BUG: Library should write to output directory whenever it is specified

Whenever the output directory is specified, the library will now write files to this directory, just like the executable does. (Before this commit, the elastix library would only create the result images in memory, even when the WriteResultImage parameter would be "true". This was an inconsistency between the library and the elastix executable.) With this commit, an empty string (`""`) is used internally to indicate that the output directory is unspecified. The use of a magical "output_path_not_set" string is abandoned.
SuperElastix · May 31, 2023 · 99902e5 · 99902e5
1 parent 691c358
commit 99902e5
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Showing 14 changed files with 248 additions and 223 deletions.
diff --git a/Components/Metrics/MissingStructurePenalty/elxMissingStructurePenalty.hxx b/Components/Metrics/MissingStructurePenalty/elxMissingStructurePenalty.hxx
@@ -190,8 +190,10 @@ MissingStructurePenalty<TElastix>::AfterEachIteration()
   this->m_Configuration->ReadParameter(
     writeResultMeshThisIteration, "WriteResultMeshAfterEachIteration", "", level, 0, false);
 
+  const std::string outputDirectoryPath = this->m_Configuration->GetCommandLineArgument("-out");
+
   /** Writing result mesh. */
-  if (writeResultMeshThisIteration)
+  if (writeResultMeshThisIteration && !outputDirectoryPath.empty())
   {
     std::string componentLabel(this->GetComponentLabel());
     std::string metricNumber = componentLabel.substr(6, 2); // strip "Metric" keep number
@@ -204,7 +206,7 @@ MissingStructurePenalty<TElastix>::AfterEachIteration()
     {
 
       std::ostringstream makeFileName;
-      makeFileName << this->m_Configuration->GetCommandLineArgument("-out") << "resultmesh" << ch << metricNumber << "."
+      makeFileName << outputDirectoryPath << "resultmesh" << ch << metricNumber << "."
                    << this->m_Configuration->GetElastixLevel() << ".R" << level << ".It" << std::setfill('0')
                    << std::setw(7) << iter << "." << resultMeshFormat;
 
@@ -238,8 +240,10 @@ MissingStructurePenalty<TElastix>::AfterEachResolution()
   this->m_Configuration->ReadParameter(
     writeResultMeshThisResolution, "WriteResultMeshAfterEachResolution", "", level, 0, false);
 
+  const std::string outputDirectoryPath = this->m_Configuration->GetCommandLineArgument("-out");
+
   /** Writing result mesh. */
-  if (writeResultMeshThisResolution)
+  if (writeResultMeshThisResolution && !outputDirectoryPath.empty())
   {
     std::string componentLabel(this->GetComponentLabel());
     std::string metricNumber = componentLabel.substr(6, 2); // strip "Metric" keep number
@@ -252,7 +256,7 @@ MissingStructurePenalty<TElastix>::AfterEachResolution()
     {
 
       std::ostringstream makeFileName;
-      makeFileName << this->m_Configuration->GetCommandLineArgument("-out") << "resultmesh" << ch << metricNumber << "."
+      makeFileName << outputDirectoryPath << "resultmesh" << ch << metricNumber << "."
                    << this->m_Configuration->GetElastixLevel() << ".R" << level << "." << resultMeshFormat;
 
       try

diff --git a/Components/Metrics/PolydataDummyPenalty/elxPolydataDummyPenalty.hxx b/Components/Metrics/PolydataDummyPenalty/elxPolydataDummyPenalty.hxx
@@ -179,8 +179,10 @@ PolydataDummyPenalty<TElastix>::AfterEachIteration()
   this->m_Configuration->ReadParameter(
     writeResultMeshThisIteration, "WriteResultMeshAfterEachIteration", "", level, 0, false);
 
+  const std::string outputDirectoryPath = this->m_Configuration->GetCommandLineArgument("-out");
+
   /** Writing result mesh. */
-  if (writeResultMeshThisIteration)
+  if (writeResultMeshThisIteration && !outputDirectoryPath.empty())
   {
     std::string componentLabel(this->GetComponentLabel());
     std::string metricNumber = componentLabel.substr(6, 2); // strip "Metric" keep number
@@ -193,7 +195,7 @@ PolydataDummyPenalty<TElastix>::AfterEachIteration()
     {
 
       std::ostringstream makeFileName;
-      makeFileName << this->m_Configuration->GetCommandLineArgument("-out") << "resultmesh" << ch << metricNumber << "."
+      makeFileName << outputDirectoryPath << "resultmesh" << ch << metricNumber << "."
                    << this->m_Configuration->GetElastixLevel() << ".R" << level << ".It" << std::setfill('0')
                    << std::setw(7) << iter << "." << resultMeshFormat;
 
