From 53960c19970ff59806725635c93aebfd9462f3cb Mon Sep 17 00:00:00 2001
From: Arnaud Jaen <arnaud.jaen@c-s.fr>
Date: Thu, 10 May 2012 17:56:53 +0200
Subject: [PATCH] ENH: Add a mask in otbStreamingVectorizedSegmentation. Pixel
with values of 0 in the mask will not be suitable for vectorization.
---
.../OBIA/otbLabelImageToOGRDataSourceFilter.h | 6 +-
.../otbLabelImageToOGRDataSourceFilter.txx | 109 ++++++++++++++++--
.../otbPersistentImageToOGRDataFilter.txx | 2 +
.../otbStreamingVectorizedSegmentationOGR.h | 14 +++
.../otbStreamingVectorizedSegmentationOGR.txx | 48 ++++++--
Testing/Code/OBIA/CMakeLists.txt | 3 +-
.../otbStreamingVectorizedSegmentationOGR.cxx | 23 ++--
7 files changed, 176 insertions(+), 29 deletions(-)
diff --git a/Code/OBIA/otbLabelImageToOGRDataSourceFilter.h b/Code/OBIA/otbLabelImageToOGRDataSourceFilter.h
index 83dbae6951..20cccb2f87 100644
--- a/Code/OBIA/otbLabelImageToOGRDataSourceFilter.h
+++ b/Code/OBIA/otbLabelImageToOGRDataSourceFilter.h
@@ -24,7 +24,7 @@
namespace otb
{
-class OGRDataSourceWrapper;
+// class OGRDataSourceWrapper;
/** \class LabelImageToOGRDataSourceFilter
* \brief this class uses GDALPolygonize method to transform a Label image into
@@ -72,6 +72,10 @@ public:
virtual void SetInput(const InputImageType *input);
virtual const InputImageType * GetInput(void);
+ /** Set/Get the input mask image. All pixels in the mask with a value of 0 will not be considered suitable for collection as polygons */
+ virtual void SetInputMask(const InputImageType *input);
+ virtual const InputImageType * GetInputMask(void);
+
itkSetMacro(FieldName, std::string);
itkGetMacro(FieldName, std::string);
diff --git a/Code/OBIA/otbLabelImageToOGRDataSourceFilter.txx b/Code/OBIA/otbLabelImageToOGRDataSourceFilter.txx
index c1818424bd..4109ea053e 100644
--- a/Code/OBIA/otbLabelImageToOGRDataSourceFilter.txx
+++ b/Code/OBIA/otbLabelImageToOGRDataSourceFilter.txx
@@ -38,6 +38,7 @@ template <class TInputImage>
LabelImageToOGRDataSourceFilter<TInputImage>
::LabelImageToOGRDataSourceFilter() : m_FieldName("DN"), m_Use8Connected(false)
{
+ this->SetNumberOfInputs(2);
this->SetNumberOfRequiredInputs(1);
this->SetNumberOfRequiredOutputs(1);
@@ -86,6 +87,28 @@ LabelImageToOGRDataSourceFilter<TInputImage>
return static_cast<const InputImageType *>(this->Superclass::GetInput(0));
}
+template <class TInputImage>
+void
+LabelImageToOGRDataSourceFilter<TInputImage>
+::SetInputMask(const InputImageType *input)
+{
+ this->Superclass::SetNthInput(1, const_cast<InputImageType *>(input));
+}
+
+template <class TInputImage>
+const typename LabelImageToOGRDataSourceFilter<TInputImage>
+::InputImageType *
+LabelImageToOGRDataSourceFilter<TInputImage>
+::GetInputMask(void)
+{
+ if (this->GetNumberOfInputs() < 2)
+ {
+ return 0;
+ }
+
+ return static_cast<const InputImageType *>(this->Superclass::GetInput(1));
+}
+
template <class TInputImage>
void
LabelImageToOGRDataSourceFilter<TInputImage>
@@ -102,10 +125,17 @@ LabelImageToOGRDataSourceFilter<TInputImage>
{
return;
}
-
// The input is necessarily the largest possible region.
