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adapt to new exp numbering
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@pjkohler
pjkohler committed Jan 19, 2018
1 parent 444c71b commit 1a3b357
Showing 1 changed file with 58 additions and 49 deletions.
107 changes: 58 additions & 49 deletions analyze_pphys.m
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Original file line number Diff line number Diff line change
Expand Up @@ -42,16 +42,12 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)
%% PRELIMINARY
% folder names
topPath = '/Volumes/Denali_4D2/kohler/EEG_EXP/DATA/motion2D3D';
if expNum == 1
dataPath = sprintf('%s/exp6_pphys1',topPath);
else
dataPath = sprintf('%s/exp7_pphys2',topPath);
end
dataPath = sprintf('%s/pphys_exp%0.0f',topPath,expNum);
subPaths = subfolders(sprintf('%s/*20*',dataPath),1);
adultExp = [1,2,4,5,8];
adultExp = [1,2,3,4,5];
% NOTE! should be path corresponding to blank (2);
rcaPath = sprintf('%s/figures/exp%0.0f/plottingData.mat',topPath,adultExp(2));
savePath = sprintf('%s/figures/paper_figures/figure4',topPath);
savePath = sprintf('%s/figures/paper_figures/pphys_exp',topPath);
% string for saving the data
saveStr = datestr(clock,26);
saveStr(strfind(saveStr,'/')) ='';
Expand Down Expand Up @@ -200,6 +196,16 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)

subPaths = subPaths(includeIdx);

%% DO PPHYS STATS
testData = exp(aveBoth(:,includeIdx));
for z = 1:2
[pphysTest(z).Sig, pphysTest(z).P,ci,testStrct] = ttest(testData(z+(z-1),:),testData(z+z,:),'dim',2,'tail','both');
pphysTest(z).df = testStrct.df;
pphysTest(z).tstat = testStrct.tstat;
factorDiff(z) = exp(bothGrand(z+z))/exp(bothGrand(z+(z-1)));
end


%% PLOT PPHYS
lWidth = 2;
fSize = 12;
Expand Down Expand Up @@ -347,7 +353,7 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)
% do this separately for each harmonic
load(rcaPath,'readyRCA');
warning('off','all')
doNR = false(1,5,8); % 1 freqs, 5 RCs, 8 conditions
doNR = false(1,6,8); % 1 freqs, 6 RCs (w/ comparison), 8 conditions
doNR([1,2,4],1,:) = true; % do fitting for first RC, first, second and fourth harmonic, all conditions
keepConditions = true;
errorType = 'SEM';
Expand Down Expand Up @@ -423,44 +429,24 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)
% tempNoiseStrct1 = aggregateData(pphysRCA(f).comparisonNoiseData.lowerSideBand,pphysRCA(f).settings,keepConditions,errorType,trialError);
% tempNoiseStrct2 = aggregateData(pphysRCA(f).comparisonNoiseData.higherSideBand,pphysRCA(f).settings,keepConditions,errorType,trialError);
% [snrVals(:,f,6,:),noiseVals(:,f,6,:)] = computeSnr(tempDataStrct,tempNoiseStrct1,tempNoiseStrct2,false);

rcStruct = aggregateData(pphysRCA(f).data,pphysRCA(f).settings,keepConditions,errorType,trialError,doNR);
compStruct = aggregateData(pphysRCA(f).comparisonData,pphysRCA(f).settings,keepConditions,errorType,trialError);
% note: no NR fitting on noise data
rcNoiseStrct1 = aggregateData(pphysRCA(f).noiseData.lowerSideBand,pphysRCA(f).settings,keepConditions,errorType,trialError,[]);
rcNoiseStrct2 = aggregateData(pphysRCA(f).noiseData.higherSideBand,pphysRCA(f).settings,keepConditions,errorType,trialError,[]);
compNoiseStrct1 = aggregateData(pphysRCA(f).comparisonNoiseData.lowerSideBand,pphysRCA(f).settings,keepConditions,errorType,trialError,[]);
compNoiseStrct2 = aggregateData(pphysRCA(f).comparisonNoiseData.higherSideBand,pphysRCA(f).settings,keepConditions,errorType,trialError,[]);
% snr
[rcSNR,rcNoiseVals] = computeSnr(rcStruct,rcNoiseStrct1,rcNoiseStrct2,false);
[compSNR,compNoiseVals] = computeSnr(compStruct,compNoiseStrct1,compNoiseStrct2,false);


