feat(PointSet): initial C++ addition

include/itkInputPointSet.h

@@ -0,0 +1,113 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  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
+ *
+ *         https://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.
+ *
+ *=========================================================================*/
+#ifndef itkInputPointSet_h
+#define itkInputPointSet_h
+
+#include "itkPipeline.h"
+
+#ifndef ITK_WASM_NO_MEMORY_IO
+#include "itkWasmExports.h"
+#include "itkWasmPointSet.h"
+#include "itkWasmPointSetToPointSetFilter.h"
+#endif
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+#include "itkMesh.h"
+#include "itkMeshFileReader.h"
+#endif
+
+namespace itk
+{
+namespace wasm
+{
+
+/**
+ *\class InputPointSet
+ * \brief Input pointSet for an itk::wasm::Pipeline
+ *
+ * This point set is read from the filesystem or memory when ITK_WASM_PARSE_ARGS is called.
+ *
+ * Call `Get()` to get the TPointSet * to use an input to a pipeline.
+ *
+ * \ingroup WebAssemblyInterface
+ */
+template <typename TPointSet>
+class ITK_TEMPLATE_EXPORT InputPointSet
+{
+public:
+  using PointSetType = TPointSet;
+
+  void Set(const PointSetType * pointSet) {
+    this->m_PointSet = pointSet;
+  }
+
+  const PointSetType * Get() const {
+    return this->m_PointSet.GetPointer();
+  }
+
+  InputPointSet() = default;
+  ~InputPointSet() = default;
+protected:
+  typename TPointSet::ConstPointer m_PointSet;
+};
+
+
+template <typename TPointSet>
+bool lexical_cast(const std::string &input, InputPointSet<TPointSet> &inputPointSet)
+{
+  if (input.empty())
+  {
+    return false;
+  }
+
+  if (wasm::Pipeline::get_use_memory_io())
+  {
+#ifndef ITK_WASM_NO_MEMORY_IO
+    using WasmPointSetToPointSetFilterType = WasmPointSetToPointSetFilter<TPointSet>;
+    auto wasmPointSetToPointSetFilter = WasmPointSetToPointSetFilterType::New();
+    auto wasmPointSet = WasmPointSetToPointSetFilterType::WasmPointSetType::New();
+    const unsigned int index = std::stoi(input);
+    auto json = getMemoryStoreInputJSON(0, index);
+    wasmPointSet->SetJSON(json);
+    wasmPointSetToPointSetFilter->SetInput(wasmPointSet);
+    wasmPointSetToPointSetFilter->Update();
+    inputPointSet.Set(wasmPointSetToPointSetFilter->GetOutput());
+#else
+    return false;
+#endif
+  }
+  else
+  {
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+    using MeshType = Mesh<typename TPointSet::PixelType, TPointSet::PointDimension>;
+    using ReaderType = MeshFileReader<MeshType>;
+    auto reader = ReaderType::New();
+    reader->SetFileName(input);
+    reader->Update();
+    auto pointSet = reader->GetOutput();
+    inputPointSet.Set(pointSet);
+#else
+    return false;
+#endif
+  }
+  return true;
+}
+
+} // end namespace wasm
+} // end namespace itk
+
+#endif

include/itkOutputPointSet.h

@@ -0,0 +1,145 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  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
+ *
+ *         https://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.
+ *
+ *=========================================================================*/
+#ifndef itkOutputPointSet_h
+#define itkOutputPointSet_h
+
+#include "itkPipeline.h"
+#include "itkMeshConvertPixelTraits.h"
+
+#ifndef ITK_WASM_NO_MEMORY_IO
+#include "itkWasmExports.h"
+#include "itkWasmPointSet.h"
+#include "itkPointSetToWasmPointSetFilter.h"
+#endif
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+#include "itkMesh.h"
+#include "itkMeshFileWriter.h"
+#endif
+
+namespace itk
+{
+namespace wasm
+{
+/**
+ *\class OutputPointSet
+ * \brief Output point set for an itk::wasm::Pipeline
+ *
+ * This point set is written to the filesystem or memory when it goes out of scope.
+ * 
+ * Call `GetPointSet()` to get the TPointSet * to use an input to a pipeline.
+ * 
+ * \ingroup WebAssemblyInterface
+ */
+template <typename TPointSet>
+class ITK_TEMPLATE_EXPORT OutputPointSet
+{
+public:
+  using PointSetType = TPointSet;
+
+  void Set(const PointSetType * pointSet) {
+    this->m_PointSet = pointSet;
+  }
+
+  const PointSetType * Get() const {
+    return this->m_PointSet.GetPointer();
+  }
+
+  /** FileName or output index. */
+  void SetIdentifier(const std::string & identifier)
+  {
+    this->m_Identifier = identifier;
+  }
+  const std::string & GetIdentifier() const
+  {
+    return this->m_Identifier;
+  }
+
+  OutputPointSet() = default;
+  ~OutputPointSet() {
+    if(wasm::Pipeline::get_use_memory_io())
+    {
+#ifndef ITK_WASM_NO_MEMORY_IO
+    if (!this->m_PointSet.IsNull() && !this->m_Identifier.empty())
+      {
+        using PointSetToWasmPointSetFilterType = PointSetToWasmPointSetFilter<PointSetType>;
+        auto pointSetToWasmPointSetFilter = PointSetToWasmPointSetFilterType::New();
+        pointSetToWasmPointSetFilter->SetInput(this->m_PointSet);
+        pointSetToWasmPointSetFilter->Update();
+        auto wasmPointSet = pointSetToWasmPointSetFilter->GetOutput();
+        const auto index = std::stoi(this->m_Identifier);
+        setMemoryStoreOutputDataObject(0, index, wasmPointSet);
+
+        if (this->m_PointSet->GetNumberOfPoints() > 0)
+        {
+          const auto pointsAddress = reinterpret_cast< size_t >( &(wasmPointSet->GetPointSet()->GetPoints()->at(0)) );
+          const auto pointsSize = wasmPointSet->GetPointSet()->GetPoints()->Size() * sizeof(typename PointSetType::CoordRepType) * PointSetType::PointDimension;
+          setMemoryStoreOutputArray(0, index, 0, pointsAddress, pointsSize);
+        }
+
+        if (this->m_PointSet->GetPointData() != nullptr && this->m_PointSet->GetPointData()->Size() > 0)
+        {
+          using PointPixelType = typename PointSetType::PixelType;
+          using ConvertPointPixelTraits = MeshConvertPixelTraits<PointPixelType>;
+          const auto pointDataAddress = reinterpret_cast< size_t >( &(wasmPointSet->GetPointSet()->GetPointData()->at(0)) );
+          const auto pointDataSize = wasmPointSet->GetPointSet()->GetPointData()->Size() * sizeof(typename ConvertPointPixelTraits::ComponentType) * ConvertPointPixelTraits::GetNumberOfComponents();
+          setMemoryStoreOutputArray(0, index, 1, pointDataAddress, pointDataSize);
+        }
+      }
+#else
+    std::cerr << "Memory IO not supported" << std::endl;
+    abort();
+#endif
+    }
+    else
+    {
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+    if (!this->m_PointSet.IsNull() && !this->m_Identifier.empty())
+      {
+      using MeshType = Mesh<typename TPointSet::PixelType, TPointSet::PointDimension>;
+      using PointSetWriterType = itk::MeshFileWriter<MeshType>;
+      auto pointSetWriter = PointSetWriterType::New();
+      pointSetWriter->SetFileName(this->m_Identifier);
+      typename MeshType::Pointer mesh = MeshType::New();
+      mesh->SetPoints(const_cast<typename MeshType::PointsContainer *>(this->m_PointSet->GetPoints()));
+      mesh->SetPointData(const_cast<typename MeshType::PointDataContainer *>(this->m_PointSet->GetPointData()));
+      pointSetWriter->SetInput(mesh);
+      pointSetWriter->Update();
+      }
+#else
+    std::cerr << "Filesystem IO not supported" << std::endl;
+    abort();
+#endif
+    }
+  }
+protected:
+  typename TPointSet::ConstPointer m_PointSet;
+
+  std::string m_Identifier;
+};
+
+template <typename TPointSet>
+bool lexical_cast(const std::string &input, OutputPointSet<TPointSet> &outputPointSet)
+{
+  outputPointSet.SetIdentifier(input);
+  return true;
+}
+
+} // namespace wasm
+} // namespace itk
+
+#endif

