molstar
Version:
A comprehensive macromolecular library.
158 lines (157 loc) • 8.37 kB
JavaScript
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { CifWriter } from '../../../../mol-io/writer/cif';
import { VOLUME_SERVER_VERSION as VERSION } from '../version';
import { ArrayEncoding } from '../../../../mol-io/common/binary-cif';
import { TypedArrayValueType } from '../../../../mol-io/common/typed-array';
export function encode(query, output) {
var w = CifWriter.createEncoder({ binary: query.params.asBinary, encoderName: "VolumeServer ".concat(VERSION) });
write(w, query);
w.encode();
w.writeTo(output);
}
function string(name, str, isSpecified) {
if (isSpecified) {
return CifWriter.Field.str(name, function (i, d) { return str(d); }, { valueKind: function (i, d) { return isSpecified(d) ? 0 /* Column.ValueKind.Present */ : 1 /* Column.ValueKind.NotPresent */; } });
}
return CifWriter.Field.str(name, function (i, d) { return str(d); });
}
function int32(name, value) {
return CifWriter.Field.int(name, function (i, d) { return value(d); });
}
function float64(name, value, digitCount) {
if (digitCount === void 0) { digitCount = 6; }
return CifWriter.Field.float(name, function (i, d) { return value(d); }, { digitCount: digitCount, typedArray: Float64Array });
}
var _volume_data_3d_info_fields = [
string('name', function (ctx) { return ctx.header.channels[ctx.channelIndex]; }),
int32('axis_order[0]', function (ctx) { return ctx.header.axisOrder[0]; }),
int32('axis_order[1]', function (ctx) { return ctx.header.axisOrder[1]; }),
int32('axis_order[2]', function (ctx) { return ctx.header.axisOrder[2]; }),
float64('origin[0]', function (ctx) { return ctx.grid.origin[0]; }),
float64('origin[1]', function (ctx) { return ctx.grid.origin[1]; }),
float64('origin[2]', function (ctx) { return ctx.grid.origin[2]; }),
float64('dimensions[0]', function (ctx) { return ctx.grid.dimensions[0]; }),
float64('dimensions[1]', function (ctx) { return ctx.grid.dimensions[1]; }),
float64('dimensions[2]', function (ctx) { return ctx.grid.dimensions[2]; }),
int32('sample_rate', function (ctx) { return ctx.sampleRate; }),
int32('sample_count[0]', function (ctx) { return ctx.grid.sampleCount[0]; }),
int32('sample_count[1]', function (ctx) { return ctx.grid.sampleCount[1]; }),
int32('sample_count[2]', function (ctx) { return ctx.grid.sampleCount[2]; }),
int32('spacegroup_number', function (ctx) { return ctx.header.spacegroup.number; }),
float64('spacegroup_cell_size[0]', function (ctx) { return ctx.header.spacegroup.size[0]; }, 3),
float64('spacegroup_cell_size[1]', function (ctx) { return ctx.header.spacegroup.size[1]; }, 3),
float64('spacegroup_cell_size[2]', function (ctx) { return ctx.header.spacegroup.size[2]; }, 3),
float64('spacegroup_cell_angles[0]', function (ctx) { return ctx.header.spacegroup.angles[0]; }, 3),
float64('spacegroup_cell_angles[1]', function (ctx) { return ctx.header.spacegroup.angles[1]; }, 3),
float64('spacegroup_cell_angles[2]', function (ctx) { return ctx.header.spacegroup.angles[2]; }, 3),
float64('mean_source', function (ctx) { return ctx.globalValuesInfo.mean; }),
float64('mean_sampled', function (ctx) { return ctx.sampledValuesInfo.mean; }),
float64('sigma_source', function (ctx) { return ctx.globalValuesInfo.sigma; }),
float64('sigma_sampled', function (ctx) { return ctx.sampledValuesInfo.sigma; }),
float64('min_source', function (ctx) { return ctx.globalValuesInfo.min; }),
float64('min_sampled', function (ctx) { return ctx.sampledValuesInfo.min; }),
float64('max_source', function (ctx) { return ctx.globalValuesInfo.max; }),
float64('max_sampled', function (ctx) { return ctx.sampledValuesInfo.max; })
