void ParallelInfo::sendZi(const Pattern &toSend)
{
int P_Tag = 0;
#if defined(TIMING_MODE)
long long elapsed, start;
elapsed = 0;
#endif
// 10-2-2002, Replaced MPI_Send with MPI_Rsend
// this assumes that the comp nodes have already
// called MPI_Recv, which they should have.
for (unsigned int i = 1; i < P_NumNodes; i++) {
#if defined(TIMING_MODE)
start = rdtsc();
#endif
int * tmpToSend = new int[totalNumNrns];
for (unsigned int nrn = 0; nrn < totalNumNrns; nrn++)
tmpToSend[nrn] = toSend.at(nrn);
MPI_Rsend(&tmpToSend[0], totalNumNrns, MPI_INT, i, P_Tag, MPI_COMM_WORLD);
#if defined(TIMING_MODE)
elapsed += rdtsc() - start;
#endif
}
#if defined(TIMING_MODE)
Output::Out() << "Elapsed root_snd time = " << elapsed * 1.0 / TICKS_PER_SEC
<< " seconds" << endl;
#endif
}
void RateMeyerHaeseler::computeFuncDerv(double value, double &df, double &ddf) {
int nseq = phylo_tree->leafNum;
int nstate = phylo_tree->getModel()->num_states;
int i, j, state1, state2;
// double lh = 0.0;
double trans, derv1, derv2;
ModelSubst *model = phylo_tree->getModel();
Pattern *pat = & phylo_tree->aln->at(optimizing_pattern);
df = ddf = 0.0;
for (i = 0; i < nseq-1; i++) if ((state1 = pat->at(i)) < nstate)
for (j = i+1; j < nseq; j++) if ((state2 = pat->at(j)) < nstate) {
double dist = dist_mat[i*nseq + j];
trans = model->computeTrans(value * dist, state1, state2, derv1, derv2);
// lh -= log(trans);
double t1 = derv1 / trans;
double t2 = derv2 / trans;
df -= t1 * dist;
ddf -= dist * dist * (t2 - t1*t1);
}
// return lh;
}
double RateMeyerHaeseler::computeFunction(double value) {
if (!rate_mh) {
if (value != cur_scale) {
ptn_tree->scaleLength(value/cur_scale);
cur_scale = value;
ptn_tree->clearAllPartialLH();
}
return -ptn_tree->computeLikelihood();
}
int nseq = phylo_tree->leafNum;
int nstate = phylo_tree->getModel()->num_states;
int i, j, state1, state2;
double lh = 0.0;
ModelSubst *model = phylo_tree->getModel();
Pattern *pat = & phylo_tree->aln->at(optimizing_pattern);
for (i = 0; i < nseq-1; i++) if ((state1 = pat->at(i)) < nstate)
for (j = i+1; j < nseq; j++) if ((state2 = pat->at(j)) < nstate)
lh -= log(model->computeTrans(value * dist_mat[i*nseq + j], state1, state2));
return lh;
}
double RateMeyerDiscrete::computeFunction(double value) {
if (!is_categorized) return RateMeyerHaeseler::computeFunction(value);
if (!rate_mh) {
if (value != cur_scale) {
ptn_tree->scaleLength(value/cur_scale);
cur_scale = value;
ptn_tree->clearAllPartialLH();
}
return -ptn_tree->computeLikelihood();
}
double lh = 0.0;
int nseq = phylo_tree->leafNum;
int nstate = phylo_tree->getModel()->num_states;
int i, j, k, state1, state2;
ModelSubst *model = phylo_tree->getModel();
int trans_size = nstate * nstate;
double *trans_mat = new double[trans_size];
int *pair_freq = new int[trans_size];
for (i = 0; i < nseq-1; i++)
for (j = i+1; j < nseq; j++) {
memset(pair_freq, 0, trans_size * sizeof(int));
for (k = 0; k < size(); k++) {
if (ptn_cat[k] != optimizing_cat) continue;
Pattern *pat = & phylo_tree->aln->at(k);
if ((state1 = pat->at(i)) < nstate && (state2 = pat->at(j)) < nstate)
pair_freq[state1*nstate + state2] += pat->frequency;
}
