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feat(mesh-filters): geogram conversion test pipeline
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11 files changed

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‎include/itkOutputMesh.h

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@@ -21,6 +21,7 @@
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#include "itkPipeline.h"
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#include "itkMeshConvertPixelTraits.h"
2323
#include "itkMesh.h"
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#include "itkQuadEdgeMesh.h"
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2526
#ifndef ITK_WASM_NO_MEMORY_IO
2627
#include "itkWasmExports.h"
@@ -144,6 +145,107 @@ class ITK_TEMPLATE_EXPORT OutputMesh
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std::string m_Identifier;
145146
};
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148+
// write a template specialization for itk::QuadEdgeMesh that does not assume
149+
// that the points, etc. are stored in itk::VectorContainers
150+
template <typename TPixel, unsigned int VDimension>
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class OutputMesh<itk::QuadEdgeMesh<TPixel, VDimension>>
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{
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public:
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using MeshType = itk::QuadEdgeMesh<TPixel, VDimension>;
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void Set(const MeshType * mesh) {
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this->m_Mesh = mesh;
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}
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const MeshType * Get() const {
161+
return this->m_Mesh.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
170+
{
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return this->m_Identifier;
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}
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OutputMesh() = default;
175+
~OutputMesh() {
176+
if(wasm::Pipeline::get_use_memory_io())
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{
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#ifndef ITK_WASM_NO_MEMORY_IO
179+
if (!this->m_Mesh.IsNull() && !this->m_Identifier.empty())
180+
{
181+
using MeshToWasmMeshFilterType = MeshToWasmMeshFilter<MeshType>;
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auto meshToWasmMeshFilter = MeshToWasmMeshFilterType::New();
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meshToWasmMeshFilter->SetInput(this->m_Mesh);
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meshToWasmMeshFilter->Update();
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auto wasmMesh = meshToWasmMeshFilter->GetOutput();
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const auto index = std::stoi(this->m_Identifier);
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setMemoryStoreOutputDataObject(0, index, wasmMesh);
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if (this->m_Mesh->GetNumberOfPoints() > 0)
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{
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const auto pointsAddress = reinterpret_cast< size_t >( &(wasmMesh->GetPointsBufferContainer().at(0)) );
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const auto pointsSize = wasmMesh->GetPointsBufferContainer().size() * sizeof(typename MeshType::PointIdentifier);
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setMemoryStoreOutputArray(0, index, 0, pointsAddress, pointsSize);
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}
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// if (this->m_Mesh->GetNumberOfCells() > 0)
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// {
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// const auto cellsAddress = reinterpret_cast< size_t >( &(wasmMesh->GetCellBuffer()->at(0)) );
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// const auto cellsSize = wasmMesh->GetCellBuffer()->Size() * sizeof(typename MeshType::CellIdentifier);
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// setMemoryStoreOutputArray(0, index, 1, cellsAddress, cellsSize);
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// }
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// if (this->m_Mesh->GetPointData() != nullptr && this->m_Mesh->GetPointData()->Size() > 0)
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// {
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// using PointPixelType = typename MeshType::PixelType;
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// using ConvertPointPixelTraits = MeshConvertPixelTraits<PointPixelType>;
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// const auto pointDataAddress = reinterpret_cast< size_t >( &(wasmMesh->GetMesh()->GetPointData()->at(0)) );
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// const auto pointDataSize = wasmMesh->GetMesh()->GetPointData()->Size() * sizeof(typename ConvertPointPixelTraits::ComponentType) * ConvertPointPixelTraits::GetNumberOfComponents();
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// setMemoryStoreOutputArray(0, index, 2, pointDataAddress, pointDataSize);
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// }
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// if (this->m_Mesh->GetCellData() != nullptr && this->m_Mesh->GetCellData()->Size() > 0)
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// {
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// using CellPixelType = typename MeshType::CellPixelType;
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// using ConvertCellPixelTraits = MeshConvertPixelTraits<CellPixelType>;
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// const auto cellDataAddress = reinterpret_cast< size_t >( &(wasmMesh->GetMesh()->GetCellData()->at(0)) );
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// const auto cellDataSize = wasmMesh->GetMesh()->GetCellData()->Size() * sizeof(typename ConvertCellPixelTraits::ComponentType) * ConvertCellPixelTraits::GetNumberOfComponents();
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// setMemoryStoreOutputArray(0, index, 3, cellDataAddress, cellDataSize);
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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
229+
if (!this->m_Mesh.IsNull() && !this->m_Identifier.empty())
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{
231+
using MeshWriterType = itk::MeshFileWriter<MeshType>;
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auto meshWriter = MeshWriterType::New();
233+
meshWriter->SetFileName(this->m_Identifier);
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meshWriter->SetInput(this->m_Mesh);
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meshWriter->Update();
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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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}
242+
}
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protected:
244+
typename MeshType::ConstPointer m_Mesh;
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std::string m_Identifier;
247+
};
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147249
template <typename TMesh>
148250
bool lexical_cast(const std::string &input, OutputMesh<TMesh> &outputMesh)
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{

