itk-vtk-viewer-imagej.imjoy.html

<config lang="json">
{
  "name": "ITK-VTK-Viewer",
  "type": "web-worker",
  "tags": [],
  "ui": "",
  "version": "0.1.2",
  "cover": "",
  "description": "This Plugin uses itk-vtk-viewer to visualize images in ImageJ.JS",
  "icon": "extension",
  "inputs": null,
  "outputs": null,
  "api_version": "0.1.8",
  "env": "",
  "permissions": [],
  "requirements": [],
  "dependencies": []
}
</config>

<script lang="javascript">
const PixelTypes = {
  Unknown: 0,
  Scalar: 1,
  RGB: 2,
  RGBA: 3,
  Offset: 4,
  Vector: 5,
  Point: 6,
  CovariantVector: 7,
  SymmetricSecondRankTensor: 8,
  DiffusionTensor3D: 9,
  Complex: 10,
  FixedArray: 11,
  Array: 12,
  Matrix: 13,
  VariableLengthVector: 14,
  VariableSizeMatrix: 15,
}
const numpy2itkType = {
  int8: {
    componentType: 'int8_t',
    arrayType: Int8Array,
  },
  uint8: {
    componentType: 'uint8_t',
    arrayType: Uint8Array,
  },
  int16: {
    componentType: 'int16_t',
    arrayType: Int16Array,
  },
  uint16: {
    componentType: 'uint16_t',
    arrayType: Uint16Array,
  },
  int32: {
    componentType: 'int32_t',
    arrayType: Int32Array,
  },
  uint32: {
    componentType: 'uint32_t',
    arrayType: Uint32Array,
  },
  float32: {
    componentType: 'float',
    arrayType: Float32Array,
  },
  float64: {
    componentType: 'double',
    arrayType: Float64Array,
  },
}

function ndarrayToItkImage(array) {
  if (array._rtype !== 'ndarray') {
    throw new Error('Invalid ndarray type: ' + array._rtype)
  }

  const { componentType, arrayType } = numpy2itkType[array._rdtype]
  if (
    array._rshape.length === 2 ||
    (array._rshape.length == 3 && array._rshape[2] <= 4)
  ) {
  
    const channels = array._rshape.length === 3 ? array._rshape[2] : 1
    let pixelType
    if(channels === 1)
        pixelType = PixelTypes.Scalar
    else if(channels === 3)
        pixelType = PixelTypes.RGB
    else if(channels === 4)
        pixelType = PixelTypes.RGBA
    else
        pixelType = PixelTypes.VariableLengthVector
    return {
      imageType: {
        dimension: 2,
        pixelType,
        componentType,
        components: channels,
      },
      name: 'Image',
      origin: [0.0, 0.0],
      spacing: [1.0, 1.0],
      direction: {
        data: [1.0, 0.0, 0.0, 1.0],
      },
      size: [array._rshape[1], array._rshape[0]],
      data: new arrayType(array._rvalue),
    }
  } else if (array._rshape.length === 3) {
    return {
      imageType: {
        dimension: 3,
        pixelType: PixelTypes.Scalar,
        componentType,
        components: 1,
      },
      name: 'Image',
      origin: [0.0, 0.0, 0.0],
      spacing: [1.0, 1.0, 1.0],
      direction: {
        data: [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0],
      },
      size: [array._rshape[2], array._rshape[1], array._rshape[0]],
      data: new arrayType(array._rvalue),
    }
  } else if (array._rshape.length === 4) {
    const channels = array._rshape[3]
    let pixelType
    if(channels === 1)
        pixelType = PixelTypes.Scalar
    else if(channels === 3)
        pixelType = PixelTypes.RGB
    else if(channels === 4)
        pixelType = PixelTypes.RGBA
    else
        pixelType = PixelTypes.VariableLengthVector
    return {
      imageType: {
        dimension: 3,
        pixelType,
        componentType,
        components: array._rshape[3],
      },
      name: 'Image',
      origin: [0.0, 0.0, 0.0],
      spacing: [1.0, 1.0, 1.0],
      direction: {
        data: [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0],
      },
      size: [array._rshape[2], array._rshape[1], array._rshape[0]],
      data: new arrayType(array._rvalue),
    }
  } else {
    throw new Error(`Unsupported shape: ${array._rshape}`)
  }
}
class ImJoyPlugin {
  async setup() {
    const ij = await api.getWindow('ImageJ.JS')
    await ij.addMenuItem({"label": "ITK/VTK Viewer (3D)", "callback": this.showInViewer})
  }
  
  async showInViewer(img){
    if(!img){
      const ij = await api.getWindow('ImageJ.JS')
      img = await ij.getImage({format: 'ndarray', all: true})
    }
    img = ndarrayToItkImage(img)
    const viewer = await api.createWindow({src: "https://unpkg.com/[email protected]/dist/index.html", name: "ITK/VTK Viewer", h: 15})
    await viewer.setImage(img)
    await viewer.setUICollapsed(true)
  }

  async run(ctx) {
    const img = ctx && ctx.data && ctx.data.image;
    if(img)
      await this.showInViewer(img);
    else
      await api.createWindow({src: "https://unpkg.com/[email protected]/dist/index.html", name: "ITK/VTK Viewer", h: 15})
  }
}

api.export(new ImJoyPlugin())
</script>