model->computeTransMatrix(value * dist_mat[i*nseq + j], trans_mat);
for (k = 0; k < trans_size; k++) if (pair_freq[k])
lh -= pair_freq[k] * log(trans_mat[k]);
}
delete [] pair_freq;
delete [] trans_mat;
return lh;
}
void ActiveConnect(ArgListType &arg) //AT_FUN
{
// process the function arguments
static string FunctionName = "ActiveConnect";
static IntArg StartNeuron("-Nstart", "start neuron", 1);
static IntArg EndNeuron("-Nend", "end neuron{-1 gives last neuron}", -1);
static IntArg StartPat("-Pstart", "start pattern(or vector)", 1);
static IntArg EndPat("-Pend", "end pattern(or vector) {-1 gives end time}",
-1);
static StrArg SeqName("-name", "sequence name");
static StrArg ResetSeq("-reset", "reset sequence", "{zeros}");
static StrArg External("-ext", "external sequence", "{zeros}");
static FlagArg DoSummary("-sum", "-nosum", "print a summary", 1);
static int argunset = true;
static CommandLine ComL(FunctionName);
if (argunset) {
ComL.HelpSet("@ActiveConnect() \n"
"\tGenerates the data about conditional probabilities of firing\n"
"\tand saves the results into the ActiveConBuffer.\n"
"\tThe reset sequence is used for the 0 time step and\n"
"\tif externals are given then they are ignored.\n"
"\tActiveConBuffer is a matrix with 6 Vectors:\n"
"\t\t1: TimeStep(Pattern Number)\n"
"\t\t2: Absolute Activity Last Time\n"
"\t\t3: Absolute Activity This Time - Externals\n"
"\t\t4: # of Conns between CoActive Neurons\n"
"\t\t5: 4/3 = Ave # of Active Conns for Active Neurons\n"
"\t\t6: 4/(2*3) = Prob cij=1 given zi=1,zj=1\n"
"\tActiveConnect also updates the variable Pczz which\n"
"\tholds the Prob(cij=1 | zi=1,zj=1) for the whole sequence\n");
ComL.IntSet(4, &StartNeuron, &EndNeuron, &StartPat, &EndPat);
ComL.StrSet(3, &SeqName, &ResetSeq, &External);
ComL.FlagSet(1, &DoSummary);
argunset = false;
}
ComL.Process(arg, Output::Err());
if (!program::Main().getNetworkCreated()) {
CALL_ERROR << "Error: You must call @CreateNetwork() before you can "
"call @ActiveConnect." << ERR_WHERE;
exit(EXIT_FAILURE);
}
UIPtnSequence Seq = SystemVar::getSequence(SeqName, FunctionName, ComL);
int SeqSize = Seq.size();
UIPtnSequence ReSeq;
if (ResetSeq.getValue() != "{zeros}") {
ReSeq = SystemVar::getSequence(ResetSeq, FunctionName, ComL);
} else {
ReSeq.resize(SeqSize, UIVector(0));
}
int lastNeuron = 0;
for (UIPtnSequenceCIt it = Seq.begin(); it != Seq.end(); it++) {
updateMax(lastNeuron, it->back());
}
if (EndNeuron.getValue() == -1) {
EndNeuron.setValue(lastNeuron);
}
if (EndPat.getValue() == -1) {
EndPat.setValue(SeqSize);
}
if (StartNeuron.getValue() < 1 ||
StartNeuron.getValue() > EndNeuron.getValue() ||
EndNeuron.getValue() > static_cast<int>(ni)) {
CALL_ERROR << "Error in " << FunctionName << ": Neuron range of "
<< StartNeuron.getValue() << "..." << EndNeuron.getValue()
<< " is invalid." << ERR_WHERE;
ComL.DisplayHelp(Output::Err());
}
if (EndPat.getValue() < 1 || EndPat.getValue() > SeqSize ||
StartPat.getValue() < 1 || StartPat.getValue() > EndPat.getValue()) {
CALL_ERROR << "Error in " << FunctionName << ": Pattern range of "
<< StartPat.getValue() << "..." << EndPat.getValue() << " is invalid."
