feat(structured-report-to-text): Initial pipeline addition

.npmignore

@@ -10,7 +10,10 @@ src/build-emscripten.js
 src/build-wasi.js
 dist/image-io/
 dist/mesh-io/
+dist/dicom/
+dist/pipelines
 dist/wasi-image-io/
 dist/wasi-mesh-io/
+dist/wasi-dicom/
 examples/
 doc/

dist/dicom/package.json

@@ -0,0 +1,46 @@
+{
+  "name": "itk-vite-example",
+  "version": "1.0.2",
+  "description": "This example demonstrates how to use itk-wasm in a Rollup project that targets the browser.",
+  "main": "index.js",
+  "scripts": {
+    "start": "vite --port 8080",
+    "build": "vite build",
+    "start:production": "vite preview --port 8080",
+    "cypress:open": "npx cypress open",
+    "cypress:run": "npx cypress run",
+    "cypress:runChrome": "npx cypress run --browser chrome",
+    "cypress:runFirefox": "npx cypress run --browser firefox",
+    "test:debug": "start-server-and-test start http-get://localhost:8080 cypress:open",
+    "test": "start-server-and-test start:production http-get://localhost:8080 cypress:run",
+    "test:chrome": "start-server-and-test start:production http-get://localhost:8080 cypress:runChrome",
+    "test:firefox": "start-server-and-test start:production http-get://localhost:8080 cypress:runFirefox"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/InsightSoftwareConsortium/itk-wasm.git"
+  },
+  "keywords": [
+    "itk",
+    "rollup",
+    "vite"
+  ],
+  "author": "Matt McCormick <[email protected]>",
+  "license": "Apache-2.0",
+  "bugs": {
+    "url": "https://github.com/InsightSoftwareConsortium/itk-wasm/issues"
+  },
+  "homepage": "https://github.com/InsightSoftwareConsortium/itk-wasm#readme",
+  "dependencies": {
+    "curry": "^1.2.0",
+    "itk-image-io": "^1.0.0-b.18",
+    "itk-mesh-io": "^1.0.0-b.18",
+    "itk-wasm": "^1.0.0-b.18"
+  },
+  "devDependencies": {
+    "cypress": "^10.3.0",
+    "rollup-plugin-copy": "^3.4.0",
+    "start-server-and-test": "^1.14.0",
+    "vite": "^3.0.9"
+  }
+}

karma.conf.cjs

@@ -38,7 +38,7 @@ module.exports = function init (config) {
       { pattern: './dist/image-io/**', watched: true, served: true, included: false },
       { pattern: './dist/mesh-io/**', watched: true, served: true, included: false },
       { pattern: './dist/web-workers/**', watched: true, served: true, included: false },
-      { pattern: './dist/pipeline/**', watched: true, served: true, included: false },
+      { pattern: './dist/pipelines/**', watched: true, served: true, included: false },
       { pattern: './build-emscripten/ExternalData/test/**', watched: true, served: true, included: false },
       { pattern: `${output.path}/**/*`, watched: false, included: false, },
     ].concat(testFiles),

src/CMakeLists.txt

@@ -41,5 +41,6 @@ add_subdirectory(io/internal/pipelines/image/convert-image)
 add_subdirectory(io/internal/pipelines/image/read-dicom)
 add_subdirectory(io/internal/pipelines/mesh/convert-mesh)
 add_subdirectory(io/internal/pipelines/mesh/mesh-to-polydata)
+add_subdirectory(io/internal/pipelines/dicom)
 
 endif() # BUILD_ITK_WASM_IO_MODULES

src/build-emscripten.js

@@ -128,6 +128,11 @@ if (options.copyBuildArtifacts) {
   } catch (err) {
     if (err.code !== 'EEXIST') throw err
   }
+  try {
+    fs.mkdirSync(path.join('dist', 'dicom', 'pipelines'), { recursive: true })
+  } catch (err) {
+    if (err.code !== 'EEXIST') throw err
+  }
   try {
     fs.mkdirSync(path.join('dist', 'web-workers'))
   } catch (err) {
@@ -161,10 +166,25 @@ if (options.copyBuildArtifacts) {
     const result = asyncMod.map(meshIOFiles, copyMeshIOModules)
     callback(null, result)
   }
+  let dicomFiles = glob.sync(path.join(buildDir, 'dicom', '*.js'))
+  dicomFiles = dicomFiles.concat(glob.sync(path.join(buildDir, 'dicom', '*.wasm')))
+  dicomFiles = dicomFiles.filter((fn) => !fn.endsWith('.umd.wasm'))
+  const copyDICOMModules = function (dicomFile, callback) {
+    const io = path.basename(dicomFile)
+    const output = path.join('dist', 'dicom', 'pipelines', io)
+    fs.copySync(dicomFile, output)
+    callback(null, io)
+  }
+  const buildDICOMParallel = function (callback) {
+    console.log('Copying dicom modules...')
+    const result = asyncMod.map(dicomFiles, copyDICOMModules)
+    callback(null, result)
+  }
 
