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Commit 0e6b022e authored by Julien Michel's avatar Julien Michel
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LSMS integration (LSMS Merging app cleanup)

parent 0a87ec6a
zonalstats_histogram
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with 256 additions and 209 deletions
+256 -209
Applications/Segmentation/otbLSMSMerging.cxx
+ 256
− 209
View file @ 0e6b022e
......@@ -50,13 +50,34 @@ public:
typedef Application Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
itkNewMacro(Self)
;
itkTypeMacro(Merging, otb::Application)
;
typedef FloatVectorImageType ImageType;
typedef ImageType::InternalPixelType ImagePixelType;
typedef UInt32ImageType LabelImageType;
typedef LabelImageType::InternalPixelType LabelImagePixelType;
typedef otb::ImageFileReader<ImageType> ImageReaderType;
typedef otb::ImageFileReader<LabelImageType> LabelImageReaderType;
typedef otb::ImageFileWriter<LabelImageType> LabelImageWriterType;
typedef otb::MultiChannelExtractROI <ImagePixelType,ImagePixelType > MultiChannelExtractROIFilterType;
typedef otb::ExtractROI<LabelImagePixelType,LabelImagePixelType> ExtractROIFilterType;
typedef otb::StreamingStatisticsImageFilter<LabelImageType> StatisticsImageFilterType;
typedef itk::ImageRegionConstIterator<LabelImageType> LabelImageIterator;
typedef itk::ImageRegionConstIterator<ImageType> ImageIterator;
typedef itk::ChangeLabelImageFilter<LabelImageType,LabelImageType> ChangeLabelImageFilterType;
typedef otb::TileImageFilter<LabelImageType> TileImageFilterType;
itkNewMacro(Self);
itkTypeMacro(Merging, otb::Application);
private:
ChangeLabelImageFilterType::Pointer m_ChangeLabelFilter;
void DoInit()
{
SetName("LSMSMerging");
......@@ -119,25 +140,6 @@ private:
unsigned int nbTilesX = GetParameterInt("nbtilesx");
unsigned int nbTilesY = GetParameterInt("nbtilesy");
typedef float ImagePixelType;
typedef otb::VectorImage<ImagePixelType, 2> ImageType;
typedef otb::ImageFileReader<ImageType> ImageReaderType;
typedef unsigned int LabelImagePixelType;
typedef otb::Image<LabelImagePixelType, 2> LabelImageType;
typedef otb::ImageFileReader<LabelImageType> LabelImageReaderType;
typedef otb::ImageFileWriter<LabelImageType> LabelImageWriterType;
typedef otb::MultiChannelExtractROI <ImagePixelType,ImagePixelType > MultiChannelExtractROIFilterType;
typedef otb::ExtractROI<LabelImagePixelType,LabelImagePixelType> ExtractROIFilterType;
typedef otb::StreamingStatisticsImageFilter<LabelImageType> StatisticsImageFilterType;
typedef itk::ImageRegionConstIterator<LabelImageType> LabelImageIterator;
typedef itk::ImageRegionConstIterator<ImageType> ImageIterator;
typedef itk::ChangeLabelImageFilter<LabelImageType,LabelImageType> ChangeLabelImageFilterType;
typedef otb::TileImageFilter<LabelImageType> TileImageFilterType;
//Acquisition of the input image dimensions
