void SigmoidNetwork::ForwardPassOutputs()
{
int i, iout;
// Output unit activations
for (iout = 0; iout < NOutputs; iout++) {
vectorIterator<float> itout(*(outputs[iout]));
float sum = 0.0;
for (i = NInputs+1, itout.init();
i < NInputs+1+NHidden+1 && ! itout;
i++, ++itout) {
sum += itout()*activations[i];
}
sums[NHidden + iout] = sum;
float act = 0.0;
switch (outputType)
{
case Linear: {act = sum; break;}
case Sigmoid: {act = Logistic(sum); break;}
case Gaussian: {act = exp(-(sum * sum)); break;}
}
activations[iout+NInputs+1+NHidden+1] = act;
}
}
void SigmoidNetwork::AdjustBiases()
{
// assuming that each hidden unit outputs 0.5, adjust the output
// biases to match the values in the targets array.
// The activation going into the output unit is
// b * 1 + (W * 0.5), where W is the hidden-to-output weight vector
// and 0.5 is a corresponding vector of 0.5's. b is the "bias" weight
// that connects to activations[NInputs + 1 + NHidden].
// Let T be the target. For sigmoid units, the desired value for b is
// ln(T/(1-T)) - (W * 0.5) = b
// For gaussian units, the desired value for b is
// +/- sqrt(- ln T) - (W * 0.5)
// We have ambiguity (unless T = 1). We will always choose the low
// side (the - sign).
// When the target is 0 or 1, we adjust it to 0.01 or 0.99.
if (outputType == Linear) return;
for (int iout = 0; iout < NOutputs; iout++) {
float tar = targets[iout];
if (tar < 0.01) tar = 0.01;
else if (tar > 0.99) tar = 0.99;
if (outputType == Sigmoid) tar = log(tar / (1.0 - tar));
else if (outputType == Gaussian) tar = -sqrt(-log(tar));
vectorIterator<float> itout(*(outputs[iout]));
float sum = 0.0;
int i;
for (i = NInputs + 1, itout.init();
i < NInputs + 1 + NHidden && ! itout;
i++, ++itout) {
sum += itout() * 0.5;
}
float bias = tar - sum;
itout() = bias;
}
}
List polyData2R(vtkSmartPointer<vtkPolyData> polydata) {
try {
//vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
//poltOutput();
int np = polydata->GetNumberOfPoints();
vtkPoints* points=polydata->GetPoints();
NumericMatrix vb(3,np);
double point[3];
for (int i=0; i< np;i++) {
polydata->GetPoints()->GetPoint(i,point);
for (int j=0; j<3; j++)
vb(j,i) = point[j];
}
//points->Delete();
int h;
vtkIdType npts=3,*pts;
int nit = polydata->GetNumberOfPolys();
std::vector<int> it;
vtkSmartPointer<vtkCellArray> oCellArr= vtkSmartPointer<vtkCellArray>::New();
polydata->GetPolys()->InitTraversal();
while(polydata->GetPolys()->GetNextCell(npts,pts)) {
//for (int i=0; i< nit;i++) {
// h = oCellArr->GetNextCell(npts,pts);
//if(h == 0){
// break;
//}
if(npts == 3){
it.push_back(pts[0]+1);
it.push_back(pts[1]+1);
it.push_back(pts[2]+1);
}
}
int ll = it.size()/3;
IntegerMatrix itout(3,ll,it.begin());
List out = List::create(Named("vb")=vb,
Named("it")=itout
);
if (it.size() > 0)
out.attr("class") = "mesh3d";
return out;
} catch(...) {
::Rf_error("PolyData to R-Data conversion failed");
return List::create(Named("error")=1);
}
}
void operator()()
{
std::ostreambuf_iterator<char> itout(m_tgtcn);
std::set<int> existingchan; //Keep track of the nb of unique channels used by the tracks
size_t nbwritten = 0;
//Reserve Header
itout = std::fill_n( itout, SMDL_Header::size(), 0 );
nbwritten += SMDL_Header::size();
//Reserve Song chunk
if( m_version == eDSEVersion::V402 )
{
itout = std::fill_n( itout, SongChunk_v402::Size, 0 );
nbwritten += SongChunk_v402::Size;
}
else if( m_version == eDSEVersion::V415 )
{
itout = std::fill_n( itout, (SongChunk_v415::SizeNoPadd + SongChunk_v415::LenMaxPadding), 0 );
nbwritten += (SongChunk_v415::SizeNoPadd + SongChunk_v415::LenMaxPadding);
}
else
throw std::runtime_error( "SMDL_Writer::operator()(): Invalid DSE version supplied!!" );
if( utils::LibWide().isLogOn() )
{
clog << "-------------------------\n"
<< "Writing SMDL\n"
<< "-------------------------\n"
<< m_src.printinfo()
<<"\n"
;
}
//Write tracks
for( uint8_t i = 0; i < m_src.getNbTracks(); ++i )
{
if( m_src[i].empty() )
continue; //ignore empty tracks
const DSE::MusicTrack & atrk = m_src[i];
TrkPreamble preamble;
preamble.trkid = i;
preamble.chanid = atrk.GetMidiChannel();
preamble.unk1 = 0;
preamble.unk2 = 0;
uint32_t lenmod = WriteTrkChunk( itout, preamble, atrk.begin(), atrk.end(), atrk.size() );
nbwritten += lenmod;
//Write padding
lenmod = (lenmod % 4);
uint32_t lenpad = lenmod;
if( lenmod != 0 )
std::fill_n( itout, lenpad, static_cast<uint8_t>(eTrkEventCodes::EndOfTrack) );
existingchan.insert( preamble.chanid );
}
//Write end chunk
DSE::ChunkHeader eoc;
eoc.label = static_cast<uint32_t>(eDSEChunks::eoc);
eoc.datlen = 0;
eoc.param1 = EocParam1Default;
eoc.param2 = EocParam2Default;
itout = eoc.WriteToContainer( itout );
//Go back to write the header and song chunk!
