Merge remote-tracking branch 'origin/master' into ShapeToDensityFeature

This merge to put image_to_mask feature inside ShapeToDensityFeature branch, to avoid conflicts later on.

Anima/diffusion/odf/tod_estimator/animaTODEstimatorImageFilter.hxx

@@ -84,6 +84,20 @@ namespace anima
             for (int i = 0; i < nbPoints; i++)
             {
                 DirType dir = GetFiberDirection(i, fiber);
+                if(output->GetDirection()[0][0] > 0)
+                {
+                    dir[0] *= -1;
+                }
+                if(output->GetDirection()[1][1] < 0)
+                {
+                    dir[1] *= -1;
+                }
+                if(output->GetDirection()[2][2] < 0)
+                {
+                    dir[2] *= -1;
+                }
+
+
                 PointType point = GetCenterVoxel(i, fiber);
                 itk::Index<3> index;
 

Anima/math-tools/common_tools/CMakeLists.txt

@@ -8,4 +8,5 @@ add_subdirectory(convert_shape)
 add_subdirectory(merge_block_images)
 add_subdirectory(shapes_to_density)
 add_subdirectory(vectorize_images)
+add_subdirectory(image_to_mask)
 

Anima/math-tools/common_tools/image_to_mask/CMakeLists.txt

@@ -0,0 +1,35 @@
+if(BUILD_TOOLS)
+
+project(animaImageToMask)
+
+## #############################################################################
+## 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}
+  ${ITKIO_LIBRARIES}
+  )
+
+## #############################################################################
+## install
+## #############################################################################
+
+set_exe_install_rules(${PROJECT_NAME})
+
+endif()

Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx

@@ -0,0 +1,143 @@
+#include <tclap/CmdLine.h>
+#include <iostream>
+#include <string>
+
+#include <itkImage.h>
+#include <itkVectorImage.h>
+#include <itkImageRegionIterator.h>
+
+#include <animaReadWriteFunctions.h>
+
+/**
+ * @brief Converts an input image (either vectorial or not) into a mask
+ * The output mask will be 0 in the voxels where the input image is 0 (or a null vector) and 1 elsewhere
+ */
+int main(int argc, char **argv)
+{
+    TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ',ANIMA_VERSION);
+
+    //Define arguments
+    TCLAP::ValueArg<std::string> inArg("i","inputfile","input image",true,"","input image",cmd);
+    TCLAP::ValueArg<std::string> outArg("o","outputfile","output mask",true,"","output mask",cmd);
+
+    //Try to parse
+    try
+    {
+        cmd.parse(argc,argv);
+    }
+    catch (TCLAP::ArgException& e)
+    {
+        std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl;
+        return(1);
+    }
+
+    //Define types
+    typedef itk::Image <double,3> ImageType;
+    typedef itk::Image <double,4> Image4DType;
+    typedef itk::VectorImage <double,3> VectorImageType;
+
+    //Read input image
+    itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(inArg.getValue().c_str(),
+                                                                           itk::IOFileModeEnum::ReadMode);
+
+    imageIO->SetFileName(inArg.getValue());
+    imageIO->ReadImageInformation();
+
+    //Initialize the output image (which is a mask) and allocate memory
+    ImageType::Pointer outImage = ImageType::New();
+
+    //Determine if the input image is a vector image (each voxel value is a vector) or not
+    bool vectorImage = (imageIO->GetNumberOfComponents() > 1);
+
+    if (vectorImage)
+    {
+        //Case of a vector image 
+
+        //Read input image and store in the correct format      
+        VectorImageType::Pointer image = anima::readImage <VectorImageType> (inArg.getValue());
+
+        //Set the output image with the same properties as the input image
+        outImage->Initialize();
+        outImage->SetDirection(image->GetDirection());
+        outImage->SetSpacing(image->GetSpacing());
+        outImage->SetOrigin(image->GetOrigin());
+
+        //Allocate the correct size for output image. region (image->GetLargestPossibleRegion()) is the whole image
+        VectorImageType::RegionType region = image->GetLargestPossibleRegion();
+        outImage->SetRegions(region);
+        outImage->Allocate();
+
+        //Create a vector with as many components as there are for each voxel, and with each component equal to 0
+        VectorImageType::PixelType zeroVec(image->GetNumberOfComponentsPerPixel());
+        zeroVec.Fill(0);
+
+        //Create iterators on input and output images
+        itk::ImageRegionIterator <VectorImageType> inItr(image,region);
+        itk::ImageRegionIterator <ImageType> outItr(outImage,outImage->GetLargestPossibleRegion());
+
+        //Main algorithm
+        while (!outItr.IsAtEnd())
+        {
+            if(inItr.Get() == zeroVec)
+            {
+                //The voxel in the input image is a constant vector equal to 0, so this voxel in the output mask will be 0.
+                outItr.Set(0);
+            }
+            else
+            {
+                //The voxel in the input image is not a constant vector equal to 0, so this voxel in the output mask will be 1.
+                outItr.Set(1);
+            }
+
+            //Move to following voxel
+            ++inItr;
+            ++outItr;
+        }
+    }
+    else
+    {
+        //Case of a non-vector image
+
+        //Read input image and store in the correct format
+        ImageType::Pointer image = anima::readImage <ImageType> (inArg.getValue());
+
+        //Set the output image with the same properties as the input image
+        outImage->Initialize();
+        outImage->SetDirection(image->GetDirection());
+        outImage->SetSpacing(image->GetSpacing());
+        outImage->SetOrigin(image->GetOrigin());
+
+        //Allocate the correct size for output image. largestRegion (image->GetLargestPossibleRegion()) is the whole image
+        ImageType::RegionType largestRegion = image->GetLargestPossibleRegion();
+        outImage->SetRegions(largestRegion);
+        outImage->Allocate();
+        outImage->FillBuffer(0.0);
+
+        //Create iterators on input and output images
+        itk::ImageRegionIterator <ImageType> inItr(image,image->GetLargestPossibleRegion());
+        itk::ImageRegionIterator <ImageType> outItr(outImage,outImage->GetLargestPossibleRegion());
+
+        //Main algorithm
+        while (!outItr.IsAtEnd())
+        {
+            if(inItr.Get() == 0.0)
+            {
+                //The voxel in the input image is 0, so this voxel in the output mask will be 0.
+                outItr.Set(0);
+            }
+            else
+            {
+                //The voxel in the input image is not 0, so this voxel in the output mask will be 1.
+                outItr.Set(1);
+            }
+
+            //Move to following voxel
+            ++inItr;
+            ++outItr;
+        }
+    }
+
+    //Write output image and exit
+    anima::writeImage <ImageType> (outArg.getValue(),outImage);
+    return EXIT_SUCCESS;
+}

superbuild/TCLAP.cmake

@@ -2,7 +2,7 @@ set (proj TCLAP)
 
 set (location "")
 if (NOT DEFINED ${proj}_SRC_DIR)
-  set(location URL https://netix.dl.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz)
+  set(location URL https://sourceforge.net/projects/tclap/files/tclap-1.2.1.tar.gz/download)
 endif()
 
 ExternalProject_Add(${proj}