diff --git a/Applications/Segmentation/otbLargeScaleSegmentation.cxx b/Applications/Segmentation/otbLargeScaleSegmentation.cxx
index 4c48de898026a8cd3c3ad9943df9e5f8ecef1762..958146fb226fcc8b336b5338becb3234104d7633 100644
--- a/Applications/Segmentation/otbLargeScaleSegmentation.cxx
+++ b/Applications/Segmentation/otbLargeScaleSegmentation.cxx
@@ -15,89 +15,77 @@
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
+// Wrappers
#include "otbWrapperApplication.h"
#include "otbWrapperApplicationFactory.h"
// Segmentation filters includes
#include "otbMeanShiftVectorImageFilter.h"
-
#include "otbMeanShiftImageFilter2.h"
-
-#include "otbStreamingVectorizedSegmentationOGR.h"
-
-//#include "otbPersistentImageToOGRDataFilter.h"
-//#include "otbPersistentFilterStreamingDecorator.h"
-
#include "otbConnectedComponentMuParserFunctor.h"
#include "itkConnectedComponentFunctorImageFilter.h"
#include "otbMaskMuParserFilter.h"
-
-#include "otbParser.h"
-
+// Large scale vectorization framework
+#include "otbStreamingVectorizedSegmentationOGR.h"
#include "otbOGRDataSourceWrapper.h"
-#include "otbMultiToMonoChannelExtractROI.h"
-#include "otbObjectList.h"
-
-
namespace otb
{
namespace Wrapper
{
-
-
class LargeScaleSegmentation : public Application
{
public:
/** Standard class typedefs. */
- typedef LargeScaleSegmentation Self;
+ typedef LargeScaleSegmentation Self;
typedef Application Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
+ /** Images typedefs */
typedef UInt32ImageType LabelImageType;
typedef UInt32ImageType MaskImageType;
-
- typedef MultiToMonoChannelExtractROI<FloatVectorImageType::InternalPixelType,
- MaskImageType::PixelType> ExtractROIFilterType;
- typedef ObjectList<ExtractROIFilterType> ExtractROIFilterListType;
-
- // typedef itk::ImageToImageFilter<FloatVectorImageType,UInt32ImageType> SegmentationFilterType;
- typedef otb::MeanShiftVectorImageFilter<FloatVectorImageType,FloatVectorImageType,LabelImageType> MSEDISONSegmentationFilterType;
-
-
- // TODO replace by new meanshift segmentation scheme
- //typedef otb::MeanShiftConnectedComponentSegmentationFilter< FloatVectorImageType, MaskImageType,LabelImageType > MeanShiftConnectedComponentSegmentationFilterType;
- // typedef otb::MeanShiftImageFilter2<FloatVectorImageType, LabelImageType> MeanShiftFilterType;
-
-
- // Mask generation
- typedef otb::Functor::ConnectedComponentMuParserFunctor<FloatVectorImageType::PixelType> FunctorType;
- typedef itk::ConnectedComponentFunctorImageFilter<
- FloatVectorImageType,
- LabelImageType,
- FunctorType,
- MaskImageType > ConnectedComponentSegmentationFilterType;
-
-
+ // Segmentation filters typedefs
+ // Edison mean-shift
+ typedef otb::MeanShiftVectorImageFilter
+ <FloatVectorImageType,
+ FloatVectorImageType,
+ LabelImageType> EdisonSegmentationFilterType;
+ // Home made mean-shift
typedef otb::MeanShiftImageFilter2
- <FloatVectorImageType, FloatVectorImageType>
- MeanShiftFilterType;
- // mask typedef
- typedef otb::MaskMuParserFilter<FloatVectorImageType, MaskImageType> MaskMuParserFilterType;
-
-
- typedef otb::StreamingVectorizedSegmentationOGR<FloatVectorImageType, ConnectedComponentSegmentationFilterType> ConnectedComponentStreamingVectorizedSegmentationOGRType;
-
- typedef otb::StreamingVectorizedSegmentationOGR<FloatVectorImageType, MSEDISONSegmentationFilterType> MSEDIONStreamingVectorizedSegmentationOGRType;
- // typedef otb::StreamingVectorizedSegmentationOGR<FloatVectorImageType, ConnectedComponentSegmentationFilterType> ConnectedComponentStreamingVectorizedSegmentationOGRType;
-
+ <FloatVectorImageType,
+ FloatVectorImageType>
+ MeanShiftFilterType;
