Merge pull request #1270 from thewtex/transform-io-high-level

transform io high level

include/itkWasmTransformIO.h

@@ -73,7 +73,7 @@ class ITK_TEMPLATE_EXPORT WasmTransformIOTemplate : public TransformIOBaseTempla
 
   /** Set the JSON representation of the image information. */
   void
-  SetJSON(const TransformListJSON & json);
+  SetJSON(const TransformListJSON & json, bool inMemory=false);
 
   /*-------- This part of the interfaces deals with writing data ----- */
 

packages/core/typescript/itk-wasm/src/cli/default-image-tag.js

@@ -1,2 +1,2 @@
-const defaultImageTag = '20241107-53b18ede'
+const defaultImageTag = '20241111-d4fcf16c'
 export default defaultImageTag

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

@@ -1,35 +1,41 @@
-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'
+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]],
-])
+  ["vtk", [vtkPolyDataReadMeshNode, vtkPolyDataWriteMeshNode]],
+  ["obj", [objReadMeshNode, objWriteMeshNode]],
+  ["stl", [stlReadMeshNode, stlWriteMeshNode]],
+  ["off", [offReadMeshNode, offWriteMeshNode]],
+  ["wasm", [wasmReadMeshNode, wasmWriteMeshNode]],
+  ["wasmZstd", [wasmZstdReadMeshNode, wasmZstdWriteMeshNode]],
+  ["swc", [swcReadMeshNode, swcWriteMeshNode]],
+  ["byu", [byuReadMeshNode, byuWriteMeshNode]],
+  [
+    "freeSurferAscii",
+    [freeSurferAsciiReadMeshNode, freeSurferAsciiWriteMeshNode],
+  ],
+  [
+    "freeSurferBinary",
+    [freeSurferBinaryReadMeshNode, freeSurferBinaryWriteMeshNode],
+  ],
+]);
 
-export default meshIoIndexNode
+export default meshIoIndexNode;

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

@@ -1,35 +1,35 @@
-import vtkPolyDataReadMesh from './vtk-poly-data-read-mesh.js'
-import vtkPolyDataWriteMesh from './vtk-poly-data-write-mesh.js'
-import objReadMesh from './obj-read-mesh.js'
-import objWriteMesh from './obj-write-mesh.js'
-import stlReadMesh from './stl-read-mesh.js'
-import stlWriteMesh from './stl-write-mesh.js'
-import offReadMesh from './off-read-mesh.js'
-import offWriteMesh from './off-write-mesh.js'
-import wasmReadMesh from './wasm-read-mesh.js'
-import wasmWriteMesh from './wasm-write-mesh.js'
-import wasmZstdReadMesh from './wasm-zstd-read-mesh.js'
-import wasmZstdWriteMesh from './wasm-zstd-write-mesh.js'
-import swcReadMesh from './swc-read-mesh.js'
-import swcWriteMesh from './swc-write-mesh.js'
-import byuReadMesh from './byu-read-mesh.js'
-import byuWriteMesh from './byu-write-mesh.js'
-import freeSurferAsciiReadMesh from './free-surfer-ascii-read-mesh.js'
-import freeSurferAsciiWriteMesh from './free-surfer-ascii-write-mesh.js'
-import freeSurferBinaryReadMesh from './free-surfer-binary-read-mesh.js'
-import freeSurferBinaryWriteMesh from './free-surfer-binary-write-mesh.js'
+import vtkPolyDataReadMesh from "./vtk-poly-data-read-mesh.js";
+import vtkPolyDataWriteMesh from "./vtk-poly-data-write-mesh.js";
+import objReadMesh from "./obj-read-mesh.js";
+import objWriteMesh from "./obj-write-mesh.js";
+import stlReadMesh from "./stl-read-mesh.js";
+import stlWriteMesh from "./stl-write-mesh.js";
+import offReadMesh from "./off-read-mesh.js";
+import offWriteMesh from "./off-write-mesh.js";
+import wasmReadMesh from "./wasm-read-mesh.js";
+import wasmWriteMesh from "./wasm-write-mesh.js";
+import wasmZstdReadMesh from "./wasm-zstd-read-mesh.js";
+import wasmZstdWriteMesh from "./wasm-zstd-write-mesh.js";
+import swcReadMesh from "./swc-read-mesh.js";
+import swcWriteMesh from "./swc-write-mesh.js";
+import byuReadMesh from "./byu-read-mesh.js";
+import byuWriteMesh from "./byu-write-mesh.js";
+import freeSurferAsciiReadMesh from "./free-surfer-ascii-read-mesh.js";
+import freeSurferAsciiWriteMesh from "./free-surfer-ascii-write-mesh.js";
+import freeSurferBinaryReadMesh from "./free-surfer-binary-read-mesh.js";
+import freeSurferBinaryWriteMesh from "./free-surfer-binary-write-mesh.js";
 