‎include/itkWasmMesh.h

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@@ -20,6 +20,7 @@
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#include "itkWasmDataObject.h"
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#include "itkVectorContainer.h"
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#include "itkQuadEdgeMesh.h"
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2425
namespace itk
2526
{
@@ -80,6 +81,54 @@ class ITK_TEMPLATE_EXPORT WasmMesh : public WasmDataObject
8081
typename CellBufferContainerType::Pointer m_CellBufferContainer;
8182
};
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84+
template <typename TPixel, unsigned int VDimension>
85+
class WasmMesh<QuadEdgeMesh<TPixel, VDimension>> : public WasmDataObject
86+
{
87+
public:
88+
ITK_DISALLOW_COPY_AND_MOVE(WasmMesh);
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90+
/** Standard class type aliases. */
91+
using Self = WasmMesh;
92+
using Superclass = WasmDataObject;
93+
using Pointer = SmartPointer<Self>;
94+
using ConstPointer = SmartPointer<const Self>;
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96+
itkNewMacro(Self);
97+
/** Run-time type information (and related methods). */
98+
itkTypeMacro(WasmMesh, WasmDataObject);
99+
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using MeshType = QuadEdgeMesh<TPixel, VDimension>;
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102+
using PointIdentifier = typename MeshType::PointIdentifier;
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using CellIdentifier = typename MeshType::CellIdentifier;
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using PointsBufferContainerType = std::vector<PointIdentifier>;
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using CellBufferContainerType = std::vector<CellIdentifier>;
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using PointDataBufferContainerType = std::vector<typename MeshType::PointDataContainer::Element>;
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using CellDataBufferContainerType = std::vector<typename MeshType::CellDataContainer::Element>;
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void SetMesh(const MeshType * mesh);
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const MeshType * GetMesh() const {
113+
return static_cast< const MeshType * >(this->GetDataObject());
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}
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const PointsBufferContainerType & GetPointsBufferContainer() const {
117+
return this->m_PointsBufferContainer;
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}
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const CellBufferContainerType & GetCellBufferContainer() const {
121+
return this->m_CellBufferContainer;
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}
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WasmMesh() = default;
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~WasmMesh() override = default;
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127+
PointsBufferContainerType m_PointsBufferContainer;
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CellBufferContainerType m_CellBufferContainer;
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};
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83132
} // namespace itk
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85134
#ifndef ITK_MANUAL_INSTANTIATION

‎include/itkWasmMesh.hxx

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@@ -32,6 +32,27 @@ WasmMesh<TMesh>
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this->SetDataObject(const_cast<MeshType *>(mesh));
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}
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35+
template <typename TPixel, unsigned int VDimension>
36+
void
37+
WasmMesh<itk::QuadEdgeMesh<TPixel, VDimension>>
38+
::SetMesh(const MeshType * mesh)
39+
{
40+
m_PointsBufferContainer.resize(mesh->GetNumberOfPoints() * VDimension);
41+
for (unsigned int i = 0; i < mesh->GetNumberOfPoints(); ++i)
42+
{
43+
const auto & point = mesh->GetPoint(i);
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for (unsigned int d = 0; d < VDimension; ++d)
45+
{
46+
m_PointsBufferContainer[i * VDimension + d] = point[d];
47+
}
48+
}
49+
// m_CellBufferContainer.reserve(mesh->GetNumberOfCells() * 5);
50+
auto cellsArray = const_cast<MeshType *>(mesh)->GetCellsArray();
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this->SetDataObject(const_cast<MeshType *>(mesh));
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}
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3556
} // end namespace itk
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#endif

