From 35d25a15a11b902c47d87cf51c9bcced92208a15 Mon Sep 17 00:00:00 2001
From: remicres <remi.cresson@teledetection.fr>
Date: Wed, 10 Aug 2016 09:50:59 +0000
Subject: [PATCH] FIX: Pierre code + itk::object inheritance implemented
---
include/lsgrmController.h | 177 +++++++++++++++++++++++-------------
include/lsgrmController.txx | 163 ++++++++++++---------------------
2 files changed, 171 insertions(+), 169 deletions(-)
diff --git a/include/lsgrmController.h b/include/lsgrmController.h
index d560f49..ef9dba7 100644
--- a/include/lsgrmController.h
+++ b/include/lsgrmController.h
@@ -3,74 +3,121 @@
#include "lsrmGetInternalMemory.h"
#include "lsgrmSplitter.h"
#include "lsgrmGraphOperations.h"
+#include "itkObject.h"
#include "itkMacro.h"
namespace lsgrm
-{
- template<class TSegmenter>
- class Controller
- {
- public:
-
- /* Some convenient typedefs */
- using SegmenterType = TSegmenter;
- using ImageType = typename SegmenterType::ImageType;
- using LabelImageType = typename SegmenterType::LabelImageType;
- using SegmentationParameterType = typename SegmenterType::ParameterType;
-
- /* Default constructor and destructor. */
- Controller();
- ~Controller();
-
- void RunSegmentation();
-
- void SetImageDivision(bool f);
- void SetInputImage(ImageType * inputImage);
- void SetTemporaryDirectory(const std::string& str);
- void SetTileWidth(const unsigned int v);
- void SetTileHeight(const unsigned int v);
- void SetNumberOfFirstIterations(const unsigned int v);
- void SetNumberOfIterations(const unsigned int v);
- void SetSpecificParameters(const SegmentationParameterType& params);
- void SetThreshold(const float& t);
- void SetInternalMemoryAvailable(long long unsigned int v); // expecting a value in Mbytes.
- void SetAutomaticTilingLayout(bool value);
-
- typename LabelImageType::Pointer GetLabeledClusteredOutput();
-
- itkGetMacro(ListOfTemporaryFiles, std::vector<std::string>);
-
- private:
-
- void GetAutomaticConfiguration();
- long unsigned int GetMaximumNumberOfNodesInMemory();
-
- /* Parameters given by the user */
- long long unsigned int m_Memory; // RAM available for the computation.
- ImageType * m_InputImage; // Input image
- std::string m_TemporaryDirectory; // Directory used to store intermediate files during the process.
- bool m_ImageDivisionActivated; // The input image must be divided.
- bool m_CleanTemporaryDirectory; // Clean the temporary directory.
-
- /* Specific segmentation parameters */
- SegmentationParameterType m_SpecificParameters;
- float m_Threshold;
-
- /* Internal attribute members.*/
- unsigned int m_NbTilesX;
- unsigned int m_NbTilesY;
- unsigned int m_NumberOfFirstIterations;
- unsigned int m_NumberOfIterations;
- unsigned int m_Margin;
- unsigned int m_TileWidth;
- unsigned int m_TileHeight;
- bool m_AutomaticTilingLayout;
-
- std::vector<ProcessingTile> m_Tiles;
- std::vector<std::string> m_ListOfTemporaryFiles;
-
- typename LabelImageType::Pointer m_LabelImage;
- };
+{
+template<class TSegmenter>
+class ITK_EXPORT Controller : public itk::Object
+{
+public:
+
+ /** Standard class typedef */
+ typedef Controller Self;
+ typedef itk::LightObject Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Runtime information support. */
+ itkTypeMacro(Controller, itk::Object);
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Enum for tiling mode */
+ enum LSGRMTilingMode
+ {
+ LSGRM_TILING_NONE,
+ LSGRM_TILING_USER,
+ LSGRM_TILING_AUTO
+ };
+
+ /* Some convenient typedefs */
+ using SegmenterType = TSegmenter;
+ using ImageType = typename SegmenterType::ImageType;
+ using LabelImageType = typename SegmenterType::LabelImageType;
+ using SegmentationParameterType = typename SegmenterType::ParameterType;
+
+ /* Default constructor and destructor. */
+ Controller();
+ ~Controller();
+
+ void RunSegmentation();
+
+ void SetSpecificParameters(const SegmentationParameterType& params);
+ void SetInputImage(ImageType * inputImage);
+ void SetInternalMemoryAvailable(long long unsigned int v); // expecting a value in Mbytes.
