BUG: Fix TransformMINC

convert MINC PositiveCoordinateOrientation RAS coordinate system to ITK PositiveCoordinateOrientation LPS
InsightSoftwareConsortium · Dec 6, 2024 · a8811a0 · a8811a0
1 parent ef1ae91
commit a8811a0
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Showing 14 changed files with 452 additions and 122 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -372,6 +372,10 @@ mark_as_advanced(ITK_NIFTI_IO_ANALYZE_FLAVOR)
 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)
 
+# Automatically convert MINC coordinate system from PositiveCoordinateOrientation RAS to PositiveCoordinateOrientation LPS
+option(ITK_MINC_IO_RAS_TO_LPS "Convert MINC coordinate system from PositiveCoordinateOrientation RAS to PositiveCoordinateOrientation LPS by default" ON)
+
+mark_as_advanced(ITK_MINC_IO_RAS_TO_LPS)
 #-----------------------------------------------------------------------------
 # ITK build classes that are in the review process
 # ITK_USE_REVIEW is deprecated, only kept for backward compatibility

diff --git a/Modules/IO/MINC/include/itkMINCImageIO.h b/Modules/IO/MINC/include/itkMINCImageIO.h
@@ -123,6 +123,11 @@ class ITKIOMINC_EXPORT MINCImageIO : public ImageIOBase
   void
   Write(const void * buffer) override;
 
+  /** Set to automatically convert from PositiveCoordinateOrientation RAS to PositiveCoordinateOrientation LPS*/
+  itkSetMacro(RAStoLPS, bool);
+  itkGetConstMacro(RAStoLPS, bool);
+  itkBooleanMacro(RAStoLPS);
+
 protected:
   MINCImageIO();
   ~MINCImageIO() override;
@@ -153,6 +158,7 @@ class ITKIOMINC_EXPORT MINCImageIO : public ImageIOBase
 
   // complex type images, composed of complex numbers
   // int m_Complex;
+  bool m_RAStoLPS;
 };
 } // end namespace itk
 

diff --git a/Modules/IO/MINC/src/CMakeLists.txt b/Modules/IO/MINC/src/CMakeLists.txt
@@ -1,3 +1,6 @@
+configure_file(itkMINCImageIOConfigurePrivate.h.in itkMINCImageIOConfigurePrivate.h @ONLY)
+include_directories("${CMAKE_CURRENT_BINARY_DIR}")
+
 set(ITKIOMINC_SRC itkMINCImageIO.cxx itkMINCImageIOFactory.cxx)
 
 add_library(ITKIOMINC ${ITK_LIBRARY_BUILD_TYPE} ${ITKIOMINC_SRC})

diff --git a/Modules/IO/MINC/src/itkMINCImageIO.cxx b/Modules/IO/MINC/src/itkMINCImageIO.cxx
@@ -29,6 +29,9 @@
 
 #include <memory> // For unique_ptr.
 
+#include "itkMINCImageIOConfigurePrivate.h"
+
+
 extern "C"
 {
   void
@@ -235,6 +238,7 @@ MINCImageIO::CloseVolume()
 
 MINCImageIO::MINCImageIO()
   : m_MINCPImpl(std::make_unique<MINCImageIOPImpl>())
+  , m_RAStoLPS(ITK_MINC_IO_RAS_TO_LPS)
 {
   for (auto & dimensionIndex : m_MINCPImpl->m_DimensionIndices)
   {
@@ -283,6 +287,7 @@ MINCImageIO::PrintSelf(std::ostream & os, Indent indent) const
 
   os << indent << "MINCPImpl: " << m_MINCPImpl.get() << std::endl;
   os << indent << "DirectionCosines: " << m_DirectionCosines << std::endl;
+  os << indent << "RAStoLPS: " << m_RAStoLPS << std::endl;
 }
 
 void
@@ -511,9 +516,11 @@ MINCImageIO::ReadImageInformation()
     }
   }
 
+
   // Transform MINC PositiveCoordinateOrientation RAS coordinates to
   // internal ITK PositiveCoordinateOrientation LPS Coordinates
-  dir_cos = RAS_tofrom_LPS * dir_cos;
+  if (this->m_RAStoLPS)
+    dir_cos = RAS_tofrom_LPS * dir_cos;
 
