From 7386b746c4f1d31a0beeb3c08048554040b1a4b4 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Tue, 26 Sep 2023 21:40:59 -0400
Subject: [PATCH 1/6] fix(bindgen): run functionName preRun on init

The constructor or the event could come first.
---
 .../compare-double-images-controller.ts       |  8 ++++---
 .../demo-app/vector-magnitude-controller.ts   |  8 ++++---
 .../demo-app/compress-stringify-controller.ts |  8 ++++---
 .../typescript/test/browser/demo-app/index.ts |  4 ++--
 .../parse-string-decompress-controller.ts     |  8 ++++---
 ...-presentation-state-to-image-controller.ts |  8 ++++---
 .../typescript/test/browser/demo-app/index.ts | 12 +++++-----
 .../demo-app/read-dicom-tags-controller.ts    |  8 ++++---
 .../structured-report-to-text-controller.ts   |  8 ++++---
 .../interface-functions-demo-typescript.js    |  8 ++++---
 src/bindgen/typescript/typescript-bindings.js | 22 ++++++++++---------
 11 files changed, 60 insertions(+), 42 deletions(-)

diff --git a/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts b/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts
index dc3841ac5..de2ddd96a 100644
--- a/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts
+++ b/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts
@@ -147,19 +147,21 @@ class CompareDoubleImagesController  {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: 'compareDoubleImages' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === 'compareDoubleImages') {
+        tabGroup.show('compareDoubleImages-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#compareDoubleImagesInputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts b/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts
index 6c9a3c94b..527503f76 100644
--- a/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts
+++ b/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts
@@ -88,19 +88,21 @@ class VectorMagnitudeController  {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: 'vectorMagnitude' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === 'vectorMagnitude') {
+        tabGroup.show('vectorMagnitude-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#vectorMagnitudeInputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/packages/compress-stringify/typescript/test/browser/demo-app/compress-stringify-controller.ts b/packages/compress-stringify/typescript/test/browser/demo-app/compress-stringify-controller.ts
index fbf209c3f..f8afafe90 100644
--- a/packages/compress-stringify/typescript/test/browser/demo-app/compress-stringify-controller.ts
+++ b/packages/compress-stringify/typescript/test/browser/demo-app/compress-stringify-controller.ts
@@ -94,19 +94,21 @@ class CompressStringifyController  {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: 'compressStringify' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === 'compressStringify') {
+        tabGroup.show('compressStringify-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#compressStringifyInputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/packages/compress-stringify/typescript/test/browser/demo-app/index.ts b/packages/compress-stringify/typescript/test/browser/demo-app/index.ts
index a539d23a6..4c93b87ca 100644
--- a/packages/compress-stringify/typescript/test/browser/demo-app/index.ts
+++ b/packages/compress-stringify/typescript/test/browser/demo-app/index.ts
@@ -8,8 +8,6 @@ compressStringify.setPipelinesBaseUrl(pipelinesBaseUrl)
 const pipelineWorkerUrl: string | URL | null = new URL('/web-workers/pipeline.worker.js', document.location.origin).href
 compressStringify.setPipelineWorkerUrl(pipelineWorkerUrl)
 
-import './compress-stringify-controller.js'
-import './parse-string-decompress-controller.js'
 
 const params = new URLSearchParams(window.location.search)
 if (!params.has('functionName')) {
@@ -18,3 +16,5 @@ if (!params.has('functionName')) {
   url.search = params
   window.history.replaceState({ functionName: 'compressStringify' }, '', url)
 }
+import './compress-stringify-controller.js'
+import './parse-string-decompress-controller.js'
diff --git a/packages/compress-stringify/typescript/test/browser/demo-app/parse-string-decompress-controller.ts b/packages/compress-stringify/typescript/test/browser/demo-app/parse-string-decompress-controller.ts
index 88026ce20..1e68f0107 100644
--- a/packages/compress-stringify/typescript/test/browser/demo-app/parse-string-decompress-controller.ts
+++ b/packages/compress-stringify/typescript/test/browser/demo-app/parse-string-decompress-controller.ts
@@ -84,19 +84,21 @@ class ParseStringDecompressController  {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: 'parseStringDecompress' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === 'parseStringDecompress') {
+        tabGroup.show('parseStringDecompress-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#parseStringDecompressInputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts b/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts
index 3c3f8c7d1..c1f22d2eb 100644
--- a/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts
+++ b/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts
@@ -133,19 +133,21 @@ class ApplyPresentationStateToImageController  {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: 'applyPresentationStateToImage' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === 'applyPresentationStateToImage') {
+        tabGroup.show('applyPresentationStateToImage-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#applyPresentationStateToImageInputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/packages/dicom/typescript/test/browser/demo-app/index.ts b/packages/dicom/typescript/test/browser/demo-app/index.ts
index 0a1459759..88d5e4b01 100644
--- a/packages/dicom/typescript/test/browser/demo-app/index.ts
+++ b/packages/dicom/typescript/test/browser/demo-app/index.ts
@@ -8,12 +8,6 @@ dicom.setPipelinesBaseUrl(pipelinesBaseUrl)
 const pipelineWorkerUrl: string | URL | null = new URL('/web-workers/pipeline.worker.js', document.location.origin).href
 dicom.setPipelineWorkerUrl(pipelineWorkerUrl)
 
-import './apply-presentation-state-to-image-controller.js'
-import './read-dicom-encapsulated-pdf-controller.js'
-import './structured-report-to-html-controller.js'
-import './structured-report-to-text-controller.js'
-import './read-dicom-tags-controller.js'
-import './read-image-dicom-file-series-controller.js'
 
 const params = new URLSearchParams(window.location.search)
 if (!params.has('functionName')) {
@@ -22,3 +16,9 @@ if (!params.has('functionName')) {
   url.search = params
   window.history.replaceState({ functionName: 'applyPresentationStateToImage' }, '', url)
 }
+import './apply-presentation-state-to-image-controller.js'
+import './read-dicom-encapsulated-pdf-controller.js'
+import './structured-report-to-html-controller.js'
+import './structured-report-to-text-controller.js'
+import './read-dicom-tags-controller.js'
+import './read-image-dicom-file-series-controller.js'
diff --git a/packages/dicom/typescript/test/browser/demo-app/read-dicom-tags-controller.ts b/packages/dicom/typescript/test/browser/demo-app/read-dicom-tags-controller.ts
index d78dc360a..0958d96af 100644
--- a/packages/dicom/typescript/test/browser/demo-app/read-dicom-tags-controller.ts
+++ b/packages/dicom/typescript/test/browser/demo-app/read-dicom-tags-controller.ts
@@ -92,19 +92,21 @@ class ReadDicomTagsController  {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: 'readDicomTags' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === 'readDicomTags') {
+        tabGroup.show('readDicomTags-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#readDicomTagsInputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/packages/dicom/typescript/test/browser/demo-app/structured-report-to-text-controller.ts b/packages/dicom/typescript/test/browser/demo-app/structured-report-to-text-controller.ts
index 28239d798..c783c2e9d 100644
--- a/packages/dicom/typescript/test/browser/demo-app/structured-report-to-text-controller.ts
+++ b/packages/dicom/typescript/test/browser/demo-app/structured-report-to-text-controller.ts
@@ -164,19 +164,21 @@ class StructuredReportToTextController  {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: 'structuredReportToText' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === 'structuredReportToText') {
+        tabGroup.show('structuredReportToText-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#structuredReportToTextInputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/src/bindgen/typescript/demo/interface-functions-demo-typescript.js b/src/bindgen/typescript/demo/interface-functions-demo-typescript.js
index 013591c0c..d3d6d2d1e 100644
--- a/src/bindgen/typescript/demo/interface-functions-demo-typescript.js
+++ b/src/bindgen/typescript/demo/interface-functions-demo-typescript.js
@@ -154,19 +154,21 @@ class ${functionNamePascalCase}Model {
           const url = new URL(document.location)
           url.search = params
           window.history.replaceState({ functionName: '${functionName}' }, '', url)
+          await preRun()
         }
-        await preRun()
       }
     }
 
