diff --git a/Modules/Applications/AppSegmentation/app/otbSmallRegionsMerging.cxx b/Modules/Applications/AppSegmentation/app/otbSmallRegionsMerging.cxx
index 4112c9da433f7c10337368dbd75a6fa64800a97d..1693322743508d869f31ad8e5019a5b95650ee30 100644
--- a/Modules/Applications/AppSegmentation/app/otbSmallRegionsMerging.cxx
+++ b/Modules/Applications/AppSegmentation/app/otbSmallRegionsMerging.cxx
@@ -45,12 +45,14 @@ public:
typedef UInt32ImageType LabelImageType;
typedef LabelImageType::InternalPixelType LabelImagePixelType;
- //typedef otb::StreamingStatisticsImageFilter<LabelImageType> StatisticsImageFilterType;
- typedef otb::StreamingStatisticsMapFromLabelImageFilter<ImageType, LabelImageType> StatisticsMapFromLabelImageFilterType;
+ typedef otb::StreamingStatisticsMapFromLabelImageFilter
+ <ImageType, LabelImageType> StatisticsMapFromLabelImageFilterType;
- typedef otb::LabelImageSmallRegionMergingFilter<LabelImageType> LabelImageSmallRegionMergingFilterType;
+ typedef otb::LabelImageSmallRegionMergingFilter<LabelImageType>
+ LabelImageSmallRegionMergingFilterType;
- typedef itk::ChangeLabelImageFilter<LabelImageType,LabelImageType> ChangeLabelImageFilterType;
+ typedef itk::ChangeLabelImageFilter<LabelImageType,LabelImageType>
+ ChangeLabelImageFilterType;
itkNewMacro(Self);
itkTypeMacro(Merging, otb::Application);
@@ -61,34 +63,43 @@ private:
void DoInit() override
{
SetName("SmallRegionsMerging");
- SetDescription("This application merges small regions of a segmentation result to connected region.");
+ SetDescription("This application merges small regions of a segmentation "
+ "result to connected region.");
SetDocName("Small Region Merging");
- SetDocLongDescription("Given a segmentation result and the original image, it will"
- " merge segments whose size in pixels is lower than minsize parameter"
- " with the adjacent segments with the adjacent segment with closest"
- " radiometry and acceptable size.\n\n"
- "Small segments will be processed by increasing size: first all segments"
- " for which area is equal to 1 pixel will be merged with adjacent"
- " segments, then all segments of area equal to 2 pixels will be processed,"
- " until segments of area minsize.");
+ SetDocLongDescription("Given a segmentation result and the original image,"
+ " it will merge segments whose size in pixels is"
+ " lower than minsize parameter with the adjacent"
+ " segments with the adjacent segment with closest"
+ " radiometry and acceptable size. \n\n"
+ "Small segments will be processed by increasing size:"
+ " first all segments for which area is equal to 1"
+ " pixel will be merged with adjacent segments, then"
+ " all segments of area equal to 2 pixels will be"
+ " processed, until segments of area minsize.");
- SetDocLimitations("This application is more efficient if the labels are contiguous, starting from 0.");
SetDocAuthors("OTB-Team");
- SetDocSeeAlso( "Segmentation");
+ SetDocSeeAlso("Segmentation");
AddDocTag(Tags::Segmentation);
AddParameter(ParameterType_InputImage, "in", "Input image");
- SetParameterDescription( "in", "The input image, containing initial spectral signatures corresponding to the segmented image (inseg)." );
- AddParameter(ParameterType_InputImage, "inseg", "Segmented image");
- SetParameterDescription( "inseg", "Segmented image where each pixel value is the unique integer label of the segment it belongs to." );
+ SetParameterDescription( "in", "The input image, containing initial"
+ " spectral signatures corresponding to the segmented image (inseg)." );
+ AddParameter(ParameterType_InputImage, "inseg", "Segmented image");
+ SetParameterDescription( "inseg", "Segmented image where each pixel value"
+ " is the unique integer label of the segment it belongs to." );
AddParameter(ParameterType_OutputImage, "out", "Output Image");
- SetParameterDescription( "out", "The output image. The output image is the segmented image where the minimal segments have been merged." );
