Improve ITKReader, testITKio and testITKReader

ChangeLog.md

@@ -49,6 +49,8 @@
     out of range. (Kacper Pluta, [#1359](https://github.com/DGtal-team/DGtal/pull/1359))
 
 - *IO*
+  - Improve ITKReader, testITKio and testITKReader (Boris Mansencal,
+    [#1379](https://github.com/DGtal-team/DGtal/pull/1379))
   - Fix wrong typedef for double case in ITKReader (Adrien Krähenbühl,
     [#1259](https://github.com/DGtal-team/DGtal/pull/1322))
   - Fix safeguard when using ImageMagick without cmake activation (David Coeurjolly,

src/DGtal/images/ImageContainerByITKImage.h

@@ -51,6 +51,7 @@
 #if defined(__GNUG__)
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
+#pragma GCC diagnostic ignored "-Wpedantic"
 #endif
 #if defined(__clang__)
 #pragma clang diagnostic push

src/DGtal/io/readers/DicomReader.ih

@@ -43,6 +43,7 @@
 #if defined(__GNUG__)
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
+#pragma GCC diagnostic ignored "-Wpedantic"
 #endif
 #if defined(__clang__)
 #pragma clang diagnostic push

src/DGtal/io/readers/ITKReader.h

@@ -47,7 +47,21 @@
 #include "DGtal/images/CImage.h"
 #include "DGtal/base/BasicFunctors.h"
 #include "DGtal/io/ITKIOTrait.h"
+#if defined(__GNUG__)
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wpedantic"
+#endif
+#if defined(__clang__)
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wdocumentation"
+#endif
 #include <itkImageFileReader.h>
+#if defined(__clang__)
+#pragma clang diagnostic pop
+#endif
+#if defined(__GNUG__)
+#endif
+#pragma GCC diagnostic pop
 
 namespace DGtal
 {

src/DGtal/io/readers/ITKReader.ih

@@ -58,71 +58,74 @@ namespace DGtal {
   const TFunctor & aFunctor )
   {
     typedef typename Image::Domain Domain;
-    typedef typename Domain::Point Point;
     typedef itk::ImageIOBase::IOComponentType IOComponentType;
     BOOST_CONCEPT_ASSERT( (concepts::CUnaryFunctor<TFunctor, ValueOut, Value>));
     const IOComponentType componentType = getITKComponentType( filename );
-    typedef unsigned char ElementType;
     switch ( componentType )
     {
 
     default:
     case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
-      std::cerr << "Unknown and unsupported component type!" << std::endl;
+      trace.warning() << "[ITKReader] Unknown and unsupported component type! File will be loaded with UCHAR component type" << std::endl;
+      //fallthrough
     case itk::ImageIOBase::UCHAR:
     {
       typedef ImageContainerByITKImage<Domain, unsigned char> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     case itk::ImageIOBase::CHAR:
     {
       typedef ImageContainerByITKImage<Domain, char> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     case itk::ImageIOBase::USHORT:
     {
       typedef ImageContainerByITKImage<Domain, unsigned short> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     case itk::ImageIOBase::SHORT:
     {
       typedef ImageContainerByITKImage<Domain, short> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
+      return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
+    }
+    case itk::ImageIOBase::UINT:
+    {
+      typedef ImageContainerByITKImage<Domain, unsigned int> DGtalITKImage;
+      return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
+    }
+    case itk::ImageIOBase::INT:
+    {
+      typedef ImageContainerByITKImage<Domain, int> DGtalITKImage;
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     case itk::ImageIOBase::ULONG:
     {
       typedef ImageContainerByITKImage<Domain, unsigned long> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     case itk::ImageIOBase::LONG:
     {
       typedef ImageContainerByITKImage<Domain, long> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
+      return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
+    }
+    case itk::ImageIOBase::ULONGLONG:
+    {
+      typedef ImageContainerByITKImage<Domain, unsigned long long> DGtalITKImage;
+      return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
+    }
+    case itk::ImageIOBase::LONGLONG:
+    {
+      typedef ImageContainerByITKImage<Domain, long long> DGtalITKImage;
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     case itk::ImageIOBase::FLOAT:
     {
       typedef ImageContainerByITKImage<Domain, float> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     case itk::ImageIOBase::DOUBLE:
     {
       typedef ImageContainerByITKImage<Domain, double> DGtalITKImage;
-      Domain d;
-      DGtalITKImage im( d );
       return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor );
     }
     }
@@ -138,9 +141,11 @@ namespace DGtal {
     {
       itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
       filename.c_str(), itk::ImageIOFactory::ReadMode );
-      imageIO->SetFileName( filename.c_str() );
-      imageIO->ReadImageInformation();
-      componentType = imageIO->GetComponentType();
+      if (imageIO) {
+	imageIO->SetFileName( filename.c_str() );
+	imageIO->ReadImageInformation();
+	componentType = imageIO->GetComponentType();
+      }
     }
     catch ( itk::ExceptionObject & e )
     {
@@ -160,7 +165,7 @@ namespace DGtal {
     typedef typename TypeDGtalImage::ITKImagePointer ITKImagePointer;
     typedef typename Image::Domain Domain;
 
