
  
    
%  #5 IHC_RP


  		




  
  137
  
    
IHC_cilia_RPParams.Cab=	4e-012;         % IHC capacitance (F)


  		




  
  138
  
    
IHC_cilia_RPParams.Cab=	1e-012;         % IHC capacitance (F)


  		




  
  139
  
    
IHC_cilia_RPParams.Et=	0.100;          % endocochlear potential (V)


  		




  
  140
  
    
% IHC_cilia_RPParams.Et=	0.07;          % endocochlear potential (V)


  		




  
  141
  
    

  		




  
  142
  
    
IHC_cilia_RPParams.Gk=	2e-008;         % 1e-8 potassium conductance (S)


  		




  
  143
  
    
IHC_cilia_RPParams.Ek=	-0.08;          % -0.084 K equilibrium potential


  		




  
  144
  
    
IHC_cilia_RPParams.Rpc=	0.04;           % combined resistances


  		




  
  145
  
    

  		




  
  146
  
    

  		




  
  147
  
    
%%  #5 IHCpreSynapse


  		




  
  148
  
    
IHCpreSynapseParams=[];


  		




  
  149
  
    
IHCpreSynapseParams.GmaxCa=	14e-9;% maximum calcium conductance


  		




  
  150
  
    
IHCpreSynapseParams.GmaxCa=	12e-9;% maximum calcium conductance


  		




  
  151
  
    
IHCpreSynapseParams.ECa=	0.066;  % calcium equilibrium potential


  		




  
  152
  
    
IHCpreSynapseParams.beta=	400;	% determine Ca channel opening


  		




  
  153
  
    
IHCpreSynapseParams.gamma=	100;	% determine Ca channel opening


  		




  
  154
  
    
IHCpreSynapseParams.tauM=	0.00005;	% membrane time constant ?0.1ms


  		




  
  155
  
    
IHCpreSynapseParams.power=	3;


  		




  
  156
  
    
% reminder: changing z has a strong effect on HF thresholds (like Et)


  		




  
  157
  
    
IHCpreSynapseParams.z=	    2e42;   % scalar Ca -> vesicle release rate


  		




  
  158
  
    

  		




  
  159
  
    
LSRtauCa=50e-6;            HSRtauCa=85e-6;            % seconds


  		




  
  160
  
    
% LSRtauCa=35e-6;            HSRtauCa=70e-6;            % seconds


  		




  
  161
  
    
IHCpreSynapseParams.tauCa= [LSRtauCa HSRtauCa]; %LSR and HSR fiber


  		




  
  162
  
    

  		




  
  163
  
    
%%  #6 AN_IHCsynapse


  		




  
  164
  
    
% c=kym/(y(l+r)+kl)	(spontaneous rate)


  		




  
  165
  
    
% c=(approx)  ym/l  (saturated rate)


  		




  
  166
  
    
AN_IHCsynapseParams=[];             % clear the structure first


  		




  
  167
  
    
AN_IHCsynapseParams.M=	12;         % maximum vesicles at synapse


  		




  
  168
  
    
AN_IHCsynapseParams.y=	4;          % depleted vesicle replacement rate


  		




  
  169
  
    
AN_IHCsynapseParams.y=	6;          % depleted vesicle replacement rate


  		




  
  170
  
    

  		




  
  171
  
    
AN_IHCsynapseParams.x=	30;         % replenishment from re-uptake store


  		




  
  172
  
    
AN_IHCsynapseParams.x=	60;         % replenishment from re-uptake store


  		




  
  173
  
    

  		




  
  174
  
    
% reduce l to increase saturated rate


  		




  
  175
  
    
AN_IHCsynapseParams.l=	100; % *loss rate of vesicles from the cleft


  		




  
  176
  
    
AN_IHCsynapseParams.l=	250; % *loss rate of vesicles from the cleft


  		




  
  177
  
    

  		




  
  178
  
    
AN_IHCsynapseParams.r=	500; % *reuptake rate from cleft into cell


  		




  
  179
  
    
% AN_IHCsynapseParams.r=	300; % *reuptake rate from cleft into cell


  		