+
+ /* Accessors */
+ void SetTilingModeNone(){m_TilingMode = LSGRM_TILING_NONE;};
+ void SetTilingModeUser(){m_TilingMode = LSGRM_TILING_USER;};
+ void SetTilingModeAuto(){m_TilingMode = LSGRM_TILING_AUTO;};
+
+ typename LabelImageType::Pointer GetLabeledClusteredOutput();
+
+ itkGetMacro(Margin, unsigned int);
+ itkGetMacro(TemporaryFilesList, std::vector<std::string>);
+
+ itkGetMacro(CleanTemporaryDirectory, bool);
+ itkSetMacro(CleanTemporaryDirectory, bool);
+
+ itkGetMacro(TemporaryDirectory, std::string);
+ itkSetMacro(TemporaryDirectory, std::string);
+
+ itkGetMacro(Threshold, float);
+ itkSetMacro(Threshold, float);
+
+ itkGetMacro(NumberOfIterations, unsigned int);
+ itkSetMacro(NumberOfIterations, unsigned int);
+
+ itkGetMacro(NbTilesX, unsigned int);
+ itkSetMacro(NbTilesX, unsigned int);
+
+ itkGetMacro(NbTilesY, unsigned int);
+ itkSetMacro(NbTilesY, unsigned int);
+
+ itkGetMacro(NumberOfFirstIterations, unsigned int);
+ itkSetMacro(NumberOfFirstIterations, unsigned int);
+
+ itkGetMacro(TileWidth, unsigned int);
+ itkSetMacro(TileWidth, unsigned int);
+
+ itkGetMacro(TileHeight, unsigned int);
+ itkSetMacro(TileHeight, unsigned int);
+
+private:
+
+ void GetAutomaticConfiguration();
+ long unsigned int GetMaximumNumberOfNodesInMemory();
+
+ /* Parameters given by the user */
+ std::string m_TemporaryDirectory; // Directory used to store intermediate files during the process.
+ bool m_CleanTemporaryDirectory; // Clean the temporary directory.
+ ImageType * m_InputImage; // Input image
+
+ /* Segmentation parameters */
+ SegmentationParameterType m_SpecificParameters; // Specific parameters
+ float m_Threshold; // Threshold
+ unsigned int m_NumberOfIterations; // Number of iterations
+
+ /* Parameters given by the user or computed automatically
+ * depending of the chosen mode
+ */
+ long long unsigned int m_Memory; // RAM available for the computation.
+ unsigned int m_NbTilesX;
+ unsigned int m_NbTilesY;
+ unsigned int m_NumberOfFirstIterations;
+ unsigned int m_TileWidth;
+ unsigned int m_TileHeight;
+
+ /* read-only variables */
+ unsigned int m_Margin;
+ std::vector<ProcessingTile> m_Tiles;
+ std::vector<std::string> m_TemporaryFilesList;
+ LSGRMTilingMode m_TilingMode;
+ typename LabelImageType::Pointer m_LabelImage;
+};
} // end of namespace lsgrm
#include "lsgrmController.txx"
diff --git a/include/lsgrmController.txx b/include/lsgrmController.txx
index ba55f0f..a1da11d 100644
--- a/include/lsgrmController.txx
+++ b/include/lsgrmController.txx
@@ -6,8 +6,7 @@ namespace lsgrm
template<class TSegmenter>
Controller<TSegmenter>::Controller()
{
- m_Memory = 0;
- m_ImageDivisionActivated = true;
+ m_TilingMode = LSGRM_TILING_AUTO;
}
template<class TSegmenter>
@@ -19,22 +18,29 @@ template<class TSegmenter>
void Controller<TSegmenter>::RunSegmentation()
{
- // TODO: smarter value?
- const unsigned int numberOfIterationsForPartialSegmentations = 3;
- unsigned int numberOfIterations = m_NumberOfIterations;
-
- // Automatic procedure
- if(m_Memory == 0)
- {
- this->GetAutomaticConfiguration();
- }
- else
+ if (m_TilingMode == LSGRM_TILING_AUTO || m_TilingMode == LSGRM_TILING_USER)
{
- m_Margin = static_cast<unsigned int>(pow(2, m_NumberOfFirstIterations + 1) - 2);
- }
+ // TODO: smarter value?
