void PlutoCore::initialize() {
const int radius = 3;
const int size = 7;
RealImage2::RegionType region;
region.SetIndex(0, -radius);
region.SetIndex(1, -radius);
region.SetSize(0, size);
region.SetSize(1, size);
_particles.resize(_images.size());
for (int i = 0; i < _images.size(); i++) {
// set up each particle per image
_particles[i] = _initialParticles;
// interpolator creation
typedef itk::LinearInterpolateImageFunction<RealImage2> InterpolatorType;
InterpolatorType::Pointer interp = InterpolatorType::New();
interp->SetInputImage(_images[i]);
Gradient2InterpolatorType::Pointer gradientInterp = Gradient2InterpolatorType::New();
gradientInterp->SetInputImage(_gradientImages[i]);
// sampler initialization
RealSamples2& samples = _samples[i];
samples.setSampleRegion(region);
samples.addInterpolator(interp);
samples.addGradientInterpolator(gradientInterp);
samples.addParticles(&_particles[i][0], _particles[i].size());
samples.allocateValues();
samples.allocateGradients();
samples.sampleValues();
samples.sampleGradients();
}
}
// ------------------------------------------------------------------------
void createLabelImage(const SeriesTransform &series,
const ImageType::Pointer &reference,
const LevelSetType::Pointer &levelSet,
const std::vector<int> &roiOffset,
ImageType::Pointer &label,
unsigned int instance)
{
// initialise the label image
createOutput(series.images[instance], label);
// create the level set interpolator
typedef itk::LinearInterpolateImageFunction<LevelSetType> InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetInputImage(levelSet);
// iterate through the output
itk::ImageRegionIterator<ImageType> it(label, label->GetLargestPossibleRegion());
it.GoToBegin();
while(!it.IsAtEnd())
{
ImageType::IndexType index = it.GetIndex();
ImageType::PointType p1, p2;
// get the point in the level set space
label->TransformIndexToPhysicalPoint(index, p1);
transformPointToPatient(reference, series, roiOffset, p1, p2);
// interpolate the level set value
if(interpolator->IsInsideBuffer(p2))
{
float val = interpolator->Evaluate(p2);
if(val >= 0) it.Set(1);
}
++it;
}
}
int main (int argc, char **argv)
{
int verbose=0, clobber=0,skip_grid=0;
int order=2;
std::string like_f,xfm_f,output_f,input_f;
double uniformize=0.0;
int invert=0;
char *history = time_stamp(argc, argv);
static struct option long_options[] = {
{"verbose", no_argument, &verbose, 1},
{"quiet", no_argument, &verbose, 0},
{"clobber", no_argument, &clobber, 1},
{"like", required_argument, 0, 'l'},
{"transform", required_argument, 0, 't'},
{"order", required_argument, 0, 'o'},
{"uniformize", required_argument, 0, 'u'},
{"invert_transform", no_argument, &invert, 1},
{0, 0, 0, 0}
};
for (;;) {
/* getopt_long stores the option index here. */
int option_index = 0;
int c = getopt_long (argc, argv, "vqcl:t:o:u:", long_options, &option_index);
/* Detect the end of the options. */
if (c == -1) break;
switch (c)
{
case 0:
break;
case 'v':
cout << "Version: 0.1" << endl;
return 0;
case 'l':
like_f=optarg; break;
case 't':
xfm_f=optarg; break;
case 'o':
order=atoi(optarg);break;
case 'u':
uniformize=atof(optarg);break;
case '?':
/* getopt_long already printed an error message. */
default:
show_usage (argv[0]);
return 1;
}
}
if ((argc - optind) < 2) {
show_usage(argv[0]);
return 1;
}
input_f=argv[optind];
output_f=argv[optind+1];
if (!clobber && !access (output_f.c_str (), F_OK))
{
std::cerr << output_f.c_str () << " Exists!" << std::endl;
return 1;
}
try
{
itk::ObjectFactoryBase::RegisterFactory(itk::MincImageIOFactory::New());
