@niivue/niivue 0.40.0 → 0.41.0

package/build/index.js

@@ -14,7 +14,7 @@ import { Subject } from "rxjs";
 import { mat4 as mat46, vec2, vec3 as vec310, vec4 as vec47 } from "gl-matrix";
 
 // package.json
-var version = "0.40.0";
+var version = "0.41.0";
 
 // src/logger.ts
 var _Log = class _Log {
@@ -1004,7 +1004,7 @@ uniform float layer;
 uniform highp sampler2D colormap;
 uniform lowp sampler3D blend3D;
 uniform float opacity;
-uniform vec3 xyzFrac;
+uniform vec4 xyzaFrac;
 uniform mat4 mtx;
 void main(void) {
 	vec4 vx = vec4(TexCoord.x, TexCoord.y, coordZ, 1.0) * mtx;
@@ -1012,41 +1012,30 @@ void main(void) {
 	FragColor = vec4(0.0, 0.0, 0.0, 0.0);
 	if (idx == uint(0))
 		return;
-	if (xyzFrac.x > 0.0) { //outline
-		vx = vec4(TexCoord.x+xyzFrac.x, TexCoord.y, coordZ, 1.0) * mtx;
+	//idx = ((idx - uint(1)) % uint(100))+uint(1);
+	float textureWidth = float(textureSize(colormap, 0).x);
+	float fx = (float(idx)+0.5) / textureWidth;
+	float nlayer = float(textureSize(colormap, 0).y);
+	float y = ((2.0 * layer) + 1.5)/nlayer;
+	FragColor = texture(colormap, vec2(fx, y)).rgba;
+	float alpha = FragColor.a;
+	FragColor.a *= opacity;
+	if (xyzaFrac.a > 0.0) { //outline
+		vx = vec4(TexCoord.x+xyzaFrac.x, TexCoord.y, coordZ, 1.0) * mtx;
 		uint R = uint(texture(intensityVol, vx.xyz).r);
-		vx = vec4(TexCoord.x-xyzFrac.x, TexCoord.y, coordZ, 1.0) * mtx;
+		vx = vec4(TexCoord.x-xyzaFrac.x, TexCoord.y, coordZ, 1.0) * mtx;
 		uint L = uint(texture(intensityVol, vx.xyz).r);
-		vx = vec4(TexCoord.x, TexCoord.y+xyzFrac.y, coordZ, 1.0) * mtx;
+		vx = vec4(TexCoord.x, TexCoord.y+xyzaFrac.y, coordZ, 1.0) * mtx;
 		uint A = uint(texture(intensityVol, vx.xyz).r);
-		vx = vec4(TexCoord.x, TexCoord.y-xyzFrac.y, coordZ, 1.0) * mtx;
+		vx = vec4(TexCoord.x, TexCoord.y-xyzaFrac.y, coordZ, 1.0) * mtx;
 		uint P = uint(texture(intensityVol, vx.xyz).r);
-		vx = vec4(TexCoord.x, TexCoord.y, coordZ+xyzFrac.z, 1.0) * mtx;
+		vx = vec4(TexCoord.x, TexCoord.y, coordZ+xyzaFrac.z, 1.0) * mtx;
 		uint S = uint(texture(intensityVol, vx.xyz).r);
-		vx = vec4(TexCoord.x, TexCoord.y, coordZ-xyzFrac.z, 1.0) * mtx;
+		vx = vec4(TexCoord.x, TexCoord.y, coordZ-xyzaFrac.z, 1.0) * mtx;
 		uint I = uint(texture(intensityVol, vx.xyz).r);
-		if ((idx == R) && (idx == L) && (idx == A) && (idx == P) && (idx == S) && (idx == I))
-			return;
+		if ((idx != R) || (idx != L) || (idx != A) || (idx != P) || (idx != S) || (idx != I))
+			FragColor.a = alpha * xyzaFrac.a;
 	}
-	idx = ((idx - uint(1)) % uint(100))+uint(1);
-	float textureWidth = float(textureSize(colormap, 0).x);
-	float fx = (float(idx)+0.5) / textureWidth;
-	float nlayer = float(textureSize(colormap, 0).y);
-	float y = ((2.0 * layer) + 1.5)/nlayer;
-	FragColor = texture(colormap, vec2(fx, y)).rgba;
-	//FragColor.a *= opacity;
-	FragColor.a = opacity;
-	return;
-
-	if (layer < 2.0) return;
-	//vec2 texXY = TexCoord.xy*0.5 +vec2(0.5,0.5);
-	//vec4 prevColor = texture(blend3D, vec3(texXY, coordZ));
-	vec4 prevColor = texture(blend3D, vec3(TexCoord.xy, coordZ));
-	// https://en.wikipedia.org/wiki/Alpha_compositing
-	float aout = FragColor.a + (1.0 - FragColor.a) * prevColor.a;
-	if (aout <= 0.0) return;
-	FragColor.rgb = ((FragColor.rgb * FragColor.a) + (prevColor.rgb * prevColor.a * (1.0 - FragColor.a))) / aout;
-	FragColor.a = aout;
 }`;
 var fragOrientShader = `#line 691
 precision highp int;
@@ -1279,9 +1268,11 @@ uniform mat4 mvpMtx;
 uniform mat4 normMtx;
 out vec4 vClr;
 out vec3 vN;
+out vec4 vP;
 void main(void) {
