COMP: Do not use file IO with Wasm

Avoid Wasm binary size issues and file access issues.
thewtex · Oct 1, 2023 · bc1829f · bc1829f
1 parent 7244b04
commit bc1829f
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Showing 15 changed files with 122 additions and 18 deletions.
diff --git a/Common/ImageSamplers/itkImageToVectorContainerFilter.hxx b/Common/ImageSamplers/itkImageToVectorContainerFilter.hxx
@@ -18,8 +18,6 @@
 #ifndef itkImageToVectorContainerFilter_hxx
 #define itkImageToVectorContainerFilter_hxx
 
-#include "itkImageToVectorContainerFilter.h"
-
 #include "itkMath.h"
 
 namespace itk

diff --git a/Common/Transforms/elxTransformIO.cxx b/Common/Transforms/elxTransformIO.cxx
@@ -32,8 +32,10 @@
 
 #include <itkTransformBase.h>
 #include <itkTransformFactoryBase.h>
+#ifndef __wasm32__
 #include <itkTransformFileReader.h>
 #include <itkTransformFileWriter.h>
+#endif
 
 #include <string>
 
@@ -191,6 +193,11 @@ elastix::TransformIO::ConvertItkTransformBaseToSingleItkTransform(const itk::Tra
 void
 elastix::TransformIO::Write(const itk::Object & itkTransform, const std::string & fileName)
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  throw std::runtime_error(message);
+#else
   try
   {
     const auto writer = itk::TransformFileWriter::New();
@@ -203,12 +210,20 @@ elastix::TransformIO::Write(const itk::Object & itkTransform, const std::string
   {
     log::error(std::ostringstream{} << "Error trying to write " << fileName << ":\n" << stdException.what());
   }
+#endif
 }
 
 
 itk::SmartPointer<itk::TransformBase>
 elastix::TransformIO::Read(const std::string & fileName)
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  throw std::runtime_error(message);
+  return nullptr;
+#else
+
   const auto reader = itk::TransformFileReader::New();
 
   reader->SetFileName(fileName);
@@ -221,6 +236,7 @@ elastix::TransformIO::Read(const std::string & fileName)
   assert(transformList->size() <= 1);
 
   return transformList->empty() ? nullptr : transformList->front();
+#endif
 }
 
 

diff --git a/Common/itkMeshFileReaderBase.h b/Common/itkMeshFileReaderBase.h
@@ -20,7 +20,11 @@
 
 #include "itkMeshSource.h"
 #include "itkMacro.h"
-#include "itkMeshFileReader.h" // for MeshFileReaderException
+#ifndef __wasm32__
+#include "itkMeshFileReaderException.h"
+#else
+#define MeshFileReaderException ExceptionObject
+#endif
 
 namespace itk
 {

diff --git a/Components/Metrics/MissingStructurePenalty/elxMissingStructurePenalty.h b/Components/Metrics/MissingStructurePenalty/elxMissingStructurePenalty.h
@@ -21,9 +21,6 @@
 #include "elxIncludes.h"
 #include "itkMissingStructurePenalty.h"
 
-#include "itkMeshFileReader.h"
-#include "itkMeshFileWriter.h"
-
 namespace elastix
 {
 

diff --git a/Components/Metrics/MissingStructurePenalty/elxMissingStructurePenalty.hxx b/Components/Metrics/MissingStructurePenalty/elxMissingStructurePenalty.hxx
@@ -21,6 +21,11 @@
 #include "elxMissingStructurePenalty.h"
 #include "itkTimeProbe.h"
 
+#ifndef __wasm32__
+#include "itkMeshFileReader.h"
+#include "itkMeshFileWriter.h"
+#endif
+
 namespace elastix
 {
 
@@ -145,6 +150,11 @@ MissingStructurePenalty<TElastix>::BeforeRegistration()
     fmeshArgument << ch << metricNumber;
     std::string                fixedMeshName = this->GetConfiguration()->GetCommandLineArgument(fmeshArgument.str());
     typename MeshType::Pointer fixedMesh; // default-constructed (null)
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  itkExceptionMacro(<< message);
+#else
     if (itksys::SystemTools::GetFilenameLastExtension(fixedMeshName) == ".txt")
     {
       this->ReadTransformixPoints(fixedMeshName, fixedMesh);
@@ -153,6 +163,7 @@ MissingStructurePenalty<TElastix>::BeforeRegistration()
     {
       this->ReadMesh(fixedMeshName, fixedMesh);
     }
+#endif
 
     meshPointerContainer->SetElement(meshNumber, fixedMesh.GetPointer());
   }
@@ -281,6 +292,12 @@ template <class TElastix>
 unsigned int
 MissingStructurePenalty<TElastix>::ReadMesh(const std::string & meshFileName, typename FixedMeshType::Pointer & mesh)
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  itkExceptionMacro(<< message);
+  return 0;
+#else
   /** Read the input mesh. */
   auto meshReader = itk::MeshFileReader<MeshType>::New();
   meshReader->SetFileName(meshFileName);
@@ -300,6 +317,7 @@ MissingStructurePenalty<TElastix>::ReadMesh(const std::string & meshFileName, ty
   log::info(std::ostringstream{} << "  Number of specified input points: " << nrofpoints);
 
   return nrofpoints;
+#endif
 } // end ReadMesh()
 
