react-science 6.0.2 → 8.0.0

package/lib-esm/app-data/enhancers/enhance.js

@@ -1,13 +0,0 @@
-export function enhance(measurements, enhancers) {
-    for (const [kind, kindEnhancers] of Object.entries(enhancers)) {
-        const kindMeasurements = measurements[kind];
-        if (kindMeasurements) {
-            for (const measurement of kindMeasurements.entries) {
-                for (const enhancer of kindEnhancers) {
-                    enhancer(measurement);
-                }
-            }
-        }
-    }
-}
-//# sourceMappingURL=enhance.js.map

package/lib-esm/app-data/enhancers/enhance.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/enhancers/index.d.ts

@@ -1,2 +0,0 @@
-export * from './enhance';
-//# sourceMappingURL=index.d.ts.map

package/lib-esm/app-data/enhancers/index.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/enhancers/index.js

@@ -1,2 +0,0 @@
-export * from './enhance';
-//# sourceMappingURL=index.js.map

package/lib-esm/app-data/enhancers/index.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/helpers/index.d.ts

@@ -1,2 +0,0 @@
-export * from './variables';
-//# sourceMappingURL=index.d.ts.map

package/lib-esm/app-data/helpers/index.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/helpers/index.js

@@ -1,2 +0,0 @@
-export * from './variables';
-//# sourceMappingURL=index.js.map

package/lib-esm/app-data/helpers/index.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/helpers/variables.d.ts

@@ -1,6 +0,0 @@
-import { MeasurementVariable } from 'cheminfo-types';
-import { MeasurementBase } from '../state/index';
-export declare function getAllVariableSymbols(measurement: MeasurementBase): string[];
-export declare function getPreferredVariable(measurement: MeasurementBase, axis: 'x' | 'y'): MeasurementVariable;
-export declare function getVariableByLabel(measurement: MeasurementBase, label: string): MeasurementVariable | null;
-//# sourceMappingURL=variables.d.ts.map

package/lib-esm/app-data/helpers/variables.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/helpers/variables.js

@@ -1,20 +0,0 @@
-export function getAllVariableSymbols(measurement) {
-    return Object.values(measurement.data[0].variables).map((v) => v.label);
-}
-export function getPreferredVariable(measurement, axis) {
-    if (axis === 'x') {
-        return measurement.data[0].variables.x || measurement.data[0].variables.a;
-    }
-    else {
-        return measurement.data[0].variables.y || measurement.data[0].variables.b;
-    }
-}
-export function getVariableByLabel(measurement, label) {
-    const variables = measurement.data[0].variables;
-    for (const value of Object.values(variables)) {
-        if (value.label === label)
-            return value;
-    }
-    return null;
-}
-//# sourceMappingURL=variables.js.map

package/lib-esm/app-data/helpers/variables.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/index.d.ts

@@ -1,7 +0,0 @@
-export * from './enhancers/index';
-export * from './helpers/index';
-export * from './kinds/index';
-export * from './loaders/index';
-export * from './state/index';
-export * from './utils';
-//# sourceMappingURL=index.d.ts.map

package/lib-esm/app-data/index.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/index.js

@@ -1,7 +0,0 @@
-export * from './enhancers/index';
-export * from './helpers/index';
-export * from './kinds/index';
-export * from './loaders/index';
-export * from './state/index';
-export * from './utils';
-//# sourceMappingURL=index.js.map

package/lib-esm/app-data/index.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/index.d.ts

@@ -1,3 +0,0 @@
-export * from './ir/index';
-export * from './iv/index';
-//# sourceMappingURL=index.d.ts.map

package/lib-esm/app-data/kinds/index.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/index.js

@@ -1,3 +0,0 @@
-export * from './ir/index';
-export * from './iv/index';
-//# sourceMappingURL=index.js.map

package/lib-esm/app-data/kinds/index.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/ir/IrMeasurement.d.ts

