@niivue/niivue 0.44.2 → 0.45.0

package/src/nvdocument.ts

@@ -96,6 +96,7 @@ export type NVConfigOptions = {
   multiplanarPadPixels: number
   // @deprecated
   multiplanarForceRender: boolean
+  multiplanarEqualSize: boolean
   multiplanarShowRender: SHOW_RENDER
   isRadiologicalConvention: boolean
   // string to allow infinity
@@ -177,6 +178,7 @@ export const DEFAULT_OPTIONS: NVConfigOptions = {
   multiplanarPadPixels: 0,
   // @deprecated
   multiplanarForceRender: false,
+  multiplanarEqualSize: false,
   multiplanarShowRender: SHOW_RENDER.AUTO, // auto is the same behaviour as multiplanarForceRender: false
   isRadiologicalConvention: false,
   meshThicknessOn2D: Infinity,
@@ -217,6 +219,7 @@ export const DEFAULT_OPTIONS: NVConfigOptions = {
 }
 
 type SceneData = {
+  gamma: number
   azimuth: number
   elevation: number
   crosshairPos: vec3
@@ -230,6 +233,7 @@ type SceneData = {
 }
 
 export const INITIAL_SCENE_DATA = {
+  gamma: 1.0,
   azimuth: 110,
   elevation: 10,
   crosshairPos: vec3.create(),
@@ -255,6 +259,7 @@ export type Scene = {
   pan2Dxyzmm: vec4
   _elevation?: number
   _azimuth?: number
+  gamma?: number
 }
 
 export type DocumentData = {
@@ -566,6 +571,12 @@ export class NVDocument {
     }
 
     data.labels = [...this.data.labels]
+
+    // remove any handlers
+    for (const label of data.labels) {
+      delete label.onClick
+    }
+
     data.customData = this.customData
 
     // volumes

package/src/nvimage/index.ts

@@ -1631,7 +1631,7 @@ export class NVImage {
             hdr.datatypeCode = NiiDataType.DT_FLOAT64
             break
           default:
-            throw new Error('Unsupported NRRD data type: ' + items[0])
+            throw new Error('Unsupported MHA data type: ' + items[0])
         }
       }
       if (line.startsWith('ObjectType') && !items[0].includes('Image')) {
@@ -1653,6 +1653,9 @@ export class NVImage {
       [mat33[2], mat33[5], mat33[8], offset[2]],
       [0, 0, 0, 1]
     ]
+    while (bytes[pos] === 10) {
+      pos++
+    }
     hdr.vox_offset = pos
     if (isDetached && pairedImgData) {
       if (isGz) {

package/src/nvlabel.ts

@@ -10,6 +10,29 @@ export enum LabelLineTerminator {
   RING = 'ring'
 }
 
+export enum LabelAnchorFlag {
+  NONE = 0,
+  LEFT = 1 << 0,
+  CENTER = 1 << 1,
+  RIGHT = 1 << 2,
+  TOP = 1 << 3,
+  MIDDLE = 1 << 4,
+  BOTTOM = 1 << 5
+}
+
+export enum LabelAnchorPoint {
+  NONE = LabelAnchorFlag.NONE,
+  TOPLEFT = LabelAnchorFlag.TOP | LabelAnchorFlag.LEFT,
+  TOPCENTER = LabelAnchorFlag.TOP | LabelAnchorFlag.CENTER,
+  TOPRIGHT = LabelAnchorFlag.TOP | LabelAnchorFlag.RIGHT,
+  MIDDLELEFT = LabelAnchorFlag.MIDDLE | LabelAnchorFlag.LEFT,
+  MIDDLECENTER = LabelAnchorFlag.MIDDLE | LabelAnchorFlag.CENTER,
+  MIDDLERIGHT = LabelAnchorFlag.MIDDLE | LabelAnchorFlag.RIGHT,
+  BOTTOMLEFT = LabelAnchorFlag.BOTTOM | LabelAnchorFlag.LEFT,
+  BOTTOMCENTER = LabelAnchorFlag.BOTTOM | LabelAnchorFlag.CENTER,
+  BOTTOMRIGHT = LabelAnchorFlag.BOTTOM | LabelAnchorFlag.RIGHT
+}
+
 /**
  * Class representing label style.
  * @ignore
@@ -65,15 +88,25 @@ export class NVLabel3D {
   text: string
   style: NVLabel3DStyle
   points?: number[] | number[][]
+  anchor: LabelAnchorPoint
+  onClick?: (label: NVLabel3D) => void
 
   /**
    * @param text - The text of the label
    * @param style - The style of the label
    * @param points - An array of points label for label lines
    */
-  constructor(text: string, style: NVLabel3DStyle, points?: number[] | number[][]) {
+  constructor(
+    text: string,
+    style: NVLabel3DStyle,
+    points?: number[] | number[][],
+    anchor?: LabelAnchorPoint,
+    onClick?: (label: NVLabel3D) => void
+  ) {
     this.text = text
     this.style = style
     this.points = points
+    this.anchor = anchor || LabelAnchorPoint.NONE
+    this.onClick = onClick
   }
 }

package/src/nvmesh-loaders.ts

@@ -709,6 +709,12 @@ export class NVMeshLoaders {
     while (lines[pos].length < 1) {
       pos++
     } // skip blank lines
+    if (lines[pos].startsWith('METADATA')) {
+      while (lines[pos].length > 1) {
+        pos++
+      } // skip until blank line
+      pos++
+    }
     items = lines[pos].trim().split(/\s+/)
     pos++
     if (items[0].includes('LINES')) {
@@ -909,7 +915,7 @@ export class NVMeshLoaders {
           layer.values = obj
         }
       }
-    } else if (ext === 'CRV' || ext === 'CURV') {
+    } else if (ext === 'CRV' || ext === 'CURV' || ext === 'THICKNESS' || ext === 'AREA') {
       layer.values = NVMeshLoaders.readCURV(buffer, n_vert)
       layer.isTransparentBelowCalMin = false
     } else if (ext === 'GII') {
@@ -935,6 +941,10 @@ export class NVMeshLoaders {
       layer.values = NVMeshLoaders.readSMP(buffer, n_vert)
     } else if (ext === 'STC') {
       layer.values = NVMeshLoaders.readSTC(buffer, n_vert)
+    } else if (NVMeshLoaders.isCurv(buffer)) {
+      // Unknown layer overlay format - hail mary assume FreeSurfer
+      layer.values = NVMeshLoaders.readCURV(buffer, n_vert)
+      layer.isTransparentBelowCalMin = false
     } else {
       log.warn('Unknown layer overlay format ' + name)
       return layer
@@ -1123,6 +1133,19 @@ export class NVMeshLoaders {
     return f32
   } // readSTC()
 
+  static isCurv(buffer: ArrayBuffer): boolean {
+    const view = new DataView(buffer) // ArrayBuffer to dataview
+    // ALWAYS big endian
+    const sig0 = view.getUint8(0)
+    const sig1 = view.getUint8(1)
+    const sig2 = view.getUint8(2)
+    if (sig0 !== 255 || sig1 !== 255 || sig2 !== 255) {
+      utiltiesLogger.debug('Unable to recognize file type: does not appear to be FreeSurfer format.')
+      return false
+    }
+    return true
+  }
+
   // read freesurfer curv big-endian format
   // https://github.com/bonilhamusclab/MRIcroS/blob/master/%2BfileUtils/%2Bpial/readPial.m
   // http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm