diff --git a/Code/lsgrmGraphOperations.h b/Code/lsgrmGraphOperations.h
index 4352c89afaf3a5c25bd5a624b0824a95ad604ed3..862f0e1534569d7e7908bcd8fe1193a0e6799343 100644
--- a/Code/lsgrmGraphOperations.h
+++ b/Code/lsgrmGraphOperations.h
@@ -2,6 +2,7 @@
#define __LSGRM_GRAPH_OPERATIONS_H
#include "lsgrmHeader.h"
#include "lsrmGraphOperations.h"
+#include "otbImage.h"
#include "otbImageFileReader.h"
namespace lsgrm
diff --git a/Code/lsgrmGraphOperations.txx b/Code/lsgrmGraphOperations.txx
index be32e32641639ac57d109738b10d4d405723cb42..02a9b002832c2e7b186aa9c2fb33e6f0e10b3750 100644
--- a/Code/lsgrmGraphOperations.txx
+++ b/Code/lsgrmGraphOperations.txx
@@ -79,6 +79,7 @@ namespace lsgrm
}
}
+<<<<<<< HEAD
if (myrank == 0)
{
std::cout << "\nAchieve segmentation process..." << std::endl;
@@ -106,6 +107,31 @@ namespace lsgrm
clusterWriter->Update();
}
}
+=======
+ std::cout << "\nAchieve segmentation process..." << std::endl;
+
+ // Segmentation of the graph
+ segmenter.SetImageWidth(imageWidth);
+ segmenter.SetImageHeight(imageHeight);
+ segmenter.SetNumberOfComponentsPerPixel(imageBands);
+ segmenter.SetParam(params);
+ segmenter.SetThreshold(threshold);
+ segmenter.SetDoBFSegmentation(true);
+ segmenter.SetNumberOfIterations(75);
+
+ lsrm::GraphOperations<TSegmenter>::PerfomAllIterationsWithLMBFAndConstThreshold(segmenter);
+
+ // Write output graph to the output graph directory
+ WriteGraph<TSegmenter>(segmenter.m_Graph, outputGraphDirectory, 0, 0);
+
+ typedef unsigned long int LabelPixelType;
+ typedef otb::Image<LabelPixelType, 2> LabelImageType;
+ typedef otb::ImageFileWriter<LabelImageType> LabelImageWriterType;
+ auto labelWriter = LabelImageWriterType::New();
+ labelWriter->SetFileName("out/labelImage.tiff");
+ labelWriter->SetInput(segmenter.GetLabeledClusteredOutput());
+ labelWriter->Update();
+>>>>>>> upstream/master
}
template<class TSegmenter>
diff --git a/Code/lsrmBaatzSegmenter.txx b/Code/lsrmBaatzSegmenter.txx
index f751ccd1208a6b7cf24185712bf33a08b629f3ac..abc0273b14c2737509515bf07190535f087ac1fe 100644
--- a/Code/lsrmBaatzSegmenter.txx
+++ b/Code/lsrmBaatzSegmenter.txx
@@ -57,7 +57,7 @@ namespace lsrm
std = std::sqrt((square_mean - 2*mean*sum + a_sum * mean* mean) / a_sum);
spect_cost += (a_sum * std - a1 * n1->m_Std[b] - a2 * n2->m_Std[b]);
}
- spect_cost *= this->m_Param.m_ShapeWeight;
+ spect_cost *= this->m_Param.m_SpectralWeight;
if(spect_cost < this->m_Threshold)
{
@@ -79,7 +79,7 @@ namespace lsrm
shape_cost = this->m_Param.m_ShapeWeight * compact_f + (1-this->m_Param.m_ShapeWeight) * smooth_f;
- return (spect_cost + (1-this->m_Param.m_ShapeWeight)*shape_cost);
+ return (spect_cost + (1-this->m_Param.m_SpectralWeight)*shape_cost);
}
else
return spect_cost;
diff --git a/Code/lsrmGraphToOtbImage.h b/Code/lsrmGraphToOtbImage.h
index 89ef969ce259a05f70f6c70432d40fab054654cf..19a448caedebff6c02fc2a8fd3cdaa1a8e61b243 100644
--- a/Code/lsrmGraphToOtbImage.h
+++ b/Code/lsrmGraphToOtbImage.h
@@ -26,18 +26,12 @@ namespace lsrm
typedef typename NodeList::const_iterator NodeConstIterator;
typedef unsigned long int LabelPixelType;
