Merge branch 'small_region_merging' into 'develop'

Refactor small region merging

See merge request !233

Modules/Applications/AppSegmentation/app/CMakeLists.txt

@@ -57,3 +57,8 @@ otb_create_application(
   NAME           LargeScaleMeanShift
   SOURCES        otbLargeScaleMeanShift.cxx
   LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
+otb_create_application(
+  NAME           SmallRegionsMerging
+  SOURCES        otbSmallRegionsMerging.cxx
+  LINK_LIBRARIES ${${otb-module}_LIBRARIES})

Modules/Applications/AppSegmentation/app/otbLSMSSmallRegionsMerging.cxx

@@ -104,6 +104,7 @@ private:
                    "[2] LSMSegmentation\n"
                    "[3] LSMSVectorization");
     AddDocTag(Tags::Segmentation);
+    AddDocTag(Tags::Deprecated);
     AddDocTag("LSMS");
 
     AddParameter(ParameterType_InputImage,  "in",    "Input image");

Modules/Applications/AppSegmentation/app/otbLargeScaleMeanShift.cxx

@@ -86,7 +86,7 @@ private:
     ClearApplications();
     AddApplication("MeanShiftSmoothing", "smoothing", "Smoothing step");
     AddApplication("LSMSSegmentation", "segmentation", "Segmentation step");
-    AddApplication("LSMSSmallRegionsMerging", "merging", "Small region merging step");
+    AddApplication("SmallRegionsMerging", "merging", "Small region merging step");
     AddApplication("LSMSVectorization", "vectorization", "Vectorization step");
 
     ShareParameter("in","smoothing.in");
@@ -130,8 +130,6 @@ private:
     Connect("merging.ram","smoothing.ram");
     Connect("vectorization.ram","smoothing.ram");
 
-    Connect("merging.tilesizex","segmentation.tilesizex");
-    Connect("merging.tilesizey","segmentation.tilesizey");
     Connect("vectorization.tilesizex","segmentation.tilesizex");
     Connect("vectorization.tilesizey","segmentation.tilesizey");
 

