Final switch to ITK 5. Requires C++17 for animaCropImage

Inria-Empenn · Jun 3, 2019 · ebdf6b5 · ebdf6b5
1 parent ba3552a
commit ebdf6b5
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Showing 26 changed files with 189 additions and 166 deletions.
diff --git a/Anima/CMakeLists.txt b/Anima/CMakeLists.txt
@@ -9,7 +9,7 @@ project(ANIMA VERSION 3.3)
 
 # On Macs, disable MACOSX_RPATH (cmake 3.x)
 set(CMAKE_MACOSX_RPATH OFF)
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 17)
 
 # Define default build type if needed
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)

diff --git a/Anima/cmake/ITKLibs.cmake b/Anima/cmake/ITKLibs.cmake
@@ -10,6 +10,7 @@ set(ITKIO_LIBRARIES
   ITKIOGE
   ITKIOHDF5
   ITKIOJPEG
+  ITKIOJPEG2000
   ITKIOLSM
   ITKIOMeta
   ITKIOMINC

diff --git a/Anima/diffusion/tractography/animaBaseProbabilisticTractographyImageFilter.h b/Anima/diffusion/tractography/animaBaseProbabilisticTractographyImageFilter.h
@@ -7,7 +7,7 @@
 #include <vtkSmartPointer.h>
 #include <itkProcessObject.h>
 #include <itkLinearInterpolateImageFunction.h>
-#include <itkFastMutexLock.h>
+#include <mutex>
 #include <itkProgressReporter.h>
 
 #include <vector>
@@ -173,7 +173,7 @@ class BaseProbabilisticTractographyImageFilter : public itk::ProcessObject
     virtual ~BaseProbabilisticTractographyImageFilter();
 
     //! Multithread util function
-    static ITK_THREAD_RETURN_TYPE ThreadTracker(void *arg);
+    static itk::ITK_THREAD_RETURN_TYPE ThreadTracker(void *arg);
 
     //! Doing the thread work dispatch
     void ThreadTrack(unsigned int numThread, FiberProcessVectorType &resultFibers, ListType &resultWeights);
@@ -273,7 +273,7 @@ class BaseProbabilisticTractographyImageFilter : public itk::ProcessObject
 
     vtkSmartPointer<vtkPolyData> m_Output;
 
-    itk::SimpleFastMutexLock m_LockHighestProcessedSeed;
+    std::mutex m_LockHighestProcessedSeed;
     int m_HighestProcessedSeed;
     itk::ProgressReporter *m_ProgressReport;
 };

diff --git a/Anima/diffusion/tractography/animaBaseProbabilisticTractographyImageFilter.hxx b/Anima/diffusion/tractography/animaBaseProbabilisticTractographyImageFilter.hxx
@@ -264,7 +264,7 @@ BaseProbabilisticTractographyImageFilter <TInputModelImageType>::GetModelInterpo
 }
 
 template <class TInputModelImageType>
-ITK_THREAD_RETURN_TYPE
+itk::ITK_THREAD_RETURN_TYPE
 BaseProbabilisticTractographyImageFilter <TInputModelImageType>
 ::ThreadTracker(void *arg)
 {
@@ -292,11 +292,11 @@ BaseProbabilisticTractographyImageFilter <TInputModelImageType>
 
     while (continueLoop)
     {
-        m_LockHighestProcessedSeed.Lock();
+        m_LockHighestProcessedSeed.lock();
 
         if (m_HighestProcessedSeed >= highestToleratedSeedIndex)
         {
-            m_LockHighestProcessedSeed.Unlock();
+            m_LockHighestProcessedSeed.unlock();
             continueLoop = false;
             continue;
         }
@@ -308,13 +308,13 @@ BaseProbabilisticTractographyImageFilter <TInputModelImageType>
 
         m_HighestProcessedSeed = endPoint;
 
-        m_LockHighestProcessedSeed.Unlock();
+        m_LockHighestProcessedSeed.unlock();
 
         this->ThreadedTrackComputer(numThread,resultFibers,resultWeights,startPoint,endPoint);
 
