From 9761a0753d23585a3316c70416e1372edd6da0e2 Mon Sep 17 00:00:00 2001
From: tctco <tctco001@163.com>
Date: Tue, 26 May 2026 00:05:59 +0800
Subject: [PATCH] Enable iterative rigid alignment

---
 localizer/src/CMakeLists.txt                   |  4 ++--
 localizer/src/README.md                        |  1 +
 localizer/src/conanfile.py                     |  2 +-
 localizer/src/core/config/Version.h            |  2 +-
 .../spatialNormalizations/rigid/RigidCLI.cpp   |  6 ++++++
 localizer/src/tests/test_normalize_cli.py      | 18 ++++++++++++++++++
 6 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/localizer/src/CMakeLists.txt b/localizer/src/CMakeLists.txt
index eeb1fd3..6628a02 100644
--- a/localizer/src/CMakeLists.txt
+++ b/localizer/src/CMakeLists.txt
@@ -1,8 +1,8 @@
 # CMakeList.txt: DCCCcore Refactored Version
 cmake_minimum_required(VERSION 3.21)
 
-project(DCCCcore VERSION 4.2.0)
-set(DCCCCORE_VERSION_SUFFIX "-alpha")
+project(DCCCcore VERSION 4.2.1)
+set(DCCCCORE_VERSION_SUFFIX "")
 set(DCCCCORE_SOFTWARE_VERSION "${PROJECT_VERSION}${DCCCCORE_VERSION_SUFFIX}")
 
 # Set C++ standard
diff --git a/localizer/src/README.md b/localizer/src/README.md
index baf68e8..20bff5f 100644
--- a/localizer/src/README.md
+++ b/localizer/src/README.md
@@ -113,6 +113,7 @@ Perform spatial standardization without metric calculation:
 # Iterative rigid registration
 ./DCCCcore normalize --input pet.nii --output normalized.nii --iterative
 ./DCCCcore adni-pet-core --input pet.nii --output normalized.nii --iterative
+./DCCCcore rigid --input pet.nii --output rigid.nii --iterative
 ```
 
 #### ADAD Analysis
diff --git a/localizer/src/conanfile.py b/localizer/src/conanfile.py
index 52ae7f2..f41356f 100644
--- a/localizer/src/conanfile.py
+++ b/localizer/src/conanfile.py
@@ -4,7 +4,7 @@
 
 class AppConan(ConanFile):
     name = "DCCCcore"
-    version = "4.2.0-alpha"
+    version = "4.2.1"
     settings = "os", "arch", "compiler", "build_type"
     generators = "CMakeDeps", "CMakeToolchain"
 
diff --git a/localizer/src/core/config/Version.h b/localizer/src/core/config/Version.h
index a28a284..8cacdb5 100644
--- a/localizer/src/core/config/Version.h
+++ b/localizer/src/core/config/Version.h
@@ -1,4 +1,4 @@
 #pragma once
 #include <string>
 
-const std::string SOFTWARE_VERSION = "4.2.0-alpha";
+const std::string SOFTWARE_VERSION = "4.2.1";
diff --git a/localizer/src/spatialNormalizations/rigid/RigidCLI.cpp b/localizer/src/spatialNormalizations/rigid/RigidCLI.cpp
index 8bfe373..902f50b 100644
--- a/localizer/src/spatialNormalizations/rigid/RigidCLI.cpp
+++ b/localizer/src/spatialNormalizations/rigid/RigidCLI.cpp
@@ -23,6 +23,10 @@ class RigidCLI final : public ISpatialNormalizationCLI {
 
     void configureArguments(argparse::ArgumentParser& parser) override {
         addBaseArguments(parser);
+        parser.add_argument("-i", "--iterative")
+            .help("Use iterative rigid transformation")
+            .default_value(false)
+            .implicit_value(true);
     }
 
     int execute(const argparse::ArgumentParser& parser, const std::string& fullCommand) override {
@@ -30,6 +34,7 @@ class RigidCLI final : public ISpatialNormalizationCLI {
         options.inputPath = parser.get<std::string>("--input");
         options.outputPath = parser.get<std::string>("--output");
         options.configPath = parser.get<std::string>("--config");
+        options.useIterativeRigid = parser.get<bool>("--iterative");
         options.enableDebugOutput = parser.get<bool>("--debug");
 
         if (!Common::fs::ensureParentDirectory(options.outputPath)) {
@@ -56,6 +61,7 @@ class RigidCLI final : public ISpatialNormalizationCLI {
         request.inputPath = options.inputPath;
         request.skip = false;
         request.options.rigidOnly = true;
+        request.options.useIterativeRigid = options.useIterativeRigid;
         request.options.enableDebugOutput = options.enableDebugOutput;
         request.options.debugOutputBasePath = options.debugOutputBasePath;
 
diff --git a/localizer/src/tests/test_normalize_cli.py b/localizer/src/tests/test_normalize_cli.py
index 8835cda..20e5932 100644
--- a/localizer/src/tests/test_normalize_cli.py
+++ b/localizer/src/tests/test_normalize_cli.py
@@ -55,3 +55,21 @@ def test_iterative_flag(self, run_subprocess, tmp_path, test_files):
         )
         assert output_path.exists(), "normalize --iterative did not create the expected output file."
 
+    def test_rigid_iterative_flag(self, run_subprocess, tmp_path, test_files):
+        output_path = tmp_path / "rigid_iterative_output.nii"
+        result = run_subprocess(
+            [
+                "rigid",
+                "--input",
+                str(test_files["input"]),
+                "--output",
+                str(output_path),
+                "--iterative",
+            ]
+        )
+
+        assert result.returncode == 0, (
+            "rigid command with --iterative failed.\n"
+            f"STDOUT:\n{result.stdout}\nSTDERR:\n{result.stderr}"
+        )
+        assert output_path.exists(), "rigid --iterative did not create the expected output file."