Comment and clean Thomas' code

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

@@ -8,13 +8,19 @@
 
 #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);
@@ -25,84 +31,113 @@ int main(int argc, char **argv)
         return(1);
     }
 
-    typedef itk::Image <unsigned int,3> ImageType;
+    //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)
     {
-        // Vectorial case       
+        //Case of a vector image 
+
+        //Read input image and store in the correct format      
         VectorImageType::Pointer image = anima::readImage <VectorImageType> (inArg.getValue());
 
-        ImageType::Pointer outImage = ImageType::New();
+        //Set the output image with the same properties as the input image
         outImage->Initialize();
-//        outImage->SetNumberOfComponentsPerPixel(image->GetNumberOfComponentsPerPixel());
         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;
         }
-
-        anima::writeImage <ImageType> (outArg.getValue(),outImage);
-
-        return EXIT_SUCCESS;
     }
+    else
+    {
+        //Case of a non-vector image
+
+        //Read input image and store in the correct format
+        ImageType::Pointer image = anima::readImage <ImageType> (inArg.getValue());
 
-    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());
+        //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());
 
-    ImageType::RegionType largestRegion = image->GetLargestPossibleRegion();
-    outImage->SetRegions(largestRegion);
-    outImage->Allocate();
-    outImage->FillBuffer(0.0);
+        //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);
 
-    itk::ImageRegionIterator <ImageType> inItr(image,image->GetLargestPossibleRegion());
-    itk::ImageRegionIterator <ImageType> outItr(outImage,outImage->GetLargestPossibleRegion());
+        //Create iterators on input and output images
+        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);
+        //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);
+            }
 
-        ++inItr;
-        ++outItr;
+            //Move to following voxel
+            ++inItr;
+            ++outItr;
+        }
     }
 
+    //Write output image and exit
     anima::writeImage <ImageType> (outArg.getValue(),outImage);
-
     return EXIT_SUCCESS;
 }