Mercurial > hg > map
changeset 15:35af36fe0a35
dt error in MAP1_14 corrected
| author | Ray Meddis <rmeddis@essex.ac.uk> |
|---|---|
| date | Mon, 06 Jun 2011 09:11:29 +0100 |
| parents | 51082e08b70b |
| children | 37a379b27cff |
| files | MAP/MAP1_14.m multithreshold 1.46/savedData/mostRecentResults.mat multithreshold 1.46/testAN.m parameterStore/MAPparamsEndo.m parameterStore/MAPparamsNormal.m testPrograms/hs_err_pid1016.log testPrograms/html/myConv.html testPrograms/html/myConv.png testPrograms/html/myConv_01.png testPrograms/html/myConv_02.png testPrograms/html/myConv_03.png testPrograms/html/myConv_04.png testPrograms/html/myConv_05.png testPrograms/html/myConv_06.png testPrograms/html/myConv_07.png testPrograms/html/myConv_08.png testPrograms/html/myConv_09.png testPrograms/html/myConv_10.png testPrograms/myConv.m testPrograms/showMAP.m testPrograms/test_MAP1_14.m |
| diffstat | 21 files changed, 639 insertions(+), 57 deletions(-) [+] |
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--- a/MAP/MAP1_14.m Thu Jun 02 14:30:01 2011 +0100 +++ b/MAP/MAP1_14.m Mon Jun 06 09:11:29 2011 +0100 @@ -83,7 +83,7 @@ segmentTime=dt*(1:segmentLength); % used in debugging plots % all spiking activity is computed using longer epochs -ANspeedUpFactor=5; % 5 times longer +ANspeedUpFactor=AN_IHCsynapseParams.ANspeedUpFactor; % e.g.5 times % inputSignal must be row vector [r c]=size(inputSignal); @@ -443,10 +443,13 @@ CNcurrentPerSpike=MacGregorMultiParams.currentPerSpike; CNspikeToCurrentTau=1/(2*pi*CNdendriteLPfreq); t=ANdt:ANdt:5*CNspikeToCurrentTau; -CNalphaFunction=... - (CNcurrentPerSpike/CNspikeToCurrentTau)*t.*exp(-t/CNspikeToCurrentTau); +CNalphaFunction= (1 / ... + CNspikeToCurrentTau)*t.*exp(-t /CNspikeToCurrentTau); +CNalphaFunction=CNalphaFunction*CNcurrentPerSpike; + % figure(98), plot(t,CNalphaFunction) % working memory for implementing convolution + CNcurrentTemp=... zeros(nCNneurons,reducedSegmentLength+length(CNalphaFunction)-1); % trailing alphas are parts of humps carried forward to the next segment @@ -877,7 +880,7 @@ for idx=1:nCNneuronsPerChannel % determine candidate fibers for this unit fibersUsed=CNinputfiberLists(synapseNo,:); - % ANpsth has a bin width of dt + % ANpsth has a bin width of ANdt % (just a simple sum across fibers) AN_PSTH(synapseNo,:) = ... sum(ANspikes(fibersUsed,:), 1); @@ -892,12 +895,14 @@ CNcurrentTemp(unitNo,:)= ... conv(AN_PSTH(unitNo,:),CNalphaFunction); end +% disp(['sum(AN_PSTH)= ' num2str(sum(AN_PSTH(1,:)))]) % add post-synaptic current left over from previous segment CNcurrentTemp(:,1:alphaCols)=... CNcurrentTemp(:,1:alphaCols)+ CNtrailingAlphas; % take post-synaptic current for this segment CNcurrentInput= CNcurrentTemp(:, 1:reducedSegmentLength); +% disp(['mean(CNcurrentInput)= ' num2str(mean(CNcurrentInput(1,:)))]) % trailingalphas are the ends of the alpha functions that % spill over into the next segment @@ -907,13 +912,14 @@ if CN_c>0 % variable threshold condition (slow) for t=1:reducedSegmentLength - CNtimeSinceLastSpike=CNtimeSinceLastSpike-dts; + CNtimeSinceLastSpike=CNtimeSinceLastSpike-ANdt; s=CN_E>CN_Th & CNtimeSinceLastSpike<0 ; CNtimeSinceLastSpike(s)=0.0005; % 0.5 ms for sodium spike dE =(-CN_E/CN_tauM + ... - CNcurrentInput(:,t)/CN_cap+(CN_Gk/CN_cap).