rcStruct = aggregateData(pphysRCA(f),keepConditions,errorType,trialError,doNR);
% RC
pphysRCA(f).stats.ampVals(:,1:5,:) = rcStruct.ampBins;
pphysRCA(f).stats.errLB(:,1:5,:) = rcStruct.ampErrBins(:,:,:,:,1);
pphysRCA(f).stats.errUB(:,1:5,:) = rcStruct.ampErrBins(:,:,:,:,2);
pphysRCA(f).stats.snrVals(:,1:5,:) = rcSNR;
pphysRCA(f).stats.noiseVals(:,1:5,:) = rcNoiseVals;
pphysRCA(f).stats.NR_pOpt(:,1:5,:) = rcStruct.NakaRushton.pOpt;
pphysRCA(f).stats.NR_JKSE(:,1:5,:) = rcStruct.NakaRushton.JKSE;
pphysRCA(f).stats.NR_R2(1:5,:) = rcStruct.NakaRushton.R2;
pphysRCA(f).stats.Amp = squeeze(rcStruct.ampBins);
pphysRCA(f).stats.SubjectAmp = squeeze(rcStruct.subjectAmp);
pphysRCA(f).stats.ErrLB = squeeze(rcStruct.ampErrBins(:,:,:,:,1));
pphysRCA(f).stats.ErrUB = squeeze(rcStruct.ampErrBins(:,:,:,:,2));
pphysRCA(f).stats.NoiseAmp = squeeze(rcStruct.ampNoiseBins);
pphysRCA(f).stats.SubjectNoiseAmp = squeeze(rcStruct.subjectAmpNoise);
% Naka-Rushton
pphysRCA(f).stats.NR_Params = squeeze(rcStruct.NakaRushton.Params);
pphysRCA(f).stats.NR_R2 = squeeze(rcStruct.NakaRushton.R2);
pphysRCA(f).stats.NR_JKSE = squeeze(rcStruct.NakaRushton.JackKnife.SE);
pphysRCA(f).stats.NR_JKParams = squeeze(rcStruct.NakaRushton.JackKnife.Params);
pphysRCA(f).stats.hModel = rcStruct.NakaRushton.hModel;
pphysRCA(f).stats.tSqrdP(:,1:5,:) = rcStruct.tSqrdP;
pphysRCA(f).stats.tSqrdSig(:,1:5,:) = rcStruct.tSqrdSig;
pphysRCA(f).stats.tSqrdVal(:,1:5,:) = rcStruct.tSqrdVal;

% COMPARISON
pphysRCA(f).stats.ampVals(:,6,:) = compStruct.ampBins;
pphysRCA(f).stats.errLB(:,6,:) = compStruct.ampErrBins(:,:,:,:,1);
pphysRCA(f).stats.errUB(:,6,:) = compStruct.ampErrBins(:,:,:,:,2);
pphysRCA(f).stats.snrVals(:,6,:) = compSNR;
pphysRCA(f).stats.noiseVals(:,6,:) = compNoiseVals;
pphysRCA(f).stats.NR_pOpt(:,6,:) = compStruct.NakaRushton.pOpt;
pphysRCA(f).stats.NR_JKSE(:,6,:) = compStruct.NakaRushton.JKSE;
pphysRCA(f).stats.NR_R2(6,:) = compStruct.NakaRushton.R2;
pphysRCA(f).stats.tSqrdP(:,6,:) = compStruct.tSqrdP;
pphysRCA(f).stats.tSqrdSig(:,6,:) = compStruct.tSqrdSig;
pphysRCA(f).stats.tSqrdVal(:,6,:) = compStruct.tSqrdVal;
pphysRCA(f).stats.tSqrdP = squeeze(rcStruct.tSqrdP);
pphysRCA(f).stats.tSqrdSig = squeeze(rcStruct.tSqrdSig);
pphysRCA(f).stats.tSqrdVal = squeeze(rcStruct.tSqrdVal);
end
warning('on','all')

