static void MaxAcf (mrs_real& max, mrs_real& mean, const realvec& beatHistogram, realvec& res,mrs_natural startSearchAt, mrs_natural stopSearchAt)
{
mrs_natural k,len = beatHistogram.getCols ();
res.setval(0.);
// compute ACF
for (k = startSearchAt; k < stopSearchAt; k++) // this can be optimized
{
mrs_real val = 0;
for (mrs_natural i = k; i < len; i++)
{
val += beatHistogram(i) * beatHistogram(i-k);
}
res(k) = val / (len-k);
}
//pkr_->process(in, pkres_);
max = res.maxval ();
mean = 1e6*res.mean ();
}
void
PeakClusterSelect::swap(realvec& rv, mrs_natural sample1, mrs_natural sample2, mrs_bool swapColumns)
{
if( swapColumns ) // swap two columns
{
int rows = rv.getRows();
mrs_real tmp;
for( int i=0 ; i<rows ; ++i )
{
tmp = rv(i, sample1);
rv(i,sample1) = rv(i,sample2);
rv(i,sample2) = tmp;
}
}
else // swap two rows
{
int cols = rv.getCols();
mrs_real tmp;
for( int i=0 ; i<cols ; ++i )
{
tmp = rv(sample1,i);
rv(sample1,i) = rv(sample2,i);
rv(sample2,i) = tmp;
}
}
}
void Map::myProcess(realvec & in, realvec & out)
{
{
MarControlAccessor input_access(m_input_ctl);
realvec & input_data = input_access.to<realvec>();
assert(input_data.getRows() == in.getRows() &&
input_data.getCols() == in.getCols());
input_data = in;
}
const realvec & output_data = m_output_ctl->to<realvec>();
assert(output_data.getRows() == out.getRows() &&
output_data.getCols() == out.getCols());
out = output_data;
}
static mrs_real SpectralFlatness (const realvec& beatHistogram, mrs_natural startIdx = 200)
{
mrs_real res = 0;
mrs_natural len = beatHistogram.getCols ();
//mrs_natural sum = beatHistogram.sum ();
//beatHistogram /= sum;
for (mrs_natural i = startIdx; i < len; i++)
res += log(beatHistogram(i)+1e-6);
return exp(res/(len-startIdx));
}
mrs_real
QGMMModel::deltaBIC(realvec C1, mrs_natural N1, realvec C2, mrs_natural N2, realvec C, mrs_real lambda)
{
//matrices should be square and equal sized
if(C1.getCols() != C2.getCols() && C1.getCols() != C.getCols() &&
C1.getCols()!= C1.getRows())
{
MRSERR("QGMMModel:deltaBIC: matrices should all be squared and equal sized...");
return MAXREAL; //just a way to sinalize the above error... [!]
}
mrs_real res;
mrs_real N = (mrs_real)(N1 + N2);
mrs_real d = (mrs_real)C1.getCols();
res = N * log(C.det());
res -= (mrs_real)N1 * log(C1.det());
res -= (mrs_real)N2 * log(C2.det());
res *= 0.5f;
res -= 0.5f * lambda * (d + 0.5f*d*(d+1.0f))* log(N);
return res;
}
static mrs_real PeriodicSpread (realvec& vector, mrs_real centroid, mrs_bool isLog = false, mrs_natural startIdx = 200)
{
mrs_natural len = vector.getCols ();
mrs_real res = 0,
norm = 0;
for (mrs_natural i = startIdx; i < len; i++)
{
mrs_real theta = (isLog)? log(i*1./startIdx)* TWOPI :(i * TWOPI) / startIdx;
res += vector(i) * abs(.5*(cos(theta)+1)-centroid);
norm += vector(i);
}
return res/norm;
}
void
MATLABengine::putVariable(realvec value, mrs_string MATLABname)
{
//----------------------------------
// send a realvec to a MATLAB matrix
//----------------------------------
mwSize dims[2]; //realvec is 2D
dims[0] = value.getRows();
dims[1] = value.getCols();
//realvec are by default double precision matrices => mxDOUBLE_CLASS
mxArray *mxMatrix = mxCreateNumericArray(2, dims, mxDOUBLE_CLASS, mxREAL);
mrs_real *data = value.getData();
memcpy((void *)mxGetPr(mxMatrix), (void *)(data), dims[0]*dims[1]*mxGetElementSize(mxMatrix));
engPutVariable(engine_, MATLABname.c_str(), mxMatrix);
mxDestroyArray(mxMatrix);
}
void PeakConvert2::ComputePeaker (mrs_realvec in, realvec& out)
{
#ifdef ORIGINAL_VERSION
peaker_->updControl("mrs_real/peakStrength", 0.2);// to be set as a control [!]