   // Transform origin coordinates
   o_origin = dir_cos * origin;
@@ -688,6 +695,9 @@ MINCImageIO::ReadImageInformation()
   std::string classname(GetNameOfClass());
   //  EncapsulateMetaData<std::string>(thisDic,ITK_InputFilterName,
   // classname);
+  // preserve information if the volume was PositiveCoordinateOrientation RAS to PositiveCoordinateOrientation LPS
+  // converted
+  EncapsulateMetaData<bool>(thisDic, "RAStoLPS", m_RAStoLPS);
 
   // store history
   size_t minc_history_length = 0;
@@ -997,8 +1007,10 @@ MINCImageIO::WriteImageInformation()
   const vnl_matrix<double> inverseDirectionCosines{ vnl_matrix_inverse<double>(dircosmatrix).as_matrix() };
   origin *= inverseDirectionCosines; // transform to minc convention
 
+
   // Convert ITK direction cosines from PositiveCoordinateOrientation LPS to PositiveCoordinateOrientation RAS
-  dircosmatrix *= RAS_tofrom_LPS;
+  if (this->m_RAStoLPS)
+    dircosmatrix *= RAS_tofrom_LPS;
 
   for (unsigned int i = 0; i < nDims; ++i)
   {
@@ -1028,38 +1040,32 @@ MINCImageIO::WriteImageInformation()
   {
     case IOComponentEnum::UCHAR:
       m_MINCPImpl->m_Volume_type = MI_TYPE_UBYTE;
-      // m_MINCPImpl->m_Volume_class=MI_CLASS_INT;
       break;
     case IOComponentEnum::CHAR:
       m_MINCPImpl->m_Volume_type = MI_TYPE_BYTE;
-      // m_MINCPImpl->m_Volume_class=MI_CLASS_INT;
       break;
     case IOComponentEnum::USHORT:
       m_MINCPImpl->m_Volume_type = MI_TYPE_USHORT;
-      // m_MINCPImpl->m_Volume_class=MI_CLASS_INT;
       break;
     case IOComponentEnum::SHORT:
       m_MINCPImpl->m_Volume_type = MI_TYPE_SHORT;
-      // m_MINCPImpl->m_Volume_class=MI_CLASS_INT;
       break;
     case IOComponentEnum::UINT:
       m_MINCPImpl->m_Volume_type = MI_TYPE_UINT;
-      // m_MINCPImpl->m_Volume_class=MI_CLASS_INT;
       break;
     case IOComponentEnum::INT:
       m_MINCPImpl->m_Volume_type = MI_TYPE_INT;
-      // m_MINCPImpl->m_Volume_class=MI_CLASS_INT;
       break;
       //     case IOComponentEnum::ULONG://TODO: make sure we are cross-platform here!
       //       volume_data_type=MI_TYPE_ULONG;
       //       break;
       //     case IOComponentEnum::LONG://TODO: make sure we are cross-platform here!
       //       volume_data_type=MI_TYPE_LONG;
       //       break;
-    case IOComponentEnum::FLOAT: // TODO: make sure we are cross-platform here!
+    case IOComponentEnum::FLOAT:
       m_MINCPImpl->m_Volume_type = MI_TYPE_FLOAT;
       break;
-    case IOComponentEnum::DOUBLE: // TODO: make sure we are cross-platform here!
+    case IOComponentEnum::DOUBLE:
       m_MINCPImpl->m_Volume_type = MI_TYPE_DOUBLE;
       break;
     default:
@@ -1099,7 +1105,6 @@ MINCImageIO::WriteImageInformation()
   if (ExposeMetaData<std::string>(thisDic, "dimension_order", dimension_order))
   {
     // the format should be ((+|-)(X|Y|Z|V|T))*
-    // std::cout<<"Restoring original dimension order:"<<dimension_order.c_str()<<std::endl;
     if (dimension_order.length() == (minc_dimensions * 2))
     {
       dimorder_good = true;
@@ -1338,6 +1343,13 @@ MINCImageIO::WriteImageInformation()
       // TODO: figure out what to do with it
     }
   }
+
+  // preserve information of MINC PositiveCoordinateOrientation RAS to ITK PositiveCoordinateOrientation LPS conversion
+  {
+    int tmp = (int)this->m_RAStoLPS;
+    miset_attr_values(m_MINCPImpl->m_Volume, MI_TYPE_INT, "itk", "RAStoLPS", 1, &tmp);
+  }
+
   mifree_volume_props(hprops);
 }
 