 
@@ -311,6 +329,11 @@ template <class TElastix>
 void
 MissingStructurePenalty<TElastix>::WriteResultMesh(const std::string & filename, MeshIdType meshId)
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  itkExceptionMacro(<< message);
+#else
   /** Setup the pipeline. */
 
   /** Set the points of the latest transformation. */
@@ -376,7 +399,7 @@ MissingStructurePenalty<TElastix>::WriteResultMesh(const std::string & filename,
     // restore celldata as undefined
     mappedMesh->SetCellData(nullptr);
   }
-
+#endif
 } // end WriteResultMesh()
 
 
@@ -389,6 +412,12 @@ unsigned int
 MissingStructurePenalty<TElastix>::ReadTransformixPoints(const std::string &          filename,
                                                          typename MeshType::Pointer & mesh) // const
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  itkExceptionMacro(<< message);
+  return 0;
+#else
   /*
   FB: Majority of the code is copied from elxTransformBase.hxx: TransformPointsSomePoints()
 Function to read 2d structures by reading elastix point files (transformix format) and connecting
@@ -528,6 +557,7 @@ the sequence of points to form a 2d connected polydata contour.
     }
   }
   return nrofpoints;
+#endif
 } // end ReadTransformixPoints()
 
 

diff --git a/Components/Metrics/PolydataDummyPenalty/elxPolydataDummyPenalty.h b/Components/Metrics/PolydataDummyPenalty/elxPolydataDummyPenalty.h
@@ -23,9 +23,6 @@
 
 //#include "elxMetricBase.h"
 
-#include "itkMeshFileReader.h"
-#include "itkMeshFileWriter.h"
-
 namespace elastix
 {
 /**

diff --git a/Components/Metrics/PolydataDummyPenalty/elxPolydataDummyPenalty.hxx b/Components/Metrics/PolydataDummyPenalty/elxPolydataDummyPenalty.hxx
@@ -20,6 +20,11 @@
 
 #include <typeinfo>
 
+#ifndef __wasm32__
+#include "itkMeshFileReader.h"
+#include "itkMeshFileWriter.h"
+#endif
+
 namespace elastix
 {
 
@@ -270,6 +275,12 @@ template <class TElastix>
 unsigned int
 PolydataDummyPenalty<TElastix>::ReadMesh(const std::string & meshFileName, typename FixedMeshType::Pointer & mesh)
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  itkExceptionMacro(<< message);
+  return 0;
+#else
   /** Read the input mesh. */
   auto meshReader = itk::MeshFileReader<MeshType>::New();
   meshReader->SetFileName(meshFileName);
@@ -291,6 +302,7 @@ PolydataDummyPenalty<TElastix>::ReadMesh(const std::string & meshFileName, typen
   log::info(std::ostringstream{} << "  Number of specified input points: " << nrofpoints);
 
   return nrofpoints;
+#endif
 } // end ReadMesh()
 
 
@@ -302,6 +314,11 @@ template <class TElastix>
 void
 PolydataDummyPenalty<TElastix>::WriteResultMesh(const std::string & filename, MeshIdType meshId)
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  itkExceptionMacro(<< message);
+#else
   /** Set the points of the latest transformation. */
   const MappedMeshContainerPointer mappedMeshContainer = this->GetModifiableMappedMeshContainer();
   FixedMeshPointer                 mappedMesh = mappedMeshContainer->ElementAt(meshId);
@@ -360,7 +377,7 @@ PolydataDummyPenalty<TElastix>::WriteResultMesh(const std::string & filename, Me
   {
     mappedMesh->SetCellData(nullptr);
   }
-
+#endif
 } // end WriteResultMesh()
 
 

diff --git a/Components/Metrics/StatisticalShapePenalty/elxStatisticalShapePenalty.hxx b/Components/Metrics/StatisticalShapePenalty/elxStatisticalShapePenalty.hxx
@@ -25,7 +25,9 @@
 #include "itkDefaultStaticMeshTraits.h"
 #include "itkTransformMeshFilter.h"
 #include <itkMesh.h>
+#ifndef __wasm32__
 #include <itkMeshFileReader.h>
+#endif
 