+ SetParameterDescription( "out", "The output image. The output image is the"
+ " segmented image where the minimal segments have been merged." );
SetDefaultOutputPixelType("out",ImagePixelType_uint32);
AddParameter(ParameterType_Int, "minsize", "Minimum Segment Size");
- SetParameterDescription("minsize", "Minimum Segment Size. If, after the segmentation, a segment is of size strictly lower than this criterion, the segment is merged with the segment that has the closest sepctral signature.");
+ SetParameterDescription("minsize", "Minimum Segment Size. If, after the "
+ " segmentation, a segment is of size strictly lower than this criterion,"
+ " the segment is merged with the segment that has the closest sepctral"
+ " signature.");
+
SetDefaultParameterInt("minsize", 50);
SetMinimumParameterIntValue("minsize", 1);
MandatoryOff("minsize");
@@ -123,7 +134,8 @@ private:
auto labelStatsFilter = StatisticsMapFromLabelImageFilterType::New();
labelStatsFilter->SetInput(imageIn);
labelStatsFilter->SetInputLabelImage(labelIn);
- AddProcess(labelStatsFilter->GetStreamer() , "Computing stats on input image ...");
+ AddProcess(labelStatsFilter->GetStreamer() , "Computing stats on input"
+ " image ...");
labelStatsFilter->Update();
// Convert Map to Unordered map
@@ -135,18 +147,19 @@ private:
labelPopulation[population.first]=population.second;
}
auto meanValueMap = labelStatsFilter->GetMeanValueMap();
- std::unordered_map< unsigned int, itk::VariableLengthVector<double> > meanValues;
+ std::unordered_map< unsigned int, itk::VariableLengthVector<double> >
+ meanValues;
for (const auto & mean : meanValueMap)
{
meanValues[mean.first] = mean.second;
}
- // Compute the LUT from the original label image to the merged output label image.
+ // Compute the LUT from the original label image to the merged output
+ // label image.
auto regionMergingFilter = LabelImageSmallRegionMergingFilterType::New();
regionMergingFilter->SetInputLabelImage( labelIn );
regionMergingFilter->SetLabelPopulation( labelPopulation );
regionMergingFilter->SetLabelStatistic( meanValues );
-
regionMergingFilter->SetMinSize( minSize);
AddProcess(regionMergingFilter, "Computing LUT ...");
@@ -168,7 +181,8 @@ private:
SetParameterOutputImage("out", changeLabelFilter->GetOutput());
RegisterPipeline();
clock_t toc = clock();
- otbAppLogINFO(<<"Elapsed time: "<<(double)(toc - tic) / CLOCKS_PER_SEC<<" seconds");
+ otbAppLogINFO(<<"Elapsed time: "<<(double)(toc - tic) / CLOCKS_PER_SEC<<
+ " seconds");
}
};
diff --git a/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.h b/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.h
index 66efb3c2cc351e44ae1f88ba179b0788cd55727e..fbfe93479119827fb6fd252b4112b6ebc00d196a 100644
--- a/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.h
+++ b/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.h
@@ -32,15 +32,17 @@ namespace otb
/** \class PersistentLabelImageSmallRegionMergingFilter
*
- * This class can be used to merge each segments of a given size in a label image to
- * the connected segment with the closest radiometry.
- * This persistent filter should be used as template parameter of a PersistentFilterStreamingDecorator
+ * This class can be used to merge each segments of a given size in a label
+ * image to the connected segment with the closest radiometry (in the sense of
+ * the euclidian squared distance).
+ * This persistent filter should be used as template parameter of a
+ * PersistentFilterStreamingDecorator.
* It computes from an input label image an equivalence table
* that gives for each pixel, the corresponding label in the merged image.
* The merged image can then be computed using a ChangeLabelImageFilter.
*
- * This filter can be updated several times for different values of size, the output
- * equivalence table will be the results of all computations.
+ * This filter can be updated several times for different values of size,
+ * the output equivalence table will be the results of all computations.