     const tabGroup = document.querySelector('sl-tab-group')
     tabGroup.addEventListener('sl-tab-show', onSelectTab)
-    document.addEventListener('DOMContentLoaded', () => {
+    function onInit() {
       const params = new URLSearchParams(window.location.search)
       if (params.has('functionName') && params.get('functionName') === '${functionName}') {
+        tabGroup.show('${functionName}-panel')
         preRun()
       }
-    })
+    }
+    onInit()
 
     const runButton = document.querySelector('#${functionName}Inputs sl-button[name="run"]')
     runButton.addEventListener('click', async (event) => {
diff --git a/src/bindgen/typescript/typescript-bindings.js b/src/bindgen/typescript/typescript-bindings.js
index c21f51bff..f9435d353 100644
--- a/src/bindgen/typescript/typescript-bindings.js
+++ b/src/bindgen/typescript/typescript-bindings.js
@@ -39,6 +39,7 @@ function typescriptBindings (outputDir, buildDir, wasmBinaries, options, forNode
   let demoFunctionsHtml = ''
   let pipelinesFunctionsTabs = ''
   let demoFunctionsTypeScript = ''
+
   const allUsedInterfaceTypes = new Set()
 
   const packageName = options.packageName
@@ -102,7 +103,17 @@ function typescriptBindings (outputDir, buildDir, wasmBinaries, options, forNode
     const moduleCamelCase = camelCase(parsedPath.name)
     const modulePascalCase = `${moduleCamelCase[0].toUpperCase()}${moduleCamelCase.substring(1)}`
     const functionName = camelCase(interfaceJson.name)
-    firstFunctionName = firstFunctionName || functionName
+    if (!firstFunctionName) {
+      firstFunctionName = functionName
+      demoFunctionsTypeScript += `\nconst params = new URLSearchParams(window.location.search)
+if (!params.has('functionName')) {
+  params.set('functionName', '${firstFunctionName}')
+  const url = new URL(document.location)
+  url.search = params
+  window.history.replaceState({ functionName: '${firstFunctionName}' }, '', url)
+}
+`
+    }
 
     const useCamelCase = true
     const functionDemoHtml = interfaceFunctionsDemoHtml(interfaceJson, functionName, useCamelCase)
@@ -144,15 +155,6 @@ function typescriptBindings (outputDir, buildDir, wasmBinaries, options, forNode
     readmePipelines += readmeResult
   })
 
-  demoFunctionsTypeScript += `\nconst params = new URLSearchParams(window.location.search)
-if (!params.has('functionName')) {
-  params.set('functionName', '${firstFunctionName}')
-  const url = new URL(document.location)
-  url.search = params
-  window.history.replaceState({ functionName: '${firstFunctionName}' }, '', url)
-}
-`
-
   if (allUsedInterfaceTypes.size > 0) {
     indexContent += '\n'
     allUsedInterfaceTypes.forEach(iType => indexContent += `export type { ${iType} } from 'itk-wasm'\n`)

From e5ecfce20b29ab4e9b4b68861d54414c35eb93fe Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Wed, 27 Sep 2023 15:21:50 -0400
Subject: [PATCH 2/6] refactor(bindgen): output file paths are passed as on
 input argument

Instead of an input option.
---
 .../compare-double-images-controller.ts       |  5 ++-
 .../demo-app/vector-magnitude-controller.ts   |  5 ++-
 ...-presentation-state-to-image-controller.ts |  3 +-
 src/bindgen/python/function-module-args.js    | 11 +++++
 .../python/function-module-docstring.js       | 15 +++++++
 .../interface-functions-demo-typescript.js    | 25 +++++++----
 src/bindgen/typescript/function-module.js     | 42 ++++++++++---------
 src/bindgen/typescript/options-module.js      | 11 -----
 src/bindgen/typescript/typescript-bindings.js |  3 +-
 9 files changed, 75 insertions(+), 45 deletions(-)

diff --git a/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts b/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts
index de2ddd96a..4031a90dc 100644
--- a/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts
+++ b/packages/compare-images/typescript/test/browser/demo-app/compare-double-images-controller.ts
@@ -1,7 +1,8 @@
 // Generated file. To retain edits, remove this comment.
 
-import { readImageFile, copyImage } from 'itk-wasm'
-import { writeImageArrayBuffer, copyImage } from 'itk-wasm'
+import { readImageFile } from 'itk-wasm'
+import { writeImageArrayBuffer } from 'itk-wasm'
+import { copyImage } from 'itk-wasm'
 import * as compareImages from '../../../dist/bundles/compare-images.js'
 import compareDoubleImagesLoadSampleInputs, { usePreRun } from "./compare-double-images-load-sample-inputs.js"
 
diff --git a/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts b/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts
index 527503f76..d2405d7c9 100644
--- a/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts
+++ b/packages/compare-images/typescript/test/browser/demo-app/vector-magnitude-controller.ts
@@ -1,7 +1,8 @@
 // Generated file. To retain edits, remove this comment.
 
-import { readImageFile, copyImage } from 'itk-wasm'
-import { writeImageArrayBuffer, copyImage } from 'itk-wasm'
+import { readImageFile } from 'itk-wasm'
+import { writeImageArrayBuffer } from 'itk-wasm'
+import { copyImage } from 'itk-wasm'
 import * as compareImages from '../../../dist/bundles/compare-images.js'
 import vectorMagnitudeLoadSampleInputs, { usePreRun } from "./vector-magnitude-load-sample-inputs.js"
 
diff --git a/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts b/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts
index c1f22d2eb..e263397c6 100644
--- a/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts
+++ b/packages/dicom/typescript/test/browser/demo-app/apply-presentation-state-to-image-controller.ts
@@ -1,6 +1,7 @@
 // Generated file. To retain edits, remove this comment.
 
