ENH: Made ITK_NIFTI_IO_SFORM_PERMISSIVE_DEFAULT OFF by default

Made ITK_NIFTI_IO_SFORM_PERMISSIVE_DEFAULT OFF by default, added support for environment variable ITK_NIFTI_SFORM_PERMISSIVE
InsightSoftwareConsortium · Apr 13, 2023 · 3e45ceb · 3e45ceb
1 parent 3d3f3e5
commit 3e45ceb
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Showing 4 changed files with 25 additions and 4 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -339,8 +339,8 @@ endif()
 mark_as_advanced(ITK_NIFTI_IO_ANALYZE_FLAVOR)
 
 # Allow non-orthogonal rotation matrix approximation in NIFTI files
-option(ITK_NIFTI_IO_SFORM_PERMISSIVE "Allow non-orthogonal rotation matrix in NIFTI sform by default" ON)
-mark_as_advanced(ITK_NIFTI_IO_SFORM_PERMISSIVE)
+option(ITK_NIFTI_IO_SFORM_PERMISSIVE_DEFAULT "Allow non-orthogonal rotation matrix in NIFTI sform by default" OFF)
+mark_as_advanced(ITK_NIFTI_IO_SFORM_PERMISSIVE_DEFAULT)
 
 
 

diff --git a/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx b/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx
@@ -23,6 +23,8 @@
 #include "itkNiftiImageIOConfigurePrivate.h"
 #include "itkMakeUniqueForOverwrite.h"
 #include "vnl/algo/vnl_svd.h"
+#include "itksys/SystemTools.hxx"
+#include "itksys/SystemInformation.hxx"
 
 namespace itk
 {
@@ -450,7 +452,7 @@ NiftiImageIO::NiftiImageIO()
   : m_NiftiImageHolder(new NiftiImageProxy(nullptr))
   , m_NiftiImage(*m_NiftiImageHolder.get())
   , m_LegacyAnalyze75Mode{ ITK_NIFTI_IO_ANALYZE_FLAVOR_DEFAULT }
-  , m_SFORM_Permissive{ ITK_NIFTI_IO_SFORM_PERMISSIVE }
+  , m_SFORM_Permissive{ ITK_NIFTI_IO_SFORM_PERMISSIVE_DEFAULT }
 {
   this->SetNumberOfDimensions(3);
   nifti_set_debug_level(0); // suppress error messages
@@ -462,6 +464,12 @@ NiftiImageIO::NiftiImageIO()
     this->AddSupportedWriteExtension(ext);
     this->AddSupportedReadExtension(ext);
   }
+  std::string envVar;
+  if (itksys::SystemTools::GetEnv("ITK_NIFTI_SFORM_PERMISSIVE", envVar))
+  {
+    envVar = itksys::SystemTools::UpperCase(envVar);
+    this->SetSFORM_Permissive(envVar != "NO" && envVar != "OFF" && envVar != "FALSE");
+  }
 }
 
 NiftiImageIO::~NiftiImageIO()

diff --git a/Modules/IO/NIFTI/src/itkNiftiImageIOConfigurePrivate.h.in b/Modules/IO/NIFTI/src/itkNiftiImageIOConfigurePrivate.h.in
@@ -24,6 +24,6 @@
 // Analyze default flavour
 #define ITK_NIFTI_IO_ANALYZE_FLAVOR_DEFAULT NiftiImageIOEnums::Analyze75Flavor::Analyze@ITK_NIFTI_IO_ANALYZE_FLAVOR@
 // Enable permissive treatment of SFORM
-#cmakedefine01 ITK_NIFTI_IO_SFORM_PERMISSIVE
+#cmakedefine01 ITK_NIFTI_IO_SFORM_PERMISSIVE_DEFAULT
 
 #endif // itkNiftiImageIOConfigurePrivate_h
diff --git a/Modules/IO/NIFTI/test/itkNiftiReadWriteDirectionTest.cxx b/Modules/IO/NIFTI/test/itkNiftiReadWriteDirectionTest.cxx
@@ -21,6 +21,8 @@
 #include "itkImageFileReader.h"
 #include "itkImageFileWriter.h"
 #include "itkTestingMacros.h"
+#include "itksys/SystemTools.hxx"
+#include "itksys/SystemInformation.hxx"
 
 // debug
 #include <map>
@@ -161,6 +163,17 @@ itkNiftiReadWriteDirectionTest(int argc, char * argv[])
   // should not read the image with non-orthogonal sform
   ITK_TRY_EXPECT_EXCEPTION(ReadImage<TestImageType>(argv[4], false));
 
+  // check if environment flag is used properly
+  // check without permissive option
+  itksys::SystemTools::PutEnv("ITK_NIFTI_SFORM_PERMISSIVE=NO");
+  ITK_TRY_EXPECT_EXCEPTION(itk::ReadImage<TestImageType>(argv[4]));
+  // check with permissive option
+  itksys::SystemTools::PutEnv("ITK_NIFTI_SFORM_PERMISSIVE=YES");
+  ITK_TRY_EXPECT_NO_EXCEPTION(itk::ReadImage<TestImageType>(argv[4]));
+  // check with permissive option, when nothing is specified
+  itksys::SystemTools::PutEnv("ITK_NIFTI_SFORM_PERMISSIVE");
+  ITK_TRY_EXPECT_NO_EXCEPTION(itk::ReadImage<TestImageType>(argv[4]));
+
   // this should work
   TestImageType::Pointer inputImageNonOrthoSform = ReadImage<TestImageType>(argv[4], true);
   dictionary = inputImageNonOrthoSform->GetMetaDataDictionary();