+ const unsigned int numberOfIterationsForPartialSegmentations = 3;
+ unsigned int numberOfIterations = m_NumberOfIterations;
+
+ if(m_TilingMode == LSGRM_TILING_AUTO)
+ {
+ this->GetAutomaticConfiguration();
+ }
+ else if (m_TilingMode == LSGRM_TILING_USER)
+ {
+ m_Margin = static_cast<unsigned int>(pow(2, m_NumberOfFirstIterations + 1) - 2);
+ }
+
+ std::cout <<
+ "--- Configuration: \n" <<
+ "\tAvailable RAM: " << m_Memory << "\n" <<
+ "\tInput image dimensions: " << m_InputImage->GetLargestPossibleRegion().GetSize() << "\n" <<
+ "\tNumber of first iterations: " << m_NumberOfFirstIterations << "\n" <<
+ "\tStability margin: " << m_Margin << "\n" <<
+ "\tComputed tile size: " << m_TileWidth << " x " << m_TileHeight << std::endl;
- if(m_ImageDivisionActivated)
- {
// Compute the splitting scheme
SplitOTBImage<ImageType>(m_InputImage, m_TileWidth, m_TileHeight, m_Margin,
m_NbTilesX, m_NbTilesY, m_Tiles);
@@ -115,20 +121,20 @@ void Controller<TSegmenter>::RunSegmentation()
m_InputImage->GetNumberOfComponentsPerPixel(),
numberOfIterations);
- // ShowTime(t);
+ ShowTime(t);
}
- else
+ else // accumulatedMemory > m_Memory
{
// That means there are no more possible fusions but we can not store the output graph
// Todo do not clean up temporary directory before copying resulting graph to the output directory
// In the output directory add an info file to give the number of tiles.
+ itkExceptionMacro(<< "No more possible fusions, but can not store the output graph");
}
-
}
- else
+ else // tiling_mode is none
{
- //TODO: use classic GRM
+ // todo use classic grm
}
@@ -158,6 +164,12 @@ long unsigned int Controller<TSegmenter>::GetMaximumNumberOfNodesInMemory()
}
+/*
+ * Compute a tiling layout such as tiles respect following constraints,
+ * sorted by priority:
+ * 1.number of nodes in a regular tile should fit the available memory
+ * 2.regular tiles compactness must be the smallest
+ */
template<class TSegmenter>
void Controller<TSegmenter>::GetAutomaticConfiguration()
{
@@ -169,7 +181,7 @@ void Controller<TSegmenter>::GetAutomaticConfiguration()
// (assuming that maxMargin = tileDimension/2)
maximumNumberOfNodesInMemory /= 4;
- // Find the largest tile with the lowest compactness
+ // Find the largest tile size
const unsigned int imageWidth = m_InputImage->GetLargestPossibleRegion().GetSize()[0];
const unsigned int imageHeight = m_InputImage->GetLargestPossibleRegion().GetSize()[1];
unsigned int nbOfTiles = 1; // total number of tiles
@@ -179,32 +191,34 @@ void Controller<TSegmenter>::GetAutomaticConfiguration()
unsigned int tileWidth(0), tileHeight(0);
while( nbOfNodesInImage / ((float) nbOfTiles) > maximumNumberOfNodesInMemory)
{
- // Get the multiples of k. For each one, compute the
- // layout which has the minimum tile compactness
- float lowestCompactness = itk::NumericTraits<float>::max();
- for (unsigned int layoutNCol = 1; layoutNCol<=nbOfTiles; layoutNCol++)
+ nbOfTiles++;
+ }
+ nbOfTiles--;
+
+ // Get the multiples of k. For each one, compute the
+ // layout which has the minimum tile compactness
+ float lowestCompactness = itk::NumericTraits<float>::max();
+ for (unsigned int layoutNCol = 1; layoutNCol<=nbOfTiles; layoutNCol++)
+ {
+ if (nbOfTiles % layoutNCol == 0) // Is it a multiple of the nb of Tiles?
{
- if (nbOfTiles % layoutNCol == 0) // Is it a multiple of the nb of Tiles?
