void
ChannelListAttribute::readValueFrom (IStream &is, int size, int version)
{
while (true)
{
//
// Read name; zero length name means end of channel list
//
char name[Name::SIZE];
Xdr::read <StreamIO> (is, sizeof (name), name);
if (name[0] == 0)
break;
//
// Read Channel struct
//
int type;
int xSampling;
int ySampling;
Xdr::read <StreamIO> (is, type);
Xdr::skip <StreamIO> (is, 4);
Xdr::read <StreamIO> (is, xSampling);
Xdr::read <StreamIO> (is, ySampling);
_value.insert (name, Channel (PixelType (type), xSampling, ySampling));
}
}
dng_image * dng_simple_image::Clone () const
{
AutoPtr<dng_simple_image> result (new dng_simple_image (Bounds (),
Planes (),
PixelType (),
fAllocator));
result->fBuffer.CopyArea (fBuffer,
Bounds (),
0,
Planes ());
return result.Release ();
}
uint32 dng_image::PixelSize () const
{
return TagTypeSize (PixelType ());
}
int main(int argc, char **argv) {
ParametersVectorType initialParameters;
std::string outPrefix, bmImageName, initFile, initMeansFile, mrfModelFile;
std::string s_minimization = DEFAULT_MRF_ALG;
float lambda1, lambda2;
ProbabilityPixelType atlas_th, mask_th;
unsigned int nClasses, emIterations, mrfIterations;
std::vector<std::string> channels, priors, geometricTerm;
std::string s_mode = "km+em";
std::string outExt = "nii.gz";
std::vector<double> dataOffsets;
std::vector<double> dataFactors;
bool useFile = false;
bool skipMRF = false;
bool usePVE = false;
bool doOutputStats,doSegmentsOutput, doOutputMRFMaps, doOutputMRFIterations,
doOutputSteps, useExplicitPVE, skipNormalization, skipBias, doBiasOutput, doCorrectedOutput,
channelsAreMasked = false;
unsigned int userBucketSize = 0;
boost::unordered_map<std::string, INIT_MODES> modes_map;
modes_map["none"] = NONE;
modes_map["km"] = KMEANS;
modes_map["em"] = EM;
modes_map["km+em"] = KMEANS_EM;
boost::unordered_map<std::string, typename MRFFilter::GCOptimizerType::MINIMIZATION_MODES > minimiz_map;
minimiz_map["expansion"] = MRFFilter::GCOptimizerType::EXPANSION;
minimiz_map["swap"] = MRFFilter::GCOptimizerType::SWAP;
bpo::options_description general("General options");
general.add_options()
("help", "show help message")
("out,o",bpo::value < std::string > (&outPrefix), "prefix for output files")
("out-ext", bpo::value< std::string >( &outExt ), "output format, if supported by ITK")
("brain-mask,x",bpo::value < std::string > (&bmImageName),"brain extracted mask")
("channels-masked,M", bpo::bool_switch(&channelsAreMasked), "set this flag if channels are already masked")
("channels,C", bpo::value< std::vector< std::string > >(&channels)->multitoken()->required(),"list of channels for multivariate segmentation")
("class,n", bpo::value<unsigned int>(&nClasses)->default_value(DEFAULT_NCLASSES), "number of tissue-type classes")
("init,I", bpo::value< std::string >(&s_mode), "operation mode for initialization [none,km,em,km+em]")
("init-file,f",bpo::value < std::string > (&initFile),"use file for initialization of tissue-type means & variances")
("init-means",bpo::value < std::string > (&initMeansFile),"use file for initialization of tissue-type means")
("segments,g", bpo::bool_switch(&doSegmentsOutput),"Output a posteriori probability for each class")
//("pv", bpo::bool_switch(&useExplicitPVE), "Use explicit PVE Gaussian Model between tissues")
("output-stats", bpo::bool_switch(&doOutputStats),"output classes statistics to CSV file")
("output-steps", bpo::bool_switch(&doOutputSteps), "Output intermediate segmentation steps")