size_t flen = static_cast<size_t>(m_tgtcn.tellp());
m_tgtcn.seekp(0);
itout = std::ostreambuf_iterator<char>(m_tgtcn);
WriteHeader( itout, existingchan, flen );
}
mitk::Image::Pointer PartialVolumeAnalysisClusteringCalculator::CaculateAngularErrorImage(
mitk::Image::Pointer comp1, mitk::Image::Pointer comp2, mitk::Image::Pointer probImg) const
{
// cast input images to itk
typedef itk::Image<float, 3> ImageType;
typedef mitk::ImageToItk<ImageType> CastType;
CastType::Pointer caster = CastType::New();
caster->SetInput(comp1);
caster->Update();
ImageType::Pointer comp1Image = caster->GetOutput();
caster = CastType::New();
caster->SetInput(comp2);
caster->Update();
ImageType::Pointer comp2Image = caster->GetOutput();
caster = CastType::New();
caster->SetInput(probImg);
caster->Update();
ImageType::Pointer probImage = caster->GetOutput();
// figure out maximum probability for fiber class
float maxProb = 0;
itk::ImageRegionConstIterator<ImageType>
itprob(probImage, probImage->GetLargestPossibleRegion());
itprob.GoToBegin();
while( !itprob.IsAtEnd() )
{
maxProb = itprob.Get() > maxProb ? itprob.Get() : maxProb;
++itprob;
}
// generate a list sample of angles at positions
// where the fiber-prob is higher than .2*maxprob
typedef float MeasurementType;
const unsigned int MeasurementVectorLength = 2;
typedef itk::Vector< MeasurementType , MeasurementVectorLength >
MeasurementVectorType;
typedef itk::Statistics::ListSample< MeasurementVectorType > ListSampleType;
ListSampleType::Pointer listSample = ListSampleType::New();
listSample->SetMeasurementVectorSize( MeasurementVectorLength );
itk::ImageRegionIterator<ImageType>
it1(comp1Image, comp1Image->GetLargestPossibleRegion());
itk::ImageRegionIterator<ImageType>
it2(comp2Image, comp2Image->GetLargestPossibleRegion());
it1.GoToBegin();
it2.GoToBegin();
itprob.GoToBegin();
while( !itprob.IsAtEnd() )
{
if(itprob.Get() > 0.2 * maxProb)
{
MeasurementVectorType mv;
mv[0] = ( MeasurementType ) it1.Get();
mv[1] = ( MeasurementType ) it2.Get();
listSample->PushBack(mv);
}
++it1;
++it2;
++itprob;
}
// generate a histogram from the list sample
typedef float HistogramMeasurementType;
typedef itk::Statistics::Histogram< HistogramMeasurementType, itk::Statistics::DenseFrequencyContainer2 > HistogramType;
typedef itk::Statistics::SampleToHistogramFilter< ListSampleType, HistogramType > GeneratorType;
GeneratorType::Pointer generator = GeneratorType::New();
GeneratorType::HistogramType::SizeType size(2);
size.Fill(30);
generator->SetHistogramSize( size );
generator->SetInput( listSample );
generator->SetMarginalScale( 10.0 );
generator->Update();
// look for frequency mode in the histogram
GeneratorType::HistogramType::ConstPointer histogram = generator->GetOutput();
GeneratorType::HistogramType::ConstIterator iter = histogram->Begin();
float maxFreq = 0;
MeasurementVectorType maxValue;
maxValue.Fill(0);
while ( iter != histogram->End() )
{
if(iter.GetFrequency() > maxFreq)
{
maxFreq = iter.GetFrequency();
maxValue[0] = iter.GetMeasurementVector()[0];
maxValue[1] = iter.GetMeasurementVector()[1];
}
++iter;
}
// generate return image that contains the angular
// error of the voxels to the histogram max measurement
ImageType::Pointer returnImage = ImageType::New();
returnImage->SetSpacing( comp1Image->GetSpacing() ); // Set the image spacing
returnImage->SetOrigin( comp1Image->GetOrigin() ); // Set the image origin
returnImage->SetDirection( comp1Image->GetDirection() ); // Set the image direction
returnImage->SetRegions( comp1Image->GetLargestPossibleRegion() );
returnImage->Allocate();
itk::ImageRegionConstIterator<ImageType>
