Fix #2338 - Mesh generation from distance transforms. (#2339)

* Fix #2338 - Mesh generation from distance transforms.

The code I had added to handle the segmentations was only meant for segmentations, not distance transforms.

Author: akenmorris

Libs/Analyze/MeshGenerator.cpp

@@ -100,8 +100,10 @@ MeshHandle MeshGenerator::build_mesh_from_image(ImageType::Pointer image, float
   try {
     // only interested in 1's and 0's
     Image itk_image = Image(image);
-    itk_image.binarize(0, 1);
-    image = itk_image.getITKImage();
+    if (!itk_image.isDistanceTransform()) {
+      itk_image.binarize(0, 1);
+      image = itk_image.getITKImage();
+    }
 
     // connect to VTK
     vtkSmartPointer<vtkImageImport> vtk_image = vtkSmartPointer<vtkImageImport>::New();

Libs/Image/Image.cpp

@@ -938,7 +938,7 @@ Point3 Image::centerOfMass(PixelType minVal, PixelType maxVal) const {
   return com;
 }
 
-Image::StatsPtr Image::statsFilter() {
+Image::StatsPtr Image::statsFilter() const {
   using FilterType = itk::StatisticsImageFilter<ImageType>;
   FilterType::Pointer filter = FilterType::New();
 
@@ -1159,6 +1159,15 @@ Image& Image::fill(PixelType value) {
   return *this;
 }
 
+//-------------------------------------------------------------------------
+bool Image::isDistanceTransform() const {
+  auto stats = statsFilter();
+  // examine scalar range of image
+  auto min = stats->GetMinimum();
+  auto max = stats->GetMaximum();
+  return (min < 0 && max > 0);
+}
+
 //-------------------------------------------------------------------------
 TransformPtr Image::createCenterOfMassTransform() {
   AffineTransformPtr xform(AffineTransform::New());

Libs/Image/Image.h

@@ -36,12 +36,13 @@ class Image {
   using InterpolatorType = itk::LinearInterpolateImageFunction<ImageType>;
 
   // constructors and assignment operators //
-  Image(const Dims dims);
-  Image(const std::string& pathname) : itk_image_(read(pathname)) {}
-  Image(ImageType::Pointer imagePtr) : itk_image_(imagePtr) {
+  explicit Image(const Dims dims);
+  explicit Image(const std::string& pathname) : itk_image_(read(pathname)) {}
+  explicit Image(ImageType::Pointer imagePtr) : itk_image_(imagePtr) {
     if (!itk_image_) throw std::invalid_argument("null imagePtr");
   }
-  Image(const vtkSmartPointer<vtkImageData> vtkImage);
+  explicit Image(const vtkSmartPointer<vtkImageData> vtkImage);
+
   Image(Image&& img) : itk_image_(nullptr) { this->itk_image_.Swap(img.itk_image_); }
   Image(const Image& img) : itk_image_(cloneData(img.itk_image_)) {}
   Image& operator=(const Image& img);  /// lvalue assignment operator
@@ -306,6 +307,9 @@ class Image {
   //! fill with value
   Image& fill(PixelType value);
 
+  //! Return if the image is a distance transform
+  bool isDistanceTransform() const;
+
   //! Return supported file types
   static std::vector<std::string> getSupportedTypes() {
     return {"nrrd", "nii", "nii.gz", "mhd", "tiff", "jpeg", "jpg", "png", "dcm", "ima"};
@@ -340,7 +344,7 @@ class Image {
   /// pad image by the given dims (always positive) in each direction
   Image& pad(Dims lowerExtendRegion, Dims upperExtendRegion, PixelType value = 0.0);
 
-  StatsPtr statsFilter();
+  StatsPtr statsFilter() const;
 
   ImageType::Pointer itk_image_;
 

Testing/ImageTests/ImageTests.cpp

@@ -328,7 +328,7 @@ TEST(ImageTests, intensityTest) {
 
 TEST(ImageTests, setlevelTest) {
   Image image(std::string(TEST_DATA_DIR) + "/1x2x2.nrrd");
-  image.applyTPLevelSetFilter(std::string(TEST_DATA_DIR) + "/curvature1.nrrd");
+  image.applyTPLevelSetFilter(Image(std::string(TEST_DATA_DIR) + "/curvature1.nrrd"));
   Image ground_truth(std::string(TEST_DATA_DIR) + "/set-level_baseline.nrrd");
 
   ASSERT_TRUE(image == ground_truth);

Testing/MeshTests/MeshTests.cpp

@@ -316,7 +316,7 @@ TEST(MeshTests, fillHolesTest) {
 
 TEST(MeshTests, probeVolumeTest) {
   Mesh femur(std::string(TEST_DATA_DIR) + "/femur.vtk");
-  femur.probeVolume(std::string(TEST_DATA_DIR) + "/femurVtkDT.nrrd");
+  femur.probeVolume(Image(std::string(TEST_DATA_DIR) + "/femurVtkDT.nrrd"));
   Mesh ground_truth(std::string(TEST_DATA_DIR) + "/probe.vtk");
 
   ASSERT_TRUE(femur == ground_truth);