void WholeCellSeg::RemoveSmallObjs(){
typedef itk::LabelGeometryImageFilter< UShortImageType, UShortImageType > GeometryFilterType;
typedef itk::LabelStatisticsImageFilter< UShortImageType,UShortImageType > StatisticsFilterType;
typedef itk::CastImageFilter< UShortImageType, UShortImageType > CastUSUSType;
typedef itk::ImageRegionIteratorWithIndex< UShortImageType > IteratorType;
typedef GeometryFilterType::LabelIndicesType labelindicestype;
std::vector< unsigned short > labelsList;
GeometryFilterType::Pointer geomfilt1 = GeometryFilterType::New();
geomfilt1->SetInput( seg_im_out );
geomfilt1->SetCalculatePixelIndices( true );
geomfilt1->Update();
labelsList = geomfilt1->GetLabels();
StatisticsFilterType::Pointer statsfilt = StatisticsFilterType::New();
statsfilt->UseHistogramsOn();
statsfilt->SetInput( intermediate_bin_im_out );
statsfilt->SetLabelInput( seg_im_out );
statsfilt->Update();
CastUSUSType::Pointer castUSUSfilter = CastUSUSType::New();
if( draw_real_bounds && draw_synth_bounds ){
castUSUSfilter->SetInput( nuclab_inp );
castUSUSfilter->Update();
nuclab_inp_cpy = castUSUSfilter->GetOutput();
}
for( unsigned short i=0; i<labelsList.size(); ++i ){
if( !labelsList[i] ) continue;
labelindicestype indices1;
indices1 = geomfilt1->GetPixelIndices( labelsList[i] );
if( !(statsfilt->GetSum( labelsList[i] )) ){
IteratorType iterator ( seg_im_out, seg_im_out->GetRequestedRegion() );
for( labelindicestype::const_iterator itPixind = indices1.begin(); itPixind != indices1.end(); ++itPixind ){
iterator.SetIndex( *itPixind );
iterator.Set( 0 );
}
}
else if( draw_real_bounds && draw_synth_bounds ){
IteratorType iterator1 ( nuclab_inp_cpy, nuclab_inp_cpy->GetRequestedRegion() );
for( labelindicestype::const_iterator itPixind = indices1.begin(); itPixind != indices1.end(); ++itPixind ){
iterator1.SetIndex( *itPixind );
if( iterator1.Get()==labelsList[i] )
iterator1.Set( 0 );
}
}
}
if( !draw_synth_bounds && draw_real_bounds )
seg_done = 1;
}
void otb::Wrapper::ObjectsRadiometricStatistics::DoExecute()
{
VectorImageType::Pointer referenceImage = GetParameterImage("im");
otb::ogr::DataSource::Pointer ogrDS;
ogrDS = otb::ogr::DataSource::New(GetParameterString("in"), otb::ogr::DataSource::Modes::Update_LayerUpdate);
m_OGRDataSourceRendering = OGRDataSourceToMapFilterType::New();
m_OGRDataSourceRendering->AddOGRDataSource(ogrDS);
m_OGRDataSourceRendering->SetOutputSize(referenceImage->GetLargestPossibleRegion().GetSize());
m_OGRDataSourceRendering->SetOutputOrigin(referenceImage->GetOrigin());
m_OGRDataSourceRendering->SetOutputSpacing(referenceImage->GetSpacing());
m_OGRDataSourceRendering->SetOutputProjectionRef(referenceImage->GetProjectionRef());
// m_OGRDataSourceRendering->SetOutputParametersFromImage(referenceImage); // A tester
m_OGRDataSourceRendering->SetBackgroundValue(GetParameterInt("background"));
m_OGRDataSourceRendering->SetBurnAttributeMode(true);
m_OGRDataSourceRendering->SetBurnAttribute(GetParameterString("field"));
// Write label image from OGR
/*
WriterType::Pointer writer = WriterType::New();
writer->SetInput(m_OGRDataSourceRendering->GetOutput());
writer->SetFileName("label_image.tif");
writer->Update();
*/
// Label image from OGR to statistics label map
ConverterStatisticsType::Pointer converterStats = ConverterStatisticsType::New();
converterStats->SetInput(m_OGRDataSourceRendering->GetOutput());
converterStats->SetBackgroundValue(GetParameterInt("background"));
converterStats->Update();
// Prepare channel extraction
ExtractROIFilterType::Pointer m_ExtractROIFilter = ExtractROIFilterType::New();
m_ExtractROIFilter->SetInput(referenceImage);
// Update dataset with new fields
otb::ogr::Layer layer = ogrDS->GetLayerChecked(0);
OGRFieldDefn fieldNbPixels("NbPixels", OFTInteger);
