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comparison parameterStore/MAPparamsNormalIC.m @ 30:1a502830d462

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author Ray Meddis <rmeddis@essex.ac.uk>
date Mon, 11 Jul 2011 14:31:29 +0100
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children 82fb37eb430e
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29:b51bf546ca3f 30:1a502830d462
1 function method=MAPparamsNormalIC ...
2 (BFlist, sampleRate, showParams, paramChanges)
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 IHC_cilia_RPParams
15 global IHC_VResp_VivoParams IHCpreSynapseParams AN_IHCsynapseParams
16 global MacGregorParams MacGregorMultiParams filteredSACFParams
17 global experiment % used by calls from multiThreshold only
18
19
20 currentFile=mfilename; % i.e. the name of this mfile
21 method.parameterSource=currentFile(10:end); % for the record
22
23 efferentDelay=0.010;
24 method.segmentDuration=efferentDelay;
25
26 if nargin<3, showParams=0; end
27 if nargin<2, sampleRate=50000; end
28 if nargin<1 || BFlist(1)<0 % if BFlist= -1, set BFlist to default
29 lowestBF=250; highestBF= 8000; numChannels=21;
30 % 21 chs (250-8k)includes BFs at 250 500 1000 2000 4000 8000
31 BFlist=round(logspace(log10(lowestBF),log10(highestBF),numChannels));
32 end
33 % BFlist=1000;
34
35 % preserve for backward campatibility
36 method.nonlinCF=BFlist;
37 method.dt=1/sampleRate;
38
39 %%%%%%%%%%%%%%%%%%%%%%%%%%%%
40 % set model parameters
41 %%%%%%%%%%%%%%%%%%%%%%%%%%%%
42
43 %% #1 inputStimulus
44 inputStimulusParams=[];
45 inputStimulusParams.sampleRate= sampleRate;
46
47 %% #2 outerMiddleEar
48 OMEParams=[]; % clear the structure first
49 % outer ear resonances band pass filter [gain lp order hp]
50 OMEParams.externalResonanceFilters= [ 10 1 1000 4000];
51
52 % highpass stapes filter
53 % Huber gives 2e-9 m at 80 dB and 1 kHz (2e-13 at 0 dB SPL)
54 OMEParams.OMEstapesLPcutoff= 1000;
55 OMEParams.stapesScalar= 45e-9;
56
57 % Acoustic reflex: maximum attenuation should be around 25 dB Price (1966)
58 % i.e. a minimum ratio of 0.056.
59 % 'spikes' model: AR based on brainstem spiking activity (LSR)
60 OMEParams.rateToAttenuationFactor=0.006; % * N(all ICspikes)
61 % OMEParams.rateToAttenuationFactor=0; % * N(all ICspikes)
62
63 % 'probability model': Ar based on AN firing probabilities (LSR)
64 OMEParams.rateToAttenuationFactorProb=0.01;% * N(all ANrates)
65 % OMEParams.rateToAttenuationFactorProb=0;% * N(all ANrates)
66
67 % asymptote should be around 100-200 ms
68 OMEParams.ARtau=.05; % AR smoothing function
69 % delay must be longer than the segment length
70 OMEParams.ARdelay=efferentDelay; %Moss gives 8.5 ms latency
71 OMEParams.ARrateThreshold=0;
72
73 %% #3 DRNL
74 DRNLParams=[]; % clear the structure first
75 DRNLParams.BFlist=BFlist;
76
77 % DRNL nonlinear path
78 DRNLParams.a=5e4; % DRNL.a=0 means no OHCs (no nonlinear path)
79 DRNLParams.a=2e4; % DRNL.a=0 means no OHCs (no nonlinear path)
80
81 DRNLParams.b=8e-6; % *compression threshold raised compression
82 % DRNLParams.b=1; % b=1 means no compression
83
84 DRNLParams.c=0.2; % compression exponent
85 % nonlinear filters
86 DRNLParams.nonlinCFs=BFlist;
87 DRNLParams.nonlinOrder= 3; % order of nonlinear gammatone filters
88 p=0.2895; q=170; % human (% p=0.14; q=366; % cat)
89 DRNLParams.nlBWs= p * BFlist + q;
90 DRNLParams.p=p; DRNLParams.q=q; % save p and q for printing only
91
92 % DRNL linear path:
93 DRNLParams.g=100; % linear path gain factor
94 % linCF is not necessarily the same as nonlinCF
95 minLinCF=153.13; coeffLinCF=0.7341; % linCF>nonlinBF for BF < 1 kHz
96 DRNLParams.linCFs=minLinCF+coeffLinCF*BFlist;
97 DRNLParams.linOrder= 3; % order of linear gammatone filters
98 minLinBW=100; coeffLinBW=0.6531;