itk::ImageFileReader<minc::image3d >::Pointer reader = itk::ImageFileReader<minc::image3d >::New();
//initializing the reader
reader->SetFileName(input_f.c_str());
reader->Update();
minc::image3d::Pointer in=reader->GetOutput();
FilterType::Pointer filter = FilterType::New();
//creating coordinate transformation objects
TransformType::Pointer transform = TransformType::New();
if(!xfm_f.empty())
{
//reading a minc style xfm file
transform->OpenXfm(xfm_f.c_str());
if(!invert) transform->Invert(); //should be inverted by default to walk through target space
filter->SetTransform( transform );
}
//creating the interpolator
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetSplineOrder(order);
filter->SetInterpolator( interpolator );
filter->SetDefaultPixelValue( 0 );
//this is for processing using batch system
filter->SetNumberOfThreads(1);
if(!like_f.empty())
{
itk::ImageFileReader<minc::image3d >::Pointer reader = itk::ImageFileReader<minc::image3d >::New();
reader->SetFileName(like_f.c_str());
reader->Update();
if(uniformize!=0.0)
{
generate_uniform_sampling(filter,reader->GetOutput(),uniformize);
} else {
filter->SetOutputParametersFromImage(reader->GetOutput());
filter->SetOutputDirection(reader->GetOutput()->GetDirection());
}
}
else
{
if(uniformize!=0.0)
{
generate_uniform_sampling(filter,in,uniformize);
} else {
//we are using original sampling
filter->SetOutputParametersFromImage(in);
filter->SetOutputDirection(in->GetDirection());
}
}
filter->SetInput(in);
filter->Update();
//copy the metadate information, for some reason it is not preserved
//filter->GetOutput()->SetMetaDataDictionary(reader->GetOutput()->GetMetaDataDictionary());
minc::image3d::Pointer out=filter->GetOutput();
minc::copy_metadata(out,in);
minc::append_history(out,history);
free(history);
//generic file writer
itk::ImageFileWriter< minc::image3d >::Pointer writer = itk::ImageFileWriter<minc::image3d >::New();
writer->SetFileName(output_f.c_str());
writer->SetInput( out );
//writer->UseInputMetaDataDictionaryOn();
writer->Update();
return 0;
} catch (const minc::generic_error & err) {
cerr << "Got an error at:" << err.file () << ":" << err.line () << endl;
return 1;
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return 2;
}
return 0;
};
int main( int argc, char *argv[] )
{
string input_name;
string output_dir;
if (argc == 3) {
input_name = argv[1];
output_dir = argv[2];
}
const unsigned int Dimension = 3;
const unsigned int OutDimension = 2;
typedef short InputPixelType;
typedef int FilterPixelType;
typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef itk::Image< FilterPixelType, Dimension > FilterImageType;
typedef itk::Image< FilterPixelType, OutDimension > OutFilterImageType;
InputImageType::Pointer image;
itk::MetaDataDictionary dict;
if (input_name.size() && output_dir.size())
{
if (boost::filesystem::is_regular_file( input_name )) {
typedef itk::ImageFileReader< InputImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( input_name );
try
{
reader->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ERROR: ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
image = reader->GetOutput();
dict = reader->GetMetaDataDictionary();
} else if (boost::filesystem::is_directory( input_name )) {
itkBasic::SeriesReader sreader( input_name );
sreader.readSeriesData( 2 );
try
{
itkBasic::ReaderType::Pointer imageReader = itkBasic::ReaderType::New();
itkBasic::FileNamesContainer fc;
sreader.getSeriesFileNames(0, fc);
image = itkBasic::getDicomSerie( fc, imageReader, 1 );