ImageType::Pointer imageIn = GetParameterImage("in");
......@@ -153,7 +155,7 @@ private:
stats->Update();
unsigned int regionCount=stats->GetMaximum();
std::vector<int>nbPixels;
std::vector<unsigned int>nbPixels;
nbPixels.clear();
nbPixels.resize(regionCount+1);
for(LabelImagePixelType curLabel = 1; curLabel <= regionCount; ++curLabel)
......@@ -164,217 +166,262 @@ private:
std::vector<ImageType::PixelType>sum(regionCount+1,defaultValue);
long nbStars = 50;
//Sums calculation per label
std::cout<<"Sums calculation (0%) [";
for(unsigned int add=0;add<nbStars;add++)
std::cout<<" ";
std::cout<<"]"<<std::flush;
unsigned int count=0;
otbAppLogINFO(<<"Sums calculation ...");
unsigned long sizeTilesX = (sizeImageX+nbTilesX-1)/nbTilesX, sizeTilesY = (sizeImageY+nbTilesY-1)/nbTilesY;
unsigned long sizeTilesX = (sizeImageX+nbTilesX-1)/nbTilesX;
unsigned long sizeTilesY = (sizeImageY+nbTilesY-1)/nbTilesY;
for(unsigned int row = 0; row < nbTilesY ; row++)
for(unsigned int column = 0; column < nbTilesX ; column++)
{
unsigned long startX = column*sizeTilesX, startY = row*sizeTilesY;
unsigned long sizeX = vcl_min(sizeTilesX,sizeImageX-startX),sizeY = vcl_min(sizeTilesY,sizeImageY-startY);
//Tiles extraction of the input image
MultiChannelExtractROIFilterType::Pointer imageROI = MultiChannelExtractROIFilterType::New();
imageROI->SetInput(imageIn);
imageROI->SetStartX(startX);
imageROI->SetStartY(startY);
imageROI->SetSizeX(sizeX);
imageROI->SetSizeY(sizeY);
imageROI->Update();
//Tiles extraction of the segmented image
ExtractROIFilterType::Pointer labelImageROI = ExtractROIFilterType::New();
labelImageROI->SetInput(labelIn);
labelImageROI->SetStartX(startX);
labelImageROI->SetStartY(startY);
labelImageROI->SetSizeX(sizeX);
labelImageROI->SetSizeY(sizeY);
labelImageROI->Update();
//Sums calculation for the mean calculation per label
LabelImageIterator itLabel( labelImageROI->GetOutput(), labelImageROI->GetOutput()->GetLargestPossibleRegion());
ImageIterator itImage( imageROI->GetOutput(), imageROI->GetOutput()->GetLargestPossibleRegion());
for (itLabel.GoToBegin(), itImage.GoToBegin(); !itLabel.IsAtEnd(); ++itLabel, ++itImage){
nbPixels[itLabel.Value()]++;
for(unsigned int comp = 0; comp<numberOfComponentsPerPixel; ++comp)
sum[itLabel.Value()][comp]+=itImage.Get()[comp];
}
count++;
unsigned int progress = (count*100)/(nbTilesX*nbTilesY);
std::cout<<"\rSums calculation ("<<progress<<"%) [";
for(unsigned int add=0;add<(progress*nbStars)/100;add++)
std::cout<<"*";
for(unsigned int add=(progress*nbStars)/100;add<nbStars;add++)
std::cout<<" ";
std::cout<<"]"<<std::flush;
}
std::cout<<std::endl;
unsigned long startX = column*sizeTilesX;
unsigned long startY = row*sizeTilesY;
unsigned long sizeX = vcl_min(sizeTilesX,sizeImageX-startX);
unsigned long sizeY = vcl_min(sizeTilesY,sizeImageY-startY);
