feat(mesh-io): add read-mesh-node

packages/mesh-io/CMakeLists.txt

@@ -54,7 +54,7 @@ set(meshios_WebAssemblyInterface itkWasmMeshIO itkWasmZstdMeshIO)
 set(meshio_id_itkWasmMeshIO 8)
 set(meshio_kebab_itkWasmMeshIO "wasm")
 set(meshio_id_itkWasmZstdMeshIO 9)
-set(meshio_kebab_itkWasmZstdMeshIO "wasm-ztd")
+set(meshio_kebab_itkWasmZstdMeshIO "wasm-zstd")
 
 set(ITK_NO_MESHIO_FACTORY_REGISTER_MANAGER 1)
 set(MeshIOIndex_ARRAY "")

packages/mesh-io/typescript/package.json

@@ -38,6 +38,7 @@
   "devDependencies": {
     "@itk-wasm/image-io": "^0.2.0",
     "@shoelace-style/shoelace": "^2.5.2",
+    "@types/mime-types": "^2.1.4",
     "@types/node": "^20.2.5",
     "ava": "^5.3.1",
     "esbuild": "^0.19.5",

packages/mesh-io/typescript/src/index-node.ts

@@ -1,4 +1,9 @@
-// Generated file. To retain edits, remove this comment.
+
+import ReadMeshOptions from './read-mesh-options.js'
+export type { ReadMeshOptions }
+
+import readMeshNode from './read-mesh-node.js'
+export { readMeshNode }
 
 
 
@@ -182,24 +187,24 @@ import wasmWriteMeshNode from './wasm-write-mesh-node.js'
 export { wasmWriteMeshNode }
 
 
-import WasmZtdReadMeshNodeResult from './wasm-ztd-read-mesh-node-result.js'
-export type { WasmZtdReadMeshNodeResult }
+import WasmZstdReadMeshNodeResult from './wasm-zstd-read-mesh-node-result.js'
+export type { WasmZstdReadMeshNodeResult }
 
-import WasmZtdReadMeshOptions from './wasm-ztd-read-mesh-options.js'
-export type { WasmZtdReadMeshOptions }
+import WasmZstdReadMeshOptions from './wasm-zstd-read-mesh-options.js'
+export type { WasmZstdReadMeshOptions }
 
-import wasmZtdReadMeshNode from './wasm-ztd-read-mesh-node.js'
-export { wasmZtdReadMeshNode }
+import wasmZstdReadMeshNode from './wasm-zstd-read-mesh-node.js'
+export { wasmZstdReadMeshNode }
 
 
-import WasmZtdWriteMeshNodeResult from './wasm-ztd-write-mesh-node-result.js'
-export type { WasmZtdWriteMeshNodeResult }
+import WasmZstdWriteMeshNodeResult from './wasm-zstd-write-mesh-node-result.js'
+export type { WasmZstdWriteMeshNodeResult }
 
-import WasmZtdWriteMeshOptions from './wasm-ztd-write-mesh-options.js'
-export type { WasmZtdWriteMeshOptions }
+import WasmZstdWriteMeshOptions from './wasm-zstd-write-mesh-options.js'
+export type { WasmZstdWriteMeshOptions }
 
-import wasmZtdWriteMeshNode from './wasm-ztd-write-mesh-node.js'
-export { wasmZtdWriteMeshNode }
+import wasmZstdWriteMeshNode from './wasm-zstd-write-mesh-node.js'
+export { wasmZstdWriteMeshNode }
 
 export type { JsonCompatible } from 'itk-wasm'
 export type { Mesh } from 'itk-wasm'

packages/mesh-io/typescript/src/index.ts

@@ -184,6 +184,26 @@ import wasmWriteMesh from './wasm-write-mesh.js'
 export { wasmWriteMesh }
 
 
+import WasmZstdReadMeshResult from './wasm-zstd-read-mesh-result.js'
+export type { WasmZstdReadMeshResult }
+
+import WasmZstdReadMeshOptions from './wasm-zstd-read-mesh-options.js'
+export type { WasmZstdReadMeshOptions }
+
+import wasmZstdReadMesh from './wasm-zstd-read-mesh.js'
+export { wasmZstdReadMesh }
+
+
+import WasmZstdWriteMeshResult from './wasm-zstd-write-mesh-result.js'
+export type { WasmZstdWriteMeshResult }
+
+import WasmZstdWriteMeshOptions from './wasm-zstd-write-mesh-options.js'
+export type { WasmZstdWriteMeshOptions }
+
+import wasmZstdWriteMesh from './wasm-zstd-write-mesh.js'
+export { wasmZstdWriteMesh }
+
+
 import WasmZtdReadMeshResult from './wasm-ztd-read-mesh-result.js'
 export type { WasmZtdReadMeshResult }
 