dict = *((*imageReader->GetMetaDataDictionaryArray())[0]);
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ERROR: ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
}
}
if (!image) {
std::cerr << argv[0] << ": input output" << std::endl;
exit(1);
}
typedef itk::SigmoidImageFilter< InputImageType, FilterImageType > SigmoidCasterType;
SigmoidCasterType::Pointer sigmoidcaster = SigmoidCasterType::New();
sigmoidcaster->SetInput( image );
sigmoidcaster->SetOutputMaximum( 4000 );
sigmoidcaster->SetOutputMinimum( 1000 );
typedef itk::AccumulateImageFilter< FilterImageType, FilterImageType > AccumulateFilter;
AccumulateFilter::Pointer accumulator = AccumulateFilter::New();
accumulator->SetAccumulateDimension(1);
accumulator->SetInput( sigmoidcaster->GetOutput() );
typedef itk::ExtractImageFilter< FilterImageType, OutFilterImageType > ExtractFilter;
ExtractFilter::Pointer extractor = ExtractFilter::New();
extractor->SetInput( accumulator->GetOutput() );
FilterImageType::Pointer accuOut = accumulator->GetOutput();
accuOut->UpdateOutputInformation();
FilterImageType::RegionType extractRegion = accuOut->GetLargestPossibleRegion();
extractRegion.SetSize(1,0);
extractor->SetExtractionRegion( extractRegion );
typedef itk::ResampleImageFilter<OutFilterImageType, OutFilterImageType > ResampleFilter;
ResampleFilter::Pointer resampler = ResampleFilter::New();
resampler->SetInput( extractor->GetOutput() );
typedef itk::BSplineInterpolateImageFunction< OutFilterImageType > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetSplineOrder(3);
resampler->SetInterpolator( interpolator );
OutFilterImageType::Pointer exOut = extractor->GetOutput();
exOut->UpdateOutputInformation();
typedef itk::CenteredRigid2DTransform< double > TransformType;
TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
OutFilterImageType::PointType exOutCenter = exOut->GetOrigin();
exOutCenter[0] += (exOut->GetLargestPossibleRegion().GetSize()[0]-1) * exOut->GetSpacing()[0] *.5;
exOutCenter[1] += (exOut->GetLargestPossibleRegion().GetSize()[1]-1) * exOut->GetSpacing()[1] *.5;
transform->SetCenter( exOutCenter );
transform->SetAngleInDegrees( 180 );
resampler->SetTransform( transform );
resampler->SetOutputParametersFromImage( exOut );
OutFilterImageType::SpacingType resampleSpacing = exOut->GetSpacing();
resampleSpacing.Fill( std::min( resampleSpacing[0], resampleSpacing[1] ) );
OutFilterImageType::SizeType resampleSize;
resampleSize[0] = exOut->GetLargestPossibleRegion().GetSize()[0] * exOut->GetSpacing()[0] / resampleSpacing[0];
resampleSize[1] = exOut->GetLargestPossibleRegion().GetSize()[1] * exOut->GetSpacing()[1] / resampleSpacing[1];
resampler->SetSize( resampleSize );
resampler->SetOutputSpacing( resampleSpacing );
OutFilterImageType::Pointer result = resampler->GetOutput();
sigmoidcaster->SetBeta( -500 );
sigmoidcaster->SetAlpha( 5 );
result->Update();
int outDicomIndex = 0;
itk::EncapsulateMetaData( dict, "0008|0008", string("DERIVED\\SECONDARY\\AXIAL"));
boost::filesystem::path outpath = output_dir;
outpath = outpath / "IM%06d";
std::vector< itk::MetaDataDictionary* > dictArray;
dictArray.push_back(&dict);
itkBasic::writeDicomSeries( itkBasic::ImageRescale(itkBasic::ImageSharp(result, 0.5), -1000, 4000), outpath.string(), &dictArray, outDicomIndex);
// itkBasic::ImageSave( itkBasic::ImageSharp(result, 0.5), boost::str( boost::format("%s.%s.png") % output_name % "lung" ), 1, 0); // Auto Level
sigmoidcaster->SetBeta( 1000 );
sigmoidcaster->SetAlpha( 300 );
