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feat(transform-io): package C++ addition
1 parent eeb4947 commit 6cc2576

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‎ITKKWStyleOverwrite.txt

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@@ -6,3 +6,4 @@ itkSupportInputMeshTypesTest\.cxx Namespace Disable
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itkSupportInputMeshTypesMemoryIOTest\.cxx Namespace Disable
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itkSupportInputPolyDataTypesTest\.cxx Namespace Disable
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itkFloatTypesJSON\.h Namespace Disable
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itkOutputTransformIO\.h Namespace Disable

‎include/itkInputTransformIO.h

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/*=========================================================================
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*
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* Copyright NumFOCUS
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* https://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#ifndef itkInputTransformIO_h
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#define itkInputTransformIO_h
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#include "itkPipeline.h"
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#include "itkWasmTransformIOBase.h"
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#include "itkWasmTransformIO.h"
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#ifndef ITK_WASM_NO_MEMORY_IO
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#include "itkWasmExports.h"
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#endif
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#ifndef ITK_WASM_NO_FILESYSTEM_IO
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#endif
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namespace itk
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{
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namespace wasm
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{
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/**
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*\class InputTransformIO
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* \brief Input transform for an itk::wasm::Pipeline from an itk::TransformIOBase
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*
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* This transform is read from the filesystem or memory when ITK_WASM_PARSE_ARGS is called.
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*
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* This class is for the WriteTransform ITK-Wasm pipeline. Most pipelines will use itk::wasm::InputTransform.
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*
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* \ingroup WebAssemblyInterface
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*/
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template <typename TParametersValueType>
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class InputTransformIO
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{
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public:
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using ParametersValueType = TParametersValueType;
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using WasmTransformIOBaseType = WasmTransformIOBase<ParametersValueType>;
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void Set(const WasmTransformIOBaseType * transformIO) {
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this->m_WasmTransformIOBase = transformIO;
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}
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const WasmTransformIOBaseType * Get() const {
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return this->m_WasmTransformIOBase.GetPointer();
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}
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InputTransformIO() = default;
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~InputTransformIO() = default;
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protected:
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typename WasmTransformIOBaseType::ConstPointer m_WasmTransformIOBase;
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};
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template <typename TParametersValueType>
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bool lexical_cast(const std::string &input, InputTransformIO<TParametersValueType> &inputTransformIO)
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{
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using ParametersValueType = TParametersValueType;
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using WasmTransformIOType = itk::WasmTransformIOTemplate<ParametersValueType>;
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using WasmTransformIOBaseType = WasmTransformIOBase<ParametersValueType>;
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using FixedParametersType = typename WasmTransformIOType::FixedParametersType;
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if (input.empty())
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{
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return false;
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}
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if (wasm::Pipeline::get_use_memory_io())
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{
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#ifndef ITK_WASM_NO_MEMORY_IO
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const unsigned int index = std::stoi(input);
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auto json = getMemoryStoreInputJSON(0, index);
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auto deserializedAttempt = glz::read_json<itk::TransformListJSON>(json);
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if (!deserializedAttempt)
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{
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const std::string descriptiveError = glz::format_error(deserializedAttempt, json);
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throw std::runtime_error("Failed to deserialize TransformJSON: " + descriptiveError);
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}
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auto transformListJSON = deserializedAttempt.value();
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if (transformListJSON.size() < 1)
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{
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throw std::runtime_error("Expected at least one transform in the list");
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}
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auto wasmTransformIO = WasmTransformIOType::New();
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wasmTransformIO->SetJSON(transformListJSON);
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auto wasmTransformIOBase = WasmTransformIOBaseType::New();
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wasmTransformIOBase->SetTransformIO(wasmTransformIO, false);
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wasmTransformIOBase->SetJSON(json);
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inputTransformIO.Set(wasmTransformIOBase);
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#else
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return false;
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#endif
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}
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else
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{
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#ifndef ITK_WASM_NO_FILESYSTEM_IO
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auto wasmTransformIO = WasmTransformIOType::New();
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wasmTransformIO->SetFileName(input);
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wasmTransformIO->Read();
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auto wasmTransformIOBase = WasmTransformIOBaseType::New();
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wasmTransformIOBase->SetTransformIO(wasmTransformIO);
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inputTransformIO.Set(wasmTransformIOBase);
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#else
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return false;
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#endif
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}
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return true;
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}
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} // end namespace wasm
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} // end namespace itk
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#endif