("normalize-off,N", bpo::bool_switch(&skipNormalization), "Do not normalize input's intensity range")
("brain-mask-th,t",bpo::value < ProbabilityPixelType > (&mask_th)->default_value(0.0), "mask probability threshold")
("version,v", "show tool version");
bpo::options_description kmeans_desc("Kmeans options");
kmeans_desc.add_options()
("bucket-size", bpo::value< unsigned int >(&userBucketSize), "bucket size for K-means operation");
bpo::options_description em_desc("Expectation-Maximization options");
em_desc.add_options()
("priors,P", bpo::value< std::vector< std::string > >(&priors)->multitoken(),"add prior to list of atlases for initializing segmentation")
("atlas-threshold",bpo::value < ProbabilityPixelType > (&atlas_th)->default_value(DEFAULT_ATLAS_TH), "threshold for atlases")
("em-iterations", bpo::value<unsigned int>(&emIterations)->default_value(DEFAULT_MAX_ITER), "maximum number of iterations");
bpo::options_description bias_desc("Bias estimator options");
bias_desc.add_options()
("bias-skip", bpo::bool_switch(&skipBias), "Do not estimate Bias field")
("bias-output", bpo::bool_switch(&doBiasOutput), "Output estimated Bias field")
("bias-corrected-output", bpo::bool_switch(&doCorrectedOutput), "Output corrected input images with estimated Bias field");
bpo::options_description mrf_desc( "MRF Segmentation options" );
mrf_desc.add_options()
("mrf-lambda,l", bpo::value<float>(&lambda1)->default_value(DEFAULT_LAMBDA),"Regularization weighting. The higher this value is, the higher smoothing. You may use a value around 0.3-1.0 for typical brain images")
("mrf-minimization,m", bpo::value < std::string > (&s_minimization)->default_value(DEFAULT_MRF_ALG), "Minimization algorithm")
("mrf-energy-model,e",bpo::value < std::string > (&mrfModelFile), "Energy Model matrix, basic Pott's Model used if missing" )
("mrf-iterations", bpo::value<unsigned int>(&mrfIterations)->default_value(DEFAULT_MRF_ITERATIONS),"MRF re-estimation iterations")
("mrf-skip,S", bpo::bool_switch(&skipMRF),"Skip MRF step")
("mrf-pve", bpo::bool_switch(&usePVE), "Compute PVE classes")
("mrf-external-lambda", bpo::value<float>(&lambda2)->default_value(1.0),"External field energy weighting. The higher this value is, the higher impact from the external field")
("mrf-external-field,E", bpo::value< std::vector< std::string > >(&geometricTerm)->multitoken(),"External field maps that manipulate the dataterm in MRF energy function")
("mrf-output-maps", bpo::bool_switch(&doOutputMRFMaps), "Output GC probabilities and energy maps")
("mrf-output-it", bpo::bool_switch(&doOutputMRFIterations), "Output intermediate segmentation steps");
bpo::options_description all("Usage");
all.add(general).add(kmeans_desc).add(bias_desc).add(em_desc).add(mrf_desc);
bpo::variables_map vmap;
bpo::store(bpo::command_line_parser(argc, argv).options(all).run(), vmap);
if ( vmap.count("version")) {
std::cout << "MBIS Segmentation tool. Version " << MBIS_VERSION_MAJOR << "." << MBIS_VERSION_MINOR << "-" << MBIS_RELEASE << "." << std::endl;
std::cout << "--------------------------------------------------------"<< std::endl;
std::cout << "Copyright (c) 2012, [email protected] (Oscar Esteban)"<< std::endl;
std::cout << "with Signal Processing Lab 5, EPFL (LTS5-EPFL)"<< std::endl;
std::cout << "and Biomedical Image Technology, UPM (BIT-UPM)"<< std::endl;
std::cout << "All rights reserved."<< std::endl;
return 0;
}
if ( vmap.empty() || vmap.count("help")) {
std::cout << all << std::endl;
return 0;
}
try {
bpo::notify(vmap);
} catch (boost::exception_detail::clone_impl<
