add of a feature to create a mask from an image.\nWritten by Thoms Du…

…rantel
Inria-Empenn · Apr 29, 2024 · 7ca5683 · 7ca5683
1 parent 185203f
commit 7ca5683
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diff --git a/Anima/math-tools/common_tools/CMakeLists.txt b/Anima/math-tools/common_tools/CMakeLists.txt
@@ -7,4 +7,5 @@ add_subdirectory(convert_image)
 add_subdirectory(convert_shape)
 add_subdirectory(merge_block_images)
 add_subdirectory(vectorize_images)
+add_subdirectory(image_to_mask)
 
diff --git a/Anima/math-tools/common_tools/image_to_mask/CMakeLists.txt b/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()
diff --git a/Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx b/Anima/math-tools/common_tools/image_to_mask/animaImageToMask.cxx
@@ -0,0 +1,108 @@
+#include <tclap/CmdLine.h>
+#include <iostream>
+#include <string>
+
+#include <itkImage.h>
+#include <itkVectorImage.h>
+#include <itkImageRegionIterator.h>
+
+#include <animaReadWriteFunctions.h>
+
+int main(int argc, char **argv)
+{
+    TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ',ANIMA_VERSION);
+
+    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
+    {
+        cmd.parse(argc,argv);
+    }
+    catch (TCLAP::ArgException& e)
+    {
+        std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl;
+        return(1);
+    }
+
+    typedef itk::Image <unsigned int,3> ImageType;
+    typedef itk::Image <double,4> Image4DType;
+    typedef itk::VectorImage <double,3> VectorImageType;
+
+    itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(inArg.getValue().c_str(),
+                                                                           itk::IOFileModeEnum::ReadMode);
+
+    imageIO->SetFileName(inArg.getValue());
+    imageIO->ReadImageInformation();
+
+    bool vectorImage = (imageIO->GetNumberOfComponents() > 1);
+
+    if (vectorImage)
+    {
+        // Vectorial case       
+        VectorImageType::Pointer image = anima::readImage <VectorImageType> (inArg.getValue());
+
+        ImageType::Pointer outImage = ImageType::New();
+        outImage->Initialize();
+//        outImage->SetNumberOfComponentsPerPixel(image->GetNumberOfComponentsPerPixel());
+        outImage->SetDirection(image->GetDirection());
+        outImage->SetSpacing(image->GetSpacing());
+        outImage->SetOrigin(image->GetOrigin());
+
+        VectorImageType::RegionType region = image->GetLargestPossibleRegion();
+        outImage->SetRegions(region);
+        outImage->Allocate();
+
+        VectorImageType::PixelType zeroVec(image->GetNumberOfComponentsPerPixel());
+        zeroVec.Fill(0);
+
+        itk::ImageRegionIterator <VectorImageType> inItr(image,region);
+        itk::ImageRegionIterator <ImageType> outItr(outImage,outImage->GetLargestPossibleRegion());
+
+        while (!outItr.IsAtEnd())
+        {
+            if(inItr.Get() == zeroVec)
+                outItr.Set(0);
+            else
+                outItr.Set(1);
+
+            ++inItr;
+            ++outItr;
+        }
+
+        anima::writeImage <ImageType> (outArg.getValue(),outImage);
+
+        return EXIT_SUCCESS;
+    }
+
+    ImageType::Pointer image = anima::readImage <ImageType> (inArg.getValue());
+
+    ImageType::Pointer outImage = ImageType::New();
+    outImage->Initialize();
+    outImage->SetDirection(image->GetDirection());
+    outImage->SetSpacing(image->GetSpacing());
+    outImage->SetOrigin(image->GetOrigin());
+
+    ImageType::RegionType largestRegion = image->GetLargestPossibleRegion();
+    outImage->SetRegions(largestRegion);
+    outImage->Allocate();
+    outImage->FillBuffer(0.0);
+
+    itk::ImageRegionIterator <ImageType> inItr(image,image->GetLargestPossibleRegion());
+    itk::ImageRegionIterator <ImageType> outItr(outImage,outImage->GetLargestPossibleRegion());
+
+    while (!outItr.IsAtEnd())
+    {
+        if(inItr.Get() == 0.0)
+            outItr.Set(0);
+        else
+            outItr.Set(1);
+
+        ++inItr;
+        ++outItr;
+    }
+
+    anima::writeImage <ImageType> (outArg.getValue(),outImage);
+
+    return EXIT_SUCCESS;
+}