-    ITKImagePointer itk_image = TypeDGtalImage::ITKImage::New();
+    ITKImagePointer itk_image = nullptr;
 
     try
     {

src/DGtal/io/writers/ITKWriter.ih

@@ -31,6 +31,7 @@
 #if defined(__GNUG__)
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
+#pragma GCC diagnostic ignored "-Wpedantic"
 #endif
 #if defined(__clang__)
 #pragma clang diagnostic push

tests/io/readers/testITKReader.cpp

@@ -68,6 +68,23 @@ TEST_CASE( "Testing ITKReader" )
     testPath + "samples/lobsterCroped16b.mhd", resc );
     REQUIRE( ( im( Z3i::Point( 35, 29, 3 ) ) == resc( 60400 ) ) );
   }
+
+  SECTION(
+  "Testing behavior of ITKReader on non existent image file" )
+  {
+    bool caughtException = false;
+    const std::string filename = testPath + "samples/null.mhd"; //non existent file
+    try {
+      Image3DUC im = ITKReader<Image3DUC>::importITK(filename);
+    }
+    catch(exception &) {
+      caughtException = true;
+      trace.info() <<"Exception was correctly caught" << std::endl;
+    }
+    REQUIRE( caughtException == true);
+  }
+
+
 }
 
 /** @ingroup Tests **/

tests/io/testITKio.cpp

@@ -65,6 +65,7 @@ test_image(const string& filename)
 
     typedef typename std::vector<typename Image::Value> Values;
     Values values;
+    values.reserve(domain.size());
     for (typename Domain::Size kk=0; kk<domain.size(); kk++)
         values.push_back(rand());
 
@@ -103,31 +104,35 @@ bool testITKio()
   unsigned int nbok = 0;
   unsigned int nb = 0;
 
-  nbok += 6;
+  nb += 8;
   trace.beginBlock ( "Testing 2D ITK image value types ..." );
-  nb += test_image<ImageSelector<Z2i::Domain, int>::Type>("image_2d_int.mha");
-  nb += test_image<ImageSelector<Z2i::Domain, bool>::Type>("image_2d_bool.mha");
-  nb += test_image<ImageSelector<Z2i::Domain, unsigned int>::Type>("image_2d_unsigned_int.mha");
-  nb += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_2d_unsigned_char.mha");
-  nb += test_image<ImageSelector<Z2i::Domain, float>::Type>("image_2d_float.mha");
-  nb += test_image<ImageSelector<Z2i::Domain, double>::Type>("image_2d_double.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, int>::Type>("image_2d_int.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, bool>::Type>("image_2d_bool.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, unsigned int>::Type>("image_2d_unsigned_int.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_2d_unsigned_char.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, unsigned long>::Type>("image_2d_unsigned_long.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, long>::Type>("image_2d_long.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, float>::Type>("image_2d_float.mha");
+  nbok += test_image<ImageSelector<Z2i::Domain, double>::Type>("image_2d_double.mha");
   trace.endBlock();
 
-  nbok += 6;
+  nb += 8;
   trace.beginBlock ( "Testing 3D ITK image value types ..." );
-  nb += test_image<ImageSelector<Z3i::Domain, int>::Type>("image_3d_int.mha");
-  nb += test_image<ImageSelector<Z3i::Domain, bool>::Type>("image_3d_bool.mha");
-  nb += test_image<ImageSelector<Z3i::Domain, unsigned int>::Type>("image_3d_unsigned_int.mha");
-  nb += test_image<ImageSelector<Z3i::Domain, unsigned char>::Type>("image_3d_unsigned_char.mha");
-  nb += test_image<ImageSelector<Z3i::Domain, float>::Type>("image_3d_float.mha");
-  nb += test_image<ImageSelector<Z3i::Domain, double>::Type>("image_3d_double.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, int>::Type>("image_3d_int.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, bool>::Type>("image_3d_bool.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, unsigned int>::Type>("image_3d_unsigned_int.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, unsigned char>::Type>("image_3d_unsigned_char.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, unsigned long>::Type>("image_3d_unsigned_long.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, long>::Type>("image_3d_long.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, float>::Type>("image_3d_float.mha");
+  nbok += test_image<ImageSelector<Z3i::Domain, double>::Type>("image_3d_double.mha");
   trace.endBlock();
 
-  nbok += 3;
+  nb += 3;
   trace.beginBlock ( "Testing 2D ITK image formats ..." );
-  nb += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_unsigned_char.jpg"); nbok--; // jpg is lossy
-  nb += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_unsigned_char.png");
-  nb += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_unsigned_char.bmp");
+  nbok += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_unsigned_char.jpg"); nb--; // jpg is lossy
+  nbok += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_unsigned_char.png");
+  nbok += test_image<ImageSelector<Z2i::Domain, unsigned char>::Type>("image_unsigned_char.bmp");
   trace.endBlock();
 
   trace.info() << "(" << nbok << "/" << nb << ") " << endl;