tweak cube clamp param

src/mol-model-formats/volume/cube.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
  */
 
 import { CubeFile } from '../../mol-io/reader/cube/parser';
@@ -11,8 +12,9 @@ import { Task } from '../../mol-task';
 import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
 import { ModelFormat } from '../format';
 import { CustomProperties } from '../../mol-model/custom-property';
+import { clamp } from '../../mol-math/interpolate';
 
-export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string, entryId?: string }): Task<Volume> {
+export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string, entryId?: string, clamp?: { min: number, max: number } }): Task<Volume> {
     return Task.create<Volume>('Create Volume', async () => {
         const { header, values: sourceValues } = source;
         const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
@@ -24,6 +26,7 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
             // get every nth value from the source values
             const [h, k, l] = header.dim;
             const nth = (params?.dataIndex || 0) + 1;
+            const { min, max } = params?.clamp || { min: -Infinity, max: Infinity };
 
             let o = 0, s = 0;
 
@@ -31,7 +34,7 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
             for (let u = 0; u < h; u++) {
                 for (let v = 0; v < k; v++) {
                     for (let w = 0; w < l; w++) {
-                        values[o++] = sourceValues[s];
+                        values[o++] = clamp(sourceValues[s], min, max);
                         s += nth;
                     }
                 }

src/mol-plugin-state/transforms/volume.ts

@@ -88,12 +88,24 @@ const VolumeFromCube = PluginStateTransform.BuiltIn({
         return {
             dataIndex,
             entryId: PD.Text(''),
+            clamp: PD.MappedStatic('off', {
+                'off': PD.EmptyGroup(),
+                'on': PD.Group({
+                    min: PD.Numeric(-1024),
+                    max: PD.Numeric(1024),
+                })
+            }, { cycle: true })
         };
     }
 })({
     apply({ a, params }) {
         return Task.create('Create volume from Cube', async ctx => {
-            const volume = await volumeFromCube(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
+            const volume = await volumeFromCube(a.data, {
+                dataIndex: params.dataIndex,
+                label: a.data.name || a.label,
+                entryId: params.entryId,
+                clamp: params.clamp.name === 'on' ? params.clamp.params : undefined,
+            }).runInContext(ctx);
             const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.dim[0]}\u00D7${a.data.header.dim[1]}\u00D7${a.data.header.dim[2]}` };
             return new SO.Volume.Data(volume, props);
         });