*
* \ingroup ImageSegmentation
*
@@ -52,13 +54,14 @@ class PersistentLabelImageSmallRegionMergingFilter
{
public:
/** Standard class typedef */
- typedef PersistentLabelImageSmallRegionMergingFilter Self;
- typedef PersistentImageFilter<TInputLabelImage, TInputLabelImage> Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef PersistentLabelImageSmallRegionMergingFilter Self;
+ typedef PersistentImageFilter<TInputLabelImage, TInputLabelImage> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
/** Type macro */
- itkTypeMacro(PersistentLabelImageSmallRegionMergingFilter, PersistentImageFilter);
+ itkTypeMacro(PersistentLabelImageSmallRegionMergingFilter,
+ PersistentImageFilter);
itkNewMacro(Self);
/** Template parameters typedefs */
@@ -70,13 +73,16 @@ public:
typedef typename InputImageType::PointType PointType;
typedef typename InputImageType::RegionType RegionType;
- typedef itk::VariableLengthVector<double> RealVectorPixelType;
+ typedef itk::VariableLengthVector<double> RealVectorPixelType;
- typedef std::unordered_map<InputLabelType, std::set<InputLabelType> > NeigboursMapType;
+ typedef std::unordered_map<InputLabelType, std::set<InputLabelType> >
+ NeigboursMapType;
- typedef std::unordered_map<InputLabelType , RealVectorPixelType > LabelStatisticType;
- typedef std::unordered_map<InputLabelType , double> LabelPopulationType;
- typedef std::unordered_map<InputLabelType , InputLabelType> LUTType;
+ typedef std::unordered_map<InputLabelType , RealVectorPixelType >
+ LabelStatisticType;
+ typedef std::unordered_map<InputLabelType , double>
+ LabelPopulationType;
+ typedef std::unordered_map<InputLabelType , InputLabelType> LUTType;
/** Set/Get size of segments to be merged */
itkGetMacro(Size , unsigned int);
@@ -122,16 +128,18 @@ public:
virtual void Synthetize(void) override;
protected:
- /** The input requested region should be padded by a radius of 1 to use the neigbourhood iterator*/
+ /** The input requested region should be padded by a radius of 1 to use the
+ * neigbourhood iterator */
void GenerateInputRequestedRegion() override;
- /** Threaded Generate Data : find the neighbours of each segments of size m_Size for each tile and store them in
- * an accumulator */
+ /** Threaded Generate Data : find the neighbours of each segments of size
+ * m_Size for each tile and store them in an accumulator */
void ThreadedGenerateData(const RegionType&
outputRegionForThread, itk::ThreadIdType threadId) override;
- // Use the LUT recursively to find the label corresponding to the input label
+ /** Use the LUT recursively to find the label corresponding to the input
+ * label */
InputLabelType FindCorrespondingLabel( InputLabelType label);
/** Constructor */
@@ -150,27 +158,30 @@ private:
/** Size of the segments to be merged */
unsigned int m_Size;
- /** Vector containing at position i the population of the segment labelled i */
+ /** Map containing at key i the population of the segment labelled i */
LabelPopulationType m_LabelPopulation;
- /** Vector containing at position i the population of mean of element of the segment labelled i*/
+ /** Map containing at key i the mean of element of the segment labelled i */
LabelStatisticType m_LabelStatistic;
/** Neigbours maps for each thread */
std::vector <NeigboursMapType > m_NeighboursMapsTmp;
- /** LUT giving correspondance between labels in the original segmentation and the merged labels */
+ /** LUT giving correspondance between labels in the original segmentation
+ * and the merged labels */
LUTType m_LUT;
};
/** \class LabelImageSmallRegionMergingFilter
*
- * This filter computes from a label image an equivalence table that gives for each pixel,
- * the corresponding label in the merged image.
- * It uses a PersistentFilterStreamingDecorator templated over a PersistentLabelImageSmallRegionMergingFilter
- * to merge the segments recursively from segment of size 1 to segment of a sized specified
- * by a parameter.
- * The merged image can then be computed using a ChangeLabelImageFilterType.
+ * This filter computes from a label image an equivalence table that gives for
+ * each pixel, the corresponding label in the merged image. It uses a
+ * PersistentFilterStreamingDecorator templated over a
+ * PersistentLabelImageSmallRegionMergingFilter
+ * to merge the segments recursively from segment of size 1 to segment of a
+ * size specified by the attribute MinSize.
+ * The equivalence table can be accessed with the method GetLut and used to
+ * compute the merged image with a ChangeLabelImageFilterType.