#else
peaker_->updControl("mrs_real/peakStrength",1e-1);
peaker_->updControl("mrs_real/peakStrengthRelMax" ,1e-2);
peaker_->updControl("mrs_real/peakStrengthAbs",1e-10 );
peaker_->updControl("mrs_real/peakStrengthTreshLpParam" ,0.95);
peaker_->updControl("mrs_real/peakStrengthRelThresh" , 1.);
#endif
peaker_->updControl("mrs_real/peakSpacing", 2e-3); // 0
peaker_->updControl("mrs_natural/peakStart", downFrequency_); // 0
peaker_->updControl("mrs_natural/peakEnd", upFrequency_); // size_
peaker_->updControl("mrs_natural/inSamples", in.getCols());
peaker_->updControl("mrs_natural/inObservations", in.getRows());
peaker_->updControl("mrs_natural/onSamples", out.getCols());
peaker_->updControl("mrs_natural/onObservations", out.getRows());
peaker_->process(in, out);
}
static mrs_real MaxHps (const realvec& beatHistogram, mrs_natural startIdx = 200)
{
const mrs_natural order = 4;
mrs_natural k,len = beatHistogram.getCols ();
mrs_realvec res = beatHistogram; // make this a member
//res.setval(-1e38);
for (k =2; k < order; k++)
{
for (mrs_natural i = startIdx; i < len; i++)
{
if (k*i >= len)
break;
res(i) += log(beatHistogram(k*i)+1e-6);
}
}
for (k = 0; k < startIdx; k++)
res(k) = -1e38;
return exp (res.maxval ());
}
void
OneRClassifier::myProcess(realvec& in, realvec& out)
{
cout << "OneRClassifier::myProcess" << endl;
cout << "in.getCols() = " << in.getCols() << endl;
cout << "in.getRows() = " << in.getRows() << endl;
//get the current mode, either train of predict mode
bool trainMode = (getctrl("mrs_string/mode")->to<mrs_string>() == "train");
row_.stretch(in.getRows());
if (trainMode)
{
if(lastModePredict_ || instances_.getCols()<=0)
{
mrs_natural nAttributes = getctrl("mrs_natural/inObservations")->to<mrs_natural>();
cout << "nAttributes = " << nAttributes << endl;
instances_.Create(nAttributes);
}
lastModePredict_ = false;
//get the incoming data and append it to the data table
for (mrs_natural ii=0; ii< inSamples_; ++ii)
{
mrs_real label = in(inObservations_-1, ii);
instances_.Append(in);
out(0,ii) = label;
out(1,ii) = label;
}//for t
}//if
else
{//predict mode
cout << "OneRClassifier::predict" << endl;
if(!lastModePredict_)
{
//get the number of class labels and build the classifier
mrs_natural nAttributes = getctrl("mrs_natural/inObservations")->to<mrs_natural>();
cout << "BUILD nAttributes = " << nAttributes << endl;
Build(nAttributes);
}//if
lastModePredict_ = true;
cout << "After lastModePredict" << endl;
//foreach row of predict data, extract the actual class, then call the
//classifier predict method. Output the actual and predicted classes.