   asyncMod.parallel([
     buildImageIOsParallel,
     buildMeshIOsParallel,
+    buildDICOMParallel,
   ])
 } // options.copySources
 
@@ -199,13 +219,13 @@ if (options.buildTestPipelines) {
     pipelineFiles = pipelineFiles.concat(glob.sync(path.join(pipelinePath, 'web-build', '*.wasm')))
     pipelineFiles.forEach((file) => {
       const filename = path.basename(file)
-      const output = path.join('dist', 'pipeline', filename)
+      const output = path.join('dist', 'pipelines', filename)
       fs.copySync(file, output)
     })
   }
 
   try {
-    fs.mkdirSync(path.join('dist', 'pipeline'))
+    fs.mkdirSync(path.join('dist', 'pipelines'))
   } catch (err) {
     if (err.code !== 'EEXIST') throw err
   }

src/build-wasi.js

@@ -145,10 +145,23 @@ if (options.copyBuildArtifacts) {
     const result = asyncMod.map(meshIOFiles, copyMeshIOModules)
     callback(null, result)
   }
+  let dicomFiles = glob.sync(path.join(buildDir, 'wasi-dicom', '*.wasm'))
+  const copyDICOMModules = function (dicomFile, callback) {
+    const io = path.basename(dicomFile)
+    const output = path.join('dist', 'wasi-dicom', io)
+    fs.copySync(dicomFile, output)
+    callback(null, io)
+  }
+  const buildDICOMParallel = function (callback) {
+    console.log('Copying wasi-dicom modules...')
+    const result = asyncMod.map(dicomFiles, copyDICOMModules)
+    callback(null, result)
+  }
 
   asyncMod.parallel([
     buildImageIOsParallel,
     buildMeshIOsParallel,
+    buildDICOMParallel,
   ])
 } // options.copySources
 

src/io/internal/pipelines/dicom/CMakeLists.txt

@@ -0,0 +1,52 @@
+cmake_minimum_required(VERSION 3.16)
+project(itkwasm-dicom)
+
+set(CMAKE_CXX_STANDARD 17)
+
+find_package(ITK REQUIRED
+  COMPONENTS
+    ITKDCMTK
+    WebAssemblyInterface
+  )
+include(${ITK_USE_FILE})
+
+set(wasm_modules )
+
+# diquant.cc required for odd linker error
+add_executable(structured-report-to-text structured-report-to-text.cxx diquant.cc)
+target_link_libraries(structured-report-to-text PUBLIC ${ITK_LIBRARIES})
+list(APPEND wasm_modules "structured-report-to-text")
+
+
+if (WASI AND DEFINED WebAssemblyInterface_BINARY_DIR)
+  foreach(target ${wasm_modules})
+    itk_module_target_label(${target})
+    itk_module_target_export(${target})
+    itk_module_target_install(${target})
+    set_property(TARGET ${target}
+      PROPERTY RUNTIME_OUTPUT_DIRECTORY
+      ${WebAssemblyInterface_BINARY_DIR}/wasi-dicom
+      )
+  endforeach()
+  return()
+endif()
+
+if (EMSCRIPTEN AND DEFINED WebAssemblyInterface_BINARY_DIR)
+  foreach(target ${wasm_modules})
+    itk_module_target_label(${target})
+    itk_module_target_export(${target})
+    itk_module_target_install(${target})
+    set_property(TARGET ${target}
+      PROPERTY RUNTIME_OUTPUT_DIRECTORY
+      ${WebAssemblyInterface_BINARY_DIR}/dicom
+      )
+    itk_module_target_label(${target}.umd)
+    itk_module_target_export(${target}.umd)
+    itk_module_target_install(${target}.umd)
+    set_property(TARGET ${target}.umd
+      PROPERTY RUNTIME_OUTPUT_DIRECTORY
+      ${WebAssemblyInterface_BINARY_DIR}/dicom
+      )
+  endforeach()
+  return()
+endif()