*
* \ingroup ImageSegmentation
*
@@ -182,10 +193,10 @@ class ITK_EXPORT LabelImageSmallRegionMergingFilter
{
public:
/** Standard Self typedef */
- typedef LabelImageSmallRegionMergingFilter Self;
- typedef itk::ProcessObject Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef LabelImageSmallRegionMergingFilter Self;
+ typedef itk::ProcessObject Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
/** Type macro */
itkNewMacro(Self);
@@ -194,12 +205,20 @@ public:
itkTypeMacro(LabelImageSmallRegionMergingFilter, itk::ProcessObject);
// Small region merging filter typedefs
- typedef PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage > PersistentLabelImageSmallRegionMergingFilterType;
- typedef PersistentFilterStreamingDecorator < PersistentLabelImageSmallRegionMergingFilterType > LabelImageSmallRegionMergingFilterType;
+ typedef PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+ PersistentLabelImageSmallRegionMergingFilterType;
+ typedef PersistentFilterStreamingDecorator
+ < PersistentLabelImageSmallRegionMergingFilterType >
+ LabelImageSmallRegionMergingFilterType;
- typedef typename PersistentLabelImageSmallRegionMergingFilterType::LabelPopulationType LabelPopulationType;
- typedef typename PersistentLabelImageSmallRegionMergingFilterType::LabelStatisticType LabelStatisticType;
- typedef typename PersistentLabelImageSmallRegionMergingFilterType::LUTType LUTType;
+ typedef typename PersistentLabelImageSmallRegionMergingFilterType
+ ::LabelPopulationType LabelPopulationType;
+
+ typedef typename PersistentLabelImageSmallRegionMergingFilterType
+ ::LabelStatisticType LabelStatisticType;
+
+ typedef typename PersistentLabelImageSmallRegionMergingFilterType::LUTType
+ LUTType;
/** Set/Get size of polygon to be merged */
@@ -215,7 +234,8 @@ public:
/** Set the Label population map */
void SetLabelPopulation( LabelPopulationType const & labelPopulation )
{
- m_SmallRegionMergingFilter->GetFilter()->SetLabelPopulation( labelPopulation );
+ m_SmallRegionMergingFilter->GetFilter()
+ ->SetLabelPopulation(labelPopulation);
}
/** Get the Label population map */
@@ -227,11 +247,11 @@ public:
/** Set the Label statistic map */
void SetLabelStatistic( LabelStatisticType const & labelStatistic )
{
- m_SmallRegionMergingFilter->GetFilter()->SetLabelStatistic( labelStatistic );
+ m_SmallRegionMergingFilter->GetFilter()->SetLabelStatistic(labelStatistic);
}
/** Get the Label statistic map */
- LabelStatisticType const & GetLabelStatistic( ) const
+ LabelStatisticType const & GetLabelStatistic() const
{
return m_SmallRegionMergingFilter->GetFilter()->GetLabelStatistic();
}
@@ -250,14 +270,19 @@ protected:
/** Destructor */
~LabelImageSmallRegionMergingFilter() override = default;
- /** Generate Data method (Update LabelImageSmallRegionMergingFilterType recursively) */
+ /** Generate Data method (Update LabelImageSmallRegionMergingFilterType
+ * recursively) */
void GenerateData() override;
private:
LabelImageSmallRegionMergingFilter(const Self &) = delete;
void operator =(const Self&) = delete;
- typename LabelImageSmallRegionMergingFilterType::Pointer m_SmallRegionMergingFilter;
+ // Filter used recursively to build the equivalence table
+ typename
+ LabelImageSmallRegionMergingFilterType::Pointer m_SmallRegionMergingFilter;
+
+ // All segments with size < m_MinSize will be merged to bigger segments.
unsigned int m_MinSize;
};
diff --git a/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.hxx b/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.hxx
index 6cabcbaf2ccca334ebd98e19fdb3896fccf27a51..57abb541ba2bbd25e172cbe0dd2af61f0c25e14f 100644
--- a/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.hxx
+++ b/Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.hxx
@@ -49,17 +49,21 @@ PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
::Synthetize()
{
NeigboursMapType neighboursMap;
+
// Merge the neighbours maps from all threads
- for( unsigned int threadId = 0; threadId < this->GetNumberOfThreads(); threadId++)
+ for( unsigned int threadId = 0; threadId < this->GetNumberOfThreads();
+ threadId++)
{
for (auto const & neighbours : m_NeighboursMapsTmp[threadId])
{
- neighboursMap[ neighbours.first ].insert( neighbours.second.begin(), neighbours.second.end() );
+ neighboursMap[ neighbours.first ].insert
+ ( neighbours.second.begin(), neighbours.second.end() );
}
}
- // For each label of the label map, find the "closest" connected label, according
- // to the euclidian distance between the corresponding m_labelStatistic elements.