//Tiles extraction of the input image
MultiChannelExtractROIFilterType::Pointer imageROI = MultiChannelExtractROIFilterType::New();
imageROI->SetInput(imageIn);
imageROI->SetStartX(startX);
imageROI->SetStartY(startY);
imageROI->SetSizeX(sizeX);
imageROI->SetSizeY(sizeY);
imageROI->Update();
//Tiles extraction of the segmented image
ExtractROIFilterType::Pointer labelImageROI = ExtractROIFilterType::New();
labelImageROI->SetInput(labelIn);
labelImageROI->SetStartX(startX);
labelImageROI->SetStartY(startY);
labelImageROI->SetSizeX(sizeX);
labelImageROI->SetSizeY(sizeY);
labelImageROI->Update();
//Sums calculation for the mean calculation per label
LabelImageIterator itLabel( labelImageROI->GetOutput(), labelImageROI->GetOutput()->GetLargestPossibleRegion());
ImageIterator itImage( imageROI->GetOutput(), imageROI->GetOutput()->GetLargestPossibleRegion());
for (itLabel.GoToBegin(), itImage.GoToBegin(); !itLabel.IsAtEnd(); ++itLabel, ++itImage)
{
nbPixels[itLabel.Value()]++;
for(unsigned int comp = 0; comp<numberOfComponentsPerPixel; ++comp)
{
sum[itLabel.Value()][comp]+=itImage.Get()[comp];
}
}
}
//LUT creation for the final relabelling
std::vector<LabelImagePixelType> LUT;
LUT.clear();
LUT.resize(regionCount+1);
for(LabelImagePixelType curLabel = 1; curLabel <= regionCount; ++curLabel)
{
LUT[curLabel] = curLabel;
std::cout<<"Region suppression (0%) [";
for(unsigned int add=0;add<nbStars;add++)
std::cout<<" ";
std::cout<<"]"<<std::flush;
count=0;
}
//Minimal size region suppression
for (int size=1;size<minSize;size++)
otbAppLogINFO(<<"Building LUT for small regions merging ...");
for (unsigned int size=1;size<minSize;size++)
{
//LUTtmp creation in order to modify the LUT only at the end of the pass
std::vector<LabelImagePixelType> LUTtmp;
LUTtmp.clear();
LUTtmp.resize(regionCount+1);
for(LabelImagePixelType curLabel = 1; curLabel <= regionCount; ++curLabel)
LUTtmp[curLabel] = LUT[curLabel];
for(unsigned int row = 0; row < nbTilesY ; row++)
for(unsigned int column = 0; column < nbTilesX ; column++)
{
std::set<int> minLabel, edgeLabel, labelMerged;
std::map<int,std::set<int> > adjMap;
unsigned long startX = column*sizeTilesX, startY = row*sizeTilesY;
unsigned long sizeX = vcl_min(sizeTilesX+size+1,sizeImageX-startX),
sizeY = vcl_min(sizeTilesY+size+1,sizeImageY-startY);
ExtractROIFilterType::Pointer labelImageROI = ExtractROIFilterType::New();
labelImageROI->SetInput(labelIn);
labelImageROI->SetStartX(startX);
labelImageROI->SetStartY(startY);
labelImageROI->SetSizeX(sizeX);
labelImageROI->SetSizeY(sizeY);
labelImageROI->Update();
LabelImageType::IndexType pixelIndex; pixelIndex[0]=0;pixelIndex[1]=0;
long &i = pixelIndex[0], &j = pixelIndex[1];
//"Adjacency map" creation for the region with nbPixels=="size"
for(i=0;i<sizeX;i++)
for(j=0;j<sizeY;j++)
{
LabelImagePixelType curLabel = labelImageROI->GetOutput()->GetPixel(pixelIndex);