packages/mesh-io/typescript/src/mesh-io-index-node.ts

@@ -0,0 +1,35 @@
+import vtkPolyDataReadMeshNode from './vtk-poly-data-read-mesh-node.js'
+import vtkPolyDataWriteMeshNode from './vtk-poly-data-write-mesh-node.js'
+import objReadMeshNode from './obj-read-mesh-node.js'
+import objWriteMeshNode from './obj-write-mesh-node.js'
+import stlReadMeshNode from './stl-read-mesh-node.js'
+import stlWriteMeshNode from './stl-write-mesh-node.js'
+import offReadMeshNode from './off-read-mesh-node.js'
+import offWriteMeshNode from './off-write-mesh-node.js'
+import wasmReadMeshNode from './wasm-read-mesh-node.js'
+import wasmWriteMeshNode from './wasm-write-mesh-node.js'
+import wasmZstdReadMeshNode from './wasm-zstd-read-mesh-node.js'
+import wasmZstdWriteMeshNode from './wasm-zstd-write-mesh-node.js'
+import swcReadMeshNode from './swc-read-mesh-node.js'
+import swcWriteMeshNode from './swc-write-mesh-node.js'
+import byuReadMeshNode from './byu-read-mesh-node.js'
+import byuWriteMeshNode from './byu-write-mesh-node.js'
+import freeSurferAsciiReadMeshNode from './free-surfer-ascii-read-mesh-node.js'
+import freeSurferAsciiWriteMeshNode from './free-surfer-ascii-write-mesh-node.js'
+import freeSurferBinaryReadMeshNode from './free-surfer-binary-read-mesh-node.js'
+import freeSurferBinaryWriteMeshNode from './free-surfer-binary-write-mesh-node.js'
+
+const meshIoIndexNode = new Map([
+  ['vtk', [vtkPolyDataReadMeshNode, vtkPolyDataWriteMeshNode]],
+  ['obj', [objReadMeshNode, objWriteMeshNode]],
+  ['stl', [stlReadMeshNode, stlWriteMeshNode]],
+  ['off', [offReadMeshNode, offWriteMeshNode]],
+  ['wasm', [wasmReadMeshNode, wasmWriteMeshNode]],
+  ['wasm-zst', [wasmZstdReadMeshNode, wasmZstdWriteMeshNode]],
+  ['swc', [swcReadMeshNode, swcWriteMeshNode]],
+  ['byu', [byuReadMeshNode, byuWriteMeshNode]],
+  ['free-surfer-ascii', [freeSurferAsciiReadMeshNode, freeSurferAsciiWriteMeshNode]],
+  ['free-surfer-binary', [freeSurferBinaryReadMeshNode, freeSurferBinaryWriteMeshNode]],
+])
+
+export default meshIoIndexNode

packages/mesh-io/typescript/src/read-mesh-node.ts

@@ -0,0 +1,72 @@
+import path from 'path'
+import mime from 'mime-types'
+
+import {
+  Mesh,
+  getFileExtension,
+} from 'itk-wasm'
+
+import mimeToMeshIo from './mime-to-mesh-io.js'
+import extensionToMeshIo from './extension-to-mesh-io.js'
+import meshIoIndexNode from './mesh-io-index-node.js'
+
+import ReadMeshOptions from './read-mesh-options.js'
+
+interface ReaderResult {
+  couldRead: boolean,
+  mesh: Mesh
+}
+interface ReaderOptions {
+  /** Only read image metadata -- do not read pixel data. */
+  informationOnly?: boolean
+}
+type Reader = (serializedMesh: string, options: ReaderOptions) => Promise<ReaderResult>
+
+
+/**
+ * Read a mesh file format and convert it to the itk-wasm file format
+ *
+ * @param {string} serializedMesh - Path to input mesh serialized in the file format
+ * @param {ReadMeshOptions} options - options to cast resulting mesh type or to only read mesh metadata
+ *
+ * @returns {Promise<Mesh>} - Mesh result
+ */
+async function readMeshNode(
+  serializedMesh: string,
+  options: ReadMeshOptions = {}
+) : Promise<Mesh> {
+
+  const absoluteFilePath = path.resolve(serializedMesh)
+  const mimeType = mime.lookup(absoluteFilePath)
+  const extension = getFileExtension(absoluteFilePath)
+
+  let io = null
+  if (mimeType && mimeToMeshIo.has(mimeType)) {
+    io = mimeToMeshIo.get(mimeType)
+  } else if (extensionToMeshIo.has(extension)) {
+    io = extensionToMeshIo.get(extension)
+  } else {
+    for (const readerWriter of meshIoIndexNode.values()) {
+      if (readerWriter[0] !== null) {
+        let { couldRead, mesh } = await (readerWriter[0] as Reader)(absoluteFilePath, { informationOnly: options.informationOnly })
+        if (couldRead) {
+          return mesh
+        }
+      }
+    }
+  }
+  if (io === null ) {
+    throw Error('Could not find IO for: ' + absoluteFilePath)
+  }
+  const readerWriter = meshIoIndexNode.get(io as string)
+
+  const reader = (readerWriter as Array<Reader>)[0]
+  let { couldRead, mesh } = await reader(absoluteFilePath, { informationOnly: options.informationOnly })
+  if (!couldRead) {
+    throw Error('Could not read: ' + absoluteFilePath)
+  }
+
+  return mesh
+}
+
+export default readMeshNode