 const meshIoIndex = new Map([
-  ['vtk', [vtkPolyDataReadMesh, vtkPolyDataWriteMesh]],
-  ['obj', [objReadMesh, objWriteMesh]],
-  ['stl', [stlReadMesh, stlWriteMesh]],
-  ['off', [offReadMesh, offWriteMesh]],
-  ['wasm', [wasmReadMesh, wasmWriteMesh]],
-  ['wasm-zst', [wasmZstdReadMesh, wasmZstdWriteMesh]],
-  ['swc', [swcReadMesh, swcWriteMesh]],
-  ['byu', [byuReadMesh, byuWriteMesh]],
-  ['free-surfer-ascii', [freeSurferAsciiReadMesh, freeSurferAsciiWriteMesh]],
-  ['free-surfer-binary', [freeSurferBinaryReadMesh, freeSurferBinaryWriteMesh]],
-])
+  ["vtk", [vtkPolyDataReadMesh, vtkPolyDataWriteMesh]],
+  ["obj", [objReadMesh, objWriteMesh]],
+  ["stl", [stlReadMesh, stlWriteMesh]],
+  ["off", [offReadMesh, offWriteMesh]],
+  ["wasm", [wasmReadMesh, wasmWriteMesh]],
+  ["wasmZstd", [wasmZstdReadMesh, wasmZstdWriteMesh]],
+  ["swc", [swcReadMesh, swcWriteMesh]],
+  ["byu", [byuReadMesh, byuWriteMesh]],
+  ["freeSurferAscii", [freeSurferAsciiReadMesh, freeSurferAsciiWriteMesh]],
+  ["freeSurferBinary", [freeSurferBinaryReadMesh, freeSurferBinaryWriteMesh]],
+]);
 
-export default meshIoIndex
+export default meshIoIndex;

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

@@ -1,25 +1,25 @@
-import path from 'path'
+import path from "path";
 
-import {
-  Mesh,
-  getFileExtension,
-} from 'itk-wasm'
+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 mimeToMeshIo from "./mime-to-mesh-io.js";
+import extensionToMeshIo from "./extension-to-mesh-io.js";
+import meshIoIndexNode from "./mesh-io-index-node.js";
 
-import WriteMeshOptions from './write-mesh-options.js'
+import WriteMeshOptions from "./write-mesh-options.js";
 
 interface WriterOptions {
-  useCompression?: boolean
-  binaryFileType?: boolean
+  useCompression?: boolean;
+  binaryFileType?: boolean;
 }
 interface WriterResult {
-  couldWrite: boolean
+  couldWrite: boolean;
 }
-type Writer = (mesh: Mesh, serializedImage: string, options: WriterOptions) => Promise<WriterResult>
-
+type Writer = (
+  mesh: Mesh,
+  serializedMesh: string,
+  options: WriterOptions
+) => Promise<WriterResult>;
 
 /**
  * Write a mesh to a serialized file format and from an the itk-wasm Mesh
@@ -34,38 +34,47 @@ async function writeMeshNode(
   mesh: Mesh,
   serializedMesh: string,
   options: WriteMeshOptions = {}
-) : Promise<void> {
-  const absoluteFilePath = path.resolve(serializedMesh)
-  const mimeType = options.mimeType
-  const extension = getFileExtension(absoluteFilePath)
+): Promise<void> {
+  const absoluteFilePath = path.resolve(serializedMesh);
+  const mimeType = options.mimeType;
+  const extension = getFileExtension(absoluteFilePath);
 
