VolumeOverlay

VolumeOverlay is a display that shows an input series with volume data overlaied on it. This is typically used by plug-ins that perform volumetry and segmentation.

Example

Synopsis

displayStrategy

[
  {
    "type": "VolumeOverlay",
    "options": {
      "colorMap": {
        "S1": "#ff000088",
        "S2": "#00ff0088"
      }
    }
  }
]

Data Preparation

The plug-in results (results.json) must contain an array data containing the volume information in the following format:

Array<{
  volumeId?: number;
  name: string;
  origin: [number, number, number];
  size: [number, number, number];
  rawFile?: string;
}>;

• volumeId: (default: 0) The volume ID which this overlaid volume corresponds to.
• name: Required The name of this volume (e.g., "spleen", "left-upper-lobe")
• origin: Required Where to overlay the volume.
• size: Required The size of the volume in pixels.
• rawFile: (default: ${name}.raw.gz) The file name of the overlaid voxel data.

For example:

{
  "results": {
    "volumes": [
      { "name": "S1", "origin": [120, 35, 80], "size": [233, 152, 25] },
      { "name": "S2", "origin": [145, 40, 93], "size": [180, 93, 19] }
    ]
  }
}

Your array should usually be located at results.volumes, but this can be configured via the dataPath option. This is useful when you want to display two different series of volumes in one screen.

Raw Voxel Data

In addition to the text/numerical data output to results.json, the plug-in must output the voxel data itself as a gzipped 1 bit/voxel RAW file. In the case of the example above, you must prepare a RAW file called S1.raw.gz, which is a gzip-compressed binary data that will be 42000 (Math.ceil(120 * 35 * 80 / 8)) bytes when decompressed. The first bit corresponds to the voxel at (0, 0, 0), and the next bit, (0, 0, 1), and so on.

📂/circus/
    📂out/
        results.json
        S1.raw.gz
        S2.raw.gz

Options

interface VolumeOverlayOptions {
  volumeId?: number;
  dataPath?: string;
  colorMap?: { [key: string]: ColorDefinition };
  defaultColor?: ColorDefinition;
  only?: string[];
}

• volumeId: (default: 0) The ID of the base volume to display.
• dataPath: (default: "results.volumes") Changes where to read the volume data from.
• colorMap: (default: {}) Colors of the overlaid volumes. The keys are the names of the volumes defined in the results file.
• defalutColor: (default: 'ffff0088') The fallback color used when there is no matching key in colorMap.
• only: (default: undefined) If an array of names is set, only shows the volumes with the names specified here.