+ // Simple connected components
+ typedef otb::Functor::ConnectedComponentMuParserFunctor
+ <FloatVectorImageType::PixelType> FunctorType;
+
+ typedef itk::ConnectedComponentFunctorImageFilter
+ <FloatVectorImageType,
+ LabelImageType,
+ FunctorType,
+ MaskImageType > ConnectedComponentSegmentationFilterType;
+
+ // mask filter
+ typedef otb::MaskMuParserFilter
+ <FloatVectorImageType, MaskImageType> MaskMuParserFilterType;
+
+ // Vectorize filters
+ // Edison mean-shift
+ typedef otb::StreamingVectorizedSegmentationOGR
+ <FloatVectorImageType,
+ EdisonSegmentationFilterType> EdisontreamingVectorizedSegmentationOGRType;
+
+ // Connected components
+ typedef otb::StreamingVectorizedSegmentationOGR
+ <FloatVectorImageType,
+ ConnectedComponentSegmentationFilterType>
+ ConnectedComponentStreamingVectorizedSegmentationOGRType;
/** Standard macro */
itkNewMacro(Self);
-
itkTypeMacro(LargeScaleSegmentation, otb::Application);
private:
@@ -131,7 +119,6 @@ private:
SetParameterDescription("lout", "The labeled output image.");
MandatoryOff("lout");
- //
AddParameter(ParameterType_Choice, "filter", "Segmentation Filter");
SetParameterDescription("filter", "Choose your segmentation filter method.");
@@ -152,40 +139,42 @@ private:
SetDefaultParameterInt("filter.meanshiftedison.minsize", 100);
SetDefaultParameterFloat("filter.meanshiftedison.scale", 100000.);
- AddChoice("filter.meanshift", "MeanShift");
- SetParameterDescription(
- "filter.meanshift",
- "MeanShift filter (MeanShift filtered output is segmented by connected component segmentation, this step will be replaced by a dedicated scheme (WIP)).");
- // MeanShift Parameters
- AddParameter(ParameterType_Int, "filter.meanshift.spatialr", "Spatial radius");
- SetParameterDescription("filter.meanshift.spatialr", "Spatial radius defining neighborhood.");
- AddParameter(ParameterType_Float, "filter.meanshift.ranger", "Range radius");
- SetParameterDescription("filter.meanshift.ranger", "Range radius defining the interval in the color space.");
- AddParameter(ParameterType_Float, "filter.meanshift.thres", "convergence threshold");
- SetParameterDescription("filter.meanshift.thres", "convergence threshold. iterative scheme will stop if MeanShift "
- "vector is below this threshold (1e-3 by default) or iteration number reached maximum iteration number.");
- AddParameter(ParameterType_Int, "filter.meanshift.maxiter", "maximum iteration number");
- SetParameterDescription("filter.meanshift.maxiter",
- "iteration process is stopped if convergence hasn't been reached after this number of iteration (10 by default).");
- AddParameter(ParameterType_Empty, "filter.meanshift.useoptim", "use optimization");
- SetParameterDescription("filter.meanshift.useoptim", "Use mode optimization.");
- MandatoryOff("filter.meanshift.useoptim");
- AddParameter(ParameterType_String, "filter.meanshift.expr", "Connected Component Expression");
- SetParameterDescription("filter.meanshift.expr", "Formula used for connected component segmentation");
- SetDefaultParameterInt("filter.meanshift.spatialr", 5);
-
- SetDefaultParameterInt("filter.meanshift.spatialr", 5);
- SetDefaultParameterFloat("filter.meanshift.ranger", 15.0);
- SetDefaultParameterFloat("filter.meanshift.thres", 1e-3);
- SetMinimumParameterFloatValue("filter.meanshift.thres", 0.);
- SetDefaultParameterInt("filter.meanshift.maxiter", 10);
- SetMinimumParameterIntValue("filter.meanshift.maxiter", 1);
+ // AddChoice("filter.meanshift", "MeanShift");
+ // SetParameterDescription(
+ // "filter.meanshift",
+ // "MeanShift filter (MeanShift filtered output is segmented by connected component segmentation, this step will be replaced by a dedicated scheme (WIP)).");
+ // // MeanShift Parameters
+ // AddParameter(ParameterType_Int, "filter.meanshift.spatialr", "Spatial radius");
+ // SetParameterDescription("filter.meanshift.spatialr", "Spatial radius defining neighborhood.");
+ // AddParameter(ParameterType_Float, "filter.meanshift.ranger", "Range radius");
+ // SetParameterDescription("filter.meanshift.ranger", "Range radius defining the interval in the color space.");
+ // AddParameter(ParameterType_Float, "filter.meanshift.thres", "convergence threshold");
+ // SetParameterDescription("filter.meanshift.thres", "convergence threshold. iterative scheme will stop if MeanShift "
+ // "vector is below this threshold (1e-3 by default) or iteration number reached maximum iteration number.");
+ // AddParameter(ParameterType_Int, "filter.meanshift.maxiter", "maximum iteration number");
+ // SetParameterDescription("filter.meanshift.maxiter",
+ // "iteration process is stopped if convergence hasn't been reached after this number of iteration (10 by default).");
+ // AddParameter(ParameterType_Empty, "filter.meanshift.useoptim", "use optimization");
+ // SetParameterDescription("filter.meanshift.useoptim", "Use mode optimization.");
+ // MandatoryOff("filter.meanshift.useoptim");
+ // AddParameter(ParameterType_String, "filter.meanshift.expr", "Connected Component Expression");
+ // SetParameterDescription("filter.meanshift.expr", "Formula used for connected component segmentation");
+ // SetDefaultParameterInt("filter.meanshift.spatialr", 5);
+
+ // SetDefaultParameterInt("filter.meanshift.spatialr", 5);
+ // SetDefaultParameterFloat("filter.meanshift.ranger", 15.0);
+ // SetDefaultParameterFloat("filter.meanshift.thres", 1e-3);
+ // SetMinimumParameterFloatValue("filter.meanshift.thres", 0.);
+ // SetDefaultParameterInt("filter.meanshift.maxiter", 10);
+ // SetMinimumParameterIntValue("filter.meanshift.maxiter", 1);
AddChoice("filter.connectedcomponent", "ConnectedComponentMuParser");
SetParameterDescription("filter.connectedcomponent", "connectedComponant muparser filter.");
AddParameter(ParameterType_String, "filter.connectedcomponent.expr", "Connected Component Expression");
SetParameterDescription("filter.connectedcomponent.expr", "Formula used for connected component segmentation");
+ MandatoryOff("filter.connectedcomponent.expr");
+
AddParameter(ParameterType_Int, "minsize", "Minimum object size");
SetParameterDescription("minsize",
@@ -194,8 +183,6 @@ private:
SetMinimumParameterIntValue("minsize", 1);
MandatoryOff("minsize");
- //
-
AddParameter(ParameterType_String, "layername", "Layer Name");
SetParameterDescription("layername", "Layer Name.(by default : Layer )");
SetParameterString("layername", "layer");
@@ -238,54 +225,57 @@ private:
void DoExecute()
{
- //
+ // Retrieve output filename as well as layer names
std::string dataSourceName = GetParameterString("outvd");
otb::ogr::DataSource::Pointer ogrDS = otb::ogr::DataSource::New(dataSourceName, otb::ogr::DataSource::Modes::write);
-
- //mask image transform vector image to LabelImage
- if (HasValue("inmask"))
- {
- m_MaskImage = this->GetParameterUInt32Image("inmask");
- m_MaskImage->UpdateOutputInformation();
- }
-
- const unsigned int minSize = static_cast<unsigned int> (this->GetParameterInt("minsize"));
- const unsigned int tileSize = static_cast<unsigned int> (this->GetParameterInt("tilesize"));
-
std::string layerName = this->GetParameterString("layername");
std::string fieldName = this->GetParameterString("fieldname");
+ // Retrieve start label parameter
const unsigned int startLabel = this->GetParameterInt("startlabel");