typedef otb::Image<LabelPixelType, 2> LabelImageType;
- typedef unsigned char ClusterPixelType;
- typedef otb::VectorImage<ClusterPixelType, 2> ClusteredImageType;
using ContourOperator = lp::ContourOperations;
LabelImageType::Pointer GetLabelImage(const GraphType& graph,
const unsigned int width,
const unsigned int height);
-
- ClusteredImageType::Pointer GetClusteredOutput(const GraphType& graph,
- const unsigned int width,
- const unsigned int height);
};
} // end of namespace lsrm
diff --git a/Code/lsrmGraphToOtbImage.h~ b/Code/lsrmGraphToOtbImage.h~
new file mode 100644
index 0000000000000000000000000000000000000000..89ef969ce259a05f70f6c70432d40fab054654cf
--- /dev/null
+++ b/Code/lsrmGraphToOtbImage.h~
@@ -0,0 +1,45 @@
+#ifndef __LSRM_GRAPH_TO_OTBIMAGE_H
+#define __LSRM_GRAPH_TO_OTBIMAGE_H
+#include <itkRGBPixel.h>
+#include <itkImageRegion.h>
+#include <otbImage.h>
+#include <otbVectorImage.h>
+#include <otbImageFileReader.h>
+#include <otbImageFileWriter.h>
+#include "lsrmGraph.h"
+#include <string>
+#include <stdlib.h>
+#include <time.h>
+#include "lpContour.h"
+
+namespace lsrm
+{
+ template<class TGraph>
+ class GraphToOtbImage
+ {
+ public:
+
+ /* Some convenient typedefs */
+ typedef TGraph GraphType;
+ typedef typename GraphType::NodeType NodeType;
+ typedef std::vector< std::shared_ptr<NodeType> > NodeList;
+ typedef typename NodeList::const_iterator NodeConstIterator;
+ typedef unsigned long int LabelPixelType;
+ typedef otb::Image<LabelPixelType, 2> LabelImageType;
+ typedef unsigned char ClusterPixelType;
+ typedef otb::VectorImage<ClusterPixelType, 2> ClusteredImageType;
+ using ContourOperator = lp::ContourOperations;
+
+
+ LabelImageType::Pointer GetLabelImage(const GraphType& graph,
+ const unsigned int width,
+ const unsigned int height);
+
+ ClusteredImageType::Pointer GetClusteredOutput(const GraphType& graph,
+ const unsigned int width,
+ const unsigned int height);
+ };
+
+} // end of namespace lsrm
+#include "lsrmGraphToOtbImage.txx"
+#endif
diff --git a/Code/lsrmGraphToOtbImage.txx b/Code/lsrmGraphToOtbImage.txx
index 66052088b818c16e71fd8396b3b1af60b6c0980e..9042bec00f32b0430d94fd1a71a940bd3a4473bd 100644
--- a/Code/lsrmGraphToOtbImage.txx
+++ b/Code/lsrmGraphToOtbImage.txx
@@ -2,6 +2,7 @@
#define __LSRM_GRAPH_TO_OTBIMAGE_TXX
#include "lsrmGraphToOtbImage.h"
#include "itkImageRegionIterator.h"
+#include "itkGrayscaleFillholeImageFilter.h"
namespace lsrm
{
@@ -45,83 +46,13 @@ namespace lsrm
++label;
}
- long unsigned int pixelValue = 0;
- for(it.GoToBegin(); !it.IsAtEnd(); ++it)
- {
- auto pixel = it.Get();
- if(pixel == 0)
- it.Set(pixelValue);
- else
- pixelValue = pixel;
- }
-
- return label_img;
- }
-
- template<class TGraph>
- typename GraphToOtbImage<TGraph>::ClusteredImageType::Pointer
- GraphToOtbImage<TGraph>::GetClusteredOutput(const GraphType& graph,
- const unsigned int width,
- const unsigned int height)
- {
- ClusteredImageType::IndexType index;
- ClusteredImageType::SizeType size;
- ClusteredImageType::RegionType region;
-
- index[0] = 0; index[1] = 0;