diff --git a/Modules/IO/MINC/src/itkMINCImageIOConfigurePrivate.h.in b/Modules/IO/MINC/src/itkMINCImageIOConfigurePrivate.h.in
@@ -0,0 +1,27 @@
+/*=========================================================================
+ *
+ *  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.
+ *
+ *=========================================================================*/
+#ifndef itkMINCImageIOConfigurePrivate_h
+#define itkMINCImageIOConfigurePrivate_h
+
+// This file is intended to hold preprocessor macros only used internally by
+// IO/MINC module and should not be installed.
+
+// Convert from PositiveCoordinateOrientation RAS to PositiveCoordinateOrientation LPS by default
+#cmakedefine01 ITK_MINC_IO_RAS_TO_LPS
+
+#endif // itkMINCImageIOConfigurePrivate_h
diff --git a/Modules/IO/MINC/test/CMakeLists.txt b/Modules/IO/MINC/test/CMakeLists.txt
@@ -1,5 +1,9 @@
 itk_module_test()
 
+# to know system default MINC PositiveCoordinateOrientation RAS to PositiveCoordinateOrientation LPS mode
+include_directories("${CMAKE_CURRENT_BINARY_DIR}/../src")
+
+
 if(NOT ITK_USE_SYSTEM_HDF5)
   include_directories("${ITKHDF5_SOURCE_DIR}/src/itkhdf5" "${ITKHDF5_SOURCE_DIR}/src/itkhdf5/src"
                       "${ITKHDF5_BINARY_DIR}/src/itkhdf5")
@@ -42,7 +46,9 @@ itk_add_test(
   ${ITK_TEST_OUTPUT_DIR}/t1_z+_byte_cor_2.mnc
   itkMINCImageIOTest4
   DATA{Input/t1_z+_byte_cor.mnc}
-  ${ITK_TEST_OUTPUT_DIR}/t1_z+_byte_cor_2.mnc)
+  ${ITK_TEST_OUTPUT_DIR}/t1_z+_byte_cor_2.mnc
+  0
+  )
 
 itk_add_test(
   NAME
@@ -54,7 +60,9 @@ itk_add_test(
   ${ITK_TEST_OUTPUT_DIR}/HeadMRVolume.mnc
   itkMINCImageIOTest4
   DATA{${ITK_DATA_ROOT}/Input/HeadMRVolume.mhd,HeadMRVolume.raw}
-  ${ITK_TEST_OUTPUT_DIR}/HeadMRVolume.mnc)
+  ${ITK_TEST_OUTPUT_DIR}/HeadMRVolume.mnc
+  -1
+  )
 
 # Test to make sure that inter-slice normalization was properly dealt with
 itk_add_test(
@@ -67,7 +75,8 @@ itk_add_test(
   ${ITK_TEST_OUTPUT_DIR}/t1_z+_ubyte_yxz_nonorm_noParams.mnc
   itkMINCImageIOTest4
   DATA{Input/t1_z+_ubyte_yxz_nonorm.mnc}
-  ${ITK_TEST_OUTPUT_DIR}/t1_z+_ubyte_yxz_nonorm_noParams.mnc)
+  ${ITK_TEST_OUTPUT_DIR}/t1_z+_ubyte_yxz_nonorm_noParams.mnc
+  0)
 
 itk_add_test(
   NAME
@@ -79,7 +88,8 @@ itk_add_test(
   ${ITK_TEST_OUTPUT_DIR}/t1_z+_float_yxz_nonorm_noParams.mnc
   itkMINCImageIOTest4
   DATA{Input/t1_z+_float_yxz_nonorm.mnc}
-  ${ITK_TEST_OUTPUT_DIR}/t1_z+_float_yxz_nonorm_noParams.mnc)
+  ${ITK_TEST_OUTPUT_DIR}/t1_z+_float_yxz_nonorm_noParams.mnc
+  0)
 
 itk_add_test(
   NAME
@@ -130,6 +140,7 @@ itk_add_test(
   itkMINCImageIOTest4
   DATA{Input/t1_z+_float_yxz_nonorm.mnc}
   ${ITK_TEST_OUTPUT_DIR}/t1_z+_float_yxz_nonorm.mnc
+  0 # RAStoLPS
   427621.7839
   -8.195741583
   72.45998819
@@ -146,6 +157,7 @@ itk_add_test(
   itkMINCImageIOTest4
   DATA{Input/t1_z+_float_yxz_norm.mnc}
   ${ITK_TEST_OUTPUT_DIR}/t1_z+_float_yxz_norm.mnc
+  0 # RAStoLPS
   427621.7839
   -8.195741583
   72.45998819
@@ -162,47 +174,51 @@ itk_add_test(
   itkMINCImageIOTest4
   DATA{Input/t1_z+_ubyte_yxz_nonorm.mnc}
   ${ITK_TEST_OUTPUT_DIR}/t1_z+_ubyte_yxz_nonorm.mnc
+  0 # RAStoLPS
   427621.7838
   -8.195741583
   72.45998819
   -3.148534512)
 
