Merge pull request #101 from Florent2305/fusion

Fusion of private and public  Anima

Anima/.gitattributes

@@ -0,0 +1,15 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.c text eol=lf
+*.h text eol=lf
+*.cxx text eol=lf
+*.hxx text eol=lf
+*.cpp text eol=lf
+*.txt text eol=lf
+
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary

Anima/.gitignore

@@ -0,0 +1,10 @@
+*~
+*.swp
+*.user
+*.orig
+*.directory
+*.DS_Store
+*.aps
+*.autosave
+CMakeLists.txt.user.*
+CMakeFiles

Anima/README.md

@@ -0,0 +1,6 @@
+ANIMA: Source Code Repository
+-----
+
+ANIMA has been created as the new place to hold the softwares from Empenn. Mainly based on ITK and VTK, it has been designed to hold C++ source code in a modular structure. People in the team are encouraged to contribute their algorithms here so that others may benefit from it easily.
+
+Refer to the [wiki](https://github.com/Inria-Visages/Anima/wiki) for more information

Anima/diffusion/CMakeLists.txt

@@ -4,10 +4,11 @@ project(ANIMA-DIFFUSION)
 # Here go the add_subdirectories, no code should be at the root of the project
 ################################################################################
 
-add_subdirectory(dti_estimator)
-add_subdirectory(dti_tools)
+add_subdirectory(dti)
 add_subdirectory(mcm)
 add_subdirectory(mcm_estimator)
+add_subdirectory(mcm_estimator/low_memory)
+add_subdirectory(mcm_model_averaging)
 add_subdirectory(mcm_tools)
 
 if(USE_VTK AND VTK_FOUND)

Anima/diffusion/dti/CMakeLists.txt

@@ -0,0 +1,6 @@
+add_subdirectory(dti_estimator)
+add_subdirectory(dti_scalar_maps)
+add_subdirectory(dwi_simulator_from_dti)
+add_subdirectory(flip_tensors)
+add_subdirectory(background_noise_variance_estimator)
+add_subdirectory(dti_non_central_chi_estimator)

Anima/diffusion/dti/background_noise_variance_estimator/CMakeLists.txt

@@ -0,0 +1,38 @@
+if(BUILD_TOOLS)
+
+project(animaBackgroundNoiseVarianceEstimator)
+
+## #############################################################################
+## List Sources
+## #############################################################################
+
+list_source_files(${PROJECT_NAME}
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  )
+
+
+## #############################################################################
+## add executable
+## #############################################################################
+
+add_executable(${PROJECT_NAME}
+  ${${PROJECT_NAME}_CFILES}
+  )
+
+
+## #############################################################################
+## Link
+## #############################################################################
+
+target_link_libraries(${PROJECT_NAME}
+  ${ITKIO_LIBRARIES}
+  AnimaStatisticalTests
+  )
+
+## #############################################################################
+## install
+## #############################################################################
+
+set_exe_install_rules(${PROJECT_NAME})
+
+endif()

Anima/diffusion/dti/background_noise_variance_estimator/animaBackgroundNoiseVarianceEstimationImageFilter.h