boost::exception_detail::error_info_injector<
boost::program_options::required_option> > &err) {
std::cout << "Error parsing options:" << err.what()
<< std::endl;
std::cout << std::endl << all << std::endl;
return EXIT_FAILURE;
}
std::cout << std::endl << "Set-up step --------------------------------------------" << std::endl;
ProbabilityImagePointer bm;
InputVector input;
PriorsVector atlas;
ClassifiedImageType::Pointer solution;
bool useFileMask = vmap.count("brain-mask") && bfs::exists(bmImageName);
bool useImplicitMasks = channelsAreMasked && !useFileMask;
if( useFileMask ) {
ProbabilityImageReader::Pointer r = ProbabilityImageReader::New();
r->SetFileName(bmImageName);
r->Update();
try {
bm = r->GetOutput();
} catch (...) {
std::cout << "Error reading brain mask" << std::endl;
return EXIT_FAILURE;
}
StatisticsImageFilterType::Pointer calc = StatisticsImageFilterType::New();
calc->SetInput(bm);
calc->Update();
ProbabilityPixelType max = calc->GetMaximum();
if (max > 1.0 ){
ProbabilityPixelType min = calc->GetMinimum();
IntensityWindowingImageFilterType::Pointer intensityFilter = IntensityWindowingImageFilterType::New();
intensityFilter->SetInput( bm );
intensityFilter->SetWindowMaximum( max );
intensityFilter->SetWindowMinimum( min );
intensityFilter->SetOutputMaximum( 1.0 );
intensityFilter->SetOutputMinimum( 0.0 );
intensityFilter->Update();
bm = intensityFilter->GetOutput();
}
std::cout << "\t* Mask: read from file " << bmImageName << ".";
if ( mask_th != 0.0 ) {
ThresholdImageFilterType::Pointer th = ThresholdImageFilterType::New();
th->SetInput( bm );
th->ThresholdBelow( mask_th );
th->Update();
bm = th->GetOutput();
std::cout << " Mask Threshold = " << mask_th << ".";
}
std::cout << std::endl;
} else {
if ( useImplicitMasks ) {
std::cout << "\t* Mask: channels are masked." << std::endl;
} else {
std::cout << "\t* Mask: not requested." << std::endl;
}
}
std::cout << "\t* Inputs normalization is " << ((!skipNormalization)?"ON":"OFF") << std::endl;
for (vector<string>::iterator it = channels.begin(); it != channels.end(); it++) {
ChannelReader::Pointer r = ChannelReader::New();
r->SetFileName( *it );
ChannelPointer p = r->GetOutput();
r->Update();
ChannelPixelType max = itk::NumericTraits< ChannelPixelType >::max();
ChannelPixelType min = 0.0;
ChannelPixelType absMin = 0.0;
if ( bm.IsNotNull() ) {
ProbabilityPixelType* mBuff = bm->GetBufferPointer();
ChannelPixelType* cBuff = r->GetOutput()->GetBufferPointer();
size_t nPix = bm->GetLargestPossibleRegion().GetNumberOfPixels();
std::vector< ChannelPixelType > sample;
for( size_t i = 0; i<nPix; i++ ) {
if ( *(mBuff+i) > 0 ) {
sample.push_back( *(cBuff+i) );
}
}
std::sort( sample.begin(), sample.end() );
max = sample[ (size_t) ((sample.size()-1)*0.98) ];
min = sample[ (size_t) ((sample.size()-1)*0.02) ];
absMin = sample[0];
} else {
StatisticsChannelFilterType::Pointer calc = StatisticsChannelFilterType::New();
calc->SetInput(p);
calc->Update();
max = calc->GetMaximum();
min = calc->GetMinimum();
absMin = min;
}
if( !skipNormalization ) {
double factor = NORM_MAX_INTENSITY / (max - min);
double constant = - factor * absMin;
if ( factor!= 1 ) {
typename MultiplyFilter::Pointer multiplier = MultiplyFilter::New();
multiplier->SetInput( p );
multiplier->SetConstant( factor );
multiplier->Update();
p = multiplier->GetOutput();
}
if ( constant!= 0 ) {
typename AddConstantFilter::Pointer adder = AddConstantFilter::New();
adder->SetInput( p );
adder->SetConstant( - constant );