 # multiple loops because of different numerical parameters
+foreach(rastoeps 0;1)
+  foreach(type byte;short;ubyte)
+    foreach(axis cor;sag;trans)
+      foreach(plusMinus -;+)
+        set(imageName t1_z${plusMinus}_${type}_${axis})
+        set(outImage ${ITK_TEST_OUTPUT_DIR}/${imageName}-${rastoeps}.mnc)
 
-foreach(type byte;short;ubyte)
-  foreach(axis cor;sag;trans)
-    foreach(plusMinus -;+)
-      set(imageName t1_z${plusMinus}_${type}_${axis})
-      set(outImage ${ITK_TEST_OUTPUT_DIR}/${imageName}.mnc)
-
-      itk_add_test(
-        NAME
-        itkMINCImageIOTest-COM-${imageName}
-        COMMAND
-        ITKIOMINCTestDriver
-        --compare
-        DATA{Input/${imageName}.mnc}
-        ${outImage}
-        itkMINCImageIOTest4
-        DATA{Input/${imageName}.mnc}
-        ${outImage}
-        427620.3115
-        -8.195582241
-        72.46002233
-        -3.148594157) # this line is different
+        itk_add_test(
+          NAME
+          itkMINCImageIOTest-COM-${imageName}-${rastoeps}
+          COMMAND
+          ITKIOMINCTestDriver
+          --compare
+          DATA{Input/${imageName}.mnc}
+          ${outImage}
+          itkMINCImageIOTest4
+          DATA{Input/${imageName}.mnc}
+          ${outImage}
+          ${rastoeps} # RAStoLPS
+          427620.3115
+          -8.195582241
+          72.46002233
+          -3.148594157) # this line is different
+      endforeach()
     endforeach()
   endforeach()
 endforeach()
 
+foreach(rastoeps 0;1)
 foreach(type double;float;long;ulong)
   foreach(axis cor;sag;trans)
     foreach(plusMinus -;+)
       set(imageName t1_z${plusMinus}_${type}_${axis})
-      set(outImage ${ITK_TEST_OUTPUT_DIR}/${imageName}.mnc)
+      set(outImage ${ITK_TEST_OUTPUT_DIR}/${imageName}_${rastoeps}.mnc)
 
       itk_add_test(
         NAME
-        itkMINCImageIOTest-COM-${imageName}
+        itkMINCImageIOTest-COM-${imageName}-${rastoeps}
         COMMAND
         ITKIOMINCTestDriver
         --compare
@@ -211,23 +227,26 @@ foreach(type double;float;long;ulong)
         itkMINCImageIOTest4
         DATA{Input/${imageName}.mnc}
         ${outImage}
+        ${rastoeps} # RAStoLPS
         427590.7631
         -8.195995507
         72.45943584
         -3.148635493) # this line is different
     endforeach()
   endforeach()
 endforeach()
+endforeach()
 
+foreach(rastoeps 0;1)
 foreach(type ushort)
   foreach(axis cor;sag;trans)
     foreach(plusMinus -;+)
       set(imageName t1_z${plusMinus}_${type}_${axis})
-      set(outImage ${ITK_TEST_OUTPUT_DIR}/${imageName}.mnc)
+      set(outImage ${ITK_TEST_OUTPUT_DIR}/${imageName}_${rastoeps}.mnc)
 
       itk_add_test(
         NAME
-        itkMINCImageIOTest-COM-${imageName}
+        itkMINCImageIOTest-COM-${imageName}-${rastoeps}
         COMMAND
         ITKIOMINCTestDriver
         --compare
@@ -236,10 +255,12 @@ foreach(type ushort)
         itkMINCImageIOTest4
         DATA{Input/${imageName}.mnc}
         ${outImage}
+        ${rastoeps} # RAStoLPS
         427590.7957
         -8.195997123
         72.45943721
         -3.148635961) # this line is different
     endforeach()
   endforeach()
 endforeach()
+endforeach()