for (mrs_natural ii=0; ii<inSamples_; ++ii)
{
//extract the actual class
mrs_natural label = (mrs_natural)in(inObservations_-1, ii);
//invoke the classifier predict method to predict the class
in.getCol(ii,row_);
mrs_natural prediction = Predict(row_);
cout << "PREDICTION = " << prediction << endl;
cout << "row_ " << row_ << endl;
//and output actual/predicted classes
out(0,ii) = (mrs_real)prediction;
out(1,ii) = (mrs_real)label;
}//for t
}//if
}//myProcess
summaryStatistics ClassificationReport::computeSummaryStatistics(const realvec& mat)
{
MRSASSERT(mat.getCols()==mat.getRows());
summaryStatistics stats;
mrs_natural size = mat.getCols();
vector<mrs_natural>rowSums(size);
for(int ii=0; ii<size; ++ii) rowSums[ii] = 0;
vector<mrs_natural>colSums(size);
for(int ii=0; ii<size; ++ii) colSums[ii] = 0;
mrs_natural diagonalSum = 0;
mrs_natural instanceCount = 0;
for(mrs_natural row=0; row<size; row++)
{
for(mrs_natural col=0; col<size; col++)
{
mrs_natural num = (mrs_natural)mat(row,col);
instanceCount += num;
rowSums[row] += num;
colSums[col] += num;
if(row==col)
diagonalSum += num;
}
}
//printf("row1 sum:%d\n",rowSums[0]);
//printf("row2 sum:%d\n",rowSums[1]);
//printf("col1 sum:%d\n",colSums[0]);
//printf("col2 sum:%d\n",colSums[1]);
//printf("diagonal sum:%d\n",diagonalSum);
//printf("instanceCount:%d\n",instanceCount);
mrs_natural N = instanceCount;
mrs_natural N2 = (N*N);
stats.instances = instanceCount;
stats.correctInstances = diagonalSum;
mrs_natural sum = 0;
for(mrs_natural ii=0; ii<size; ++ii)
{
sum += (rowSums[ii] * colSums[ii]);
}
mrs_real PE = (mrs_real)sum / (mrs_real)N2;
mrs_real PA = (mrs_real)diagonalSum / (mrs_real)N;
stats.kappa = (PA - PE) / (1.0 - PE);
mrs_natural not_diagonal_sum = instanceCount - diagonalSum;
mrs_real MeanAbsoluteError = (mrs_real)not_diagonal_sum / (mrs_real)instanceCount;
//printf("MeanAbsoluteError:%f\n",MeanAbsoluteError);
stats.meanAbsoluteError = MeanAbsoluteError;
mrs_real RootMeanSquaredError = sqrt(MeanAbsoluteError);
//printf("RootMeanSquaredError:%f\n",RootMeanSquaredError);
stats.rootMeanSquaredError = RootMeanSquaredError;
mrs_real RelativeAbsoluteError = (MeanAbsoluteError / 0.5) * 100.0;
//printf("RelativeAbsoluteError:%f%%\n",RelativeAbsoluteError);
stats.relativeAbsoluteError = RelativeAbsoluteError;
mrs_real RootRelativeSquaredError = (RootMeanSquaredError / (0.5)) * 100.0;
//printf("RootRelativeSquaredError:%f%%\n",RootRelativeSquaredError);
stats.rootRelativeSquaredError = RootRelativeSquaredError;
return stats;
}//computeSummaryStatistics
void
PeakViewMerge::myProcess(realvec& in, realvec& out)
{
peakView *In[kNumMatrices],
Out (out);
mrs_natural i, rowIdx = 0,
numPeaks[kNumMatrices],
outputIdx = 0;
const mrs_bool discNegGroups = ctrl_noNegativeGroups_->to<mrs_bool>();
out.setval(0.);
for (i = 0; i < kNumMatrices; i++)
{
mrs_natural numRows = (i==kMat1)? ctrl_frameMaxNumPeaks1_->to<mrs_natural>() : ctrl_frameMaxNumPeaks2_->to<mrs_natural>();
numRows *= peakView::nbPkParameters;
if (numRows == 0) // if the controls have not been set assume both matrixes to be of equal size
numRows = in.getRows ()/kNumMatrices;
peakViewIn_[i].stretch (numRows, in.getCols ());
in.getSubMatrix (rowIdx, 0, peakViewIn_[i]);
rowIdx += numRows;
In[i] = new peakView(peakViewIn_[i]);
numPeaks[i] = In[i]->getTotalNumPeaks ();
}
if (ctrl_mode_->to<mrs_string>() == "OR")
{
// write all entries of the second peakView to output
for (i = 0; i < numPeaks[1]; i++)
{
if (discNegGroups && (*In[1])(i,peakView::pkGroup) < 0)
continue;
