BUG: GDCM reporting wrong spacing for some Media Types

Noticed and reported by Andriy Federov.  Andriy encountered a dataset
that reported spacing of 1,1,1, when the actual spacing was 0.178038,
0x.174924, 1. I traced the problem to some tortured logic in
gdcmImageHelper.cxx.  Since that is a 3rd party library, I modified
itkGDCMImageIO.cxx to work around the problem rather than fix the
version of GDCM in ITK.

Change-Id: I3ebfc828da36bca86d78123cedb29b0e88aca4c7

Modules/IO/GDCM/src/itkGDCMImageIO.cxx

@@ -51,6 +51,7 @@
 #include "gdcmUIDGenerator.h"
 #include "gdcmAttribute.h"
 #include "gdcmGlobal.h"
+#include "gdcmMediaStorage.h"
 
 #include <fstream>
 
@@ -356,16 +357,110 @@ void GDCMImageIO::InternalReadImageInformation()
   m_Dimensions[0] = dims[0];
   m_Dimensions[1] = dims[1];
 
-  const double *spacing = image.GetSpacing();
-  m_Spacing[0] = spacing[0];
-  m_Spacing[1] = spacing[1];
-  m_Spacing[2] = spacing[2];
+  double spacing[3];
 
-  const double *origin = image.GetOrigin();
-  m_Origin[0] = origin[0];
-  m_Origin[1] = origin[1];
-  m_Origin[2] = origin[2];
+  //
+  //
+  // This is a WORKAROUND for a bug in GDCM -- in
+  // ImageHeplper::GetSpacingTagFromMediaStorage it was not
+  // handling some MediaStorage types
+  // so we have to punt here.
+  gdcm::MediaStorage ms;
+
+  ms.SetFromFile(f);
+  switch(ms)
+    {
+    case gdcm::MediaStorage::HardcopyGrayscaleImageStorage:
+    case gdcm::MediaStorage::GEPrivate3DModelStorage:
+    case gdcm::MediaStorage::Philips3D:
+    case gdcm::MediaStorage::VideoEndoscopicImageStorage:
+    case gdcm::MediaStorage::UltrasoundMultiFrameImageStorage:
+    case gdcm::MediaStorage::UltrasoundImageStorage: // ??
+    case gdcm::MediaStorage::UltrasoundImageStorageRetired:
+    case gdcm::MediaStorage::UltrasoundMultiFrameImageStorageRetired:
+      {
+      std::vector<double> sp;
+      gdcm::Tag spacingTag(0x0028,0x0030);
+      if(ds.FindDataElement(spacingTag) &&
+         !ds.GetDataElement(spacingTag).IsEmpty())
+        {
+        gdcm::DataElement de = ds.GetDataElement(spacingTag);
+        const gdcm::Global &g = gdcm::GlobalInstance;
+        const gdcm::Dicts &dicts = g.GetDicts();
+        const gdcm::DictEntry &entry = dicts.GetDictEntry(de.GetTag());
+        const gdcm::VR & vr = entry.GetVR();
+        switch(vr)
+          {
+          case gdcm::VR::DS:
+            {
+            std::stringstream m_Ss;
+
+            gdcm::Element<gdcm::VR::DS,gdcm::VM::VM1_n> m_El;
+
+            const gdcm::ByteValue *                     bv = de.GetByteValue();
+            assert( bv );
+
+            std::string s = std::string( bv->GetPointer(), bv->GetLength() );
+
+            m_Ss.str( s );
+            // Stupid file: CT-MONO2-8-abdo.dcm
+            // The spacing is something like that: [0.2\0\0.200000]
+            // I would need to throw an expection that VM is not compatible
+            m_El.SetLength( entry.GetVM().GetLength() * entry.GetVR().GetSizeof() );
+            m_El.Read( m_Ss );
+
+            assert( m_El.GetLength() == 2 );
+            for(unsigned long i = 0; i < m_El.GetLength(); ++i)
+              sp.push_back( m_El.GetValue(i) );
+            std::swap( sp[0], sp[1]);
+            assert( sp.size() == (unsigned int)entry.GetVM() );
+            }
+            break;
+          case gdcm::VR::IS:
+            {
+            std::stringstream m_Ss;
 