‎include/itkOutputTransformIO.h

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/*=========================================================================
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*
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* Copyright NumFOCUS
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* https://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#ifndef itkOutputTransformIO_h
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#define itkOutputTransformIO_h
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#include "itkTransformBase.h"
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#include "itkPipeline.h"
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#include "itkTransformIOBase.h"
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#include "itkWasmTransformIOBase.h"
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#include "itkWasmTransformIO.h"
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#include "itkTransformJSON.h"
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#ifndef ITK_WASM_NO_MEMORY_IO
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#include "itkWasmExports.h"
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#endif
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#ifndef ITK_WASM_NO_FILESYSTEM_IO
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#endif
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namespace
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{
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template <typename TParametersValueType>
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void
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addTransformBuffersToMemoryStore(const itk::TransformListJSON & transformListJSON, size_t index)
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{
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using ParametersValueType = TParametersValueType;
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using TransformBaseType = itk::TransformBaseTemplate<ParametersValueType>;
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using FixedParametersValueType = typename TransformBaseType::FixedParametersValueType;
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unsigned int dataCount = 0;
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// iterate through the transform list and store each transfrom's fixed parameters and parameters
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for (const auto & transformJSON: transformListJSON)
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{
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if (transformJSON.transformType.transformParameterization == itk::JSONTransformParameterizationEnum::Composite)
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{
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continue;
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}
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const auto fixedParamsAddress = static_cast< size_t >( std::strtoull(transformJSON.fixedParameters.substr(35).c_str(), nullptr, 10) );
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const auto fixedParamsSize = transformJSON.numberOfFixedParameters * sizeof(FixedParametersValueType);
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itk::wasm::setMemoryStoreOutputArray(0, index, dataCount, fixedParamsAddress, fixedParamsSize);
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++dataCount;
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const auto paramsAddress = static_cast< size_t >( std::strtoull(transformJSON.parameters.substr(35).c_str(), nullptr, 10) );
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const auto paramsSize = transformJSON.numberOfParameters * sizeof(ParametersValueType);
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itk::wasm::setMemoryStoreOutputArray(0, index, dataCount, paramsAddress, paramsSize);
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++dataCount;
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}
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}
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} // end anonymous namespace
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namespace itk
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{
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namespace wasm
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{
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/**
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*\class OutputTransformIO
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* \brief Output transform for an itk::wasm::Pipeline from an itk::TransformIOBaseTemplate
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*
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* This transform is written to the filesystem or memory when it goes out of scope.
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*
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* This class is for the ReadTransform ITK-Wasm pipeline. Most pipelines will use itk::wasm::OutputTransform.
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*
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* \ingroup WebAssemblyInterface
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*/
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template <typename TParametersValueType>
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class OutputTransformIO
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{
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public:
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using ParametersValueType = TParametersValueType;
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using TransformIOBaseType = itk::TransformIOBaseTemplate<ParametersValueType>;
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void Set(TransformIOBaseType * transformIO) {
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this->m_TransformIO = transformIO;
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}
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TransformIOBaseType * Get() const {
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return this->m_TransformIO.GetPointer();
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}
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/** FileName or output index. */
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void SetIdentifier(const std::string & identifier)
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{
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this->m_Identifier = identifier;
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}
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const std::string & GetIdentifier() const
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{
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return this->m_Identifier;
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}
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OutputTransformIO() = default;
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~OutputTransformIO() {
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if(wasm::Pipeline::get_use_memory_io())
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{
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#ifndef ITK_WASM_NO_MEMORY_IO
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if (!this->m_TransformIO.IsNull() && !this->m_Identifier.empty())
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{
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const auto index = std::stoi(this->m_Identifier);
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auto wasmTransformIOBase = WasmTransformIOBase<ParametersValueType>::New();
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wasmTransformIOBase->SetTransformIO(this->m_TransformIO);
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setMemoryStoreOutputDataObject(0, index, wasmTransformIOBase);
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const auto transformListJSON = wasmTransformIOBase->GetTransformListJSON();
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if (transformListJSON.size() > 0)
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{
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addTransformBuffersToMemoryStore<ParametersValueType>(transformListJSON, index);
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}
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}
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#else
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std::cerr << "Memory IO not supported" << std::endl;
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abort();
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#endif
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}
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else
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{
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#ifndef ITK_WASM_NO_FILESYSTEM_IO
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if (!this->m_TransformIO.IsNull() && !this->m_Identifier.empty())
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{
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this->m_TransformIO->Read();
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using WasmTransformIOType = itk::WasmTransformIOTemplate<ParametersValueType>;
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auto wasmTransformIO = WasmTransformIOType::New();
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wasmTransformIO->SetTransformList(*(reinterpret_cast<typename WasmTransformIOType::ConstTransformListType *>(&(this->m_TransformIO->GetTransformList()))));
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wasmTransformIO->SetFileName(this->m_Identifier);
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wasmTransformIO->Write();
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}
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#else
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std::cerr << "Filesystem IO not supported" << std::endl;
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abort();
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#endif
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}
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}
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protected:
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typename TransformIOBaseType::Pointer m_TransformIO;
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std::string m_Identifier;
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};
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template<typename TParametersValueType>
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bool lexical_cast(const std::string &input, OutputTransformIO<TParametersValueType> &outputTransformIO)
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{
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outputTransformIO.SetIdentifier(input);
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return true;
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}
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} // namespace wasm
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} // namespace itk
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#endif