  
  180
  
    

  		




  
  181
  
    
AN_IHCsynapseParams.refractory_period=	0.00075;


  		




  
  182
  
    
% number of AN fibers at each BF (used only for spike generation)


  		




  
  183
  
    
AN_IHCsynapseParams.numFibers=	100; 


  		




  
  184
  
    
AN_IHCsynapseParams.TWdelay=0.004;  % ?delay before stimulus first spike


  		




  
  185
  
    

  		




  
  186
  
    
%%  #7 MacGregorMulti (first order brainstem neurons)


  		




  
  187
  
    
MacGregorMultiParams=[];


  		




  
  188
  
    
MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose


  		




  
  189
  
    
switch MacGregorMultiType


  		




  
  190
  
    
    case 'primary-like'


  		




  
  191
  
    
        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF


  		




  
  192
  
    
        MacGregorMultiParams.type = 'primary-like cell';


  		




  
  193
  
    
        MacGregorMultiParams.fibersPerNeuron=4;   % N input fibers


  		




  
  194
  
    
        MacGregorMultiParams.dendriteLPfreq=200;  % dendritic filter


  		




  
  195
  
    
        MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike


  		




  
  196
  
    
        MacGregorMultiParams.Cap=4.55e-9;   % cell capacitance (Siemens)


  		




  
  197
  
    
        MacGregorMultiParams.tauM=5e-4;     % membrane time constant (s)


  		




  
  198
  
    
        MacGregorMultiParams.Ek=-0.01;      % K+ eq. potential (V)


  		




  
  199
  
    
        MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S


  		




  
  200
  
    
        MacGregorMultiParams.tauGk=	0.0012; % K+ conductance tau (s)


  		




  
  201
  
    
        MacGregorMultiParams.Th0=	0.01;   % equilibrium threshold (V)


  		




  
  202
  
    
        MacGregorMultiParams.c=	0.01;       % threshold shift on spike, (V)


  		




  
  203
  
    
        MacGregorMultiParams.tauTh=	0.015;  % variable threshold tau


  		




  
  204
  
    
        MacGregorMultiParams.Er=-0.06;      % resting potential (V)


  		




  
  205
  
    
        MacGregorMultiParams.Eb=0.06;       % spike height (V)


  		




  
  206
  
    

  		




  
  207
  
    
    case 'chopper'


  		




  
  208
  
    
        MacGregorMultiParams.nNeuronsPerBF=	10;   % N neurons per BF


  		




  
  209
  
    
        MacGregorMultiParams.type = 'chopper cell';


  		




  
  210
  
    
        MacGregorMultiParams.fibersPerNeuron=10;  % N input fibers


  		




  
  211
  
    
%         MacGregorMultiParams.fibersPerNeuron=6;  % N input fibers


  		




  
  212
  
    

  		




  
  213
  
    
        MacGregorMultiParams.dendriteLPfreq=50;   % dendritic filter


  		




  
  214
  
    
        MacGregorMultiParams.currentPerSpike=35e-9; % *per spike


  		




  
  215
  
    
%         MacGregorMultiParams.currentPerSpike=45e-9; % *per spike


  		




  
  216
  
    
        


  		




  
  217
  
    
        MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)


  		




  
  218
  
    
        MacGregorMultiParams.tauM=0.002;  % membrane time constant (s)


  		




  
  219
  
    
        MacGregorMultiParams.Ek=-0.01;    % K+ eq. potential (V)


  		




  
  220
  
    
        MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S


  		




  
  221
  
    
        MacGregorMultiParams.tauGk=	0.0001;% K+ conductance tau (s)


  		




  
  222
  
    
        MacGregorMultiParams.Th0=	0.01; % equilibrium threshold (V)


  		




  
  223
  
    
        MacGregorMultiParams.c=	0;        % threshold shift on spike, (V)


  		




  
  224
  
    
        MacGregorMultiParams.tauTh=	0.02; % variable threshold tau


  		




  
  225
  
    
        MacGregorMultiParams.Er=-0.06;    % resting potential (V)


  		




  
  226
  
    
        MacGregorMultiParams.Eb=0.06;     % spike height (V)