+            gdcm::Element<gdcm::VR::IS,gdcm::VM::VM1_n> m_El;
+
+            const gdcm::ByteValue *bv = de.GetByteValue();
+            assert( bv );
+
+            std::string s = std::string( bv->GetPointer(), bv->GetLength() );
+            m_Ss.str( s );
+            m_El.SetLength( entry.GetVM().GetLength() * entry.GetVR().GetSizeof() );
+            m_El.Read( m_Ss );
+            for(unsigned long i = 0; i < m_El.GetLength(); ++i)
+              sp.push_back( m_El.GetValue(i) );
+            assert( sp.size() == (unsigned int)entry.GetVM() );
+            }
+            break;
+          default:
+            assert(0);
+            break;
+          }
+        }
+        spacing[0] = sp[0];
+        spacing[1] = sp[1];
+        spacing[2] = 1.0; // punt?
+      }
+      break;
+    default:
+      {
+      const double *sp;
+      sp = image.GetSpacing();
+      spacing[0] = sp[0];
+      spacing[1] = sp[1];
+      spacing[2] = sp[2];
+      }
+    break;
+    }
+
+  const double *origin = image.GetOrigin();
+  for(unsigned i = 0; i < 3; ++i)
+    {
+    m_Spacing[i] = spacing[i];
+    m_Origin[i] = origin[i];
+    }
   if ( image.GetNumberOfDimensions() == 3 )
     {
     m_Dimensions[2] = dims[2];

Modules/IO/GDCM/test/CMakeLists.txt

@@ -10,6 +10,7 @@ itkGDCMSeriesStreamReadImageWriteTest.cxx
 itkGDCMImagePositionPatientTest.cxx
 itkGDCMImageIOOrthoDirTest.cxx
 itkGDCMImageOrientationPatientTest.cxx
+itkGDCMLoadImageSpacingTest.cxx
 )
 
 CreateTestDriver(ITKIOGDCM  "${ITKIOGDCM-Test_LIBRARIES}" "${ITKIOGDCMTests}")
@@ -80,3 +81,8 @@ set_property(TEST itkGDCMSeriesMissingDicomTagTest APPEND PROPERTY DEPENDS ITKDa
 
 itk_add_test(NAME itkGDCMImageIONoCrashTest
              COMMAND ITKIOGDCMTestDriver itkGDCMImageIONoCrashTest DATA{${ITK_DATA_ROOT}/Input/OT-PAL-8-face.dcm})
+
+itk_add_test(NAME itkGDCMLoadImageSpacingTest
+  COMMAND ITKIOGDCMTestDriver itkGDCMLoadImageSpacingTest
+  DATA{Input/gdcmSpacingTest.dcm}
+  )

Modules/IO/GDCM/test/Input/gdcmSpacingTest.dcm.md5

@@ -0,0 +1 @@
+6772e7ad0331fed4832ee98ecae4c70d

Modules/IO/GDCM/test/itkGDCMLoadImageSpacingTest.cxx

@@ -0,0 +1,73 @@
+/*=========================================================================
+ *
+ *  Copyright Insight Software Consortium
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+#include <iostream>
+#include "itkGDCMSeriesFileNames.h"
+#include "itkGDCMImageIO.h"
+#include "itkImageFileReader.h"
+#include "gdcmImageHelper.h"
+
+typedef itk::Image<unsigned short, 2>   ImageType;
+typedef itk::ImageFileReader<ImageType> ReaderType;
+
+//
+// This test is specifically for a problem detected in GDCMImageIO
+// by Andriy Fedorov, who noticed that the DCMTK reader
+// reported the correct spacing for this DICOM dataset, but GDCM
+// report spacing of 1,1,1 ... looking through the gdcm library
+// code in Modules/ThirdParty/GDCM, I noticed that in
+// gdcmImageHelper.cxx there was a bunch of elaborate code that in the
+// case of Andriy's dataset, used the wrong tag to find the spacing,
+// ignored the error when the tag wasn't found, and silenetly returned
+// 1,1,1 for the spacing.
+// The patch that this test is part of has a fallback for the case of
+// the MediaStorageTypes for which gdcm has trouble with the spacing tag.
+
+template <typename TIO, typename TSeriesNames>
+int
+ReadFile(const char *fname)
+{
+  typename TIO::Pointer imageIO = TIO::New();
+  typename ReaderType::Pointer reader = ReaderType::New();
+
+  reader->SetImageIO(imageIO);
+  reader->SetFileName(fname);
+
+  reader->Update();
+  typename ImageType::Pointer image = reader->GetOutput();
+  std::cout << image << std::endl;
+  typename ImageType::SpacingType spacing = image->GetSpacing();
+  if(vcl_abs(spacing[0]-0.178038) >= 0.000001 ||
+     vcl_abs(spacing[1]-0.174924) >= 0.000001)
+    {
+    return EXIT_FAILURE;
+    }
+
+  return EXIT_SUCCESS;
+}
+
+int itkGDCMLoadImageSpacingTest(int argc, char *argv[])
+{
+  if(argc < 2)
+    {
+    std::cerr << "Missing image filename argument" << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  const char *fname = argv[1];
+  return ReadFile<itk::GDCMImageIO,itk::GDCMSeriesFileNames>(fname);
+}