99 DRNLParams.linBWs=minLinBW + coeffLinBW*BFlist; % bandwidths of linear filters
100
101 % DRNL MOC efferents
102 DRNLParams.MOCdelay = efferentDelay; % must be < segment length!
103
104 % 'spikes' model: MOC based on brainstem spiking activity (HSR)
105 DRNLParams.rateToAttenuationFactor = .01; % strength of MOC
106 % DRNLParams.rateToAttenuationFactor = 0; % strength of MOC
107 % 'probability' model: MOC based on AN spiking activity (HSR)
108 DRNLParams.rateToAttenuationFactorProb = .0055; % strength of MOC
109 % DRNLParams.rateToAttenuationFactorProb = .0; % strength of MOC
110 DRNLParams.MOCrateThresholdProb =70; % spikes/s probability only
111
112 DRNLParams.MOCtau =.1; % smoothing for MOC
113
114
115 %% #4 IHC_cilia_RPParams
116
117 IHC_cilia_RPParams.tc= 0.0003; % 0.0003 filter time simulates viscocity
118 % IHC_cilia_RPParams.tc= 0.0005; % 0.0003 filter time simulates viscocity
119 IHC_cilia_RPParams.C= 0.03; % 0.1 scalar (C_cilia )
120 IHC_cilia_RPParams.u0= 5e-9;
121 IHC_cilia_RPParams.s0= 30e-9;
122 IHC_cilia_RPParams.u1= 1e-9;
123 IHC_cilia_RPParams.s1= 1e-9;
124
125 IHC_cilia_RPParams.Gmax= 6e-9; % 2.5e-9 maximum conductance (Siemens)
126 IHC_cilia_RPParams.Ga= 1e-9; % 4.3e-9 fixed apical membrane conductance
127 IHC_cilia_RPParams.Ga= .8e-9; % 4.3e-9 fixed apical membrane conductance
128
129 % #5 IHC_RP
130 IHC_cilia_RPParams.Cab= 4e-012; % IHC capacitance (F)
131 % IHC_cilia_RPParams.Cab= 1e-012; % IHC capacitance (F)
132 IHC_cilia_RPParams.Et= 0.100; % endocochlear potential (V)
133
134 IHC_cilia_RPParams.Gk= 2e-008; % 1e-8 potassium conductance (S)
135 IHC_cilia_RPParams.Ek= -0.08; % -0.084 K equilibrium potential
136 IHC_cilia_RPParams.Rpc= 0.04; % combined resistances
137
138
139 %% #5 IHCpreSynapse
140 IHCpreSynapseParams=[];
141 IHCpreSynapseParams.GmaxCa= 14e-9;% maximum calcium conductance
142 IHCpreSynapseParams.GmaxCa= 12e-9;% maximum calcium conductance
143 IHCpreSynapseParams.ECa= 0.066; % calcium equilibrium potential
144 IHCpreSynapseParams.beta= 400; % determine Ca channel opening
145 IHCpreSynapseParams.gamma= 100; % determine Ca channel opening
146 IHCpreSynapseParams.tauM= 0.00005; % membrane time constant ?0.1ms
147 IHCpreSynapseParams.power= 3;
148 % reminder: changing z has a strong effect on HF thresholds (like Et)
149 IHCpreSynapseParams.z= 2e42; % scalar Ca -> vesicle release rate
150
151 LSRtauCa=35e-6; HSRtauCa=85e-6; % seconds
152 % LSRtauCa=35e-6; HSRtauCa=70e-6; % seconds
153 IHCpreSynapseParams.tauCa= [ HSRtauCa]; %LSR and HSR fiber
154
155 %% #6 AN_IHCsynapse
156 % c=kym/(y(l+r)+kl) (spontaneous rate)
157 % c=(approx) ym/l (saturated rate)
158 AN_IHCsynapseParams=[]; % clear the structure first
159 AN_IHCsynapseParams.M= 12; % maximum vesicles at synapse
160 AN_IHCsynapseParams.y= 4; % depleted vesicle replacement rate
161 AN_IHCsynapseParams.y= 6; % depleted vesicle replacement rate
162
163 AN_IHCsynapseParams.x= 30; % replenishment from re-uptake store
164 AN_IHCsynapseParams.x= 60; % replenishment from re-uptake store
165
166 % reduce l to increase saturated rate