<< ERR_WHERE;
ComL.DisplayHelp(Output::Err());
}
// get externals
UIMatrix ExtSeq;
if (External.getValue() != "{zeros}") {
ExtSeq = SystemVar::getSequence(External, FunctionName, ComL);
} else {
ExtSeq.resize(SeqSize, UIVector(0));
}
// Do the loops
int NumPats = EndPat.getValue() - StartPat.getValue() + 1;
DataList Ave(NumPats);
DataList Sum(NumPats);
DataList Pats(NumPats);
DataList jNumFired(NumPats);
DataList iNumFired(NumPats);
DataList PczzV(NumPats);
int index = 0;
UIPtnSequenceCIt SeqConstIterator = Seq.begin();
UIPtnSequenceCIt ExtConstIterator = ExtSeq.begin();
UIVector pat_b4;
if (StartPat.getValue() == 1) {
pat_b4 = ReSeq.front();
} else {
for (int inc = 0; inc < StartPat.getValue() - 2; ++inc) ++SeqConstIterator;
pat_b4 = *(SeqConstIterator++);
}
for (int t = StartPat.getValue(); t <= EndPat.getValue(); ++t, ++index, ++SeqConstIterator, ++ExtConstIterator) {
Pats.at(index) = static_cast<float>(t);
Pattern pat = UIVectorToPtn(*SeqConstIterator, lastNeuron);
Pattern pat_ext = UIVectorToPtn(*ExtConstIterator, lastNeuron);
for (int j = StartNeuron.getValue(); j <= EndNeuron.getValue(); j++) {
// count the number on
if (pat_b4.at(j-1)) ++iNumFired.at(index);
// do the calculation for non-externals and active
if (pat.at(j-1) && (!(pat_ext.at(j-1)))) {
++jNumFired.at(index);
for (unsigned int c = 0; c < FanInCon.at(j-1); c++) {
if (pat_b4.at(inMatrix[j-1][c].getSrcNeuron()))
++Sum.at(index);
}
}
}
pat_b4 = pat;
}
// Output the data
Output::Out() << "\nSummed Active Connections in sequence " << SeqName.getValue()
<< " using neurons " << StartNeuron.getValue() << "..."
<< EndNeuron.getValue() << " and patterns " << StartPat.getValue()
<< "..." << EndPat.getValue() << "\n\tignoring externals given by "
<< External.getValue();
if (DoSummary.getValue()) {
Output::Out() << "\n" << std::setw(11) << "1:TimeStep"
<< std::setw(9) << "2:#z(t-1)"
<< std::setw(9) << "3:#z(t)"
<< std::setw(15) << "4:#cz(t-1)z(t)"
<< std::setw(9) << "4/3" << std::setw(9) << "4/(2*3)" << "\n";
}
float TotalSumC = 0.0f;
float TotalSumZ = 0.0f;
for (int i = 0; i < index; i++) {
if (fabs(Sum.at(i)) < verySmallFloat) {
Ave.at(i) = 0.0f;
PczzV.at(i) = 0.0f;
} else {
Ave.at(i) = Sum.at(i) / jNumFired.at(i);
PczzV.at(i) = Ave.at(i) / iNumFired.at(i);
}
TotalSumC += Sum.at(i);
TotalSumZ += iNumFired.at(i) * jNumFired.at(i);
if (DoSummary.getValue()) {
Output::Out() << "\n" << std::setw(11) << static_cast<int>(Pats.at(i))
<< std::setw(9) << static_cast<int>(iNumFired.at(i))
<< std::setw(9) << static_cast<int>(jNumFired.at(i))
<< std::setw(15) << static_cast<int>(Sum.at(i))
<< std::setw(9) << Ave.at(i)
<< std::setw(9) << PczzV.at(i);
}
}
Output::Out() << "\n";
float Pczz;
if (fabs(TotalSumC) < verySmallFloat) {
Pczz = 0.0f;
} else {
Pczz = TotalSumC / TotalSumZ;
}
SystemVar::SetFloatVar("Pczz", Pczz);
if (DoSummary.getValue()) {
Output::Out() << "Average: " << Pczz << "\n";
}
// Save the vector to the ActiveConBuffer
DataMatrix ActiveConMat;
ActiveConMat.push_back(Pats);
ActiveConMat.push_back(iNumFired);
ActiveConMat.push_back(jNumFired);
ActiveConMat.push_back(Sum);
ActiveConMat.push_back(Ave);
ActiveConMat.push_back(PczzV);
SystemVar::insertData("ActiveConBuffer", ActiveConMat, DLT_matrix);
return;
}
void RateMeyerDiscrete::computeFuncDerv(double value, double &df, double &ddf) {
if (!is_categorized) {
RateMeyerHaeseler::computeFuncDerv(value, df, ddf);
