diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 2d2b5057eb24c4645b50f9cf55ea6ea565e36a36..f3d4b585753df0eee9c410d048e2ec2ad5fe9389 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -9,6 +9,7 @@ import Iterator from 'mol-data/iterator'
import { Column, Table } from 'mol-data/db'
import { Tensor } from 'mol-math/linear-algebra'
import Encoder from '../encoder'
+import { ArrayEncoder, ArrayEncoding } from '../../common/binary-cif';
// TODO: support for "coordinate fields", make "coordinate precision" a parameter of the encoder
// TODO: automatically detect "precision" of floating point arrays.
@@ -28,21 +29,19 @@ export const enum FieldType {
export interface FieldDefinitionBase<Key, Data> {
name: string,
valueKind?: (key: Key, data: Data) => Column.ValueKind,
- // TODO:
- // shouldInclude?: (data: Data) => boolean
+ encoder?: ArrayEncoder
}
export type FieldDefinition<Key = any, Data = any> =
| FieldDefinitionBase<Key, Data> & { type: FieldType.Str, value(key: Key, data: Data): string }
- | FieldDefinitionBase<Key, Data> & { type: FieldType.Int, value(key: Key, data: Data): number }
- | FieldDefinitionBase<Key, Data> & { type: FieldType.Float, value(key: Key, data: Data): number }
+ | FieldDefinitionBase<Key, Data> & { type: FieldType.Int, value(key: Key, data: Data): number, typedArray?: ArrayEncoding.TypedArrayCtor }
+ | FieldDefinitionBase<Key, Data> & { type: FieldType.Float, value(key: Key, data: Data): number, digitCount?: number, typedArray?: ArrayEncoding.TypedArrayCtor }
export interface FieldFormat {
// TODO: do we actually need this?
- // textDecimalPlaces: number,
- // stringEncoder: ArrayEncoder,
- // numericEncoder: ArrayEncoder,
- // typedArray?: E.TypedArrayCtor
+ // digitCount?: number,
+ // encoder?: ArrayEncoder,
+ // typedArray?: ArrayEncoding.TypedArrayCtor
}
export namespace FieldFormat {
@@ -55,7 +54,8 @@ export namespace FieldFormat {
export interface CategoryDefinition<Key = any, Data = any> {
name: string,
- fields: FieldDefinition<Key, Data>[]
+ fields: FieldDefinition<Key, Data>[],
+ format?: { [name: string]: FieldFormat }
}
export interface CategoryInstance<Key = any, Data = any> {
diff --git a/src/mol-io/writer/cif/encoder/binary.ts b/src/mol-io/writer/cif/encoder/binary.ts
index 4e369e7cc394a2334c464ba3f9c1de5e3b47f6c0..762592b131eb0e9c966da65a3b8a71156cfb3d4d 100644
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -77,16 +77,22 @@ export default class BinaryCIFWriter<Context> implements CIFEncoder<Uint8Array,
}
}
-function encodeField(field: FieldDefinition, data: { data: any, keys: () => Iterator<any> }[], totalCount: number, format: FieldFormat): EncodedColumn {
- const isStr = field.type === FieldType.Str
- let array: any[], encoder: ArrayEncoder;
+function createArray(field: FieldDefinition, count: number) {
+ if (field.type === FieldType.Str) return new Array(count) as any;
+ else if (field.typedArray) return new field.typedArray(count) as any;
+ else return (field.type === FieldType.Int ? new Int32Array(count) : new Float32Array(count)) as any;
+}
- if (isStr) {
- array = new Array(totalCount);
- encoder = ArrayEncoder.by(E.stringArray); //format.stringEncoder;
+function encodeField(field: FieldDefinition, data: { data: any, keys: () => Iterator<any> }[], totalCount: number, format: FieldFormat): EncodedColumn {
+ const isStr = field.type === FieldType.Str;
+ const array = createArray(field, totalCount);
+ let encoder: ArrayEncoder;
+
+ if (field.encoder) {
+ encoder = field.encoder;
+ } else if (isStr) {
+ encoder = ArrayEncoder.by(E.stringArray);
} else {
