Press n or j to go to the next uncovered block, b, p or k for the previous block.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 | import { Sphere } from "./WebGL/shapes"; import { Vector3, Matrix4 } from "./WebGL/math"; import { VolumetricMaterial, Mesh, Texture, Object3D } from "./WebGL"; import { CC } from "./WebGL"; import { GLShape } from "./GLShape"; /** * A GLVolumetricRender is a "shape" for representing volumetric data as a density distribution. * * @class * * @param {VolumeData} data - volumetric data * @param {VolumetricRenderSpec} spec - specification of volumetric render * @returns {$3Dmol.GLShape} */ export class GLVolumetricRender { static interpolateArray(data, fitCount) { function linearInterpolate(before, after, atPoint) { return before + (after - before) * atPoint; } var newData = []; var springFactor = (data.length - 1) / (fitCount - 1); newData[0] = data[0]; // for new allocation for (var i = 1; i < fitCount - 1; i++) { var tmp = i * springFactor; var before = Math.floor(tmp); var after = Math.ceil(tmp); var atPoint = tmp - before; newData[i] = linearInterpolate(data[before], data[after], atPoint); } newData[fitCount - 1] = data[data.length - 1]; // for new allocation return newData; } hidden = false; boundingSphere = new Sphere(); shapePosition: any; renderedShapeObj: any = null; shapeObj: any = null; geo: any; subsamples = 5.0; data: any = null; transferfunctionbuffer: any = []; min:number = 0; max:number = 0; extent: any; maxdepth: number; texmatrix: any; minunit: any; constructor(data, spec) { spec = spec || {}; var transferfn = Object.assign([], spec.transferfn); this.subsamples = spec.subsamples || 5.0; let TRANSFER_BUFFER_SIZE = 256; // arrange points based on position property transferfn.forEach(function (a) { a.value = parseFloat(a.value); }); transferfn.sort(function (a, b) { return a.value - b.value; }); this.min = transferfn[0].value; Iif (transferfn.length == 0) transferfn.push(transferfn[0]); //need at least two this.max = transferfn[transferfn.length - 1].value; // create and fill an array of interpolated values per 2 colors var pos1, pos2, color1, color2, R, G, B, A, alpha1, alpha2; for (let i = 0; i < transferfn.length - 1; i++) { color1 = CC.color(transferfn[i].color); color2 = CC.color(transferfn[i + 1].color); alpha1 = transferfn[i].opacity; alpha2 = transferfn[i + 1].opacity; pos1 = Math.floor((transferfn[i].value - this.min) * TRANSFER_BUFFER_SIZE / (this.max - this.min)); pos2 = Math.floor((transferfn[i + 1].value - this.min) * TRANSFER_BUFFER_SIZE / (this.max - this.min)); Iif (pos1 == pos2) continue; R = GLVolumetricRender.interpolateArray([color1.r * 255, color2.r * 255], pos2 - pos1); G = GLVolumetricRender.interpolateArray([color1.g * 255, color2.g * 255], pos2 - pos1); B = GLVolumetricRender.interpolateArray([color1.b * 255, color2.b * 255], pos2 - pos1); A = GLVolumetricRender.interpolateArray([alpha1 * 255, alpha2 * 255], pos2 - pos1); for (let j = 0; j < R.length; j++) { this.transferfunctionbuffer.push(R[j]); this.transferfunctionbuffer.push(G[j]); this.transferfunctionbuffer.push(B[j]); this.transferfunctionbuffer.push(A[j]); // opacity will be added later } } this.transferfunctionbuffer = new Uint8ClampedArray(this.transferfunctionbuffer); //need to create transformation matrix that maps model points into //texture space // need extent (bounding box dimensions), maxdepth (box diagonal), // texmatrix (conversion from model to texture coords), minunit, // possibly non-orthnormal basis if matrix if (data.matrix) { //figure out bounding box of transformed grid let start = new Vector3(0, 0, 0); let end = new Vector3(data.size.x, data.size.y, data.size.z); let unit = new Vector3(1, 1, 1); start.applyMatrix4(data.matrix); end.applyMatrix4(data.matrix); unit.applyMatrix4(data.matrix).sub(start); this.extent = [[start.x, start.y, start.z], [end.x, end.y, end.z]]; //check all corners, these may not be the farthest apart for (let i = 1; i < 7; i++) { end.x = (i & 1) ? data.size.x : 0; end.y = (i & 2) ? data.size.y : 0; end.z = (i & 4) ? data.size.z : 0; end.applyMatrix4(data.matrix); this.extent[0][0] = Math.min(this.extent[0][0], end.x); this.extent[0][1] = Math.min(this.extent[0][1], end.y); this.extent[0][2] = Math.min(this.extent[0][2], end.z); this.extent[1][0] = Math.max(this.extent[1][0], end.x); this.extent[1][1] = Math.max(this.extent[1][1], end.y); this.extent[1][2] = Math.max(this.extent[1][2], end.z); } let xoff = end.x - start.x; let yoff = end.y - start.y; let zoff = end.z - start.z; this.maxdepth = Math.sqrt(xoff * xoff + yoff * yoff + zoff * zoff); this.minunit = Math.min(Math.min(unit.x, unit.y), unit.z); //invert onto grid, then scale by grid dimensions to get //normalized texture coordinates this.texmatrix = new Matrix4().identity().scale({ x: data.size.x, y: data.size.y, z: data.size.z }); this.texmatrix = this.texmatrix.multiplyMatrices(data.matrix, this.texmatrix); this.texmatrix = this.texmatrix.getInverse(this.texmatrix); } else { this.texmatrix = new Matrix4().identity(); let xoff = data.unit.x * data.size.x; let yoff = data.unit.y * data.size.y; let zoff = data.unit.z * data.size.z; //scale doesn't apply to the translation vector, so preapply it this.texmatrix.makeTranslation(-data.origin.x / xoff, -data.origin.y / yoff, -data.origin.z / zoff); this.texmatrix.scale({ x: 1.0 / xoff, y: 1.0 / yoff, z: 1.0 / zoff }); this.minunit = Math.min(Math.min(data.unit.x, data.unit.y), data.unit.z); //need the bounding box so we can intersect with rays this.extent = [[data.origin.x, data.origin.y, data.origin.z], [data.origin.x + xoff, data.origin.y + yoff, data.origin.z + zoff]]; this.maxdepth = Math.sqrt(xoff * xoff + yoff * yoff + zoff * zoff); } //use GLShape to construct box var shape = new GLShape({}); shape.addBox({ corner: { x: this.extent[0][0], y: this.extent[0][1], z: this.extent[0][2] }, dimensions: { w: this.extent[1][0] - this.extent[0][0], h: this.extent[1][1] - this.extent[0][1], d: this.extent[1][2] - this.extent[0][2] } }); this.geo = shape.finalize(); this.boundingSphere.center = new Vector3( (this.extent[0][0] + this.extent[1][0]) / 2.0, (this.extent[0][1] + this.extent[1][1]) / 2.0, (this.extent[0][2] + this.extent[1][2]) / 2.0 ); this.boundingSphere.radius = this.maxdepth / 2; // volume selectivity based on given coords and distance Iif (spec.coords !== undefined && spec.seldist !== undefined) { let mask = new Uint8Array(data.data.length); //for each coordinate let d = spec.seldist; let d2 = d * d; for (let i = 0, n = spec.coords.length; i < n; i++) { let c = spec.coords[i]; let minx = c.x - d, miny = c.y - d, minz = c.z - d; let maxx = c.x + d, maxy = c.y + d, maxz = c.z + d; Iif (data.getIndex(minx, miny, minz) >= 0 || data.getIndex(maxx, maxy, maxz) >= 0) { //bounding box overlaps grid //iterate over the grid points in the seldist bounding box //minunit may be inefficient if axes have very different units. oh well. for (let x = minx; x < maxx; x += this.minunit) { for (let y = miny; y < maxy; y += this.minunit) { for (let z = minz; z < maxz; z += this.minunit) { let idx = data.getIndex(x, y, z); Iif (idx >= 0 && !mask[idx]) { //if not already masked, check distance let distsq = (x - c.x) * (x - c.x) + (y - c.y) * (y - c.y) + (z - c.z) * (z - c.z); Iif (distsq < d2) { mask[idx] = 1; } } } } } } } //any place mask is zero, make infinite in data for (let i = 0, n = data.data.length; i < n; i++) { Iif (mask[i] == 0) data.data[i] = Infinity; } } this.data = data; } /** * Initialize webgl objects for rendering * @param {Object3D} group * */ globj(group) { Iif (this.renderedShapeObj) { group.remove(this.renderedShapeObj); this.renderedShapeObj = null; } Iif (this.hidden) return; this.shapeObj = new Object3D(); var material = null; var texture = new Texture(this.data, true); var transfertexture = new Texture(this.transferfunctionbuffer, false); texture.needsUpdate = true; transfertexture.needsUpdate = true; transfertexture.flipY = false; material = new VolumetricMaterial({ transferfn: transfertexture, transfermin: this.min, transfermax: this.max, map: texture, extent: this.extent, maxdepth: this.maxdepth, texmatrix: this.texmatrix, unit: this.minunit, subsamples: this.subsamples, }); var mesh = new Mesh(this.geo, material); this.shapeObj.add(mesh); this.renderedShapeObj = this.shapeObj.clone(); group.add(this.renderedShapeObj); }; removegl(group) { Iif (this.renderedShapeObj) { // dispose of geos and materials Iif (this.renderedShapeObj.geometry !== undefined) this.renderedShapeObj.geometry.dispose(); Iif (this.renderedShapeObj.material !== undefined) this.renderedShapeObj.material.dispose(); group.remove(this.renderedShapeObj); this.renderedShapeObj = null; } this.shapeObj = null; }; get position() { return this.boundingSphere.center; } get x() { return this.boundingSphere.center.x; } get y() { return this.boundingSphere.center.y; } get z() { return this.boundingSphere.center.z; } } |