@@ -1,13 +0,0 @@
-import type { MeasurementBase } from '../../index';
-import type { IrPeak } from './IrPeak';
-/**
- * When we have a simple measurement like uv, ir, etc, data should only contain one element
- * Sometimes measurements are more complex like in GC / MS, GC / MS / MS, raman images, etc. In this case we will add the meta and info properties
- * to differentiate each measurement
- * If we have isotherm with gaz absorption / desorption this format should also be used.
- * The 'info'for each 'Measurement' should be normalized.
- */
-export interface IrMeasurement extends MeasurementBase {
-    peaks?: IrPeak[];
-}
-//# sourceMappingURL=IrMeasurement.d.ts.map

package/lib-esm/app-data/kinds/ir/IrMeasurement.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/ir/IrMeasurement.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=IrMeasurement.js.map

package/lib-esm/app-data/kinds/ir/IrMeasurement.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"IrMeasurement.js","sourceRoot":"","sources":["../../../../src/app-data/kinds/ir/IrMeasurement.ts"],"names":[],"mappings":""}

package/lib-esm/app-data/kinds/ir/IrPeak.d.ts

@@ -1,8 +0,0 @@
-export type IrPeakKind = 'S' | 'w' | 'm';
-export interface IrPeak {
-    wavenumber: number;
-    absorbance: number;
-    transmittance: number;
-    kind: IrPeakKind;
-}
-//# sourceMappingURL=IrPeak.d.ts.map

package/lib-esm/app-data/kinds/ir/IrPeak.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"IrPeak.d.ts","sourceRoot":"","sources":["../../../../src/app-data/kinds/ir/IrPeak.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,UAAU,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;AAEzC,MAAM,WAAW,MAAM;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,MAAM,CAAC;IACtB,IAAI,EAAE,UAAU,CAAC;CAClB"}

package/lib-esm/app-data/kinds/ir/IrPeak.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=IrPeak.js.map

package/lib-esm/app-data/kinds/ir/IrPeak.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"IrPeak.js","sourceRoot":"","sources":["../../../../src/app-data/kinds/ir/IrPeak.ts"],"names":[],"mappings":""}

package/lib-esm/app-data/kinds/ir/index.d.ts

@@ -1,5 +0,0 @@
-export * from './irAutoPeakPickingEnhancer';
-export * from './IrMeasurement';
-export * from './irMeasurementEnhancer';
-export * from './IrPeak';
-//# sourceMappingURL=index.d.ts.map

package/lib-esm/app-data/kinds/ir/index.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/ir/index.js

@@ -1,5 +0,0 @@
-export * from './irAutoPeakPickingEnhancer';
-export * from './IrMeasurement';
-export * from './irMeasurementEnhancer';
-export * from './IrPeak';
-//# sourceMappingURL=index.js.map

package/lib-esm/app-data/kinds/ir/index.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/ir/irAutoPeakPickingEnhancer.d.ts

@@ -1,20 +0,0 @@
-import { GSDOptions } from 'ml-gsd';
-import type { Shape1D } from 'ml-peak-shape-generator';
-import type { IrMeasurement } from './IrMeasurement';
-export interface AutoPeakPickingOptions extends GSDOptions {
-    /** x variable label, by default 'x' */
-    xVariable?: string;
-    /** y variable label, by default 'y' */
-    yVariable?: string;
-    shape?: Shape1D;
-    /** First X value for the peak picking (default: first X value */
-    from?: number;
-    /** Last X value for the peak picking (default: last X value */
-    to?: number;
-    /** Minimal peak width */
-    minPeakWidth?: number;
-}
-/** Based on a x value we will return a peak*/
-export declare function irAutoPeakPickingEnhancer(measurement: IrMeasurement, options?: AutoPeakPickingOptions): never[] | undefined;
-export declare function getIrAutoPeakPickingEnhancer(options: AutoPeakPickingOptions | undefined): (measurement: IrMeasurement) => never[] | undefined;
-//# sourceMappingURL=irAutoPeakPickingEnhancer.d.ts.map

package/lib-esm/app-data/kinds/ir/irAutoPeakPickingEnhancer.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/ir/irAutoPeakPickingEnhancer.js

