WIP: pnpm build

itkwasm-sub-mesh/CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.16)
-project(sub-mesh)
+project(itkwasm-sub-mesh LANGUAGES CXX)
 
-set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD 20)
 
 set(io_components)
 if(NOT EMSCRIPTEN)
@@ -15,12 +15,8 @@ find_package(ITK REQUIRED
   )
 include(${ITK_USE_FILE})
 
-add_executable(sub-mesh sub-mesh.cxx)
-target_link_libraries(sub-mesh PUBLIC ${ITK_LIBRARIES})
-
 enable_testing()
-add_test(NAME sub-mesh
-  COMMAND sub-mesh ${CMAKE_CURRENT_SOURCE_DIR}/cow.vtk
-  ${CMAKE_CURRENT_SOURCE_DIR}/cow-cells-to-extract.json
-  ${CMAKE_CURRENT_BINARY_DIR}/sub-cow.vtk
-  )
+
+# Begin create-itk-wasm added pipelines.
+add_subdirectory(sub-mesh)
+# End create-itk-wasm added pipelines.

itkwasm-sub-mesh/README.md

@@ -1,3 +1,3 @@
 # itkwasm-sub-mesh
 
-Extract subset of a mesh given by the cell identifiers.
+Extract a subset of a mesh given by the cell identifiers.

itkwasm-sub-mesh/cow-cells-to-extract.json

@@ -0,0 +1 @@
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199]

itkwasm-sub-mesh/environment.yml

@@ -0,0 +1,9 @@
+name: itkwasm-sub-mesh
+channels:
+  - conda-forge
+dependencies:
+  - pytest
+  - python=3.11
+  - pip
+  - pip:
+    - hatch

itkwasm-sub-mesh/package.json

@@ -0,0 +1,48 @@
+{
+  "name": "itkwasm-sub-mesh-build",
+  "version": "0.1.0",
+  "private": true,
+  "packageManager": "[email protected]",
+  "description": "Scripts to generate itkwasm-sub-mesh itk-wasm artifacts.",
+  "type": "module",
+  "itk-wasm": {
+    "package-description": "Extract a subset of a mesh given by the cell identifiers.",
+    "typescript-package-name": "@itk-wasm/sub-mesh",
+    "python-package-name": "itkwasm-sub-mesh",
+    "repository": "https://github.com/uncbiag/OAI_analysis_2"
+  },
+  "license": "Apache-2.0",
+  "scripts": {
+    "build": "pnpm build:gen:typescript && pnpm build:gen:python",
+    "build:emscripten": "itk-wasm pnpm-script build:emscripten",
+    "build:emscripten:debug": "itk-wasm pnpm-script build:emscripten:debug",
+    "build:wasi": "itk-wasm pnpm-script build:wasi",
+    "build:wasi:debug": "itk-wasm pnpm-script build:wasi:debug",
+    "build:python:wasi": "itk-wasm pnpm-script build:python:wasi",
+    "bindgen:typescript": "itk-wasm pnpm-script bindgen:typescript",
+    "bindgen:python": "itk-wasm pnpm-script bindgen:python",
+    "build:gen:typescript": "itk-wasm pnpm-script build:gen:typescript",
+    "build:gen:python": "itk-wasm pnpm-script build:gen:python",
+    "build:micromamba": "itk-wasm pnpm-script build:micromamba",
+    "build:python:versionSync": "itk-wasm pnpm-script build:python:versionSync",
+    "publish:python": "itk-wasm pnpm-script publish:python",
+    "test": "pnpm test:data:download && pnpm build:gen:python && pnpm test:python",
+    "test:data:download": "dam download test/data test/data.tar.gz bafkreigpkk3pqcoqzjzcauogw6dml52yig3ksmcrobau5pkoictymizzri https://github.com/InsightSoftwareConsortium/itk-wasm/releases/download/itk-wasm-v1.0.0-b.163/create-itk-wasm-test-data.tar.gz https://bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca.ipfs.w3s.link/ipfs/bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca/create-itk-wasm-test-data.tar.gz https://ipfs.filebase.io/ipfs/QmcxyvUKnaoTTwUqEPXwp1sdcbrFh3XnnwckLKVRpctJx9",
+    "test:data:pack": "dam pack test/data test/data.tar.gz",
+    "test:python:wasi": "itk-wasm pnpm-script test:python:wasi",
+    "test:python:emscripten": "itk-wasm pnpm-script test:python:emscripten",
+    "test:python:dispatch": "itk-wasm pnpm-script test:python:emscripten",
+    "test:python": "itk-wasm pnpm-script test:python",
+    "test:wasi": "itk-wasm pnpm-script test:wasi"
+  },
+  "devDependencies": {
+    "@itk-wasm/dam": "^1.1.1",
+    "@thewtex/setup-micromamba": "^1.9.7",
+    "itk-wasm": "1.0.0-b.167"
+  },
+  "author": "Matt McCormick",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/uncbiag/OAI_analysis_2"
+  }
+}