-import { writeImageArrayBuffer, copyImage } from 'itk-wasm'
+import { writeImageArrayBuffer } from 'itk-wasm'
+import { copyImage } from 'itk-wasm'
 import * as dicom from '../../../dist/bundles/dicom.js'
 import applyPresentationStateToImageLoadSampleInputs, { usePreRun } from "./apply-presentation-state-to-image-load-sample-inputs.js"
 
diff --git a/src/bindgen/python/function-module-args.js b/src/bindgen/python/function-module-args.js
index 2b76f2a75..3822417ef 100644
--- a/src/bindgen/python/function-module-args.js
+++ b/src/bindgen/python/function-module-args.js
@@ -11,6 +11,16 @@ function functionModuleArgs(interfaceJson) {
     const pythonType = interfaceJsonTypeToPythonType.get(canonical)
     functionArgs += `    ${snakeCase(value.name)}: ${pythonType},\n`
   })
+  const outputFiles = interfaceJson.outputs.filter(o => { return o.type.includes('FILE') })
+  outputFiles.forEach((output) => {
+    const isArray = output.itemsExpectedMax > 1
+    const optionName = `${output.name}`
+    if (isArray) {
+      functionArgs += `    ${snakeCase(optionName)}: List[str],\n`
+    } else {
+      functionArgs += `    ${snakeCase(optionName)}: str,\n`
+    }
+  })
   interfaceJson['parameters'].forEach((value) => {
     if (value.name === "memory-io" || value.name === "version") {
       return
@@ -45,6 +55,7 @@ function functionModuleArgs(interfaceJson) {
       }
     }
   })
+
   return functionArgs
 }
 
diff --git a/src/bindgen/python/function-module-docstring.js b/src/bindgen/python/function-module-docstring.js
index 3a685c2b2..a1fc650a2 100644
--- a/src/bindgen/python/function-module-docstring.js
+++ b/src/bindgen/python/function-module-docstring.js
@@ -13,6 +13,18 @@ function functionModuleDocstring(interfaceJson) {
     docstring += `\n    :param ${snakeCase(value.name)}: ${description}\n`
     docstring += `    :type  ${snakeCase(value.name)}: ${pythonType}\n`
   })
+  const outputFiles = interfaceJson.outputs.filter(o => { return o.type.includes('FILE') })
+  outputFiles.forEach((output) => {
+    const isArray = output.itemsExpectedMax > 1
+    const optionName = `${output.name}`
+    const description = output.description.replaceAll('\n', ' ')
+    docstring += `\n    :param ${snakeCase(optionName)}: ${description}\n`
+    if (isArray) {
+      docstring += `    :type  ${snakeCase(optionName)}: List[str]\n`
+    } else {
+      docstring += `    :type  ${snakeCase(optionName)}: str\n`
+    }
+  })
   interfaceJson['parameters'].forEach((value) => {
     if (value.name === "memory-io" || value.name === "version") {
       return
@@ -25,6 +37,9 @@ function functionModuleDocstring(interfaceJson) {
   })
   const jsonOutputs = interfaceJson['outputs']
   jsonOutputs.forEach((value) => {
+    if (value.type.includes('FILE')) {
+      return
+    }
     const description = value.description.replaceAll('\n', ' ')
     const canonical = canonicalType(value.type)
     const pythonType = interfaceJsonTypeToPythonType.get(canonical)
diff --git a/src/bindgen/typescript/demo/interface-functions-demo-typescript.js b/src/bindgen/typescript/demo/interface-functions-demo-typescript.js
index d3d6d2d1e..bfb2f797e 100644
--- a/src/bindgen/typescript/demo/interface-functions-demo-typescript.js
+++ b/src/bindgen/typescript/demo/interface-functions-demo-typescript.js
@@ -27,7 +27,7 @@ function interfaceFunctionsDemoTypeScript(packageName, interfaceJson, outputPath
     result += `import { readMeshFile } from 'itk-wasm'\n`
   }
   if (needReadImage) {
-    result += `import { readImageFile, copyImage } from 'itk-wasm'\n`
+    result += `import { readImageFile } from 'itk-wasm'\n`
   }
   const needWriteMesh = interfaceJson.outputs.filter((value) => interfaceJsonTypeToInterfaceType.get(value.type) === 'Mesh').length > 0
   if (needWriteMesh) {
@@ -35,7 +35,10 @@ function interfaceFunctionsDemoTypeScript(packageName, interfaceJson, outputPath
   }
   const needWriteImage = interfaceJson.outputs.filter((value) => interfaceJsonTypeToInterfaceType.get(value.type) === 'Image').length > 0
   if (needWriteImage) {
-    result += `import { writeImageArrayBuffer, copyImage } from 'itk-wasm'\n`
+    result += `import { writeImageArrayBuffer } from 'itk-wasm'\n`
+  }
+  if (needReadImage || needWriteImage) {
+    result += `import { copyImage } from 'itk-wasm'\n`
   }
 
   result += `import * as ${camelCase(bundleName)} from '../../../dist/bundles/${bundleName}.js'\n`
@@ -117,6 +120,12 @@ class ${functionNamePascalCase}Model {
     result += inputParametersDemoTypeScript(functionName, indent, input, true, 'inputs')
   })
 
+  interfaceJson.outputs.forEach((output) => {
+    if (output.type.includes('FILE')) {
+      result += inputParametersDemoTypeScript(functionName, indent, output, true, 'inputs')
+    }
+  })
+
   if (interfaceJson.parameters.length > 1) {
     result += `${indent}// ----------------------------------------------\n${indent}// Options\n`
     interfaceJson.parameters.forEach((parameter) => {
@@ -128,12 +137,6 @@ class ${functionNamePascalCase}Model {
     })
   }
 