@@ -1,50 +0,0 @@
-import { gsd } from 'ml-gsd';
-import { xMinMaxValues } from 'ml-spectra-processing';
-/** Based on a x value we will return a peak*/
-export function irAutoPeakPickingEnhancer(measurement, options = {}) {
-    const { xVariable = 'x', yVariable = 'y', minPeakWidth } = options;
-    // we throw if there are more than one spectrum
-    if (measurement.data.length > 1) {
-        throw new Error('autoPeakPickingEnhancer can only be applied if there is only on measurement data');
-    }
-    if (measurement.data.length === 0)
-        return;
-    const datum = measurement.data[0];
-    const x = datum.variables[xVariable]?.data;
-    const y = datum.variables[yVariable]?.data;
-    if (!x || !y)
-        return [];
-    const { from, to } = options;
-    let peaks = gsd({ x, y }, options);
-    if (from !== undefined) {
-        peaks = peaks.filter((peak) => peak.x >= from);
-    }
-    if (to !== undefined) {
-        peaks = peaks.filter((peak) => peak.x <= to);
-    }
-    if (minPeakWidth) {
-        peaks = peaks.filter((peak) => peak.width >= minPeakWidth);
-    }
-    const minMaxTransmittance = xMinMaxValues(datum.variables.t.data);
-    const results = peaks.map((peak) => ({
-        wavenumber: datum.variables.x.data[peak.index],
-        absorbance: datum.variables.a.data[peak.index],
-        transmittance: datum.variables.t.data[peak.index] / 100,
-        kind: getPeakKind(datum.variables.t.data[peak.index], minMaxTransmittance.min, minMaxTransmittance.max),
-    }));
-    measurement.peaks = results;
-}
-export function getIrAutoPeakPickingEnhancer(options) {
-    return (measurement) => irAutoPeakPickingEnhancer(measurement, options);
-}
-function getPeakKind(transmittance, minTransmittance, maxTransmittance) {
-    const position = (maxTransmittance - transmittance) / (maxTransmittance - minTransmittance);
-    if (position < 0.33) {
-        return 'w';
-    }
-    else if (position < 0.66) {
-        return 'm';
-    }
-    return 'S';
-}
-//# sourceMappingURL=irAutoPeakPickingEnhancer.js.map

package/lib-esm/app-data/kinds/ir/irAutoPeakPickingEnhancer.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/ir/irMeasurementEnhancer.d.ts

@@ -1,8 +0,0 @@
-import type { MeasurementBase } from '../../index';
-/**
- * we add missing absorbance / transmittance
- * variable a = absorbance
- * variable t = transmittance
- */
-export declare function irMeasurementEnhancer(measurement: MeasurementBase): void;
-//# sourceMappingURL=irMeasurementEnhancer.d.ts.map

package/lib-esm/app-data/kinds/ir/irMeasurementEnhancer.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/ir/irMeasurementEnhancer.js

@@ -1,47 +0,0 @@
-/**
- * we add missing absorbance / transmittance
- * variable a = absorbance
- * variable t = transmittance
- */
-export function irMeasurementEnhancer(measurement) {
-    for (const datum of measurement.data) {
-        const variables = datum.variables;
-        const yVariable = variables.y;
-        let absorbance = true;
-        if (yVariable.label.toLowerCase().includes('trans')) {
-            absorbance = false;
-        }
-        if (absorbance) {
-            variables.a = { ...yVariable };
-            variables.a.data = variables.a.data.slice();
-            variables.t = {
-                data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
-                label: 'Transmittance (%)',
-                units: '',
-            };
-        }
-        else {
-            const factor = yVariable.label.includes('%') ||
-                yVariable.label.toLowerCase().includes('percent')
-                ? 100
-                : 1;
-            variables.a = {
-                data: yVariable.data.map((transmittance) => -Math.log10(transmittance / factor)),
-                label: 'Absorbance',
-                units: '',
-            };
-            if (factor === 100) {
-                variables.t = { ...yVariable };
-                variables.t.data = variables.t.data.slice();
-            }
-            else {
-                variables.t = {
-                    units: '',
-                    label: 'Transmittance (%)',
-                    data: yVariable.data.map((transmittance) => transmittance * 100),
-                };
-            }
-        }
-    }
-}
-//# sourceMappingURL=irMeasurementEnhancer.js.map