WriteOutput (Out, In[1], i, outputIdx);
outputIdx++;
}
// write all entries of the first peakView to output except duplicates
for (i = 0; i < numPeaks[0]; i++)
{
mrs_natural Idx;
if (discNegGroups && (*In[0])(i,peakView::pkGroup) < 0)
continue;
for (mrs_natural k = 1; k < kNumMatrices; k++)
Idx = FindDuplicate (In[k], (*In[0])(i, peakView::pkFrequency), numPeaks[k]);
if (Idx < 0)
{
WriteOutput (Out, In[0], i, outputIdx);
outputIdx++;
}
}
}
else if (ctrl_mode_->to<mrs_string>() == "AND")
{
// find duplicates and write only them to output
for (i = 0; i < numPeaks[0]; i++)
{
mrs_natural Idx;
if (discNegGroups && (*In[0])(i,peakView::pkGroup) < 0)
continue;
for (mrs_natural k = 1; k < kNumMatrices; k++)
Idx = FindDuplicate (In[k], (*In[0])(i, peakView::pkFrequency), numPeaks[k]);
if (Idx >= 0)
{
if (discNegGroups && (*In[1])(Idx,peakView::pkGroup) < 0)
continue;
WriteOutput (Out, In[0], i, outputIdx);
outputIdx++;
}
}
}
else if (ctrl_mode_->to<mrs_string>() == "ANDOR")
{
// keep the input[0] peaks that are not in input[1]
for (i = 0; i < numPeaks[0]; i++)
{
mrs_natural Idx;
if (discNegGroups && (*In[0])(i,peakView::pkGroup) < 0)
continue;
for (mrs_natural k = 1; k < kNumMatrices; k++)
Idx = FindDuplicate (In[k], (*In[0])(i, peakView::pkFrequency), numPeaks[k]);
if (Idx < 0)
{
WriteOutput (Out, In[0], i, outputIdx);
outputIdx++;
}
}
}
else if (ctrl_mode_->to<mrs_string>() == "XOR")
{
// find duplicates and write only residual to output
for (i = 0; i < numPeaks[0]; i++)
{
if (discNegGroups && (*In[0])(i,peakView::pkGroup) < 0)
continue;
mrs_natural Idx = FindDuplicate (In[1], (*In[0])(i, peakView::pkFrequency), numPeaks[1]);
if (Idx < 0)
{
WriteOutput (Out, In[0], i, outputIdx);
outputIdx++;
}
}
// find duplicates and write only residual to output
for (i = 0; i < numPeaks[1]; i++)
{
if (discNegGroups && (*In[1])(i,peakView::pkGroup) < 0)
continue;
mrs_natural Idx= FindDuplicate (In[0], (*In[1])(i, peakView::pkFrequency), numPeaks[0]);
if (Idx < 0)
{
WriteOutput (Out, In[1], i, outputIdx);
outputIdx++;
}
}
}
else
{
MRSERR("PeakViewMerfe::myProcess() : illegal mode string: " << ctrl_mode_->to<mrs_string>());
}
for (i = 0; i < kNumMatrices; i++)
{
delete In[i];
}
ctrl_totalNumPeaks_->setValue(outputIdx);
}
mrs_real
McAulayQuatieri::peakTrack(realvec& vec, mrs_natural frame, mrs_natural grpOne, mrs_natural grpTwo)
{
mrs_real dist;
mrs_natural candidate;
mrs_natural lastMatched = -1;
mrs_natural matchedTracks = 0;
mrs_real delta = ctrl_delta_->to<mrs_real>();
if(frame+1 >= vec.getCols())
{
MRSERR("McAulayQuatieri::peakTrack - frame index is bigger than the input vector!");
return -1.0;
}
peakView tmpPeakView(vec);
//get the trackID for any future track to be born (in STEP 3 - see below)
mrs_natural nextTrack = tmpPeakView.getFrameNumPeaks(0, grpOne);
//iterate over peaks in current frame
for(mrs_natural n = 0; n < tmpPeakView.getFrameNumPeaks(frame, grpOne); ++n)
{
mrs_real lastdist = MAXREAL;
candidate = -1;
// STEP 1
// find a candidate match on the next frame for each peak (i.e. track) in current frame
for(mrs_natural m = lastMatched + 1; m < tmpPeakView.getFrameNumPeaks(frame+1, grpTwo); ++m)
{
//set track parameter of all peaks of next frame to -1 so we know later
//which ones were not matched (=> BIRTH of new tracks)
tmpPeakView(m, peakView::pkTrack, frame+1, grpTwo) = -1.0;
dist = abs(tmpPeakView(n, peakView::pkFrequency, frame, grpOne) - tmpPeakView(m, peakView::pkFrequency, frame+1, grpTwo));
if (dist < delta && dist < lastdist)
{
//found a candidate!