return;
}
// double lh = 0.0;
int nseq = phylo_tree->leafNum;
int nstate = phylo_tree->getModel()->num_states;
int i, j, k, state1, state2;
ModelSubst *model = phylo_tree->getModel();
int trans_size = nstate * nstate;
double *trans_mat = new double[trans_size];
double *trans_derv1 = new double[trans_size];
double *trans_derv2 = new double[trans_size];
df = ddf = 0.0;
int *pair_freq = new int[trans_size];
for (i = 0; i < nseq-1; i++)
for (j = i+1; j < nseq; j++) {
memset(pair_freq, 0, trans_size * sizeof(int));
for (k = 0; k < size(); k++) {
if (ptn_cat[k] != optimizing_cat) continue;
Pattern *pat = & phylo_tree->aln->at(k);
if ((state1 = pat->at(i)) < nstate && (state2 = pat->at(j)) < nstate)
pair_freq[state1*nstate + state2] += pat->frequency;
}
double dist = dist_mat[i*nseq + j];
double derv1 = 0.0, derv2 = 0.0;
model->computeTransDerv(value * dist, trans_mat, trans_derv1, trans_derv2);
for (k = 0; k < trans_size; k++) if (pair_freq[k]) {
double t1 = trans_derv1[k] / trans_mat[k];
double t2 = trans_derv2[k] / trans_mat[k];
trans_derv1[k] = t1;
trans_derv2[k] = (t2 - t1*t1);
// lh -= log(trans_mat[k]) * pair_freq[k];
derv1 += trans_derv1[k] * pair_freq[k];
derv2 += trans_derv2[k] * pair_freq[k];
}
df -= derv1 * dist;
ddf -= derv2 * dist * dist;
}
delete [] pair_freq;
delete [] trans_derv2;
delete [] trans_derv1;
delete [] trans_mat;
// return lh;
/* double lh = 0.0, derv1, derv2;
df = 0.0; ddf = 0.0;
for (int i = 0; i < size(); i++)
if (ptn_cat[i] == optimizing_cat) {
optimizing_pattern = i;
int freq = phylo_tree->aln->at(i).frequency;
lh += RateMeyerHaeseler::computeFuncDerv(value, derv1, derv2) * freq;
df += derv1 * freq;
ddf += derv2 * freq;
}
return lh;*/
}
void Preprocessor::correctSlanting ()
{
boost::timer timer;
timer.restart();
const double PI = 3.1415926535;
for ( std::vector<Pattern>::iterator i = patterns_.begin(); i != patterns_.end(); ++i )
{
const unsigned int rotationLimit = 20;
double shearingFactor;;
// This vector stores the greatest number of ink pixels counted in any column of a rotated pattern.
std::vector<unsigned int> columnPixelMaximalCounts(rotationLimit);
// Rotate the pattern and count the number of ink pixels per column
for ( double angle = 0; angle < rotationLimit; ++angle )
{
std::map<unsigned int, std::set<unsigned int> > pixelsPerColumn;
shearingFactor = tan(-angle * PI / 180.0);
// Store the columns of rotated pixels
for ( unsigned int j = 0; j < i->height(); ++j )
{
for ( unsigned int k = 0; k < i->width(); ++k )
{
if ( i->at(j,k) == 1 ) // Ink pixel
{
double jp = j;
double kp = k;
kp = round(kp - jp * shearingFactor);
if ( kp < i->width() && kp > 0 )
pixelsPerColumn[kp].insert(j);
}
}
}
unsigned int columnPixelMaximalCount = 0;
for ( std::map<unsigned int, std::set<unsigned int> >::iterator row = pixelsPerColumn.begin(); row != pixelsPerColumn.end(); ++row )
{
if ( row->second.size() > columnPixelMaximalCount )
columnPixelMaximalCount = row->second.size();
}
columnPixelMaximalCounts.at(angle) = columnPixelMaximalCount;
}
// Get the angle to rotate selecting the rotation that generates the maximal number of pixels in a column
double targetAngle = distance( columnPixelMaximalCounts.begin(), std::max_element(columnPixelMaximalCounts.begin(), columnPixelMaximalCounts.end()) );
shearingFactor = tan(-targetAngle * PI / 180.0);