  		




  
  227
  
    
        MacGregorMultiParams.PSTHbinWidth=	1e-4;


  		




  
  228
  
    
end


  		




  
  229
  
    

  		




  
  230
  
    
%%  #8 MacGregor (second-order neuron). Only one per channel


  		




  
  231
  
    
MacGregorParams=[];                 % clear the structure first


  		




  
  232
  
    
MacGregorParams.type = 'chopper cell';


  		




  
  233
  
    
MacGregorParams.fibersPerNeuron=10; % N input fibers


  		




  
  234
  
    
MacGregorParams.dendriteLPfreq=100; % dendritic filter


  		




  
  235
  
    
MacGregorParams.currentPerSpike=120e-9;% *(A) per spike


  		




  
  236
  
    

  		




  
  237
  
    
MacGregorParams.Cap=16.7e-9;        % cell capacitance (Siemens)


  		




  
  238
  
    
MacGregorParams.tauM=0.002;         % membrane time constant (s)


  		




  
  239
  
    
MacGregorParams.Ek=-0.01;           % K+ eq. potential (V)


  		




  
  240
  
    
MacGregorParams.dGkSpike=1.33e-4;   % K+ cond.shift on spike,S


  		




  
  241
  
    
MacGregorParams.tauGk=	0.0003;     % K+ conductance tau (s)


  		




  
  242
  
    
MacGregorParams.Th0=	0.01;       % equilibrium threshold (V)


  		




  
  243
  
    
MacGregorParams.c=	0;              % threshold shift on spike, (V)


  		




  
  244
  
    
MacGregorParams.tauTh=	0.02;       % variable threshold tau


  		




  
  245
  
    
MacGregorParams.Er=-0.06;           % resting potential (V)


  		




  
  246
  
    
MacGregorParams.Eb=0.06;            % spike height (V)


  		




  
  247
  
    
MacGregorParams.debugging=0;        % (special)


  		




  
  248
  
    
% wideband accepts input from all channels (of same fiber type)


  		




  
  249
  
    
% use wideband to create inhibitory units


  		




  
  250
  
    
MacGregorParams.wideband=0;         % special for wideband units


  		




  
  251
  
    
% MacGregorParams.saveAllData=0;


  		




  
  252
  
    

  		




  
  253
  
    
%%  #9 filteredSACF


  		




  
  254
  
    
minPitch=	300; maxPitch=	3000; numPitches=60;    % specify lags


  		




  
  255
  
    
pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));


  		




  
  256
  
    
filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector


  		




  
  257
  
    
filteredSACFParams.acfTau=	.003;       % time constant of running ACF


  		




  
  258
  
    
filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF


  		




  
  259
  
    
filteredSACFParams.plotFilteredSACF=1;  % 0 plots unfiltered ACFs


  		




  
  260
  
    
filteredSACFParams.plotACFs=0;          % special plot (see code)


  		




  
  261
  
    
%  filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags


  		




  
  262
  
    
filteredSACFParams.lagsProcedure=  'useAllLags';


  		




  
  263
  
    
% filteredSACFParams.lagsProcedure=  'useBernsteinLagWeights';


  		




  
  264
  
    
% filteredSACFParams.lagsProcedure=  'omitShortLags';


  		




  
  265
  
    
filteredSACFParams.criterionForOmittingLags=3;


  		




  
  266
  
    

  		




  
  267
  
    
% checks


  		




  
  268
  
    
if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron


  		




  
  269
  
    
    error('MacGregorMulti: too few input fibers for input to MacG unit')


  		




  
  270
  
    
end


  		




  
  271
  
    

  		




  
  272
  
    

  		




  
  273
  
    
%% write all parameters to the command window


  		




  
  274
  
    
% showParams is currently set at the top of htis function


  		




  
  275
  
    
if showParams


  		




  
  276
  
    
    fprintf('\n %%%%%%%%\n')


  		




  
  277
  
    
    fprintf('\n%s\n', method.parameterSource)


  		




  
  278
  
    
    fprintf('\n')


  		