lastdist = dist;
candidate = m;
}
}
// STEP 2
// must confirm candidate (if any)
if(candidate >= 0) //check if a candidate was found
{
//confirm if this is not the last peak in current frame
if(n < tmpPeakView.getFrameNumPeaks(frame, grpOne)-1)
{
//check the next remaining peak in current frame and see if it is a better match for the found candidate
dist = abs(tmpPeakView(n+1, peakView::pkFrequency, frame, grpOne) - tmpPeakView(candidate, peakView::pkFrequency, frame+1, grpTwo));
if(dist < lastdist)
{
// it is a better match! Check two additional conditions:
// 1. an unmatched lower freq candidate should exist
// 2. it is inside the frequency interval specified by delta
if(candidate - 1 > lastMatched)
{
if(abs(tmpPeakView(n, peakView::pkFrequency, frame, grpOne) - tmpPeakView(candidate-1, peakView::pkFrequency, frame+1, grpTwo)) < delta)
{
//found a peak to continue the track -> confirm candidate!
tmpPeakView(candidate-1, peakView::pkTrack, frame+1, grpTwo) = tmpPeakView(n, peakView::pkTrack, frame, grpOne);
lastMatched = candidate-1;
matchedTracks++;
}
}
}
else
{
//no better match than this one, so confirm candidate!
tmpPeakView(candidate, peakView::pkTrack, frame+1, grpTwo) = tmpPeakView(n, peakView::pkTrack, frame, grpOne);
lastMatched = candidate;
matchedTracks++;
}
}
else
{
//if this was the last peak in current frame, so inherently it was the best match.
//Candidate is therefore automatically confirmed and can be propagated.
tmpPeakView(candidate, peakView::pkTrack, frame+1, grpTwo) = tmpPeakView(n, peakView::pkTrack, frame, grpOne);
lastMatched = candidate;
matchedTracks++;
}
}
} //end of loop on peaks of current frame
// STEP 3
// check for any unmatched peaks in the next frame and give BIRTH to new tracks!
for(mrs_natural m = 0; m < tmpPeakView.getFrameNumPeaks(frame+1, grpTwo); ++m)
{
if(tmpPeakView(m, peakView::pkTrack, frame+1, grpTwo) == -1.0)
tmpPeakView(m, peakView::pkTrack, frame+1, grpTwo) = nextTrack++; //BIRTH of new track
}
return matchedTracks;
}
void
BeatHistoFeatures::beatHistoFeatures(realvec& in, realvec& out)
{
mrs_real sum = 0;
for (mrs_natural o=0; o < inObservations_; o++)
for (mrs_natural t = 0; t < inSamples_; t++)
{
sum += in(o,t);
}
mrs_real result[2];
mrs_natural i,startIdx = 200;
// zero-out below 50BPM
for (i=0; i < startIdx; i++)
in(i) = 0;
for (i = startIdx; i < in.getCols (); i++)
if (in(i) < 0)
in(i) = 0;
pkr1_->process(in, pkres1_);
mxr_->process(pkres1_,mxres_);
vector<mrs_real> bpms;
bpms.push_back(mxres_(0,1));
bpms.push_back(mxres_(0,3));
bpms.push_back(mxres_(0,5));
sort(bpms.begin(), bpms.end());
out(0,0) = sum;
for (unsigned int i=0; i<bpms.size(); i++)
for (unsigned int j =0; j < bpms.size(); j++)
{
if (bpms[i] == mxres_(0,2*j+1))
out(i+1,0) = mxres_(0,2*j);
}
out(4,0) = bpms[0] /4.0;
out(5,0) = bpms[1] /4.0;
out(6,0) = bpms[2] /4.0;
out(7,0) = out(4,0) / out(5,0);