// Correct slanting of the actual pattern
if ( targetAngle != 0 )
{
Pattern rotatedPattern;
rotatedPattern.clean();
for ( unsigned int j = 0; j < i->height(); ++j )
{
for ( unsigned int k = 0; k < i->width(); ++k )
{
if ( i->at(j,k) == 1 )
{
double jp = j;
double kp = k;
kp = round(kp - jp * shearingFactor);
if ( kp < i->width() && kp > 0 )
rotatedPattern.at(jp, kp) = 1;
}
}
}
*i = rotatedPattern;
}
}
statistics_.slantingCorrectionTime(timer.elapsed());;
}
void Preprocessor::buildPatterns ()
{
boost::timer timer;
timer.restart();
patterns_.clear();
patterns_.reserve(regions_.size());
Pattern pattern;
// Traverse the list of iterators to regions creating a Pattern object for each region
for( RegionLines::iterator k = inlineRegions_.begin(); k != inlineRegions_.end(); ++k )
{
std::list<RegionIterator> line(k->second);
for( std::list<RegionIterator>::iterator i = line.begin(); i != line.end(); ++i )
{
(*i)->normalizeCoordinates();
// Normalize region using Magick++ facilities
Magick::Image image( Magick::Geometry((*i)->width(), (*i)->height()), Magick::ColorGray(1.0) );
image.type( Magick::BilevelType );
Magick::Pixels view(image);
Magick::PixelPacket *originPixel = view.get(0, 0, (*i)->width(), (*i)->height());
Magick::PixelPacket *pixel;
for ( unsigned int j = 0; j < (*i)->size(); ++j )
{
pixel = originPixel + ((*i)->at(j).first * view.columns() + (*i)->at(j).second);
*pixel = Magick::ColorGray (0.0);
}
view.sync();
image.syncPixels();
image.scale( Magick::Geometry(Pattern::planeSize(), Pattern::planeSize()) );
// Preprocess the normalized region
Preprocessor temporalPreprocessor (image, 0, 0, image.rows(), image.columns());
temporalPreprocessor.applyGlobalThresholding();
temporalPreprocessor.isolateRegions();
Region normalizedRegion;
if ( ! temporalPreprocessor.regions_.empty() )
{
// Merge subregions if preprocessing split the original region
if ( temporalPreprocessor.regions_.size() > 1 )
{
for ( RegionIterator j = temporalPreprocessor.regions_.begin(); j != temporalPreprocessor.regions_.end(); ++j )
normalizedRegion = normalizedRegion + *j;
temporalPreprocessor.regions_.clear();
temporalPreprocessor.regions_.push_back(normalizedRegion);
}
else
normalizedRegion = temporalPreprocessor.regions_.front();
}
// Build the pattern
pattern.clean();
for ( unsigned int i = 0; i < normalizedRegion.size(); ++i )
pattern.at(normalizedRegion.at(i).first, normalizedRegion.at(i).second) = 1;
// Correct shifting
if ( image.rows() < Pattern::planeSize() ) // Shift rows from top to the center
{
unsigned int offset = (Pattern::planeSize() - image.rows()) / 2;
while ( offset != 0 )
{
for ( int i = Pattern::planeSize()-2; i >= 0; --i )
{
for ( unsigned int j = 0; j < Pattern::planeSize(); ++j )
pattern.at(i+1, j) = pattern.at(i, j);
}
for ( unsigned int j = 0; j < Pattern::planeSize(); ++j )
pattern.at(0, j) = 0;
--offset;
}
}
if ( image.columns() < Pattern::planeSize() ) // Shift columns from left to center
{
unsigned int offset = (Pattern::planeSize() - image.columns()) / 2;
while ( offset != 0 )
{
for ( unsigned int i = 0; i < Pattern::planeSize(); ++i )
{
for ( int j = Pattern::planeSize()-2; j >= 0; --j )
pattern.at(i, j+1) = pattern.at(i, j);
}
for ( unsigned int i = 0; i < Pattern::planeSize(); ++i )
pattern.at(i, 0) = 0;
--offset;
}
}
patterns_.push_back( pattern );
}
}
statistics_.patternsBuildingTime(timer.elapsed());
}