layer.CreateField(fieldNbPixels, true);
OGRFieldDefn fieldFlatness("Flat", OFTReal);
layer.CreateField(fieldFlatness, true);
OGRFieldDefn fieldRoundness("Round", OFTReal);
layer.CreateField(fieldRoundness, true);
OGRFieldDefn fieldElongation("Elong", OFTReal);
layer.CreateField(fieldElongation, true);
OGRFieldDefn fieldPerimeter("Perim", OFTReal);
layer.CreateField(fieldPerimeter, true);
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"meanB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"stdB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"MedB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"VarB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"KurtB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"SkewB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
// Channel selection
m_ExtractROIFilter->SetChannel(i + 1);
// Statistics computation
StatisticsFilterType::Pointer statistics = StatisticsFilterType::New();
statistics->SetInput(converterStats->GetOutput());
statistics->SetFeatureImage(m_ExtractROIFilter->GetOutput());
statistics->SetComputePerimeter(true);
statistics->Update();
// Write shape attributes only one time
if(i==0)
{
for(otb::ogr::Layer::iterator featIt = layer.begin(); featIt!=layer.end(); ++featIt)
{
otb::ogr::Feature m_Feature = *featIt;
unsigned int label = m_Feature.ogr().GetFieldAsInteger(layer.GetLayerDefn().GetFieldIndex(GetParameterString("field").c_str()));
if(statistics->GetOutput()->HasLabel(label))
{
const StatisticsLabelObjectType *labelObjectStats = statistics->GetOutput()->GetLabelObject(label);
m_Feature.ogr().SetField("NbPixels", (int)labelObjectStats->GetNumberOfPixels());
m_Feature.ogr().SetField("Flat", labelObjectStats->GetFlatness());
m_Feature.ogr().SetField("Round", labelObjectStats->GetRoundness());
m_Feature.ogr().SetField("Elong", labelObjectStats->GetElongation());
m_Feature.ogr().SetField("Perim", labelObjectStats->GetPerimeter());
layer.SetFeature(m_Feature);
}
}
}
// Features iteration
for(otb::ogr::Layer::iterator featIt = layer.begin(); featIt!=layer.end(); ++featIt)
{
otb::ogr::Feature m_Feature = *featIt;
unsigned int label = m_Feature.ogr().GetFieldAsInteger(layer.GetLayerDefn().GetFieldIndex(GetParameterString("field").c_str()));
if(statistics->GetOutput()->HasLabel(label))
{
const StatisticsLabelObjectType *labelObjectStats = statistics->GetOutput()->GetLabelObject(label);
std::ostringstream fieldoss;
fieldoss<<"meanB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetMean());
fieldoss.str("");
fieldoss<<"stdB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetStandardDeviation());
fieldoss.str("");
fieldoss<<"medB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetMedian());
fieldoss.str("");
fieldoss<<"varB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetVariance());
fieldoss.str("");
fieldoss<<"kurtB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetKurtosis());
fieldoss.str("");
fieldoss<<"skewB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetSkewness());
fieldoss.str("");
}
else
{
otbAppLogINFO( << "Object number " << label << " is skipped. This could happen during the rasterisation process when an object is smaller than 1 pixel.");
}
}
}
}
void otb::Wrapper::Aggregate::DoExecute()
{
// Récupération de la labelmap
LabelImageType::Pointer labelIn = GetParameterUInt32Image("inseg");
labelIn->SetRequestedRegionToLargestPossibleRegion();
labelIn->Update();
// Filtre statistique pour récupérer le nombre de label dans la labelmap
StatisticsImageFilterType::Pointer stats = StatisticsImageFilterType::New();
stats->SetInput(labelIn);
stats->Update();
unsigned int regionCount=stats->GetMaximum();
otbAppLogINFO(<<"Number of objects: "<<regionCount);
//Récupération de la classification et statistique pour connaître le nombre de classes