include/itkPointSetJSON.h

@@ -0,0 +1,128 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  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
+ *
+ *         https://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.
+ *
+ *=========================================================================*/
+#ifndef itkPointSetJSON_h
+#define itkPointSetJSON_h
+
+#include "itkMeshConvertPixelTraits.h"
+
+#include "itkWasmMapComponentType.h"
+#include "itkWasmMapPixelType.h"
+#include "itkIntTypesJSON.h"
+#include "itkFloatTypesJSON.h"
+#include "itkPixelTypesJSON.h"
+#include "itkWasmPointSet.h"
+#include "itkMetaDataDictionaryJSON.h"
+
+#include "glaze/glaze.hpp"
+
+namespace itk
+{
+  /** \class PointSetTypeJSON
+   *
+   * \brief PointSet type JSON representation data structure.
+   *
+   * \ingroup WebAssemblyInterface
+   */
+  struct PointSetTypeJSON
+  {
+    unsigned int dimension { 2 };
+    JSONFloatTypesEnum pointComponentType { JSONFloatTypesEnum::float32 };
+    JSONComponentTypesEnum pointPixelComponentType { JSONComponentTypesEnum::float32 };
+    JSONPixelTypesEnum pointPixelType { JSONPixelTypesEnum::Scalar };
+    unsigned int pointPixelComponents { 1 };
+  };
+
+  /** \class PointSetJSON
+   *
+   * \brief PointSet JSON representation data structure.
+   *
+   * \ingroup WebAssemblyInterface
+   */
+  struct PointSetJSON
+  {
+    PointSetTypeJSON pointSetType;
+
+    std::string name { "PointSet"};
+
+    size_t numberOfPoints{ 0 };
+    std::string points;
+
+    size_t numberOfPointPixels{ 0 };
+    std::string pointData;
+
+    MetadataJSON metadata;
+  };
+
+template<typename TPointSet>
+auto pointSetToPointSetJSON(const TPointSet * pointSet, const WasmPointSet<TPointSet> * wasmPointSet, bool inMemory) -> PointSetJSON
+{
+  using PointSetType = TPointSet;
+
+  PointSetJSON pointSetJSON;
+
+  pointSetJSON.pointSetType.dimension = PointSetType::PointDimension;
+
+  pointSetJSON.pointSetType.pointComponentType = wasm::MapComponentType<typename PointSetType::CoordRepType>::JSONFloatTypeEnum;
+  using PointPixelType = typename TPointSet::PixelType;
+  using ConvertPointPixelTraits = MeshConvertPixelTraits<PointPixelType>;
+  pointSetJSON.pointSetType.pointPixelComponentType = wasm::MapComponentType<typename ConvertPointPixelTraits::ComponentType>::JSONComponentEnum;
+  pointSetJSON.pointSetType.pointPixelType = wasm::MapPixelType<PointPixelType>::JSONPixelEnum;
+  pointSetJSON.pointSetType.pointPixelComponents = ConvertPointPixelTraits::GetNumberOfComponents();
+
+  pointSetJSON.name = pointSet->GetObjectName();
+  pointSetJSON.numberOfPoints = pointSet->GetNumberOfPoints();
+  if (pointSet->GetPointData() == nullptr)
+  {
+    pointSetJSON.numberOfPointPixels = 0;
+  }
+  else
+  {
+    pointSetJSON.numberOfPointPixels = pointSet->GetPointData()->Size();
+  }
+  if (inMemory)
+  {
+    const auto pointsAddress = reinterpret_cast< size_t >( &(pointSet->GetPoints()->at(0)) );
+    std::ostringstream pointsStream;
+    pointsStream << "data:application/vnd.itk.address,0:";
+    pointsStream << pointsAddress;
+    pointSetJSON.points = pointsStream.str();
+
+    size_t pointDataAddress = 0;
+    if (pointSet->GetPointData() != nullptr && pointSet->GetPointData()->Size() > 0)
+    {
+      pointDataAddress = reinterpret_cast< size_t >( &(pointSet->GetPointData()->at(0)) );
+    }
+    std::ostringstream pointDataStream;
+    pointDataStream << "data:application/vnd.itk.address,0:";
+    pointDataStream << pointDataAddress;
+    pointSetJSON.pointData = pointDataStream.str();
+  }
+  else
+  {
+    pointSetJSON.points = "data:application/vnd.itk.path,data/points.raw";
+    pointSetJSON.pointData = "data:application/vnd.itk.path,data/point-data.raw";
+  }
+
+  auto dictionary = pointSet->GetMetaDataDictionary();
+  metaDataDictionaryToJSON(dictionary, pointSetJSON.metadata);
+
+  return pointSetJSON;
+}
+} // end namespace itk
+
+#endif // itkPointSetJSON_h