transform interface

docs/cxx/interface_types.md

@@ -66,4 +66,6 @@ For binding generation, set the `type_name` an the options accordingly. The type
 - `INPUT_MESH`
 - `OUTPUT_MESH`
 - `INPUT_POLYDATA`
-- `OUTPUT_POLYDATA`
+- `OUTPUT_POLYDATA`
+- `INPUT_TRANSFORM`
+- `OUTPUT_TRANSFORM`

include/itkInputTransform.h

@@ -0,0 +1,121 @@
+/*=========================================================================
+ *
+ *  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 itkInputTransform_h
+#define itkInputTransform_h
+
+#include "itkPipeline.h"
+
+#ifndef ITK_WASM_NO_MEMORY_IO
+#include "itkWasmExports.h"
+#include "itkWasmTransform.h"
+#include "itkWasmTransformToTransformFilter.h"
+#endif
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+#include "itkTransformFileReader.h"
+#endif
+
+namespace itk
+{
+namespace wasm
+{
+
+/**
+ *\class InputTransform
+ * \brief Input transform for an itk::wasm::Pipeline
+ *
+ * This transform is read from the filesystem or memory when ITK_WASM_PARSE_ARGS is called.
+ *
+ * Call `Get()` to get the TTransform * to use an input to a pipeline.
+ *
+ * \ingroup WebAssemblyInterface
+ */
+template <typename TTransform>
+class ITK_TEMPLATE_EXPORT InputTransform
+{
+public:
+  using TransformType = TTransform;
+
+  void Set(const TransformType * transform) {
+    this->m_Transform = transform;
+  }
+
+  const TransformType * Get() const {
+    return this->m_Transform.GetPointer();
+  }
+
+  InputTransform() = default;
+  ~InputTransform() = default;
+protected:
+  typename TTransform::ConstPointer m_Transform;
+};
+
+
+template <typename TTransform>
+bool lexical_cast(const std::string &input, InputTransform<TTransform> &inputTransform)
+{
+  if (input.empty())
+  {
+    return false;
+  }
+
+  if (wasm::Pipeline::get_use_memory_io())
+  {
+#ifndef ITK_WASM_NO_MEMORY_IO
+    using WasmTransformToTransformFilterType = WasmTransformToTransformFilter<TTransform>;
+    auto wasmTransformToTransformFilter = WasmTransformToTransformFilterType::New();
+    auto wasmTransform = WasmTransformToTransformFilterType::WasmTransformType::New();
+    const unsigned int index = std::stoi(input);
+    auto json = getMemoryStoreInputJSON(0, index);
+    wasmTransform->SetJSON(json);
+    wasmTransformToTransformFilter->SetInput(wasmTransform);
+    wasmTransformToTransformFilter->Update();
+    inputTransform.Set(wasmTransformToTransformFilter->GetOutput());
+#else
+    return false;
+#endif
+  }
+  else
+  {
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+    using ParametersValueType = typename TTransform::ParametersValueType;
+    using ReaderType = itk::TransformFileReaderTemplate<ParametersValueType>;
+    auto reader = ReaderType::New();
+    reader->SetFileName(input);
+    reader->Update();
+    auto transformList = reader->GetTransformList();
+    if (transformList->empty())
+    {
+      return false;
+    }
+    auto transform = dynamic_cast<const TTransform *>(transformList->front().GetPointer());
+    if (!transform)
+    {
+      return false;
+    }
+    inputTransform.Set(transform);
+#else
+    return false;
+#endif
+  }
+  return true;
+}
+
+} // end namespace wasm
+} // end namespace itk
+
+#endif