*(CN_Ek-CN_E))*dt; - dGk=-CN_Gk*dt./tauGk + CN_b*s; - dTh=-(CN_Th-CN_Th0)*dt/CN_tauTh + CN_c*s; + CNcurrentInput(:,t)/CN_cap+(... + CN_Gk/CN_cap).*(CN_Ek-CN_E))*ANdt; + dGk=-CN_Gk*ANdt./tauGk + CN_b*s; + dTh=-(CN_Th-CN_Th0)*ANdt/CN_tauTh + CN_c*s; CN_E=CN_E+dE; CN_Gk=CN_Gk+dGk; CN_Th=CN_Th+dTh; @@ -921,30 +927,48 @@ end else % static threshold (faster) + E=zeros(1,reducedSegmentLength); + Gk=zeros(1,reducedSegmentLength); + ss=zeros(1,reducedSegmentLength); for t=1:reducedSegmentLength - CNtimeSinceLastSpike=CNtimeSinceLastSpike-dt; - s=CN_E>CN_Th0 & CNtimeSinceLastSpike<0 ; % =1 if both conditions met - CNtimeSinceLastSpike(s)=0.0005; % 0.5 ms for sodium spike + % time of previous spike moves back in time + CNtimeSinceLastSpike=CNtimeSinceLastSpike-ANdt; + % action potential if E>threshold + % allow time for s to reset between events + s=CN_E>CN_Th0 & CNtimeSinceLastSpike<0 ; + ss(t)=s(1); + CNtimeSinceLastSpike(s)=0.0005; % 0.5 ms for sodium spike dE = (-CN_E/CN_tauM + ... - CNcurrentInput(:,t)/CN_cap+(CN_Gk/CN_cap).*(CN_Ek-CN_E))*dt; - dGk=-CN_Gk*dt./tauGk +CN_b*s; + CNcurrentInput(:,t)/CN_cap +... + (CN_Gk/CN_cap).*(CN_Ek-CN_E))*ANdt; + dGk=-CN_Gk*ANdt./tauGk +CN_b*s; CN_E=CN_E+dE; CN_Gk=CN_Gk+dGk; + E(t)=CN_E(1); + Gk(t)=CN_Gk(1); % add spike to CN_E and add resting potential (-60 mV) - CNmembranePotential(:,t)=CN_E+s.*(CN_Eb-CN_E)+CN_Er; + CNmembranePotential(:,t)=CN_E +s.*(CN_Eb-CN_E)+CN_Er; end end +% disp(['CN_E= ' num2str(sum(CN_E(1,:)))]) +% disp(['CN_Gk= ' num2str(sum(CN_Gk(1,:)))]) +% disp(['CNmembranePotential= ' num2str(sum(CNmembranePotential(1,:)))]) +% plot(CNmembranePotential(1,:)) + % extract spikes. A spike is a substantial upswing in voltage - CN_spikes=CNmembranePotential> -0.01; + CN_spikes=CNmembranePotential> -0.02; +% disp(['CNspikesbefore= ' num2str(sum(sum(CN_spikes)))]) % now remove any spike that is immediately followed by a spike % NB 'find' works on columns (whence the transposing) + % for each spike put a zero in the next epoch CN_spikes=CN_spikes'; idx=find(CN_spikes); idx=idx(1:end-1); CN_spikes(idx+1)=0; CN_spikes=CN_spikes'; +% disp(['CNspikes= ' num2str(sum(sum(CN_spikes)))]) % segment debugging % plotInstructions.figureNo=98; @@ -988,8 +1012,8 @@ for t=1:reducedSegmentLength s=IC_E>IC_Th0; dE = (-IC_E/IC_tauM + inputCurrent(:,t)/IC_cap +... - (IC_Gk/IC_cap).*(IC_Ek-IC_E))*dt; - dGk=-IC_Gk*dt/IC_tauGk +IC_b*s; + (IC_Gk/IC_cap).*(IC_Ek-IC_E))*ANdt; + dGk=-IC_Gk*ANdt/IC_tauGk +IC_b*s; IC_E=IC_E+dE; IC_Gk=IC_Gk+dGk; ICmembranePotential(:,t)=IC_E+s.*(IC_Eb-IC_E)+IC_Er; @@ -999,16 +1023,16 @@ for t=1:reducedSegmentLength dE = (-IC_E/IC_tauM + ... inputCurrent(:,t)/IC_cap + (IC_Gk/IC_cap)... - .*(IC_Ek-IC_E))*dt; + .*(IC_Ek-IC_E))*ANdt; IC_E=IC_E+dE; s=IC_E>IC_Th; ICmembranePotential(:,t)=IC_E+s.*(IC_Eb-IC_E)+IC_Er; - dGk=-IC_Gk*dt/IC_tauGk +IC_b*s; + dGk=-IC_Gk*ANdt/IC_tauGk +IC_b*s; IC_Gk=IC_Gk+dGk; % After a spike, the threshold is raised % otherwise it settles to its baseline - dTh=-(IC_Th-Th0)*dt/IC_tauTh +s*IC_c; + dTh=-(IC_Th-Th0)*ANdt/IC_tauTh +s*IC_c; IC_Th=IC_Th+dTh; end end @@ -1027,6 +1051,7 @@ lastCell=nCellsPerTau; for tauCount=1:nANfiberTypes % separate rates according to fiber types + % currently only the last segment is saved ICfiberTypeRates(tauCount, ... reducedSegmentPTR:shorterSegmentEndPTR)=... sum(ICspikes(firstCell:lastCell, :))... @@ -1034,13 +1059,16 @@ firstCell=firstCell+nCellsPerTau; lastCell=lastCell+nCellsPerTau; end - ICoutput(:, reducedSegmentPTR:shorterSegmentEndPTR)=ICspikes; - + + ICoutput(:,reducedSegmentPTR:shorterSegmentEndPTR)=ICspikes; + + % store membrane output on original dt scale if nBFs==1 % single channel x= repmat(ICmembranePotential(1,:), ANspeedUpFactor,1); x= reshape(x,1,segmentLength); if nANfiberTypes>1 % save HSR and LSR - y= repmat(ICmembranePotential(end,:), ANspeedUpFactor,1); + y=repmat(ICmembranePotential(end,:),... + ANspeedUpFactor,1); y= reshape(y,1,segmentLength); x=[x; y]; end
--- a/multithreshold 1.46/testAN.m Thu Jun 02 14:30:01 2011 +0100 +++ b/multithreshold 1.46/testAN.m Mon Jun 06 09:11:29 2011 +0100 @@ -6,6 +6,9 @@ global IHC_VResp_VivoParams IHC_cilia_RPParams IHCpreSynapseParams global AN_IHCsynapseParams + global ANoutput ANdt CNoutput ICoutput ICmembraneOutput tauCas + global ARattenuation MOCattenuation + dbstop if error addpath (['..' filesep 'MAP'], ['..' filesep 'utilities'], ... @@ -47,7 +50,6 @@ set(gcf,'position',[980 356 401 321]) figure(5), clf set(gcf,'position', [980 34 400 295]) -set(gcf,'name',[num2str(BFlist), ' Hz']); drawnow %% guarantee that the sample rate is at least 10 times the frequency @@ -93,8 +95,6 @@ MAPparamsName=experiment.name; showPlotsAndDetails=0; - global ANoutput ANdt CNoutput ICoutput ICmembraneOutput tauCas - global ARattenuation MOCattenuation MAP1_14(inputSignal, 1/dt, BFlist, ... MAPparamsName, AN_spikesOrProbability); @@ -127,6 +127,7 @@ hold on, bar(PSTHtime,PSTHLSR,'r') ylim([0 1000]) xlim([0 length(PSTH)*localPSTHbinwidth]) + set(gcf,'name',[num2str(BFlist), ' Hz: ' num2str(leveldB) ' dB']); % AN - CV % CV is computed 5 times. Use the middle one (3) as most typical @@ -188,7 +189,7 @@ AR(levelNo)=min(ARattenuation); MOC(levelNo)=min(MOCattenuation(length(MOCattenuation)/2:end)); - time=ANdt:ANdt:ANdt*size(ICmembraneOutput,2); + time=dt:dt:dt*size(ICmembraneOutput,2); figure(5), subplot(2,2,4) plot(time,ICmembraneOutput(2, 1:end),'k') ylim([-0.07 0])
--- a/parameterStore/MAPparamsEndo.m Thu Jun 02 14:30:01 2011 +0100 +++ b/parameterStore/MAPparamsEndo.m Mon Jun 06 09:11:29 2011 +0100 @@ -130,13 +130,13 @@ IHC_cilia_RPParams.u1= 1e-9; IHC_cilia_RPParams.s1= 1e-9; -IHC_cilia_RPParams.Gmax= 5e-9; % 2.5e-9 maximum conductance (Siemens) -IHC_cilia_RPParams.Ga= 1e-9; % 4.3e-9 fixed apical membrane conductance +IHC_cilia_RPParams.Gmax= 5e-9; % 2.5e-9 maximum conductance (Siemens) +IHC_cilia_RPParams.Ga= 1e-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.Et= 0.100; % endocochlear potential (V) IHC_cilia_RPParams.Et= 0.07; % endocochlear potential (V) IHC_cilia_RPParams.Gk= 2e-008; % 1e-8 potassium conductance (S) @@ -183,6 +183,8 @@ AN_IHCsynapseParams.numFibers= 100; AN_IHCsynapseParams.TWdelay=0.004; % ?delay before stimulus first spike +AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes. + %% #7 MacGregorMulti (first order brainstem neurons) MacGregorMultiParams=[]; MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose @@ -212,13 +214,13 @@ MacGregorMultiParams.dendriteLPfreq=50; % dendritic filter MacGregorMultiParams.currentPerSpike=35e-9; % *per spike -% MacGregorMultiParams.currentPerSpike=45e-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= 0.0001;% K+ conductance tau (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 @@ -233,12 +235,13 @@ MacGregorParams.fibersPerNeuron=10; % N input fibers MacGregorParams.dendriteLPfreq=100; % dendritic filter MacGregorParams.currentPerSpike=120e-9;% *(A) per spike +MacGregorParams.currentPerSpike=30e-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= 0.0003; % K+ conductance tau (s) +MacGregorParams.tauGk= 0.0005; % K+ conductance tau (s) MacGregorParams.Th0= 0.01; % equilibrium threshold (V) MacGregorParams.c= 0; % threshold shift on spike, (V) MacGregorParams.tauTh= 0.02; % variable threshold tau
--- a/parameterStore/MAPparamsNormal.m Thu Jun 02 14:30:01 2011 +0100 +++ b/parameterStore/MAPparamsNormal.m Mon Jun 06 09:11:29 2011 +0100 @@ -137,7 +137,7 @@ 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.Et= 0.07; % endocochlear potential (V) +IHC_cilia_RPParams.Et= 0.07; % 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 @@ -183,6 +183,8 @@ AN_IHCsynapseParams.numFibers= 100; AN_IHCsynapseParams.TWdelay=0.004; % ?delay before stimulus first spike +AN_IHCsynapseParams.ANspeedUpFactor=5; % longer epochs for computing spikes. + %% #7 MacGregorMulti (first order brainstem neurons) MacGregorMultiParams=[]; MacGregorMultiType='chopper'; % MacGregorMultiType='primary-like'; %choose @@ -212,13 +214,13 @@ MacGregorMultiParams.dendriteLPfreq=50; % dendritic filter MacGregorMultiParams.currentPerSpike=35e-9; % *per spike -% MacGregorMultiParams.currentPerSpike=45e-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= 0.0001;% K+ conductance tau (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 @@ -233,12 +235,13 @@ MacGregorParams.fibersPerNeuron=10; % N input fibers MacGregorParams.dendriteLPfreq=100; % dendritic filter MacGregorParams.currentPerSpike=120e-9;% *(A) per spike +MacGregorParams.currentPerSpike=30e-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= 0.0003; % K+ conductance tau (s) +MacGregorParams.tauGk= 0.0005; % K+ conductance tau (s) MacGregorParams.Th0= 0.01; % equilibrium threshold (V) MacGregorParams.c= 0; % threshold shift on spike, (V) MacGregorParams.tauTh= 0.02; % variable threshold tau
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/testPrograms/hs_err_pid1016.log Mon Jun 06 09:11:29 2011 +0100 @@ -0,0 +1,300 @@ +# +# An unexpected error has been detected by Java Runtime Environment: +# +# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x000000000fef5110, pid=1016, tid=6396 +# +# Java VM: Java HotSpot(TM) 64-Bit Server VM (1.6.0-b105 mixed mode) +# Problematic frame: +# C [awt.dll+0x185110] +# +# If you would like to submit a bug report, please visit: +# http://java.sun.com/webapps/bugreport/crash.jsp +# + +--------------- T H R E A D --------------- + +Current thread (0x000000001181c800): JavaThread "AWT-EventQueue-0" [_thread_in_native, id=6396] + +siginfo: ExceptionCode=0xc0000005, reading address 0xffffffffffffffff + +Registers: +EAX=0x800000ea47fdfdc2, EBX=0x0000000000000001, ECX=0x00000000111de260, EDX=0x0000000011238318 +ESP=0x00000000309cdb80, EBP=0x000000000e690f00, ESI=0x000000001181c990, EDI=0x0000000000000000 +EIP=0x000000000fef5110, EFLAGS=0x0000000000010202 + +Top of Stack: (sp=0x00000000309cdb80) +0x00000000309cdb80: 000000001181c800 0000000000000000 +0x00000000309cdb90: 00000000309cdcd0 0000000015dfd008 +0x00000000309cdba0: 0000000000000001 000000000fef6dd3 +0x00000000309cdbb0: 0000000000000001 000000000e690f00 +0x00000000309cdbc0: 000000001181c990 0000000000000000 +0x00000000309cdbd0: 0000000011238318 00000000169b9f50 +0x00000000309cdbe0: 0000000000000004 00000000152cd810 +0x00000000309cdbf0: 0000000000000000 0000000000000000 +0x00000000309cdc00: 0000000000000001 0000000000000102 +0x00000000309cdc10: 00000000122a308e 0000000000000001 +0x00000000309cdc20: 00000000309cdca8 00000000122afc24 +0x00000000309cdc30: 0000000000000000 0000000026cb7e80 +0x00000000309cdc40: 0000000000000000 0000000015dfd008 +0x00000000309cdc50: 0000000000000001 0000000000000000 +0x00000000309cdc60: 00000000309cdc50 00000000309cdc68 +0x00000000309cdc70: 0000000000000000 00000000309cdcd0 + +Instructions: (pc=0x000000000fef5110) 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Solution\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\Intel\DMIX;C:\Program Files (x86)\NTRU Cryptosystems\NTRU TCG Software Stack\bin\;C:\Program Files\NTRU Cryptosystems\NTRU TCG Software Stack\bin\;C:\Program Files\Wave Systems Corp\Gemalto\Access Client\v5\;c:\Program Files\WIDCOMM\Bluetooth Software\;c:\Program Files\WIDCOMM\Bluetooth Software\syswow64;C:\Program Files (x86)\Common Files\Roxio Shared\DLLShared\;C:\Program Files (x86)\Common Files\Roxio Shared\10.0\DLLShared\;C:\Program Files (x86)\Common Files\Adobe\AGL;C:\Program Files\MATLAB\R2010b\bin;C:\Program Files\MATLAB\R2010a\bin;C:\Program Files\MATLAB\R2008a\bin;C:\Program Files\MATLAB\R2008a\bin\win64;C:\Program Files (x86)\QuickTime\QTSystem\;C:\Program Files\Microsoft Windows Performance Toolkit\ +USERNAME=rmeddis +OS=Windows_NT +PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 37 Stepping 2, GenuineIntel + + + +--------------- S Y S T E M --------------- + +OS: Windows NT 6.1 Build 7601 Service Pack 1 + +CPU:total 4 em64t ht + +Memory: 4k page, physical 8181592k(5524620k free), swap 16361336k(13575508k free) + +vm_info: Java HotSpot(TM) 64-Bit Server VM (1.6.0-b105) for windows-amd64, built on Nov 29 2006 00:38:01 by "java_re" with unknown MS VC++:1400 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/testPrograms/html/myConv.html Mon Jun 06 09:11:29 2011 +0100 @@ -0,0 +1,172 @@ + +<!DOCTYPE html + PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"> +<html xmlns:mwsh="http://www.mathworks.com/namespace/mcode/v1/syntaxhighlight.dtd"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> + + <!-- +This HTML is auto-generated from an M-file. +To make changes, update the M-file and republish this document. + --> + <title>myConv</title> + <meta name="generator" content="MATLAB 7.6"> + <meta name="date" content="2011-06-05"> + <meta name="m-file" content="myConv"><style> + +body { + background-color: white; + margin:10px; +} + +h1 { + color: #990000; + font-size: x-large; +} + +h2 { + color: #990000; + font-size: medium; +} + +/* Make the text shrink to fit narrow windows, but not stretch too far in +wide windows. */ +p,h1,h2,div.content div { + max-width: 600px; + /* Hack for IE6 */ + width: auto !important; width: 600px; +} + +pre.codeinput { + background: #EEEEEE; + padding: 10px; +} +@media print { + pre.codeinput {word-wrap:break-word; width:100%;} +} + +span.keyword {color: #0000FF} +span.comment {color: #228B22} +span.string {color: #A020F0} +span.untermstring {color: #B20000} +span.syscmd {color: #B28C00} + +pre.codeoutput { + color: #666666; + padding: 10px; +} + +pre.error { + color: red; +} + +p.footer { + text-align: right; + font-size: xx-small; + font-weight: lighter; + font-style: italic; + color: gray; +} + + </style></head> + <body> + <div class="content"> + <h2>Contents</h2> + <div> + <ul> + <li><a href="#3">testing convolution speculation</a></li> + <li><a href="#4">convolution function</a></li> + <li><a href="#5">normalise conv function</a></li> + <li><a href="#6">adjust for spike current</a></li> + <li><a href="#7">convolution</a></li> + </ul> + </div><pre class="codeinput">signalDuration=.1; +spikeTime= signalDuration/2; +<span class="keyword">for</span> sampleRate=[1000 2000]; +</pre><pre class="codeinput"> disp([<span class="string">'sample rate= '</span> num2str(sampleRate)]) +</pre><pre class="codeoutput">sample rate= 1000 +</pre><pre class="codeoutput">sample rate= 2000 +</pre><h2>testing convolution speculation<a name="3"></a></h2><pre class="codeinput">dt= 1/sampleRate; +signalLength=round(signalDuration/dt); +spikeArray=zeros(1,signalLength); +spikeLocation=round(spikeTime/dt); +spikeArray(spikeLocation)=1; +disp([<span class="string">'length of spike array= '</span> num2str(length(spikeArray))]) +t=dt*(1:length(spikeArray)); +plot(t, spikeArray) +</pre><pre class="codeoutput">length of spike array= 100 +</pre><img vspace="5" hspace="5" src="myConv_01.png"> <pre class="codeoutput">length of spike array= 200 +</pre><img vspace="5" hspace="5" src="myConv_06.png"> <h2>convolution function<a name="4"></a></h2><pre class="codeinput">CNspikeToCurrentTau=0.01; +t=dt:dt:3*CNspikeToCurrentTau; +CNalphaFunction=<span class="keyword">...</span> + (1/CNspikeToCurrentTau)*t.*exp(-t/CNspikeToCurrentTau); + +plot(t, CNalphaFunction) +</pre><img vspace="5" hspace="5" src="myConv_02.png"> <img vspace="5" hspace="5" src="myConv_07.png"> <h2>normalise conv function<a name="5"></a></h2><pre class="codeinput">CNalphaFunction=CNalphaFunction/sum(CNalphaFunction); +plot(t, CNalphaFunction) +disp([<span class="string">'area under function= '</span> num2str(sum(CNalphaFunction))]) +</pre><pre class="codeoutput">area under function= 1 +</pre><img vspace="5" hspace="5" src="myConv_03.png"> <pre class="codeoutput">area under function= 1 +</pre><img vspace="5" hspace="5" src="myConv_08.png"> <h2>adjust for spike current<a name="6"></a></h2><pre class="codeinput">CNcurrentPerSpike=2; +CNalphaFunction=CNalphaFunction*CNcurrentPerSpike; +plot(t, CNalphaFunction) +</pre><img vspace="5" hspace="5" src="myConv_04.png"> <img vspace="5" hspace="5" src="myConv_09.png"> <h2>convolution<a name="7"></a></h2><pre class="codeinput">result=conv(spikeArray,CNalphaFunction); +t=dt*(1:length(result)); +plot(t, result) +disp([<span class="string">'area under function= '</span> num2str(sum(result))]) +</pre><pre class="codeoutput">area under function= 2 +</pre><img vspace="5" hspace="5" src="myConv_05.png"> <pre class="codeoutput">area under function= 2 +</pre><img vspace="5" hspace="5" src="myConv_10.png"> <pre class="codeinput"><span class="keyword">end</span> +</pre><p class="footer"><br> + Published with MATLAB® 7.6<br></p> + </div> + <!