-  interfaceJson.outputs.forEach((output) => {
-    if (output.type.includes('FILE')) {
-      result += inputParametersDemoTypeScript(functionName, indent, output, true, 'options')
-    }
-  })
-
   result += `${indent}// ----------------------------------------------\n${indent}// Outputs`
   interfaceJson.outputs.forEach((output) => {
     result += outputDemoTypeScript(functionName, '', indent, output)
@@ -222,6 +225,12 @@ class ${functionNamePascalCase}Model {
       result += `      this.model.inputs.get('${camelCase(input.name)}'),\n`
     }
   })
+  interfaceJson.outputs.forEach((output) => {
+    const defaultData = output.type.includes('BINARY') ? 'new Uint8Array()' : "''"
+    if (output.type.startsWith('OUTPUT_BINARY_FILE') || output.type.startsWith('OUTPUT_TEXT_FILE')) {
+      result += `      this.model.inputs.get('${camelCase(output.name)}'),\n`
+    }
+  })
   result += '      Object.fromEntries(this.model.options.entries())\n'
   result += '    )\n'
   result += '    this.webWorker = webWorker\n'
diff --git a/src/bindgen/typescript/function-module.js b/src/bindgen/typescript/function-module.js
index 0d49afcd7..09700fc13 100644
--- a/src/bindgen/typescript/function-module.js
+++ b/src/bindgen/typescript/function-module.js
@@ -99,6 +99,14 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
     functionContent += ` * @param {${typescriptType}} ${camelCase(input.name)} - ${input.description}\n`
     readmeParametersTable.push([`\`${camelCase(input.name)}\``, `*${typescriptType}*`, input.description])
   })
+  const outputFiles = interfaceJson.outputs.filter(o => { return o.type.includes('FILE') })
+  outputFiles.forEach((output) => {
+    const isArray = output.itemsExpectedMax > 1 ? '[]' : ''
+    const typescriptType = `string${isArray}`
+    functionContent += ` * @param {${typescriptType}} ${camelCase(output.name)} - ${output.description}\n`
+    readmeParametersTable.push([`\`${camelCase(output.name)}\``, `*${typescriptType}*`, output.description])
+  })
+
   if (haveOptions) {
     functionContent += ` * @param {${modulePascalCase}Options} options - options object\n`
   }
@@ -113,7 +121,7 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
   }
   interfaceJson.inputs.forEach((input, index) => {
     let typescriptType = interfaceJsonTypeToTypeScriptType.get(input.type)
-    const end = index === interfaceJson.inputs.length - 1 && !haveOptions ? '\n' : ',\n'
+    const end = index === interfaceJson.inputs.length - 1 && !haveOptions && !outputFiles.length ? '\n' : ',\n'
     const isArray = input.itemsExpectedMax > 1 ? '[]' : ''
     const fileType = forNode ? 'string' : 'File'
     if (typescriptType === 'TextFile' || typescriptType === 'BinaryFile') {
@@ -127,6 +135,12 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
     }
     functionCall += `  ${camelCase(input.name)}: ${typescriptType}${end}`
   })
+  outputFiles.forEach((output, index) => {
+    const end = index === interfaceJson.outputs.length - 1 && !haveOptions ? '\n' : ',\n'
+    const isArray = output.itemsExpectedMax > 1 ? '[]' : ''
+    const typescriptType = `string${isArray}`
+    functionCall += `  ${camelCase(output.name)}: ${typescriptType}${end}`
+  })
   if (haveOptions) {
     let requiredOptions = ''
     interfaceJson.parameters.forEach((parameter) => {
@@ -179,9 +193,7 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
           const camel = camelCase(output.name)
           if (isArray) {
             const defaultData = interfaceType === 'BinaryFile' ? 'new Uint8Array()' : "''"
-            functionContent += `  const ${camel}PipelineOutputs = typeof options.${camel}Path !== 'undefined' ? options.${camel}Path.map((p) => { return { type: InterfaceTypes.${interfaceType}, data: { path: p, data: ${defaultData} }}}) : []\n`
-          } else {
-            functionContent += `  const ${camel}Path = options.${camel}Path ?? '${camel}'\n`
+            functionContent += `  const ${camel}PipelineOutputs = ${camel}.map((p) => { return { type: InterfaceTypes.${interfaceType}, data: { path: p, data: ${defaultData} }}})\n`
           }
         }
       }
@@ -200,7 +212,7 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
           haveArray = true
           functionContent += `    ...${camel}PipelineOutputs,\n`
         } else {
-          functionContent += `    { type: InterfaceTypes.${interfaceType}, data: { path: ${camel}Path, data: ${defaultData} }},\n`
+          functionContent += `    { type: InterfaceTypes.${interfaceType}, data: { path: ${camel}, data: ${defaultData} }},\n`
         }
       } else if (!interfaceType.includes('File')) {
         functionContent += `    { type: InterfaceTypes.${interfaceType} },\n`
@@ -218,7 +230,7 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
           const isArray = output.itemsExpectedMax > 1
           if (isArray) {
             functionContent += `  const ${camel}Start = outputIndex\n`
-            functionContent += `  outputIndex += options.${camel}Path ? options.${camel}Path.length : 0\n`
+            functionContent += `  outputIndex += ${camel}.length\n`
             functionContent += `  const ${camel}End = outputIndex\n`
           } else {
             functionContent += `  const ${camel}Index = outputIndex\n`
@@ -296,25 +308,17 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
       let name = `  const ${camel}Name = '${outputCount.toString()}'\n`
       const isArray = output.itemsExpectedMax > 1 ? '[]' : ''
       if (interfaceType.includes('File')) {
-        if (forNode) {
-          if (isArray) {
-            name = ''
-          } else {
-            name = `  const ${camel}Name = options.${camel}Path ?? '${camel}'\n`
-          }
+        if (isArray) {
+          name = ''
         } else {
-          if (isArray) {
-            name = ''
-          } else {
-            name = `  const ${camel}Name = ${camel}Path\n`
-          }
+          name = `  const ${camel}Name = ${camel}?? '${camel}'\n`
         }
       }
       functionContent += name
       if (isArray) {
-        functionContent += `  options.${camel}Path?.forEach((p) => args.push(p))\n`
+        functionContent += `  ${camel}.forEach((p) => args.push(p))\n`
         if (forNode && interfaceType.includes('File')) {
-          functionContent += `  options.${camel}Path?.forEach((p) => mountDirs.add(path.dirname(p)))\n`
+          functionContent += `  ${camel}.forEach((p) => mountDirs.add(path.dirname(p)))\n`
         }
       } else {
         functionContent += `  args.push(${camel}Name)\n`
diff --git a/src/bindgen/typescript/options-module.js b/src/bindgen/typescript/options-module.js
index 6486aed39..046dd573c 100644
--- a/src/bindgen/typescript/options-module.js
+++ b/src/bindgen/typescript/options-module.js
@@ -49,17 +49,6 @@ function optionsModule (srcOutputDir, interfaceJson, modulePascalCase, nodeTextC
     readmeOptionsTable.push([`\`${camelCase(parameter.name)}\``, `*${parameterType}*`, parameter.description])
   })
 