 	vec3 lightPosition = vec3(0.0, 0.0, -10.0);
-	gl_Position = mvpMtx * vec4(pos, 1.0);
+	vP = vec4(pos, 1.0);
+	gl_Position = mvpMtx * vP;
 	vN = normalize((normMtx * vec4(norm.xyz,1.0)).xyz);
 	//vV = -vec3(modelMtx*vec4(pos,1.0));
 	vClr = clr;
@@ -11044,7 +11035,7 @@ var ColorTables = class {
     const cmap = this.colormapFromKey(key);
     return this.makeLut(cmap.R, cmap.G, cmap.B, cmap.A, cmap.I, isInvert);
   }
-  makeLabelLut(cm, alphaFill = 64) {
+  makeLabelLut(cm, alphaFill = 255) {
     if (cm.R === void 0 || cm.G === void 0 || cm.B === void 0) {
       throw new Error(`Invalid colormap table: ${cm}`);
     }
@@ -12174,7 +12165,7 @@ var NVMeshLoaders = class _NVMeshLoaders {
   }
   // readTxtVTK()
   // read mesh overlay to influence vertex colors
-  static readLayer(name = "", buffer, nvmesh, opacity = 0.5, colormap = "warm", colormapNegative = "winter", useNegativeCmap = false, cal_min = null, cal_max = null, isOutlineBorder = false) {
+  static readLayer(name = "", buffer, nvmesh, opacity = 0.5, colormap = "warm", colormapNegative = "winter", useNegativeCmap = false, cal_min = null, cal_max = null, outlineBorder = 0) {
     const layer = {
       colormapInvert: false,
       alphaThreshold: false,
@@ -12271,7 +12262,7 @@ var NVMeshLoaders = class _NVMeshLoaders {
     }
     layer.nFrame4D = layer.values.length / n_vert;
     layer.frame4D = 0;
-    layer.isOutlineBorder = isOutlineBorder;
+    layer.outlineBorder = outlineBorder;
     let mn = layer.values[0];
     let mx = layer.values[0];
     for (let i = 0; i < layer.values.length; i++) {
@@ -12941,7 +12932,11 @@ var NVMeshLoaders = class _NVMeshLoaders {
       isSCALAR = true;
     }
     if (isSCALAR) {
-      const FSizeWoScalars = 16 + nskip + (isFace ? 1 : 0) * nface * 12 + (isVert ? 1 : 0) * n_vert * 12 + (isRGBA ? 1 : 0) * n_vert * 4;
+      let nv = n_vert;
+      if (n_vert === 0) {
+        nv = nvert;
+      }
+      const FSizeWoScalars = 16 + nskip + (isFace ? 1 : 0) * nface * 12 + (isVert ? 1 : 0) * nv * 12 + (isRGBA ? 1 : 0) * nv * 4;
       const scalarFloats = Math.floor((_buffer.byteLength - FSizeWoScalars) / bytesPerScalar);
       if (nvert !== n_vert && scalarFloats % n_vert === 0) {
         log.warn("Issue 729: mz3 mismatch scalar NVERT does not match mesh NVERT");
@@ -13405,9 +13400,51 @@ var NVMeshLoaders = class _NVMeshLoaders {
     };
   }
   // readOFF()
+  static readOBJMNI(buffer) {
+    const enc = new TextDecoder("utf-8");
+    const txt = enc.decode(buffer);
+    const items = txt.trim().split(/\s*,\s*|\s+/);
+    if (items.length < 1 || items[0] !== "P") {
+      log.warn("This is not a valid MNI OBJ mesh.");
+    }
+    let j = 6;
+    const nVert = parseInt(items[j++]);
+    const nVertX3 = nVert * 3;
+    const positions = new Float32Array(nVertX3);
+    for (let i = 0; i < nVertX3; i++) {
+      positions[i] = parseFloat(items[j++]);
+    }
+    j += nVertX3;
+    const nTri = parseInt(items[j++]);
+    const colour_flag = parseInt(items[j++]);
+    if (nTri < 1 || colour_flag < 0 || colour_flag > 2) {
+      log.warn("This is not a valid MNI OBJ mesh.");
+    }
+    let num_c = 1;
+    if (colour_flag === 1) {
+      num_c = nTri;
+    } else if (colour_flag === 1) {
+      num_c = nVert;
+    }
+    j += num_c * 4;
+    j += nTri;
+    const nTriX3 = nTri * 3;
+    const indices = new Int32Array(nTriX3);
+    for (let i = 0; i < nTriX3; i++) {
+      indices[i] = parseInt(items[j++]);
+    }
+    return {
