feat(registration): example (poc)

packages/core/examples/registration/RegistrationConsole.ts

@@ -0,0 +1,106 @@
+import * as hdf5 from 'jsfive';
+import { getFormatedDateTime } from './utils';
+
+class RegistrationConsole {
+  private _consoleRoot: HTMLElement;
+  private _logRoot: HTMLDivElement;
+
+  constructor(container) {
+    const { consoleRoot, logRoot } =
+      RegistrationConsole.createLogWindow(container);
+
+    this._consoleRoot = consoleRoot;
+    this._logRoot = logRoot;
+  }
+
+  private static createLogWindow(container) {
+    const statusFieldset = document.createElement('fieldset');
+    const statusFieldsetLegent = document.createElement('legend');
+    const logRoot = document.createElement('div');
+
+    Object.assign(statusFieldset.style, {
+      fontSize: '12px',
+      height: '200px',
+      overflow: 'scroll',
+    });
+
+    statusFieldsetLegent.innerText = 'Processing logs';
+    logRoot.style.fontFamily = 'monospace';
+
+    statusFieldset.appendChild(statusFieldsetLegent);
+    statusFieldset.appendChild(logRoot);
+    container.appendChild(statusFieldset);
+
+    return {
+      consoleRoot: statusFieldset,
+      logRoot,
+    };
+  }
+
+  public log(text, preFormated = false) {
+    const { _consoleRoot: consoleRoot, _logRoot: logRoot } = this;
+    const node = document.createElement(preFormated ? 'pre' : 'p');
+
+    node.innerHTML = `${getFormatedDateTime()} ${text}`;
+    node.style.margin = '0';
+    node.style.fontSize = '10px';
+    logRoot.appendChild(node);
+
+    // Scroll to the end
+    consoleRoot.scrollBy(0, consoleRoot.scrollHeight - consoleRoot.scrollTop);
+  }
+
+  public clear() {
+    const { _logRoot: logRoot } = this;
+    while (logRoot.hasChildNodes()) {
+      logRoot.removeChild(logRoot.firstChild);
+    }
+  }
+
+  /**
+   * Log all image information
+   */
+  public logImageInfo(image) {
+    this.log(`image "${image.name}"`);
+    this.log(`    origin: ${image.origin.join(', ')}`, true);
+    this.log(`    spacing: ${image.spacing.join(', ')}`, true);
+    this.log(`    direction: ${image.direction.join(', ')}`, true);
+    this.log(`    size: ${image.size.join(', ')}`, true);
+    this.log(`    imageType:`, true);
+    this.log(`        dimension: ${image.imageType.dimension}`, true);
+    this.log(`        components: ${image.imageType.components}`, true);
+    this.log(`        componentType: ${image.imageType.componentType}`, true);
+    this.log(`        pixelType: ${image.imageType.pixelType}`, true);
+  }
+
+  /**
+   * Log HDF5 transform and make it available for download
+   */
+  public logTransform(transform) {
+    let buffer = transform.data.buffer;
+
+    // Convert SharedArrayBuffer into ArrayBuffer
+    if (buffer instanceof SharedArrayBuffer) {
+      buffer = new Uint8ClampedArray(buffer).slice().buffer;
+    }
+
+    const fileName = transform.path;
+    const hdfFile = new hdf5.File(buffer, transform.path);
+    const transformBlob = new Blob([buffer], { type: 'application/x-hdf5' });
+    const url = URL.createObjectURL(transformBlob);
+
+    this.log(
+      `Download <a href="${url}" download="${fileName}">${fileName}</a>`
+    );
+
+    console.log('Transform (HDF5):', hdfFile);
+  }
+
+  destroy() {
+    this._consoleRoot.remove();
+    this._consoleRoot = null;
+    this._logRoot = null;
+  }
+}
+
+export { RegistrationConsole as default, RegistrationConsole };