+
+ // Retrieve the 8-connected option
bool use8connected = IsParameterEnabled("neighbor");
+ // Retrieve min object size parameter
+ const unsigned int minSize = static_cast<unsigned int> (this->GetParameterInt("minsize"));
+
+ // Retrieve tile size parameter
+ const unsigned int tileSize = static_cast<unsigned int> (this->GetParameterInt("tilesize"));
+
+
+ // Switch on segmentation filter case
switch (GetParameterInt("filter"))
{
- // MeanShiftEDISON based filtering
+ // Edison mean-shift
case 0:
{
+ EdisontreamingVectorizedSegmentationOGRType::Pointer
+ edisonVectorizationFilter = EdisontreamingVectorizedSegmentationOGRType::New();
- MSEDIONStreamingVectorizedSegmentationOGRType::Pointer
- EDISONVectorizationFilter = MSEDIONStreamingVectorizedSegmentationOGRType::New();
- m_VectorizationFilter = EDISONVectorizationFilter;
+ edisonVectorizationFilter->SetInput(GetParameterFloatVectorImage("in"));
- EDISONVectorizationFilter->SetInput(GetParameterFloatVectorImage("in"));
if (HasValue("inmask"))
{
- EDISONVectorizationFilter->SetInputMask(this->GetParameterUInt32Image("inmask"));
+ edisonVectorizationFilter->SetInputMask(this->GetParameterUInt32Image("inmask"));
}
- EDISONVectorizationFilter->SetOGRDataSource(ogrDS);
+ edisonVectorizationFilter->SetOGRDataSource(ogrDS);
- //filter->GetStreamer()->SetNumberOfLinesStrippedStreaming(atoi(argv[3]));
if (tileSize != 0)
- EDISONVectorizationFilter->GetStreamer()->SetTileDimensionTiledStreaming(tileSize);
- else EDISONVectorizationFilter->GetStreamer()->SetAutomaticTiledStreaming();
+ {
+ edisonVectorizationFilter->GetStreamer()->SetTileDimensionTiledStreaming(tileSize);
+ }
+ else
+ {
+ edisonVectorizationFilter->GetStreamer()->SetAutomaticAdaptativeStreaming();
+ }
- EDISONVectorizationFilter->SetLayerName(layerName);
- EDISONVectorizationFilter->SetFieldName(fieldName);
- EDISONVectorizationFilter->SetStartLabel(startLabel);
+ edisonVectorizationFilter->SetLayerName(layerName);
+ edisonVectorizationFilter->SetFieldName(fieldName);
+ edisonVectorizationFilter->SetStartLabel(startLabel);
if (use8connected)
otbAppLogINFO(<<"Use 8 connected neighborhood."<<std::endl);
- EDISONVectorizationFilter->SetUse8Connected(use8connected);
+ edisonVectorizationFilter->SetUse8Connected(use8connected);
//segmentation paramters
const unsigned int
@@ -296,117 +286,71 @@ private:
minimumObjectSize = static_cast<unsigned int> (this->GetParameterInt("filter.meanshiftedison.minsize"));
const float scale = this->GetParameterFloat("filter.meanshiftedison.scale");
- EDISONVectorizationFilter->GetSegmentationFilter()->SetSpatialRadius(spatialRadius);
- EDISONVectorizationFilter->GetSegmentationFilter()->SetRangeRadius(rangeRadius);
- EDISONVectorizationFilter->GetSegmentationFilter()->SetMinimumRegionSize(minimumObjectSize);
- EDISONVectorizationFilter->GetSegmentationFilter()->SetScale(scale);
+ edisonVectorizationFilter->GetSegmentationFilter()->SetSpatialRadius(spatialRadius);
+ edisonVectorizationFilter->GetSegmentationFilter()->SetRangeRadius(rangeRadius);
+ edisonVectorizationFilter->GetSegmentationFilter()->SetMinimumRegionSize(minimumObjectSize);
+ edisonVectorizationFilter->GetSegmentationFilter()->SetScale(scale);
if (minSize > 1)
{
otbAppLogINFO(<<"Object with size under "<<minSize<<" will be suppressed."<<std::endl);
- EDISONVectorizationFilter->SetFilterSmallObject(true);
- EDISONVectorizationFilter->SetMinimumObjectSize(minSize);
+ edisonVectorizationFilter->SetFilterSmallObject(true);
+ edisonVectorizationFilter->SetMinimumObjectSize(minSize);
}
- EDISONVectorizationFilter->Initialize(); //must be called !
