Commit 1bf5351a authored by Cresson Remi's avatar Cresson Remi
Browse files

Merge branch 'master' of gitlab-ssh.irstea.fr:remi.cresson/SimpleExtractionTools

parents be3c5d10 db2cc25e
......@@ -43,15 +43,15 @@ MeanResampleImageFilter<TImage>
// The new output image has the same origin
ImagePointType origin = inputImage->GetOrigin();
origin[0] += 0.5 * inputImage->GetSignedSpacing()[0] * (m_StepX - 1);
origin[1] += 0.5 * inputImage->GetSignedSpacing()[1] * (m_StepY - 1);
origin[0] += 0.5 * inputImage->GetSpacing()[0] * (m_StepX - 1);
origin[1] += 0.5 * inputImage->GetSpacing()[1] * (m_StepY - 1);
outputPtr->SetOrigin ( origin );
// New spacing for the output image
ImageSpacingType spacing = inputImage->GetSignedSpacing();
ImageSpacingType spacing = inputImage->GetSpacing();
spacing[0] *= m_StepX;
spacing[1] *= m_StepY;
outputPtr->SetSignedSpacing (spacing);
outputPtr->SetSpacing (spacing);
// New size for the output image
ImageRegionType inRegion = inputImage->GetLargestPossibleRegion();
......
/*
* otbMosaicFromDirectoryHandler.h
*
* Created on: 24 mars 2016
* Author: cresson
*/
#ifndef MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_H_
#define MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_H_
#include "itkImageSource.h"
#include "itkExceptionObject.h"
#include "itkImageRegion.h"
#include "otbStreamingSimpleMosaicFilter.h"
#include "otbImageFileReader.h"
#include "itkDirectory.h"
#include "otbImageIOBase.h"
#include "otbImageIOFactory.h"
#include "otbMultiToMonoChannelExtractROI.h"
#include "otbGenericRSResampleImageFilter.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
namespace otb
{
/** \class MosaicFromDirectoryHandler
* \brief This ImageSource produces an otb::image from multiple rasters
* stored in the m_Directory.
* TODO: Currently only .tif extension is supported. Might be nice to change it.
*
*
* \ingroup OTBMosaic
*
*/
template <class TOutputImage, class TReferenceImage>
class ITK_EXPORT MosaicFromDirectoryHandler : public itk::ImageSource<TOutputImage>
{
public:
/** Standard class typedefs. */
typedef MosaicFromDirectoryHandler Self;
typedef itk::ImageSource<TOutputImage> Superclass;
typedef itk::SmartPointer<Self> Pointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(MosaicFromDirectoryHandler, ImageSource);
/** Typedefs for output image */
typedef typename TOutputImage::SizeType SizeType;
typedef typename TOutputImage::IndexType IndexType;
typedef typename TOutputImage::SpacingType SpacingType;
typedef typename TOutputImage::PointType PointType;
typedef typename TOutputImage::RegionType ImageRegionType;
typedef typename TOutputImage::InternalPixelType OutputImagePixelType;
/** Typedefs for mosaic filter */
typedef otb::VectorImage<OutputImagePixelType> InternalMaskImageType;
typedef otb::StreamingSimpleMosaicFilter<
InternalMaskImageType> MosaicFilterType;
typedef typename MosaicFilterType::Pointer MosaicFilterPointerType;
/** Typedefs for image reader */
typedef otb::ImageFileReader<InternalMaskImageType> ReaderType;
typedef typename ReaderType::Pointer ReaderPointerType;
/** Typedefs for casting the image */
typedef otb::MultiToMonoChannelExtractROI<
OutputImagePixelType, OutputImagePixelType> CastFilterType;
typedef typename CastFilterType::Pointer CastFilterPointerType;
/** Typedefs for image reprojection */
typedef otb::GenericRSResampleImageFilter<
InternalMaskImageType, InternalMaskImageType> ResamplerType;
typedef typename ResamplerType::Pointer ResamplerPointerType;
typedef itk::NearestNeighborInterpolateImageFunction<
InternalMaskImageType, double> NNInterpolatorType;
