Merge pull request #4804 from blowekamp/add_anatomical_orientation

Add AnatomicalOrientation class

Modules/Core/Common/src/CMakeLists.txt

@@ -145,7 +145,9 @@ set(ITKCommon_SRCS
     itkFrustumSpatialFunction.cxx
     itkObjectStore.cxx
     itkGaussianDerivativeOperator.cxx
-    itkSpatialOrientation.cxx)
+    itkSpatialOrientation.cxx
+    itkAnatomicalOrientation.cxx
+)
 
 if(WIN32)
   list(APPEND ITKCommon_SRCS itkWin32OutputWindow.cxx)

Modules/Core/Common/src/itkAnatomicalOrientation.cxx

@@ -0,0 +1,328 @@
+/*=========================================================================
+ *
+ *  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 "itkAnatomicalOrientation.h"
+#ifndef ITK_FUTURE_LEGACY_REMOVE
+#  include "itkSpatialOrientationAdapter.h"
+#endif
+
+namespace itk
+{
+
+
+#ifndef ITK_FUTURE_LEGACY_REMOVE
+AnatomicalOrientation::AnatomicalOrientation(LegacyOrientationType legacyOrientation)
+  : AnatomicalOrientation(SpatialOrientationAdapter().ToDirectionCosines(legacyOrientation))
+{
+  assert(uint32_t(legacyOrientation) == uint32_t(m_Value));
+}
+#endif
+
+
+std::string
+AnatomicalOrientation::GetAsPositiveStringEncoding() const
+{
+
+  // a lambda function to convert a CoordinateEnum to a char
+  auto enumAsChar = [](CoordinateEnum coord) -> char {
+    switch (coord)
+    {
+      case CoordinateEnum::RightToLeft:
+        return 'L';
+      case CoordinateEnum::LeftToRight:
+        return 'R';
+      case CoordinateEnum::AnteriorToPosterior:
+        return 'P';
+      case CoordinateEnum::PosteriorToAnterior:
+        return 'A';
+      case CoordinateEnum::InferiorToSuperior:
+        return 'S';
+      case CoordinateEnum::SuperiorToInferior:
+        return 'I';
+      default:
+        return 'X';
+    }
+  };
+
+  if (m_Value == PositiveEnum::INVALID)
+  {
+    return "INVALID";
+  }
+
+  return std::string({ enumAsChar(GetPrimaryTerm()), enumAsChar(GetSecondaryTerm()), enumAsChar(GetTertiaryTerm()) });
+}
+
+
+std::string
+AnatomicalOrientation::GetAsNegativeStringEncoding() const
+{
+  return ConvertStringEncoding(GetAsPositiveStringEncoding());
+}
+
+
+AnatomicalOrientation
+AnatomicalOrientation::CreateFromPositiveStringEncoding(std::string str)
+{
+  std::transform(str.begin(), str.end(), str.begin(), ::toupper);
+
+  const std::map<std::string, typename AnatomicalOrientation::PositiveEnum> & stringToCode = GetStringToCode();
+  auto                                                                        iter = stringToCode.find(str);
+  if (iter == stringToCode.end())
+  {
+    return AnatomicalOrientation(PositiveEnum::INVALID);
+  }
+  return AnatomicalOrientation(iter->second);
+}
+
+AnatomicalOrientation
+AnatomicalOrientation::CreateFromNegativeStringEncoding(std::string str)
+{
+  return AnatomicalOrientation::CreateFromPositiveStringEncoding(ConvertStringEncoding(str));
+}
+
+
+std::string
+AnatomicalOrientation::ConvertStringEncoding(std::string str)
+{
+
+  auto flip = [](char c) -> char {
+    switch (::toupper(c))
+    {
+      case 'R':
+        return 'L';
+      case 'L':
+        return 'R';
+      case 'A':
+        return 'P';
+      case 'P':
+        return 'A';
+      case 'S':
+        return 'I';
+      case 'I':
+        return 'S';
+      case 'X':
+        return 'X';
+      default:
+        return c;
+    }
+  };
+
+  for (auto & c : str)
+  {
+    c = flip(c);
+  }
+  return str;
+}
+
+
+AnatomicalOrientation::CoordinateEnum
+AnatomicalOrientation::GetCoordinateTerm(CoordinateMajornessTermsEnum cmt) const
+{
+  return static_cast<CoordinateEnum>(static_cast<uint32_t>(m_Value) >> static_cast<uint8_t>(cmt) & 0xff);
+}
+
+
+const std::map<typename AnatomicalOrientation::PositiveEnum, std::string> &