Modules/Applications/AppSegmentation/app/otbSmallRegionsMerging.cxx

+/*
+ * Copyright (C) 2005-2017 Centre National d'Etudes Spatiales (CNES)
+ *
+ * This file is part of Orfeo Toolbox
+ *
+ *     https://www.orfeo-toolbox.org/
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#include "otbWrapperApplication.h"
+#include "otbWrapperApplicationFactory.h"
+
+#include "otbStreamingStatisticsMapFromLabelImageFilter.h"
+#include "otbLabelImageSmallRegionMergingFilter.h"
+#include "itkChangeLabelImageFilter.h"
+
+#include "otbStopwatch.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+class SmallRegionsMerging : public Application
+{
+public:
+  typedef SmallRegionsMerging Self;
+  typedef Application Superclass;
+  typedef itk::SmartPointer<Self> Pointer;
+  typedef itk::SmartPointer<const Self> ConstPointer;
+
+  typedef FloatVectorImageType              ImageType;
+  typedef ImageType::InternalPixelType      ImagePixelType;
+  typedef UInt32ImageType                   LabelImageType;
+  typedef LabelImageType::InternalPixelType LabelImagePixelType;
+
+  typedef otb::StreamingStatisticsMapFromLabelImageFilter
+      <ImageType, LabelImageType> StatisticsMapFromLabelImageFilterType;
+
+  typedef otb::LabelImageSmallRegionMergingFilter<LabelImageType> 
+                                  LabelImageSmallRegionMergingFilterType;
+
+  typedef itk::ChangeLabelImageFilter<LabelImageType,LabelImageType> 
+                                  ChangeLabelImageFilterType;
+ 
+  itkNewMacro(Self);
+  itkTypeMacro(Merging, otb::Application);
+
+private:
+  ChangeLabelImageFilterType::Pointer m_ChangeLabelFilter;
+
+  void DoInit() override
+  {
+    SetName("SmallRegionsMerging");
+    SetDescription("This application merges small regions of a segmentation "
+      "result.");
+
+    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.");
+    
+    SetDocLimitations( "None") ;
+    
+    SetDocAuthors("OTB-Team");
+    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." );
+
+    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." );
+    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.");
+    
+    SetDefaultParameterInt("minsize", 50);
+    SetMinimumParameterIntValue("minsize", 1);
+    MandatoryOff("minsize");
+
+    AddRAMParameter();
+
+    // Doc example parameter settings
+    SetDocExampleParameterValue("in","smooth.tif");
+    SetDocExampleParameterValue("inseg","segmentation.tif");
+    SetDocExampleParameterValue("out","merged.tif");
+    SetDocExampleParameterValue("minsize","50");
+
+    SetOfficialDocLink();
+  }
+
+  void DoUpdateParameters() override
+  {
+  }
+
+  void DoExecute() override
+  {
+    // Start Timer for the application
+    auto Timer = Stopwatch::StartNew();
+    
+    unsigned int minSize     = GetParameterInt("minsize");
+
+    //Acquisition of the input image dimensions
+    ImageType::Pointer imageIn = GetParameterImage("in");
+
+    LabelImageType::Pointer labelIn = GetParameterUInt32Image("inseg");
+
+    // Compute statistics for each segment
+    auto labelStatsFilter = StatisticsMapFromLabelImageFilterType::New();
+    labelStatsFilter->SetInput(imageIn);
+    labelStatsFilter->SetInputLabelImage(labelIn);
+    AddProcess(labelStatsFilter->GetStreamer() , "Computing stats on input"
+      " image ...");
+    labelStatsFilter->Update();
+
+    // Convert Map to Unordered map
+
+    auto  labelPopulationMap = labelStatsFilter->GetLabelPopulationMap();
+    std::unordered_map< unsigned int,double> labelPopulation;
+    for (auto population : labelPopulationMap)
+      {
+      labelPopulation[population.first]=population.second;
+      }
+    auto  meanValueMap = labelStatsFilter->GetMeanValueMap();
+    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.
+    auto regionMergingFilter = LabelImageSmallRegionMergingFilterType::New();
+    regionMergingFilter->SetInputLabelImage( labelIn );
+    regionMergingFilter->SetLabelPopulation( labelPopulation );
+    regionMergingFilter->SetLabelStatistic( meanValues );
+    regionMergingFilter->SetMinSize( minSize);
+    
+    AddProcess(regionMergingFilter, "Computing LUT ...");
+    regionMergingFilter->Update();
+    
+    // Relabelling using the LUT
+    auto changeLabelFilter = ChangeLabelImageFilterType::New();
+    changeLabelFilter->SetInput(labelIn);
+    
+    const auto & LUT = regionMergingFilter->GetLUT();
+
+    for (auto const & label : LUT)
+    {
+      if (label.first != label.second)
+      {
+        changeLabelFilter->SetChange(label.first, label.second);
+      }
+    }
+    SetParameterOutputImage("out", changeLabelFilter->GetOutput());
+    RegisterPipeline();
+
+    Timer.Stop();
+    otbAppLogINFO( "Total elapsed time: "<< 
+      float(Timer.GetElapsedMilliseconds())/1000 <<" seconds.");
+
+  }
+  
+};
+}
+}
+
+OTB_APPLICATION_EXPORT(otb::Wrapper::SmallRegionsMerging)
+
+

Modules/Applications/AppSegmentation/test/CMakeLists.txt

@@ -250,6 +250,20 @@ otb_test_application(NAME     apTvLSMS3SmallRegionsMerging
 
 set_property(TEST apTvLSMS3SmallRegionsMerging PROPERTY DEPENDS apTvLSMS2Segmentation)
 
+#----------- SmallRegionsMerging TESTS ----------------
+otb_test_application(NAME     apTvSmallRegionsMerging
+                     APP      SmallRegionsMerging
+                     OPTIONS  -in ${TEMP}/apTvLSMS1_filtered_range.tif
+                              -inseg  ${TEMP}/apTvLSMS2_Segmentation.tif
+                              -out ${TEMP}/apTvSmallMerged.tif uint32
+                              -minsize 10
+                     VALID    --compare-image ${NOTOL}
+                              ${BASELINE}/apTvSmallMerged.tif
+                              ${TEMP}/apTvSmallMerged.tif
+                     )
+                     
+set_property(TEST apTvSmallRegionsMerging PROPERTY DEPENDS apTvLSMS2Segmentation)
+
 #----------- LSMSVectorization TESTS ----------------
 otb_test_application(NAME     apTvLSMS4Vectorization_SmallMerged
                      APP      LSMSVectorization
@@ -308,3 +322,4 @@ otb_test_application(NAME     apTvSeLargeScaleMeanShiftTest
                               ${BASELINE_FILES}/apTvSeLargeScaleMeanShiftTestOut.shp
                               ${TEMP}/apTvSeLargeScaleMeanShiftTestOut.shp
                      )
+                     

Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.h

+/*
+ * Copyright (C) 2005-2017 Centre National d'Etudes Spatiales (CNES)
+ *
+ * This file is part of Orfeo Toolbox
+ *
+ *     https://www.orfeo-toolbox.org/
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#ifndef otbLabelImageSmallRegionMergingFilter_h
+#define otbLabelImageSmallRegionMergingFilter_h
+
+#include "otbPersistentImageFilter.h"
+#include "otbPersistentFilterStreamingDecorator.h"
+
+#include <unordered_map>
+
+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 (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.
+ *
+ * \ingroup ImageSegmentation
+ *
+ * \ingroup OTBConversion
+ */
+template <class TInputLabelImage>
+class ITK_EXPORT PersistentLabelImageSmallRegionMergingFilter
+  : public PersistentImageFilter<TInputLabelImage, TInputLabelImage>
+{
+public:
+  /** Standard class typedef */
+  typedef PersistentLabelImageSmallRegionMergingFilter               Self;
+  typedef PersistentImageFilter<TInputLabelImage, TInputLabelImage>  Superclass;
+  typedef itk::SmartPointer<Self>                                    Pointer;
+  typedef itk::SmartPointer<const Self>                            ConstPointer;
+
+  /** Type macro */
+  itkTypeMacro(PersistentLabelImageSmallRegionMergingFilter, 
+    PersistentImageFilter);
+  itkNewMacro(Self);
+
+  /** Template parameters typedefs */
+
+  typedef TInputLabelImage                        InputImageType;
+  typedef typename InputImageType::Pointer        InputImagePointerType;
+  typedef typename InputImageType::PixelType      InputLabelType;
+  typedef typename InputImageType::SizeType       InputSizeType;
+  typedef typename InputImageType::PointType      PointType;
+  typedef typename InputImageType::RegionType     RegionType;
+
+  typedef itk::VariableLengthVector<double>               RealVectorPixelType;
+  
+  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;
+  
+  /** Set/Get size of segments to be merged */
+  itkGetMacro(Size , unsigned int);
+  itkSetMacro(Size , unsigned int);
+
+  /** Set the Label population  and initialize the LUT */
+  void SetLabelPopulation( LabelPopulationType const & labelPopulation );
+
+  /** Get the Label population */
+  LabelPopulationType const & GetLabelPopulation() const;
+
+  /** Set the label statistic */
+  void SetLabelStatistic( LabelStatisticType const & labelStatistic );
+
+  /** Get the label statistic */
+  LabelStatisticType const & GetLabelStatistic() const;
+
+  /** Get the LUT */
+  LUTType const & GetLUT() const;
+
+  virtual void Reset(void) override;
+  virtual void Synthetize(void) override;
+
+protected:
+  /** 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 */ 
+  void ThreadedGenerateData(const RegionType&
+                outputRegionForThread, itk::ThreadIdType threadId) override;
+
+
+  /** Use the LUT recursively to find the label corresponding to the input 
+   * label */
+  InputLabelType FindCorrespondingLabel( InputLabelType label);
+
+  /** Constructor */
+  PersistentLabelImageSmallRegionMergingFilter();
+
+  /** Destructor */
+  ~PersistentLabelImageSmallRegionMergingFilter() override = default;
+
+  /** PrintSelf method */
+  void PrintSelf(std::ostream& os, itk::Indent indent) const override;
+
+private:
+  PersistentLabelImageSmallRegionMergingFilter(const Self &) = delete;
+  void operator =(const Self&) = delete;
+  
+  /** Size of the segments to be merged */
+  unsigned int m_Size;
+  
+  /** Map containing at key i the population of the segment labelled i */
+  LabelPopulationType m_LabelPopulation;
+  
+  /** 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 */
+  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 
+ * 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
+ *
+ * \ingroup OTBConversion
+ */
+template <class TInputLabelImage>
+class ITK_EXPORT LabelImageSmallRegionMergingFilter 
+  : public itk::ProcessObject
+{
+public:
+  /** Standard Self typedef */
+  typedef LabelImageSmallRegionMergingFilter                      Self;
+  typedef itk::ProcessObject                                      Superclass;
+  typedef itk::SmartPointer<Self>                                 Pointer;
+  typedef itk::SmartPointer<const Self>                           ConstPointer;
+
+  /** Type macro */
+  itkNewMacro(Self);
+
+  /** Creation through object factory macro */
+  itkTypeMacro(LabelImageSmallRegionMergingFilter, itk::ProcessObject);
+
+  // Small region merging filter typedefs
+  typedef PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage > 
+                            PersistentLabelImageSmallRegionMergingFilterType;
+  typedef PersistentFilterStreamingDecorator 
+    < PersistentLabelImageSmallRegionMergingFilterType >  
+                            LabelImageSmallRegionMergingFilterType;
+  
+  typedef typename PersistentLabelImageSmallRegionMergingFilterType
+    ::LabelPopulationType       LabelPopulationType;
+  
+  typedef typename PersistentLabelImageSmallRegionMergingFilterType
+    ::LabelStatisticType        LabelStatisticType;
+  
+  typedef typename PersistentLabelImageSmallRegionMergingFilterType::LUTType
+                                LUTType;
+  
+  
+  /** Set/Get size of polygon to be merged */
+  itkGetMacro(MinSize , unsigned int);
+  itkSetMacro(MinSize , unsigned int);
+
+  /** Set the Label population map */
+  void SetInputLabelImage( const TInputLabelImage * labelImage );
+  
+  /** Set the Label population map */
+  void SetLabelPopulation( LabelPopulationType const & labelPopulation );
+
+  /** Get the Label population map */
+  LabelPopulationType const & GetLabelPopulation() const;
+  
+  /** Set the Label statistic map */
+  void SetLabelStatistic( LabelStatisticType const & labelStatistic );
+  
+  /** Get the Label statistic map */
+  LabelStatisticType const & GetLabelStatistic() const;
+
+  /** Get the Label statistic map */
+  LUTType const & GetLUT() const;
+  
+  /** Call GenerateData() */
+  void Update() override;
+
+protected:
+  /** Constructor */
+  LabelImageSmallRegionMergingFilter();
+  /** Destructor */
+  ~LabelImageSmallRegionMergingFilter() override = default;
+
+  /** Generate Data method (Update LabelImageSmallRegionMergingFilterType 
+   * recursively) */
+  void GenerateData() override;
+  
+private:
+  LabelImageSmallRegionMergingFilter(const Self &) = delete;
+  void operator =(const Self&) = delete;
+
+  // 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;
+};
+
+} // end namespace otb
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include "otbLabelImageSmallRegionMergingFilter.hxx"
+#endif
+
+#endif