-  let inputMesh = mesh
+  let inputMesh = mesh;
 
-  let io = null
-  if (typeof mimeType !== 'undefined' && mimeToMeshIo.has(mimeType)) {
-    io = mimeToMeshIo.get(mimeType)
+  let io = null;
+  if (typeof mimeType !== "undefined" && mimeToMeshIo.has(mimeType)) {
+    io = mimeToMeshIo.get(mimeType);
   } else if (extensionToMeshIo.has(extension)) {
-    io = extensionToMeshIo.get(extension)
+    io = extensionToMeshIo.get(extension);
   } else {
     for (const readerWriter of meshIoIndexNode.values()) {
       if (readerWriter[1] !== null) {
-        let { couldWrite } = await (readerWriter[1] as Writer)(inputMesh, absoluteFilePath, { useCompression: options.useCompression, binaryFileType: options.binaryFileType })
+        let { couldWrite } = await (readerWriter[1] as Writer)(
+          inputMesh,
+          absoluteFilePath,
+          {
+            useCompression: options.useCompression,
+            binaryFileType: options.binaryFileType,
+          }
+        );
         if (couldWrite) {
-          return
+          return;
         }
       }
     }
   }
-  if (io === null ) {
-    throw Error('Could not find IO for: ' + absoluteFilePath)
+  if (io === null) {
+    throw Error("Could not find IO for: " + absoluteFilePath);
   }
-  const readerWriter = meshIoIndexNode.get(io as string)
+  const readerWriter = meshIoIndexNode.get(io as string);
 
-  const writer = (readerWriter as Array<Writer>)[1]
-  let { couldWrite } = await writer(inputMesh, absoluteFilePath, { useCompression: options.useCompression })
+  const writer = (readerWriter as Array<Writer>)[1];
+  let { couldWrite } = await writer(inputMesh, absoluteFilePath, {
+    useCompression: options.useCompression,
+  });
   if (!couldWrite) {
-    throw Error('Could not write: ' + absoluteFilePath)
+    throw Error("Could not write: " + absoluteFilePath);
   }
 }
 
-export default writeMeshNode
+export default writeMeshNode;

packages/transform-io/itkInputTransformIO.h

@@ -96,11 +96,11 @@ bool lexical_cast(const std::string &input, InputTransformIO<TParametersValueTyp
     }
 
     auto wasmTransformIO = WasmTransformIOType::New();
-    wasmTransformIO->SetJSON(transformListJSON);
+    constexpr bool inMemory = true;
+    wasmTransformIO->SetJSON(transformListJSON, inMemory);
 
     auto wasmTransformIOBase = WasmTransformIOBaseType::New();
-    wasmTransformIOBase->SetTransformIO(wasmTransformIO, false);
-    wasmTransformIOBase->SetJSON(json);
+    wasmTransformIOBase->SetTransformIO(wasmTransformIO, inMemory);
 
     inputTransformIO.Set(wasmTransformIOBase);
 #else

packages/transform-io/typescript/package.json

@@ -34,12 +34,14 @@
   "author": "",
   "license": "Apache-2.0",
   "dependencies": {
-    "itk-wasm": "workspace:^"
+    "itk-wasm": "workspace:^",
+    "mime-types": "^2.1.35"
   },
   "devDependencies": {
     "@itk-wasm/demo-app": "workspace:*",
     "@itk-wasm/transform-io-build": "workspace:*",
     "@types/node": "^20.2.5",
+    "@types/mime-types": "^2.1.4",
     "ava": "^6.1.3",
     "esbuild": "^0.19.8",
     "shx": "^0.3.4",

packages/transform-io/typescript/src/extension-to-transform-io.ts

@@ -0,0 +1,12 @@
+const extensionToTransformIo = new Map([
+  ["h5", "hdf5"],
+  ["hdf5", "hdf5"],
+  ["txt", "txt"],
+  ["mat", "mat"],
+  ["xfm", "mnc"],
+  ["iwt", "wasm"],
+  ["iwt.cbor", "wasm"],
+  ["iwt.cbor.zst", "wasm-zstd"],
+]);
+
+export default extensionToTransformIo;