NormInPlace (in);
#ifdef MARSYAS_MATLAB
#ifdef MTLB_DBG_LOG
MATLAB_PUT(in, "beathist");
MATLAB_EVAL("figure(1);plot((201:800)/4, beathist(201:800)),grid on");
#endif
#endif
MaxAcf (result[0], result[1],in, flag_, startIdx, 600);
out(8,0) = result[0];
out(9,0) = result[1];
out(10,0) = MaxHps (in, startIdx);
out(11,0) = SpectralFlatness (in, startIdx);
out(12,0) = Std(in);
out(13,0) = PeriodicCentroid(in, false, startIdx);
out(14,0) = PeriodicCentroid(in, true, startIdx);
out(15,0) = PeriodicSpread(in, out(13,0), false, startIdx);
out(16,0) = PeriodicSpread(in, out(14,0), true, startIdx);
out(17,0) = NumMax(in);
}
void
Filter::myProcess(realvec& in, realvec& out)
{
//checkFlow(in,out);
mrs_natural i,j,c;
mrs_natural size = in.getCols();
mrs_natural stateSize = state_.getCols();
mrs_natural channels = in.getRows();
mrs_real gain = getctrl("mrs_real/fgain")->to<mrs_real>();
// State array holds the various delays for the difference equation
// of the filter. Similar implementation as described in the manual
// for MATLAB Signal Processing Toolbox. State corresponds to
// the z, num_coefs to the b and denom_coefs to the a vector respectively
// in_window is the input x(n) and out_window is the output y(n)
//dcoeffs_/=10;
// state_.setval(0);
if (norder_ == dorder_) {
for (c = 0; c < channels; ++c) {
for (i = 0; i < size; ++i) {
out(c,i) = ncoeffs_(0) * in(c,i) + state_(c,0);
for (j = 0; j < stateSize - 1; j++)
{
state_(c,j) = ncoeffs_(j+1) * in(c,i) + state_(c,j+1) - dcoeffs_(j+1) * out(c,i);
}
state_(c,stateSize - 1) = ncoeffs_(order_-1) * in(c,i) - dcoeffs_(order_-1) * out(c,i);
}
}
}
else if (norder_ < dorder_) {
for (c = 0; c < channels; ++c) {
for (i = 0; i < size; ++i) {
out(c,i) = ncoeffs_(0) * in(c,i) + state_(c,0);
for (j = 0; j < norder_ - 1; j++)
{
state_(c,j) = ncoeffs_(j+1) * in(c,i) + state_(c,j+1) - dcoeffs_(j+1) * out(c,i);
}
for (j = norder_ - 1; j < stateSize - 1; j++)
{
state_(c,j) = state_(c,j+1) - dcoeffs_(j+1) * out(c,i);
}
state_(c,stateSize - 1) = -dcoeffs_(order_ - 1) * out(c,i);
}
}
}
else {
for (c = 0; c < channels; ++c) {
for (i = 0; i < size; ++i) {
out(c,i) = ncoeffs_(0) * in(c,i) + state_(c,0);
for (j = 0; j < dorder_ - 1; j++)
{
state_(c,j) = ncoeffs_(j+1) * in(c,i) + state_(c,j+1) - dcoeffs_(j+1) * out(c,i);
}
for (j = dorder_ - 1; j < stateSize - 1; j++)
{
state_(c,j) = ncoeffs_(j+1) * in(c,i) + state_(c,j+1);
}
state_(c,stateSize - 1) = ncoeffs_(order_-1) * in(c,i);
}
}
}
out *= gain;
// MATLAB_PUT(in, "Filter_in");
// MATLAB_PUT(out, "Filter_out");
// MATLAB_PUT(ncoeffs_, "ncoeffs_");
// MATLAB_PUT(dcoeffs_, "dcoeffs_");
// MATLAB_EVAL("MAT_out = filter(ncoeffs_, dcoeffs_, Filter_in)");
//
// MATLAB_EVAL("spec_in = abs(fft(Filter_in));");
// MATLAB_EVAL("spec_out = abs(fft(Filter_out));");
// MATLAB_EVAL("spec_mat = abs(fft(MAT_out));");
//
