From 73a0d3a97912910db52a396ec187050bcf1a1299 Mon Sep 17 00:00:00 2001
From: Niels Dekker <N.Dekker@lumc.nl>
Date: Sun, 7 May 2023 09:58:51 +0200
Subject: [PATCH] BUG: Ignore "InitialTransformParametersFileName" when
 configurations > 1

When there are two or more "TransformConfigurations", the sequence of transforms is entirely specified by those configurations, and not by transform parameter files. The "InitialTransformParametersFileName" parameter should then be ignored.

Aims to fix a test failure that occurred when running itkElastixRegistrationMethodTest from
https://github.com/InsightSoftwareConsortium/ITKElastix/blob/v0.16.0/test/itkElastixRegistrationMethodTest.cxx at the current revision of the elastix main branch.

The bug appears introduced with pull request https://github.com/SuperElastix/elastix/pull/837 commit 1d75664d7d2bcac9ff9c80b11281a9bce6d86212 "ENH: Find previous configuration without interpreting filename as index" (merged on March 17, 2023).
---
 .../ComponentBaseClasses/elxTransformBase.hxx | 53 +++++++++----------
 1 file changed, 26 insertions(+), 27 deletions(-)

diff --git a/Core/ComponentBaseClasses/elxTransformBase.hxx b/Core/ComponentBaseClasses/elxTransformBase.hxx
index f9a66663b..0897bb981 100644
--- a/Core/ComponentBaseClasses/elxTransformBase.hxx
+++ b/Core/ComponentBaseClasses/elxTransformBase.hxx
@@ -348,43 +348,42 @@ TransformBase<TElastix>::ReadFromFile()
   } // end if this->m_ReadWriteTransformParameters
 
   /** Task 2 - Get the InitialTransform. */
-
-  /** Get the InitialTransformName. */
-  std::string fileName = "NoInitialTransform";
-  configuration.ReadParameter(fileName, "InitialTransformParametersFileName", 0);
-
   const ElastixBase & elastixBase = Deref(Superclass::GetElastix());
 
-  /** Call the function ReadInitialTransformFromFile. */
-  if (fileName == "NoInitialTransform")
+  if (elastixBase.GetNumberOfTransformConfigurations() > 1)
   {
-    if (elastixBase.GetNumberOfTransformConfigurations() > 1)
-    {
-      const Configuration::ConstPointer previousTransformConfiguration =
-        elastixBase.GetPreviousTransformConfiguration(configuration);
+    const Configuration::ConstPointer previousTransformConfiguration =
+      elastixBase.GetPreviousTransformConfiguration(configuration);
 
-      if (previousTransformConfiguration)
-      {
-        this->ReadInitialTransformFromConfiguration(previousTransformConfiguration);
-      }
+    if (previousTransformConfiguration)
+    {
+      this->ReadInitialTransformFromConfiguration(previousTransformConfiguration);
     }
   }
   else
   {
-    /** Check if the initial transform of this transform parameter file
-     * 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)
+    /** Get the InitialTransformName. */
+    std::string fileName = "NoInitialTransform";
+    configuration.ReadParameter(fileName, "InitialTransformParametersFileName", 0);
+
+    /** Call the function ReadInitialTransformFromFile. */
+    if (fileName != "NoInitialTransform")
     {
-      itkExceptionMacro(<< "ERROR: The InitialTransformParametersFileName is identical to the current "
-                           "TransformParameters filename! An infinite loop is not allowed.");
-    }
+      /** Check if the initial transform of this transform parameter file
+       * 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)
+      {
+        itkExceptionMacro(<< "ERROR: The InitialTransformParametersFileName 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());
+      /** We can safely read the initial transform. */
+      this->ReadInitialTransformFromFile(fileName.c_str());
+    }
   }
 
   /** Task 3 - Read from the configuration file how to combine the