-  const outputFiles = interfaceJson.outputs.filter(o => { return o.type.includes('FILE') })
-  outputFiles.forEach((output) => {
-    const outputDescription = `${output.description} path`
-    optionsInterfaceContent += `  /** ${outputDescription} */\n`
-    const isArray = output.itemsExpectedMax > 1 ? '[]' : ''
-    const parameterType = `string${isArray}`
-    const optionName = `${output.name}-path`
-    optionsInterfaceContent += `  ${camelCase(optionName)}?: ${parameterType}\n\n`
-    readmeOptionsTable.push([`\`${camelCase(optionName)}\``, `*${parameterType}*`, outputDescription])
-  })
-
   // Insert the import statement in the beginning for the file.
   if (optionsImportTypes.size !== 0) {
     optionsContent += `import { ${Array.from(optionsImportTypes).join(',')} } from 'itk-wasm'\n\n`
diff --git a/src/bindgen/typescript/typescript-bindings.js b/src/bindgen/typescript/typescript-bindings.js
index f9435d353..d6e14c0de 100644
--- a/src/bindgen/typescript/typescript-bindings.js
+++ b/src/bindgen/typescript/typescript-bindings.js
@@ -135,8 +135,7 @@ if (!params.has('functionName')) {
     indexContent += `export type { ${modulePascalCase}${nodeTextCamel}Result }\n\n`
 
     const filteredParameters = interfaceJson.parameters.filter(p => { return p.name !== 'memory-io' && p.name !== 'version'})
-    const haveOutputFile = interfaceJson.outputs.some(o => { return o.type.includes('FILE') })
-    const haveOptions = !!filteredParameters.length || haveOutputFile
+    const haveOptions = !!filteredParameters.length
 
     const { readmeOptions } = optionsModule(srcOutputDir, interfaceJson, modulePascalCase, nodeTextCamel, moduleKebabCase, haveOptions)
     if (haveOptions) {

From 2cf3c7eb68e8a6bea710467a2f1783ba9833beaa Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Wed, 27 Sep 2023 21:34:47 -0400
Subject: [PATCH 3/6] feat(bindgen): Python output file support

---
 .../python/function-module-return-type.js     |   9 +-
 .../python/wasi/wasi-function-module.js       | 140 ++++++++++++++----
 src/bindgen/typescript/function-module.js     |   4 +-
 3 files changed, 124 insertions(+), 29 deletions(-)

diff --git a/src/bindgen/python/function-module-return-type.js b/src/bindgen/python/function-module-return-type.js
index 44ee43b8d..407dae055 100644
--- a/src/bindgen/python/function-module-return-type.js
+++ b/src/bindgen/python/function-module-return-type.js
@@ -9,7 +9,14 @@ function functionModuleReturnType(interfaceJson) {
     jsonOutputs.forEach((value) => {
       const canonical = canonicalType(value.type)
       const pythonType = interfaceJsonTypeToPythonType.get(canonical)
-      returnType += `${pythonType}, `
+      if (value.type.includes('FILE')) {
+        return
+      }
+      if (value.itemsExpectedMax > 1) {
+        returnType += `List[${pythonType}], `
+      } else {
+        returnType += `${pythonType}, `
+      }
     })
     returnType = returnType.substring(0, returnType.length - 2)
     returnType += "]"
diff --git a/src/bindgen/python/wasi/wasi-function-module.js b/src/bindgen/python/wasi/wasi-function-module.js
index d7caed5ed..934a6a0d1 100644
--- a/src/bindgen/python/wasi/wasi-function-module.js
+++ b/src/bindgen/python/wasi/wasi-function-module.js
@@ -13,9 +13,7 @@ import writeIfOverrideNotPresent from '../../write-if-override-not-present.js'
 
 function wasiFunctionModule(interfaceJson, pypackage, modulePath) {
   const functionName = snakeCase(interfaceJson.name)
-  let moduleContent = `# Generated file. Do not edit.
-
-from pathlib import Path, PurePosixPath
+  let moduleContent = `from pathlib import Path, PurePosixPath
 import os
 from typing import Dict, Tuple, Optional, List, Any
 
@@ -34,20 +32,65 @@ from itkwasm import (
   const returnType = functionModuleReturnType(interfaceJson)
   const docstring = functionModuleDocstring(interfaceJson)
 
+  let pipelineOutputFilePrep = ''
+  interfaceJson.outputs.forEach((output) => {
+    if (interfaceJsonTypeToInterfaceType.has(output.type)) {
+      const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
+      const isArray = output.itemsExpectedMax > 1
+      if (interfaceType.includes('File')) {
+        const snake = snakeCase(output.name)
+        if (isArray) {
+          pipelineOutputFilePrep += `    ${snake}_pipeline_outputs = [PipelineOutput(InterfaceTypes.${interfaceType}, ${interfaceType}(PurePosixPath(p))) for p in ${snake}]\n`
+        }
+      }
+    }
+  })
+
   let pipelineOutputs = ''
+  let haveArray = false
   interfaceJson.outputs.forEach((output) => {
     if (interfaceJsonTypeToInterfaceType.has(output.type)) {
       const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
+      const isArray = output.itemsExpectedMax > 1
       switch (interfaceType) {
         case "TextFile":
         case "BinaryFile":
-          pipelineOutputs += `        PipelineOutput(InterfaceTypes.${interfaceType}, ${interfaceType}(PurePosixPath(${snakeCase(output.name)}))),\n`
+          if (isArray) {
+            haveArray = true
+            pipelineOutputs += `        *${snakeCase(output.name)}_pipeline_outputs,\n`
+          } else {
+            pipelineOutputs += `        PipelineOutput(InterfaceTypes.${interfaceType}, ${interfaceType}(PurePosixPath(${snakeCase(output.name)}))),\n`
+          }
           break
         default:
           pipelineOutputs += `        PipelineOutput(InterfaceTypes.${interfaceType}),\n`
       }
     }
   })
+  let pipelineOutputIndices = ''
+  if (haveArray) {
+    pipelineOutputIndices += `    output_index = 0\n`
+    interfaceJson.outputs.forEach((output) => {
+      if (interfaceJsonTypeToInterfaceType.has(output.type)) {
+        const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
+        if (interfaceType.includes('File')) {
+          const snake = snakeCase(output.name)
+          const isArray = output.itemsExpectedMax > 1
+          if (isArray) {
+            pipelineOutputIndices += `    ${snake}_start = output_index\n`
+            pipelineOutputIndices += `    output_index += len(${snake})\n`
+            pipelineOutputIndices += `    ${snake}_end = output_index\n`
+          } else {
+            pipelineOutputIndices += `    ${snake}_index = output_index\n`
+            pipelineOutputIndices += `    output_index += 1\n`
+          }
+        } else if (!interfaceType.includes('File')) {
+          pipelineOutputIndices += `    ${snake}_index = output_index\n`
+          pipelineOutputIndices += `    output_index += 1\n`
+        }
+      }
+    })
+  }
 
   let pipelineInputs = ''
   interfaceJson['inputs'].forEach((input) => {
@@ -90,18 +133,33 @@ from itkwasm import (
   let outputCount = 0
   args += "    # Outputs\n"
   interfaceJson.outputs.forEach((output) => {
+    const snake = snakeCase(output.name)
     if (interfaceJsonTypeToInterfaceType.has(output.type)) {
       const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
-      const name = interfaceType.includes('File') ?  `str(PurePosixPath(${snakeCase(output.name)}))` : `'${outputCount.toString()}'`
-      args += `    args.append(${name})\n`
+      const isArray = output.itemsExpectedMax > 1
+      let name = `    ${snake}_name = '${outputCount.toString()}'\n`
+      if (interfaceType.includes('File')) {
+        if (isArray) {
+          name = ''
+        } else {
+          name = `    ${snake}_name = str(PurePosixPath(${snake}))\n`
+        }
+      }
+      args += name
+      if (isArray) {
+        args += `    args.extend([str(PurePosixPath(p)) for p in ${snake}])\n`
+      } else {
+        args += `    args.append(${snake}_name)\n`
+      }
+      args += '\n'
       outputCount++
     } else {
-      const snake = snakeCase(output.name)
       args += `    args.append(str(${snake}))\n`
     }
   })
 