packages/mesh-io/typescript/src/read-mesh-options.ts

@@ -0,0 +1,6 @@
+interface ReadMeshOptions {
+  /** Only read mesh metadata -- do not read pixel data. */
+  informationOnly?: boolean
+}
+
+export default ReadMeshOptions

packages/mesh-io/typescript/src/wasm-zstd-read-mesh-node-result.ts

@@ -0,0 +1,14 @@
+// Generated file. To retain edits, remove this comment.
+
+import { JsonCompatible, Mesh } from 'itk-wasm'
+
+interface WasmZstdReadMeshNodeResult {
+  /** Whether the input could be read. If false, the output mesh is not valid. */
+  couldRead: JsonCompatible
+
+  /** Output mesh */
+  mesh: Mesh
+
+}
+
+export default WasmZstdReadMeshNodeResult

packages/mesh-io/typescript/src/wasm-zstd-read-mesh-node.ts

@@ -0,0 +1,78 @@
+// Generated file. To retain edits, remove this comment.
+
+import {
+  JsonCompatible,
+  Mesh,
+  InterfaceTypes,
+  PipelineOutput,
+  PipelineInput,
+  runPipelineNode
+} from 'itk-wasm'
+
+import WasmZstdReadMeshOptions from './wasm-zstd-read-mesh-options.js'
+import WasmZstdReadMeshNodeResult from './wasm-zstd-read-mesh-node-result.js'
+
+import path from 'path'
+
+/**
+ * Read a mesh file format and convert it to the itk-wasm file format
+ *
+ * @param {string} serializedMesh - Input mesh serialized in the file format
+ * @param {WasmZstdReadMeshOptions} options - options object
+ *
+ * @returns {Promise<WasmZstdReadMeshNodeResult>} - result object
+ */
+async function wasmZstdReadMeshNode(
+  serializedMesh: string,
+  options: WasmZstdReadMeshOptions = {}
+) : Promise<WasmZstdReadMeshNodeResult> {
+
+  const mountDirs: Set<string> = new Set()
+
+  const desiredOutputs: Array<PipelineOutput> = [
+    { type: InterfaceTypes.JsonCompatible },
+    { type: InterfaceTypes.Mesh },
+  ]
+
+  mountDirs.add(path.dirname(serializedMesh as string))
+  const inputs: Array<PipelineInput> = [
+  ]
+
+  const args = []
+  // Inputs
+  const serializedMeshName = serializedMesh
+  args.push(serializedMeshName)
+  mountDirs.add(path.dirname(serializedMeshName))
+
+  // Outputs
+  const couldReadName = '0'
+  args.push(couldReadName)
+
+  const meshName = '1'
+  args.push(meshName)
+
+  // Options
+  args.push('--memory-io')
+  if (typeof options.informationOnly !== "undefined") {
+    options.informationOnly && args.push('--information-only')
+  }
+
+  const pipelinePath = path.join(path.dirname(import.meta.url.substring(7)), 'pipelines', 'wasm-zstd-read-mesh')
+
+  const {
+    returnValue,
+    stderr,
+    outputs
+  } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
+  if (returnValue !== 0 && stderr !== "") {
+    throw new Error(stderr)
+  }
+
+  const result = {
+    couldRead: outputs[0]?.data as JsonCompatible,
+    mesh: outputs[1]?.data as Mesh,
+  }
+  return result
+}
+
+export default wasmZstdReadMeshNode

packages/mesh-io/typescript/src/wasm-zstd-read-mesh-options.ts

@@ -0,0 +1,9 @@
+// Generated file. To retain edits, remove this comment.
+
+interface WasmZstdReadMeshOptions {
+  /** Only read image metadata -- do not read pixel data. */
+  informationOnly?: boolean
+
+}
+
+export default WasmZstdReadMeshOptions

packages/mesh-io/typescript/src/wasm-zstd-read-mesh-result.ts

@@ -0,0 +1,17 @@
+// Generated file. To retain edits, remove this comment.
+
+import { JsonCompatible, Mesh } from 'itk-wasm'
+
+interface WasmZstdReadMeshResult {
+  /** WebWorker used for computation */
+  webWorker: Worker | null
+
+  /** Whether the input could be read. If false, the output mesh is not valid. */
+  couldRead: JsonCompatible
+
+  /** Output mesh */
+  mesh: Mesh
+
+}
+
+export default WasmZstdReadMeshResult