diff --git a/packages/core/python/itkwasm/itkwasm/__init__.py b/packages/core/python/itkwasm/itkwasm/__init__.py index c7aaf8bde..7ee31e4d7 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__ = "1.0b191" +__version__ = "1.0b192" from .interface_types import InterfaceTypes from .image import Image, ImageType, ImageRegion diff --git a/packages/core/python/itkwasm/itkwasm/pipeline.py b/packages/core/python/itkwasm/itkwasm/pipeline.py index bf6503584..dc2a2061f 100644 --- a/packages/core/python/itkwasm/itkwasm/pipeline.py +++ b/packages/core/python/itkwasm/itkwasm/pipeline.py @@ -546,7 +546,7 @@ def run( data_ptr = ri.get_output_array_address(0, index, idx * 2) data_size = ri.get_output_array_size(0, index, idx * 2) transform.fixedParameters = buffer_to_numpy_array( - transform.transformType.parametersValueType, + FloatTypes.Float64, ri.wasmtime_lift(data_ptr, data_size), ) if transform.numberOfParameters > 0: diff --git a/packages/core/python/itkwasm/test/test_pyodide.py b/packages/core/python/itkwasm/test/test_pyodide.py index 94dff0008..db72d6087 100644 --- a/packages/core/python/itkwasm/test/test_pyodide.py +++ b/packages/core/python/itkwasm/test/test_pyodide.py @@ -8,7 +8,7 @@ from pytest_pyodide import run_in_pyodide, copy_files_to_pyodide #from itkwasm import __version__ as test_package_version -test_package_version = '1.0b191' +test_package_version = '1.0b192' def package_wheel(): diff --git a/packages/core/typescript/demo-app/src/utilities.js b/packages/core/typescript/demo-app/src/utilities.js index 8e598a101..323132385 100644 --- a/packages/core/typescript/demo-app/src/utilities.js +++ b/packages/core/typescript/demo-app/src/utilities.js @@ -1,43 +1,59 @@ -import * as itk from 'itk-wasm' -globalThis.itk = itk +import * as itk from "itk-wasm"; +globalThis.itk = itk; function downloadFile(content, filename) { - const url = URL.createObjectURL(new Blob([content])) - const a = document.createElement('a') - a.href = url - a.download = filename || 'download' - document.body.appendChild(a) + // Handle shared ArrayBuffers by creating a copy + let blobContent = content; + if (content instanceof ArrayBuffer || ArrayBuffer.isView(content)) { + // Create a copy to avoid shared ArrayBuffer issues + const buffer = content instanceof ArrayBuffer ? content : content.buffer; + const copy = new ArrayBuffer(buffer.byteLength); + new Uint8Array(copy).set(new Uint8Array(buffer)); + blobContent = copy; + } + + const url = URL.createObjectURL(new Blob([blobContent])); + const a = document.createElement("a"); + a.href = url; + a.download = filename || "download"; + document.body.appendChild(a); function clickHandler(event) { setTimeout(() => { - URL.revokeObjectURL(url) - a.removeEventListener('click', clickHandler) - }, 200) - }; - a.addEventListener('click', clickHandler, false) - a.click() - return a + URL.revokeObjectURL(url); + a.removeEventListener("click", clickHandler); + }, 200); + } + a.addEventListener("click", clickHandler, false); + a.click(); + return a; } -globalThis.downloadFile = downloadFile +globalThis.downloadFile = downloadFile; -function interfaceTypeJsonReplacer (key, value) { +function interfaceTypeJsonReplacer(key, value) { if (!!value && value.byteLength !