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Speed up #68

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merged 5 commits into from
Aug 30, 2022
Merged

Speed up #68

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5ae2cf7
Speed up
RoyalBoggs Aug 29, 2022
015bfcc
Merge branch 'main' into delx_adapt
RoyalBoggs Aug 29, 2022
5ab952c
Codacity clean up
RoyalBoggs Aug 29, 2022
2e06b55
Merge branch 'delx_adapt' of https://github.com/RoyalBoggs/Tripoli in…
RoyalBoggs Aug 29, 2022
a29115c
Correcting main merge error
RoyalBoggs Aug 29, 2022
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30 changes: 11 additions & 19 deletions ...ns/analysis/massSpectrometerModels/dataOutputModels/rjmcmc/DataModelDriverExperiment.java
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Original file line number Diff line number Diff line change
Expand Up @@ -330,12 +330,9 @@ static AbstractPlotBuilder[] applyInversionWithRJMCMC(MassSpecOutputDataRecord m

% Size of model: # isotopes + # intensity knots + # baselines + # df gain
Nmod = d0.Niso + sum(d0.Ncycle) + d0.Nfar + Ndf ;
sizeOfModel
% Data and data covariance vectors
xmean = zeros(Nmod,1);
xDataMean
xcov = zeros(Nmod,Nmod);
xDataCovariance

% Adaptive MCMC proposal term
delx_adapt=zeros(Nmod,datsav);
Expand Down Expand Up @@ -439,7 +436,7 @@ static AbstractPlotBuilder[] applyInversionWithRJMCMC(MassSpecOutputDataRecord m
adaptiveFlag,
allFlag
);

boolean noiseOperation = operation.toLowerCase(Locale.ROOT).startsWith("n");

/*
%% Create updated data based on new model
Expand Down Expand Up @@ -501,7 +498,7 @@ static AbstractPlotBuilder[] applyInversionWithRJMCMC(MassSpecOutputDataRecord m
prev = interval1 + prev;

// todo: reminder only 1 block here
// remove zeroes from firstblockinterpolations
// todo: remove zeroes from firstblockinterpolations
ArrayList<double[]> intensity2 = new ArrayList<>(1);
PhysicalStore<Double> tempIntensity = storeFactory.make(massSpecOutputDataRecord.allBlockInterpolations()[0].countRows(),
storeFactory.columns(dataModelUpdaterOutputRecord_x2.blockIntensities()).getColDim());
Expand Down Expand Up @@ -542,22 +539,20 @@ static AbstractPlotBuilder[] applyInversionWithRJMCMC(MassSpecOutputDataRecord m
prev = interval3 + prev;

for (int row = 0; row < massSpecOutputDataRecord.rawDataColumn().length; row++) {
double term1 = StrictMath.pow(dataModelUpdaterOutputRecord_x2.signalNoise()[(int) massSpecOutputDataRecord.detectorIndicesForRawDataColumn()[row] - 1], 2);
double term1 = pow(dataModelUpdaterOutputRecord_x2.signalNoise()[(int) massSpecOutputDataRecord.detectorIndicesForRawDataColumn()[row] - 1], 2);
double term2 = dataModelUpdaterOutputRecord_x2.signalNoise()[(int) massSpecOutputDataRecord.isotopeIndicesForRawDataColumn()[row] - 1 + massSpecOutputDataRecord.faradayCount() + 1];
dSignalNoise2Array[row] = term1 + term2 * dnobl2[row];
double residualValue = StrictMath.pow(massSpecOutputDataRecord.rawDataColumn()[row] - dataModelInit.dataArray()[row], 2);
double residualValue = pow(massSpecOutputDataRecord.rawDataColumn()[row] - dataModelInit.dataArray()[row], 2);
E0 += residualValue;
// remove strictmath try regular
double residualValue2 = StrictMath.pow(massSpecOutputDataRecord.rawDataColumn()[row] - d2[row], 2);
double residualValue2 = pow(massSpecOutputDataRecord.rawDataColumn()[row] - d2[row], 2);
E02 += residualValue2;

/*
% Decide whether to accept or reject model
keep = AcceptItMS(oper,dE,psig,delx,prior,Dsig,Dsig2,d0);
*/
// make variable for bool calculate before for loop, right after its declared
// bool noiseOperation
if (operation.toLowerCase(Locale.ROOT).startsWith("n")) {
// todo: make variable for bool calculate before for loop, right after its declared
if (noiseOperation) {
E += residualValue / dSignalNoiseArray[row];
E2 += residualValue2 / dSignalNoise2Array[row];
sumLogDSignalNoise += -1.0 * Math.log(dSignalNoiseArray[row]);
Expand All @@ -571,7 +566,7 @@ static AbstractPlotBuilder[] applyInversionWithRJMCMC(MassSpecOutputDataRecord m
long interval4 = System.nanoTime() - prev;
prev = interval4 + prev;

if (operation.toLowerCase(Locale.ROOT).startsWith("n")) {
if (noiseOperation) {
dE = E2 - E;
double deltaLogNoise = sumLogDSignalNoise2 - sumLogDSignalNoise;
keep = min(1.0, exp(deltaLogNoise / 2.0 - (dE) / 2.0));//keep = min(1,exp(X/2-(dE)/2));
Expand Down Expand Up @@ -701,16 +696,13 @@ static AbstractPlotBuilder[] applyInversionWithRJMCMC(MassSpecOutputDataRecord m
t = diag(sigma);
r(:,t==0) = mu(:,t==0); % force exact mean when variance is 0
*/
Cholesky<Double> cholesky = Cholesky.PRIMITIVE.make();
Normal tmpNormDistribution = new Normal();
Primitive64Store distribution = Primitive64Store.FACTORY.makeFilled(100, 21, tmpNormDistribution);
Primitive64Store distribution = Primitive64Store.FACTORY.makeFilled(stepCountForcedSave, sizeOfModel, tmpNormDistribution);

Cholesky<Double> cholesky = Cholesky.PRIMITIVE.make();
cholesky.decompose(storeFactory.columns(xDataCovariance).multiply(pow(2.38, 2) / sizeOfModel));
PhysicalStore<Double> test = distribution.multiply(cholesky.getL()).copy();
//MatrixStore<Double> tempCov = storeFactory.columns(xDataCovariance).diagonal();
//test.fillColumn(1,tempCov);

delx_adapt = test.transpose().copy();
delx_adapt = distribution.multiply(cholesky.getR()).transpose().copy();
}
}

Expand Down
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