From 65f3020d8748165ae2655a5b658dc36b4a9d854b Mon Sep 17 00:00:00 2001
From: Pierre Lassalle <lassallep@cesbio.cnes.fr>
Date: Fri, 26 Feb 2016 20:55:11 +0100
Subject: [PATCH] Fix bug generation of labels
---
Code/lsrmGraphToOtbImage.h | 4 +-
Code/lsrmGraphToOtbImage.h~ | 45 ++++++++++++
Code/lsrmGraphToOtbImage.txx | 21 +++---
Code/lsrmGraphToOtbImage.txx~ | 125 ++++++++++++++++++++++++++++++++++
4 files changed, 181 insertions(+), 14 deletions(-)
create mode 100644 Code/lsrmGraphToOtbImage.h~
create mode 100644 Code/lsrmGraphToOtbImage.txx~
diff --git a/Code/lsrmGraphToOtbImage.h b/Code/lsrmGraphToOtbImage.h
index 89ef969..0cd93ce 100644
--- a/Code/lsrmGraphToOtbImage.h
+++ b/Code/lsrmGraphToOtbImage.h
@@ -35,9 +35,9 @@ namespace lsrm
const unsigned int width,
const unsigned int height);
- ClusteredImageType::Pointer GetClusteredOutput(const GraphType& graph,
+ /*ClusteredImageType::Pointer GetClusteredOutput(const GraphType& graph,
const unsigned int width,
- const unsigned int height);
+ const unsigned int height);*/
};
} // end of namespace lsrm
diff --git a/Code/lsrmGraphToOtbImage.h~ b/Code/lsrmGraphToOtbImage.h~
new file mode 100644
index 0000000..89ef969
--- /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 6605208..48d7084 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
{
@@ -45,20 +46,16 @@ 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;
- }
+ // Fill holes
+ typedef itk::GrayscaleFillholeImageFilter<LabelImageType,LabelImageType> FillholeFilterType;
+ FillholeFilterType::Pointer fillFilter = FillholeFilterType::New();
+ fillFilter->SetInput(label_img);
+ fillFilter->Update();
- return label_img;
+ return fillFilter->GetOutput();
}
- template<class TGraph>
+ /*template<class TGraph>
typename GraphToOtbImage<TGraph>::ClusteredImageType::Pointer
GraphToOtbImage<TGraph>::GetClusteredOutput(const GraphType& graph,
const unsigned int width,
@@ -122,7 +119,7 @@ namespace lsrm
}
return clusterImg;
- }
+ }*/
} // end of namespace lsrm
#endif
diff --git a/Code/lsrmGraphToOtbImage.txx~ b/Code/lsrmGraphToOtbImage.txx~
new file mode 100644
index 0000000..5fb16c5
--- /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
--
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