adder->Update();
p = adder->GetOutput();
}
dataOffsets.push_back( constant );
dataFactors.push_back( factor );
if ( bm.IsNotNull() ) {
ChannelImageType::DirectionType dir = bm->GetDirection();
p->SetDirection( dir );
p->SetOrigin( bm->GetOrigin() );
MaskChannelFilterType::Pointer m = MaskChannelFilterType::New();
m->SetInput( p );
m->SetMaskImage( bm );
m->Update();
p = m->GetOutput();
}
if( doOutputSteps ) {
itk::ImageFileWriter< ChannelImageType >::Pointer wc = itk::ImageFileWriter< ChannelImageType >::New();
wc->SetInput( p );
std::stringstream ss;
ss << outPrefix << "_normin_" << input.size() << "." << outExt;
wc->SetFileName( ss.str() );
wc->Update();
}
}
InputComponentConstPointer im;
typename ChannelToComponentCaster::Pointer c = ChannelToComponentCaster::New();
c->SetInput(p);
c->Update();
im = c->GetOutput();
input.push_back( im );
std::cout << "\t* Channel [" << std::setw(2) << input.size() << "] read: " << (*it) << std::endl;
}
if ( useImplicitMasks ) {
bm = ProbabilityImageType::New();
bm->SetRegions( input[0]->GetLargestPossibleRegion() );
bm->CopyInformation( input[0] );
bm->Allocate();
bm->FillBuffer( 1.0 );
bm->Update();
ProbabilityPixelType* buffer = bm->GetBufferPointer();
size_t numberOfPixels = bm->GetLargestPossibleRegion().GetNumberOfPixels();
for ( size_t i = 0; i < input.size(); i++) {
const PixelType* buffer2 = input[i]->GetBufferPointer();
for( size_t offset = 0; offset < numberOfPixels; offset++ ) {
if( *( buffer + offset ) > 0.0 ) {
*( buffer + offset ) = PixelType ( *( buffer2 + offset ) > 1e-5);
}
}
}
if( doOutputSteps ) {
itk::ImageFileWriter< ProbabilityImageType >::Pointer wc = itk::ImageFileWriter< ProbabilityImageType >::New();
wc->SetInput( bm );
std::stringstream ss;
ss << outPrefix << "_mask." << outExt;
wc->SetFileName( ss.str() );
wc->Update();
}
}
unsigned int init_mode = modes_map[s_mode];
unsigned int nComponents = input.size();
unsigned int nElements = nComponents * (1+nComponents);
if( priors.size() > 0 ) {
if (init_mode== KMEANS ) init_mode = MANUAL;
if (init_mode == KMEANS_EM ) init_mode = EM;
for (vector<string>::iterator it = priors.begin(); it != priors.end(); it++) {
ProbabilityImageReader::Pointer r = ProbabilityImageReader::New();
r->SetFileName( *it );
ProbabilityImageType::ConstPointer p = r->GetOutput();
r->Update();
StatisticsImageFilterType::Pointer calc = StatisticsImageFilterType::New();
calc->SetInput(p);
calc->Update();
ProbabilityPixelType max = calc->GetMaximum();
if (max > 1.0 ){
ProbabilityPixelType min = calc->GetMinimum();
IntensityWindowingImageFilterType::Pointer intensityFilter = IntensityWindowingImageFilterType::New();
intensityFilter->SetInput( p );
intensityFilter->SetWindowMaximum( max );
intensityFilter->SetWindowMinimum( min );
intensityFilter->SetOutputMaximum( 1.0 );
intensityFilter->SetOutputMinimum( 0.0 );
intensityFilter->Update();
p = intensityFilter->GetOutput();
}
atlas.push_back(p);
std::cout << "\t* Prior [" << std::setw(2) << atlas.size() << "] read: " << (*it) << std::endl;
ParameterEstimator::Pointer est = ParameterEstimator::New();
est->SetInputVector( input );
est->SetPrior( p );
if ( bm.IsNotNull() ) {
est->SetMaskImage( bm );
}
est->Update();
initialParameters.push_back( est->GetOutputParameters() );
}
}
if ( bfs::exists(initFile)) {
if (init_mode== KMEANS ) init_mode = MANUAL;
if (init_mode == KMEANS_EM ) init_mode = EM;
std::cout << "\t* Parsing tissue parameters file: " << initFile << std::endl;
initialParameters = ReadParametersFile(initFile);
