From 004a461ec61c87fa1e7e9eeaeb2d6c3856a573ff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ga=C3=ABlle=20USSEGLIO?= <gaelle.usseglio@cnes.fr>
Date: Tue, 2 Jun 2020 14:50:01 +0000
Subject: [PATCH] ENH : Fix streaming into TilesAnalysisWith Step filter with
buffer to store previous output region
---
app/otbSARPhaseFiltering.cxx | 11 +-
include/otbTilesAnalysisWithStepImageFilter.h | 15 ++
.../otbTilesAnalysisWithStepImageFilter.txx | 229 ++++++++++++++----
3 files changed, 208 insertions(+), 47 deletions(-)
diff --git a/app/otbSARPhaseFiltering.cxx b/app/otbSARPhaseFiltering.cxx
index f7a863c..9307df6 100644
--- a/app/otbSARPhaseFiltering.cxx
+++ b/app/otbSARPhaseFiltering.cxx
@@ -226,7 +226,8 @@ namespace otb
functor->SetSizeTiles(sizeTiles);
functor->Setalpha(alpha);
- // Instanciate the Coregistration filter
+ // Instanciate the Tiles Analysis (with Step) filter
+ // Limitation : Works only with a streaming by strips
TilesFilterType::Pointer filterPhase = TilesFilterType::New();
m_Ref.push_back(filterPhase.GetPointer());
filterPhase->SetSizeTiles(sizeTiles);
@@ -293,10 +294,10 @@ namespace otb
m_Ref.push_back(filterGroupedBy.GetPointer());
// Only for phase and coherence
- std::vector<std::string> bands;
- bands.push_back("pha");
- bands.push_back("coh");
- filterGroupedBy->bandSelection(bands);
+ // std::vector<std::string> bands;
+ // bands.push_back("pha");
+ // bands.push_back("coh");
+ // filterGroupedBy->bandSelection(bands);
filterGroupedBy->SetInput(filterPhase->GetOutput());
filterGroupedBy->SetMLRan(factor_ran);
diff --git a/include/otbTilesAnalysisWithStepImageFilter.h b/include/otbTilesAnalysisWithStepImageFilter.h
index 1d62afe..bd2f65a 100644
--- a/include/otbTilesAnalysisWithStepImageFilter.h
+++ b/include/otbTilesAnalysisWithStepImageFilter.h
@@ -46,6 +46,8 @@ namespace otb
* _ assign output with accumulations
*
* This filter can be used for phase filtering.
+ *
+ * Limitations : This filter works only with a streaming by strips
* \ingroup DiapOTBModule
*/
@@ -156,6 +158,8 @@ protected:
void BeforeThreadedGenerateData();
+ void AfterThreadedGenerateData();
+
/** Static function used as a "callback" by the MultiThreader. The threading
* library will call this routine for each thread, which will delegate the
* control to ThreadedGenerateData(). */
@@ -183,6 +187,17 @@ protected:
MutexType * m_Mutex;
+ // Store previous/effective index and size of output requested region and expect new ones
+ // Used into GenerateInputRequestedRegion to define output requested region
+ ImageOutIndexType m_expectedIndex;
+ ImageOutSizeType m_expectedSize;
+ ImageOutIndexType m_saveIndex;
+ ImageOutSizeType m_saveSize;
+
+ // Store previous output region with it size : to initialize correctly current output region
+ ImageOutSizeType m_oldSize;
+ ImageOutPixelType * m_saveOutputBuffer;
+
};
} // End namespace otb
diff --git a/include/otbTilesAnalysisWithStepImageFilter.txx b/include/otbTilesAnalysisWithStepImageFilter.txx
index be9861b..208da01 100644
--- a/include/otbTilesAnalysisWithStepImageFilter.txx
+++ b/include/otbTilesAnalysisWithStepImageFilter.txx
@@ -46,6 +46,8 @@ namespace otb
this->m_Margin = 0;
m_Mutex = new MutexType();
+
+ m_saveOutputBuffer = 0;
}
/**