-- +##### SOURCE BEGIN ##### +signalDuration=.1; +spikeTime= signalDuration/2; +for sampleRate=[1000 2000]; + disp(['sample rate= ' num2str(sampleRate)]) + +%% testing convolution speculation +dt= 1/sampleRate; +signalLength=round(signalDuration/dt); +spikeArray=zeros(1,signalLength); +spikeLocation=round(spikeTime/dt); +spikeArray(spikeLocation)=1; +disp(['length of spike array= ' num2str(length(spikeArray))]) +t=dt*(1:length(spikeArray)); +plot(t, spikeArray) + +%% convolution function +CNspikeToCurrentTau=0.01; +t=dt:dt:3*CNspikeToCurrentTau; +CNalphaFunction=... + (1/CNspikeToCurrentTau)*t.*exp(-t/CNspikeToCurrentTau); + +plot(t, CNalphaFunction) + +%% normalise conv function +CNalphaFunction=CNalphaFunction/sum(CNalphaFunction); +plot(t, CNalphaFunction) +disp(['area under function= ' num2str(sum(CNalphaFunction))]) + +%% adjust for spike current +CNcurrentPerSpike=2; +CNalphaFunction=CNalphaFunction*CNcurrentPerSpike; +plot(t, CNalphaFunction) + +%% convolution +result=conv(spikeArray,CNalphaFunction); +t=dt*(1:length(result)); +plot(t, result) +disp(['area under function= ' num2str(sum(result))]) + +end + + + + +##### SOURCE END ##### +--> + </body> +</html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/testPrograms/myConv.m Mon Jun 06 09:11:29 2011 +0100 @@ -0,0 +1,43 @@ +signalDuration=.1; +spikeTime= signalDuration/2; +for sampleRate=[1000 2000]; + disp(['sample rate= ' num2str(sampleRate)]) + +%% testing convolution speculation +dt= 1/sampleRate; +signalLength=round(signalDuration/dt); +spikeArray=zeros(1,signalLength); +spikeLocation=round(spikeTime/dt); +spikeArray(spikeLocation)=1; +disp(['length of spike array= ' num2str(length(spikeArray))]) +t=dt*(1:length(spikeArray)); +plot(t, spikeArray) + +%% convolution function +CNspikeToCurrentTau=0.01; +t=dt:dt:3*CNspikeToCurrentTau; +CNalphaFunction=... + (1/CNspikeToCurrentTau)*t.*exp(-t/CNspikeToCurrentTau); + +plot(t, CNalphaFunction) + +%% normalise conv function +CNalphaFunction=CNalphaFunction/sum(CNalphaFunction); +plot(t, CNalphaFunction) +disp(['area under function= ' num2str(sum(CNalphaFunction))]) + +%% adjust for spike current +CNcurrentPerSpike=2; +CNalphaFunction=CNalphaFunction*CNcurrentPerSpike; +plot(t, CNalphaFunction) + +%% convolution +result=conv(spikeArray,CNalphaFunction); +t=dt*(1:length(result)); +plot(t, result) +disp(['area under function= ' num2str(sum(result))]) + +end + + +
--- a/testPrograms/showMAP.m Thu Jun 02 14:30:01 2011 +0100 +++ b/testPrograms/showMAP.m Mon Jun 06 09:11:29 2011 +0100 @@ -51,8 +51,8 @@ nHSRCNneuronss=nCNneurons/nANfiberTypes; disp(['CN: ' num2str(sum(sum(CNoutput(end-nHSRCNneuronss+1:end,:)))... /(nHSRCNneuronss*duration))]) - disp(['IC: ' num2str(sum(sum(ICoutput)))]) - disp(['IC by type: ' num2str(mean(ICfiberTypeRates,2)')]) + disp(['IC: ' num2str(sum(sum(ICoutput))/duration)]) +% disp(['IC by type: ' num2str(mean(ICfiberTypeRates,2)')]) else disp(['AN: ' num2str(mean(mean(ANprobRateOutput)))]) end @@ -237,4 +237,4 @@ set(gca,'xtickLabel', round(100*t(tt))/100) end -path(restorePath) \ No newline at end of file +path(restorePath)