for ( ParametersVectorType::iterator it = initialParameters.begin(); it!=initialParameters.end(); it++) {
size_t n = (*it).size();
if ( n != nElements ) {
std::cerr << "Parameters file is incorrect or badly interpreted" << std::endl;
}
if ( !skipNormalization ) {
for( size_t i = 0; i<nComponents; i++ ) {
(*it)[i] *= dataFactors[i];
(*it)[i] += dataOffsets[i];
}
for( size_t i = nComponents; i<n; i++ ) {
(*it)[i] = dataFactors[i%nComponents] * (*it)[i];
}
}
}
useFile = true;
std::cout << "\t* Manual Parameters: " << std::endl;
for (size_t i = 0; i<initialParameters.size(); i++)
std::cout << "\t\t" << initialParameters[i] << std::endl;
}
if ( bfs::exists(initMeansFile)) {
std::cout << "\t* Parsing tissue means file: " << initMeansFile << std::endl;
initialParameters = ReadParametersFile( initMeansFile );
for ( ParametersVectorType::iterator it = initialParameters.begin(); it!=initialParameters.end(); it++) {
size_t n = (*it).size();
if ( n != nComponents ) {
std::cerr << "Means file is incorrect or badly interpreted" << std::endl;
}
if ( !skipNormalization ) {
for( size_t i = 0; i<n; i++ ) {
(*it)[i] *= dataFactors[i];
(*it)[i] += dataOffsets[i];
}
}
}
useFile = true;
std::cout << "\t* Manual Parameters: " << std::endl;
for (size_t i = 0; i<initialParameters.size(); i++)
std::cout << "\t\t" << initialParameters[i] << std::endl;
}
EMFilter::Pointer em_filter;
KMeansFilter::Pointer kmeans;
if (init_mode == KMEANS || init_mode == KMEANS_EM ) {
std::cout << std::endl << "Kmeans step --------------------------------------------" << std::endl;
kmeans = KMeansFilter::New();
kmeans->SetInputVector( input );
if ( bm.IsNotNull() ) kmeans->SetMaskImage( bm );
kmeans->SetNumberOfClasses(nClasses);
if(vmap.count("bucket-size")) {
kmeans->SetUserBucketSize(userBucketSize);
}
if( useFile ) {
kmeans->SetInitialParameters( initialParameters );
}
kmeans->Compute();
initialParameters = kmeans->GetOutputParameters();
if (doOutputStats) {
stringstream s;
s << outPrefix << "_stats_kmeans.csv";
std::ofstream outputCSVfile ( s.str().c_str() );
for ( unsigned int i = 0; i < initialParameters.size(); i++)
outputCSVfile << initialParameters[i] << "\n";
outputCSVfile.close();
}
kmeans->Update();
}
// Check for sanity initial parameters
if( initialParameters.size()!=nClasses ) {
std::cerr << "Error: initial parameters size (" << initialParameters.size() << ") doesn't match number of classes (" << (int) nClasses << std::endl;
} else if ( initialParameters[0].size() != nElements ) {
typename MLClassifierFilter::Pointer ml_classifier = MLClassifierFilter::New();
ml_classifier->SetInputVector( input );
if ( bm.IsNotNull() ) ml_classifier->SetMaskImage(bm);
ml_classifier->SetParameters( initialParameters );
ml_classifier->Update();
solution = ml_classifier->GetOutput();
if ( doOutputSteps ) {
ClassifiedImageWriter::Pointer w = ClassifiedImageWriter::New();
w->SetInput( solution );
w->SetFileName(outPrefix + "_means." + outExt );
w->Update();
}
ProbabilityImagePointer unoImage = ProbabilityImageType::New();
unoImage->SetRegions( input[0]->GetLargestPossibleRegion() );
unoImage->CopyInformation( input[0] );
unoImage->Allocate();
unoImage->FillBuffer( 1.0 );
unoImage->Update();
// Initialize Covariance matrix --------------------------------------
ParameterEstimator::Pointer est = ParameterEstimator::New();
est->SetInputVector( input );
typedef itk::LabelImageToLabelMapFilter< ClassifiedImageType > ClassifiedToLabelMapFilter;
typedef typename ClassifiedToLabelMapFilter::OutputImageType LabelMap;