if(labelMerged.count(LUT[curLabel])) edgeLabel.insert(LUT[curLabel]);
if((i==0)&&(startX!=0)) edgeLabel.insert(LUT[curLabel]);
if((j==0)&&(startY!=0)) edgeLabel.insert(LUT[curLabel]);
if(i==sizeX-1){if(startX!=(nbTilesX-1)*sizeTilesX) edgeLabel.insert(LUT[curLabel]);}
else{
i++;LabelImagePixelType adjLabelX = labelImageROI->GetOutput()->GetPixel(pixelIndex);i--;
if(LUT[adjLabelX]!=LUT[curLabel])
{
if((nbPixels[LUT[curLabel]]>0)&&(nbPixels[LUT[curLabel]]==size))
{adjMap[LUT[curLabel]].insert(LUT[adjLabelX]);minLabel.insert(LUT[curLabel]);}
if((nbPixels[LUT[adjLabelX]]>0)&&(nbPixels[LUT[adjLabelX]]==size))
{adjMap[LUT[adjLabelX]].insert(LUT[curLabel]);minLabel.insert(LUT[adjLabelX]);}
}}
if(j==sizeY-1){if(startY!=(nbTilesY-1)*sizeTilesY) edgeLabel.insert(LUT[curLabel]);}
else{
j++;LabelImagePixelType adjLabelY = labelImageROI->GetOutput()->GetPixel(pixelIndex);j--;
if(LUT[adjLabelY]!=LUT[curLabel])
{
if((nbPixels[LUT[curLabel]]>0)&&(nbPixels[LUT[curLabel]]==size))
{adjMap[LUT[curLabel]].insert(LUT[adjLabelY]);minLabel.insert(LUT[curLabel]);}
if((nbPixels[LUT[adjLabelY]]>0)&&(nbPixels[LUT[adjLabelY]]==size))
{adjMap[LUT[adjLabelY]].insert(LUT[curLabel]);minLabel.insert(LUT[adjLabelY]);}
}}
}
//Searching the "nearest" region
for (std::set<int>::iterator itMinLabel=minLabel.begin(); itMinLabel!=minLabel.end(); ++itMinLabel)
{
LabelImagePixelType curLabel = *itMinLabel, adjLabel, err = INT_MAX;
if(edgeLabel.count(curLabel)==0){
if(nbPixels[curLabel]==size){
edgeLabel.insert(curLabel);
for (std::set<int>::iterator itAdjLabel=adjMap[curLabel].begin(); itAdjLabel!=adjMap[curLabel].end(); ++itAdjLabel)
{
int tmpError = 0; LabelImagePixelType tmpLabel = *itAdjLabel;
if(tmpLabel!=curLabel){
for(unsigned int comp = 0; comp<numberOfComponentsPerPixel; ++comp)
{
int curComp = sum[curLabel][comp]/nbPixels[curLabel];
int tmpComp = sum[tmpLabel][comp]/nbPixels[tmpLabel];
tmpError += (curComp-tmpComp)*(curComp-tmpComp);
}
if(tmpError<err)
{
err = tmpError;
adjLabel = tmpLabel;
}}
}
// LUTtmp creation in order to modify the LUT only at the end of the pass
std::vector<LabelImagePixelType> LUTtmp;
LUTtmp.clear();
LUTtmp.resize(regionCount+1);
for(LabelImagePixelType curLabel = 1; curLabel <= regionCount; ++curLabel)
{
LUTtmp[curLabel] = LUT[curLabel];
}
for(unsigned int row = 0; row < nbTilesY ; row++)
{
for(unsigned int column = 0; column < nbTilesX ; column++)
{
std::set<int> minLabel, edgeLabel, labelMerged;
std::map<int,std::set<int> > adjMap;
unsigned long startX = column*sizeTilesX, startY = row*sizeTilesY;
unsigned long sizeX = vcl_min(sizeTilesX+size+1,sizeImageX-startX),
sizeY = vcl_min(sizeTilesY+size+1,sizeImageY-startY);
ExtractROIFilterType::Pointer labelImageROI = ExtractROIFilterType::New();
labelImageROI->SetInput(labelIn);
labelImageROI->SetStartX(startX);