+      positions,
+      indices
+    };
+  }
+  // readOBJMNI()
   static readOBJ(buffer) {
     const enc = new TextDecoder("utf-8");
     const txt = enc.decode(buffer);
+    if (txt[0] === "P") {
+      return this.readOBJMNI(buffer);
+    }
     const lines = txt.split("\n");
     const n = lines.length;
     const pts = [];
@@ -14099,33 +14136,20 @@ var NVMeshLoaders = class _NVMeshLoaders {
   static readX3D(buffer) {
     const len = buffer.byteLength;
     if (len < 20) {
-      throw new Error("File too small to be GII: bytes = " + len);
+      throw new Error("File too small to be X3D: bytes = " + len);
     }
     const bytes = new Uint8Array(buffer);
     let pos = 0;
-    function readStrX() {
-      while (pos < len && bytes[pos] === 10) {
+    function readStr() {
+      while (pos < len && bytes[pos] !== 60) {
         pos++;
       }
-      const startPos = pos;
-      while (pos < len && bytes[pos] !== 10) {
+      const startP = pos;
+      while (pos < len && bytes[pos] !== 62) {
         pos++;
       }
-      pos++;
-      if (pos - startPos < 1) {
-        return "";
-      }
-      return new TextDecoder().decode(buffer.slice(startPos, pos - 1)).trim();
-    }
-    function readStr() {
-      let line2 = readStrX();
-      if (!line2.startsWith("<") || line2.endsWith(">")) {
-        return line2;
-      }
-      while (pos < len && !line2.endsWith(">")) {
-        line2 += readStrX();
-      }
-      return line2;
+      const endP = pos;
+      return new TextDecoder().decode(buffer.slice(startP, endP + 1)).trim();
     }
     let line = readStr();
     function readStringTag(TagName) {
@@ -14146,22 +14170,30 @@ var NVMeshLoaders = class _NVMeshLoaders {
       const delimiter = line[fpos + TagName.length + 1];
       const spos = line.indexOf(delimiter, fpos) + 1;
       const epos = line.indexOf(delimiter, spos);
-      const str = line.slice(spos, epos).trim();
-      const items = str.trim().split(/\s+/);
+      let str = line.slice(spos, epos).trim();
+      str = str.replace(/,\s*$/, "");
+      const items = str.trim().split(/\s*,\s*|\s+/);
       if (items.length < 2) {
         return parseFloat(str);
       }
-      const ret = [];
+      let ret = new Array(items.length);
+      let j = 0;
       for (let i = 0; i < items.length; i++) {
-        ret.push(parseFloat(items[i]));
+        const v = parseFloat(items[i]);
+        if (!isFinite(v)) {
+          continue;
+        }
+        ret[j] = v;
+        j++;
       }
+      ret = ret.slice(0, j);
       return ret;
     }
     if (!line.includes("xml version")) {
       log.warn("Not a X3D image");
     }
     let positions = [];
-    const indices = [];
+    let indices = [];
     let rgba255 = [];
     let color = [];
     let translation = [0, 0, 0, 0];
@@ -14239,12 +14271,20 @@ var NVMeshLoaders = class _NVMeshLoaders {
             height = -2;
             coordIndex = readNumericTag("coordIndex");
           }
+          if (line.startsWith("<IndexedTriangleSet")) {
+            height = -7;
+            coordIndex = readNumericTag("index");
+          }
           if (line.startsWith("<IndexedTriangleStripSet")) {
             height = -3;
             coordIndex = readNumericTag("index");
           }
           if (line.startsWith("<Coordinate")) {
             point = readNumericTag("point");
+            const rem = point.length % 3;
+            if (rem !== 0) {
+              point = point.slice(0, -rem);
+            }
           }