@@ -57,6 +59,12 @@ namespace otb
{
delete m_Mutex;
m_Mutex = 0;
+
+ if (m_saveOutputBuffer)
+ {
+ delete m_saveOutputBuffer;
+ m_saveOutputBuffer = 0;
+ }
}
@@ -126,27 +134,49 @@ namespace otb
{
////// Set Output Requestion Region (Contruct Tiles with given size and step for output) ///////
ImageOutRegionType outputRequestedRegion = this->GetOutput()->GetRequestedRegion();
-
- //std::cout << "Before outputRequestedRegion : " << outputRequestedRegion << std::endl;
- // New Index : closest inf multiple of Step
+ // New Index : closest inf multiple of Step and shift to this->m_SizeTiles - m_Step
ImageOutIndexType outputIndex;
- outputIndex[0] = (static_cast<int>(outputRequestedRegion.GetIndex()[0]/this->m_Step))*
- this->m_Step;
+
- outputIndex[1] = (static_cast<int>(outputRequestedRegion.GetIndex()[1]/this->m_Step))*
- this->m_Step;
+ if (outputRequestedRegion.GetIndex()[0]/this->m_Step < (this->m_SizeTiles/m_Step))
+ {
+ outputIndex[0] = outputRequestedRegion.GetIndex()[0];
- // New Size : closest sup multiple of SizeTiles with addtional when difference between new and
- // old index is too important
+ m_expectedIndex[0] = outputIndex[0];
+ }
+ else
+ {
+ outputIndex[0] = (static_cast<int>(outputRequestedRegion.GetIndex()[0]/this->m_Step))*
+ this->m_Step - (this->m_SizeTiles - m_Step) ;
+
+ m_expectedIndex[0] = m_saveIndex[0] + m_saveSize[0] - (this->m_SizeTiles - m_Step);
+ }
+
+ if (outputRequestedRegion.GetIndex()[1]/this->m_Step < (this->m_SizeTiles/m_Step))
+ {
+ outputIndex[1] = outputRequestedRegion.GetIndex()[1];
+ m_expectedIndex[1] = outputIndex[1];
+ }
+ else
+ {
+ outputIndex[1] = (static_cast<int>(outputRequestedRegion.GetIndex()[1]/this->m_Step))*
+ this->m_Step - (this->m_SizeTiles - m_Step);
+
+ m_expectedIndex[1] = m_saveIndex[1] + m_saveSize[1] - (this->m_SizeTiles - m_Step);
+ }
+
+
+ // New Size : closest sup multiple of Step with addtional when difference between new and
+ // old index and SizeTiles to handles the last tiles
ImageOutSizeType outputSize;
+
outputSize[0] = (static_cast<int>((outputRequestedRegion.GetIndex()[0] - outputIndex[0] +
- outputRequestedRegion.GetSize()[0])/this->m_SizeTiles) +
- 1)*this->m_SizeTiles + m_Step;
+ outputRequestedRegion.GetSize()[0])/this->m_Step))*
+ this->m_Step + this->m_SizeTiles;
outputSize[1] = (static_cast<int>((outputRequestedRegion.GetIndex()[1] - outputIndex[1] +
- outputRequestedRegion.GetSize()[1])/this->m_SizeTiles) +
- 1)*this->m_SizeTiles + m_Step;
-
+ outputRequestedRegion.GetSize()[1])/this->m_Step))*
+ this->m_Step + this->m_SizeTiles;
// Region affectation (with Crop to respect image dimension)
outputRequestedRegion.SetSize(outputSize);
@@ -154,13 +184,133 @@ namespace otb
outputRequestedRegion.Crop(this->GetOutput()->GetLargestPossibleRegion());
this->GetOutput()->SetRequestedRegion(outputRequestedRegion);
- //std::cout << "After outputRequestedRegion : " << outputRequestedRegion << std::endl;
- ///////////// With the new output requested region, find the region into input image /////////////
+ // input requested region same than output
ImageInRegionType inputRequestedRegion = outputRequestedRegion;
ImageInPointer inputPtr = const_cast< ImageInType * >( this->GetImageInput() );