+ // Compute tile compactness
+ unsigned int layoutNRow = nbOfTiles / layoutNCol;
+ tileWidth = imageWidth / layoutNCol;
+ tileHeight = imageHeight / layoutNRow;
+ float perimeter = tileWidth + tileHeight;
+ float surface = tileWidth * tileHeight;
+ float compactness = perimeter / surface;
+
+ // Update minimum compactness
+ if (lowestCompactness > compactness)
{
- // Compute tile compactness
- unsigned int layoutNRow = nbOfTiles / layoutNCol;
- tileWidth = imageWidth / layoutNCol;
- tileHeight = imageHeight / layoutNRow;
- float perimeter = tileWidth + tileHeight;
- float surface = tileWidth * tileHeight;
- float compactness = perimeter / surface;
-
- // Update minimum compactness
- if (lowestCompactness > compactness)
- {
- lowestCompactness = compactness;
- m_NbTilesX = layoutNCol;
- m_NbTilesY = layoutNRow;
- }
+ lowestCompactness = compactness;
+ m_NbTilesX = layoutNCol;
+ m_NbTilesY = layoutNRow;
}
- } // for each multiple of k
- nbOfTiles++;
- } // while
+ }
+ } // for each multiple of k
// Compute the tile size
m_TileWidth = static_cast<unsigned int>(imageWidth/m_NbTilesX);
@@ -227,22 +241,6 @@ void Controller<TSegmenter>::GetAutomaticConfiguration()
m_Margin = prevMargin;
m_NumberOfFirstIterations = niter - 1;
- std::cout <<
- "--- Configuration: \n" <<
- "\tAvailable RAM: " << m_Memory << "\n" <<
- "\tInput image dimensions: " << imageWidth << " x " << imageHeight << "\n" <<
- "\tMaximum number of nodes in memory: " << maximumNumberOfNodesInMemory << "\n" <<
- "\tOptimal square tile size: " << tileDimension << "\n" <<
- "\tNumber of first iterations: " << niter << "\n" <<
- "\tStability margin: " << prevMargin << "\n" <<
- "\tComputed tile size: " << m_TileWidth << " x " << m_TileHeight << std::endl;
-
-}
-
-template <class TSegmenter>
-void Controller<TSegmenter>::SetTemporaryDirectory(const std::string& str)
-{
- m_TemporaryDirectory = str;
}
template <class TSegmenter>
@@ -252,61 +250,18 @@ void Controller<TSegmenter>::SetInternalMemoryAvailable(long long unsigned int v
m_Memory = v * 1024ul * 1024ul;
}
-template<class TSegmenter>
-void Controller<TSegmenter>::SetImageDivision(bool f)
-{
- m_ImageDivisionActivated = f;
-}
-
-template<class TSegmenter>
-void Controller<TSegmenter>::SetAutomaticTilingLayout(bool value)
-{
- m_AutomaticTilingLayout = value;
-}
-
template<class TSegmenter>
void Controller<TSegmenter>::SetInputImage(ImageType * inputImage)
{
m_InputImage = inputImage;
}
-template<class TSegmenter>
-void Controller<TSegmenter>::SetTileWidth(const unsigned int v)
-{
- m_TileWidth = v;
-}
-
-template<class TSegmenter>
-void Controller<TSegmenter>::SetTileHeight(const unsigned int v)
-{
- m_TileHeight = v;
-}
-
-template<class TSegmenter>
-void Controller<TSegmenter>::SetNumberOfFirstIterations(const unsigned int v)
-{
- m_NumberOfFirstIterations = v;
- m_Margin = static_cast<unsigned int>(pow(2, m_NumberOfFirstIterations + 1) - 2);// 2^{n+1}-2
-}
-
-template<class TSegmenter>
-void Controller<TSegmenter>::SetNumberOfIterations(const unsigned int v)
-{
- m_NumberOfIterations = v;
-}
-
template<class TSegmenter>
void Controller<TSegmenter>::SetSpecificParameters(const SegmentationParameterType& params)
{
m_SpecificParameters = params;
}
-template<class TSegmenter>
-void Controller<TSegmenter>::SetThreshold(const float& t)
-{
- m_Threshold = t;
-}
-
template<class TSegmenter>
typename Controller<TSegmenter>::LabelImageType::Pointer
Controller<TSegmenter>::GetLabeledClusteredOutput()
--
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