];
var _volume_data_3d_info = {
name: 'volume_data_3d_info',
instance: function (result) {
var ctx = {
header: result.query.data.header,
channelIndex: result.channelIndex,
grid: result.query.samplingInfo.gridDomain,
sampleRate: result.query.samplingInfo.sampling.rate,
globalValuesInfo: result.query.data.header.sampling[0].valuesInfo[result.channelIndex],
sampledValuesInfo: result.query.data.header.sampling[result.query.samplingInfo.sampling.index].valuesInfo[result.channelIndex]
};
return { fields: _volume_data_3d_info_fields, source: [{ data: ctx, rowCount: 1 }] };
}
};
function _volume_data_3d_number(i, ctx) {
return ctx[i];
}
var _volume_data_3d = {
name: 'volume_data_3d',
instance: function (ctx) {
var data = ctx.query.values[ctx.channelIndex];
var E = ArrayEncoding;
var encoder;
var typedArray;
if (ctx.query.data.header.valueType === TypedArrayValueType.Float32 || ctx.query.data.header.valueType === TypedArrayValueType.Int16) {
var min = void 0, max = void 0;
min = data[0], max = data[0];
for (var i = 0, n = data.length; i < n; i++) {
var v = data[i];
if (v < min)
min = v;
else if (v > max)
max = v;
}
typedArray = Float32Array;
// encode into 255 steps and store each value in 1 byte.
encoder = E.by(E.intervalQuantizaiton(min, max, 255, Uint8Array)).and(E.byteArray);
}
else {
typedArray = Int8Array;
// just encode the bytes
encoder = E.by(E.byteArray);
}
var fields = [CifWriter.Field.float('values', _volume_data_3d_number, { encoder: encoder, typedArray: typedArray, digitCount: 6 })];
return CifWriter.categoryInstance(fields, { data: data, rowCount: data.length });
}
};
function pickQueryBoxDimension(ctx, e, d) {
var box = ctx.params.box;
switch (box.kind) {
case 'Cartesian':
case 'Fractional':
return "".concat(Math.round(1000000 * box[e][d]) / 1000000);
default: return '';
}
}
function queryBoxDimension(e, d) {
return string("query_box_".concat(e, "[").concat(d, "]"), function (ctx) { return pickQueryBoxDimension(ctx, e, d); }, function (ctx) { return ctx.params.box.kind !== 'Cell'; });
}
var _density_server_result_fields = [
string('server_version', function (ctx) { return VERSION; }),
string('datetime_utc', function (ctx) { return new Date().toISOString().replace(/T/, ' ').replace(/\..+/, ''); }),
string('guid', function (ctx) { return ctx.guid; }),
string('is_empty', function (ctx) { return ctx.kind === 'Empty' || ctx.kind === 'Error' ? 'yes' : 'no'; }),
string('has_error', function (ctx) { return ctx.kind === 'Error' ? 'yes' : 'no'; }),
string('error', function (ctx) { return ctx.kind === 'Error' ? ctx.message : ''; }, function (ctx) { return ctx.kind === 'Error'; }),
string('query_source_id', function (ctx) { return ctx.params.sourceId; }),
string('query_type', function (ctx) { return 'box'; }),
string('query_box_type', function (ctx) { return ctx.params.box.kind.toLowerCase(); }),
queryBoxDimension('a', 0),
queryBoxDimension('a', 1),
queryBoxDimension('a', 2),
queryBoxDimension('b', 0),
queryBoxDimension('b', 1),
queryBoxDimension('b', 2)
];
var _density_server_result = {
name: 'density_server_result',
instance: function (ctx) { return CifWriter.categoryInstance(_density_server_result_fields, { data: ctx, rowCount: 1 }); }
};
function write(encoder, query) {
encoder.startDataBlock('SERVER');
encoder.writeCategory(_density_server_result, query);
switch (query.kind) {
case 'Data':
}
if (query.kind === 'Data') {
var header = query.data.header;
for (var i = 0; i < header.channels.length; i++) {
encoder.startDataBlock(header.channels[i]);
var ctx = { query: query, channelIndex: i };
encoder.writeCategory(_volume_data_3d_info, ctx);
encoder.writeCategory(_volume_data_3d, ctx);
}
}
}