Executable linked to elastix.lib, offering subset of elastix.exe functionality

Core/CMakeLists.txt

@@ -169,6 +169,12 @@ set_target_properties( elastix_lib PROPERTIES OUTPUT_NAME elastix )
 target_compile_definitions( elastix_lib PRIVATE ELX_CMAKE_VERSION="${CMAKE_VERSION}" )
 target_link_libraries( elastix_lib ${ELASTIX_TARGET_LINK_LIBRARIES} )
 
+add_executable( ElastixLibBasedExe
+   Main/ElastixLibBasedExe.cxx
+)
+target_link_libraries( ElastixLibBasedExe elastix_lib )
+target_compile_definitions(ElastixLibBasedExe PRIVATE ELX_CMAKE_VERSION="${CMAKE_VERSION}")
+
 #---------------------------------------------------------------------
 # Create the transformix executable.
 

Core/Main/ElastixLibBasedExe.cxx

@@ -0,0 +1,352 @@
+/*=========================================================================
+ *
+ *  Copyright UMC Utrecht and contributors
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *        http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+
+// Elastix header files:
+#include "elastix.h"
+#include "elastixlib.h"
+#include "elxConversion.h"
+#include "elxElastixMain.h"
+#include <Core/elxVersionMacros.h>
+#include "itkUseMevisDicomTiff.h"
+
+// ITK header files:
+#include <itkTimeProbe.h>
+#include <itksys/SystemInformation.hxx>
+#include <itksys/SystemTools.hxx>
+
+// Standard C++ header files:
+#include <cassert>
+#include <climits> // For UINT_MAX.
+#include <cstddef> // For size_t.
+#include <deque>
+#include <iostream>
+#include <limits>
+#include <vector>
+
+constexpr const char * elastixHelpText =
+  /** Print the version. */
+  "elastix version: " ELASTIX_VERSION_STRING "\n\n"
+
+  /** What is elastix? */
+  "elastix registers a moving image to a fixed image.\n"
+  "The registration-process is specified in the parameter file.\n"
+  "  --help, -h displays this message and exit\n"
+  "  --version  output version information and exit\n"
+  "  --extended-version  output extended version information and exit\n\n"
+
+  /** Mandatory arguments.*/
+  "Call elastix from the command line with mandatory arguments:\n"
+  "  -f        fixed image\n"
+  "  -m        moving image\n"
+  "  -out      output directory\n"
+  "  -p        parameter file, elastix handles 1 or more \"-p\"\n\n"
+
+  /** Optional arguments.*/
+  "Optional extra commands:\n"
+  "  -fMask    mask for fixed image\n"
+  "  -mMask    mask for moving image\n"
+  "  -fp       point set for fixed image\n"
+  "  -mp       point set for moving image\n"
+  "  -t0       parameter file for initial transform\n"
+  "  -priority set the process priority to high, abovenormal, normal (default),\n"
+  "            belownormal, or idle (Windows only option)\n"
+  "  -threads  set the maximum number of threads of elastix\n\n"
+
+  /** The parameter file.*/
+  "The parameter-file must contain all the information "
+  "necessary for elastix to run properly. That includes which metric to "
+  "use, which optimizer, which transform, etc. It must also contain "
+  "information specific for the metric, optimizer, transform, etc. "
+  "For a usable parameter-file, see the website.\n\n"
+
+  "Need further help? Please check:\n"
+  " * the elastix website: https://elastix.lumc.nl\n"
+  " * the source code repository site: https://github.com/SuperElastix/elastix\n"
+  " * the discussion forum: https://groups.google.com/g/elastix-imageregistration";
+
+
+namespace
+{
+using ImageType = itk::Image<float>;
+
+// TODO: Check GenerateImageContainer calls in ElastixMain::Run() for
+// more extensive reading.
+ImageType::Pointer
+ReadImage(const std::string & filename)
+{
+  /** Setup reader. */
+  const auto imageFileReader = itk::ImageFileReader<ImageType>::New();
+  imageFileReader->SetFileName(filename);
+  imageFileReader->Update();
+  return imageFileReader->GetOutput();
+}
+} // namespace
+
+int
+Main(const int argc, const char * const * const argv)
+{
+
+  /** Check if "--help" or "--version" was asked for. */
+  if (argc == 1)
+  {
+    std::cout << "Use \"elastix --help\" for information about elastix-usage." << std::endl;
+    return 0;
+  }
+  else if (argc == 2)
+  {
+    std::string argument(argv[1]);
+    if (argument == "-help" || argument == "--help" || argument == "-h")
+    {
+      std::cout << elastixHelpText << std::endl;
+      return 0;
+    }
+    else if (argument == "--version")
+    {
+      std::cout << "elastix version: " ELASTIX_VERSION_STRING << std::endl;
+      return 0;
+    }
+    else if (argument == "--extended-version")
+    {
+      std::cout << "elastix version: " ELASTIX_VERSION_STRING << "\nITK version: " << ITK_VERSION_MAJOR << '.'
+                << ITK_VERSION_MINOR << '.' << ITK_VERSION_PATCH << "\nBuild date: " << __DATE__ << ' ' << __TIME__
+#ifdef _MSC_FULL_VER
+                << "\nCompiler: Visual C++ version " << _MSC_FULL_VER << '.' << _MSC_BUILD
+#endif
+#ifdef __clang__
+                << "\nCompiler: Clang"
+#  ifdef __VERSION__
+                << " version " << __VERSION__
+#  endif
+#endif
+#if defined(__GNUC__)
+                << "\nCompiler: GCC"
+#  ifdef __VERSION__
+                << " version " << __VERSION__
+#  endif
+#endif
+                << "\nMemory address size: " << std::numeric_limits<std::size_t>::digits
+                << "-bit\nCMake version: " << ELX_CMAKE_VERSION << std::endl;
+      return 0;
+    }
+    else
+    {
+      std::cout << "Use \"elastix --help\" for information about elastix-usage." << std::endl;
+      return 0;
+    }
+  }
+
+  /** Some typedef's. */
+  typedef elx::ElastixMain                            ElastixMainType;
+  typedef ElastixMainType::ObjectPointer              ObjectPointer;
+  typedef ElastixMainType::DataObjectContainerPointer DataObjectContainerPointer;
+  typedef ElastixMainType::FlatDirectionCosinesType   FlatDirectionCosinesType;
+
+  typedef ElastixMainType::ArgumentMapType ArgumentMapType;
+  typedef ArgumentMapType::value_type      ArgumentMapEntryType;
+
+  /** Support Mevis Dicom Tiff (if selected in cmake) */
+  RegisterMevisDicomTiff();
+
+  ArgumentMapType         argMap;
+  std::deque<std::string> parameterFileList;