// MATLAB_EVAL("subplot(2,1,1);plot(Filter_in);hold on; plot(Filter_out, 'r'); plot(MAT_out, 'g');hold off");
// MATLAB_EVAL("subplot(2,1,2);plot(spec_in(1:end/2));hold on; plot(spec_out(1:end/2),'r');plot(spec_mat(1:end/2),'g');hold off;");
// MATLAB_EVAL("h = abs(fft([1 -.97], length(Filter_in)));");
// MATLAB_EVAL("hold on; plot(h(1:end/2), 'k'); hold off");
// //MATLAB_GET("MAT_out", out)
//
}
void
SelfSimilarityMatrix::myProcess(realvec& in, realvec& out)
{
if(this->getctrl("mrs_natural/mode")->to<mrs_natural>() == SelfSimilarityMatrix::outputDistanceMatrix)
{
//check if there are any elements to process at the input
//(in some cases, they may not exist!) - otherwise, do nothing
//(i.e. output will be zeroed out)
if(inSamples_ > 0)
{
unsigned int child_count = marsystems_.size();
if(child_count == 1)
{
mrs_natural nfeats = in.getRows();
//normalize input features if necessary
if(ctrl_normalize_->to<mrs_string>() == "MinMax")
in.normObsMinMax(); // (x - min)/(max - min)
else if(ctrl_normalize_->to<mrs_string>() == "MeanStd")
in.normObs(); // (x - mean)/std
//calculate the Covariance Matrix from the input, if defined
if(ctrl_calcCovMatrix_->to<mrs_natural>() & SelfSimilarityMatrix::fixedStdDev)
{
//fill covMatrix diagonal with fixed value (remaining values are zero)
MarControlAccessor acc(ctrl_covMatrix_);
realvec& covMatrix = acc.to<mrs_realvec>();
covMatrix.create(inObservations_, inObservations_);
mrs_real var = ctrl_stdDev_->to<mrs_real>();
var *= var;
for(mrs_natural i=0; i< inObservations_; ++i)
{
covMatrix(i,i) = var;
}
}
else if(ctrl_calcCovMatrix_->to<mrs_natural>() & SelfSimilarityMatrix::diagCovMatrix)
{
in.varObs(vars_); //FASTER -> only get the vars for each feature
mrs_natural dim = vars_.getSize();
//fill covMatrix diagonal with var values (remaining values are zero)
MarControlAccessor acc(ctrl_covMatrix_);
realvec& covMatrix = acc.to<mrs_realvec>();
covMatrix.create(dim, dim);
for(mrs_natural i=0; i< dim; ++i)
{
covMatrix(i,i) = vars_(i);
}
}
else if(ctrl_calcCovMatrix_->to<mrs_natural>() & SelfSimilarityMatrix::fullCovMatrix)
{
MarControlAccessor acc(ctrl_covMatrix_);
realvec& covMatrix = acc.to<mrs_realvec>();
in.covariance(covMatrix); //SLOWER -> estimate the full cov matrix
}
else if(ctrl_calcCovMatrix_->to<mrs_natural>() == SelfSimilarityMatrix::noCovMatrix)
{
ctrl_covMatrix_->setValue(realvec());
}
for(mrs_natural i=0; i < in.getCols(); ++i)
{
in.getCol(i, i_featVec_);
for(mrs_natural j=0; j <= i; ++j)
{
in.getCol(j, j_featVec_);
//stack i and j feat vecs
for(mrs_natural r=0; r < nfeats; ++r)
{
stackedFeatVecs_(r, 0) = i_featVec_(r);
stackedFeatVecs_(r+nfeats, 0) = j_featVec_(r);
}
//do the metric calculation for these two feat vectors
//and store it in the similarity matrix (which is symmetric)
marsystems_[0]->process(stackedFeatVecs_, metricResult_);
out(i,j) = metricResult_(0,0);
//metric should be symmetric!