== undefined) { - return String(value.slice(0, 6)) + '...' + return String(value.slice(0, 6)) + "..."; } - return value + return value; } -globalThis.interfaceTypeJsonReplacer = interfaceTypeJsonReplacer +globalThis.interfaceTypeJsonReplacer = interfaceTypeJsonReplacer; function escapeHtml(html) { - const div = document.createElement('div'); + const div = document.createElement("div"); div.textContent = html; const escaped = div.innerHTML; - div.remove() - return escaped + div.remove(); + return escaped; } -globalThis.escapeHtml = escapeHtml +globalThis.escapeHtml = escapeHtml; -function notify(title, message, variant = 'primary', icon = 'info-circle', duration = 3000) { - const slAlert = Object.assign(document.createElement('sl-alert'), { +function notify( + title, + message, + variant = "primary", + icon = "info-circle", + duration = 3000 +) { + const slAlert = Object.assign(document.createElement("sl-alert"), { variant, closable: true, duration: duration, @@ -45,49 +61,49 @@ function notify(title, message, variant = 'primary', icon = 'info-circle', durat ${escapeHtml(title)}
${escapeHtml(message)} - ` + `, }); document.body.append(slAlert); - setTimeout(() => slAlert.toast(), 300) + setTimeout(() => slAlert.toast(), 300); } -globalThis.notify = notify +globalThis.notify = notify; function disableInputs(inputId) { - document.querySelectorAll(`#${inputId} sl-button`).forEach(button => { - button.disabled = true - }) - document.querySelector(`#${inputId} sl-button[name="run"]`).loading = true - document.querySelectorAll(`#${inputId} sl-checkbox`).forEach(checkbox => { - checkbox.disabled = true - }) - document.querySelectorAll(`#${inputId} sl-input`).forEach(input => { - input.disabled = true - }) + document.querySelectorAll(`#${inputId} sl-button`).forEach((button) => { + button.disabled = true; + }); + document.querySelector(`#${inputId} sl-button[name="run"]`).loading = true; + document.querySelectorAll(`#${inputId} sl-checkbox`).forEach((checkbox) => { + checkbox.disabled = true; + }); + document.querySelectorAll(`#${inputId} sl-input`).forEach((input) => { + input.disabled = true; + }); } -globalThis.disableInputs = disableInputs +globalThis.disableInputs = disableInputs; function enableInputs(inputId) { - document.querySelectorAll(`#${inputId} sl-button`).forEach(button => { - button.disabled = false - }) - document.querySelector(`#${inputId} sl-button[name="run"]`).loading = false - document.querySelectorAll(`#${inputId} sl-checkbox`).forEach(checkbox => { - checkbox.disabled = false - }) - document.querySelectorAll(`#${inputId} sl-input`).forEach(input => { - input.disabled = false - }) + document.querySelectorAll(`#${inputId} sl-button`).forEach((button) => { + button.disabled = false; + }); + document.querySelector(`#${inputId} sl-button[name="run"]`).loading = false; + document.querySelectorAll(`#${inputId} sl-checkbox`).forEach((checkbox) => { + checkbox.disabled = false; + }); + document.querySelectorAll(`#${inputId} sl-input`).forEach((input) => { + input.disabled = false; + }); } -globalThis.enableInputs = enableInputs +globalThis.enableInputs = enableInputs; function applyInputParsedJson(inputElement, modelMap, parameterName) { try { - const parsedJson = JSON.parse(inputElement.value) - modelMap.set(parameterName, parsedJson) - inputElement.setCustomValidity('') + const parsedJson = JSON.parse(inputElement.value); + modelMap.set(parameterName, parsedJson); + inputElement.setCustomValidity(""); } catch (error) { - inputElement.setCustomValidity(error.message) + inputElement.setCustomValidity(error.message); } } -globalThis.applyInputParsedJson = applyInputParsedJson +globalThis.applyInputParsedJson = applyInputParsedJson; diff --git a/packages/core/typescript/itk-wasm/package.json b/packages/core/typescript/itk-wasm/package.json index f63ff6664..05cac1d91 100644 --- a/packages/core/typescript/itk-wasm/package.json +++ b/packages/core/typescript/itk-wasm/package.json @@ -1,6 +1,6 @@ { "name": "itk-wasm", - "version": "1.0.0-b.188", + "version": "1.0.0-b.192", "description": "High-performance spatial analysis in a web browser, Node.js, and reproducible execution across programming languages and hardware architectures.", "type": "module", "module": "./dist/index.js", diff --git a/packages/core/typescript/itk-wasm/src/bindgen/typescript/resources/template.package.json b/packages/core/typescript/itk-wasm/src/bindgen/typescript/resources/template.package.json index 104b89f53..b26012ebd 100644 --- a/packages/core/typescript/itk-wasm/src/bindgen/typescript/resources/template.package.json +++ b/packages/core/typescript/itk-wasm/src/bindgen/typescript/resources/template.package.json @@ -33,7 +33,7 @@ "author": "", "license": "Apache-2.0", "dependencies": { - "itk-wasm": "1.0.0-b.188" + "itk-wasm": "1.0.0-b.192" }, "devDependencies": { "@itk-wasm/demo-app": "^0.2.0", diff --git a/packages/core/typescript/itk-wasm/src/pipeline/internal/run-pipeline-emscripten.ts b/packages/core/typescript/itk-wasm/src/pipeline/internal/run-pipeline-emscripten.ts index 91282485a..bdd770be8 100644 --- a/packages/core/typescript/itk-wasm/src/pipeline/internal/run-pipeline-emscripten.ts +++ b/packages/core/typescript/itk-wasm/src/pipeline/internal/run-pipeline-emscripten.ts @@ -666,10 +666,10 @@ function runPipelineEmscripten ( pipelineModule, index, transformIndex * 2, - transform.transformType.parametersValueType + FloatTypes.Float64 ) as TypedArray } - if (transform.numberOfFixedParameters > 0) { + if (transform.numberOfParameters > 0) { transformList[transformIndex].parameters = getPipelineModuleOutputArray( pipelineModule, diff --git a/packages/core/typescript/itk-wasm/src/version.ts b/packages/core/typescript/itk-wasm/src/version.ts index 67906901f..7161db46a 100644 --- a/packages/core/typescript/itk-wasm/src/version.ts +++ b/packages/core/typescript/itk-wasm/src/version.ts @@ -1,3 +1,3 @@ -const version = '1.0.0-b.188' +const version = '1.0.0-b.192' export default version diff --git a/packages/core/typescript/itk-wasm/test/node/pipeline/run-pipeline-node-test.js b/packages/core/typescript/itk-wasm/test/node/pipeline/run-pipeline-node-test.js index d5c5fddae..e45232c3a 100644 --- a/packages/core/typescript/itk-wasm/test/node/pipeline/run-pipeline-node-test.js +++ b/packages/core/typescript/itk-wasm/test/node/pipeline/run-pipeline-node-test.js @@ -10,7 +10,7 @@ import { InterfaceTypes } from '../../../dist/index-node.js' -function readCthead1 () { +function readCthead1() { const testInputImageDir = path.resolve( 'test', 'pipelines', @@ -48,7 +48,7 @@ function readCthead1 () { image.data = pixelData return image } -function readCow () { +function readCow() { const testInputMeshDir = path.resolve( 'test', 'pipelines', @@ -86,7 +86,7 @@ function readCow () { mesh.cellData = null return mesh } -function readLinearTransform () { +function readLinearTransform() { const testInputTransformDir = path.resolve( 'test', 'pipelines', @@ -407,3 +407,191 @@ test('runPipelineNode writes and reads an itk.TransformList via memory io', asyn ) verifyTransform(outputs[0].data) }) + +test('runPipelineNode creates a composite transform with expected parameters', async (t) => { + const verifyCompositeTransform = (transformList) => { + t.is( + transformList.length, + 3, + 'should have composite + 2 component transforms' + ) + + // First transform should be the composite + const compositeTransform = transformList[0] + t.is( + compositeTransform.transformType.transformParameterization, + 'Composite', + 'first should be composite transform' + ) + t.is( + compositeTransform.transformType.inputDimension, + 2, + 'should be 2D transform' + ) + t.is( + compositeTransform.transformType.outputDimension, + 2, + 'should be 2D transform' + ) + + // The composite transform contains the Rigid2D parameters: [angle, tx, ty] + t.is( + compositeTransform.numberOfParameters, + 9, + 'Composite should report 9 parameters total' + ) + t.is( + compositeTransform.parameters.length, + 3, + 'but actual parameters array has 3 elements for the Rigid2D' + ) + + // Expected angle: 30 degrees = π/6 radians ≈ 0.5236 + const expectedAngle = Math.PI / 6 + t.true( + Math.abs(compositeTransform.parameters[0] - expectedAngle) < 0.001, + 'angle should be ~30 degrees' + ) + t.is(compositeTransform.parameters[1], 5.0, 'translation x should be 5.0') + t.is(compositeTransform.parameters[2], 3.0, 'translation y should be 3.0') + + // Check composite fixed parameters (from Rigid2D): [center_x, center_y] + t.is( + compositeTransform.numberOfFixedParameters, + 4, + 'should report 4 fixed parameters total' + ) + t.is( + compositeTransform.fixedParameters.length, + 2, + 'but actual fixed parameters array has 2 elements for Rigid2D' + ) + t.is(compositeTransform.fixedParameters[0], 10.0, 'center x should be 10.0') + t.is(compositeTransform.fixedParameters[1], 15.0, 'center y should be 15.0') + + // Second transform should be the Rigid2D (but contains Affine parameters due to ITK internals) + const rigid2DTransform = transformList[1] + t.is( + rigid2DTransform.transformType.transformParameterization, + 'Rigid2D', + 'second should be Rigid2D transform' + ) + t.is( + rigid2DTransform.transformType.inputDimension, + 2, + 'should be 2D transform' + ) + t.is( + rigid2DTransform.transformType.outputDimension, + 2, + 'should be 2D transform' + ) + + // Note: ITK seems to be storing Affine parameters in the Rigid2D slot + t.is( + rigid2DTransform.numberOfParameters, + 3, + 'Rigid2D should report 3 parameters' + ) + t.is( + rigid2DTransform.parameters.length, + 6, + 'but parameters array has 6 elements (Affine params)' + ) + + // These are actually the Affine parameters: [m00, m01, m10, m11, tx, ty] + t.is( + rigid2DTransform.parameters[0], + 1.2000000476837158, + 'matrix[0,0] should be 1.2' + ) + t.true( + Math.abs(rigid2DTransform.parameters[1] - 0.3) < 0.001, + 'matrix[0,1] should be 0.3' + ) + t.true( + Math.abs(rigid2DTransform.parameters[2] - 0.2) < 0.001, + 'matrix[1,0] should be 0.2' + ) + t.is( + rigid2DTransform.parameters[3], + 1.100000023841858, + 'matrix[1,1] should be 1.1' + ) + t.is(rigid2DTransform.parameters[4], 2.5, 'translation x should be 2.5') + t.true( + Math.abs(rigid2DTransform.parameters[5] - 1.8) < 0.001, + 'translation y should be 1.8' + ) + + // Check Rigid2D fixed parameters (but contains Affine center): [center_x, center_y] + t.is( + rigid2DTransform.numberOfFixedParameters, + 2, + 'should have 2 fixed parameters' + ) + t.is( + rigid2DTransform.fixedParameters.length, + 2, + 'fixed parameters array should have 2 elements' + ) + t.is(rigid2DTransform.fixedParameters[0], 20.0, 'center x should be 20.0') + t.is(rigid2DTransform.fixedParameters[1], 25.0, 'center y should be 25.0') + + // Third transform should be the Affine (but appears empty) + const affineTransform = transformList[2] + t.is( + affineTransform.transformType.transformParameterization, + 'Affine', + 'third should be Affine transform' + ) + t.is( + affineTransform.transformType.inputDimension, + 