- size[0] = width; size[1] = height;
- region.SetIndex(index);
- region.SetSize(size);
-
- ClusteredImageType::Pointer clusterImg = ClusteredImageType::New();
- clusterImg->SetRegions(region);
- clusterImg->SetNumberOfComponentsPerPixel(3);
- clusterImg->Allocate();
-
- ClusteredImageType::PixelType pixelValue;
- pixelValue.Reserve(3);
- pixelValue[0] = 0;
- pixelValue[1] = 0;
- pixelValue[2] = 0;
-
- using ClusterImageIterator = itk::ImageRegionIterator<ClusteredImageType>;
- ClusterImageIterator it(clusterImg, clusterImg->GetLargestPossibleRegion());
- for(it.GoToBegin();!it.IsAtEnd(); ++it)
- it.Set(pixelValue);
-
- srand(time(NULL));
- unsigned char c1, c2, c3;
- for(auto& region : graph.m_Nodes)
- {
- c1 = rand() % 256;
- c2 = rand() % 256;
- c3 = rand() % 256;
-
- lp::CellLists borderPixels;
- ContourOperator::GenerateBorderCells(borderPixels, region->m_Contour, region->m_Id, width);
-
- for (auto& pix : borderPixels)
- {
- index[0] = pix % width;
- index[1] = pix / width;
- pixelValue[0] = c1;
- pixelValue[1] = c2;
- pixelValue[2] = c3;
- clusterImg->SetPixel(index, pixelValue);
- }
- }
-
-
- for(it.GoToBegin(); !it.IsAtEnd(); ++it)
- {
- auto pixel = it.Get();
- if(pixel[0] == 0 && pixel[1] == 0 && pixel[2] == 0)
- it.Set(pixelValue);
- else
- pixelValue = pixel;
- }
+ // Fill holes
+ typedef itk::GrayscaleFillholeImageFilter<LabelImageType,LabelImageType> FillholeFilterType;
+ FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
+ fillFilter->SetInput(label_img);
+ fillFilter->Update();
- return clusterImg;
+ return fillFilter->GetOutput();
}
} // end of namespace lsrm
diff --git a/Code/lsrmGraphToOtbImage.txx~ b/Code/lsrmGraphToOtbImage.txx~
new file mode 100644
index 0000000000000000000000000000000000000000..5fb16c51b876a86c25e0911ea65641d2ee50fd20
--- /dev/null
+++ b/Code/lsrmGraphToOtbImage.txx~
@@ -0,0 +1,125 @@
+#ifndef __LSRM_GRAPH_TO_OTBIMAGE_TXX
+#define __LSRM_GRAPH_TO_OTBIMAGE_TXX
+#include "lsrmGraphToOtbImage.h"
+#include "itkImageRegionIterator.h"
+#include "itkGrayscaleFillholeImageFilter.h"
+
+namespace lsrm
+{
+ template<class TGraph>
+ typename GraphToOtbImage<TGraph>::LabelImageType::Pointer
+ GraphToOtbImage<TGraph>::GetLabelImage(const GraphType& graph,
+ const unsigned int width,
+ const unsigned int height)
+ {
+ LabelImageType::IndexType index;
+ LabelImageType::SizeType size;
+ LabelImageType::RegionType region;
+
+ index[0] = 0; index[1] = 0;
+ size[0] = width; size[1] = height;
+ region.SetIndex(index);
+ region.SetSize(size);
+
+ LabelImageType::Pointer label_img = LabelImageType::New();
+ label_img->SetRegions(region);
+ label_img->Allocate();
+
+ using LabelImageIterator = itk::ImageRegionIterator<LabelImageType>;
+ LabelImageIterator it(label_img, label_img->GetLargestPossibleRegion());
+ for(it.GoToBegin();!it.IsAtEnd(); ++it)
+ it.Set(0);
+
+ // Start at 1 (value 0 can be used for invalid pixels)
+ long unsigned int label = 1;
+ for(auto& region : graph.m_Nodes)
+ {
+ lp::CellLists borderPixels;
+ ContourOperator::GenerateBorderCells(borderPixels, region->m_Contour, region->m_Id, width);
