ENH: allow Nifti with wrong scales in sform

Allow loading of Nifti files incorrectly written by by VINCI with wrong scales in sform, s. InsightSoftwareConsortium#3514
issakomi · Aug 16, 2022 · 3e84173 · 3e84173
1 parent b9005b8
commit 3e84173
Showing 1 changed file with 12 additions and 7 deletions.
diff --git a/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx b/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx
@@ -1912,22 +1912,27 @@ NiftiImageIO::SetImageIOOrientationFromNIfTI(unsigned short dims)
           vnl_matrix_fixed<float, 3, 3> rotation = sto_xyz.extract(3, 3, 0, 0);
           {
             // Ensure that the scales are approximately the same for spacing directions
+            bool                       sform_scales_ok{ true };
             vnl_vector_fixed<float, 3> scale;
             scale[0] = rotation.get_column(0).magnitude();
+            scale[1] = rotation.get_column(1).magnitude();
+            scale[2] = rotation.get_column(2).magnitude();
             constexpr float large_value_tolerance = 1e-3; // Numerical precision of sform is not very good
             if (itk::Math::abs(this->m_NiftiImage->dx - scale[0]) > large_value_tolerance)
             {
-              return false;
+              sform_scales_ok = false;
             }
-            scale[1] = rotation.get_column(1).magnitude();
-            if (itk::Math::abs(this->m_NiftiImage->dy - scale[1]) > large_value_tolerance)
+            else if (itk::Math::abs(this->m_NiftiImage->dy - scale[1]) > large_value_tolerance)
             {
-              return false;
+              sform_scales_ok = false;
             }
-            scale[2] = rotation.get_column(2).magnitude();
-            if (itk::Math::abs(this->m_NiftiImage->dz - scale[2]) > large_value_tolerance)
+            else if (itk::Math::abs(this->m_NiftiImage->dz - scale[2]) > large_value_tolerance)
+            {
+              sform_scales_ok = false;
+            }
+            if (!sform_scales_ok)
             {
-              return false;
+              itkWarningMacro(<< this->GetFileName() << " has unexpected scales in sform");
             }
           }
           // Remove scale from columns