--- a/testPrograms/test_MAP1_14.m Thu Jun 02 14:30:01 2011 +0100 +++ b/testPrograms/test_MAP1_14.m Mon Jun 06 09:11:29 2011 +0100 @@ -1,9 +1,37 @@ function test_MAP1_14 +% test_MAP1_14 is a general purpose test routine that can be adjusted to +% test a number of different applications of MAP1_14 +% +% A range of options are supplied in the early part of the program +% +% One use of the function is to create demonstrations; filenames <demoxx> +% to illustrate particular features +% +% #1 +% Identify the file (in 'MAPparamsName') containing the model parameters +% +% #2 +% Identify the kind of model required (in 'AN_spikesOrProbability'). +% A full brainstem model (spikes) can be computed or a shorter model +% (probability) that computes only so far as the auditory nerve +% +% #3 +% Choose between a tone signal or file input (in 'signalType') +% +% #4 +% Set the signal rms level (in leveldBSPL) +% +% #5 +% Indentify the channels in terms of their best frequencies in the vector +% BFlist. +% +% Last minute changes to the parameters fetched earlier can be made using +% the cell array of strings 'paramChanges'. +% Each string must have the same format as the corresponding line in the +% file identified in 'MAPparamsName' +% +% When the demonstration is satisfactory, freeze it by renaming it <demoxx> -% MAPdemo runs the MATLAB auditory periphery model (MAP1_14) as far as -% the AN (probabilities) or IC (spikes) with graphical output - -% Things you might want to change; #1 - #5 %% #1 parameter file name MAPparamsName='Normal'; @@ -18,7 +46,7 @@ %% #3 pure tone, harmonic sequence or speech file input signalType= 'tones'; duration=0.100; % seconds -duration=0.020; % seconds +% duration=0.020; % seconds sampleRate= 64000; % toneFrequency= 250:250:8000; % harmonic sequence (Hz) toneFrequency= 2000; % or a pure tone (Hz8 @@ -26,14 +54,14 @@ rampDuration=.005; % seconds % or -signalType= 'file'; -fileName='twister_44kHz'; +% signalType= 'file'; +% fileName='twister_44kHz'; % fileName='new-da-44khz'; %% #4 rms level % signal details -leveldBSPL=70; % dB SPL +leveldBSPL= 90; % dB SPL %% #5 number of channels in the model @@ -43,7 +71,7 @@ BFlist=round(logspace(log10(lowestBF), log10(highestBF), numChannels)); % or specify your own channel BFs -% BFlist=toneFrequency; +BFlist=toneFrequency; %% #6 change model parameters @@ -54,18 +82,14 @@ % *after* the MAPparams file has been read % This example declares only one fiber type with a calcium clearance time % constant of 80e-6 s (HSR fiber) when the probability option is selected. -% switch AN_spikesOrProbability -% case 'probability' -% paramChanges={'IHCpreSynapseParams.tauCa=80e-6;'}; -% otherwise -% paramChanges=[]; -% end + paramChanges={'AN_IHCsynapseParams.ANspeedUpFactor=5;', ... + 'IHCpreSynapseParams.tauCa=86e-6;'}; %% delare showMap options showMapOptions=[]; % use defaults % or (example: show everything including an smoothed SACF output - showMapOptions.showModelParameters=1; + showMapOptions.showModelParameters=0; showMapOptions.showModelOutput=1; showMapOptions.printFiringRates=1; showMapOptions.showACF=0; @@ -98,12 +122,20 @@ disp(['Signal duration= ' num2str(length(inputSignal)/sampleRate)]) disp([num2str(numChannels) ' channel model']) disp('Computing ...') + +restorePath=path; +addpath (['..' filesep 'MAP']) + MAP1_14(inputSignal, sampleRate, BFlist, ... MAPparamsName, AN_spikesOrProbability, paramChanges); +path(restorePath) toc % the model run is now complete. Now display the results showMAP(showMapOptions) +for i=1:length(paramChanges) +disp(paramChanges{i}) +end toc path(restorePath) @@ -130,5 +162,5 @@ % add 10 ms silence silence= zeros(1,round(0.03/dt)); -% inputSignal= [silence inputSignal silence]; +inputSignal= [silence inputSignal silence];