+AnatomicalOrientation::GetCodeToString()
+{
+  auto createCodeToString = []() -> std::map<PositiveEnum, std::string> {
+    std::map<PositiveEnum, std::string> orientToString;
+
+    for (auto code : { PositiveEnum::RIP, PositiveEnum::LIP, PositiveEnum::RSP, PositiveEnum::LSP,    PositiveEnum::RIA,
+                       PositiveEnum::LIA, PositiveEnum::RSA, PositiveEnum::LSA, PositiveEnum::IRP,    PositiveEnum::ILP,
+                       PositiveEnum::SRP, PositiveEnum::SLP, PositiveEnum::IRA, PositiveEnum::ILA,    PositiveEnum::SRA,
+                       PositiveEnum::SLA, PositiveEnum::RPI, PositiveEnum::LPI, PositiveEnum::RAI,    PositiveEnum::LAI,
+                       PositiveEnum::RPS, PositiveEnum::LPS, PositiveEnum::RAS, PositiveEnum::LAS,    PositiveEnum::PRI,
+                       PositiveEnum::PLI, PositiveEnum::ARI, PositiveEnum::ALI, PositiveEnum::PRS,    PositiveEnum::PLS,
+                       PositiveEnum::ARS, PositiveEnum::ALS, PositiveEnum::IPR, PositiveEnum::SPR,    PositiveEnum::IAR,
+                       PositiveEnum::SAR, PositiveEnum::IPL, PositiveEnum::SPL, PositiveEnum::IAL,    PositiveEnum::SAL,
+                       PositiveEnum::PIR, PositiveEnum::PSR, PositiveEnum::AIR, PositiveEnum::ASR,    PositiveEnum::PIL,
+                       PositiveEnum::PSL, PositiveEnum::AIL, PositiveEnum::ASL, PositiveEnum::INVALID })
+    {
+      orientToString[code] = AnatomicalOrientation(code).GetAsPositiveStringEncoding();
+    }
+
+    return orientToString;
+  };
+  static const std::map<PositiveEnum, std::string> codeToString = createCodeToString();
+  return codeToString;
+}
+
+const std::map<std::string, AnatomicalOrientation::PositiveEnum> &
+AnatomicalOrientation::GetStringToCode()
+{
+
+  auto createStringToCode = []() -> std::map<std::string, PositiveEnum> {
+    std::map<std::string, PositiveEnum>         stringToCode;
+    const std::map<PositiveEnum, std::string> & codeToString = GetCodeToString();
+
+    for (const auto & kv : codeToString)
+    {
+      stringToCode[kv.second] = kv.first;
+    }
+    return stringToCode;
+  };
+
+  static const std::map<std::string, AnatomicalOrientation::PositiveEnum> stringToCode = createStringToCode();
+  return stringToCode;
+}
+
+
+AnatomicalOrientation::PositiveEnum
+AnatomicalOrientation::ConvertDirectionToPositiveEnum(const DirectionType & dir)
+{
+  // NOTE: This method was based off of itk::SpatialObjectAdaptor::FromDirectionCosines
+  // but it is DIFFERENT in the meaning of direction in terms of sign-ness.
+  CoordinateEnum terms[3] = { CoordinateEnum::UNKNOWN, CoordinateEnum::UNKNOWN, CoordinateEnum::UNKNOWN };
+
+  std::multimap<double, std::pair<unsigned, unsigned>> value_to_idx;
+  for (unsigned int c = 0; c < 3; ++c)
+  {
+    for (unsigned int r = 0; r < 3; ++r)
+    {
+      value_to_idx.emplace(std::abs(dir[c][r]), std::make_pair(c, r));
+    }
+  }
+
+  for (unsigned i = 0; i < 3; ++i)
+  {
+
+    auto               max_idx = value_to_idx.rbegin()->second;
+    const unsigned int max_c = max_idx.first;
+    const unsigned int max_r = max_idx.second;
+
+    const int max_sgn = Math::sgn(dir[max_c][max_r]);
+
+    for (auto it = value_to_idx.begin(); it != value_to_idx.end();)
+    {
+      if (it->second.first == max_c || it->second.second == max_r)
+      {
+        value_to_idx.erase(it++);
+      }
+      else
+      {
+        ++it;
+      }
+    }
+
+    switch (max_c)
+    {
+      case 0:
+      {
+        // When the dominant axis sign is positive, assign the coordinate for the direction we are increasing towards.
+        // ITK is in LPS, so that is the positive direction