inputPtr->SetRequestedRegion(inputRequestedRegion);
+ // Store index and size (for next call of this function)
+ m_saveIndex[0] = outputIndex[0];
+ m_saveIndex[1] = outputIndex[1];
+ m_saveSize[0] = outputSize[0];
+ m_saveSize[1] = outputSize[1];
+ }
+
+ /**
+ * Method BeforeThreadedGenerateData
+ */
+ template<class TImageIn, class TImageOut, class TFunction>
+ void
+ TilesAnalysisWithStepImageFilter< TImageIn, TImageOut, TFunction >
+ ::BeforeThreadedGenerateData()
+ {
+ // Typedef for Iterators on selected region
+ typedef itk::ImageRegionIterator<ImageOutType> OutItType;
+
+ // Initialize output region
+ ImageOutRegionType outputRequestedRegion = this->GetOutput()->GetRequestedRegion();
+
+
+ OutItType OutIt(this->GetOutput(), outputRequestedRegion);
+ OutIt.GoToBegin();
+
+ ImageOutIndexType first_index = OutIt.GetIndex();
+
+ // Limitations : Works only with a streaing by strips
+ // TODO : See to allow others kind of streamings
+ int counter = (m_oldSize[1] - (this->m_SizeTiles - m_Step +
+ m_expectedIndex[1]-m_saveIndex[1])) * m_oldSize[0];
+
+
+ while (!OutIt.IsAtEnd())
+ {
+ ImageOutIndexType index_current = OutIt.GetIndex();
+
+ // First Streaming
+ if (first_index[0] < (this->m_SizeTiles-m_Step) &&
+ first_index[1] < (this->m_SizeTiles-m_Step))
+ {
+ OutIt.Set(0);
+ }
+ else
+ {
+ // First pixels have already been initialized or estimated => saveBuffer
+ // and 0 for others
+ // TODO : See to allow another kind of streaming (not only strips)
+ if ((index_current[1]) >= (m_expectedIndex[1] + this->m_SizeTiles - m_Step))
+ {
+ // Init for accumulations
+ OutIt.Set(0);
+ }
+ else
+ {
+ // Keep values from last streaming
+ OutIt.Set(m_saveOutputBuffer[counter]);
+
+ counter++;
+ }
+
+ }
+
+ ++OutIt;
+ }
+
+ // Free memory
+ delete m_saveOutputBuffer;
+ m_saveOutputBuffer = 0;
+ }
+
+
+ /**
+ * Method AfterThreadedGenerateData
+ */
+ template<class TImageIn, class TImageOut, class TFunction>
+ void
+ TilesAnalysisWithStepImageFilter< TImageIn, TImageOut, TFunction >
+ ::AfterThreadedGenerateData()
+ {
+ ImageOutRegionType outputRequestedRegion = this->GetOutput()->GetRequestedRegion();
+
+ // Store all output region
+ ImageOutIndexType saveOutputIndex;
+ saveOutputIndex[0] = outputRequestedRegion.GetIndex()[0];
+ saveOutputIndex[1] = outputRequestedRegion.GetIndex()[1];
+
+ ImageOutSizeType saveOutputSize;
+ saveOutputSize[0] = outputRequestedRegion.GetSize()[0];
+ saveOutputSize[1] = outputRequestedRegion.GetSize()[1];
+
+ ImageOutRegionType saveOutputRegion;
+ saveOutputRegion.SetSize(saveOutputSize);
+ saveOutputRegion.SetIndex(saveOutputIndex);
+ saveOutputRegion.Crop(this->GetOutput()->GetLargestPossibleRegion());
+
+ m_oldSize[0] = saveOutputSize[0];
+ m_oldSize[1] = saveOutputSize[1];
+
+ // Typedef for Iterators on selected region
+ typedef itk::ImageRegionIterator<ImageOutType> OutItType;
+
+ OutItType OutIt(this->GetOutput(), saveOutputRegion);
+ OutIt.GoToBegin();
+
+
+ m_saveOutputBuffer = new ImageOutPixelType[outputRequestedRegion.GetSize()[0]*
+ outputRequestedRegion.GetSize()[1]];
+
+
+ // Loop for assignations
+ int counter = 0;
+ while (!OutIt.IsAtEnd())
+ {
+
+ m_saveOutputBuffer[counter] = OutIt.Get();
+
+ ++counter;
+ ++OutIt;
+ }
+
}
@@ -181,9 +331,10 @@ namespace otb