result->Update();
itkBasic::writeDicomSeries( itkBasic::ImageRescale(itkBasic::ImageSharp(result, 0.5), -1000, 4000), outpath.string(), &dictArray, outDicomIndex);
// itkBasic::ImageSave( itkBasic::ImageSharp(result, 0.5), boost::str( boost::format("%s.%s.png") % output_name % "bone" ), 1, 0); // Auto Level
sigmoidcaster->SetBeta( 0 );
sigmoidcaster->SetAlpha( 2000 );
result->Update();
itkBasic::writeDicomSeries( itkBasic::ImageRescale(itkBasic::ImageSharp(result, 0.5), -1000, 4000), outpath.string(), &dictArray, outDicomIndex);
// itkBasic::ImageSave( itkBasic::ImageSharp(result, 0.5), boost::str( boost::format("%s.%s.png") % output_name % "normal" ), 1, 0); // Auto Level
}
int main (int argc, char **argv)
{
int verbose=0,clobber=0;
int order=2;
static struct option long_options[] = {
{"verbose", no_argument, &verbose, 1},
{"quiet", no_argument, &verbose, 0},
{"clobber", no_argument, &clobber, 1},
{"order", required_argument, 0, 'o'},
{0, 0, 0, 0}
};
for (;;) {
/* getopt_long stores the option index here. */
int option_index = 0;
int c = getopt_long (argc, argv, "vo:", long_options, &option_index);
/* Detect the end of the options. */
if (c == -1) break;
switch (c)
{
case 0:
break;
case 'o':
order=atoi(optarg);break;
case 'v':
cout << "Version: 0.1" << endl;
return 0;
case '?':
/* getopt_long already printed an error message. */
default:
show_usage (argv[0]);
return 1;
}
}
if((argc - optind) < 3) {
show_usage (argv[0]);
return 1;
}
std::string in_volume=argv[optind];
std::string in_obj=argv[optind+1];
std::string out_csv=argv[optind+2];
if (!clobber && !access(out_csv.c_str(), F_OK))
{
cerr << out_csv.c_str() << " Exists!" << endl;
return 1;
}
try
{
itk::ObjectFactoryBase::RegisterFactory(itk::MincImageIOFactory::New());
itk::ImageFileReader<minc::image3d >::Pointer reader = itk::ImageFileReader<minc::image3d >::New();
//initializing the reader
reader->SetFileName(in_volume.c_str());
reader->Update();
minc::image3d::Pointer in=reader->GetOutput();
std::cout<<"Building BSpline interpolator , order="<<order<<std::endl;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetSplineOrder(order);
interpolator->SetInputImage(in);
std::ofstream output(out_csv.c_str());
VIO_File_formats format;
object_struct **object_list;
int n_objects=0;
//bicpl sucks!
if( input_graphics_file( (char*)in_obj.c_str(), &format, &n_objects,
&object_list ) != VIO_OK )
{
std::cerr << " Error reading "<<in_obj.c_str() << std::endl;
return 1;
}
//const int segment_length=10;
std::vector<minc::tag_point> lines;
std::vector<int> line_index;
std::cout<<"Processing "<<n_objects<<" objects"<<std::endl;
output<<"x,y,z,v"<<std::endl;
for(int i=0;i< n_objects;i++ )
{
if( get_object_type( object_list[i] ) == POLYGONS )
{
polygons_struct *polygons;
polygons = get_polygons_ptr(object_list[i]);
/*object_struct * lobj= create_object( LINES );
lines_struct * lines = get_lines_ptr(lobj);
initialize_lines( lines, WHITE );
lines->n_points = polygons->n_items*segment_length;
ALLOC( lines->points, lines->n_points );*/
for(int pnt=0;pnt< polygons->n_points;pnt++ )
{
VIO_Point p_=polygons->points[pnt];//seeding point
minc::tag_point p_orig,p;
p_orig[0]=p_.coords[0];p_orig[1]=p_.coords[1];p_orig[2]=p_.coords[2];
//line_index.push_back(lines.size());
//lines.push_back(p_orig);
p=p_orig;
double _in=interpolator->Evaluate(p);
/* polygons->points[pnt].coords[0]=p[0];
polygons->points[pnt].coords[1]=p[1];
polygons->points[pnt].coords[2]=p[2];*/
//int size = GET_OBJECT_SIZE( *polygons, poly );
//if(size<3) continue; //?