Expand Down Expand Up @@ -505,10 +491,10 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)
freqFig(f) = figure;
curFreq = freqsToUse(f);

valSet = pphysRCA(curFreq).stats.ampVals;
errSet1 = pphysRCA(curFreq).stats.errLB;
errSet2 = pphysRCA(curFreq).stats.errUB;
NRset = pphysRCA(curFreq).stats.NR_pOpt;
valSet = pphysRCA(curFreq).stats.Amp;
errSet1 = pphysRCA(curFreq).stats.ErrLB;
errSet2 = pphysRCA(curFreq).stats.ErrUB;
NRset = pphysRCA(curFreq).stats.NR_Params;
NRmodel = pphysRCA(curFreq).stats.hModel;
for r = 1:(nComp+1)
if r<6
Expand Down Expand Up @@ -584,7 +570,7 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)
ylim([0,yMax])

% plot noise patch
meanNoise = max(pphysRCA(curFreq).stats.noiseVals(:,r,curConds),[],3)';
meanNoise = max(pphysRCA(curFreq).stats.NoiseAmp(:,r,curConds),[],3)';
yNoiseVals = [0,meanNoise(1),meanNoise,meanNoise(end),0]; % start and end points just repeats of first and last
xNoiseVals = [xMin,xMin,binVals',xMax,xMax];
pH = patch(xNoiseVals,yNoiseVals,[.75 .75 .75],'edgecolor','none');
Expand Down Expand Up @@ -656,6 +642,22 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)
rc_tSqrdSig(b,3+(s-1)*3) = tempStrct.H;
diffMag(b,s) = tempStrct.testAmp;
end

% make Naka-Rushton values

NRvals = pphysRCA(curFreq).stats.NR_Params;
NRerrs = pphysRCA(curFreq).stats.NR_JKSE;
NRmodel = pphysRCA(curFreq).stats.hModel;

% do paired tests
testVal = squeeze(pphysRCA(curFreq).stats.NR_JKParams(:,:,rcNum,curConds));
testVal = permute(testVal,[2,1,3]); % move subjects to first dim
paramIdx = [1,2,3,4];% only look at c50 and rMax
jkDf = size(testVal,1)-1;
diffErr = jackKnifeErr(testVal(:,paramIdx,1)-testVal(:,paramIdx,2));
grandDiff = NRvals(paramIdx,rcNum,curConds(1)) - NRvals(paramIdx,rcNum,curConds(2));
paramPairedT(:,s) = grandDiff'./diffErr;
paramPairedP(:,s) = 2*tcdf( -abs(paramPairedT(:,s)) , jkDf);
else
end
hold off;
Expand All @@ -680,6 +682,13 @@ function analyze_pphys(expNum,taskFig,logConvert,rcaType)
export_fig(sprintf('%s/pphys%0.0f_rc%d_%s.pdf',savePath,expNum,curFreq,rcaType),'-pdf','-transparent',gcf);
end
close all;

for z=1:4
subplot(1,4,z);
hold on
plot(1:4,squeeze(NRvals(z,1,:)),'o')
errorb(1:4,squeeze(NRvals(z,1,:)),squeeze(NRerrs(z,1,:)))
end

%% PLOT TASK ILLUSTRATION
if taskFig
Expand Down

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