ImageOutRegionType outputRegion = this->GetOutput()->GetRequestedRegion();
// Define the number of tiles for processing
- int nbTiles_Lines = outputRegion.GetSize()[1]/m_Step - this->m_SizeTiles/m_Step;
- int nbTiles_Col = outputRegion.GetSize()[0]/m_Step - this->m_SizeTiles/m_Step;
+ int nbTiles_Lines = (outputRegion.GetSize()[1]-this->m_SizeTiles)/m_Step;
+ int nbTiles_Col = (outputRegion.GetSize()[0]-this->m_SizeTiles)/m_Step;
+
// Check if additionnal tiles are required
if (outputRegion.GetSize()[1] % m_Step != 0)
{
@@ -195,9 +346,19 @@ namespace otb
}
// First Tile = index of output requested region
- int IndL_FirstTiles = outputRegion.GetIndex()[1];
- int IndC_FirstTiles = outputRegion.GetIndex()[0];
+ //int IndL_FirstTiles = outputRegion.GetIndex()[1];
+ //int IndC_FirstTiles = outputRegion.GetIndex()[0];
+
+ // First Tile = index of expected output requested region (real output region might be larger
+ // than expected) => do not process all tiles because some of its had been estimated.
+ int IndL_FirstTiles = m_expectedIndex[1];
+ int IndC_FirstTiles = m_expectedIndex[0];
+ nbTiles_Lines -= (m_expectedIndex[1] - outputRegion.GetIndex()[1])/m_Step;
+ nbTiles_Col -= (m_expectedIndex[0] - outputRegion.GetIndex()[0])/m_Step;
+
+ nbTiles_Lines++;
+
///////////////////////// Pre Processing ///////////////////////
// Call Function initialization
this->m_FunctionOnTiles->Initialize(nbThreads);
@@ -222,33 +383,13 @@ namespace otb
this->GetMultiThreader()->SingleMethodExecute();
///////////// Post Processing ////////////
+ this->AfterThreadedGenerateData();
+
// Call Function terminate
this->m_FunctionOnTiles->Terminate();
}
- template<class TImageIn, class TImageOut, class TFunction>
- void
- TilesAnalysisWithStepImageFilter< TImageIn, TImageOut, TFunction >
- ::BeforeThreadedGenerateData()
- {
- // Typedef for Iterators on selected region
- typedef itk::ImageRegionIterator<ImageOutType> OutItType;
-
- // Initialize output region
- ImageOutRegionType outputRequestedRegion = this->GetOutput()->GetRequestedRegion();
-
-
- OutItType OutIt(this->GetOutput(), outputRequestedRegion);
- OutIt.GoToBegin();
- while (!OutIt.IsAtEnd())
- {
- // For accumulations
- OutIt.Set(0);
- ++OutIt;
- }
- }
-
template<class TImageIn, class TImageOut, class TFunction>
void
@@ -262,6 +403,7 @@ namespace otb
// Typedef for Iterators on selected region
typedef itk::ImageRegionIterator<ImageOutType> OutItType;
+
for (unsigned int k = startTileId; k < stopTileId; k++) //<= ??????
{
// Transform Tiles id into index
@@ -299,6 +441,7 @@ namespace otb
int compteur = 0;
// Assignate Output with function result
+ // Mutex to guarantee Thread-Safety
// Iterators on output
OutItType OutIt(this->GetOutput(), outputCurrentRegion);
OutIt.GoToBegin();
@@ -308,6 +451,7 @@ namespace otb
// Accumulations
ImageOutPixelType outTmp = OutIt.Get();
OutIt.Set(outTmp + TilesCache[compteur]);
+
++compteur;
++OutIt;
}
@@ -350,6 +494,7 @@ namespace otb
static_cast<unsigned int>((threadId+1) *
std::ceil(static_cast<double>(total)/(static_cast<double>(threadCount))));
+
if (stop > total) stop = total;
// For very small graphs it might occur that start = stop. In this
--
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