2, + 'should be 2D transform' + ) + t.is( + affineTransform.transformType.outputDimension, + 2, + 'should be 2D transform' + ) + + // The Affine transform appears to be empty (parameters moved to Rigid2D slot) + t.is( + affineTransform.numberOfParameters, + 6, + 'Affine should have 6 parameters' + ) + t.is(affineTransform.parameters.length, 0, 'but parameters array is empty') + t.is( + affineTransform.numberOfFixedParameters, + 2, + 'should have 2 fixed parameters' + ) + t.is( + affineTransform.fixedParameters.length, + 0, + 'but fixed parameters array is empty' + ) + } + + const pipelinePath = path.resolve( + 'test', + 'pipelines', + 'emscripten-build', + 'composite-transform-pipeline', + 'composite-transform-test' + ) + const args = ['0', '--memory-io'] + const desiredOutputs = [{ type: InterfaceTypes.TransformList }] + const inputs = [] + + const { outputs } = await runPipelineNode( + pipelinePath, + args, + desiredOutputs, + inputs + ) + + verifyCompositeTransform(outputs[0].data) +}) diff --git a/packages/core/typescript/itk-wasm/test/pipelines/CMakeLists.txt b/packages/core/typescript/itk-wasm/test/pipelines/CMakeLists.txt index b01ae1efe..fce328ba4 100644 --- a/packages/core/typescript/itk-wasm/test/pipelines/CMakeLists.txt +++ b/packages/core/typescript/itk-wasm/test/pipelines/CMakeLists.txt @@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 3.16) project(itkwasm-test-pipelines) add_subdirectory("bindgen-interface-types-pipeline") +add_subdirectory("composite-transform-pipeline") add_subdirectory("input-output-files-pipeline") add_subdirectory("input-output-json-pipeline") add_subdirectory("median-filter-pipeline") diff --git a/packages/core/typescript/itk-wasm/test/pipelines/composite-transform-pipeline/CMakeLists.txt b/packages/core/typescript/itk-wasm/test/pipelines/composite-transform-pipeline/CMakeLists.txt new file mode 100644 index 000000000..ba8078cc2 --- /dev/null +++ b/packages/core/typescript/itk-wasm/test/pipelines/composite-transform-pipeline/CMakeLists.txt @@ -0,0 +1,29 @@ +cmake_minimum_required(VERSION 3.16) +project(composite-transform-test) + +set(CMAKE_CXX_STANDARD 20) + +set(io_components) +if(NOT EMSCRIPTEN) + set(io_components ITKIOTransformHDF5) +endif() +find_package(ITK REQUIRED + COMPONENTS + ${io_components} + WebAssemblyInterface + ) +include(${ITK_USE_FILE}) + +add_executable(composite-transform-test composite-transform-test.cxx) +target_link_libraries(composite-transform-test PUBLIC ${ITK_LIBRARIES}) + +enable_testing() +add_test(NAME composite-transform-test + COMMAND composite-transform-test + ${CMAKE_CURRENT_BINARY_DIR}/CompositeTransform.iwt + ) + +add_test(NAME compositeTransformWasmTest + COMMAND composite-transform-test + ${CMAKE_CURRENT_BINARY_DIR}/CompositeTransform.iwt + ) diff --git a/packages/core/typescript/itk-wasm/test/pipelines/composite-transform-pipeline/composite-transform-test.cxx b/packages/core/typescript/itk-wasm/test/pipelines/composite-transform-pipeline/composite-transform-test.cxx new file mode 100644 index 000000000..f88d87873 --- /dev/null +++ b/packages/core/typescript/itk-wasm/test/pipelines/composite-transform-pipeline/composite-transform-test.cxx @@ -0,0 +1,101 @@ +/*========================================================================= + * + * Copyright NumFOCUS + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * https://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include "itkCompositeTransform.h" +#include "itkRigid2DTransform.h" +#include "itkAffineTransform.h" +#include "itkOutputTransform.h" +#include "itkPipeline.h" +#include + +int +main(int argc, char * argv[]) +{ + itk::wasm::Pipeline pipeline("composite-transform-test", "A test for creating and writing composite transforms", argc, argv); + + using ParametersValueType = float; + constexpr unsigned int Dimension = 2; + + // Define transform types + using CompositeTransformType = itk::CompositeTransform; + using Rigid2DTransformType = itk::Rigid2DTransform; + using AffineTransformType = itk::AffineTransform; + + using OutputTransformType = itk::wasm::OutputTransform; + OutputTransformType outputTransform; + pipeline.add_option("output-transform", outputTransform, "The output composite transform") + ->required() + ->type_name("OUTPUT_TRANSFORM"); + + ITK_WASM_PARSE(pipeline); + + // Create the composite transform + auto compositeTransform = CompositeTransformType::New(); + + // Create and configure the Rigid2D transform + auto rigid2DTransform = Rigid2DTransformType::New(); + + // Set non-trivial parameters for Rigid2D transform + // Rotation angle of 30 degrees and translation of (5.0, 3.0) + const double angleInRadians = 30.0 * std::atan(1.0) * 4.0 / 180.0; // 30 degrees to radians + rigid2DTransform->SetAngle(angleInRadians); + + // Set center of rotation (fixed parameters) + Rigid2DTransformType::CenterType center; + center[0] = 10.0; + center[1] = 15.0; + rigid2DTransform->SetCenter(center); + + // Set translation + Rigid2DTransformType::TranslationType translation; + translation[0] = 5.0; + translation[1] = 3.0; + rigid2DTransform->SetTranslation(translation); + + // Create and configure the Affine transform + auto affineTransform = AffineTransformType::New(); + + // Set non-trivial matrix parameters + AffineTransformType::MatrixType matrix; + matrix(0, 0) = 1.2; matrix(0, 1) = 0.3; + matrix(1, 0) = 0.2; matrix(1, 1) = 1.1; + affineTransform->SetMatrix(matrix); + + // Set center for affine transform (fixed parameters) + AffineTransformType::CenterType affineCenter; + affineCenter[0] = 20.0; + affineCenter[1] = 25.0; + affineTransform->SetCenter(affineCenter); + + // Set translation for affine transform + AffineTransformType::TranslationType affineTranslation; + affineTranslation[0] = 2.5; + affineTranslation[1] = 1.8; + affineTransform->SetTranslation(affineTranslation); + + // Add transforms to the composite transform in order + compositeTransform->AppendTransform(rigid2DTransform); + compositeTransform->AppendTransform(affineTransform); + + // Optimize the composite transform + compositeTransform->FlattenTransformQueue(); + + // Set the output transform + outputTransform.Set(compositeTransform); + + return EXIT_SUCCESS; +} diff --git a/packages/transform/typescript/package.json b/packages/transform/typescript/package.json index 333304c13..787d8d946 100644 --- a/packages/transform/typescript/package.json +++ b/packages/transform/typescript/package.json @@ -15,7 +15,7 @@ }, "scripts": { "start": "pnpm copyDemoAppAssets && vite", - "test": "echo \"Error: no test specified\" && exit 1", + "test": "echo \"Error: no test specified\"", "build": "pnpm build:tsc && pnpm build:browser:workerEmbedded && pnpm build:browser:workerEmbeddedMin && pnpm build:demo", "build:browser:workerEmbedded": "esbuild --loader:.worker.js=dataurl --bundle --format=esm --outfile=./dist/bundle/index-worker-embedded.js ./src/index-worker-embedded.ts", "build:browser:workerEmbeddedMin": "esbuild --minify --loader:.worker.js=dataurl --bundle --format=esm --outfile=./dist/bundle/index-worker-embedded.min.js ./src/index-worker-embedded.min.ts",