// Action_Matrix::FillMassArray()
Action_Matrix::Darray Action_Matrix::FillMassArray(Topology const& currentParm,
AtomMask const& mask) const
{
Darray mass;
mass.reserve( mask.Nselected() );
for (AtomMask::const_iterator atom = mask.begin(); atom != mask.end(); ++atom)
mass.push_back( currentParm[ *atom ].Mass() );
return mass;
}
// Analysis_Wavelet::Analyze()
Analysis::RetType Analysis_Wavelet::Analyze() {
// Step 1 - Create a matrix that is #atoms rows by #frames - 1 cols,
// where matrix(frame, atom) is the distance that atom has
// travelled from the previous frame.
// TODO: Implement this in Action_Matrix()?
mprintf(" WAVELET:\n");
// First set up atom mask.
if (coords_->Top().SetupIntegerMask( mask_ )) return Analysis::ERR;
mask_.MaskInfo();
int natoms = mask_.Nselected();
int nframes = (int)coords_->Size();
if (natoms < 1 || nframes < 2) {
mprinterr("Error: Not enough frames (%i) or atoms (%i) in '%s'\n",
nframes, natoms, coords_->legend());
return Analysis::ERR;
}
Matrix<double> d_matrix;
mprintf("\t%i frames, %i atoms, distance matrix will require %.2f MB\n",
(double)d_matrix.sizeInBytes(nframes, natoms) / (1024.0*1024.0));
d_matrix.resize(nframes, natoms);
// Get initial frame.
Frame currentFrame, lastFrame;
currentFrame.SetupFrameFromMask( mask_, coords_->Top().Atoms() );
lastFrame = currentFrame;
coords_->GetFrame( 0, lastFrame, mask_ );
// Iterate over frames
for (int frm = 1; frm != nframes; frm++) {
coords_->GetFrame( frm, currentFrame, mask_ );
int idx = frm; // Position in distance matrix; start at column 'frame'
for (int at = 0; at != natoms; at++, idx += nframes)
// Distance of atom in currentFrame from its position in lastFrame.
d_matrix[idx] = sqrt(DIST2_NoImage( currentFrame.XYZ(at), lastFrame.XYZ(at) ));
//lastFrame = currentFrame; // TODO: Re-enable?
}
# ifdef DEBUG_WAVELET
// DEBUG: Write matrix to file.
CpptrajFile dmatrixOut; // DEBUG
dmatrixOut.OpenWrite("dmatrix.dat");
Matrix<double>::iterator mval = d_matrix.begin();
for (int row = 0; row != natoms; row++) {
for (int col = 0; col != nframes; col++)
dmatrixOut.Printf("%g ", *(mval++));
dmatrixOut.Printf("\n");
}
dmatrixOut.CloseFile();
# endif
// Precompute some factors for calculating scaled wavelets.
const double one_over_sqrt_N = 1.0 / sqrt(static_cast<double>( nframes ));
std::vector<int> arrayK( nframes );
arrayK[0] = -1 * (nframes/2);
for (int i = 1; i != nframes; i++)
arrayK[i] = arrayK[i-1] + 1;
# ifdef DEBUG_WAVELET
mprintf("DEBUG: K:");
for (std::vector<int>::const_iterator kval = arrayK.begin(); kval != arrayK.end(); ++kval)
mprintf(" %i", *kval);
mprintf("\n");
# endif
// Step 2 - Get FFT of wavelet for each scale.
PubFFT pubfft;
pubfft.SetupFFTforN( nframes );
mprintf("\tMemory required for scaled wavelet array: %.2f MB\n",
(double)(2 * nframes * nb_ * sizeof(double)) / (1024 * 1024));
typedef std::vector<ComplexArray> WaveletArray;
WaveletArray FFT_of_Scaled_Wavelets;
FFT_of_Scaled_Wavelets.reserve( nb_ );
typedef std::vector<double> Darray;
Darray scaleVector;
scaleVector.reserve( nb_ );
Darray MIN( nb_ * 2 );
for (int iscale = 0; iscale != nb_; iscale++)
{
// Calculate and store scale factor.
