molstar
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A comprehensive macromolecular library.
135 lines (134 loc) • 6.1 kB
JavaScript
;
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.SegcifFormat = void 0;
exports.volumeFromSegmentationData = volumeFromSegmentationData;
const volume_1 = require("../../mol-model/volume");
const mol_task_1 = require("../../mol-task");
const geometry_1 = require("../../mol-math/geometry");
const linear_algebra_1 = require("../../mol-math/linear-algebra");
const custom_property_1 = require("../../mol-model/custom-property");
const object_1 = require("../../mol-util/object");
function volumeFromSegmentationData(source, params) {
return mol_task_1.Task.create('Create Segmentation Volume', async (ctx) => {
var _a;
const { volume_data_3d_info: info, segmentation_data_3d: values } = source;
const cell = geometry_1.SpacegroupCell.create(info.spacegroup_number.value(0), linear_algebra_1.Vec3.ofArray(info.spacegroup_cell_size.value(0)), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180));
const axis_order_fast_to_slow = info.axis_order.value(0);
const normalizeOrder = linear_algebra_1.Tensor.convertToCanonicalAxisIndicesFastToSlow(axis_order_fast_to_slow);
// sample count is in "axis order" and needs to be reordered
const sample_count = normalizeOrder(info.sample_count.value(0));
const tensorSpace = linear_algebra_1.Tensor.Space(sample_count, linear_algebra_1.Tensor.invertAxisOrder(axis_order_fast_to_slow), Float32Array);
const t = linear_algebra_1.Tensor.create(tensorSpace, linear_algebra_1.Tensor.Data1(values.values.toArray({ array: Float32Array })));
// origin and dimensions are in "axis order" and need to be reordered
const origin = linear_algebra_1.Vec3.ofArray(normalizeOrder(info.origin.value(0)));
const dimensions = linear_algebra_1.Vec3.ofArray(normalizeOrder(info.dimensions.value(0)));
const v = {
label: params === null || params === void 0 ? void 0 : params.label,
entryId: undefined,
grid: {
transform: {
kind: 'spacegroup',
cell,
fractionalBox: geometry_1.Box3D.create(origin, linear_algebra_1.Vec3.add((0, linear_algebra_1.Vec3)(), origin, dimensions))
},
cells: t,
stats: {
min: 0, max: 1, mean: 0, sigma: 1
},
},
sourceData: SegcifFormat.create(source),
customProperties: new custom_property_1.CustomProperties(),
_propertyData: { ownerId: params === null || params === void 0 ? void 0 : params.ownerId },
};
volume_1.Volume.PickingGranularity.set(v, 'object');
const segments = new Map();
const sets = new Map();
const { segment_id, set_id } = source.segmentation_data_table;
for (let i = 0, il = segment_id.rowCount; i < il; ++i) {
const segment = segment_id.value(i);
const set = set_id.value(i);
if (set === 0 || segment === 0)
continue;
if (!sets.has(set))
sets.set(set, new Set());
sets.get(set).add(segment);
}
sets.forEach((segs, set) => {
segs.forEach(seg => {
if (!segments.has(seg))
segments.set(seg, new Set());
segments.get(seg).add(set);
});
});
const c = [0, 0, 0];
const getCoords = t.space.getCoords;
const d = t.data;
const [xn, yn, zn] = v.grid.cells.space.dimensions;
const xn1 = xn - 1;
const yn1 = yn - 1;
const zn1 = zn - 1;
const setBounds = {};
sets.forEach((v, k) => {
setBounds[k] = [xn1, yn1, zn1, -1, -1, -1];
});
for (let i = 0, il = d.length; i < il; ++i) {
const v = d[i];
if (v === 0)
continue;
getCoords(i, c);
const b = setBounds[v];
if (c[0] < b[0])
b[0] = c[0];
if (c[1] < b[1])
b[1] = c[1];
if (c[2] < b[2])
b[2] = c[2];
if (c[0] > b[3])
b[3] = c[0];
if (c[1] > b[4])
b[4] = c[1];
if (c[2] > b[5])
b[5] = c[2];
}
const bounds = {};
segments.forEach((v, k) => {
bounds[k] = geometry_1.Box3D.create(linear_algebra_1.Vec3.create(xn1, yn1, zn1), linear_algebra_1.Vec3.create(-1, -1, -1));
});
(0, object_1.objectForEach)(setBounds, (b, s) => {
sets.get(parseInt(s)).forEach(seg => {
const sb = bounds[seg];
if (b[0] < sb.min[0])
sb.min[0] = b[0];
if (b[1] < sb.min[1])
sb.min[1] = b[1];
if (b[2] < sb.min[2])
sb.min[2] = b[2];
if (b[3] > sb.max[0])
sb.max[0] = b[3];
if (b[4] > sb.max[1])
sb.max[1] = b[4];
if (b[5] > sb.max[2])
sb.max[2] = b[5];
});
});
volume_1.Volume.Segmentation.set(v, { segments, sets, bounds, labels: (_a = params === null || params === void 0 ? void 0 : params.segmentLabels) !== null && _a !== void 0 ? _a : {} });
return v;
});
}
var SegcifFormat;
(function (SegcifFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'segcif';
}
SegcifFormat.is = is;
function create(segcif) {
return { kind: 'segcif', name: segcif._name, data: segcif };
}
SegcifFormat.create = create;
})(SegcifFormat || (exports.SegcifFormat = SegcifFormat = {}));