feat(JsonObject): Add JSON_OUTPUT as output type

Add JSON_OUTPUT as a possible output type which will be generated by an operation (.cxx) as a string, but will be parsed as a generic Javascript object when receiving results on the JS side of the pipeline. Use JSON_OUTPUT for the second output of applyPresentationStateToImage operation. Add convenience command 'npm run bindgen' to package.json.
InsightSoftwareConsortium · Nov 1, 2022 · ec4176f · ec4176f
1 parent d057456
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Showing 14 changed files with 45 additions and 19 deletions.
diff --git a/dist/dicom/src/ApplyPresentationStateToImageNodeResult.ts b/dist/dicom/src/ApplyPresentationStateToImageNodeResult.ts
@@ -2,7 +2,7 @@ import { Image } from 'itk-wasm'
 
 interface ApplyPresentationStateToImageNodeResult {
   /** Output overlay information */
-  presentationStateOutStream: string
+  presentationStateOutStream: Object
 
   /** Output image */
   outputImage: Image

diff --git a/dist/dicom/src/ApplyPresentationStateToImageResult.ts b/dist/dicom/src/ApplyPresentationStateToImageResult.ts
@@ -5,7 +5,7 @@ interface ApplyPresentationStateToImageResult {
   webWorker: Worker | null
 
   /** Output overlay information */
-  presentationStateOutStream: string
+  presentationStateOutStream: Object
 
   /** Output image */
   outputImage: Image

diff --git a/dist/dicom/src/applyPresentationStateToImage.ts b/dist/dicom/src/applyPresentationStateToImage.ts
@@ -1,5 +1,5 @@
 import {
-  TextStream,
+  JsonObject,
   Image,
   InterfaceTypes,
   PipelineInput,
@@ -23,7 +23,7 @@ async function applyPresentationStateToImage(
     : Promise<ApplyPresentationStateToImageResult> {
 
   const desiredOutputs = [
-    { type: InterfaceTypes.TextStream },
+    { type: InterfaceTypes.JsonObject },
     { type: InterfaceTypes.Image },
   ]
   const inputs: [ PipelineInput ] = [
@@ -76,7 +76,7 @@ async function applyPresentationStateToImage(
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    presentationStateOutStream: (outputs[0].data as TextStream).data,
+    presentationStateOutStream: (outputs[0].data as JsonObject).data,
     outputImage: outputs[1].data as Image,
   }
   return result

diff --git a/dist/dicom/src/applyPresentationStateToImageNode.ts b/dist/dicom/src/applyPresentationStateToImageNode.ts
@@ -1,5 +1,5 @@
 import {
-  TextStream,
+  JsonObject,
   Image,
   InterfaceTypes,
   PipelineInput,
@@ -24,7 +24,7 @@ async function applyPresentationStateToImageNode(  imageIn: Uint8Array,
     : Promise<ApplyPresentationStateToImageNodeResult> {
 
   const desiredOutputs = [
-    { type: InterfaceTypes.TextStream },
+    { type: InterfaceTypes.JsonObject },
     { type: InterfaceTypes.Image },
   ]
   const inputs: [ PipelineInput ] = [
@@ -75,7 +75,7 @@ async function applyPresentationStateToImageNode(  imageIn: Uint8Array,
   }
 
   const result = {
-    presentationStateOutStream: (outputs[0].data as TextStream).data,
+    presentationStateOutStream: (outputs[0].data as JsonObject).data,
     outputImage: outputs[1].data as Image,
   }
   return result

diff --git a/dist/dicom/test/node.js b/dist/dicom/test/node.js
@@ -123,9 +123,9 @@ test('Apply presentation state to dicom image.', async t => {
   const pstateFileBuffer = fs.readFileSync(pstateFilePath)
   const inputPState = new Uint8Array(pstateFileBuffer)
 
-  const { presentationStateOutStream, outputImage } = await applyPresentationStateToImageNode(inputImage, {presentationStateFile: inputPState})
+  const { presentationStateOutStream: pstateJsonOut, outputImage } = await applyPresentationStateToImageNode(inputImage, {presentationStateFile: inputPState})
 
