BUG: Set NIFTI header xyzt_units field correctly

Previously, the correct xyzt code was assigned to the 'xyz_units' variable,
but time gets masked out because it's only for space units, resulting in
xyzt_units=2.

Fix by setting 'time_units' to NIFTI_UNITS_SEC.

This produces images with xyzt_units == 10, which is correct for ITK output
(NIFTI_UNITS_MM | NIFTI_UNITS_SEC)

Modules/IO/NIFTI/src/itkNiftiImageIO.cxx

@@ -1503,13 +1503,14 @@ NiftiImageIO::WriteImageInformation()
   //                   dim[2] is required for 2-D volumes,
   //                   dim[3] for 3-D volumes, etc.
   this->m_NiftiImage->nvox = 1;
-  // Spacial dims in ITK are given in mm.
+  // Spatial dims in ITK are given in mm.
   // If 4D assume 4thD is in SECONDS, for all of ITK.
   // NOTE: Due to an ambiguity in the nifti specification, some developers
   // external tools believe that the time units must be set, even if there
-  // is only one dataset.  Having the time specified for a purly spatial
+  // is only one dataset.  Having the time specified for a purely spatial
   // image has no consequence, so go ahead and set it to seconds.
-  this->m_NiftiImage->xyz_units = static_cast<int>(NIFTI_UNITS_MM | NIFTI_UNITS_SEC);
+  this->m_NiftiImage->xyz_units = static_cast<int>(NIFTI_UNITS_MM);
+  this->m_NiftiImage->time_units = static_cast<int>(NIFTI_UNITS_SEC);
   this->m_NiftiImage->dim[7] = this->m_NiftiImage->nw = 1;
   this->m_NiftiImage->dim[6] = this->m_NiftiImage->nv = 1;
   this->m_NiftiImage->dim[5] = this->m_NiftiImage->nu = 1;
@@ -2364,7 +2365,7 @@ NiftiImageIO::Write(const void * buffer)
                                         // so will destructor of the image that really owns it.
     if (nifti_write_status)
     {
-      itkExceptionMacro("ERROR: nifti library failed to write image" << this->GetFileName());
+      itkExceptionMacro("ERROR: nifti library failed to write image: " << this->GetFileName());
     }
   }
   else /// Image intent is vector image
@@ -2469,7 +2470,7 @@ NiftiImageIO::Write(const void * buffer)
     this->m_NiftiImage->data = nullptr; // if left pointing to data buffer
     if (nifti_write_status)
     {
-      itkExceptionMacro("ERROR: nifti library failed to write image" << this->GetFileName());
+      itkExceptionMacro("ERROR: nifti library failed to write image: " << this->GetFileName());
     }
   }
 }

Modules/IO/NIFTI/test/CMakeLists.txt

@@ -13,6 +13,7 @@ set(ITKIONIFTITests
     itkNiftiImageIOTest11.cxx
     itkNiftiImageIOTest12.cxx
     itkNiftiImageIOTest13.cxx
+    itkNiftiImageIOTest14.cxx
     itkNiftiLargeImageRegionReadTest.cxx
     itkNiftiReadAnalyzeTest.cxx
     itkNiftiReadWriteDirectionTest.cxx
@@ -245,6 +246,14 @@ itk_add_test(
   itkNiftiImageIOTest13
   DATA{Input/SmallVoxels_AffinePrecision.nii.gz})
 
+itk_add_test(
+  NAME
+  itkNiftiSpatialTemporalUnitsTest
+  COMMAND
+  ITKIONIFTITestDriver
+  itkNiftiImageIOTest14
+  ${ITK_TEST_OUTPUT_DIR})
+
 itk_add_test(
   NAME
   itkNiftiQFormSFormDifferentSpacingTest

Modules/IO/NIFTI/test/itkNiftiImageIOTest14.cxx

@@ -0,0 +1,109 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  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
+ *
+ *         https://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 "itkNiftiImageIOTest.h"
+#include "itkTestingMacros.h"
+
+// Test writing NIFTI xyzt_units field - should be 10 (mm, sec)
+int
+itkNiftiImageIOTest14(int argc, char * argv[])
+{
+
+  if (argc > 1)
+  {
+    char * testdir = argv[1];
+    itksys::SystemTools::ChangeDirectory(testdir);
+  }
+  else
+  {
+    return EXIT_FAILURE;
+  }
+
+  constexpr unsigned int Dimension = 3;
+
+  using PixelType = float;
+  using ImageType = itk::Image<PixelType, Dimension>;
+
+  ImageType::Pointer image;
+
+  // fill out an image and write it as nifti.
+  const char * filename = "xyzt_unit_check.nii";
+  using OutputImageType = itk::Image<PixelType, Dimension>;
+  typename OutputImageType::RegionType region;
+  typename OutputImageType::IndexType  start;
+  typename OutputImageType::SizeType   size;
+  size[0] = 8;
+  size[1] = 8;
+  size[2] = 4;
+  region.SetSize(size);
+  region.SetIndex(start);
+  auto outputimage = OutputImageType::New();
+  outputimage->SetRegions(region);
+  outputimage->Allocate();
+
+  auto writer = itk::ImageFileWriter<OutputImageType>::New();
+  auto niftiImageIO = itk::NiftiImageIO::New();
+  writer->SetImageIO(niftiImageIO);
+  writer->SetFileName(filename);
+  writer->SetInput(outputimage);
+  try
+  {
+    writer->Update();
+  }
+  catch (const itk::ExceptionObject & err)
+  {
+    std::cerr << "Exception Object caught: " << std::endl << err << std::endl;
+    throw;
+  }
+
+  bool fileHasCorrectXYZTTUnits = false;
+
+  try
+  {
+    // read the image back in
+    ImageType::Pointer image_from_disk = itk::IOTestHelper::ReadImage<ImageType>(std::string(filename));
+    // check the metadata for xyzt_units
+    itk::MetaDataDictionary & dictionary = image_from_disk->GetMetaDataDictionary();
+    std::string               xyzt_units;
+    if (!itk::ExposeMetaData<std::string>(dictionary, "xyzt_units", xyzt_units))
+    {
+      std::cerr << "xyzt_units not found in metadata" << std::endl;
+    }
+    if (xyzt_units == "10")
+    {
+      fileHasCorrectXYZTTUnits = true;
+    }
+    else
+    {
+      std::cerr << "xyzt_units not set correctly in metadata" << std::endl;
+      fileHasCorrectXYZTTUnits = false;
+    }
+  }
+  catch (...)
+  {
+    std::cerr << "Exception caught while reading image back in" << std::endl;
+  }
+
+  itk::IOTestHelper::Remove(filename);
+
+  if (fileHasCorrectXYZTTUnits)
+  {
+    return EXIT_SUCCESS;
+  }
+  return EXIT_FAILURE;
+}