-        m_LockHighestProcessedSeed.Lock();
+        m_LockHighestProcessedSeed.lock();
         m_ProgressReport->CompletedPixel();
-        m_LockHighestProcessedSeed.Unlock();
+        m_LockHighestProcessedSeed.unlock();
     }
 }
 

diff --git a/Anima/diffusion/tractography/animaBaseTractographyImageFilter.cxx b/Anima/diffusion/tractography/animaBaseTractographyImageFilter.cxx
@@ -171,7 +171,7 @@ void BaseTractographyImageFilter::PrepareTractography()
     std::cout << "Generated " << m_PointsToProcess.size() << " seed points from ROI mask" << std::endl;
 }
 
-ITK_THREAD_RETURN_TYPE BaseTractographyImageFilter::ThreadTracker(void *arg)
+itk::ITK_THREAD_RETURN_TYPE BaseTractographyImageFilter::ThreadTracker(void *arg)
 {
     itk::MultiThreaderBase::WorkUnitInfo *threadArgs = (itk::MultiThreaderBase::WorkUnitInfo *)arg;
     unsigned int nbThread = threadArgs->WorkUnitID;
@@ -193,11 +193,11 @@ void BaseTractographyImageFilter::ThreadTrack(unsigned int numThread, std::vecto
 
     while (continueLoop)
     {
-        m_LockHighestProcessedSeed.Lock();
+        m_LockHighestProcessedSeed.lock();
 
         if (m_HighestProcessedSeed >= highestToleratedSeedIndex)
         {
-            m_LockHighestProcessedSeed.Unlock();
+            m_LockHighestProcessedSeed.unlock();
             continueLoop = false;
             continue;
         }
@@ -209,13 +209,13 @@ void BaseTractographyImageFilter::ThreadTrack(unsigned int numThread, std::vecto
 
         m_HighestProcessedSeed = endPoint;
 
-        m_LockHighestProcessedSeed.Unlock();
+        m_LockHighestProcessedSeed.unlock();
 
         this->ThreadedTrackComputer(numThread,resultFibers,startPoint,endPoint);
 
-        m_LockHighestProcessedSeed.Lock();
+        m_LockHighestProcessedSeed.lock();
         m_ProgressReport->CompletedPixel();
-        m_LockHighestProcessedSeed.Unlock();
+        m_LockHighestProcessedSeed.unlock();
     }
 }
 

diff --git a/Anima/diffusion/tractography/animaBaseTractographyImageFilter.h b/Anima/diffusion/tractography/animaBaseTractographyImageFilter.h
@@ -7,7 +7,7 @@
 #include <vtkSmartPointer.h>
 #include <itkLinearInterpolateImageFunction.h>
 #include <itkProcessObject.h>
-#include <itkFastMutexLock.h>
+#include <mutex>
 #include <itkProgressReporter.h>
 
 #include "AnimaTractographyExport.h"
@@ -83,7 +83,7 @@ class ANIMATRACTOGRAPHY_EXPORT BaseTractographyImageFilter : public itk::Process
     BaseTractographyImageFilter();
     virtual ~BaseTractographyImageFilter();
 
-    static ITK_THREAD_RETURN_TYPE ThreadTracker(void *arg);
+    static itk::ITK_THREAD_RETURN_TYPE ThreadTracker(void *arg);
     void ThreadTrack(unsigned int numThread, std::vector <FiberType> &resultFibers);
     void ThreadedTrackComputer(unsigned int numThread, std::vector <FiberType> &resultFibers,
                                unsigned int startSeedIndex, unsigned int endSeedIndex);
@@ -130,7 +130,7 @@ class ANIMATRACTOGRAPHY_EXPORT BaseTractographyImageFilter : public itk::Process
     bool m_ComputeLocalColors;
     vtkSmartPointer<vtkPolyData> m_Output;
 