/** Input directory accessors */
itkGetMacro(Directory, std::string);
itkSetMacro(Directory, std::string);
/** Output parameters setters */
itkSetMacro(OutputSpacing, SpacingType);
itkSetMacro(OutputSize, SizeType);
itkSetMacro(OutputOrigin, PointType);
void SetReferenceImage(TReferenceImage * ptr){m_RefImagePtr = ptr;}
itkSetMacro(UseReferenceImage, bool);
/** Prepare image allocation at the first call of the pipeline processing */
virtual void GenerateOutputInformation(void);
/** Does the real work. */
virtual void GenerateData();
protected:
MosaicFromDirectoryHandler();
virtual ~MosaicFromDirectoryHandler();
// Masks directory
std::string m_Directory;
// Output parameters
SpacingType m_OutputSpacing;
SizeType m_OutputSize;
PointType m_OutputOrigin;
// Internal filters
MosaicFilterPointerType mosaicFilter;
CastFilterPointerType castFilter;
std::vector<ReaderPointerType> readers;
std::vector<ResamplerPointerType> resamplers;
// Reference image pointer
bool m_UseReferenceImage;
TReferenceImage * m_RefImagePtr;
private:
MosaicFromDirectoryHandler(const Self &); //purposely not implemented
void operator =(const Self&); //purposely not implemented
};
} //namespace otb
#ifndef OTB_MANUAL_INSTANTIATION
#include <otbMosaicFromDirectoryHandler.txx>
#endif
#endif /* MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_H_ */
/*
* otbMosaicFromDirectoryHandler.hxx
*
* Created on: 24 mars 2016
* Author: cresson
*/
#ifndef MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_HXX_
#define MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_HXX_
#include "otbMosaicFromDirectoryHandler.h"
#include "otbImageFileWriter.h"
namespace otb
{
template <class TOutputImage, class TReferenceImage>
MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
::MosaicFromDirectoryHandler()
{
mosaicFilter = MosaicFilterType::New();
castFilter = CastFilterType::New();
m_UseReferenceImage = false;
m_RefImagePtr = 0;
}
template <class TOutputImage, class TReferenceImage>
MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
::~MosaicFromDirectoryHandler()
{
}
template <class TOutputImage, class TReferenceImage>
void
MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
::GenerateOutputInformation()
{
if (m_Directory[m_Directory.size()-1] != '/')
{
// If not, we add the separator
m_Directory.append("/");
}
// Get the list of files in the directory
itk::Directory::Pointer dir = itk::Directory::New();
if (!dir->Load(m_Directory.c_str()))
{
itkExceptionMacro(<< "Unable to browse directory " << m_Directory);
}
// Instanciate a new mosaic filter
mosaicFilter = MosaicFilterType::New();
mosaicFilter->SetGlobalWarningDisplay(false);
readers.clear();
resamplers.clear();
// Browse the directory
for (unsigned int i = 0; i < dir->GetNumberOfFiles(); i++)
{
const char *filename = dir->GetFile(i);
std::string sfilename(filename);
sfilename = m_Directory + sfilename;
// Try to read the file
otb::ImageIOBase::Pointer imageIO =
otb::ImageIOFactory::CreateImageIO(sfilename.c_str(),otb::ImageIOFactory::ReadMode);
if( imageIO.IsNotNull() )
{
// create reader
ReaderPointerType reader = ReaderType::New();
reader->SetFileName(sfilename);
reader->UpdateOutputInformation();
readers.push_back(reader);
if (m_UseReferenceImage)
{
ResamplerPointerType resampler = ResamplerType::New();
resampler->SetInput(reader->GetOutput());
// Setup transform through projRef and Keywordlist
SpacingType defSpacing = m_RefImagePtr->GetSignedSpacing();
defSpacing[0] *= 10;
defSpacing[1] *= 10;
resampler->SetDisplacementFieldSpacing(defSpacing);