labelImageROI->SetStartY(startY);
labelImageROI->SetSizeX(sizeX);
labelImageROI->SetSizeY(sizeY);
labelImageROI->Update();
LabelImageType::IndexType pixelIndex;
//"Adjacency map" creation for the region with nbPixels=="size"
for(pixelIndex[0]=0;pixelIndex[0]<static_cast<long>(sizeX);++pixelIndex[0])
for(pixelIndex[1]=0;pixelIndex[1]<static_cast<long>(sizeY);++pixelIndex[1])
{
LabelImagePixelType curLabel = labelImageROI->GetOutput()->GetPixel(pixelIndex);
if(labelMerged.count(LUT[curLabel]))
{
edgeLabel.insert(LUT[curLabel]);
}
if((pixelIndex[0]==0)&&(startX!=0))
{
edgeLabel.insert(LUT[curLabel]);
}
if((pixelIndex[1]==0)&&(startY!=0))
{
edgeLabel.insert(LUT[curLabel]);
}
if(pixelIndex[0]==static_cast<long>(sizeX)-1)
{
if(startX!=(nbTilesX-1)*sizeTilesX) edgeLabel.insert(LUT[curLabel]);
}
else
{
++pixelIndex[0];
LabelImagePixelType adjLabelX = labelImageROI->GetOutput()->GetPixel(pixelIndex);
--pixelIndex[0];
if(LUT[adjLabelX]!=LUT[curLabel])
{
if((nbPixels[LUT[curLabel]]>0)&&(nbPixels[LUT[curLabel]]==size))
{
adjMap[LUT[curLabel]].insert(LUT[adjLabelX]);
minLabel.insert(LUT[curLabel]);
}
if((nbPixels[LUT[adjLabelX]]>0)&&(nbPixels[LUT[adjLabelX]]==size))
{
adjMap[LUT[adjLabelX]].insert(LUT[curLabel]);
minLabel.insert(LUT[adjLabelX]);
}
}
}
if(pixelIndex[1]==static_cast<long>(sizeY)-1)
{
if(startY!=(nbTilesY-1)*sizeTilesY) edgeLabel.insert(LUT[curLabel]);
}
else
{
++pixelIndex[1];
LabelImagePixelType adjLabelY = labelImageROI->GetOutput()->GetPixel(pixelIndex);
--pixelIndex[1];
if(LUT[adjLabelY]!=LUT[curLabel])
{
if((nbPixels[LUT[curLabel]]>0)&&(nbPixels[LUT[curLabel]]==size))
{
adjMap[LUT[curLabel]].insert(LUT[adjLabelY]);
minLabel.insert(LUT[curLabel]);
}
if((nbPixels[LUT[adjLabelY]]>0)&&(nbPixels[LUT[adjLabelY]]==size))
{
adjMap[LUT[adjLabelY]].insert(LUT[curLabel]);
minLabel.insert(LUT[adjLabelY]);}
}
}
}
//Searching the "nearest" region
for(std::set<int>::iterator itMinLabel=minLabel.begin(); itMinLabel!=minLabel.end(); ++itMinLabel)
{
LabelImagePixelType curLabel = *itMinLabel, adjLabel;
double err = itk::NumericTraits<double>::max();
if(edgeLabel.count(curLabel)==0)
{
if(nbPixels[curLabel]==size)
{
edgeLabel.insert(curLabel);
for(std::set<int>::iterator itAdjLabel=adjMap[curLabel].begin();
itAdjLabel!=adjMap[curLabel].end(); ++itAdjLabel)
{
double tmpError = 0;
LabelImagePixelType tmpLabel = *itAdjLabel;
if(tmpLabel!=curLabel)
{
for(unsigned int comp = 0; comp<numberOfComponentsPerPixel; ++comp)
{
double curComp = static_cast<double>(sum[curLabel][comp])/nbPixels[curLabel];
int tmpComp = static_cast<double>(sum[tmpLabel][comp])/nbPixels[tmpLabel];
tmpError += (curComp-tmpComp)*(curComp-tmpComp);
}
if(tmpError<err)
{
err = tmpError;
adjLabel = tmpLabel;
}
}
}
//Fusion of the two regions
if(adjLabel!=curLabel){
int curLabelLUT = curLabel, adjLabelLUT = adjLabel;
while(LUTtmp[curLabelLUT] != curLabelLUT) curLabelLUT = LUTtmp[curLabelLUT];