‎itk_wasm_env.bash

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@@ -40,6 +40,9 @@ export ITK_WASM_DICOM_TEST_DATA_URLS=${ITK_WASM_DICOM_TEST_DATA_URLS:-$(cat pack
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export ITK_WASM_DOWNSAMPLE_TEST_DATA_HASH=${ITK_WASM_DOWNSAMPLE_TEST_DATA_HASH:-$(cat packages/downsample/package.json | jq -e -r '."itk-wasm"."test-data-hash"')}
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export ITK_WASM_DOWNSAMPLE_TEST_DATA_URLS=${ITK_WASM_DOWNSAMPLE_TEST_DATA_URLS:-$(cat packages/downsample/package.json | jq -e -r '."itk-wasm"."test-data-urls" | join(" ")')}
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export ITK_WASM_MESH_FILTERS_TEST_DATA_HASH=${ITK_WASM_MESH_FILTERS_TEST_DATA_HASH:-$(cat packages/mesh-filters/package.json | jq -e -r '."itk-wasm"."test-data-hash"')}
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export ITK_WASM_MESH_FILTERS_TEST_DATA_URLS=${ITK_WASM_MESH_FILTERS_TEST_DATA_URLS:-$(cat packages/mesh-filters/package.json | jq -e -r '."itk-wasm"."test-data-urls" | join(" ")')}
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export ITK_WASM_MESH_IO_TEST_DATA_HASH=${ITK_WASM_MESH_IO_TEST_DATA_HASH:-$(cat packages/mesh-io/package.json | jq -e -r '."itk-wasm"."test-data-hash"')}
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export ITK_WASM_MESH_IO_TEST_DATA_URLS=${ITK_WASM_MESH_IO_TEST_DATA_URLS:-$(cat packages/mesh-io/package.json | jq -e -r '."itk-wasm"."test-data-urls" | join(" ")')}
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‎packages/mesh-filters/.gitignore

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emscripten-build/
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wasi-build/
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python/itkwasm-mesh-filters-wasi/itkwasm_mesh-filters_wasi/wasm_modules/
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typescript/dist/
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typescript/test/browser/demo-app/public/
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typescript/demo-app/
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typescript/src/version.ts
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test/pyodide-dispatch.tar.bz2
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test/pyodide-emscripten.tar.bz2
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test/data.tar.gz
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test/data/baseline/
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test/data/python/
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python/itkwasm-mesh-filters-emscripten/dist/
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python/itkwasm-mesh-filters-wasi/dist/
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python/itkwasm-mesh-filters/dist/
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pyodide/