   args += "    # Options\n"
+  args += `    input_count = len(pipeline_inputs)\n`
   interfaceJson.parameters.forEach((parameter) => {
     if (parameter.name === 'memory-io' || parameter.name === 'version') {
       // Internal
@@ -126,14 +184,14 @@ from itkwasm import (
           args += `            args.append(input_file)\n`
         } else if (interfaceType.includes('Stream')) {
           // for streams
-          args += `            input_count_string = str(len(pipeline_inputs))\n`
           args += `            pipeline_inputs.append(PipelineInput(InterfaceTypes.${interfaceType}, ${interfaceType}(value)))\n`
-          args += `            args.append(input_count_spring)\n`
+          args += `            args.append(str(input_count))\n`
+          args += `            input_count += 1\n`
         } else {
           // Image, Mesh, PolyData, JsonCompatible
-          args += `            input_count_string = str(len(pipeline_inputs))\n`
           args += `            pipeline_inputs.append(PipelineInput(InterfaceTypes.${interfaceType}, value))\n`
-          args += `            args.append(input_count_string)\n`
+          args += `            args.append(str(input_count))\n`
+          args += `            input_count += 1\n`
         }
       } else {
         args += `            args.append(str(value))\n`
@@ -150,16 +208,16 @@ from itkwasm import (
           args += `        args.append(input_file)\n`
         } else if (interfaceType.includes('Stream')) {
           // for streams
-          args += `        input_count_string = str(len(pipeline_inputs))\n`
           args += `        pipeline_inputs.append(PipelineInput(InterfaceTypes.${interfaceType}, ${interfaceType}(${snake})))\n`
           args += `        args.append('--${parameter.name}')\n`
-          args += `        args.append(input_count_string)\n`
+          args += `        args.append(str(input_count))\n`
+          args += `        input_count += 1\n`
         } else {
           // Image, Mesh, PolyData, JsonCompatible
-          args += `        input_count_string = str(len(pipeline_inputs))\n`
           args += `        pipeline_inputs.append(PipelineInput(InterfaceTypes.${interfaceType}, ${snake}))\n`
           args += `        args.append('--${parameter.name}')\n`
-          args += `        args.append(input_count_string)\n`
+          args += `        args.append(str(input_count))\n`
+          args += `        input_count += 1\n`
         }
       } else {
         args += `    if ${snake}:\n`
@@ -192,24 +250,54 @@ from itkwasm import (
       case "float":
         return `float(${value})`
       case "Any":
-        return `${value}.data.data`
+        return `${value}.data`
       default:
         return `${value}.data`
     }
   }
+  outputCount = 0
   const jsonOutputs = interfaceJson['outputs']
-  if (jsonOutputs.length > 1) {
+  const numOutputs = interfaceJson.outputs.filter(o => !o.type.includes('FILE')).length
+  if (numOutputs > 1) {
     postOutput += '    result = (\n'
-    jsonOutputs.forEach((value, index) => {
-      const outputValue = `outputs[${index}]`
-      postOutput += `        ${toPythonType(value.type, outputValue)},\n`
+  } else if (numOutputs === 1){
+    postOutput = '    result = '
+  }
+
+  if (numOutputs > 0) {
+    // const outputValue = "outputs[0]"
+    // postOutput = `    result = ${toPythonType(jsonOutputs[0].type, outputValue)}\n`
+    const indent = numOutputs > 1 ? '        ' : ''
+    const comma = numOutputs > 1 ? ',' : ''
+    jsonOutputs.forEach((value) => {
+      if (value.type.includes('FILE')) {
+        outputCount++
+        return
+      }
+      const snake = snakeCase(value.name)
+      const outputIndex = haveArray ? `${snake}_index` : outputCount.toString()
+      if (haveArray) {
+        const isArray = value.itemsExpectedMax > 1
+        if (isArray) {
+          const outputValue = `outputs[${snake}_start:${snake}_end]`
+          postOutput += `${indent}*[${toPythonType(value.type, 'v')} for v in ${outputValue}]${comma}\n`
+        } else {
+          const outputValue = `outputs[${snake}_index]`
+          postOutput += `${indent}${toPythonType(value.type, outputValue)}${comma}\n`
+        }
+      } else {
+        const outputValue = `outputs[${outputIndex}]`
+        postOutput += `${indent}${toPythonType(value.type, outputValue)}${comma}\n`
+      }
+      outputCount++
     })
+  }
+  if (numOutputs > 1) {
     postOutput += '    )\n'
-  } else {
-    const outputValue = "outputs[0]"
-    postOutput = `    result = ${toPythonType(jsonOutputs[0].type, outputValue)}\n`
   }
-  postOutput += '    return result\n'
+  if (numOutputs > 0) {
+    postOutput += '    return result\n'
+  }
 
   moduleContent += `def ${functionName}(
 ${functionArgs}) -> ${returnType}:
@@ -217,10 +305,10 @@ ${functionArgs}) -> ${returnType}:
     global _pipeline
     if _pipeline is None:
         _pipeline = Pipeline(file_resources('${pypackage}').joinpath(Path('wasm_modules') / Path('${interfaceJson.name}.wasi.wasm')))
-
+${pipelineOutputFilePrep}
     pipeline_outputs: List[PipelineOutput] = [
 ${pipelineOutputs}    ]
-
+${pipelineOutputIndices}
     pipeline_inputs: List[PipelineInput] = [
 ${pipelineInputs}    ]
 
diff --git a/src/bindgen/typescript/function-module.js b/src/bindgen/typescript/function-module.js
index 09700fc13..2666eec0a 100644
--- a/src/bindgen/typescript/function-module.js
+++ b/src/bindgen/typescript/function-module.js
@@ -306,12 +306,12 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
     if (interfaceJsonTypeToInterfaceType.has(output.type)) {
       const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
       let name = `  const ${camel}Name = '${outputCount.toString()}'\n`
-      const isArray = output.itemsExpectedMax > 1 ? '[]' : ''
+      const isArray = output.itemsExpectedMax > 1
       if (interfaceType.includes('File')) {
         if (isArray) {
           name = ''
         } else {
-          name = `  const ${camel}Name = ${camel}?? '${camel}'\n`
+          name = `  const ${camel}Name = ${camel}\n`
         }
       }
       functionContent += name

From 4b07cda335b164b24a04dcc27028cbaa3398cc45 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Thu, 28 Sep 2023 08:42:24 -0400
Subject: [PATCH 4/6] feat(bindgen): Check for positional input of an array of
 files

Still todo: dynamic input indexing with multiple arguments.

