ENH: Allow InitialTransformParameterFileName relative to parameter file

Allow the file name specified by the "InitialTransformParameterFileName" parameter in a transform parameter file to be relative to that transform parameter file.

Core/ComponentBaseClasses/elxTransformBase.hxx

@@ -388,16 +388,43 @@ TransformBase<TElastix>::ReadFromFile()
        * is not the same as this transform parameter file. Otherwise,
        * we will have an infinite loop.
        */
-      std::string fullFileName1 = itksys::SystemTools::CollapseFullPath(fileName);
-      std::string fullFileName2 = itksys::SystemTools::CollapseFullPath(configuration.GetParameterFileName());
-      if (fullFileName1 == fullFileName2)
+
+      const std::string configurationParameterFileName = configuration.GetParameterFileName();
+
+      if (itksys::SystemTools::CollapseFullPath(fileName) ==
+          itksys::SystemTools::CollapseFullPath(configurationParameterFileName))
       {
         itkExceptionMacro("ERROR: The InitialTransformParameterFileName is identical to the current "
                           "TransformParameters filename! An infinite loop is not allowed.");
       }
 
       /** We can safely read the initial transform. */
-      this->ReadInitialTransformFromFile(fileName.c_str());
+
+      // Find the last separator (slash or backslash) in the current transform parameter file path.
+      const auto lastConfigurationParameterFilePathSeparator = configurationParameterFileName.find_last_of("\\/");
+      const char firstFileNameLetter = fileName.front();
+
+      if (const bool isAbsoluteFilePath{ firstFileNameLetter == '\\' || firstFileNameLetter == '/' ||
+                                         (firstFileNameLetter > 0 && std::isalpha(firstFileNameLetter) &&
+                                          fileName.size() > 1 && fileName[1] == ':') };
+          isAbsoluteFilePath || (lastConfigurationParameterFilePathSeparator == std::string::npos) ||
+          itksys::SystemTools::FileExists(fileName))
+      {
+        // The file name is an absolute path, or the current transform parameter file name does not have any separator,
+        // or the file exists in the current working directory. So use it!
+        this->ReadInitialTransformFromFile(fileName.c_str());
+      }
+      else
+      {
+        // The file name of the initial transform is a relative path, so now assume that it is relative to the current
+        // transform parameter file (the current configuration). Try to read the initial transform from the same
+        // directory as the current transform, by concatenating the current configuration file path up to that last
+        // separator with the string specified by "InitialTransformParameterFileName".
+        this->ReadInitialTransformFromFile(
+          configurationParameterFileName.substr(0, lastConfigurationParameterFilePathSeparator + 1)
+            .append(fileName)
+            .c_str());
+      }
     }
   }
 

Core/Main/GTesting/itkElastixRegistrationMethodGTest.cxx

@@ -976,6 +976,62 @@ GTEST_TEST(itkElastixRegistrationMethod, InitialTransformParameterFile)
 }
 
 
+GTEST_TEST(itkElastixRegistrationMethod, InitialTransformParameterFileWithInitialTransformParameterFile)
+{
+  using PixelType = float;
+  enum
+  {
+    ImageDimension = 2U
+  };
+  using ImageType = itk::Image<PixelType, ImageDimension>;
+
+  const auto doDummyRegistration =
+    [](const std::string & initialTransformParameterFileName) -> itk::SmartPointer<ImageType> {
+    const ImageType::SizeType imageSize{ { 5, 6 } };
+
+    std::mt19937 randomNumberEngine{};
+
+    const auto fillImageBufferRandomly = [&randomNumberEngine](ImageType & image) {
+      const itk::ImageBufferRange<ImageType> imageBufferRange(image);
+
+      std::generate(imageBufferRange.begin(), imageBufferRange.end(), [&randomNumberEngine] {
+        return std::uniform_real_distribution<PixelType>{ PixelType{ 1 }, PixelType{ 2 } }(randomNumberEngine);
+      });
+    };
+
+    elx::DefaultConstruct<ImageType> fixedImage{};
+    fixedImage.SetRegions(imageSize);
+    fixedImage.Allocate(true);
+    fillImageBufferRandomly(fixedImage);
+
+    elx::DefaultConstruct<ImageType> movingImage{};
+    movingImage.SetRegions(imageSize);
+    movingImage.Allocate(true);
+    fillImageBufferRandomly(movingImage);
+
+    elx::DefaultConstruct<ElastixRegistrationMethodType<ImageType>> registration{};
+    registration.SetFixedImage(&fixedImage);
+    registration.SetMovingImage(&movingImage);
+    registration.SetInitialTransformParameterFileName(initialTransformParameterFileName);
+
+    registration.SetParameterObject(CreateParameterObject({ // Parameters in alphabetic order:
+                                                            { "AutomaticTransformInitialization", "false" },
+                                                            { "ImageSampler", "Full" },
+                                                            { "MaximumNumberOfIterations", "0" },
+                                                            { "Metric", "AdvancedNormalizedCorrelation" },
+                                                            { "Optimizer", "AdaptiveStochasticGradientDescent" },
+                                                            { "Transform", "TranslationTransform" } }));
+    registration.Update();
+    return registration.GetOutput();
+  };
+
+  EXPECT_EQ(
+    DerefSmartPointer(doDummyRegistration(
+      GetDataDirectoryPath() + "/Translation(1,-2)/TransformParametersWithInitialTransformParameterFile.txt")),
+    DerefSmartPointer(doDummyRegistration(GetDataDirectoryPath() + "/Translation(1,-2)/TransformParameters.txt")));
+}
+
+
 GTEST_TEST(itkElastixRegistrationMethod, SetInitialTransformParameterObject)
 {
   using PixelType = float;

Testing/Data/Translation(1,-2)/InitialTransformParameters.txt

@@ -0,0 +1,4 @@
+(InitialTransformParameterFileName "NoInitialTransform")
+(NumberOfParameters 2)
+(Transform "TranslationTransform")
+(TransformParameters 1 0)

Testing/Data/Translation(1,-2)/TransformParametersWithInitialTransformParameterFile.txt

@@ -0,0 +1,4 @@
+(InitialTransformParameterFileName "InitialTransformParameters.txt")
+(NumberOfParameters 2)
+(Transform "TranslationTransform")
+(TransformParameters 0 -2)