+  std::string             outFolder;
+
+  /** Put command line parameters into parameterFileList. */
+  for (unsigned int i = 1; static_cast<long>(i) < (argc - 1); i += 2)
+  {
+    std::string key(argv[i]);
+    std::string value(argv[i + 1]);
+
+    if (key == "-p")
+    {
+      /** Queue the ParameterFileNames. */
+      parameterFileList.push_back(value);
+      /** The different '-p' are stored in the argMap, with
+       * keys p(1), p(2), etc. */
+      std::ostringstream tempPname;
+      tempPname << "-p(" << parameterFileList.size() << ")";
+      std::string tempPName = tempPname.str();
+      argMap.insert(ArgumentMapEntryType(tempPName, value));
+    }
+    else
+    {
+      if (key == "-out")
+      {
+        /** Make sure that last character of the output folder equals a '/' or '\'. */
+        const char last = value.back();
+        if (last != '/' && last != '\\')
+        {
+          value.append("/");
+        }
+        value = elx::Conversion::ToNativePathNameSeparators(value);
+
+        /** Save this information. */
+        outFolder = value;
+
+      } // end if key == "-out"
+
+      /** Attempt to save the arguments in the ArgumentMap. */
+      if (argMap.count(key) == 0)
+      {
+        argMap.insert(ArgumentMapEntryType(key, value));
+      }
+      else
+      {
+        /** Duplicate arguments. */
+        std::cerr << "WARNING!" << std::endl;
+        std::cerr << "Argument " << key << "is only required once." << std::endl;
+        std::cerr << "Arguments " << key << " " << value << "are ignored" << std::endl;
+      }
+
+    } // end else (so, if key does not equal "-p")
+
+  } // end for loop
+
+  /** The argv0 argument, required for finding the component.dll/so's. */
+  argMap.insert(ArgumentMapEntryType("-argv0", argv[0]));
+
+  int returndummy{};
+
+  /** Check if at least once the option "-p" is given. */
+  if (parameterFileList.empty())
+  {
+    std::cerr << "ERROR: No CommandLine option \"-p\" given!" << std::endl;
+    returndummy |= -1;
+  }
+
+  /** Check if the -out option is given. */
+  if (!outFolder.empty())
+  {
+    /** Check if the output directory exists. */
+    if (!itksys::SystemTools::FileIsDirectory(outFolder))
+    {
+      std::cerr << "ERROR: the output directory \"" << outFolder << "\" does not exist." << std::endl;
+      std::cerr << "You are responsible for creating it." << std::endl;
+      returndummy |= -2;
+    }
+    else
+    {
+      /** Setup xout. */
+      const std::string logFileName = outFolder + "elastix.log";
+      const int         returndummy2{ elx::xoutSetup(logFileName.c_str(), true, true) };
+      if (returndummy2 != 0)
+      {
+        std::cerr << "ERROR while setting up xout." << std::endl;
+      }
+      returndummy |= returndummy2;
+    }
+  }
+  else
+  {
+    returndummy = -2;
+    std::cerr << "ERROR: No CommandLine option \"-out\" given!" << std::endl;
+  }
+
+  /** Stop if some fatal errors occurred. */
+  if (returndummy != 0)
+  {
+    return returndummy;
+  }
+
+  elxout << std::endl;
+
+  /** Declare a timer, start it and print the start time. */
+  itk::TimeProbe totaltimer;
+  totaltimer.Start();
+  elxout << "elastix is started at " << GetCurrentDateAndTime() << ".\n" << std::endl;
+
+  /** Print where elastix was run. */
+  elxout << "which elastix:   " << argv[0] << std::endl;
+  itksys::SystemInformation info;
+  info.RunCPUCheck();
+  info.RunOSCheck();
+  info.RunMemoryCheck();
+  elxout << "elastix runs at: " << info.GetHostname() << std::endl;
+  elxout << "  " << info.GetOSName() << " " << info.GetOSRelease() << (info.Is64Bits() ? " (x64), " : ", ")
+         << info.GetOSVersion() << std::endl;
+  elxout << "  with " << info.GetTotalPhysicalMemory() << " MB memory, and " << info.GetNumberOfPhysicalCPU()
+         << " cores @ " << static_cast<unsigned int>(info.GetProcessorClockFrequency()) << " MHz." << std::endl;
+
+
+  /**
+   * ********************* START REGISTRATION *********************
+   *
+   * Do the (possibly multiple) registration(s).
+   */
+
+
+  const int result = [parameterFileList, outFolder, argMap] {
+    const auto nrOfParameterFiles = parameterFileList.size();
+
+    const auto fixedImageFilename = argMap.at("-f");
+    const auto movingImageFilename = argMap.at("-m");
+
+    using elastix::ELASTIX;
+    ELASTIX    elastixObject;
+    const auto fixedImage = ReadImage(fixedImageFilename);
+    const auto movingImage = ReadImage(movingImageFilename);
+
+    std::vector<ELASTIX::ParameterMapType> parameterMaps(nrOfParameterFiles);
+
+    for (std::size_t i{}; i < nrOfParameterFiles; ++i)
+    {
+      const auto parameterFileParser = itk::ParameterFileParser::New();
+      parameterFileParser->SetParameterFileName(parameterFileList[i]);
+      parameterFileParser->ReadParameterFile();
+      auto parameterMap = parameterFileParser->GetParameterMap();
+
+      parameterMap["FixedImageDimension"] = { std::to_string(fixedImage->GetImageDimension()) };
+      parameterMap["MovingImageDimension"] = { std::to_string(movingImage->GetImageDimension()) };
+      parameterMaps[i] = parameterMap;
+    }
+
+    const bool            performLogging{ true };
+    const bool            performCout{ true };
+    ELASTIX::ImagePointer fixedMask{};
+    ELASTIX::ImagePointer movingMask{};
+
+    return elastixObject.RegisterImages(
+      fixedImage, movingImage, parameterMaps, outFolder, performLogging, performCout, fixedMask, movingMask);
+  }();
+
+
+  elxout << "-------------------------------------------------------------------------\n" << std::endl;
+
+  /** Stop totaltimer and print it. */
+  totaltimer.Stop();
+  elxout << "Total time elapsed: " << ConvertSecondsToDHMS(totaltimer.GetMean(), 1) << ".\n" << std::endl;
+
+  /** Exit and return the error code. */
+  return result;
+
+} // end Main
+
+
+int
+main(int argc, char ** argv)
+{
+  try
+  {
+    return Main(argc, argv);
+  }
+  catch (const std::exception & stdException)
+  {
+    std::cerr << "An error occurred! Exception: " << stdException.what() << '\n';
+    return EXIT_FAILURE;
+  }
+}