- //array = format.typedArray ? new format.typedArray(totalCount) as any : field.type === FieldType.Int ? new Int32Array(totalCount) : new Float32Array(totalCount);
- array = (field.type === FieldType.Int ? new Int32Array(totalCount) : new Float32Array(totalCount)) as any;
encoder = ArrayEncoder.by(E.byteArray);
}
diff --git a/src/mol-io/writer/cif/encoder/text.ts b/src/mol-io/writer/cif/encoder/text.ts
index 9ded26f16babe9f20cb9f6fd825e69c17c616533..318eb74f146652b516b5cfa131528317ddc05690 100644
--- a/src/mol-io/writer/cif/encoder/text.ts
+++ b/src/mol-io/writer/cif/encoder/text.ts
@@ -60,7 +60,7 @@ export default class TextCIFEncoder<Context> implements Enc.CIFEncoder<string, C
}
}
-function writeValue(builder: StringBuilder, data: any, key: any, f: Enc.FieldDefinition<any, any>): boolean {
+function writeValue(builder: StringBuilder, data: any, key: any, f: Enc.FieldDefinition<any, any>, floatPrecision: number): boolean {
const kind = f.valueKind;
const p = kind ? kind(key, data) : Column.ValueKind.Present;
if (p !== Column.ValueKind.Present) {
@@ -79,12 +79,20 @@ function writeValue(builder: StringBuilder, data: any, key: any, f: Enc.FieldDef
} else if (t === Enc.FieldType.Int) {
writeInteger(builder, val as number);
} else {
- writeFloat(builder, val as number, 1000000);
+ writeFloat(builder, val as number, floatPrecision);
}
}
return false;
}
+function getFloatPrecisions(cat: Enc.CategoryInstance) {
+ const ret: number[] = [];
+ for (const f of cat.definition.fields) {
+ ret[ret.length] = f.type === Enc.FieldType.Float ? Math.pow(10, typeof f.digitCount === 'undefined' ? 6 : f.digitCount) : 0;
+ }
+ return ret;
+}
+
function writeCifSingleRecord(category: Enc.CategoryInstance<any>, builder: StringBuilder) {
const fields = category.definition.fields;
const data = category.data;
@@ -93,10 +101,12 @@ function writeCifSingleRecord(category: Enc.CategoryInstance<any>, builder: Stri
const it = category.keys();
const key = it.move();
+ const precisions = getFloatPrecisions(category);
+
for (let _f = 0; _f < fields.length; _f++) {
const f = fields[_f];
StringBuilder.writePadRight(builder, `_${category.definition.name}.${f.name}`, width);
- const multiline = writeValue(builder, data, key, f);
+ const multiline = writeValue(builder, data, key, f, precisions[_f]);
if (!multiline) StringBuilder.newline(builder);
}
StringBuilder.write(builder, '#\n');
@@ -106,6 +116,7 @@ function writeCifLoop(categories: Enc.CategoryInstance[], builder: StringBuilder
const first = categories[0];
const fields = first.definition.fields;
const fieldCount = fields.length;
+ const precisions = getFloatPrecisions(first);
writeLine(builder, 'loop_');
for (let i = 0; i < fieldCount; i++) {
@@ -124,7 +135,7 @@ function writeCifLoop(categories: Enc.CategoryInstance[], builder: StringBuilder
let multiline = false;
for (let _f = 0; _f < fieldCount; _f++) {
- multiline = writeValue(builder, data, key, fields[_f]);
+ multiline = writeValue(builder, data, key, fields[_f], precisions[_f]);
}
if (!multiline) StringBuilder.newline(builder);
}
diff --git a/src/servers/volume/server/query/encode.ts b/src/servers/volume/server/query/encode.ts
index 67277cccb2f2db4e10fac1c5791aeaf366cdbf1c..525e365ea1de97ed074abf06249a0d897c52628a 100644
--- a/src/servers/volume/server/query/encode.ts
+++ b/src/servers/volume/server/query/encode.ts
@@ -13,7 +13,7 @@ import VERSION from '../version'
import * as DataFormat from '../../common/data-format'
import { Column } from 'mol-data/db';
import { Iterator } from 'mol-data';
-//import { ArrayEncoding, ArrayEncoder } from 'mol-io/common/binary-cif';
