From 23ef4329e25e0751ebf26ba59d8c85c539f13f80 Mon Sep 17 00:00:00 2001
From: Niels Dekker <N.Dekker@lumc.nl>
Date: Mon, 22 May 2023 16:47:24 +0200
Subject: [PATCH] ENH: Exclude retrieval of filenames of masks from elastix
 library

Avoided confusing log messages saying "-fMask    unspecified, so no fixed mask used" and "-mMask    unspecified, so no moving mask used" for library users (including ITKElastix).

Relates to issue https://github.com/InsightSoftwareConsortium/ITKElastix/issues/127 "registration with mask does not work", reported by jslalu, June 11, 2021.
---
 Core/Kernel/elxElastixBase.cxx | 44 ++++++++++++++++++----------------
 1 file changed, 24 insertions(+), 20 deletions(-)

diff --git a/Core/Kernel/elxElastixBase.cxx b/Core/Kernel/elxElastixBase.cxx
index a03b01c1b..43baa4ff2 100644
--- a/Core/Kernel/elxElastixBase.cxx
+++ b/Core/Kernel/elxElastixBase.cxx
@@ -180,30 +180,34 @@ ElastixBase::BeforeAllBase()
   log::info("ELASTIX version: " ELASTIX_VERSION_STRING "\nCommand line options from ElastixBase:");
   std::string check = "";
 
-  /** Read the fixed and moving image filenames. These are obliged options,
-   * so print an error if they are not present.
-   * Print also some info (second boolean = true).
-   */
   if (!BaseComponent::IsElastixLibrary())
   {
+    // Note: The filenames of the input images and the masks are only relevant to the elastix executable, not the
+    // library.
+
+    /** Read the fixed and moving image filenames. These are obliged options,
+     * so print an error if they are not present.
+     * Print also some info (second boolean = true).
+     */
     m_FixedImageFileNameContainer = GenerateFileNameContainer(*m_Configuration, "-f", returndummy, true, true);
     m_MovingImageFileNameContainer = GenerateFileNameContainer(*m_Configuration, "-m", returndummy, true, true);
-  }
-  /** Read the fixed and moving mask filenames. These are not obliged options,
-   * so do not print any errors if they are not present.
-   * Do print some info (second boolean = true).
-   */
-  int maskreturndummy = 0;
-  m_FixedMaskFileNameContainer = GenerateFileNameContainer(*m_Configuration, "-fMask", maskreturndummy, false, true);
-  if (maskreturndummy != 0)
-  {
-    log::info("-fMask    unspecified, so no fixed mask used");
-  }
-  maskreturndummy = 0;
-  m_MovingMaskFileNameContainer = GenerateFileNameContainer(*m_Configuration, "-mMask", maskreturndummy, false, true);
-  if (maskreturndummy != 0)
-  {
-    log::info("-mMask    unspecified, so no moving mask used");
+
+    /** Read the fixed and moving mask filenames. These are not obliged options,
+     * so do not print any errors if they are not present.
+     * Do print some info (second boolean = true).
+     */
+    int maskreturndummy = 0;
+    m_FixedMaskFileNameContainer = GenerateFileNameContainer(*m_Configuration, "-fMask", maskreturndummy, false, true);
+    if (maskreturndummy != 0)
+    {
+      log::info("-fMask    unspecified, so no fixed mask used");
+    }
+    maskreturndummy = 0;
+    m_MovingMaskFileNameContainer = GenerateFileNameContainer(*m_Configuration, "-mMask", maskreturndummy, false, true);
+    if (maskreturndummy != 0)
+    {
+      log::info("-mMask    unspecified, so no moving mask used");
+    }
   }
 
   /** Check for appearance of "-out".