- // For a streamed implementation, use the StreamingLineSegmentDetector filter
input->SetRequestedRegionToLargestPossibleRegion();
+
+ typename InputImageType::Pointer mask =
+ const_cast<InputImageType *> (this->GetInputMask());
+ if(!mask)
+ {
+ return;
+ }
+ // The input is necessarily the largest possible region.
+ mask->SetRequestedRegionToLargestPossibleRegion();
}
@@ -118,15 +148,16 @@ LabelImageToOGRDataSourceFilter<TInputImage>
{
itkExceptionMacro(<< "Not streamed filter. ERROR : requested region is not the largest possible region.");
}
-
- typename InputImageType::Pointer inImage = const_cast<InputImageType *>(this->GetInput());
- SizeType size = this->GetInput()->GetLargestPossibleRegion().GetSize();
-
- unsigned int nbBands = this->GetInput()->GetNumberOfComponentsPerPixel();
- unsigned int bytePerPixel = sizeof(InputPixelType);
+ SizeType size;
+ unsigned int nbBands = 0;
+ unsigned int bytePerPixel = 0;
- /** Convert Input image into a OGRLayer using GDALPolygonize */
+ /* Convert the input image into a GDAL raster needed by GDALPolygonize */
+ size = this->GetInput()->GetLargestPossibleRegion().GetSize();
+ nbBands = this->GetInput()->GetNumberOfComponentsPerPixel();
+ bytePerPixel = sizeof(InputPixelType);
+
// buffer casted in unsigned long cause under Win32 the adress
// don't begin with 0x, the adress in not interpreted as
// hexadecimal but alpha numeric value, then the conversion to
@@ -192,8 +223,64 @@ LabelImageToOGRDataSourceFilter<TInputImage>
options=option;
}
- GDALPolygonize(dataset->GetRasterBand(1), NULL, &outputLayer.ogr(), 0, options, NULL, NULL);
-
+ /* Convert the mask input into a GDAL raster needed by GDALPolygonize */
+ typename InputImageType::ConstPointer inputMask = this->GetInputMask();
+ if (!inputMask.IsNull())
+ {
+ size = this->GetInputMask()->GetLargestPossibleRegion().GetSize();
+ nbBands = this->GetInputMask()->GetNumberOfComponentsPerPixel();
+ bytePerPixel = sizeof(InputPixelType);
+ // buffer casted in unsigned long cause under Win32 the adress
+ // don't begin with 0x, the adress in not interpreted as
+ // hexadecimal but alpha numeric value, then the conversion to
+ // integer make us pointing to an non allowed memory block => Crash.
+ std::ostringstream maskstream;
+ maskstream << "MEM:::"
+ << "DATAPOINTER=" << (unsigned long)(this->GetInputMask()->GetBufferPointer()) << ","
+ << "PIXELS=" << size[0] << ","
+ << "LINES=" << size[1] << ","
+ << "BANDS=" << nbBands << ","
+ << "DATATYPE=" << GDALGetDataTypeName(GdalDataTypeBridge::GetGDALDataType<InputPixelType>()) << ","
+ << "PIXELOFFSET=" << bytePerPixel * nbBands << ","
+ << "LINEOFFSET=" << bytePerPixel * nbBands * size[0] << ","
+ << "BANDOFFSET=" << bytePerPixel;
+
+ GDALDataset * maskDataset = static_cast<GDALDataset *> (GDALOpen(maskstream.str().c_str(), GA_ReadOnly));
+
+ //Set input Projection ref and Geo transform to the dataset.