+import { ArrayEncoding, ArrayEncoder } from 'mol-io/common/binary-cif';
export default function encode(query: Data.QueryContext, output: Data.QueryOutputStream) {
let w = Encoder.create({ binary: query.params.asBinary, encoderName: `VolumeServer ${VERSION}` });
@@ -45,8 +45,8 @@ function int32<T>(name: string, value: (data: T) => number): FieldDesc<T> {
return { name, type: Encoder.FieldType.Int, value: (i, d) => value(d) };
}
-function float64<T>(name: string, value: (data: T) => number, precisionMultiplier: number = 1000000): FieldDesc<T> {
- return { name, type: Encoder.FieldType.Float, value: (i, d) => value(d) };
+function float64<T>(name: string, value: (data: T) => number, digitCount: number = 6): FieldDesc<T> {
+ return { name, type: Encoder.FieldType.Float, value: (i, d) => value(d), digitCount };
}
interface _vd3d_Ctx {
@@ -80,13 +80,13 @@ const _volume_data_3d_info_fields: FieldDesc<_vd3d_Ctx>[] = [
int32<_vd3d_Ctx>('spacegroup_number', ctx => ctx.header.spacegroup.number),
- float64<_vd3d_Ctx>('spacegroup_cell_size[0]', ctx => ctx.header.spacegroup.size[0], 1000),
- float64<_vd3d_Ctx>('spacegroup_cell_size[1]', ctx => ctx.header.spacegroup.size[1], 1000),
- float64<_vd3d_Ctx>('spacegroup_cell_size[2]', ctx => ctx.header.spacegroup.size[2], 1000),
+ float64<_vd3d_Ctx>('spacegroup_cell_size[0]', ctx => ctx.header.spacegroup.size[0], 3),
+ float64<_vd3d_Ctx>('spacegroup_cell_size[1]', ctx => ctx.header.spacegroup.size[1], 3),
+ float64<_vd3d_Ctx>('spacegroup_cell_size[2]', ctx => ctx.header.spacegroup.size[2], 3),
- float64<_vd3d_Ctx>('spacegroup_cell_angles[0]', ctx => ctx.header.spacegroup.angles[0], 1000),
- float64<_vd3d_Ctx>('spacegroup_cell_angles[1]', ctx => ctx.header.spacegroup.angles[1], 1000),
- float64<_vd3d_Ctx>('spacegroup_cell_angles[2]', ctx => ctx.header.spacegroup.angles[2], 1000),
+ float64<_vd3d_Ctx>('spacegroup_cell_angles[0]', ctx => ctx.header.spacegroup.angles[0], 3),
+ float64<_vd3d_Ctx>('spacegroup_cell_angles[1]', ctx => ctx.header.spacegroup.angles[1], 3),
+ float64<_vd3d_Ctx>('spacegroup_cell_angles[2]', ctx => ctx.header.spacegroup.angles[2], 3),
float64<_vd3d_Ctx>('mean_source', ctx => ctx.globalValuesInfo.mean),
float64<_vd3d_Ctx>('mean_sampled', ctx => ctx.sampledValuesInfo.mean),
@@ -123,29 +123,27 @@ function _volume_data_3d_number(i: number, ctx: DataFormat.ValueArray): number {
function _volume_data_3d(ctx: ResultContext) {
const data = ctx.query.values[ctx.channelIndex];
- // const E = ArrayEncoding;
- // let encoder: ArrayEncoder;
- // let typedArray: any;
- // if (ctx.query.data.header.valueType === DataFormat.ValueType.Float32 || ctx.query.data.header.valueType === DataFormat.ValueType.Int16) {
- // let min: number, max: number;
- // min = data[0], max = data[0];
- // for (let i = 0, n = data.length; i < n; i++) {
- // let 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)
- // }
-
- let fields: FieldDesc<typeof data>[] = [{
- name: 'values', type: Encoder.FieldType.Float, value: _volume_data_3d_number
- }];
+ const E = ArrayEncoding;
+ let encoder: ArrayEncoder;
+ let typedArray: any;
+ if (ctx.query.data.header.valueType === DataFormat.ValueType.Float32 || ctx.query.data.header.valueType === DataFormat.ValueType.Int16) {
+ let min: number, max: number;
+ min = data[0], max = data[0];
+ for (let i = 0, n = data.length; i < n; i++) {
+ let 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)
+ }
+
+ let fields: FieldDesc<typeof data>[] = [{ name: 'values', type: Encoder.FieldType.Float, value: _volume_data_3d_number, encoder, typedArray, digitCount: 6 }];
return {
data,