/* p1=polygons->points[POINT_INDEX( polygons->end_indices, poly, 0 )];
p2=polygons->points[POINT_INDEX( polygons->end_indices, poly, 1 )];
p3=polygons->points[POINT_INDEX( polygons->end_indices, poly, 2 )];*/
/*
std::cout<<poly<<"\t"<<POINT_INDEX( polygons->end_indices, poly, 0 )<<" "
<<POINT_INDEX( polygons->end_indices, poly, 1 )<<" "
<<POINT_INDEX( polygons->end_indices, poly, 2 )<<std::endl;*/
//std::cout<<poly<<"\t"<<p1.coords[0]<<" "<<p1.coords[1]<<" "<<p1.coords[2]<<std::endl;
//center
output<<p[0]<<","<<p[1]<<","<<p[2]<<","<<
_in<<std::endl;
}
}
}
//int status = output_graphics_file( (char*)out_objf.c_str(), format,n_objects, object_list );
//free up memory
delete_object_list( n_objects, object_list );
//return( status != OK );
/*
//outputting lines
FILE *fp=fopen(out_objf.c_str(),"w");
// IL want to write in binary
fprintf(fp,"L 0.1 %d\n",lines.size());
//WRITING cordinates
for (int i=0;i<lines.size();i++) {
fprintf(fp,"%f %f %f\n",lines[i][0],lines[i][1],lines[i][2]);
}
fprintf(fp,"%d\n1 ",line_index.size()); //1 color per line
for (int i=0;i<line_index.size();i++) { //random colors
fprintf(fp,"%f %f %f 1.0\n",rand()/(double)RAND_MAX,rand()/(double)RAND_MAX,rand()/(double)RAND_MAX);
}
for (int i=0;i<line_index.size();i++) {
if(i<(line_index.size()-1))
fprintf(fp,"%d ",line_index[i+1]);
else
fprintf(fp,"%d ",lines.size());//last line lasts untill the end
}
fprintf(fp,"\n");
for (int i=0;i<line_index.size();i++)
{
int end=i<(line_index.size()-1)?line_index[i+1]:lines.size();
for(int j=line_index[i];j<end;j++)
fprintf(fp," %d",j);
fprintf(fp,"\n");
}
fclose(fp);*/
} catch (const minc::generic_error & err) {
cerr << "Got an error at:" << err.file () << ":" << err.line () << endl;
return 1;
}
return 0;
};
//calculate segmentation values
bool CTImageTreeItem::internalGetSegmentationValues( SegmentationValues &values) const {
//get ITK image
ImageType::Pointer image = getITKImage();
if (image.IsNull())
return false;
//get buffered region of the image
ImageType::RegionType ctregion = image->GetBufferedRegion();
//define an iterator for the binary segment
typedef itk::ImageRegionConstIteratorWithIndex< BinaryImageType > BinaryIteratorType;
//get binary segment
BinaryImageTreeItem::ImageType::Pointer segment = values.m_segment->getITKImage();
if (segment.IsNull())
return false;
/* typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( "test.dcm" );
writer->SetInput( image );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception catched !" << std::endl;
std::cerr << excep << std::endl;
}
*/
//create a binary iterator for the segment and its buffered region
BinaryIteratorType binIter( segment, segment->GetBufferedRegion() );
ImageType::PointType point;
//The Accumulators Framework is framework for performing incremental calculations
using namespace boost::accumulators;
//http://boost-sandbox.sourceforge.net/libs/accumulators/doc/html/accumulators/user_s_guide.html#accumulators.user_s_guide.the_accumulators_framework
accumulator_set<double,features<tag::count, tag::min, tag::mean, tag::max, tag::variance> > acc;
//check selected accuracy
if (values.m_accuracy == SegmentationValues::SimpleAccuracy) {
ImageType::IndexType index;
//iterate over the pixel of the binary segment
for(binIter.GoToBegin(); !binIter.IsAtEnd(); ++binIter) {
//if actual value = 255
if (binIter.Value() == BinaryPixelOn) {