packages/core/examples/registration/elastixParametersSettings.ts

@@ -0,0 +1,196 @@
+const defaultNumberOfResolutions = 2;
+const defaultFinalGridSpacing = 8;
+
+const parametersSettings = {
+  NumberOfResolutions: {
+    inputType: 'number',
+    defaultValue: defaultNumberOfResolutions,
+  },
+  MaximumNumberOfIterations: {
+    inputType: 'number',
+    defaultValue: 256,
+  },
+  Registration: {
+    inputType: 'dropdown',
+    values: [
+      'MultiResolutionRegistration',
+      'MultiResolutionRegistrationWithFeatures',
+      'MultiMetricMultiResolutionRegistration',
+    ],
+  },
+  Metric: {
+    inputType: 'dropdown',
+    values: [
+      'AdvancedKappaStatistic',
+      'AdvancedMattesMutualInformation',
+      'AdvancedMeanSquares',
+      'AdvancedNormalizedCorrelation',
+      'CorrespondingPointsEuclideanDistanceMetric',
+      'DisplacementMagnitudePenalty',
+      'DistancePreservingRigidityPenalty',
+      'GradientDifference',
+      'KNNGraphAlphaMutualInformation',
+      'MissingStructurePenalty',
+      'NormalizedGradientCorrelation',
+      'NormalizedMutualInformation',
+      'PCAMetric',
+      'PCAMetric2',
+      'PatternIntensity',
+      'PolydataDummyPenalty',
+      'StatisticalShapePenalty',
+      'SumOfPairwiseCorrelationCoefficientsMetric',
+      'SumSquaredTissueVolumeDifference',
+      'TransformBendingEnergyPenalty',
+      'TransformRigidityPenalty',
+      'VarianceOverLastDimensionMetric',
+    ],
+  },
+  Interpolator: {
+    inputType: 'dropdown',
+    values: [
+      'BSplineInterpolator',
+      'BSplineInterpolatorFloat',
+      'LinearInterpolator',
+      'NearestNeighborInterpolator',
+      'RayCastInterpolator',
+      'ReducedDimensionBSplineInterpolator',
+    ],
+  },
+  FixedImagePyramid: {
+    inputType: 'dropdown',
+    values: [
+      'FixedGenericImagePyramid',
+      'FixedRecursiveImagePyramid',
+      'FixedSmoothingImagePyramid',
+      'FixedShrinkingImagePyramid',
+      'OpenCLFixedGenericImagePyramid',
+    ],
+  },
+  MovingImagePyramid: {
+    inputType: 'dropdown',
+    values: [
+      'MovingGenericImagePyramid',
+      'MovingRecursiveImagePyramid',
+      'MovingShrinkingImagePyramid',
+      'MovingSmoothingImagePyramid',
+      'OpenCLMovingGenericImagePyramid',
+    ],
+  },
+  Optimizer: {
+    inputType: 'dropdown',
+    values: [
+      'AdaGrad',
+      'AdaptiveStochasticGradientDescent',
+      'AdaptiveStochasticLBFGS',
+      'AdaptiveStochasticVarianceReducedGradient',
+      'CMAEvolutionStrategy',
+      'ConjugateGradient',
+      'ConjugateGradientFRPR',
+      'FiniteDifferenceGradientDescent',
+      'FullSearch',
+      'Powell',
+      'PreconditionedGradientDescent',
+      'PreconditionedStochasticGradientDescent',
+      'QuasiNewtonLBFGS',
+      'RSGDEachParameterApart',
+      'RegularStepGradientDescent',
+      'Simplex',
+      'SimultaneousPerturbation',
+      'StandardGradientDescent',
+    ],
+  },
+  Resampler: {
+    inputType: 'dropdown',
+    values: ['DefaultResampler', 'OpenCLResampler'],
+  },
+  ResampleInterpolator: {
+    inputType: 'dropdown',
+    values: [
+      'FinalBSplineInterpolator',
+      'FinalBSplineInterpolatorFloat',
+      'FinalLinearInterpolator',
+      'FinalNearestNeighborInterpolator',
+      'FinalReducedDimensionBSplineInterpolator',
+      'FinalRayCastInterpolator',
+    ],
+  },
+  FinalBSplineInterpolationOrder: {
+    inputType: 'number',
+  },
+  ImageSampler: {
+    inputType: 'dropdown',
+    values: [
+      'Random',
+      'RandomCoordinate',
+      'Full',
+      'Grid',
+      'MultiInputRandomCoordinate',
+      'RandomSparseMask',
+    ],
+  },
+  NumberOfSpatialSamples: {
+    inputType: 'number',
+    defaultValue: 2048,
+  },
+  CheckNumberOfSamples: {
+    inputType: 'dropdown',
+    values: ['true', 'false'],
+    defaultValue: 'true',
+  },
+  MaximumNumberOfSamplingAttempts: {
+    inputType: 'number',
+    defaultValue: 8,
+  },
+  NewSamplesEveryIteration: {
+    inputType: 'dropdown',
+    values: ['true', 'false'],
+    defaultValue: 'true',
+  },
+  NumberOfSamplesForExactGradient: {
+    inputType: 'number',
+    defaultValue: 4096,
+  },
+  DefaultPixelValue: {
+    inputType: 'number',
+    defaultValue: 0,
+  },
+  AutomaticParameterEstimation: {
+    inputType: 'dropdown',
+    values: ['true', 'false'],
+    defaultValue: 'true',
+  },
+  AutomaticScalesEstimation: {
+    inputType: 'dropdown',
+    values: ['true', 'false'],
+    defaultValue: 'true',
+  },
+  AutomaticTransformInitialization: {
+    inputType: 'dropdown',
+    values: ['true', 'false'],
+    defaultValue: 'true',
+  },
+  Metric0Weight: {
+    inputType: 'number',
+    defaultValue: '1.0',
+    step: 0.1,
+  },
+  Metric1Weight: {
+    inputType: 'number',
+    defaultValue: '1.0',
+    step: 0.1,
+  },
+  FinalGridSpacing: {
+    inputType: 'number',
+    defaultValue: defaultFinalGridSpacing,
+  },
+  // ResultImageFormat: {
+  //   inputType: 'dropdown',
+  //   values: ['mhd', 'nii', 'nrrd', 'vti'],
+  // },
+};
+
+export {
+  defaultNumberOfResolutions,
+  defaultFinalGridSpacing,
+  parametersSettings,
+};