+        terms[max_r] = (max_sgn == 1) ? CoordinateEnum::RightToLeft : CoordinateEnum::LeftToRight;
+        break;
+      }
+      case 1:
+      {
+        terms[max_r] = (max_sgn == 1) ? CoordinateEnum::AnteriorToPosterior : CoordinateEnum::PosteriorToAnterior;
+        break;
+      }
+      case 2:
+      {
+        terms[max_r] = (max_sgn == 1) ? CoordinateEnum::InferiorToSuperior : CoordinateEnum::SuperiorToInferior;
+        break;
+      }
+      default:
+        itkGenericExceptionMacro("Unexpected Axis");
+    }
+  }
+
+  return AnatomicalOrientation(terms[0], terms[1], terms[2]);
+}
+
+
+typename AnatomicalOrientation::DirectionType
+AnatomicalOrientation::ConvertPositiveEnumToDirection(PositiveEnum orientationEnum)
+{
+  const AnatomicalOrientation o(orientationEnum);
+
+  CoordinateEnum terms[Dimension] = { o.GetPrimaryTerm(), o.GetSecondaryTerm(), o.GetTertiaryTerm() };
+  DirectionType  direction;
+  direction.Fill(0.0);
+
+  for (unsigned int i = 0; i < Dimension; ++i)
+  {
+    const int sign = (static_cast<uint8_t>(terms[i]) & 0x1) ? 1 : -1;
+
+    switch (terms[i])
+    {
+      case CoordinateEnum::LeftToRight:
+      case CoordinateEnum::RightToLeft:
+        direction[0][i] = -1 * sign;
+        break;
+      case CoordinateEnum::AnteriorToPosterior:
+      case CoordinateEnum::PosteriorToAnterior:
+        direction[1][i] = 1 * sign;
+        break;
+      case CoordinateEnum::InferiorToSuperior:
+      case CoordinateEnum::SuperiorToInferior:
+        direction[2][i] = -1 * sign;
+        break;
+      case CoordinateEnum::UNKNOWN:
+        break;
+    }
+  }
+  return direction;
+}
+
+std::ostream &
+operator<<(std::ostream & out, typename AnatomicalOrientation::CoordinateEnum value)
+{
+  switch (value)
+  {
+    case AnatomicalOrientation::CoordinateEnum::RightToLeft:
+      return out << "right-to-left";
+    case AnatomicalOrientation::CoordinateEnum::LeftToRight:
+      return out << "left-to-right";
+    case AnatomicalOrientation::CoordinateEnum::AnteriorToPosterior:
+      return out << "anterior-to-posterior";
+    case AnatomicalOrientation::CoordinateEnum::PosteriorToAnterior:
+      return out << "posterior-to-anterior";
+    case AnatomicalOrientation::CoordinateEnum::InferiorToSuperior:
+      return out << "inferior-to-superior";
+    case AnatomicalOrientation::CoordinateEnum::SuperiorToInferior:
+      return out << "superior-to-inferior";
+    case AnatomicalOrientation::CoordinateEnum::UNKNOWN:
+      return out << "unknown";
+    default:
+      return out << "invalid";
+  }
+}
+
+std::ostream &
+operator<<(std::ostream & out, typename AnatomicalOrientation::PositiveEnum value)
+{
+  return (out << AnatomicalOrientation(value).GetAsPositiveStringEncoding());
+}
+
+std::ostream &
+operator<<(std::ostream & out, typename AnatomicalOrientation::NegativeEnum value)
+{
+  return (out << AnatomicalOrientation(value).GetAsNegativeStringEncoding());
+}
+
+std::ostream &
+operator<<(std::ostream & out, const AnatomicalOrientation & orientation)
+{
+  const auto terms = orientation.GetTerms();
+  static_assert(std::tuple_size<decltype(terms)>{} == 3);
+  return out << terms[0] << " " << terms[1] << " " << terms[2];
+}
+
+} // namespace itk

Modules/Core/Common/test/CMakeLists.txt

@@ -1760,7 +1760,9 @@ set(ITKCommonGTests
     itkWeakPointerGTest.cxx
     itkCommonTypeTraitsGTest.cxx
     itkMetaDataDictionaryGTest.cxx
-    itkSpatialOrientationAdaptorGTest.cxx)
+    itkSpatialOrientationAdaptorGTest.cxx
+    itkAnatomicalOrientationGTest.cxx
+)
 creategoogletestdriver(ITKCommon "${ITKCommon-Test_LIBRARIES}" "${ITKCommonGTests}")
 # If `-static` was passed to CMAKE_EXE_LINKER_FLAGS, compilation fails. No need to
 # test this case.