- EDISONVectorizationFilter->Update(); //must be called !
- //m_VectorizationFilter->Update();
- m_LabelImage = EDISONVectorizationFilter->GetSegmentationFilter()->GetLabeledClusteredOutput();
+
+ edisonVectorizationFilter->SetSimplify(false);
+
+ std::cout<<"Edison branch"<<std::endl;
+
+ edisonVectorizationFilter->Initialize(); //must be called !
+ edisonVectorizationFilter->Update(); //must be called !
+ m_LabelImage = edisonVectorizationFilter->GetSegmentationFilter()->GetLabeledClusteredOutput();
break;
}
- //MeanShift filter
+ // Home made mean-shift
case 1:
{
-
- ConnectedComponentStreamingVectorizedSegmentationOGRType::Pointer
- MSVectorizationFilter = ConnectedComponentStreamingVectorizedSegmentationOGRType::New();
- m_VectorizationFilter = MSVectorizationFilter;
-
- MeanShiftFilterType::Pointer MSFilter = MeanShiftFilterType::New();
- // MeanShift filtering
- // Set filter parameters
-
- //segmentation paramters
- const unsigned int
- spatialRadius = static_cast<unsigned int> (this->GetParameterInt("filter.meanshift.spatialr"));
- const unsigned int rangeRadius = static_cast<unsigned int> (this->GetParameterInt("filter.meanshift.ranger"));
- const unsigned int maxIter = static_cast<unsigned int> (this->GetParameterInt("filter.meanshift.maxiter"));
- const float threshold = this->GetParameterFloat("filter.meanshift.thres");
-
- MSFilter->SetSpatialBandwidth(spatialRadius);
- MSFilter->SetRangeBandwidth(rangeRadius);
- MSFilter->SetThreshold(threshold);
- MSFilter->SetMaxIterationNumber(maxIter);
- MSFilter->SetInput(GetParameterFloatVectorImage("in"));
- MSFilter->SetModeSearchOptimization(IsParameterEnabled("filter.meanshift.useoptim"));
-
- MSVectorizationFilter->SetInput(GetParameterFloatVectorImage("in"));
- AddProcess(MSVectorizationFilter, "Computing Filtering");
-
- MSVectorizationFilter->SetInput(MSFilter->GetRangeOutput());
- if (HasValue("inmask"))
- {
- MSVectorizationFilter->SetInputMask(this->GetParameterUInt32Image("inmask"));
- MSVectorizationFilter->GetSegmentationFilter()->SetMaskImage(this->GetParameterUInt32Image("inmask"));
-
- }
- MSVectorizationFilter->SetOGRDataSource(ogrDS);
-
- //filter->GetStreamer()->SetNumberOfLinesStrippedStreaming(atoi(argv[3]));
- if (tileSize != 0)
- MSVectorizationFilter->GetStreamer()->SetTileDimensionTiledStreaming(tileSize);
- else MSVectorizationFilter->GetStreamer()->SetAutomaticTiledStreaming();
-
- MSVectorizationFilter->SetLayerName(layerName);
- MSVectorizationFilter->SetFieldName(fieldName);
- MSVectorizationFilter->SetStartLabel(startLabel);
- MSVectorizationFilter->SetUse8Connected(use8connected);
-
- MSVectorizationFilter->GetSegmentationFilter()->GetFunctor().SetExpression(
- GetParameterString(
- "filter.meanshift.expr"));
- AddProcess(MSVectorizationFilter->GetSegmentationFilter(), "Computing segmentation");
-
- MSVectorizationFilter->Initialize(); //must be called !