@@ -0,0 +1,119 @@
+#pragma once
+
+#include <iostream>
+#include <animaNumberedThreadImageToImageFilter.h>
+#include <itkVectorImage.h>
+#include <itkImage.h>
+#include <vnl/vnl_matrix.h>
+#include <vector>
+
+namespace anima
+{
+template <typename TInputImage>
+class BackgroundNoiseVarianceEstimationImageFilter :
+        public anima::NumberedThreadImageToImageFilter < TInputImage, itk::Image<unsigned char,3> >
+{
+public:
+    /** Standard class typedefs. */
+    typedef BackgroundNoiseVarianceEstimationImageFilter Self;
+    typedef itk::Image<unsigned char,3> TOutputImage;
+    typedef itk::VectorImage <double,3> VectorImageType;
+    typedef VectorImageType::Pointer VectorImagePointer;
+
+    typedef anima::NumberedThreadImageToImageFilter <TInputImage, TOutputImage> Superclass;
+    typedef itk::SmartPointer<Self> Pointer;
+    typedef itk::SmartPointer<const Self>  ConstPointer;
+
+    /** Method for creation through the object factory. */
+    itkNewMacro(Self)
+
+    /** Run-time type information (and related methods) */
+    itkTypeMacro(BackgroundNoiseVarianceEstimationImageFilter, anima::NumberedThreadImageToImageFilter)
+
+    typedef typename TOutputImage::PixelType OutputPixelType;
+    typedef typename TInputImage::PixelType InputPixelType;
+
+    /** Image typedef support */
+    typedef TInputImage  InputImageType;
+    typedef TOutputImage OutputImageType;
+    typedef typename InputImageType::Pointer InputImagePointer;
+    typedef typename InputImageType::IndexType InputImageIndexType;
+    typedef typename InputImageType::PixelType InputImagePixelType;
+    typedef typename OutputImageType::Pointer OutputImagePointer;
+
+    /** Superclass typedefs. */
+    typedef typename Superclass::InputImageRegionType InputImageRegionType;
+    typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
+
+    //! Actually computes partial variances for this region
+    void ComputePartialVariance(const OutputImageRegionType &region);
+
+    //! Actually updates output for this region
+    void PartialUpdateOutput(const OutputImageRegionType &region);
+
+    itkSetMacro(PValueThreshold, double)
+    itkGetMacro(OutputVariance, double)
+
+    itkSetMacro(NumberOfCoils, unsigned int)
+
+    void SetTheoreticalSnr(std::vector <double> theoreticalSnr ){m_TheoreticalSnr = theoreticalSnr;}
+    void SetBValuesList(std::vector <double> bValuesList ){m_BValuesList = bValuesList;}
+
+    itkSetMacro(QuantileInitialization, double)
+
+    itkSetMacro(EstimatedB0Image, InputImagePointer)
+    itkSetMacro(DTIImage, VectorImagePointer)
+
+    void AddGradientDirection(unsigned int i, std::vector <double> &grad);
+
+protected:
+    BackgroundNoiseVarianceEstimationImageFilter()
+        : Superclass()
+    {
+        m_NumberOfCoils = 1;
+        m_PValueThreshold = 0.05;
+        m_OutputVariance = 0;
+        m_SlopeInterceptDesignPart = 0;
+        m_QuantileInitialization = 0.5;
+
+        m_EstimatedB0Image = NULL;
+        m_DTIImage = NULL;
+    }
+
+    virtual ~BackgroundNoiseVarianceEstimationImageFilter() {}
+
+    //Redefine virtual functions
+    void GenerateData() ITK_OVERRIDE;
+
+    unsigned int ComputeInitialOutputFromDTI();
+    unsigned int UpdateOutputFromPValues();
+
+private:
+    ITK_DISALLOW_COPY_AND_ASSIGN(BackgroundNoiseVarianceEstimationImageFilter);
+
+    std::vector <double> m_PartialVariances;
+    std::vector <unsigned int> m_PartialNumberOfCoils;
+
+    itk::Image<double,3>::Pointer m_WorkPValImage;
+    InputImagePointer m_EstimatedB0Image;
+    VectorImagePointer m_DTIImage;
+
+    std::vector <double> m_BValuesList;
+    std::vector< std::vector <double> > m_GradientDirections;
+    vnl_matrix <double> m_DesignMatrix;
+    double m_SlopeInterceptDesignPart;
+    double m_QuantileInitialization;
+
+    double m_OutputVariance;
+    unsigned int m_TotalNumberOfCoils;
+    unsigned int m_NumPixels;
+    unsigned int m_NumberOfCoils;
+    std::vector <double> m_TheoreticalSnr;
+    double m_PValueThreshold;
+
+    static const unsigned int m_NumberOfComponents = 6;
+};
+
+} // end of namespace anima
+
+#include "animaBackgroundNoiseVarianceEstimationImageFilter.hxx"