‎include/itkWasmMeshIO.h

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@@ -32,11 +32,11 @@ namespace itk
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* \brief Read and write the an itk::Mesh in a format for interfacing in WebAssembly (Wasm).
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*
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* This format is intended to facilitate data exchange in itk-wasm.
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* It reads and writes an itk-wasm Mesh object where TypedArrays are
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* It reads and writes an ITK-Wasm Mesh object where TypedArrays are
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* replaced by binary files on the filesystem or in a CBOR file.
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*
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* The file extensions used are .iwm and .iwm.cbor.
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*
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*
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* \ingroup IOFilters
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* \ingroup WebAssemblyInterface
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*/

‎include/itkWasmTransformIO.h

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@@ -86,7 +86,7 @@ class ITK_TEMPLATE_EXPORT WasmTransformIOTemplate : public TransformIOBaseTempla
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#if !defined(ITK_WRAPPING_PARSER)
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/** Get the JSON representation of the mesh information. */
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auto
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GetJSON() -> TransformListJSON;
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GetJSON(bool inMemory=false) -> TransformListJSON;
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#endif
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protected:
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void
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PrintSelf(std::ostream & os, Indent indent) const override;
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auto
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virtual auto
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ReadTransformInformation() -> const TransformListJSON;
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void
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ReadFixedParameters(const TransformListJSON & json);
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void
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WriteParameters();
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/** Reads in the transform information and populates the related buffers. */
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void
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ReadCBOR();
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/** Writes the buffers into the CBOR item and the buffer out to disk. */
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void
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WriteCBOR();
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void ReadCBOR(void * buffer = nullptr, unsigned char * cborBuffer = nullptr, size_t cborBufferLength = 0);
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size_t WriteCBOR(const void * buffer = nullptr, unsigned char ** cborBuffer = nullptr, bool allocateCBORBuffer = false);
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cbor_item_t * m_CBORRoot{ nullptr };
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