itkwasm-sub-mesh/pnpm-workspace.yaml

@@ -0,0 +1,2 @@
+packages:
+  - 'typescript'

itkwasm-sub-mesh/sub-mesh/CMakeLists.txt

@@ -0,0 +1,4 @@
+add_executable(sub-mesh sub-mesh.cxx)
+target_link_libraries(sub-mesh PUBLIC ${ITK_LIBRARIES})
+
+add_test(NAME sub-mesh-help COMMAND sub-mesh --help)

itkwasm-sub-mesh/sub-mesh/sub-mesh.cxx

@@ -0,0 +1,91 @@
+/*=========================================================================
+
+ *  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.
+ *
+ *=========================================================================*/
+
+#include "itkPipeline.h"
+#include "itkInputMesh.h"
+#include "itkInputTextStream.h"
+#include "itkOutputMesh.h"
+#include "itkSupportInputMeshTypes.h"
+
+#include "itkTriangleCell.h"
+#include "itkVertexCell.h"
+#include "itkQuadrilateralCell.h"
+#include "itkTetrahedronCell.h"
+#include "itkHexahedronCell.h"
+
+#include "itkAutomaticTopologyMeshSource.h"
+
+template <typename TMesh>
+int subMesh(itk::wasm::Pipeline &pipeline, const TMesh *mesh)
+{
+  using MeshType = TMesh;
+  constexpr unsigned int Dimension = MeshType::PointDimension;
+  using PixelType = typename MeshType::PixelType;
+
+  pipeline.get_option("mesh")->required()->type_name("INPUT_MESH");
+
+  std::vector< uint32_t > cellIdentifiers;
+  pipeline.add_option("cell-identifiers", cellIdentifiers, "Cell identifiers for output mesh.")->required();
+
+  itk::wasm::OutputMesh<MeshType> subMesh;
+  pipeline.add_option("sub-mesh", subMesh, "Sub mesh.")->required()->type_name("OUTPUT_MESH");
+
+  ITK_WASM_PARSE(pipeline);
+
+  std::set< itk::IdentifierType > usedPoints;
+  for (auto cellIdentifier : cellIdentifiers)
+  {
+    const typename MeshType::CellType * cell = mesh->GetCell(cellIdentifier);
+
+    // meshSource->AddCellIdentifier(cellIdentifier);
+  }
+
+  using MeshSourceType = itk::AutomaticTopologyMeshSource< MeshType >;
+  auto meshSource = MeshSourceType::New();
+
+  subMesh.Set(mesh);
+
+  return EXIT_SUCCESS;
+}
+
+template <typename TMesh>
+class PipelineFunctor
+{
+public:
+  int operator()(itk::wasm::Pipeline &pipeline)
+  {
+    using MeshType = TMesh;
+
+    itk::wasm::InputMesh<MeshType> mesh;
+    pipeline.add_option("mesh", mesh, "Full mesh")->type_name("INPUT_MESH");
+
+    ITK_WASM_PRE_PARSE(pipeline);
+
+    typename MeshType::ConstPointer meshRef = mesh.Get();
+    return subMesh<MeshType>(pipeline, meshRef);
+  }
+};
+
+int main(int argc, char * argv[])
+{
+  itk::wasm::Pipeline pipeline("sub-mesh", "Extract a subset of a mesh given by the cell identifiers.", argc, argv);
+
+  return itk::wasm::SupportInputMeshTypes<PipelineFunctor,
+    uint8_t, uint16_t, int16_t, float, double>
+    ::Dimensions<3U>("mesh", pipeline);
+}