167 AN_IHCsynapseParams.l= 100; % *loss rate of vesicles from the cleft
168 AN_IHCsynapseParams.l= 250; % *loss rate of vesicles from the cleft
169
170 AN_IHCsynapseParams.r= 500; % *reuptake rate from cleft into cell
171 % AN_IHCsynapseParams.r= 300; % *reuptake rate from cleft into cell
172
173 AN_IHCsynapseParams.refractory_period= 0.00075;
174 % number of AN fibers at each BF (used only for spike generation)
175 AN_IHCsynapseParams.numFibers= 100;
176 AN_IHCsynapseParams.TWdelay=0.004; % ?delay before stimulus first spike
177
178 AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes.
179
180 %% #7 MacGregorMulti (first order brainstem neurons)
181 MacGregorMultiParams=[];
182 MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose
183 switch MacGregorMultiType
184 case 'primary-like'
185 MacGregorMultiParams.nNeuronsPerBF= 10; % N neurons per BF
186 MacGregorMultiParams.type = 'primary-like cell';
187 MacGregorMultiParams.fibersPerNeuron=4; % N input fibers
188 MacGregorMultiParams.dendriteLPfreq=200; % dendritic filter
189 MacGregorMultiParams.currentPerSpike=0.11e-6; % (A) per spike
190 MacGregorMultiParams.Cap=4.55e-9; % cell capacitance (Siemens)
191 MacGregorMultiParams.tauM=5e-4; % membrane time constant (s)
192 MacGregorMultiParams.Ek=-0.01; % K+ eq. potential (V)
193 MacGregorMultiParams.dGkSpike=3.64e-5; % K+ cond.shift on spike,S
194 MacGregorMultiParams.tauGk= 0.0012; % K+ conductance tau (s)
195 MacGregorMultiParams.Th0= 0.01; % equilibrium threshold (V)
196 MacGregorMultiParams.c= 0.01; % threshold shift on spike, (V)
197 MacGregorMultiParams.tauTh= 0.015; % variable threshold tau
198 MacGregorMultiParams.Er=-0.06; % resting potential (V)
199 MacGregorMultiParams.Eb=0.06; % spike height (V)
200
201 case 'chopper'
202 MacGregorMultiParams.nNeuronsPerBF= 10; % N neurons per BF
203 MacGregorMultiParams.type = 'chopper cell';
204 MacGregorMultiParams.fibersPerNeuron=10; % N input fibers
205 % MacGregorMultiParams.fibersPerNeuron=6; % N input fibers
206
207 MacGregorMultiParams.dendriteLPfreq=50; % dendritic filter
208 MacGregorMultiParams.currentPerSpike=35e-9; % *per spike
209 % MacGregorMultiParams.currentPerSpike=30e-9; % *per spike
210
211 MacGregorMultiParams.Cap=1.67e-8; % ??cell capacitance (Siemens)
212 MacGregorMultiParams.tauM=0.002; % membrane time constant (s)
213 MacGregorMultiParams.Ek=-0.01; % K+ eq. potential (V)
214 MacGregorMultiParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S
215 MacGregorMultiParams.tauGk= [0.001 0.0005];% K+ conductance tau (s)
216 MacGregorMultiParams.Th0= 0.01; % equilibrium threshold (V)
217 MacGregorMultiParams.c= 0; % threshold shift on spike, (V)
218 MacGregorMultiParams.tauTh= 0.02; % variable threshold tau
219 MacGregorMultiParams.Er=-0.06; % resting potential (V)
220 MacGregorMultiParams.Eb=0.06; % spike height (V)
221 MacGregorMultiParams.PSTHbinWidth= 1e-4;
222 end
223
224 %% #8 MacGregor (second-order neuron). Only one per channel
225 MacGregorParams=[]; % clear the structure first
226 MacGregorParams.type = 'chopper cell';