out(j, i) = out(i, j);
}
}
}
else
{
out.setval(0.0);
if(child_count == 0)
{
MRSWARN("SelfSimilarityMatrix::myProcess - no Child Metric MarSystem added - outputting zero similarity matrix!");
}
else
{
MRSWARN("SelfSimilarityMatrix::myProcess - more than one Child MarSystem exists (i.e. invalid metric) - outputting zero similarity matrix!");
}
}
}
//MATLAB_PUT(out, "simMatrix");
//MATLAB_EVAL("figure(1);imagesc(simMatrix);");
//MATLAB_PUT(out, "simMat");
//MATLAB_EVAL(name_+"=["+name_+",simMat(:)'];");
}
else if(this->getctrl("mrs_natural/mode")->to<mrs_natural>() == SelfSimilarityMatrix::outputPairDistance)
{
if(inSamples_ == 2) //we always need two column vector instances at input
{
unsigned int child_count = marsystems_.size();
if(child_count == 1)
{
MarControlAccessor acc(ctrl_instanceIndexes_);
realvec& instIdxs = acc.to<mrs_realvec>();
mrs_natural i = mrs_natural(instIdxs(0));
mrs_natural j = mrs_natural(instIdxs(1));
//check for out of bound indexes (which could have been set
//by someone outside changing the value of the ctrl_instanceIndexes control)
mrs_natural nInstances = ctrl_nInstances_->to<mrs_natural>();
if(i >= nInstances || j >= nInstances)
ctrl_done_->setValue(true);
if(!ctrl_done_->isTrue())
{
mrs_natural nfeats = in.getRows();
//COMPUTE DISTANCE between the two column vector at input
in.getCol(0, i_featVec_);
in.getCol(1, j_featVec_);
//stack i and j feat vecs
for(mrs_natural r=0; r < nfeats; ++r)
{
stackedFeatVecs_(r, 0) = i_featVec_(r);
stackedFeatVecs_(r+nfeats, 0) = j_featVec_(r);
}
//do the metric calculation for these two feat vectors
//and send it to the output
marsystems_[0]->process(stackedFeatVecs_, out);
//out(0) = metricResult_(0,0);
}
else
{
//Self Similarity has completed all pair-wise similarity computations
//so, it will just send zero valued values and a warning
out(0) = 0.0;
MRSWARN("SelfSimilarityMatrix::myProcess - no more pairwise similarity computations to be performed - outputting zero similarity value!")
}
//Select indexes for next pair of instances for distance computation
//Similarity matrix is tringular simetric, so we should just compute
//half of it (including diagonal). These indexes are to be used by some
//source MarSystem that has a control linked to ctrl_instanceIndexes (e.g. WekaSource)
if (i < j)
++i;
else
{
++j;
i = 0;
}
if (j >= nInstances)
{
ctrl_done_->setValue(true);
j = -1; //used to signal that there are no more instance pairs to compute
i = -1; //used to signal that there are no more instance pairs to compute
}
else
ctrl_done_->setValue(false);
//set indexes into the ctrl_instanceIndexes_ control
instIdxs(0) = i;
instIdxs(1) = j;
}
else
{
void
peakView::fromTable(const realvec& vecTable)
{
//get data from header
fs_ = vecTable(0, 1);
frameSize_ = (mrs_natural)vecTable(0, 2);
frameMaxNumPeaks_ = (mrs_natural)vecTable(0, 3);
numFrames_ = (mrs_natural)vecTable(0, 4);
//get the first frame in table (it may not be 0!!!)
mrs_natural frame = (mrs_natural)vecTable(1, pkFrame); // start frame [!]
//resize (and set to zero) vec_ for new peak data
//(should accommodate empty frames before the first frame in table!)
vec_.create(frameMaxNumPeaks_*nbPkParameters, numFrames_+frame); //[!]
mrs_natural p = 0; // peak index inside each frame
mrs_natural r = 1;//peak index in table (i.e. row index) - ignore header row
//check in case realvec has less parameters than nbPkParameters
mrs_natural actualNbPkParams = (mrs_natural)min((mrs_real)nbPkParameters, (mrs_real)vecTable.getCols());
//iterate over table rows (i.e. peaks) - excluding header row
while(r < vecTable.getRows()-1)
{
//get parameters for this peak
for(mrs_natural prm = 0; prm < actualNbPkParams; ++prm)
{
(*this)(p, pkParameter(prm), frame) = vecTable(r, prm);
}
++r; //move on to next table row (i.e. peak)
p++;
//if the next row in table is form a different frame,
//reset peak index and get new frame index
if(vecTable(r, pkFrame) != frame)
{
frame = (mrs_natural)vecTable(r, pkFrame);
p = 0;
}
}
}