while(LUTtmp[adjLabelLUT] != adjLabelLUT) adjLabelLUT = LUTtmp[adjLabelLUT];
if(curLabelLUT < adjLabelLUT) LUTtmp[adjLabelLUT] = curLabelLUT;
else{LUTtmp[LUTtmp[curLabelLUT]] = adjLabelLUT; LUTtmp[curLabelLUT] = adjLabelLUT;}}
}}
}
//Fusion of the two regions
if(adjLabel!=curLabel)
{
unsigned int curLabelLUT = curLabel, adjLabelLUT = adjLabel;
while(LUTtmp[curLabelLUT] != curLabelLUT)
{
curLabelLUT = LUTtmp[curLabelLUT];
}
while(LUTtmp[adjLabelLUT] != adjLabelLUT)
{
adjLabelLUT = LUTtmp[adjLabelLUT];
}
if(curLabelLUT < adjLabelLUT)
{
LUTtmp[adjLabelLUT] = curLabelLUT;
}
else
{
LUTtmp[LUTtmp[curLabelLUT]] = adjLabelLUT; LUTtmp[curLabelLUT] = adjLabelLUT;
}
}
}
}
}
for(LabelImagePixelType label = 1; label < regionCount+1; ++label)
{
LabelImagePixelType can = label;
while(LUTtmp[can] != can) can = LUTtmp[can];
LUTtmp[label] = can;
}
}
for(LabelImagePixelType label = 1; label < regionCount+1; ++label)
{
LabelImagePixelType can = label;
while(LUTtmp[can] != can)
{
can = LUTtmp[can];
}
LUTtmp[label] = can;
}
}
}
for(LabelImagePixelType label = 1; label < regionCount+1; ++label)
{
LUT[label]=LUTtmp[label];
if((nbPixels[label]!=0)&&(LUT[label]!=label))
{
nbPixels[LUT[label]]+=nbPixels[label];
nbPixels[label]=0;
for(unsigned int comp = 0; comp<numberOfComponentsPerPixel; ++comp)
sum[LUT[label]][comp]+=sum[label][comp];
}
}
unsigned int progress = (size*100)/(minSize-1);
std::cout<<"\rRegion suppression ("<<progress<<"%) [";
for(unsigned int add=0;add<(progress*nbStars)/100;add++)
std::cout<<"*";
for(unsigned int add=(progress*nbStars)/100;add<nbStars;add++)
std::cout<<" ";
std::cout<<"]"<<std::flush;
for(LabelImagePixelType label = 1; label < regionCount+1; ++label)
{
LUT[label]=LUTtmp[label];
if((nbPixels[label]!=0)&&(LUT[label]!=label))
{
nbPixels[LUT[label]]+=nbPixels[label];
nbPixels[label]=0;
for(unsigned int comp = 0; comp<numberOfComponentsPerPixel; ++comp)
{
sum[LUT[label]][comp]+=sum[label][comp];
}
}
}
}
std::cout<<std::endl;
//Relabelling
ChangeLabelImageFilterType::Pointer changeLabel = ChangeLabelImageFilterType::New();
changeLabel->SetInput(labelIn);
m_ChangeLabelFilter = ChangeLabelImageFilterType::New();
m_ChangeLabelFilter->SetInput(labelIn);
for(LabelImagePixelType label = 1;label<regionCount+1; ++label)
if(label!=LUT[label]) changeLabel->SetChange(label,LUT[label]);
changeLabel->Update();
SetParameterOutputImage("out", changeLabel->GetOutput());
{
if(label!=LUT[label])
{
m_ChangeLabelFilter->SetChange(label,LUT[label]);
}
}
clock_t toc = clock();
SetParameterOutputImage("out", m_ChangeLabelFilter->GetOutput());
printf("Elapsed: %f seconds\n", (double)(toc - tic) / CLOCKS_PER_SEC);
clock_t toc = clock();
otbAppLogINFO(<<"Elapsed time: "<<(double)(toc - tic) / CLOCKS_PER_SEC<<" seconds");
}
};
}
}
......
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