react-science 7.0.0 → 8.0.0

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 @@
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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

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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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package/lib-esm/app-data/loaders/cdfLoader.js

@@ -1,164 +0,0 @@
-import { NetCDFReader } from 'netcdfjs';
-import { assert } from '../../components/index';
-import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
-export async function cdfLoader(fileCollection, logger) {
-    const newMeasurements = {};
-    let kind;
-    let count = 0;
-    for (const file of fileCollection) {
-        if (/\.cdf$/i.test(file.name)) {
-            try {
-                // TODO: load in parallel
-                // eslint-disable-next-line no-await-in-loop
-                const reader = new NetCDFReader(await file.arrayBuffer());
-                if (reader.dataVariableExists('mass_values') &&
-                    reader.dataVariableExists('time_values')) {
-                    kind = 'gclcms';
-                }
-                else if (reader.dataVariableExists('ordinate_values') &&
-                    reader.getAttribute('detector_name')?.match(/dad|tic/i)) {
-                    kind = 'gclc';
-                }
-                else {
-                    return newMeasurements;
-                }
-                addMeta(reader, reader.globalAttributes);
-                if (!newMeasurements[kind]) {
-                    newMeasurements[kind] = { entries: [] };
-                }
-                assert(newMeasurements[kind], 'Error while loading, kind is not defined');
-                const newMeasurement = {
-                    ...getMeasurementInfoFromFile(file, reader.getAttribute('experiment_title')),
-                    // @ts-expect-error meta is not defined in reader.
-                    meta: reader.header.meta,
-                    data: kind === 'gclcms'
-                        ? chromatogramWithMassSpectra(reader)
-                        : chromatogram(reader),
-                };
-                newMeasurements[kind]?.entries.push(newMeasurement);
-                count++;
-            }
-            catch (error) {
-                if (error instanceof Error) {
-                    //send error to UI ?
-                    if (logger) {
-                        logger.error(error);
-                    }
-                    else {
-                        throw error;
-                    }
-                }
-            }
-        }
-    }
-    logger?.debug(`Loaded ${count} measurements with cdfLoader`);
-    return newMeasurements;
-}
-function chromatogramWithMassSpectra(reader) {
-    // Taken from: https://github.com/cheminfo/netcdf-gcms
-    const pointCount = reader.getDataVariable('point_count');
-    const massValues = reader.getDataVariable('mass_values');
-    const intensityValues = reader.getDataVariable('intensity_values');
-    const times = reader.getDataVariable('scan_acquisition_time');
-    const tics = reader.getDataVariable('total_intensity');
-    let index = 0;
-    const allMasses = [];
-    const allIntensities = [];
-    for (const size of pointCount) {
-        const masses = new Float64Array(size);
-        const intensities = new Float64Array(size);
-        for (let j = 0; j < size; j++) {
-            masses[j] = massValues[index];
-            intensities[j] = intensityValues[index++];
-        }
-        allIntensities.push(intensities);
-        allMasses.push(masses);
-    }
-    const data = [];
-    for (let i = 0; i < times.length; i++) {
-        data.push({
-            info: {
-                time: { value: times[i], units: 's' },
-                tic: tics[i],
-            },
-            variables: {
-                x: {
-                    symbol: 'X',
-                    label: 'm/z',
-                    units: '',
-                    data: allMasses[i] || [],
-                },
-                y: {
-                    symbol: 'Y',
-                    label: 'relative intensity',
-                    units: '',
-                    data: allIntensities[i] || [],
-                },
-            },
-        });
-    }
-    return data;
-}
-function chromatogram(reader) {
-    // Taken from: https://github.com/cheminfo/netcdf-gcms
-    const data = [];
-    const intensities = reader.getDataVariable('ordinate_values');
-    const numberPoints = intensities.length;
-    const detector = reader.getAttribute('detector_name');
-    let channel;
-    if (/dad/i.test(detector)) {
-        const uvNumber = detector.match(/.*Sig=(?<uvNumber>\d+).*/)?.groups
-            ?.uvNumber;
-        channel = `uv${Number(uvNumber) || ''}`;
-    }
-    else if (/tic/i.test(detector)) {
-        channel = 'tic';
-    }
-    else {
-        channel = 'unknown';
-    }
-    const delayTime = reader.getDataVariable('actual_delay_time')[0];
-    const runtimeLength = reader.getDataVariable('actual_run_time_length')[0];
-    let samplingInterval;
-    if (reader.dataVariableExists('actual_sampling_interval')) {
-        samplingInterval = reader.getDataVariable('actual_sampling_interval')[0];
-        if (Math.abs(delayTime + samplingInterval * numberPoints - runtimeLength) > 3) {
-            throw new Error('The expected last time does not correspond to the runtimeLength');
-        }
-    }
-    else {
-        samplingInterval = (runtimeLength - delayTime) / numberPoints;
-    }
-    const times = [];
-    let time = delayTime;
-    for (let i = 0; i < numberPoints; i++) {
-        times.push(time);
-        time += samplingInterval;
-    }
-    data.push({
-        variables: {
-            x: {
-                symbol: 'X',
-                label: 'time',
-                units: 's',
-                data: times || [],
-            },
-            y: {
-                symbol: 'Y',
-                label: channel,
-                units: '',
-                data: intensities || [],
-            },
-        },
-    });
-    return data;
-}
-function addMeta(reader, globalAttributes) {
-    // @ts-expect-error meta is not defined in reader.
-    reader.header.meta = {};
-    for (const item of globalAttributes) {
-        // @ts-expect-error meta is not defined in reader.
-        reader.header.meta[item.name] = item.value;
-    }
-}
-//# sourceMappingURL=cdfLoader.js.map

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

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

@@ -1,9 +0,0 @@
-export * from './proprietary/agilent/cary500Loader';
-export * from './utility/index';
-export * from './biologicLoader';
-export * from './cdfLoader';
-export * from './jcampLoader';
-export * from './loadMeasurements';
-export * from './spcLoader';
-export * from './wdfLoader';
-//# sourceMappingURL=index.d.ts.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/app-data/loaders/index.ts"],"names":[],"mappings":"AAAA,cAAc,qCAAqC,CAAC;AACpD,cAAc,iBAAiB,CAAC;AAChC,cAAc,kBAAkB,CAAC;AACjC,cAAc,aAAa,CAAC;AAC5B,cAAc,eAAe,CAAC;AAC9B,cAAc,oBAAoB,CAAC;AACnC,cAAc,aAAa,CAAC;AAC5B,cAAc,aAAa,CAAC"}

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

@@ -1,9 +0,0 @@
-export * from './proprietary/agilent/cary500Loader';
-export * from './utility/index';
-export * from './biologicLoader';
-export * from './cdfLoader';
-export * from './jcampLoader';
-export * from './loadMeasurements';
-export * from './spcLoader';
-export * from './wdfLoader';
-//# sourceMappingURL=index.js.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/app-data/loaders/index.ts"],"names":[],"mappings":"AAAA,cAAc,qCAAqC,CAAC;AACpD,cAAc,iBAAiB,CAAC;AAChC,cAAc,kBAAkB,CAAC;AACjC,cAAc,aAAa,CAAC;AAC5B,cAAc,eAAe,CAAC;AAC9B,cAAc,oBAAoB,CAAC;AACnC,cAAc,aAAa,CAAC;AAC5B,cAAc,aAAa,CAAC"}

package/lib-esm/app-data/loaders/jcampLoader.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 logger - whether to log to console or not
- * @returns - new measurements object to be merged
- */
-export declare function jcampLoader(fileCollection: FileCollection, logger?: FifoLogger): Promise<Partial<Measurements>>;
-//# sourceMappingURL=jcampLoader.d.ts.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"jcampLoader.d.ts","sourceRoot":"","sources":["../../../src/app-data/loaders/jcampLoader.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAC9C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAC;AAIrD,OAAO,KAAK,EAAmB,YAAY,EAAE,MAAM,UAAU,CAAC;AAI9D;;;;;GAKG;AACH,wBAAsB,WAAW,CAC/B,cAAc,EAAE,cAAc,EAC9B,MAAM,CAAC,EAAE,UAAU,GAClB,OAAO,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAsDhC"}