//transforms the index to a physical point in the binary segment
segment->TransformIndexToPhysicalPoint(binIter.GetIndex(),point);
//transform that point to an index of the CT image
image->TransformPhysicalPointToIndex(point, index);
//check if that index is inside the CT region
if (ctregion.IsInside(index)) {
//get the pixel value at the index
int t = image->GetPixel(index);
//check if pixel value != -2048
if (isRealHUvalue(t)) {
//accumulate pixel value
acc( t );
}
}
}
}
//check selected accuracy
} else if (values.m_accuracy == SegmentationValues::PreventDoubleSamplingAccuracy) {
ImageType::IndexType index;
//definition for a set of indices, which can be compared
typedef std::set< ImageType::IndexType, IndexCompareFunctor > IndexSetType;
IndexSetType indexSet;
//iterate over the pixel of the binary segment
for(binIter.GoToBegin(); !binIter.IsAtEnd(); ++binIter) {
//if actual value = 255
if (binIter.Value() == BinaryPixelOn) {
//transforms the index to a physical point in the binary segment
segment->TransformIndexToPhysicalPoint(binIter.GetIndex(),point);
//transform that point to an index of the CT image
image->TransformPhysicalPointToIndex(point, index);
//check if that index is inside the CT region
if (ctregion.IsInside(index)) {
std::pair<IndexSetType::iterator,IndexSetType::iterator> ret;
//
ret = indexSet.equal_range(index);
//If x does not match any key in the container, the range returned has a length of zero,
//with both iterators pointing to the nearest value greater than x, if any,
//or to set::end if x is greater than all the elements in the container.
if (ret.first == ret.second) {
indexSet.insert(ret.first, index);
//get the pixel value at the index
int t = image->GetPixel(index);
//check if pixel value != -2048
if (isRealHUvalue(t)) {
//accumulate pixel value
acc( t );
}
}
}
}
}
//check selected accuracy
} else if (values.m_accuracy == SegmentationValues::InterpolatedAccuracy) {
//define an interpolate function
typedef itk::LinearInterpolateImageFunction< CTImageType > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
//set input to the interpolator
interpolator->SetInputImage( image );
InterpolatorType::ContinuousIndexType index;
//iterate over the pixel of the binary segment
for(binIter.GoToBegin(); !binIter.IsAtEnd(); ++binIter) {
//if actual value = 255
if (binIter.Value() == BinaryPixelOn) {
//transforms the index to a physical point in the binary segment
segment->TransformIndexToPhysicalPoint(binIter.GetIndex(),point);
//transform that point to an index of the CT image
image->TransformPhysicalPointToContinuousIndex(point, index);
//check if the index is inside the buffer of the interpolator
if (interpolator->IsInsideBuffer(index)) {
//Returns the linearly interpolated image intensity
int t = interpolator->EvaluateAtContinuousIndex(index);
//check if pixel value != -2048
if (isRealHUvalue(t)) {
//accumulate pixel value
acc( t );
}
}
}
}
}
//set sample count, min, mean, max and standard deviation
//from the accumulated intensities
values.m_sampleCount = count( acc );
values.m_min = min( acc );
values.m_mean = mean( acc );
values.m_max = max( acc );
values.m_stddev = std::sqrt( variance( acc ) );
//set the image modification time
values.m_mtime = segment->GetMTime();
const_cast<CTImageTreeItem*>(this)->m_segmentationValueCache[ values.m_segment ] = values;
return values.m_sampleCount > 0;
}