@@ -227,8 +229,10 @@ PolydataDummyPenalty<TElastix>::AfterEachResolution()
   this->m_Configuration->ReadParameter(
     writeResultMeshThisResolution, "WriteResultMeshAfterEachResolution", "", level, 0, false);
 
+  const std::string outputDirectoryPath = this->m_Configuration->GetCommandLineArgument("-out");
+
   /** Writing result mesh. */
-  if (writeResultMeshThisResolution)
+  if (writeResultMeshThisResolution && !outputDirectoryPath.empty())
   {
     std::string componentLabel(this->GetComponentLabel());
     std::string metricNumber = componentLabel.substr(6, 2); // strip "Metric" keep number
@@ -241,7 +245,7 @@ PolydataDummyPenalty<TElastix>::AfterEachResolution()
     {
 
       std::ostringstream makeFileName;
-      makeFileName << this->m_Configuration->GetCommandLineArgument("-out") << "resultmesh" << ch << metricNumber << "."
+      makeFileName << outputDirectoryPath << "resultmesh" << ch << metricNumber << "."
                    << this->m_Configuration->GetElastixLevel() << ".R" << level << "." << resultMeshFormat;
 
       try

diff --git a/Components/Optimizers/FullSearch/elxFullSearchOptimizer.hxx b/Components/Optimizers/FullSearch/elxFullSearchOptimizer.hxx
@@ -160,13 +160,18 @@ FullSearch<TElastix>::BeforeEachResolution()
     this->m_OptimizationSurface->Allocate();
     /** \todo try/catch block around Allocate? */
 
-    /** Set the name of this image on disk. */
-    std::string resultImageFormat = "mhd";
-    configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
-    makeString.str("");
-    makeString << configuration.GetCommandLineArgument("-out") << "OptimizationSurface."
-               << configuration.GetElastixLevel() << ".R" << level << "." << resultImageFormat;
-    this->m_OptimizationSurface->SetOutputFileName(makeString.str().c_str());
+    if (const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
+        !outputDirectoryPath.empty())
+    {
+      /** Set the name of this image on disk. */
+      std::string resultImageFormat = "mhd";
+      configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
+
+      makeString.str("");
+      makeString << outputDirectoryPath << "OptimizationSurface." << configuration.GetElastixLevel() << ".R" << level
+                 << "." << resultImageFormat;
+      this->m_OptimizationSurface->SetOutputFileName(makeString.str().c_str());
+    }
 
     log::info(std::ostringstream{} << "Total number of iterations needed in this resolution: "
                                    << this->GetNumberOfIterations() << ".");
@@ -239,7 +244,8 @@ FullSearch<TElastix>::AfterEachResolution()
   /** Write the optimization surface to disk */
   bool writeSurfaceEachResolution = false;
   configuration.ReadParameter(writeSurfaceEachResolution, "WriteOptimizationSurfaceEachResolution", 0, false);
-  if (writeSurfaceEachResolution)
+
+  if (writeSurfaceEachResolution && !configuration.GetCommandLineArgument("-out").empty())
   {
     try
     {

diff --git a/Core/ComponentBaseClasses/elxFixedImagePyramidBase.hxx b/Core/ComponentBaseClasses/elxFixedImagePyramidBase.hxx
@@ -60,12 +60,14 @@ FixedImagePyramidBase<TElastix>::BeforeEachResolutionBase()
   std::string resultImageFormat = "mhd";
   configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
 
+  const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
+
   /** Writing result image. */
-  if (writePyramidImage)
+  if (writePyramidImage && !outputDirectoryPath.empty())
   {
     /** Create a name for the final result. */
     std::ostringstream makeFileName;
-    makeFileName << configuration.GetCommandLineArgument("-out");
+    makeFileName << outputDirectoryPath;
     makeFileName << this->GetComponentLabel() << "." << configuration.GetElastixLevel() << ".R" << level << "."
                  << resultImageFormat;
 

diff --git a/Core/ComponentBaseClasses/elxMovingImagePyramidBase.hxx b/Core/ComponentBaseClasses/elxMovingImagePyramidBase.hxx
@@ -61,12 +61,14 @@ MovingImagePyramidBase<TElastix>::BeforeEachResolutionBase()
   std::string resultImageFormat = "mhd";
   configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
 
+  const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
+
   /** Writing result image. */
-  if (writePyramidImage)
+  if (writePyramidImage && !outputDirectoryPath.empty())
   {
     /** Create a name for the final result. */
     std::ostringstream makeFileName;
-    makeFileName << configuration.GetCommandLineArgument("-out");
+    makeFileName << outputDirectoryPath;
     makeFileName << this->GetComponentLabel() << "." << configuration.GetElastixLevel() << ".R" << level << "."
                  << resultImageFormat;
 

diff --git a/Core/ComponentBaseClasses/elxResamplerBase.hxx b/Core/ComponentBaseClasses/elxResamplerBase.hxx
@@ -92,16 +92,18 @@ ResamplerBase<TElastix>::AfterEachResolutionBase()
   configuration.ReadParameter(
     writeResultImageThisResolution, "WriteResultImageAfterEachResolution", "", level, 0, false);
 