‎packages/mesh-filters/.npmrc

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git-checks=false

‎packages/mesh-filters/CMakeLists.txt

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cmake_minimum_required(VERSION 3.16)
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project(itkwasm-mesh-filters LANGUAGES CXX)
3+
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set(CMAKE_CXX_STANDARD 20)
5+
6+
if(EMSCRIPTEN)
7+
set(io_components
8+
)
9+
elseif(WASI)
10+
set(io_components
11+
ITKIOOFF
12+
)
13+
else()
14+
set(io_components
15+
ITKMeshIO
16+
)
17+
endif()
18+
19+
find_package(ITK REQUIRED
20+
COMPONENTS
21+
WebAssemblyInterface
22+
ITKQuadEdgeMeshFiltering
23+
${io_components}
24+
)
25+
include(${ITK_USE_FILE})
26+
27+
include(FetchContent)
28+
29+
set(PMP_BUILD_DOCS OFF)
30+
set(PMP_BUILD_EXAMPLES OFF)
31+
set(PMP_BUILD_REGRESSIONS OFF)
32+
set(PMP_BUILD_TESTS OFF)
33+
set(PMP_BUILD_VIS OFF)
34+
set(PMP_INSTALL OFF)
35+
36+
set(PMP_GIT_REPOSITORY "https://github.com/pmp-library/pmp-library.git")
37+
# v3.0.0
38+
set(PMP_GIT_TAG "f2fb04f4a4188a5c1ab137e83b96e62fa99c639f")
39+
set(BUILD_SHARED_LIBS OFF)
40+
FetchContent_Declare(
41+
pmp
42+
GIT_REPOSITORY ${PMP_GIT_REPOSITORY}
43+
GIT_TAG ${PMP_GIT_TAG}
44+
GIT_SHALLOW TRUE
45+
)
46+
47+
if (POLICY CMP0077)
48+
cmake_policy(SET CMP0077 NEW)
49+
endif()
50+
set(GEOGRAM_WITH_GARGATUA OFF CACHE BOOL "64-bit indices")
51+
set(GEOGRAM_WITH_GRAPHICS OFF CACHE BOOL "Viewers and geogram_gfx library")
52+
set(GEOGRAM_WITH_HLBFGS OFF CACHE BOOL "HLBFGS non-linear solver library")
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set(GEOGRAM_WITH_LUA OFF CACHE BOOL "Lua scripting")
54+
set(GEOGRAM_WITH_TBB OFF CACHE BOOL "Intel TBB")
55+
set(GEOGRAM_WITH_TETGEN OFF CACHE BOOL "Tetrahedral mesh generation (Hang Si's TetGen)")
56+
set(GEOGRAM_WITH_TRIANGLE OFF CACHE BOOL "Triangle mesher (Jonathan Shewchuk's Triangle)")
57+
58+
set(GEOGRAM_GIT_REPOSITORY "https://github.com/BrunoLevy/geogram.git")
59+
# v1.9.1
60+
set(GEOGRAM_GIT_TAG "fd3db7f141e570ebc68585e15d01a2f2c8ddb02e")
61+
set(BUILD_SHARED_LIBS OFF)
62+
FetchContent_Declare(
63+
geogram
64+
GIT_REPOSITORY ${GEOGRAM_GIT_REPOSITORY}
65+
GIT_TAG ${GEOGRAM_GIT_TAG}
66+
GIT_SHALLOW TRUE
67+
)
68+
69+
FetchContent_MakeAvailable(pmp geogram)
70+
include_directories(${pmp_SOURCE_DIR}/src)
71+
72+
foreach(pipeline geogram-conversion)
73+
# foreach(pipeline mesh-filters mesh-filters-sigma gaussian-kernel-radius mesh-filters-bin-shrink mesh-filters-label-image)
74+
add_executable(${pipeline} ${pipeline}.cxx)
75+
target_link_libraries(${pipeline} PUBLIC ${ITK_LIBRARIES} pmp)
76+
target_include_directories(${pipeline} PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
77+
endforeach()
78+
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enable_testing()
80+
add_test(NAME geogram-conversion
81+
COMMAND geogram-conversion
82+
${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/suzanne.off
83+
${CMAKE_CURRENT_BINARY_DIR}/suzanne-geogram.off
84+
)
85+
# # Interesting backtrace on exit
86+
# if (NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
87+
# add_test(NAME mesh-filters
88+
# COMMAND mesh-filters
89+
# ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
90+
# ${CMAKE_CURRENT_BINARY_DIR}/cthead1_mesh-filtersd.png
91+
# --shrink-factors 2 2
92+
# )
93+
# endif()
94+
95+
# add_test(NAME mesh-filters-sigma
96+
# COMMAND mesh-filters-sigma
97+
# ${CMAKE_CURRENT_BINARY_DIR}/mesh-filters-sigma.json
98+
# --shrink-factors 2 4
99+
# )
100+
101+
# add_test(NAME gaussian-kernel-radius
102+
# COMMAND gaussian-kernel-radius
103+
# ${CMAKE_CURRENT_BINARY_DIR}/gaussian-kernel-radius.json
104+
# --size 64 64 32
105+
# --sigma 2.0 4.0 2.0
106+
# )
107+
108+
# add_test(NAME mesh-filters-bin-shrink
109+
# COMMAND mesh-filters-bin-shrink
110+
# ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
111+
# ${CMAKE_CURRENT_BINARY_DIR}/cthead1_mesh-filtersd_bin_shrink.png
112+
# --shrink-factors 2 2
113+
# )
114+
115+
# add_test(NAME mesh-filters-label-image
116+
# COMMAND mesh-filters-label-image
117+
# ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/2th_cthead1.png
118+
# ${CMAKE_CURRENT_BINARY_DIR}/cthead1_mesh-filtersd_label_image.png
119+
# --shrink-factors 2 2
120+
# )

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