package/lib-esm/app-data/kinds/ir/irMeasurementEnhancer.js.map

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package/lib-esm/app-data/kinds/iv/IvMeasurement.d.ts

@@ -1,3 +0,0 @@
-import type { MeasurementBase } from '../../index';
-export type IvMeasurement = MeasurementBase;
-//# sourceMappingURL=IvMeasurement.d.ts.map

package/lib-esm/app-data/kinds/iv/IvMeasurement.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"IvMeasurement.d.ts","sourceRoot":"","sources":["../../../../src/app-data/kinds/iv/IvMeasurement.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,aAAa,CAAC;AAEnD,MAAM,MAAM,aAAa,GAAG,eAAe,CAAC"}

package/lib-esm/app-data/kinds/iv/IvMeasurement.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=IvMeasurement.js.map

package/lib-esm/app-data/kinds/iv/IvMeasurement.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"IvMeasurement.js","sourceRoot":"","sources":["../../../../src/app-data/kinds/iv/IvMeasurement.ts"],"names":[],"mappings":""}

package/lib-esm/app-data/kinds/iv/index.d.ts

@@ -1,2 +0,0 @@
-export * from './IvMeasurement';
-//# sourceMappingURL=index.d.ts.map

package/lib-esm/app-data/kinds/iv/index.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/kinds/iv/index.js

@@ -1,2 +0,0 @@
-export * from './IvMeasurement';
-//# sourceMappingURL=index.js.map

package/lib-esm/app-data/kinds/iv/index.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/loaders/biologicLoader.d.ts

@@ -1,11 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import type { Measurements } from '../index';
-/**
- *
- * @param fileCollection - the dragged file/files
- * @param logs - pass to append errors to the logs, it mutates the external array.
- * @returns - new measurements object to be merged
- */
-export declare function biologicLoader(fileCollection: FileCollection, logger?: FifoLogger): Promise<Partial<Measurements>>;
-//# sourceMappingURL=biologicLoader.d.ts.map

package/lib-esm/app-data/loaders/biologicLoader.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/loaders/biologicLoader.js