+ maskDataset->SetProjection(this->GetInputMask()->GetProjectionRef().c_str());
+
+ projSize = this->GetInputMask()->GetGeoTransform().size();
+
+ //Set the geo transform of the input mask image (if any)
+ // Reporting origin and spacing of the buffered region
+ // the spacing is unchanged, the origin is relative to the buffered region
+ bufferIndexOrigin = this->GetInputMask()->GetBufferedRegion().GetIndex();
+ this->GetInputMask()->TransformIndexToPhysicalPoint(bufferIndexOrigin, bufferOrigin);
+ geoTransform[0] = bufferOrigin[0];
+ geoTransform[3] = bufferOrigin[1];
+ geoTransform[1] = this->GetInput()->GetSpacing()[0];
+ geoTransform[5] = this->GetInput()->GetSpacing()[1];
+ // FIXME: Here component 1 and 4 should be replaced by the orientation parameters
+ if (projSize == 0)
+ {
+ geoTransform[2] = 0.;
+ geoTransform[4] = 0.;
+ }
+ else
+ {
+ geoTransform[2] = this->GetInput()->GetGeoTransform()[2];
+ geoTransform[4] = this->GetInput()->GetGeoTransform()[4];
+ }
+ maskDataset->SetGeoTransform(geoTransform);
+
+ GDALPolygonize(dataset->GetRasterBand(1), maskDataset->GetRasterBand(1), &outputLayer.ogr(), 0, options, NULL, NULL);
+ GDALClose(maskDataset);
+ }
+ else
+ {
+ GDALPolygonize(dataset->GetRasterBand(1), NULL, &outputLayer.ogr(), 0, options, NULL, NULL);
+ }
this->SetNthOutput(0,ogrDS);
diff --git a/Code/OBIA/otbPersistentImageToOGRDataFilter.txx b/Code/OBIA/otbPersistentImageToOGRDataFilter.txx
index ccaf2b7435..5abec263dd 100644
--- a/Code/OBIA/otbPersistentImageToOGRDataFilter.txx
+++ b/Code/OBIA/otbPersistentImageToOGRDataFilter.txx
@@ -33,6 +33,8 @@ template<class TImage>
PersistentImageToOGRDataFilter<TImage>
::PersistentImageToOGRDataFilter() : m_FieldName("DN"), m_LayerName("Layer"), m_GeometryType(wkbMultiPolygon)
{
+ this->SetNumberOfInputs(2);
+ this->SetNumberOfRequiredInputs(2);
m_StreamSize.Fill(0);
}
diff --git a/Code/OBIA/otbStreamingVectorizedSegmentationOGR.h b/Code/OBIA/otbStreamingVectorizedSegmentationOGR.h
index 36bb5a81fd..a683793f77 100644
--- a/Code/OBIA/otbStreamingVectorizedSegmentationOGR.h
+++ b/Code/OBIA/otbStreamingVectorizedSegmentationOGR.h
@@ -133,6 +133,9 @@ public:
itkSetMacro(Use8Connected, bool);
itkGetMacro(Use8Connected, bool);
+
+ virtual void SetInputMask(const LabelImageType *mask);
+ virtual const LabelImageType * GetInputMask(void);
protected:
PersistentStreamingLabelImageToOGRDataFilter();
@@ -181,6 +184,8 @@ public:
typedef TImageType InputImageType;
typedef typename PersistentStreamingLabelImageToOGRDataFilter<TImageType,
TSegmentationFilter>::LabelPixelType LabelPixelType;
+ typedef typename PersistentStreamingLabelImageToOGRDataFilter<TImageType,
+ TSegmentationFilter>::LabelImageType LabelImageType;
typedef typename PersistentStreamingLabelImageToOGRDataFilter<TImageType,
TSegmentationFilter>::OGRDataSourcePointerType OGRDataSourcePointerType;
@@ -193,6 +198,15 @@ public:
return this->GetFilter()->GetInput();
}
+ void SetInputMask(LabelImageType * mask)
+ {
+ this->GetFilter()->SetInputMask(mask);
+ }
+ const LabelImageType * GetInputMask()
+ {
+ return this->GetFilter()->GetInputMask();
+ }
+
void SetOGRDataSource( OGRDataSourcePointerType ogrDS )
{
this->GetFilter()->SetOGRDataSource(ogrDS);
diff --git a/Code/OBIA/otbStreamingVectorizedSegmentationOGR.txx b/Code/OBIA/otbStreamingVectorizedSegmentationOGR.txx
index 819bd26a6e..a37796b99e 100644
--- a/Code/OBIA/otbStreamingVectorizedSegmentationOGR.txx