+  const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
+
   /** Writing result image. */
-  if (writeResultImageThisResolution)
+  if (writeResultImageThisResolution && !outputDirectoryPath.empty())
   {
     /** Create a name for the final result. */
     const auto  resultImageName = configuration.RetrieveParameterStringValue("result", "ResultImageName", 0, false);
     std::string resultImageFormat = "mhd";
     configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
     std::ostringstream makeFileName;
-    makeFileName << configuration.GetCommandLineArgument("-out") << resultImageName << '.'
-                 << configuration.GetElastixLevel() << ".R" << level << "." << resultImageFormat;
+    makeFileName << outputDirectoryPath << resultImageName << '.' << configuration.GetElastixLevel() << ".R" << level
+                 << "." << resultImageFormat;
 
     /** Time the resampling. */
     itk::TimeProbe timer;
@@ -147,8 +149,10 @@ ResamplerBase<TElastix>::AfterEachIterationBase()
   bool writeResultImageThisIteration = false;
   configuration.ReadParameter(writeResultImageThisIteration, "WriteResultImageAfterEachIteration", "", level, 0, false);
 
+  const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
+
   /** Writing result image. */
-  if (writeResultImageThisIteration)
+  if (writeResultImageThisIteration && !outputDirectoryPath.empty())
   {
     /** Set the final transform parameters. */
     this->GetElastix()->GetElxTransformBase()->SetFinalParameters();
@@ -158,9 +162,8 @@ ResamplerBase<TElastix>::AfterEachIterationBase()
     std::string resultImageFormat = "mhd";
     configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
     std::ostringstream makeFileName;
-    makeFileName << configuration.GetCommandLineArgument("-out") << resultImageName << '.'
-                 << configuration.GetElastixLevel() << ".R" << level << ".It" << std::setfill('0') << std::setw(7)
-                 << iter << "." << resultImageFormat;
+    makeFileName << outputDirectoryPath << resultImageName << '.' << configuration.GetElastixLevel() << ".R" << level
+                 << ".It" << std::setfill('0') << std::setw(7) << iter << "." << resultImageFormat;
 
     /** Apply the final transform, and save the result. */
     try
@@ -210,29 +213,28 @@ ResamplerBase<TElastix>::AfterRegistrationBase()
     this->ReleaseMemory();
   }
 
-  /**
-   * Create the result image and put it in ResultImageContainer
-   * Only necessary when compiling elastix as a library!
-   */
-  if (isElastixLibrary)
+  /** Writing result image. */
+  if (writeResultImage == "true")
   {
-    if (writeResultImage == "true")
+    /**
+     * Create the result image and put it in ResultImageContainer
+     * Only necessary when compiling elastix as a library!
+     */
+    if (isElastixLibrary)
     {
       this->CreateItkResultImage();
     }
-  }
-  else
-  {
-    /** Writing result image. */
-    if (writeResultImage == "true")
+
+    if (const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
+        !outputDirectoryPath.empty())
     {
       /** Create a name for the final result. */
       const auto  resultImageName = configuration.RetrieveParameterStringValue("result", "ResultImageName", 0, false);
       std::string resultImageFormat = "mhd";
       configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0);
       std::ostringstream makeFileName;
-      makeFileName << configuration.GetCommandLineArgument("-out") << resultImageName << '.'
-                   << configuration.GetElastixLevel() << "." << resultImageFormat;
+      makeFileName << outputDirectoryPath << resultImageName << '.' << configuration.GetElastixLevel() << "."
+                   << resultImageFormat;
 
       /** Time the resampling. */
       itk::TimeProbe timer;
@@ -256,13 +258,13 @@ ResamplerBase<TElastix>::AfterRegistrationBase()
       log::info(std::ostringstream{} << "  Applying final transform took "
                                      << Conversion::SecondsToDHMS(timer.GetMean(), 2));
     }
-    else
-    {
-      /** Do not apply the final transform. */
-      log::info(std::ostringstream{} << '\n'
-                                     << "Skipping applying final transform, no resulting output image generated.");
-    } // end if
   }
+  else
+  {
+    /** Do not apply the final transform. */
+    log::info(std::ostringstream{} << '\n'
+                                   << "Skipping applying final transform, no resulting output image generated.");
+  } // end if
 
 } // end AfterRegistrationBase()