208 structure info

[allemangD]

Adds structure to each control point in JSON output. This value is ignored during file loading, only used as metadata in consuming applications. Resolves #208. Note this change requires each Annotation instance hold a reference to the HomeLogic instance. Looking toward #196, it may make sense to introduce a "AtlasLogic" or similar which contains the volume node, color node, and related metadata for only one atlas. This metadata could then be serialized within Annotation.toDict.

Adds methods to HomeLogic

• getWorldRASToIJKTransform
• getAllenLabelIndex
• getAnnotation

Updates getCrosshairPixelString and getPixelString to use them.

Those methods, along with these attributes, could probably go in an AtlasLogic class:

• AllenStructurePaths
• AllenLayerStructurePaths
• AllenStructureNames
• SlicerToAllenMapping
• AllenToSlicerMapping

[allemangD]

Some sample JSON in the new format:

Note there's only one markup with three control points, and each point is in a different structure. Point 2 is outside the atlas, so its structure is null.

Such a case might not be "realistic" however it's important the file format is robust to such edge-cases.

{
  "version": "0.2.1+2022.03.04",
  "markups": [
    {
      "markup": {
        "type": "ClosedCurve",
        "coordinateSystem": "LPS",
        "controlPoints": [
          {
            "id": "1",
            "position": [
              -6897.8740234375,
              6575.0,
              -1308.8443603515625
            ],
            "orientation": [
              -1.0,
              -0.0,
              -0.0,
              -0.0,
              -1.0,
              -0.0,
              0.0,
              0.0,
              1.0
            ],
            "structure": {
              "id": 9,
              "acronym": "SSp-tr6a"
            }
          },
          {
            "id": "2",
            "position": [
              -5673.08349609375,
              6575.0,
              -607.249267578125
            ],
            "orientation": [
              -1.0,
              -0.0,
              -0.0,
              -0.0,
              -1.0,
              -0.0,
              0.0,
              0.0,
              1.0
            ],
            "structure": null
          },
          {
            "id": "3",
            "position": [
              -5143.537109375,
              6575.0,
              -2108.5126953125
            ],
            "orientation": [
              -1.0,
              -0.0,
              -0.0,
              -0.0,
              -1.0,
              -0.0,
              0.0,
              0.0,
              1.0
            ],
            "structure": {
              "id": 382,
              "acronym": "CA1"
            }
          }
        ]
      },
      "name": "Curve",
      "orientation": [
        1.0,
        0.0,
        0.0,
        5686.499999999999,
        0.0,
        0.0,
        1.0,
        -6574.999999999999,
        0.0,
        1.0,
        0.0,
        -3987.4999999999995,
        0.0,
        0.0,
        0.0,
        1.0
      ],
      "representationType": "spline",
      "thickness": 50
    }
  ],
  "currentId": 0,
  "referenceView": "Coronal",
  "ontology": "Structure",
  "stepSize": 24.999999999999996,
  "cameraPosition": [
    5873.272365267856,
    -50203.60366698136,
    -4026.6211672287745
  ],
  "cameraViewUp": [
    0.0,
    0.0,
    1.0
  ]
}

[wbwakeman]

This looks good to me. Thank you @allemangD !