void test_iterators(test_harness& t, sam::alignment& aln) {
sam::alignment::iterator it;
it = aln.begin();
sam::alignment::iterator it1 = it;
sam::alignment::iterator it2(it);
sam::alignment::const_iterator cit;
cit = aln.begin();
sam::alignment::const_iterator cit1 = cit;
sam::alignment::const_iterator cit2(cit);
t.check(it1 == it2, "iterator.==");
t.check(!(it1 != it2), "iterator.!=");
t.check(cit1 == cit2, "const_iterator.==");
t.check(!(cit1 != cit2), "const_iterator.!=");
t.check(it1 == cit2, "iterator__const_iterator.==");
t.check(cit1 == it2, "const_iterator__iterator.==");
t.check(!(it1 != cit2), "iterator__const_iterator.!=");
t.check(!(cit1 != it2), "const_iterator__iterator.!=");
std::cout << "begin: " << aln.begin() << ", end: " << aln.end() << "\n";
std::string foo = "foo";
int bar = 37;
aln.dump_on(std::cout);
std::cout << aln << "\npush_back.X1\n";
aln.push_back("X1", foo);
aln.dump_on(std::cout, aln.find("X1"));
std::cout << aln << "\npush_back.X2\n";
aln.push_back("X2", bar);
//aln.push_back("X3", cit2);
aln.dump_on(std::cout);
std::cout << aln << "\ninsert.Y1\n";
aln.insert(aln.begin(), "Y1", foo);
aln.dump_on(std::cout, aln.begin());
std::cout << aln << "\ninsert.Y2\n";
aln.insert(aln.begin(), "Y2", bar);
//aln.insert(aln.begin(), "Y3", cit2);
//aln.replace(aln.begin(), aln.end(), "Y3", it2);
aln.dump_on(std::cout);
std::cout << aln << "\nset_aux.Z1\n";
aln.set_aux("Z1", foo);
aln.dump_on(std::cout);
std::cout << aln << "\nset_aux.Z2\n";
aln.set_aux("Z2", bar);
aln.dump_on(std::cout);
std::cout << aln << "\nset_aux.Z3\n";
sam::alignment aln2 = aln;
cit2 = aln2.find("X1");
aln.set_aux("Z3", cit2);
std::cout << "begin: " << aln.begin() << ", end: " << aln.end() << "\nauxen:";
for (cit = aln.begin(); cit != aln.end(); ++cit)
std::cout << " {" << *cit << "}";
std::cout << "\n";
it1 = aln.begin(), ++it1, ++it1;
aln.dump_on(std::cout, it1);
std::cout << aln << "\nset_aux.it1\n";
aln.set_aux(it1, foo);
aln.dump_on(std::cout, it1);
std::cout << aln << "\nset_aux.it1\n";
aln.set_aux(it1, bar);
//aln.set_aux(it1, cit2);
it = aln.begin();
std::cout << "And finally...\n";
aln.dump_on(std::cout, it);
std::cout << "pre: it: " << it << "\n";
it++;
std::cout << "post: it: " << it << "\n";
aln.dump_on(std::cout, it);
std::cout << "End of test_iterators()\n";
}
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;
}