Testing/CMakeLists.txt

@@ -301,7 +301,7 @@ macro( elx_add_run_test testbasename howtocompare )
   # Set maximum test length to 10 minutes
   add_test( NAME ${testname}_OUTPUT
     CONFIGURATIONS Release
-    COMMAND ${EXECUTABLE_OUTPUT_PATH}/elastix
+    COMMAND ${EXECUTABLE_OUTPUT_PATH}/ElastixLibBasedExe
     ${elastixargs} -out ${output_dir} )
   set_tests_properties( ${testname}_OUTPUT
     PROPERTIES TIMEOUT 600 )
@@ -449,7 +449,7 @@ file( MAKE_DIRECTORY "${TestOutputDir}/OutputDirectoryPathContainingSpacesTest"
 file( MAKE_DIRECTORY "${TestOutputDir}/OutputDirectoryPathContainingSpacesTest/path with spaces" )
 file( MAKE_DIRECTORY "${TestOutputDir}/OutputDirectoryPathContainingSpacesTest/path with spaces/name with spaces" )
 add_test( NAME OutputDirectoryPathContainingSpacesTest
-  COMMAND ${EXECUTABLE_OUTPUT_PATH}/elastix
+  COMMAND ${EXECUTABLE_OUTPUT_PATH}/ElastixLibBasedExe
   -f "${TestDataDir}/2D_2x2_square_object_at_(1,3).mhd" 
   -m "${TestDataDir}/2D_2x2_square_object_at_(2,1).mhd"
   -p "${TestDataDir}/parameters.2D.NC.translation.ASGD.txt"