Modules/Segmentation/Conversion/include/otbLabelImageSmallRegionMergingFilter.hxx

+/*
+ * Copyright (C) 2005-2017 Centre National d'Etudes Spatiales (CNES)
+ *
+ * This file is part of Orfeo Toolbox
+ *
+ *     https://www.orfeo-toolbox.org/
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+#ifndef otbLabelImageSmallRegionMergingFilter_hxx
+#define otbLabelImageSmallRegionMergingFilter_hxx
+
+#include "otbLabelImageSmallRegionMergingFilter.h"
+#include "itkConstShapedNeighborhoodIterator.h"
+#include "itkProgressReporter.h"
+
+namespace otb
+{
+template <class TInputLabelImage >
+PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+::PersistentLabelImageSmallRegionMergingFilter() : m_Size(1)
+{
+}
+
+template <class TInputLabelImage >
+void
+PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+::SetLabelPopulation( LabelPopulationType const & labelPopulation )
+{
+  m_LabelPopulation = labelPopulation; 
+    
+  // Initialize m_CorrespondingMap to the identity (i.e. m[label] = label)
+  for (auto label : m_LabelPopulation)
+    {
+    m_LUT[label.first] = label.first;
+    }  
+}
+  
+template <class TInputLabelImage >
+typename PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+::LabelPopulationType const &
+PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+::GetLabelPopulation() const
+{
+  return m_LabelPopulation;
+}
+
+  
+template <class TInputLabelImage >
+void
+PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+::SetLabelStatistic( LabelStatisticType const & labelStatistic )
+{
+  m_LabelStatistic = labelStatistic;
+}
+
+template <class TInputLabelImage >
+typename PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >
+::LabelStatisticType const &
+PersistentLabelImageSmallRegionMergingFilter< TInputLabelImage >