ImageType::Pointer imageIn = GetParameterUInt32Image("in");
stats->SetInput(imageIn);
stats->Update();
unsigned int nbclass=stats->GetMaximum()-stats->GetMinimum()+1;
otbAppLogINFO(<<"Number of classes: "<<nbclass);
unsigned int minimum =stats->GetMinimum();
otbAppLogINFO(<<"Minimum: "<<minimum);
// Filtre LabelImage vers LabelMap(StatisticsLabelObject)
ConverterStatisticsType::Pointer converterStats = ConverterStatisticsType::New();
converterStats->SetInput(labelIn);
converterStats->SetBackgroundValue(0);
converterStats->Update();
// Calcul des statistiques par objet de la LabelMap
StatisticsFilterType::Pointer statistics = StatisticsFilterType::New();
statistics->SetInput(converterStats->GetOutput());
statistics->SetFeatureImage(imageIn);
statistics->SetNumberOfBins(nbclass);
statistics->Update();
// Définition du filtre ChangeLabel
m_ChangeLabelFilter = ChangeLabelImageFilterType::New();
m_ChangeLabelFilter->SetInput(labelIn);
// Iteration sur les objets, récupération de l'histogramme, extraction de la valeur mojoritaire
// Changement de la valeur du label par la valeur majoritaire dans la label map => obtention d'une classification corrigée
for(unsigned int i=0; i<regionCount+1; i++)
{
if(statistics->GetOutput()->HasLabel(i))
{
const StatisticsLabelObjectType *labelObjectStats = statistics->GetOutput()->GetLabelObject(i);
const HistogramType *histogram = labelObjectStats->GetHistogram();
unsigned int var = 0;
unsigned int classe = minimum;
for(unsigned int j=0; j< nbclass; j++)
{
if(histogram->GetFrequency(j)>var)
{
var = histogram->GetFrequency(j);
classe = j+minimum;
}
}
m_ChangeLabelFilter->SetChange(i,classe);
}
}
SetParameterOutputImage("outim", m_ChangeLabelFilter->GetOutput());
//Vectorisation
otbAppLogINFO(<<"Vectorization...");
//Définition du shapefile
const std::string shapefile = GetParameterString("out");
otb::ogr::DataSource::Pointer ogrDS;
otb::ogr::Layer layer(NULL, false);
std::string projRef = imageIn->GetProjectionRef();
OGRSpatialReference oSRS(projRef.c_str());
otbAppLogINFO(<< projRef);
std::vector<std::string> options;
ogrDS = otb::ogr::DataSource::New(shapefile, otb::ogr::DataSource::Modes::Overwrite);
std::string layername = itksys::SystemTools::GetFilenameName(shapefile.c_str());
std::string const extension = itksys::SystemTools::GetFilenameLastExtension(shapefile.c_str());
layername = layername.substr(0,layername.size()-(extension.size()));
layer = ogrDS->CreateLayer(layername, &oSRS, wkbMultiPolygon, options);
OGRFieldDefn labelField("label", OFTInteger);
layer.CreateField(labelField, true);
OGRFieldDefn MajorityField("Majority", OFTInteger);
layer.CreateField(MajorityField, true);
// Write label image
/*
WriterType::Pointer writer = WriterType::New();
writer->SetInput(m_ChangeLabelFilter->GetOutput());
writer->SetFileName("label_image.tif");
writer->Update();
*/
// Filtre LabelImage vers OGRDataSource
LabelImageToOGRDataSourceFilterType::Pointer labelToOGR = LabelImageToOGRDataSourceFilterType::New();
labelToOGR->SetInput(m_ChangeLabelFilter->GetOutput());
labelToOGR->SetInputMask(m_ChangeLabelFilter->GetOutput()); // La classe 0 est considérée comme du background et n'est pas vectorisée
labelToOGR->SetFieldName("Majority");
labelToOGR->Update();
otb::ogr::DataSource::ConstPointer ogrDSTmp = labelToOGR->GetOutput();
otb::ogr::Layer layerTmp = ogrDSTmp->GetLayerChecked(0);
otb::ogr::Layer::const_iterator featIt = layerTmp.begin();
int nveau_label = 1;
for(; featIt!=layerTmp.end(); ++featIt)
{
otb::ogr::Feature dstFeature(layer.GetLayerDefn());
dstFeature.SetFrom( *featIt, TRUE );
layer.CreateFeature( dstFeature );
dstFeature.ogr().SetField("label",nveau_label);
layer.SetFeature(dstFeature);
nveau_label +=1;
}
otbAppLogINFO(<<"Processing complete.");
}