typedef itk::LabelMapMaskImageFilter< LabelMap, ProbabilityImageType > LabelMapMaskFilter;
unsigned int maskOffset = (unsigned int) bm.IsNotNull();
for ( typename ClassifiedImageType::PixelType i = 0 ; i < nClasses ; i++ ) {
typename ClassifiedToLabelMapFilter::Pointer lfilter = ClassifiedToLabelMapFilter::New();
lfilter->SetInput( solution );
lfilter->Update();
typename LabelMapMaskFilter::Pointer lmask = LabelMapMaskFilter::New();
lmask->SetInput1( lfilter->GetOutput() );
lmask->SetInput2( unoImage );
lmask->SetLabel( i + maskOffset );
lmask->Update();
est->SetPrior( lmask->GetOutput());
est->Update();
initialParameters[i] = est->GetOutputParameters();
}
// End initialize covariance matrix -------------------------------------------
}
if (init_mode == EM || init_mode == KMEANS_EM ) {
std::cout << std::endl << "E-M Step -----------------------------------------------" << std::endl;
em_filter = EMFilter::New();
em_filter->SetMaskImage( bm );
em_filter->SetNumberOfClasses( nClasses );
em_filter->SetMaximumIteration( emIterations );
em_filter->SetMaxBiasEstimationIterations( 5 );
em_filter->SetInputVector( input );
em_filter->SetInitialParameters( initialParameters );
em_filter->SetUseExplicitPVModel( useExplicitPVE );
em_filter->SetUseBiasCorrection( !skipBias );
if ( atlas.size() != 0 ) {
em_filter->SetPriors( atlas );
em_filter->SetUsePriorProbabilityImages( true );
}
em_filter->Update();
// TODO change to GetModelParameters()
initialParameters = em_filter->GetInitialParameters();
solution = em_filter->GetOutput();
if ( doOutputSteps || skipMRF ) {
ClassifiedImageWriter::Pointer w = ClassifiedImageWriter::New();
w->SetInput( solution );
w->SetFileName(outPrefix + "_em." + outExt );
w->Update();
}
//
// Output file with initial stats if switch is true
//
if (doOutputStats) {
stringstream s;
s << outPrefix << "_stats_em.csv";
std::ofstream outputCSVfile ( s.str().c_str() );
for ( unsigned int i = 0; i < initialParameters.size(); i++)
outputCSVfile << initialParameters[i] << "\n";
outputCSVfile.close();
}
if( em_filter->GetUseBiasCorrection() ) {
typedef typename EMFilter::EstimatorType::InputVectorImageType VectorImage;
typedef typename itk::ImageFileWriter< ChannelImageType > ChannelWriter;
typedef itk::VectorIndexSelectionCastImageFilter< VectorImage, ChannelImageType> SelectorType;
typename VectorImage::ConstPointer vec = em_filter->GetEstimator()->GetCorrectedInput();
for( int channel = 0; channel< input.size(); channel++ ) {
typename SelectorType::Pointer channelSelector = SelectorType::New();
channelSelector->SetInput( vec );
channelSelector->SetIndex( channel );
channelSelector->Update();
channelSelector->GetOutput()->SetRegions( vec->GetRequestedRegion() );
input[channel] = channelSelector->GetOutput();
if ( doCorrectedOutput ) {
char name[50];
sprintf(name, "_corrected_ch%02d.%s" , channel, outExt.c_str() );
typename ChannelWriter::Pointer chW = ChannelWriter::New();
chW->SetInput(input[channel]);
chW->SetFileName( outPrefix + name );
chW->Update();
}
}
if( doBiasOutput ) {
typedef typename EMFilter::EstimatorType::InputVectorImageType VectorImage;
typedef typename itk::ImageFileWriter< ChannelImageType > ChannelWriter;
typename VectorImage::ConstPointer bias = em_filter->GetEstimator()->GetCurrentBias();
for( int channel = 0; channel< input.size(); channel++ ) {
typename SelectorType::Pointer channelSelector = SelectorType::New();
channelSelector->SetInput( bias );
channelSelector->SetIndex( channel );