           if (line.startsWith("<Color")) {
             color = readNumericTag("color");
@@ -14262,7 +14302,7 @@ var NVMeshLoaders = class _NVMeshLoaders {
             log.warn("Unsupported x3d shape: ElevationGrid");
           }
         }
-        if (height < -3) {
+        if (height < -3 && height !== -7) {
         } else if (height < -1) {
           if (coordIndex.length < 1 || point.length < 3 || point.length === void 0) {
             log.warn("Indexed mesh must specify indices and points");
@@ -14270,7 +14310,9 @@ var NVMeshLoaders = class _NVMeshLoaders {
           }
           const idx0 = Math.floor(positions.length / 3);
           let j = 2;
-          if (height === -2) {
+          if (height === -7) {
+            indices = [...indices, ...coordIndex];
+          } else if (height === -2) {
             let triStart = 0;
             while (j < coordIndex.length) {
               if (coordIndex[j] >= 0) {
@@ -14329,7 +14371,7 @@ var NVMeshLoaders = class _NVMeshLoaders {
       }
     }
     return {
-      positions,
+      positions: Float32Array.from(positions),
       indices: Int32Array.from(indices),
       rgba255
     };
@@ -15359,6 +15401,9 @@ var NVMesh = class _NVMesh {
         if (opacity <= 0 || layer.cal_min > layer.cal_max) {
           continue;
         }
+        if (layer.outlineBorder === void 0) {
+          layer.outlineBorder = 0;
+        }
         if (layer.isAdditiveBlend === void 0) {
           layer.isAdditiveBlend = false;
         }
@@ -15380,23 +15425,23 @@ var NVMesh = class _NVMesh {
             rgba8[k + 2] = lut2[idx + 2];
             k += 4;
           }
-          let opaque = new Array(nvtx).fill(true);
-          if (layer.isOutlineBorder) {
+          let opaque = new Array(nvtx).fill(false);
+          if (layer.outlineBorder > 0) {
             opaque = NVMeshUtilities.getClusterBoundary(rgba8, this.tris);
           }
           k = 0;
           for (let j = 0; j < layer.values.length; j++) {
-            if (!opaque[j]) {
-              k += 4;
-              continue;
+            let opa = opacity;
+            if (opaque[j]) {
+              opa = layer.outlineBorder;
             }
             let vtx = j * 28 + 24;
             if (this.f32PerVertex !== 7) {
               vtx = j * 20 + 16;
             }
-            u8[vtx + 0] = lerp(u8[vtx + 0], rgba8[k + 0], opacity);
-            u8[vtx + 1] = lerp(u8[vtx + 1], rgba8[k + 1], opacity);
-            u8[vtx + 2] = lerp(u8[vtx + 2], rgba8[k + 2], opacity);
+            u8[vtx + 0] = lerp(u8[vtx + 0], rgba8[k + 0], opa);
+            u8[vtx + 1] = lerp(u8[vtx + 1], rgba8[k + 1], opa);
+            u8[vtx + 2] = lerp(u8[vtx + 2], rgba8[k + 2], opa);
             k += 4;
           }
           continue;
@@ -15404,7 +15449,7 @@ var NVMesh = class _NVMesh {
         if (layer.values instanceof Uint8Array) {
           const rgba8 = new Uint8Array(layer.values.buffer);
           let opaque = new Array(nvtx).fill(true);
-          if (layer.isOutlineBorder) {
+          if (layer.outlineBorder > 0) {
             opaque = NVMeshUtilities.getClusterBoundary(rgba8, this.tris);
           }
           let k = 0;
@@ -15413,14 +15458,13 @@ var NVMesh = class _NVMesh {
             if (this.f32PerVertex !== 7) {
               vtx = j * 20 + 16;
             }
-            if (!opaque[j]) {
-              u8[vtx + 3] = 0;
-              k += 4;
-              continue;
+            let opa = opacity;
+            if (opaque[j]) {
+              opa = layer.outlineBorder;
             }
-            u8[vtx + 0] = lerp(u8[vtx + 0], rgba8[k + 0], opacity);
-            u8[vtx + 1] = lerp(u8[vtx + 1], rgba8[k + 1], opacity);
-            u8[vtx + 2] = lerp(u8[vtx + 2], rgba8[k + 2], opacity);
+            u8[vtx + 0] = lerp(u8[vtx + 0], rgba8[k + 0], opa);
+            u8[vtx + 1] = lerp(u8[vtx + 1], rgba8[k + 1], opa);
+            u8[vtx + 2] = lerp(u8[vtx + 2], rgba8[k + 2], opa);
             k += 4;
           }
           continue;
@@ -15447,7 +15491,7 @@ var NVMesh = class _NVMesh {
         if (!layer.isTransparentBelowCalMin) {
           mnCal = Number.NEGATIVE_INFINITY;
         }
-        if (!layer.isOutlineBorder) {
+        if (layer.outlineBorder <= 0) {
           for (let j = 0; j < nvtx; j++) {
             const v = layer.values[j + frameOffset];
             if (v < mnCal) {
@@ -15470,9 +15514,10 @@ var NVMesh = class _NVMesh {
               additiveRGBA[j4 + 2] = additiveBlend(additiveRGBA[j4 + 2], lut[v255 + 2]);
               additiveRGBA[j4 + 3] = additiveBlend(additiveRGBA[j4 + 3], 255);
             } else {
-              u8[vtx + 0] = lerp(u8[vtx + 0], lut[v255 + 0], opacity);
-              u8[vtx + 1] = lerp(u8[vtx + 1], lut[v255 + 1], opacity);
-              u8[vtx + 2] = lerp(u8[vtx + 2], lut[v255 + 2], opacity);
+              const opa = opacity;
+              u8[vtx + 0] = lerp(u8[vtx + 0], lut[v255 + 0], opa);
+              u8[vtx + 1] = lerp(u8[vtx + 1], lut[v255 + 1], opa);
+              u8[vtx + 2] = lerp(u8[vtx + 2], lut[v255 + 2], opa);
             }
           }
         } else {
@@ -15487,23 +15532,26 @@ var NVMesh = class _NVMesh {
           }
           const opaque = NVMeshUtilities.getClusterBoundaryU8(v255s, this.tris);
           for (let j = 0; j < nvtx; j++) {
-            let v255 = 255;
-            if (!opaque[j]) {
+            if (v255s[j] < 1) {
               continue;
             }
-            v255 = Math.min(255, v255) * 4;
+            let opa = opacity;
+            if (opaque[j]) {
+              opa = layer.outlineBorder;
+            }
+            const v255 = v255s[j] * 4;
             let vtx = j * 28 + 24;
             if (this.f32PerVertex !== 7) {
               vtx = j * 20 + 16;
             }
-            u8[vtx + 0] = lerp(u8[vtx + 0], lut[v255 + 0], opacity);
-            u8[vtx + 1] = lerp(u8[vtx + 1], lut[v255 + 1], opacity);
-            u8[vtx + 2] = lerp(u8[vtx + 2], lut[v255 + 2], opacity);
+            u8[vtx + 0] = lerp(u8[vtx + 0], lut[v255 + 0], opa);
+            u8[vtx + 1] = lerp(u8[vtx + 1], lut[v255 + 1], opa);
+            u8[vtx + 2] = lerp(u8[vtx + 2], lut[v255 + 2], opa);
           }
         }
         if (layer.useNegativeCmap) {
           const lut2 = cmapper.colormap(layer.colormapNegative, layer.colormapInvert);
-          if (!layer.isOutlineBorder) {
+          if (layer.outlineBorder <= 0) {
             let mn2 = layer.cal_min;
             let mx = layer.cal_max;
             if (isFinite(layer.cal_minNeg) && isFinite(layer.cal_minNeg)) {
@@ -15560,17 +15608,18 @@ var NVMesh = class _NVMesh {
             const opaque = NVMeshUtilities.getClusterBoundaryU8(v255s, this.tris);
             for (let j = 0; j < nvtx; j++) {
               let v255 = 255;
-              if (!opaque[j]) {
-                continue;
+              let opa = opacity;
+              if (opaque[j]) {
+                opa = layer.outlineBorder;
               }
               v255 = Math.min(255, v255) * 4;
               let vtx = j * 28 + 24;
               if (this.f32PerVertex !== 7) {
                 vtx = j * 20 + 16;
               }
-              u8[vtx + 0] = lerp(u8[vtx + 0], lut2[v255 + 0], opacity);
-              u8[vtx + 1] = lerp(u8[vtx + 1], lut2[v255 + 1], opacity);
-              u8[vtx + 2] = lerp(u8[vtx + 2], lut2[v255 + 2], opacity);
+              u8[vtx + 0] = lerp(u8[vtx + 0], lut2[v255 + 0], opa);
+              u8[vtx + 1] = lerp(u8[vtx + 1], lut2[v255 + 1], opa);
+              u8[vtx + 2] = lerp(u8[vtx + 2], lut2[v255 + 2], opa);
             }
           }
         }
@@ -17950,7 +17999,7 @@ var NVIMAGE_TYPE = Object.freeze({
     return imageType;
   }
 });
-var NVImageFromUrlOptions = (url, urlImageData = "", name = "", colormap = "gray", opacity = 1, cal_min = NaN, cal_max = NaN, trustCalMinMax = true, percentileFrac = 0.02, ignoreZeroVoxels = false, visible = true, useQFormNotSForm = false, colormapNegative = "", frame4D = 0, imageType = NVIMAGE_TYPE.UNKNOWN, cal_minNeg = NaN, cal_maxNeg = NaN, colorbarVisible = true, alphaThreshold = false, colormapLabel = []) => {
+var NVImageFromUrlOptions = (url, urlImageData = "", name = "", colormap = "gray", opacity = 1, cal_min = NaN, cal_max = NaN, trustCalMinMax = true, percentileFrac = 0.02, ignoreZeroVoxels = false, useQFormNotSForm = false, colormapNegative = "", frame4D = 0, imageType = NVIMAGE_TYPE.UNKNOWN, cal_minNeg = NaN, cal_maxNeg = NaN, colorbarVisible = true, alphaThreshold = false, colormapLabel = []) => {
   return {
     url,
     urlImageData,
@@ -17963,7 +18012,6 @@ var NVImageFromUrlOptions = (url, urlImageData = "", name = "", colormap = "gray
     trustCalMinMax,
     percentileFrac,
     ignoreZeroVoxels,
-    visible,
     useQFormNotSForm,
     colormapNegative,
     imageType,
@@ -18165,7 +18213,6 @@ var NVImage = class _NVImage {
    * @param trustCalMinMax - whether or not to trust cal_min and cal_max from the nifti header (trusting results in faster loading)
    * @param percentileFrac - the percentile to use for setting the robust range of the display values (smart intensity setting for images with large ranges)
    * @param ignoreZeroVoxels - whether or not to ignore zero voxels in setting the robust range of display values
-   * @param visible - whether or not this image is to be visible
    * @param useQFormNotSForm - give precedence to QForm (Quaternion) or SForm (Matrix)
    * @param colormapNegative - a color map to use for symmetrical negative intensities
    * @param frame4D - volume displayed, 0 indexed, must be less than nFrame4D
@@ -18181,7 +18228,7 @@ var NVImage = class _NVImage {
    * @param colorbarVisible - TODO
    * @param colormapLabel - TODO
    */
-  constructor(dataBuffer = null, name = "", colormap = "gray", opacity = 1, pairedImgData = null, cal_min = NaN, cal_max = NaN, trustCalMinMax = true, percentileFrac = 0.02, ignoreZeroVoxels = false, visible = true, useQFormNotSForm = false, colormapNegative = "", frame4D = 0, imageType = NVIMAGE_TYPE.UNKNOWN, cal_minNeg = NaN, cal_maxNeg = NaN, colorbarVisible = true, colormapLabel = null) {
+  constructor(dataBuffer = null, name = "", colormap = "gray", opacity = 1, pairedImgData = null, cal_min = NaN, cal_max = NaN, trustCalMinMax = true, percentileFrac = 0.02, ignoreZeroVoxels = false, useQFormNotSForm = false, colormapNegative = "", frame4D = 0, imageType = NVIMAGE_TYPE.UNKNOWN, cal_minNeg = NaN, cal_maxNeg = NaN, colorbarVisible = true, colormapLabel = null) {
     __publicField(this, "name");
     __publicField(this, "id");
     __publicField(this, "url");
@@ -18202,7 +18249,6 @@ var NVImage = class _NVImage {
     __publicField(this, "cal_minNeg");
     __publicField(this, "cal_maxNeg");
     __publicField(this, "colorbarVisible", true);
-    __publicField(this, "visible");
     __publicField(this, "modulationImage", null);
     __publicField(this, "modulateAlpha", 0);
     // if !=0, mod transparency with expon power |Alpha|
@@ -18305,7 +18351,6 @@ var NVImage = class _NVImage {
     this.cal_minNeg = cal_minNeg;
     this.cal_maxNeg = cal_maxNeg;
     this.colorbarVisible = colorbarVisible;
-    this.visible = visible;
     this.useQFormNotSForm = useQFormNotSForm;
     if (!dataBuffer) {
       return;
@@ -20568,7 +20613,6 @@ var NVImage = class _NVImage {
     trustCalMinMax = true,
     percentileFrac = 0.02,
     ignoreZeroVoxels = false,
-    visible = true,
     useQFormNotSForm = false,
     colormapNegative = "",
     frame4D = 0,
@@ -20710,7 +20754,6 @@ var NVImage = class _NVImage {
       trustCalMinMax,
       percentileFrac,
       ignoreZeroVoxels,
-      visible,
       useQFormNotSForm,
       colormapNegative,
       frame4D,
@@ -20755,7 +20798,6 @@ var NVImage = class _NVImage {
     trustCalMinMax = true,
     percentileFrac = 0.02,
     ignoreZeroVoxels = false,
-    visible = true,
     useQFormNotSForm = false,
     colormapNegative = "",
     frame4D = 0,
@@ -20845,7 +20887,6 @@ var NVImage = class _NVImage {
         trustCalMinMax,
         percentileFrac,
         ignoreZeroVoxels,
-        visible,
         useQFormNotSForm,
         colormapNegative,
         frame4D,
@@ -20877,8 +20918,7 @@ var NVImage = class _NVImage {
     cal_max = NaN,
     trustCalMinMax = true,
     percentileFrac = 0.02,
-    ignoreZeroVoxels = false,
-    visible = true
+    ignoreZeroVoxels = false
   }) {
     function base64ToArrayBuffer(base642) {
       const binary_string = window.atob(base642);
@@ -20903,8 +20943,7 @@ var NVImage = class _NVImage {
         cal_max,
         trustCalMinMax,
         percentileFrac,
-        ignoreZeroVoxels,
-        visible
+        ignoreZeroVoxels
       );
     } catch (err) {
       log.debug(err);
@@ -21172,8 +21211,6 @@ var NVImage = class _NVImage {
       // percentileFrac
       this.ignoreZeroVoxels,
       // ignoreZeroVoxels
-      this.visible,
-      // visible
       this.useQFormNotSForm,
       // useQFormNotSForm
       this.colormapNegative,
@@ -21373,7 +21410,7 @@ var DEFAULT_OPTIONS = {
   keyDebounceTime: 50,
   isNearestInterpolation: false,
   isResizeCanvas: true,
-  isAtlasOutline: false,
+  atlasOutline: 0,
   isRuler: false,
   isColorbar: false,
   isOrientCube: false,
@@ -21649,7 +21686,6 @@ var NVDocument = class _NVDocument {
           trustCalMinMax: true,
           percentileFrac: 0.02,
           ignoreZeroVoxels: false,
-          visible: true,
           useQFormNotSForm: false,
           colormapNegative: "",
           colormapLabel: [],
@@ -21695,7 +21731,6 @@ var NVDocument = class _NVDocument {
             trustCalMinMax: true,
             percentileFrac: 0.02,
             ignoreZeroVoxels: false,
-            visible: true,
             useQFormNotSForm: false,
             colormapNegative: "",
             colormapLabel: [],
@@ -21748,7 +21783,7 @@ var NVDocument = class _NVDocument {
           values: layer.values,
           nFrame4D: layer.nFrame4D,
           frame4D: 0,
-          isOutlineBorder: layer.isOutlineBorder,
+          outlineBorder: layer.outlineBorder,
           global_min: layer.global_min,
           global_max: layer.global_max,
           cal_min: layer.cal_min,
@@ -23115,6 +23150,8 @@ var Niivue = class _Niivue {
     __publicField(this, "position");
     __publicField(this, "extentsMin");
     __publicField(this, "extentsMax");
+    // ResizeObserver
+    __publicField(this, "resizeObserver", null);
     __publicField(this, "syncOpts", {});
     __publicField(this, "readyForSync", false);
     // UI Data
@@ -23606,6 +23643,8 @@ var Niivue = class _Niivue {
       this.canvas.width = this.canvas.offsetWidth;
       this.canvas.height = this.canvas.offsetHeight;
       window.addEventListener("resize", this.resizeListener.bind(this));
+      this.resizeObserver = new ResizeObserver(this.resizeListener.bind(this));
+      this.resizeObserver.observe(this.canvas.parentElement);
     }
     this.registerInteractions();
     await this.init();
@@ -25211,6 +25250,24 @@ var Niivue = class _Niivue {
     this.updateGLVolume();
     this.onMeshPropertyChanged(idx, key, val);
   }
+  /**
+   * returns the index of the mesh vertex that is closest to the provided coordinates
+   * @param id - identity of mesh to change
+   * @param Xmm - location in left/right dimension
+   * @param Ymm - location in posterior/anterior dimension
+   * @param Zmm - location in foot/head dimension
+   * @returns the an array where ret[0] is the mesh index and ret[1] is distance from vertex to coordinates
+   * @example niivue.indexNearestXYZmm(niivue.meshes[0].id, -22, 42, 13)
+   * @see {@link https://niivue.github.io/niivue/features/clipplanes.html | live demo usage}
+   */
+  indexNearestXYZmm(mesh, Xmm, Ymm, Zmm) {
+    const idx = this.getMeshIndexByID(mesh);
+    if (idx < 0) {
+      log.warn("indexNearestXYZmm() id not loaded", mesh);
+      return [NaN, NaN];
+    }
+    return this.meshes[idx].indexNearestXYZmm(Xmm, Ymm, Zmm);
+  }
   /**
    * reverse triangle winding of mesh (swap front and back faces)
    * @param id - identity of mesh to change
@@ -27880,13 +27937,16 @@ var Niivue = class _Niivue {
     if (!this.back.dims) {
       throw new Error("back.dims undefined");
     }
+    let outline = 0;
     if (hdr.intent_code === 1002) {
-      let x = 1 / this.back.dims[1];
-      if (!this.opts.isAtlasOutline) {
-        x = -x;
-      }
-      this.gl.uniform3fv(orientShader.uniforms.xyzFrac, [x, 1 / this.back.dims[2], 1 / this.back.dims[3]]);
+      outline = this.opts.atlasOutline;
     }
+    this.gl.uniform4fv(orientShader.uniforms.xyzaFrac, [
+      1 / this.back.dims[1],
+      1 / this.back.dims[2],
+      1 / this.back.dims[3],
+      outline
+    ]);
     log.debug("back dims: ", this.back.dims);
     for (let i = 0; i < this.back.dims[3]; i++) {
       const coordZ = 1 / this.back.dims[3] * (i + 0.5);
@@ -28100,7 +28160,7 @@ var Niivue = class _Niivue {
    */
   getFrame4D(id) {
     const idx = this.getVolumeIndexByID(id);
-    return this.volumes[idx].nFrame4D;
+    return this.volumes[idx].frame4D;
   }
   // not included in public docs
   colormapFromKey(name) {
@@ -29013,7 +29073,7 @@ var Niivue = class _Niivue {
   }
   // not included in public docs
   setAtlasOutline(isOutline) {
-    this.opts.isAtlasOutline = isOutline;
+    this.opts.atlasOutline = isOutline;
     this.updateGLVolume();
     this.drawScene();
   }