-  t.assert(presentationStateOutStream != null)
+  t.assert(pstateJsonOut != null)
   t.assert(outputImage != null)
 
   t.assert(outputImage.imageType.dimension === 2)
@@ -138,14 +138,15 @@ test('Apply presentation state to dicom image.', async t => {
   t.assert(arrayEquals(outputImage.direction, [1, 0, 0, 1]))
   t.assert(arrayEquals(outputImage.size, [512, 512]))
 
-  const baselineJson = 'gsps-pstate-baseline.json'
-  const baselineJsonFilePath = `../../build-emscripten/ExternalData/test/Input/${baselineJson}`
+  const baselineJsonFile = 'gsps-pstate-baseline.json'
+  const baselineJsonFilePath = `../../build-emscripten/ExternalData/test/Input/${baselineJsonFile}`
   const baselineJsonFileBuffer = fs.readFileSync(baselineJsonFilePath)
   // the slice operation removes the last EOF char from the baseline file.
   const baselineJsonString = baselineJsonFileBuffer.toString().slice(0, -1)
-
-  t.assert(baselineJsonString === presentationStateOutStream)
-  t.assert(baselineJsonString.length === presentationStateOutStream.length)
+  const baselineJsonObject = JSON.parse(baselineJsonString)
+  t.assert(baselineJsonObject.PresentationLabel === pstateJsonOut.PresentationLabel)
+  t.assert(baselineJsonObject.PresentationSizeMode === pstateJsonOut.PresentationSizeMode)
+  t.assert(baselineJsonObject.toString() === pstateJsonOut.toString())
 
   const baselineImage = 'gsps-pstate-image-baseline.pgm'
   const baselineImageFilePath = `../../build-emscripten/ExternalData/test/Input/${baselineImage}`

diff --git a/doc/content/api/JsonObject.md b/doc/content/api/JsonObject.md
@@ -0,0 +1,6 @@
+title: JsonObject
+---
+
+A `JsonObject` represents a javascript object parsed from an arbitrary JSON string. `JsonObject` is a JavaScript object with the following properties:
+
+**data**: Of type `Object`, contains the javascript object parsed from a generated JSON text/string.
diff --git a/doc/content/docs/interface_types.md b/doc/content/docs/interface_types.md
@@ -1,7 +1,7 @@
 title: Interface Types
 ---
 
-itk-wasm execution pipelines support the following [interface types](https://github.com/InsightSoftwareConsortum/itk-wasm/tree/master/src/core/InterfaceTypes.ts):
+itk-wasm execution pipelines support the following [interface types](https://github.com/InsightSoftwareConsortium/itk-wasm/tree/master/src/core/InterfaceTypes.ts):
 
 - [TextFile](../api/TextFile.html)
 - [BinaryFile](../api/BinaryFile.html)
@@ -10,6 +10,7 @@ itk-wasm execution pipelines support the following [interface types](https://git
 - [Image](../api/Image.html)
 - [Mesh](../api/Mesh.html)
 - [PolyData](../api/PolyData.html)
+- [JsonObject](../api/JsonObject.html)
 
 These interfaces types are supported in the [Emscripten interface](../api/runPipeline.html), WASI embedding interfaces, and native or virtual [filesystem IO](./file_formats.html).
 

diff --git a/package.json b/package.json
@@ -25,6 +25,7 @@
     "doc": "kw-doc -c ./doc/config.cjs",
     "doc:www": "kw-doc -c ./doc/config.cjs -s",
     "commit": "git cz",
+    "bindgen": "node ./src/itk-wasm-cli.js bindgen ./dist/dicom/src ./dist/dicom/public/pipelines/*.wasm",
     "build": "npm run build:emscripten && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack && node ./src/io/internal/packages/package-json-gen.cjs",
     "build:debug": "npm run build:emscripten -- --debug && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack -- --mode development",
     "build:tsc": "tsc --pretty",

diff --git a/src/core/InterfaceTypes.ts b/src/core/InterfaceTypes.ts
@@ -6,7 +6,8 @@ const InterfaceTypes = {
   BinaryStream: 'InterfaceBinaryStream',
   Image: 'InterfaceImage',
   Mesh: 'InterfaceMesh',
-  PolyData: 'InterfacePolyData'
+  PolyData: 'InterfacePolyData',
+  JsonObject: 'InterfaceJsonObject',
 } as const
 