227 MacGregorParams.fibersPerNeuron=10; % N input fibers
228 MacGregorParams.dendriteLPfreq=100; % dendritic filter
229 MacGregorParams.currentPerSpike=120e-9;% *(A) per spike
230 MacGregorParams.currentPerSpike=40e-9;% *(A) per spike
231
232 MacGregorParams.Cap=16.7e-9; % cell capacitance (Siemens)
233 MacGregorParams.tauM=0.002; % membrane time constant (s)
234 MacGregorParams.Ek=-0.01; % K+ eq. potential (V)
235 MacGregorParams.dGkSpike=1.33e-4; % K+ cond.shift on spike,S
236 MacGregorParams.tauGk= 0.0005; % K+ conductance tau (s)
237 MacGregorParams.Th0= 0.01; % equilibrium threshold (V)
238 MacGregorParams.c= 0; % threshold shift on spike, (V)
239 MacGregorParams.tauTh= 0.02; % variable threshold tau
240 MacGregorParams.Er=-0.06; % resting potential (V)
241 MacGregorParams.Eb=0.06; % spike height (V)
242 MacGregorParams.debugging=0; % (special)
243 % wideband accepts input from all channels (of same fiber type)
244 % use wideband to create inhibitory units
245 MacGregorParams.wideband=0; % special for wideband units
246 % MacGregorParams.saveAllData=0;
247
248 %% #9 filteredSACF
249 minPitch= 300; maxPitch= 3000; numPitches=60; % specify lags
250 pitches=100*log10(logspace(minPitch/100, maxPitch/100, numPitches));
251 filteredSACFParams.lags=1./pitches; % autocorrelation lags vector
252 filteredSACFParams.acfTau= .003; % time constant of running ACF
253 filteredSACFParams.lambda= 0.12; % slower filter to smooth ACF
254 filteredSACFParams.plotFilteredSACF=1; % 0 plots unfiltered ACFs
255 filteredSACFParams.plotACFs=0; % special plot (see code)
256 % filteredSACFParams.usePressnitzer=0; % attenuates ACF at long lags
257 filteredSACFParams.lagsProcedure= 'useAllLags';
258 % filteredSACFParams.lagsProcedure= 'useBernsteinLagWeights';
259 % filteredSACFParams.lagsProcedure= 'omitShortLags';
260 filteredSACFParams.criterionForOmittingLags=3;
261
262 % checks
263 if AN_IHCsynapseParams.numFibers<MacGregorMultiParams.fibersPerNeuron
264 error('MacGregorMulti: too few input fibers for input to MacG unit')
265 end
266
267
268 %% now accept last minute parameter changes required by the calling program
269 % paramChanges
270 if nargin>3 && ~isempty(paramChanges)
271 nChanges=length(paramChanges);
272 for idx=1:nChanges
273 eval(paramChanges{idx})
274 end
275 end
276
277
278 %% write all parameters to the command window
279 % showParams is currently set at the top of htis function
280 if showParams
281 fprintf('\n %%%%%%%%\n')
282 fprintf('\n%s\n', method.parameterSource)
283 fprintf('\n')
284 nm=UTIL_paramsList(whos);
285 for i=1:length(nm)
286 % eval(['UTIL_showStruct(' nm{i} ', ''' nm{i} ''')'])
287 if ~strcmp(nm(i), 'method')
288 eval(['UTIL_showStructureSummary(' nm{i} ', ''' nm{i} ''', 10)'])
289 end
290 end
291
292 % highlight parameter changes made locally
293 if nargin>3 && ~isempty(paramChanges)
294 fprintf('\n Local parameter changes:\n')
295 for i=1:length(paramChanges)
296 disp(paramChanges{i})
297 end
298 end
299 end
300
301 % for backward compatibility
302 experiment.comparisonData=[];