Also, cli11 currently does not distinguish between the end of a input
array set of arguments and a positional output.
---
 src/bindgen/input-array-check.js              | 12 +++++
 src/bindgen/typescript/function-module.js     | 44 +++++++++++++++----
 src/bindgen/typescript/typescript-bindings.js |  2 +
 3 files changed, 50 insertions(+), 8 deletions(-)
 create mode 100644 src/bindgen/input-array-check.js

diff --git a/src/bindgen/input-array-check.js b/src/bindgen/input-array-check.js
new file mode 100644
index 000000000..5b55ef995
--- /dev/null
+++ b/src/bindgen/input-array-check.js
@@ -0,0 +1,12 @@
+function inputArrayCheck(interfaceJson) {
+  interfaceJson.inputs.forEach((input) => {
+    const isArray = input.itemsExpectedMax > 1
+    if (isArray) {
+      console.error('Positional multi-value inputs are currently not supported -- please use an option instead')
+      console.error(`Violating option: ${input.name}`)
+      process.exit(1)
+    }
+  })
+}
+
+export default inputArrayCheck
diff --git a/src/bindgen/typescript/function-module.js b/src/bindgen/typescript/function-module.js
index 2666eec0a..0d5b53eda 100644
--- a/src/bindgen/typescript/function-module.js
+++ b/src/bindgen/typescript/function-module.js
@@ -10,7 +10,7 @@ import writeIfOverrideNotPresent from '../write-if-override-not-present.js'
 function readFileIfNotInterfaceType(forNode, interfaceType, varName, indent, isArray) {
   if (forNode) {
     if (isArray) {
-      return `${indent}value.forEach((p) => mountDirs.add(path.dirname(p) as string))\n`
+      return `${indent}${varName}.forEach((p) => mountDirs.add(path.dirname(p) as string))\n`
     } else {
       return `${indent}mountDirs.add(path.dirname(${varName} as string))\n`
     }
@@ -18,13 +18,13 @@ function readFileIfNotInterfaceType(forNode, interfaceType, varName, indent, isA
   } else {
     if (interfaceType === 'TextFile') {
       if (isArray) {
-        return `${indent}${varName}.map((v) => {\n${indent}${indent}let vFile = v\n${indent}${indent}if (v instanceof File) {\n${indent}${indent}  const vBuffer = await v.arrayBuffer()\n${indent}${indent}  vFile = { path: v.name, data: new TextDecoder().decode(vBuffer) }\n${indent}${indent}}\n${indent}})\n`
+        return `${indent}const ${varName}File = await Promise.all(${varName}.map(async (v) => {\n${indent}${indent}let vFile = v\n${indent}${indent}if (v instanceof File) {\n${indent}${indent}  const vBuffer = await v.arrayBuffer()\n${indent}${indent}  vFile = { path: v.name, data: new TextDecoder().decode(vBuffer) }\n${indent}${indent}}\n${indent}${indent}return vFile\n${indent}}))\n`
       } else {
         return `${indent}let ${varName}File = ${varName}\n${indent}if (${varName} instanceof File) {\n${indent}  const ${varName}Buffer = await ${varName}.arrayBuffer()\n${indent}  ${varName}File = { path: ${varName}.name, data: new TextDecoder().decode(${varName}Buffer) }\n${indent}}\n`
       }
     } else {
       if (isArray) {
-        return `${indent}${varName}.map((v) => {\n${indent}let vFile = v\n${indent}${indent}if (v instanceof File) {\n${indent}${indent}  const vBuffer = await v.arrayBuffer()\n${indent}${indent}  vFile = { path: v.name, data: new Uint8Array(vBuffer) }\n${indent}${indent}}\n${indent}})\n`
+        return `${indent}const ${varName}File = await Promise.all(${varName}.map(async (v) => {\n${indent}let vFile = v\n${indent}${indent}if (v instanceof File) {\n${indent}${indent}  const vBuffer = await v.arrayBuffer()\n${indent}${indent}  vFile = { path: v.name, data: new Uint8Array(vBuffer) }\n${indent}${indent}}${indent}${indent}\nreturn vFile\n${indent}}))\n`
       } else {
         return `${indent}let ${varName}File = ${varName}\n${indent}if (${varName} instanceof File) {\n${indent}  const ${varName}Buffer = await ${varName}.arrayBuffer()\n${indent}  ${varName}File = { path: ${varName}.name, data: new Uint8Array(${varName}Buffer) }\n${indent}}\n`
 
@@ -251,6 +251,9 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
         const camel = camelCase(input.name)
         const isArray = input.itemsExpectedMax > 1
         functionContent += readFileIfNotInterfaceType(forNode, interfaceType, camel, '  ', isArray)
+        if (!forNode && isArray) {
+          functionContent += `  const ${camel}PipelineInputs = ${camel}File.map(i => { return { type: InterfaceTypes.${interfaceType}, data: i as ${interfaceType} }})\n`
+        }
       }
     }
   })
@@ -259,9 +262,14 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
     if (interfaceJsonTypeToInterfaceType.has(input.type)) {
       const interfaceType = interfaceJsonTypeToInterfaceType.get(input.type)
       const camel = camelCase(input.name)
+      const isArray = input.itemsExpectedMax > 1
       if (interfaceType.includes('File')) {
         if (!forNode) {
-          functionContent += `    { type: InterfaceTypes.${interfaceType}, data: ${camel}File as ${interfaceType} },\n`
+          if (isArray) {
+            functionContent += `    ...${camel}PipelineInputs,\n`
+          } else {
+            functionContent += `    { type: InterfaceTypes.${interfaceType}, data: ${camel}File as ${interfaceType} },\n`
+          }
         }
       } else {
         let data = camel
@@ -283,16 +291,36 @@ function functionModule (srcOutputDir, forNode, interfaceJson, modulePascalCase,
     const camel = camelCase(input.name)
     if (interfaceJsonTypeToInterfaceType.has(input.type)) {
       const interfaceType = interfaceJsonTypeToInterfaceType.get(input.type)
+      const isArray = input.itemsExpectedMax > 1
       let name = `  const ${camel}Name = '${inputCount.toString()}'\n`
       if (interfaceType.includes('File')) {
-        if (forNode) {
-          name = `  const ${camel}Name = ${camel}\n`
+        if (isArray) {
+          name = ''
         } else {
-          name = `  const ${camel}Name = (${camel}File as ${interfaceType}).path\n`
+          if (forNode) {
+            name = `  const ${camel}Name = ${camel}\n`
+          } else {
+            name = `  const ${camel}Name = (${camel}File as ${interfaceType}).path\n`
+          }
         }
       }
       functionContent += name
-      functionContent += `  args.push(${camel}Name as string)\n\n`
+      if (isArray) {
+        if (forNode) {
+          functionContent += `  ${camel}.forEach((p) => args.push(p))\n`
+        } else {
+          functionContent += `  ${camel}File.forEach((p) => args.push((p as ${interfaceType}).path))\n`
+        }
+        if (forNode && interfaceType.includes('File')) {
+          functionContent += `  ${camel}.forEach((p) => mountDirs.add(path.dirname(p)))\n`
+        }
+      } else {
+        functionContent += `  args.push(${camel}Name)\n`
+        if (forNode && interfaceType.includes('File')) {
+          functionContent += `  mountDirs.add(path.dirname(${camel}Name))\n`
+        }
+      }
+      functionContent += '\n'
       inputCount++
     } else {
       functionContent += `  args.push(${camel}.toString())\n\n`
diff --git a/src/bindgen/typescript/typescript-bindings.js b/src/bindgen/typescript/typescript-bindings.js
index d6e14c0de..005ddcb0a 100644
--- a/src/bindgen/typescript/typescript-bindings.js
+++ b/src/bindgen/typescript/typescript-bindings.js
@@ -15,6 +15,7 @@ import resultsModule from './results-module.js'
 import optionsModule from './options-module.js'
 import functionModule from './function-module.js'
 import outputOptionsCheck from '../output-options-check.js'
+import inputArrayCheck from '../input-array-check.js'
 