+++ b/Code/OBIA/otbStreamingVectorizedSegmentationOGR.txx
@@ -35,6 +35,8 @@ template <class TImageType, class TSegmentationFilter>
PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
::PersistentStreamingLabelImageToOGRDataFilter() : m_TileMaxLabel(0), m_StartLabel(0), m_Use8Connected(false)
{
+ this->SetNumberOfInputs(3);
+ this->SetNumberOfRequiredInputs(2);
m_SegmentationFilter = SegmentationFilterType::New();
m_TileNumber = 1;
}
@@ -45,6 +47,28 @@ PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
{
}
+template <class TImageType, class TSegmentationFilter>
+void
+PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
+::SetInputMask(const LabelImageType *mask)
+{
+ this->itk::ProcessObject::SetNthInput(2, const_cast<LabelImageType *>(mask));
+}
+
+template <class TImageType, class TSegmentationFilter>
+const typename PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
+::LabelImageType *
+PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
+::GetInputMask(void)
+{
+ if (this->GetNumberOfInputs() < 3)
+ {
+ return 0;
+ }
+
+ return static_cast<const LabelImageType *>(this->itk::ProcessObject::GetInput(2));
+}
+
template <class TImageType, class TSegmentationFilter>
void
PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
@@ -63,18 +87,12 @@ PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
itk::TimeProbe tileChrono;
tileChrono.Start();
-
- itk::TimeProbe chrono;
- chrono.Start();
// Apply an ExtractImageFilter to avoid problems with filters asking for the LargestPossibleRegion
typedef itk::ExtractImageFilter<InputImageType, InputImageType> ExtractImageFilterType;
typename ExtractImageFilterType::Pointer extract = ExtractImageFilterType::New();
extract->SetInput( this->GetInput() );
extract->SetExtractionRegion( this->GetInput()->GetRequestedRegion() );
extract->Update();
-
- chrono.Stop();
- //std::cout<< "extract took " << chrono.GetTotal() << " sec"<<std::endl;
// WARNING: itk::ExtractImageFilter does not copy the MetadataDictionnary
extract->GetOutput()->SetMetaDataDictionary(this->GetInput()->GetMetaDataDictionary());
@@ -84,7 +102,6 @@ PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
typename LabelImageToOGRDataSourceFilterType::Pointer labelImageToOGRDataFilter =
LabelImageToOGRDataSourceFilterType::New();
-
itk::TimeProbe chrono1;
chrono1.Start();
m_SegmentationFilter->SetInput(extract->GetOutput());
@@ -97,7 +114,22 @@ PersistentStreamingLabelImageToOGRDataFilter<TImageType, TSegmentationFilter>
itk::TimeProbe chrono2;
chrono2.Start();
-
+
+ typename LabelImageType::ConstPointer inputMask = this->GetInputMask();
+ if (!inputMask.IsNull())
+ {
+ // Apply an ExtractImageFilter to avoid problems with filters asking for the LargestPossibleRegion
+ typedef itk::ExtractImageFilter<LabelImageType, LabelImageType> ExtractLabelImageFilterType;
+ typename ExtractLabelImageFilterType::Pointer maskExtract = ExtractLabelImageFilterType::New();
+ maskExtract->SetInput( this->GetInputMask() );
+ maskExtract->SetExtractionRegion( this->GetInputMask()->GetRequestedRegion() );
+ maskExtract->Update();
+
+ // WARNING: itk::ExtractImageFilter does not copy the MetadataDictionnary
+ maskExtract->GetOutput()->SetMetaDataDictionary(this->GetInputMask()->GetMetaDataDictionary());
+
+ labelImageToOGRDataFilter->SetInputMask(maskExtract->GetOutput());
+ }
labelImageToOGRDataFilter->SetInput(dynamic_cast<LabelImageType *>(m_SegmentationFilter->GetOutputs().at(labelImageIndex).GetPointer()));