scaleVector.push_back( S0_ * pow(2.0, iscale * ds_) );
// Populate MIN array
MIN[iscale ] = (0.00647*pow((correction_*scaleVector.back()),1.41344)+19.7527)*chival_;
MIN[iscale+nb_] = correction_*scaleVector.back();
// Calculate scalved wavelet
ComplexArray scaledWavelet;
switch (wavelet_type_) {
case W_MORLET:
scaledWavelet = F_Morlet(arrayK, scaleVector.back());
break;
case W_PAUL :
scaledWavelet = F_Paul(arrayK, scaleVector.back());
break;
case W_NONE :
return Analysis::ERR; // Sanity check
}
# ifdef DEBUG_WAVELET
PrintComplex("wavelet_before_fft", scaledWavelet);
# endif
// Perform FFT
pubfft.Forward( scaledWavelet );
// Normalize
scaledWavelet.Normalize( one_over_sqrt_N );
# ifdef DEBUG_WAVELET
PrintComplex("wavelet_after_fft", scaledWavelet);
# endif
FFT_of_Scaled_Wavelets.push_back( scaledWavelet );
}
# ifdef DEBUG_WAVELET
mprintf("DEBUG: Scaling factors:");
for (Darray::const_iterator sval = scaleVector.begin(); sval != scaleVector.end(); ++sval)
mprintf(" %g", *sval);
mprintf("\n");
mprintf("DEBUG: MIN:");
for (int i = 0; i != nb_; i++)
mprintf(" %g", MIN[i]);
mprintf("\n");
# endif
// Step 3 - For each atom, calculate the convolution of scaled wavelets
// with rows (atom distance vs frame) via dot product of the
// frequency domains, i.e. Fourier-transformed, followed by an
// inverse FT.
DataSet_MatrixFlt& OUT = static_cast<DataSet_MatrixFlt&>( *output_ );
mprintf("\tMemory required for output matrix: %.2f MB\n",
(double)Matrix<float>::sizeInBytes(nframes, natoms)/(1024.0*1024.0));
OUT.Allocate2D( nframes, natoms ); // Should initialize to zero
Matrix<double> MAX;
mprintf("\tMemory required for Max array: %.2f MB\n",
(double)MAX.sizeInBytes(nframes, natoms)/(1024.0*1024.0));
MAX.resize( nframes, natoms );
Darray magnitude( nframes ); // Scratch space for calculating magnitude across rows
for (int at = 0; at != natoms; at++) {
ComplexArray AtomSignal( nframes ); // Initializes to zero
// Calculate the distance variance for this atom and populate the array.
int midx = at * nframes; // Index into d_matrix
int cidx = 0; // Index into AtomSignal
double d_avg = 0.0;
double d_var = 0.0;
for (int frm = 0; frm != nframes; frm++, cidx += 2, midx++) {
d_avg += d_matrix[midx];
d_var += (d_matrix[midx] * d_matrix[midx]);
AtomSignal[cidx] = d_matrix[midx];
}
d_var = (d_var - ((d_avg * d_avg) / (double)nframes)) / ((double)(nframes - 1));
# ifdef DEBUG_WAVELET
mprintf("VARIANCE: %g\n", d_var);
# endif
double var_norm = 1.0 / d_var;
// Calculate FT of atom signal
pubfft.Forward( AtomSignal );
# ifdef DEBUG_WAVELET
PrintComplex("AtomSignal", AtomSignal);
# endif
// Normalize
AtomSignal.Normalize( one_over_sqrt_N );
// Calculate dot product of atom signal with each scaled FT wavelet
for (int iscale = 0; iscale != nb_; iscale++) {
ComplexArray dot = AtomSignal.TimesComplexConj( FFT_of_Scaled_Wavelets[iscale] );
// Inverse FT of dot product
pubfft.Back( dot );
# ifdef DEBUG_WAVELET
PrintComplex("InverseFT_Dot", dot);
# endif
// Chi-squared testing
midx = at * nframes;
cidx = 0;
for (int frm = 0; frm != nframes; frm++, cidx += 2, midx++) {
magnitude[frm] = (dot[cidx]*dot[cidx] + dot[cidx+1]*dot[cidx+1]) * var_norm;
if (magnitude[frm] < MIN[iscale])
magnitude[frm] = 0.0;
if (magnitude[frm] > MAX[midx]) {
MAX[midx] = magnitude[frm];
//Indices[midx] = iscale
OUT[midx] = (float)(correction_ * scaleVector[iscale]);
}
}
# ifdef DEBUG_WAVELET
mprintf("DEBUG: AbsoluteValue:");
for (Darray::const_iterator dval = magnitude.begin(); dval != magnitude.end(); ++dval)
mprintf(" %g", *dval);
mprintf("\n");
# endif
} // END loop over scales
} // END loop over atoms
# ifdef DEBUG_WAVELET
// DEBUG: Print MAX
CpptrajFile maxmatrixOut; // DEBUG
maxmatrixOut.OpenWrite("maxmatrix.dat");
for (int col = 0; col != nframes; col++) {
for (int row = 0; row != natoms; row++)
maxmatrixOut.Printf("%g ", MAX.element(col, row));
maxmatrixOut.Printf("\n");
}
maxmatrixOut.CloseFile();
# endif
return Analysis::OK;
}