 #include <fstream>
 #include <typeinfo>
@@ -352,6 +354,12 @@ StatisticalShapePenalty<TElastix>::ReadShape(const std::string &
                                              typename PointSetType::Pointer &       pointSet,
                                              const typename ImageType::ConstPointer image)
 {
+#ifdef __wasm32__
+  const std::string message = "File IO not supported in WebAssembly builds.";
+  log::error(message);
+  itkExceptionMacro(<< message);
+  return 0;
+#else
   /** Typedef's. \todo test DummyIPPPixelType=bool. */
   using DummyIPPPixelType = double;
   using MeshTraitsType =
@@ -380,7 +388,7 @@ StatisticalShapePenalty<TElastix>::ReadShape(const std::string &
   pointSet = PointSetType::New();
   pointSet->SetPoints(mesh->GetPoints());
   return nrofpoints;
-
+#endif
 } // end ReadShape()
 
 

diff --git a/Core/ComponentBaseClasses/elxFixedImagePyramidBase.hxx b/Core/ComponentBaseClasses/elxFixedImagePyramidBase.hxx
@@ -178,21 +178,30 @@ FixedImagePyramidBase<TElastix>::WritePyramidImage(const std::string & filename,
 
   /** Do the writing. */
   log::to_stdout("  Writing fixed pyramid image ...");
+#ifndef __wasm32__
   try
   {
-    itk::WriteCastedImage(*(this->GetAsITKBaseType()->GetOutput(level)), filename, resultImagePixelType, doCompression);
+ itk::WriteCastedImage(*(this->GetAsITKBaseType()->GetOutput(level)), filename, resultImagePixelType, doCompression);
   }
   catch (itk::ExceptionObject & excp)
   {
+#else
+// Always throw -- do not include support code or access filesystem with wasm
+    itk::ExceptionObject excp;
+#endif
     /** Add information to the exception. */
     excp.SetLocation("FixedImagePyramidBase - BeforeEachResolutionBase()");
     std::string err_str = excp.GetDescription();
     err_str += "\nError occurred while writing pyramid image.\n";
     excp.SetDescription(err_str);
 
     /** Pass the exception to an higher level. */
+#ifndef __wasm32__
     throw;
   }
+#else
+    throw excp;
+#endif
 
 } // end WritePyramidImage()
 

diff --git a/Core/ComponentBaseClasses/elxMovingImagePyramidBase.hxx b/Core/ComponentBaseClasses/elxMovingImagePyramidBase.hxx
@@ -179,21 +179,30 @@ MovingImagePyramidBase<TElastix>::WritePyramidImage(const std::string & filename
 
   /** Do the writing. */
   log::to_stdout("  Writing moving pyramid image ...");
+#ifndef __wasm32__
   try
   {
     itk::WriteCastedImage(*(this->GetAsITKBaseType()->GetOutput(level)), filename, resultImagePixelType, doCompression);
   }
   catch (itk::ExceptionObject & excp)
   {
+#else
+// Always throw -- do not include support code or access filesystem with wasm
+    itk::ExceptionObject excp;
+#endif
     /** Add information to the exception. */
     excp.SetLocation("MovingImagePyramidBase - BeforeEachResolutionBase()");
     std::string err_str = excp.GetDescription();
     err_str += "\nError occurred while writing pyramid image.\n";
     excp.SetDescription(err_str);
 
     /** Pass the exception to an higher level. */
+#ifndef __wasm32__
     throw;
   }
+#else
+    throw excp;
+#endif
 
 } // end WritePyramidImage()
 

diff --git a/Core/ComponentBaseClasses/elxResamplerBase.hxx b/Core/ComponentBaseClasses/elxResamplerBase.hxx
@@ -395,21 +395,30 @@ ResamplerBase<TElastix>::WriteResultImage(OutputImageType *   image,
   {
     log::to_stdout("\n  Writing image ...");
   }
+#ifndef __wasm32__
   try
   {
-    itk::WriteCastedImage(*(infoChanger->GetOutput()), filename, resultImagePixelType, doCompression);
+   itk::WriteCastedImage(*(infoChanger->GetOutput()), filename, resultImagePixelType, doCompression);
   }
   catch (itk::ExceptionObject & excp)
   {
+#else
+// Always throw -- do not include support code or access filesystem with wasm
+    itk::ExceptionObject excp;
+#endif
     /** Add information to the exception. */
     excp.SetLocation("ResamplerBase - AfterRegistrationBase()");
     std::string err_str = excp.GetDescription();
     err_str += "\nError occurred while writing resampled image.\n";
     excp.SetDescription(err_str);
 
     /** Pass the exception to an higher level. */
+#ifndef __wasm32__
     throw;
   }
+#else
+    throw excp;
+#endif
 } // end WriteResultImage()