+
+ for (auto& pix: borderPixels)
+ {
+ index[0] = pix % width;
+ index[1] = pix / width;
+ label_img->SetPixel(index, label);
+ }
+ ++label;
+ }
+
+ // Fill holes
+ typedef itk::GrayscaleFillholeImageFilter<LabelImageType,LabelImageType> FillholeFilterType;
+ FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
+ fillFilter->SetInput(label_img);
+ fillFilter->Update();
+
+ return fillFilter->GetOutput();
+ }
+
+ template<class TGraph>
+ typename GraphToOtbImage<TGraph>::ClusteredImageType::Pointer
+ GraphToOtbImage<TGraph>::GetClusteredOutput(const GraphType& graph,
+ const unsigned int width,
+ const unsigned int height)
+ {
+ ClusteredImageType::IndexType index;
+ ClusteredImageType::SizeType size;
+ ClusteredImageType::RegionType region;
+
+ index[0] = 0; index[1] = 0;
+ size[0] = width; size[1] = height;
+ region.SetIndex(index);
+ region.SetSize(size);
+
+ ClusteredImageType::Pointer clusterImg = ClusteredImageType::New();
+ clusterImg->SetRegions(region);
+ clusterImg->SetNumberOfComponentsPerPixel(3);
+ clusterImg->Allocate();
+
+ ClusteredImageType::PixelType pixelValue;
+ pixelValue.Reserve(3);
+ pixelValue[0] = 0;
+ pixelValue[1] = 0;
+ pixelValue[2] = 0;
+
+ using ClusterImageIterator = itk::ImageRegionIterator<ClusteredImageType>;
+ ClusterImageIterator it(clusterImg, clusterImg->GetLargestPossibleRegion());
+ for(it.GoToBegin();!it.IsAtEnd(); ++it)
+ it.Set(pixelValue);
+
+ srand(time(NULL));
+ unsigned char c1, c2, c3;
+ for(auto& region : graph.m_Nodes)
+ {
+ c1 = rand() % 256;
+ c2 = rand() % 256;
+ c3 = rand() % 256;
+
+ lp::CellLists borderPixels;
+ ContourOperator::GenerateBorderCells(borderPixels, region->m_Contour, region->m_Id, width);
+
+ for (auto& pix : borderPixels)
+ {
+ index[0] = pix % width;
+ index[1] = pix / width;
+ pixelValue[0] = c1;
+ pixelValue[1] = c2;
+ pixelValue[2] = c3;
+ clusterImg->SetPixel(index, pixelValue);
+ }
+ }
+
+
+ for(it.GoToBegin(); !it.IsAtEnd(); ++it)
+ {
+ auto pixel = it.Get();
+ if(pixel[0] == 0 && pixel[1] == 0 && pixel[2] == 0)
+ it.Set(pixelValue);
+ else
+ pixelValue = pixel;
+ }
+
+ return clusterImg;
+ }
+
+} // end of namespace lsrm
+#endif
diff --git a/Code/lsrmSegmenter.h b/Code/lsrmSegmenter.h
index f48f9290d0abfdfa357c1b8b9a343d04003bc775..92771b9b902aa2d64984e7f2626322c927c7718b 100644
--- a/Code/lsrmSegmenter.h
+++ b/Code/lsrmSegmenter.h
@@ -24,7 +24,6 @@ namespace lsrm
typedef typename GraphOperatorType::NodePointerType NodePointerType;
typedef GraphToOtbImage<GraphType> IOType;
typedef typename IOType::LabelImageType LabelImageType;
- typedef typename IOType::ClusteredImageType ClusteredImageType;
/* Default constructor and destructor */
@@ -81,13 +80,6 @@ namespace lsrm
auto labelImg = io.GetLabelImage(this->m_Graph, this->m_ImageWidth, this->m_ImageHeight);
return labelImg;
}
-
- inline typename ClusteredImageType::Pointer GetClusteredImageOutput()
- {
- IOType io;
- auto clusteredImg = io.GetClusteredOutput(this->m_Graph, this->m_ImageWidth, this->m_ImageHeight);
- return clusteredImg;
- }
/* Set methods */
SetMacro(bool, DoBFSegmentation);