 // Array of types that will require an import from itk-wasm
 function bindgenResource(filePath) {
@@ -98,6 +99,7 @@ function typescriptBindings (outputDir, buildDir, wasmBinaries, options, forNode
     const { interfaceJson, parsedPath } = wasmBinaryInterfaceJson(outputDir, buildDir, wasmBinaryName)
 
     outputOptionsCheck(interfaceJson)
+    inputArrayCheck(interfaceJson)
 
     const moduleKebabCase = parsedPath.name
     const moduleCamelCase = camelCase(parsedPath.name)

From ce051631569741a0264598fbd789d653ebba609f Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Thu, 28 Sep 2023 20:36:57 -0400
Subject: [PATCH 5/6] feat(bindgen): python emescripten function output file
 support

---
 .../core/python/itkwasm/itkwasm/__init__.py     |  2 +-
 packages/core/python/itkwasm/itkwasm/pyodide.py |  4 ++--
 .../emscripten/emscripten-function-module.js    | 17 ++++++++++++++---
 3 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/packages/core/python/itkwasm/itkwasm/__init__.py b/packages/core/python/itkwasm/itkwasm/__init__.py
index bc4b61213..bd795f7ce 100644
--- a/packages/core/python/itkwasm/itkwasm/__init__.py
+++ b/packages/core/python/itkwasm/itkwasm/__init__.py
@@ -1,6 +1,6 @@
 """itkwasm: Python interface to itk-wasm WebAssembly modules."""
 
-__version__ = "1.0b141"
+__version__ = "1.0b142"
 
 from .interface_types import InterfaceTypes
 from .image import Image, ImageType
diff --git a/packages/core/python/itkwasm/itkwasm/pyodide.py b/packages/core/python/itkwasm/itkwasm/pyodide.py
index 70beeb0c2..8538cdd6d 100644
--- a/packages/core/python/itkwasm/itkwasm/pyodide.py
+++ b/packages/core/python/itkwasm/itkwasm/pyodide.py
@@ -150,7 +150,7 @@ def to_py(js_proxy):
     # int, etc
     return js_proxy
 
-def to_js(py):
+def to_js(py, **kwargs):
     import pyodide
     import js
     if isinstance(py, list):
@@ -222,4 +222,4 @@ def to_js(py):
         text_file_dict['data'] = data
         return pyodide.ffi.to_js(text_file_dict, dict_converter=js.Object.fromEntries)
 
-    return pyodide.ffi.to_js(py)
+    return pyodide.ffi.to_js(py, **kwargs)
diff --git a/src/bindgen/python/emscripten/emscripten-function-module.js b/src/bindgen/python/emscripten/emscripten-function-module.js
index bd2a1a59b..8809de801 100644
--- a/src/bindgen/python/emscripten/emscripten-function-module.js
+++ b/src/bindgen/python/emscripten/emscripten-function-module.js
@@ -12,9 +12,7 @@ import writeIfOverrideNotPresent from '../../write-if-override-not-present.js'
 
 function emscriptenFunctionModule(interfaceJson, pypackage, modulePath) {
   const functionName = snakeCase(interfaceJson.name)
-  let moduleContent = `# Generated file. Do not edit.
-
-from pathlib import Path
+  let moduleContent = `from pathlib import Path
 import os
 from typing import Dict, Tuple, Optional, List, Any
 
@@ -49,6 +47,19 @@ from itkwasm import (
       args += `to_js(${snakeCase(input.name)}), `
     }
   })
+  interfaceJson.outputs.forEach((output) => {
+    if (interfaceJsonTypeToInterfaceType.has(output.type)) {
+      const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
+      switch (interfaceType) {
+        case "TextFile":
+        case "BinaryFile":
+          args += `to_js(${snakeCase(output.name)}), `
+          break
+        default:
+          //
+      }
+    }
+  })
 
   let addKwargs = ''
   interfaceJson.parameters.forEach((parameter) => {

From e171721d9fbc34e1a66532f203c77106045f899f Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Thu, 28 Sep 2023 21:20:44 -0400
Subject: [PATCH 6/6] feat(bindgen): python dispatch function output file
 support

---
 src/bindgen/python/dispatch-function-module.js | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/bindgen/python/dispatch-function-module.js b/src/bindgen/python/dispatch-function-module.js
index 34a6ed32a..ab4fdaeb8 100644
--- a/src/bindgen/python/dispatch-function-module.js
+++ b/src/bindgen/python/dispatch-function-module.js
@@ -6,6 +6,7 @@ import functionModuleImports from './function-module-imports.js'
 import functionModuleArgs from './function-module-args.js'
 import functionModuleDocstring from './function-module-docstring.js'
 import functionModuleReturnType from './function-module-return-type.js'
+import interfaceJsonTypeToInterfaceType from '../interface-json-type-to-interface-type.js'
 
 function dispatchFunctionModule(interfaceJson, pypackage, modulePath) {
   const functionName = snakeCase(interfaceJson.name)
@@ -24,9 +25,22 @@ from itkwasm import (
   const docstring = functionModuleDocstring(interfaceJson)
 
   let functionArgsToPass = ""
-  interfaceJson['inputs'].forEach((value) => {
+  interfaceJson.inputs.forEach((value) => {
     functionArgsToPass += `${snakeCase(value.name)}, `
   })
+  interfaceJson.outputs.forEach((output) => {
+    if (interfaceJsonTypeToInterfaceType.has(output.type)) {
+      const interfaceType = interfaceJsonTypeToInterfaceType.get(output.type)
+      switch (interfaceType) {
+        case "TextFile":
+        case "BinaryFile":
+          functionArgsToPass += `${snakeCase(output.name)}, `
+          break
+        default:
+          //
+      }
+    }
+  })
   interfaceJson['parameters'].forEach((value) => {
     if (value.name === "memory-io" || value.name === "version") {
       return