@@ -1,141 +0,0 @@
-import { parseMPR, parseMPT } from 'biologic-converter';
-import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
-/**
- *
- * @param fileCollection - the dragged file/files
- * @param logs - pass to append errors to the logs, it mutates the external array.
- * @returns - new measurements object to be merged
- */
-export async function biologicLoader(fileCollection, logger) {
-    const measurements = {};
-    const entries = [];
-    for (const file of fileCollection.files) {
-        try {
-            if (/\.mpr$/i.test(file.name)) {
-                // TODO: load in parallel
-                // eslint-disable-next-line no-await-in-loop
-                const mpr = parseMPR(await file.arrayBuffer());
-                const meta = mpr.settings.variables;
-                const info = getMeasurementInfoFromFile(file, `Experiment: ${meta.technique}`);
-                // puts the "useful" variables at x and y for default plot.
-                const variables = preferredXY(meta.technique, mpr.data.variables);
-                const result = {
-                    ...info,
-                    meta,
-                    data: [{ variables }],
-                };
-                entries.push(result);
-            }
-            else if (/\.mpt$/i.test(file.name)) {
-                // TODO: load in parallel
-                // eslint-disable-next-line no-await-in-loop
-                const { data, settings } = parseMPT(await file.arrayBuffer());
-                if (data.variables) {
-                    const metaData = settings?.variables;
-                    const info = getMeasurementInfoFromFile(file, metaData?.technique
-                        ? `Experiment: ${metaData.technique}`
-                        : file.name);
-                    // puts the "useful" variables at x and y for default plot.
-                    const variables = preferredXY(metaData?.technique, data.variables);
-                    const result = {
-                        ...info,
-                        meta: metaData || {},
-                        data: [{ variables }],
-                    };
-                    entries.push(result);
-                }
-            }
-        }
-        catch (error) {
-            //send error to UI to show to User ?
-            if (error instanceof Error) {
-                if (logger) {
-                    logger.error(error);
-                }
-                else {
-                    throw error;
-                }
-            }
-        }
-    }
-    logger?.debug(`Loaded ${entries.length} entries with biologicLoader`);
-    measurements.iv = { entries };
-    return measurements;
-}
-/**
- * Each biologic experiment stores measurement variables (not just `x` and `y`) in the
- * `data.variables` object.
- * this function takes "useful ones", and place them as `x` and `y`.
- * so they are default for the plot.
- * @param technique technique used in the experiment
- * @param variables experiment variables
- * @returns the same data (and type) with rearranged variables.
- * (does not need return type as it is inferred)
- */
-function preferredXY(technique, variables) {
-    if (!technique)
-        return variables;
-    switch (technique) {
-        case 'CA': {
-            //Chronoamperometry or Chronocoulometry (distinguish?)
-            variables = setDefault(variables, 'I', 'y');
-            variables = setDefault(variables, 'time', 'x');
-            break;
-        }
-        case 'CP': {
-            //Chronopotentiometry. <average>
-            variables = setDefault(variables, '<Ewe>', 'y');
-            variables = setDefault(variables, 'time', 'x');
-            break;
-        }
-        case 'CV': {
-            //cyclic voltammetry. <average>
-            variables = setDefault(variables, '<I>', 'y');
-            variables = setDefault(variables, 'Ewe', 'x');
-            break;
-        }
-        case 'GCPL': {
-            variables = setDefault(variables, 'Ewe', 'y');
-            variables = setDefault(variables, 'time', 'x');
-            break;
-        }
-        case 'OCV': {
-            variables = setDefault(variables, 'Ewe', 'y');
-            variables = setDefault(variables, 'time', 'x');
-            break;
-        }
-        default:
-            break;
-    }
-    return variables;
-}
-/**
- * Stores object with "label" at either "x" or "y".
- * the data stored is still the same.
- * @param variables experimental variables
- * @param label label to search for in the variables object (time, potential, current, etc)
- * @param storeAt which key to move that data to
- * @returns the new variables object.
- */
-function setDefault(variables, label, storeAt) {
-    for (const varum in variables) {
-        // find the key with `label` (or skip if not found)
-        if (variables[varum].label === label && //if not already at the right key
-            varum !== storeAt) {
-            // populate key, if there is no data there.
-            if (!variables[storeAt]) {
-                variables[storeAt] = variables[varum];
-                delete variables[varum];
-            }
-            else {
-                // if the storeAt is already occupied, swap the two
-                const originalX = variables[storeAt];
-                const newX = variables[varum];
-                variables[storeAt] = newX;
-                variables[varum] = originalX;
-            }
-        }
-    }
-    return variables;
-}
-//# sourceMappingURL=biologicLoader.js.map

package/lib-esm/app-data/loaders/biologicLoader.js.map

@@ -1 +0,0 @@
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package/lib-esm/app-data/loaders/cdfLoader.d.ts

@@ -1,5 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import type { Measurements } from '../index';
-export declare function cdfLoader(fileCollection: FileCollection, logger?: FifoLogger): Promise<Partial<Measurements>>;
-//# sourceMappingURL=cdfLoader.d.ts.map

package/lib-esm/app-data/loaders/cdfLoader.d.ts.map

@@ -1 +0,0 @@
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