Enable iterative rigid alignment

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

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

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"
 

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";

localizer/src/spatialNormalizations/rigid/RigidCLI.cpp

@@ -23,13 +23,18 @@ 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 {
         NormalizeCommandOptions options;
         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;
 

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."