channelSelector->Update();
channelSelector->GetOutput()->SetRegions( bias->GetRequestedRegion() );
char name[50];
sprintf(name, "_bias_ch%02d.%s" , channel, outExt.c_str() );
typename ChannelWriter::Pointer chW = ChannelWriter::New();
chW->SetInput(channelSelector->GetOutput());
chW->SetFileName( outPrefix + name );
chW->Update();
}
}
}
}
//
// MRF Segmentation
//
if( !skipMRF ) {
std::cout << std::endl << "MRF Step -----------------------------------------------" << std::endl;
MRFFilter::Pointer mrf = MRFFilter::New();
mrf->SetUseExplicitPVModel( useExplicitPVE );
mrf->SetNumberOfClasses( nClasses );
mrf->SetMaskImage( bm );
mrf->SetInputVector( input );
mrf->SetLambda( lambda1 );
mrf->SetExternalLambda( lambda2 );
mrf->SetUseOutputPriors( doSegmentsOutput );
mrf->SetInitialParameters( initialParameters );
mrf->SetMRFIterations( mrfIterations );
mrf->SetMinimizationMode( minimiz_map[s_minimization] );
mrf->SetOutputPrefix( outPrefix );
if( doOutputMRFIterations ) {
typedef itk::SimpleMemberCommand< MRFFilter > ObserverType;
ObserverType::Pointer obs = ObserverType::New();
obs->SetCallbackFunction( mrf, &MRFFilter::WriteIteration );
mrf->AddObserver( itk::IterationEvent(), obs );
}
if( doOutputMRFMaps ) {
typedef itk::SimpleMemberCommand< MRFFilter > ObserverType;
ObserverType::Pointer obs = ObserverType::New();
obs->SetCallbackFunction( mrf, &MRFFilter::WriteMaps );
mrf->AddObserver( itk::IterationEvent(), obs );
}
if ( doOutputSteps && init_mode == NONE ) {
EMFilter::Pointer em_classifier = EMFilter::New();
em_classifier->SetMaskImage( bm );
em_classifier->SetNumberOfClasses( nClasses );
em_classifier->SetInputVector( input );
em_classifier->SetInitialParameters( initialParameters );
em_classifier->SetUseExplicitPVModel( useExplicitPVE );
em_classifier->SetUseOnlyClassify(true);
em_classifier->Update();
ClassifiedImageWriter::Pointer w = ClassifiedImageWriter::New();
w->SetInput( em_classifier->GetOutput() );
w->SetFileName(outPrefix + "_mrf_initialization." + outExt );
w->Update();
}
if( bfs::exists( mrfModelFile ) ) {
std::cout << "\t* Loading Energy Model Matrix: " << mrfModelFile << std::endl;
mrf->SetMatrixFile( mrfModelFile );
}
for (vector<string>::iterator it = geometricTerm.begin(); it != geometricTerm.end(); it++) {
if( bfs::exists(*it) ) {
size_t label = (it - geometricTerm.begin()) + 1;
ProbabilityImageReader::Pointer r = ProbabilityImageReader::New();
r->SetFileName( *it );
ProbabilityImageType::Pointer p = r->GetOutput();
r->Update();
mrf->SetSpatialEnergyMap(label, p );
std::cout << "\t* Geometrical constraint [" << std::setw(2) << label << "] read: " << (*it) << std::endl;
}
}
mrf->Update();
solution = mrf->GetOutput();
ClassifiedImageWriter::Pointer w2 = ClassifiedImageWriter::New();
w2->SetInput( solution );
w2->SetFileName(outPrefix + "_mrf." + outExt );
w2->Update();
if ( doSegmentsOutput ) {
for ( unsigned int i = 1; i<=nClasses; i++ ) {
ProbabilityImageWriter::Pointer wProb = ProbabilityImageWriter::New();
wProb->SetInput( mrf->GetPosteriorProbabilityImage(i) );
char name[50];
sprintf(name, "_mrf_seg%02d.%s" , i, outExt.c_str() );
wProb->SetFileName( outPrefix + name );
wProb->Update();
}
}
if (doOutputStats) {
initialParameters = mrf->GetInitialParameters();
stringstream s;
s << outPrefix << "_stats_final.csv";
std::ofstream outputCSVfile ( s.str().c_str() );
for ( unsigned int i = 0; i < initialParameters.size(); i++)
outputCSVfile << initialParameters[i] << "\n";
outputCSVfile.close();
}
}
return EXIT_SUCCESS;
}