  
  279
  
    
    nm=UTIL_paramsList(whos);


  		




  
  280
  
    
    for i=1:length(nm)


  		




  
  281
  
    
        %         eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])


  		




  
  282
  
    
        if ~strcmp(nm(i), 'method')


  		




  
  283
  
    
            eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])


  		




  
  284
  
    
        end


  		




  
  285
  
    
    end


  		




  
  286
  
    
end


  		




  
  287
  
    

  		




  
  288
  
    

  		




  
  289
  
    

  		




  
  290
  
    
% **********************************************************************  comparison data


  		




  
  291
  
    
% store individual data here for display on the multiThreshold GUI (if used)


  		




  
  292
  
    
% the final value in each vector is an identifier (BF or duration))


  		




  
  293
  
    
if isstruct(experiment)


  		




  
  294
  
    
    switch experiment.paradigm


  		




  
  295
  
    
        case {'IFMC','IFMC_8ms'}


  		




  
  296
  
    
            % based on MPa


  		




  
  297
  
    
            comparisonData=[


  		




  
  298
  
    
                66	51	49	48	46	45	54	250;


  		




  
  299
  
    
                60	54	46	42	39	49	65	500;


  		




  
  300
  
    
                64	51	38	32	33	59	75	1000;


  		




  
  301
  
    
                59	51	36	30	41	81	93	2000;


  		




  
  302
  
    
                71	63	53	44	36	76	95	4000;


  		




  
  303
  
    
                70	64	43	35	35	66	88	6000;


  		




  
  304
  
    
                110	110	110	110	110	110	110	8000;


  		




  
  305
  
    
                ];


  		




  
  306
  
    
            if length(BFlist)==1 && ~isempty(comparisonData)


  		




  
  307
  
    
                availableFrequencies=comparisonData(:,end)';


  		




  
  308
  
    
                findRow= find(BFlist==availableFrequencies);


  		




  
  309
  
    
                if ~isempty (findRow)


  		




  
  310
  
    
                    experiment.comparisonData=comparisonData(findRow,:);


  		




  
  311
  
    
                end


  		




  
  312
  
    
            end


  		




  
  313
  
    

  		




  
  314
  
    
        case {'TMC','TMC_8ms'}


  		




  
  315
  
    
            % based on MPa


  		




  
  316
  
    
            comparisonData=[


  		




  
  317
  
    
                48	58	63	68	75	80	85	92	99	250;


  		




  
  318
  
    
                33	39	40	49	52	61	64	77	79	500;


  		




  
  319
  
    
                39	42	50	81	83	92	96	97	110	1000;


  		




  
  320
  
    
                24	26	32	37	46	51	59	71	78	2000;


  		




  
  321
  
    
                65	68	77	85	91	93	110	110	110	4000;


  		




  
  322
  
    
                20	19	26	44	80	95	96	110	110	6000;


  		




  
  323
  
    
                ];


  		




  
  324
  
    
            if length(BFlist)==1 && ~isempty(comparisonData)


  		




  
  325
  
    
                availableFrequencies=comparisonData(:,end)';


  		




  
  326
  
    
                findRow= find(BFlist==availableFrequencies);


  		




  
  327
  
    
                if ~isempty (findRow)


  		




  
  328
  
    
                    experiment.comparisonData=comparisonData(findRow,:);


  		




  
  329
  
    
                end


  		




  
  330
  
    
            end


  		




  
  331
  
    

  		




  
  332
  
    
        case { 'absThreshold',  'absThreshold_8'}


  		




  
  333
  
    
            % MPa thresholds


  		




  
  334
  
    
            experiment.comparisonData=[


  		




  
  335
  
    
                32	26	16	18	22	22 0.008;


  		




  
  336
  
    
                16	13	6	9	15	11 0.500


  		




  
  337
  
    
                ];


  		




  
  338
  
    

  		




  
  339
  
    

  		




  
  340
  
    
        otherwise


  		




  
  341
  
    
            experiment.comparisonData=[];


  		




  
  342
  
    
    end


  		




  
  343
  
    
end


  		




  
  344
  
    

  		




  
  345
  
    

  		












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