 export default InterfaceTypes
diff --git a/src/core/JsonObject.ts b/src/core/JsonObject.ts
@@ -0,0 +1,5 @@
+interface JsonObject {
+  data: Object
+}
+
+export default JsonObject
diff --git a/src/core/index.ts b/src/core/index.ts
@@ -6,6 +6,7 @@ export { default as TextStream } from './TextStream.js'
 export { default as BinaryStream } from './BinaryStream.js'
 export { default as TextFile } from './TextFile.js'
 export { default as BinaryFile } from './BinaryFile.js'
+export { default as JsonObject } from './JsonObject.js'
 
 export { default as TypedArray } from './TypedArray.js'
 export { default as IntTypes } from './IntTypes.js'

diff --git a/src/io/internal/pipelines/dicom/apply-presentation-state-to-image.cxx b/src/io/internal/pipelines/dicom/apply-presentation-state-to-image.cxx
@@ -479,7 +479,7 @@ int main(int argc, char *argv[])
   // Outputs
   // Metadata output regarding overlays
   itk::wasm::OutputTextStream pstateOutStream;
-  pipeline.add_option("presentation-state-out-stream", pstateOutStream, "Output overlay information")->type_name("OUTPUT_TEXT_STREAM");
+  pipeline.add_option("presentation-state-out-stream", pstateOutStream, "Output overlay information")->type_name("OUTPUT_JSON");
   // Processed output image
   constexpr unsigned int Dimension = 2;
   using PixelType = unsigned char;

diff --git a/src/itk-wasm-cli.js b/src/itk-wasm-cli.js
@@ -245,6 +245,7 @@ const interfaceJsonTypeToTypeScriptType = new Map([
   ['BOOL', 'boolean'],
   ['TEXT', 'string'],
   ['INT', 'number'],
+  ['OUTPUT_JSON', 'Object'],
 ])
 
 const interfaceJsonTypeToInterfaceType = new Map([
@@ -262,6 +263,7 @@ const interfaceJsonTypeToInterfaceType = new Map([
   ['OUTPUT_MESH', 'Mesh'],
   ['INPUT_POLYDATA', 'PolyData'],
   ['OUTPUT_POLYDATA', 'PolyData'],
+  ['OUTPUT_JSON', 'JsonObject'],
 ])
 
 function typescriptBindings(srcOutputDir, buildDir, wasmBinaries, forNode=false) {
@@ -511,7 +513,7 @@ function typescriptBindings(srcOutputDir, buildDir, wasmBinaries, forNode=false)
     interfaceJson.outputs.forEach((output, index) => {
       const camel = camelCase(output.name)
       const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
-      if (interfaceType.includes('Text') || interfaceType.includes('Binary')) {
+      if (interfaceType.includes('Text') || interfaceType.includes('Binary') || interfaceType.includes('JsonObject')) {
         functionContent += `    ${camel}: (outputs[${index.toString()}].data as ${interfaceType}).data,\n`
       } else {
         functionContent += `    ${camel}: outputs[${index.toString()}].data as ${interfaceType},\n`

diff --git a/src/pipeline/internal/runPipelineEmscripten.ts b/src/pipeline/internal/runPipelineEmscripten.ts
@@ -319,6 +319,14 @@ function runPipelineEmscripten (pipelineModule: PipelineEmscriptenModule, args:
           outputData = { data: decoder.decode(dataArrayView) }
           break
         }
+        case InterfaceTypes.JsonObject:
+        {
+          const dataPtr = pipelineModule.ccall('itk_wasm_output_array_address', 'number', ['number', 'number', 'number'], [0, index, 0])
+          const dataSize = pipelineModule.ccall('itk_wasm_output_array_size', 'number', ['number', 'number', 'number'], [0, index, 0])
+          const dataArrayView = new Uint8Array(pipelineModule.HEAPU8.buffer, dataPtr, dataSize)
+          outputData = { data: JSON.parse(decoder.decode(dataArrayView)) }
+          break
+        }
         case InterfaceTypes.BinaryStream:
         {
           // const jsonPtr = pipelineModule.ccall('itk_wasm_output_json_address', 'number', ['number', 'number'], [0, index])