+ // For each label of the label map, find the "closest" connected label,
+ // according to the euclidian distance between the corresponding
+ // m_labelStatistic elements.
for (auto const & neighbours : neighboursMap)
{
double proximity = itk::NumericTraits<double>::max();
@@ -82,6 +86,8 @@ PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
auto curLabelLUT = FindCorrespondingLabel(label);
auto adjLabelLUT = FindCorrespondingLabel(closestNeighbour);
+ // Keep the smallest label (this prevents infinite loop in the LUT
+ // (like LUT[i]=j and LUT[j]=i)
if(curLabelLUT < adjLabelLUT)
{
m_LUT[adjLabelLUT] = curLabelLUT;
@@ -98,24 +104,31 @@ PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
label.second = FindCorrespondingLabel( label.first );
}
- // Update statistics
+ // Update statistics : for each newly merged segments, sum the population, and
+ // recompute the mean.
for (auto label : m_LUT)
{
if((m_LabelPopulation[label.first]!=0) && (label.second != label.first))
{
- m_LabelStatistic[ label.second ] = (m_LabelStatistic[label.second]*m_LabelPopulation[label.second] +
- m_LabelStatistic[label.first]*m_LabelPopulation[label.first] ) / (m_LabelPopulation[label.first]+m_LabelPopulation[label.second]);
+ m_LabelStatistic[ label.second ] =
+ ( m_LabelStatistic[label.first]*m_LabelPopulation[label.first]
+ + m_LabelStatistic[label.second]*m_LabelPopulation[label.second] )
+ / (m_LabelPopulation[label.first]+m_LabelPopulation[label.second]);
+
m_LabelPopulation[ label.second ] += m_LabelPopulation[ label.first ] ;
+
+ // Do not use this label anymore
m_LabelPopulation[ label.first ] = 0;
}
}
}
template <class TInputLabelImage >
-typename PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >::InputLabelType
+typename PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+::InputLabelType
PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
-::FindCorrespondingLabel( typename PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
- ::InputLabelType label)
+::FindCorrespondingLabel( typename PersistentLabelImageSmallRegionMergingFilter
+ < TInputLabelImage >::InputLabelType label)
{
auto correspondingLabel = m_LUT[label];
while (label != correspondingLabel)
@@ -160,7 +173,8 @@ PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
// build an exception
itk::InvalidRequestedRegionError e(__FILE__, __LINE__);
e.SetLocation(ITK_LOCATION);
- e.SetDescription("Requested region is (at least partially) outside the largest possible region.");
+ e.SetDescription("Requested region is (at least partially) outside the "
+ "largest possible region.");
e.SetDataObject(inputPtr);
throw e;
}
@@ -170,10 +184,12 @@ PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
template <class TInputLabelImage >
void
PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
-::ThreadedGenerateData(const RegionType& outputRegionForThread, itk::ThreadIdType threadId )
+::ThreadedGenerateData(const RegionType& outputRegionForThread,
+ itk::ThreadIdType threadId )
{
using IteratorType = itk::ImageRegionConstIterator< TInputLabelImage >;
- using NeighborhoodIteratorType = itk::ConstShapedNeighborhoodIterator< TInputLabelImage >;
+ using NeighborhoodIteratorType =
+ itk::ConstShapedNeighborhoodIterator< TInputLabelImage >;
typename NeighborhoodIteratorType::RadiusType radius;
radius.Fill(1);
@@ -204,7 +220,7 @@ PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
{
int neighbourLabel = m_LUT[ ci.Get() ];
if (neighbourLabel != currentLabel)
- m_NeighboursMapsTmp[threadId][ currentLabel ].insert( neighbourLabel );
+ m_NeighboursMapsTmp[threadId][ currentLabel ].insert(neighbourLabel);
}
}
}