- m_VectorizationFilter->Update();
- m_LabelImage = MSVectorizationFilter->GetSegmentationFilter()->GetOutput();
-
+ otbAppLogFATAL(<<"Standard mean-shift not implemented yet");
break;
}
- // CC filter
+ // Connected component segmentation
case 2:
{
ConnectedComponentStreamingVectorizedSegmentationOGRType::Pointer
- CCVectorizationFilter = ConnectedComponentStreamingVectorizedSegmentationOGRType::New();
- m_VectorizationFilter = CCVectorizationFilter;
+ ccVectorizationFilter = ConnectedComponentStreamingVectorizedSegmentationOGRType::New();
- CCVectorizationFilter->SetInput(GetParameterFloatVectorImage("in"));
+ ccVectorizationFilter->SetInput(GetParameterFloatVectorImage("in"));
if (HasValue("inmask"))
{
- CCVectorizationFilter->SetInputMask(this->GetParameterUInt32Image("inmask"));
- CCVectorizationFilter->GetSegmentationFilter()->SetMaskImage(this->GetParameterUInt32Image("inmask"));
+ ccVectorizationFilter->SetInputMask(this->GetParameterUInt32Image("inmask"));
+ ccVectorizationFilter->GetSegmentationFilter()->SetMaskImage(this->GetParameterUInt32Image("inmask"));
}
- CCVectorizationFilter->SetOGRDataSource(ogrDS);
+ ccVectorizationFilter->SetOGRDataSource(ogrDS);
- //filter->GetStreamer()->SetNumberOfLinesStrippedStreaming(atoi(argv[3]));
if (tileSize != 0)
- CCVectorizationFilter->GetStreamer()->SetTileDimensionTiledStreaming(tileSize);
- else CCVectorizationFilter->GetStreamer()->SetAutomaticTiledStreaming();
+ {
+ ccVectorizationFilter->GetStreamer()->SetTileDimensionTiledStreaming(tileSize);
+ }
+ else
+ {
+ ccVectorizationFilter->GetStreamer()->SetAutomaticTiledStreaming();
+ }
- CCVectorizationFilter->SetLayerName(layerName);
- CCVectorizationFilter->SetFieldName(fieldName);
- CCVectorizationFilter->SetStartLabel(startLabel);
- CCVectorizationFilter->SetUse8Connected(use8connected);
+ ccVectorizationFilter->SetLayerName(layerName);
+ ccVectorizationFilter->SetFieldName(fieldName);
+ ccVectorizationFilter->SetStartLabel(startLabel);
+ ccVectorizationFilter->SetUse8Connected(use8connected);
- CCVectorizationFilter->GetSegmentationFilter()->GetFunctor().SetExpression(
+ ccVectorizationFilter->GetSegmentationFilter()->GetFunctor().SetExpression(
GetParameterString(
"filter.connectedcomponent.expr"));
- AddProcess(CCVectorizationFilter->GetSegmentationFilter(), "Computing segmentation");
+ AddProcess(ccVectorizationFilter->GetSegmentationFilter(), "Computing segmentation");
- CCVectorizationFilter->Initialize(); //must be called !
- m_VectorizationFilter->Update();
- m_LabelImage = CCVectorizationFilter->GetSegmentationFilter()->GetOutput();
+ ccVectorizationFilter->Initialize(); //must be called !
+ ccVectorizationFilter->Update();
+ m_LabelImage = ccVectorizationFilter->GetSegmentationFilter()->GetOutput();
break;
}
@@ -424,10 +368,6 @@ private:
SetParameterOutputImage<LabelImageType> ("lout", m_LabelImage);
}
-
- itk::ProcessObject::Pointer m_SegmentationFilter;
- itk::ProcessObject::Pointer m_VectorizationFilter;
- MaskImageType::Pointer m_MaskImage;
LabelImageType::Pointer m_LabelImage;
};