-    itk::SimpleFastMutexLock m_LockHighestProcessedSeed;
+    std::mutex m_LockHighestProcessedSeed;
     int m_HighestProcessedSeed;
     itk::ProgressReporter *m_ProgressReport;
 };

diff --git a/Anima/diffusion/tractography/fibers_filterer/animaFibersFilterer.cxx b/Anima/diffusion/tractography/fibers_filterer/animaFibersFilterer.cxx
@@ -94,7 +94,7 @@ typedef struct
     std::vector <unsigned int> forbiddenLabels;
 } ThreaderArguments;
 
-ITK_THREAD_RETURN_TYPE ThreadFilterer(void *arg)
+itk::ITK_THREAD_RETURN_TYPE ThreadFilterer(void *arg)
 {
     itk::MultiThreaderBase::WorkUnitInfo *threadArgs = (itk::MultiThreaderBase::WorkUnitInfo *)arg;
     unsigned int nbThread = threadArgs->WorkUnitID;

diff --git a/Anima/math-tools/common/animaNumberedThreadImageToImageFilter.h b/Anima/math-tools/common/animaNumberedThreadImageToImageFilter.h
@@ -1,7 +1,7 @@
 #pragma once
 
 #include <itkImageToImageFilter.h>
-#include <itkFastMutexLock.h>
+#include <mutex>
 
 namespace anima
 {
@@ -51,10 +51,10 @@ class NumberedThreadImageToImageFilter :
 private:
     ITK_DISALLOW_COPY_AND_ASSIGN(NumberedThreadImageToImageFilter);
 
-    itk::SimpleFastMutexLock m_LockThreadIdNumber;
+    std::mutex m_LockThreadIdNumber;
     std::vector <unsigned int> m_ThreadIdsVector;
 
-    itk::SimpleFastMutexLock m_LockProcessedPoints;
+    std::mutex m_LockProcessedPoints;
     unsigned int m_NumberOfProcessedPoints;
     unsigned int m_NumberOfPointsToProcess;
 };

diff --git a/Anima/math-tools/common/animaNumberedThreadImageToImageFilter.hxx b/Anima/math-tools/common/animaNumberedThreadImageToImageFilter.hxx
@@ -55,22 +55,22 @@ void
 NumberedThreadImageToImageFilter <TInputImage, TOutputImage>
 ::IncrementNumberOfProcessedPoints()
 {
-    m_LockProcessedPoints.Lock();
+    m_LockProcessedPoints.lock();
 
     ++m_NumberOfProcessedPoints;
 
     double ratio = static_cast <double> (m_NumberOfProcessedPoints) / m_NumberOfPointsToProcess;
     this->UpdateProgress(ratio);
 
-    m_LockProcessedPoints.Unlock();
+    m_LockProcessedPoints.unlock();
 }
 
 template <typename TInputImage, typename TOutputImage>
 unsigned int
 NumberedThreadImageToImageFilter <TInputImage, TOutputImage>
 ::GetSafeThreadId()
 {
-    m_LockThreadIdNumber.Lock();
+    m_LockThreadIdNumber.lock();
 
     unsigned int threadId = 0;
     bool presentInIdsVector = true;
@@ -92,7 +92,7 @@ NumberedThreadImageToImageFilter <TInputImage, TOutputImage>
 
     m_ThreadIdsVector.push_back(threadId);
 
-    m_LockThreadIdNumber.Unlock();
+    m_LockThreadIdNumber.unlock();
 
     return threadId;
 }
@@ -102,7 +102,7 @@ void
 NumberedThreadImageToImageFilter <TInputImage, TOutputImage>
 ::SafeReleaseThreadId(unsigned int threadId)
 {
-    m_LockThreadIdNumber.Lock();
+    m_LockThreadIdNumber.lock();
 
     unsigned int indexThreadId = 0;
     for (unsigned int i = 0;i < m_ThreadIdsVector.size();++i)
@@ -116,7 +116,7 @@ NumberedThreadImageToImageFilter <TInputImage, TOutputImage>
 
     m_ThreadIdsVector.erase(m_ThreadIdsVector.begin() + indexThreadId);
 
-    m_LockThreadIdNumber.Unlock();
+    m_LockThreadIdNumber.unlock();
 }
 
 } // end namespace anima