resampler->SetInputKeywordList(reader->GetOutput()->GetImageKeywordlist());
resampler->SetInputProjectionRef(reader->GetOutput()->GetProjectionRef());
resampler->SetOutputKeywordList(m_RefImagePtr->GetImageKeywordlist());
resampler->SetOutputProjectionRef(m_RefImagePtr->GetProjectionRef());
resampler->SetOutputOrigin(m_RefImagePtr->GetOrigin());
resampler->SetOutputSpacing(m_RefImagePtr->GetSignedSpacing());
resampler->SetOutputSize(m_RefImagePtr->GetLargestPossibleRegion().GetSize());
resampler->SetOutputStartIndex(m_RefImagePtr->GetLargestPossibleRegion().GetIndex());
typename NNInterpolatorType::Pointer interpolator = NNInterpolatorType::New();
resampler->SetInterpolator(interpolator);
resamplers.push_back(resampler);
mosaicFilter->PushBackInput(resampler->GetOutput());
}
else
{
mosaicFilter->PushBackInput(reader->GetOutput());
}
}
else
{
// itkWarningMacro(<<"Unable to read file " << sfilename);
}
}
if (m_UseReferenceImage)
{
mosaicFilter->SetOutputOrigin(m_RefImagePtr->GetOrigin());
mosaicFilter->SetOutputSpacing(m_RefImagePtr->GetSignedSpacing());
mosaicFilter->SetOutputSize(m_RefImagePtr->GetLargestPossibleRegion().GetSize());
}
else
{
mosaicFilter->SetOutputOrigin(m_OutputOrigin);
mosaicFilter->SetOutputSpacing(m_OutputSpacing);
mosaicFilter->SetOutputSize(m_OutputSize);
}
mosaicFilter->SetAutomaticOutputParametersComputation(false);
castFilter->SetInput(mosaicFilter->GetOutput());
castFilter->GraftOutput( this->GetOutput() );
castFilter->UpdateOutputInformation();
this->GraftOutput( castFilter->GetOutput() );
}
template <class TOutputImage, class TReferenceImage>
void
MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
::GenerateData()
{
castFilter->GraftOutput( this->GetOutput() );
castFilter->Update();
this->GraftOutput( castFilter->GetOutput() );
}
} // end namespace otb
#endif /* MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_HXX_ */
......@@ -119,7 +119,7 @@ VectorDataToLabelImageCustomFilter<TVectorData, TOutputImage>
::SetOutputParametersFromImage(const ImageBaseType * src)
{
this->SetOutputOrigin ( src->GetOrigin() );
this->SetOutputSignedSpacing ( src->GetSignedSpacing() );
this->SetOutputSpacing ( src->GetSignedSpacing() );
this->SetOutputSize ( src->GetLargestPossibleRegion().GetSize() );
otb::ImageMetadataInterfaceBase::Pointer imi = otb::ImageMetadataInterfaceFactory::CreateIMI(src->GetMetaDataDictionary());
this->SetOutputProjectionRef(imi->GetProjectionRef());
......@@ -144,7 +144,7 @@ VectorDataToLabelImageCustomFilter<TVectorData, TOutputImage>
outputPtr->SetLargestPossibleRegion(outputLargestPossibleRegion);
// Set spacing and origin
outputPtr->SetSignedSpacing(m_OutputSpacing);
outputPtr->SetSpacing(m_OutputSpacing);
outputPtr->SetOrigin(m_OutputOrigin);
itk::MetaDataDictionary& dict = outputPtr->GetMetaDataDictionary();
......@@ -295,8 +295,8 @@ VectorDataToLabelImageCustomFilter<TVectorData, TOutputImage>::GenerateData()
this->GetOutput()->TransformIndexToPhysicalPoint(bufferIndexOrigin, bufferOrigin);
geoTransform[0] = bufferOrigin[0];
geoTransform[3] = bufferOrigin[1];
geoTransform[1] = this->GetOutput()->GetSignedSpacing()[0];
geoTransform[5] = this->GetOutput()->GetSignedSpacing()[1];
geoTransform[1] = this->GetOutput()->GetSpacing()[0];
geoTransform[5] = this->GetOutput()->GetSpacing()[1];
// FIXME: Here component 1 and 4 should be replaced by the orientation parameters
geoTransform[2] = 0.;
......
......@@ -8,6 +8,7 @@ otb_module(SimpleExtractionTools
OTBImageBase
OTBImageIO
OTBStatistics
OTBMosaic
TEST_DEPENDS
OTBTestKernel
......
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