cit1(comp1Image, comp1Image->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<ImageType>
cit2(comp2Image, comp2Image->GetLargestPossibleRegion());
itk::ImageRegionIterator<ImageType>
itout(returnImage, returnImage->GetLargestPossibleRegion());
cit1.GoToBegin();
cit2.GoToBegin();
itout.GoToBegin();
vnl_vector<float> v(3);
v[0] = cos( maxValue[0] ) * sin( maxValue[1] );
v[1] = sin( maxValue[0] ) * sin( maxValue[1] );
v[2] = cos( maxValue[1] );
// MITK_INFO << "max vector: " << v;
while( !cit1.IsAtEnd() )
{
vnl_vector<float> v1(3);
v1[0] = cos( cit1.Get() ) * sin( cit2.Get() );
v1[1] = sin( cit1.Get() ) * sin( cit2.Get() );
v1[2] = cos( cit2.Get() );
itout.Set(fabs(angle(v,v1)));
// MITK_INFO << "ang_error " << v1 << ": " << fabs(angle(v,v1));
++cit1;
++cit2;
++itout;
}
mitk::Image::Pointer retval = mitk::Image::New();
retval->InitializeByItk(returnImage.GetPointer());
retval->SetVolume(returnImage->GetBufferPointer());
return retval;
}
CodAddMsgDialog::CodAddMsgDialog(CodObjCanvas * from, CodObjCanvas * to,
CodMsgSupport * i, ColDiagramView * v,
bool fo)
: QDialog(0, "add msg dialog", TRUE), in(i), view(v), forward(fo) {
setCaption(TR("Add message dialog"));
QVBoxLayout * vbox = new QVBoxLayout(this);
QHBoxLayout * hbox;
vbox->setMargin(5);
hbox = new QHBoxLayout(vbox);
hbox->setMargin(10);
QLabel * label1 = new QLabel(TR("Add message to %1", to->get_full_name()), this);
label1->setAlignment(AlignCenter);
hbox->addWidget(label1);
QGrid * grid = new QGrid(2, this);
vbox->addWidget(grid);
new QLabel(TR("rank : "), grid);
cbrank = new QComboBox(FALSE, grid);
ColMsgList all_in;
ColMsgList all_out;
from->get_all_in_all_out(all_in, all_out);
ColMsg * m;
QStringList new_ones;
QListIterator<ColMsg> itout(all_out);
for (; (m = itout.current()) != 0; ++itout) {
QString s = m->next_hierarchical_rank();
if ((s.find('.') != - 1) && (ColMsg::find(s, all_out) == 0)) {
cbrank->insertItem(QString::number(m->get_rank() + 1) + " : " + s);
new_ones.append(s);
}
}
QListIterator<ColMsg> itin(all_in);
for (; (m = itin.current()) != 0; ++itin) {
QString s = m->get_hierarchical_rank() + ".1";
if ((ColMsg::find(s, all_out) == 0) && (new_ones.findIndex(s) == -1)) {
cbrank->insertItem(QString::number(m->get_rank() + 1) + " : " + s);
new_ones.append(s);
}
}
// add a the rank for a new toplevel link
cbrank->insertItem(QString::number(ColMsg::last_rank(view->get_msgs()) + 1)
+ " : "
+ QString::number(view->get_msgs().count() + 1));
// the default new one follow the last input or output or view's last msg
cbrank->setCurrentItem((cbrank->count() == 1) ? 0 : cbrank->count() - 2);
QSizePolicy sp = cbrank->sizePolicy();
sp.setHorData(QSizePolicy::Expanding);
cbrank->setSizePolicy(sp);
new QLabel("", grid);
new QLabel("", grid);
// the operations
SmallPushButton * b = new SmallPushButton(TR("message :"), grid);
connect(b, SIGNAL(clicked()), this, SLOT(menu_op()));
edoper = new QComboBox(TRUE, grid);
edoper->setAutoCompletion(completion());
// gets operations
cl = to->get_class();
if (cl != 0) {
cl->get_opers(opers, list);
edoper->insertStringList(list);
if (!cl->is_writable())
cl = 0;
}
edoper->setSizePolicy(sp);
new QLabel("", grid);
new QLabel("", grid);
// ok & cancel
hbox = new QHBoxLayout(vbox);
hbox->setMargin(5);
QPushButton * ok = new QPushButton(TR("&OK"), this);
QPushButton * cancel = new QPushButton(TR("&Cancel"), this);
QSize bs(cancel->sizeHint());
ok->setDefault(TRUE);
ok->setFixedSize(bs);
cancel->setFixedSize(bs);
hbox->addWidget(ok);
hbox->addWidget(cancel);
connect(ok, SIGNAL(clicked()), this, SLOT(accept()));
connect(cancel, SIGNAL(clicked()), this, SLOT(reject()));
}