labelImageToOGRDataFilter->SetFieldName(this->GetFieldName());
labelImageToOGRDataFilter->SetUse8Connected(m_Use8Connected);
diff --git a/Testing/Code/OBIA/CMakeLists.txt b/Testing/Code/OBIA/CMakeLists.txt
index 0875354b42..8507eb8667 100644
--- a/Testing/Code/OBIA/CMakeLists.txt
+++ b/Testing/Code/OBIA/CMakeLists.txt
@@ -251,7 +251,8 @@ ADD_TEST(obTvStreamingVectorizedSegmentationOGR ${OBIA_TESTS1}
#${TEMP}/obTvStreamingVectorizedSegmentationOutput.sqlite
otbStreamingVectorizedSegmentationOGR
${INPUTDATA}/QB_Toulouse_Ortho_PAN.tif
- ${TEMP}/obTvStreamingVectorizedSegmentationOGR.shp
+ ${INPUTDATA}/QB_Toulouse_Ortho_PAN_Mask.tif
+ ${TEMP}/obTvStreamingVectorizedSegmentationOGR.sqlite
NewLayer
100
5
diff --git a/Testing/Code/OBIA/otbStreamingVectorizedSegmentationOGR.cxx b/Testing/Code/OBIA/otbStreamingVectorizedSegmentationOGR.cxx
index 52542f7f48..2f5aebcf54 100644
--- a/Testing/Code/OBIA/otbStreamingVectorizedSegmentationOGR.cxx
+++ b/Testing/Code/OBIA/otbStreamingVectorizedSegmentationOGR.cxx
@@ -49,20 +49,21 @@ int otbStreamingVectorizedSegmentationOGRNew(int argc, char * argv[])
int otbStreamingVectorizedSegmentationOGR(int argc, char * argv[])
{
- if (argc != 8)
+ if (argc != 9)
{
std::cerr << "Usage: " << argv[0];
- std::cerr << " inputImage outputVec layerName TileDimension spatialRadius rangeRadius minObjectSize" << std::endl;
+ std::cerr << " inputImage maskImage outputVec layerName TileDimension spatialRadius rangeRadius minObjectSize" << std::endl;
return EXIT_FAILURE;
}
const char * imageName = argv[1];
- const char * dataSourceName = argv[2];
- const char * layerName = argv[3];
- const unsigned int tileSize = atoi(argv[4]);
- const unsigned int spatialRadiusOldMS = atoi(argv[5]);
- const double rangeRadiusOldMS = atof(argv[6]);
- const unsigned int minimumObjectSizeOldMS = atoi(argv[7]);
+ const char * maskName = argv[2];
+ const char * dataSourceName = argv[3];
+ const char * layerName = argv[4];
+ const unsigned int tileSize = atoi(argv[5]);
+ const unsigned int spatialRadiusOldMS = atoi(argv[6]);
+ const double rangeRadiusOldMS = atof(argv[7]);
+ const unsigned int minimumObjectSizeOldMS = atoi(argv[8]);
typedef float InputPixelType;
@@ -77,16 +78,22 @@ int otbStreamingVectorizedSegmentationOGR(int argc, char * argv[])
typedef otb::MeanShiftVectorImageFilter<ImageType, ImageType, LabelImageType> SegmentationFilterType;
typedef otb::StreamingVectorizedSegmentationOGR<ImageType, SegmentationFilterType> StreamingVectorizedSegmentationOGRType;
typedef otb::ImageFileReader<ImageType> ReaderType;
+ typedef otb::ImageFileReader<LabelImageType> MaskReaderType;
ReaderType::Pointer reader = ReaderType::New();
+ MaskReaderType::Pointer maskReader = MaskReaderType::New();
StreamingVectorizedSegmentationOGRType::Pointer filter = StreamingVectorizedSegmentationOGRType::New();
reader->SetFileName(imageName);
reader->UpdateOutputInformation();
+ maskReader->SetFileName(maskName);
+ maskReader->UpdateOutputInformation();
+
otb::ogr::DataSource::Pointer ogrDS = otb::ogr::DataSource::New(dataSourceName, otb::ogr::DataSource::Modes::write);
filter->SetInput(reader->GetOutput());
+ filter->SetInputMask(maskReader->GetOutput());
filter->SetOGRDataSource(ogrDS);
//filter->GetStreamer()->SetNumberOfLinesStrippedStreaming(atoi(argv[3]));
filter->GetStreamer()->SetTileDimensionTiledStreaming(tileSize);
--
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