include/itkOutputTransform.h

@@ -0,0 +1,162 @@
+/*=========================================================================
+ *
+ *  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 itkOutputTransform_h
+#define itkOutputTransform_h
+
+#include "itkPipeline.h"
+
+#ifndef ITK_WASM_NO_MEMORY_IO
+#include "itkWasmExports.h"
+#include "itkWasmTransform.h"
+#include "itkTransformToWasmTransformFilter.h"
+#include "itkCompositeTransform.h"
+#include "itkCompositeTransformIOHelper.h"
+#endif
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+#include "itkTransformFileWriter.h"
+#endif
+
+namespace itk
+{
+namespace wasm
+{
+/**
+ *\class OutputTransform
+ * \brief Output transform for an itk::wasm::Pipeline
+ *
+ * This transform is written to the filesystem or memory when it goes out of scope.
+ * 
+ * Call `GetTransform()` to get the TTransform * to use an input to a pipeline.
+ * 
+ * \ingroup WebAssemblyInterface
+ */
+template <typename TTransform>
+class ITK_TEMPLATE_EXPORT OutputTransform
+{
+public:
+  using TransformType = TTransform;
+
+  void Set(const TransformType * transform) {
+    this->m_Transform = transform;
+  }
+
+  const TransformType * Get() const {
+    return this->m_Transform.GetPointer();
+  }
+
+  /** FileName or output index. */
+  void SetIdentifier(const std::string & identifier)
+  {
+    this->m_Identifier = identifier;
+  }
+  const std::string & GetIdentifier() const
+  {
+    return this->m_Identifier;
+  }
+
+  OutputTransform() = default;
+  ~OutputTransform() {
+    if(wasm::Pipeline::get_use_memory_io())
+    {
+#ifndef ITK_WASM_NO_MEMORY_IO
+    if (!this->m_Transform.IsNull() && !this->m_Identifier.empty())
+      {
+        using TransformToWasmTransformFilterType = TransformToWasmTransformFilter<TransformType>;
+        auto transformToWasmTransformFilter = TransformToWasmTransformFilterType::New();
+        transformToWasmTransformFilter->SetTransform(this->m_Transform.GetPointer());
+        transformToWasmTransformFilter->Update();
+        auto wasmTransform = transformToWasmTransformFilter->GetOutput();
+        const auto index = std::stoi(this->m_Identifier);
+        setMemoryStoreOutputDataObject(0, index, wasmTransform);
+
+        using ParametersValueType = typename TransformType::ParametersValueType;
+        using FixedParametersValueType = typename TransformType::FixedParametersValueType;
+        using CompositeTransformType = CompositeTransform<ParametersValueType, TransformType::InputSpaceDimension>;
+        auto compositeTransform = dynamic_cast<const CompositeTransformType *>(wasmTransform->GetTransform());
+        if (compositeTransform)
+        {
+          unsigned int dataCount = 0;
+          CompositeTransformIOHelperTemplate<ParametersValueType> helper;
+          auto transformList = helper.GetTransformList(compositeTransform);
+          // composite transform
+          transformList.pop_front();
+          // iterate through the transform list and store each transfrom's fixed parameters and parameters
+          for (const auto & transform: transformList)
+          {
+            const auto fixedParamsAddress = reinterpret_cast< size_t >( transform->GetFixedParameters().data_block() );
+            const auto fixedParamsSize = transform->GetFixedParameters().Size() * sizeof(FixedParametersValueType);
+            setMemoryStoreOutputArray(0, index, dataCount, fixedParamsAddress, fixedParamsSize);
+            ++dataCount;
+
+            const auto paramsAddress = reinterpret_cast< size_t >( transform->GetParameters().data_block() );
+            const auto paramsSize = transform->GetParameters().Size() * sizeof(ParametersValueType);
+            setMemoryStoreOutputArray(0, index, dataCount, paramsAddress, paramsSize);
+            ++dataCount;
+          }
+        }
+        else
+        {
+          const auto fixedParamsAddress = reinterpret_cast< size_t >( wasmTransform->GetTransform()->GetFixedParameters().data_block() );
+          const auto fixedParamsSize = wasmTransform->GetTransform()->GetFixedParameters().Size() * sizeof(FixedParametersValueType);
+          setMemoryStoreOutputArray(0, index, 0, fixedParamsAddress, fixedParamsSize);
+
+          const auto paramsAddress = reinterpret_cast< size_t >( wasmTransform->GetTransform()->GetParameters().data_block() );
+          const auto paramsSize = wasmTransform->GetTransform()->GetParameters().Size() * sizeof(ParametersValueType);
+          setMemoryStoreOutputArray(0, index, 1, paramsAddress, paramsSize);
+        }
+      }
+#else
+    std::cerr << "Memory IO not supported" << std::endl;
+    abort();
+#endif
+    }
+    else
+    {
+#ifndef ITK_WASM_NO_FILESYSTEM_IO
+    if (!this->m_Transform.IsNull() && !this->m_Identifier.empty())
+      {
+        using ParametersValueType = typename TransformType::ParametersValueType;
+        using WriterType = TransformFileWriterTemplate<ParametersValueType>;
+        auto writer = WriterType::New();
+        writer->SetFileName(this->m_Identifier);
+        writer->SetInput(this->m_Transform);
+        writer->Update();
+      }
+#else
+    std::cerr << "Filesystem IO not supported" << std::endl;
+    abort();
+#endif
+    }
+  }
+protected:
+  typename TTransform::ConstPointer m_Transform;
+
+  std::string m_Identifier;
+};
+
+template <typename TTransform>
+bool lexical_cast(const std::string &input, OutputTransform<TTransform> &outputTransform)
+{
+  outputTransform.SetIdentifier(input);
+  return true;
+}
+
+} // namespace wasm
+} // namespace itk
+
+#endif