package/lib-esm/app-data/loaders/jcampLoader.js

@@ -1,100 +0,0 @@
-import { convert } from 'jcampconverter';
-import { assert } from '../../components/index';
-import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
-/**
- *
- * @param fileCollection - the dragged file/files
- * @param logger - whether to log to console or not
- * @returns - new measurements object to be merged
- */
-export async function jcampLoader(fileCollection, logger) {
-    let count = 0;
-    const newMeasurements = {};
-    for (const file of fileCollection) {
-        if (/(?:\.jdx|\.dx)$/i.test(file.name)) {
-            try {
-                // TODO: load in parallel
-                // eslint-disable-next-line no-await-in-loop
-                const parsed = convert(await file.text(), { keepRecordsRegExp: /.*/ });
-                for (const measurement of parsed.flatten) {
-                    let kind;
-                    if (measurement?.dataType?.match(/infrared|ir/i)) {
-                        kind = 'ir';
-                    }
-                    else if (measurement?.dataType?.match(/raman/i)) {
-                        kind = 'raman';
-                    }
-                    else if (measurement?.dataType?.match(/uv/i)) {
-                        kind = 'uv';
-                    }
-                    else if (measurement?.dataType?.match(/mass/i)) {
-                        kind = 'mass';
-                    }
-                    else if (measurement?.dataType?.match(/nmr/i)) {
-                        kind = 'nmr';
-                    }
-                    if (kind) {
-                        if (!newMeasurements[kind]) {
-                            newMeasurements[kind] = { entries: [] };
-                        }
-                        assert(newMeasurements[kind], 'Error while loading, kind is not defined');
-                        const newMeasurement = {
-                            ...getMeasurementInfoFromFile(file, measurement.title || ''),
-                            meta: measurement.meta,
-                            data: normalizeSpectra(measurement.spectra),
-                        };
-                        count++;
-                        Object.assign(newMeasurement.info, measurement.info);
-                        newMeasurements[kind]?.entries.push(newMeasurement);
-                    }
-                }
-            }
-            catch (error) {
-                if (error instanceof Error) {
-                    if (logger) {
-                        logger?.error(error);
-                    }
-                    else {
-                        throw error;
-                    }
-                }
-            }
-        }
-    }
-    logger?.debug(`Loaded ${count} measurements with jcampLoader`);
-    return newMeasurements;
-}
-function normalizeSpectra(spectra) {
-    const data = [];
-    for (const spectrum of spectra) {
-        let variables = spectrum.variables;
-        if (!variables) {
-            variables = {};
-            variables.x = {
-                label: spectrum.xUnits,
-                symbol: 'X',
-                data: spectrum.data.x || spectrum.data.X,
-            };
-            variables.y = {
-                label: spectrum.yUnits,
-                symbol: 'Y',
-                data: spectrum.data.y || spectrum.data.Y,
-            };
-        }
-        else {
-            for (const key in variables) {
-                const variable = variables[key];
-                if (variable.label)
-                    continue;
-                let label = variable.name || variable.symbol || key;
-                if (variable.units && !label.includes(variable.units)) {
-                    label += ` [${variable.units}]`;
-                }
-                variable.label = label;
-            }
-        }
-        data.push({ variables });
-    }
-    return data;
-}
-//# sourceMappingURL=jcampLoader.js.map

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

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

@@ -1,15 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import { Enhancers, Measurements } from '../index';
-import { MeasurementsLoader } from './utility/measurementLoader';
-import type { ParserLog } from './utility/parserLog';
-export interface LoadOptions {
-    loaders?: MeasurementsLoader[];
-    enhancers?: Partial<Enhancers>;
-    logger?: FifoLogger;
-}
-export declare function loadMeasurements(fileCollection: FileCollection, options: LoadOptions): Promise<{
-    measurements: Partial<Measurements>;
-    logs: ParserLog[];
-}>;
-//# sourceMappingURL=loadMeasurements.d.ts.map

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

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

@@ -1,37 +0,0 @@
-import { xMinMaxValues } from 'ml-spectra-processing';
-import { enhance } from '../index';
-import { mergeMeasurements, } from './utility/measurementLoader';
-export async function loadMeasurements(fileCollection, options) {
-    const measurements = {};
-    const logs = [];
-    const { loaders = [], enhancers = {}, logger } = options;
-    for (const loader of loaders) {
-        // TODO: load in parallel
-        // eslint-disable-next-line no-await-in-loop
-        const loaderData = await loader(fileCollection, logger);
-        for (const { entries } of Object.values(loaderData)) {
-            for (const entry of entries) {
-                computeMinMax(entry);
-            }
-        }
-        enhance(loaderData, enhancers);
-        mergeMeasurements(measurements, loaderData);
-    }
-    return { measurements, logs };
-}
-function computeMinMax(measurement) {
-    for (const datum of measurement.data) {
-        for (const variable of Object.values(datum.variables)) {
-            if (variable.data.length === 0) {
-                // TODO: should we accept empty data?
-                return;
-            }
-            if (variable.min === undefined || variable.max === undefined) {
-                const { min, max } = xMinMaxValues(variable.data);
-                variable.min = min;
-                variable.max = max;
-            }
-        }
-    }
-}
-//# sourceMappingURL=loadMeasurements.js.map

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

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package/lib-esm/app-data/loaders/proprietary/agilent/cary500Loader.d.ts

@@ -1,5 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import { Measurements } from '../../../index';
-export declare function cary500Loader(fileCollection: FileCollection, logger?: FifoLogger): Promise<Partial<Measurements>>;
-//# sourceMappingURL=cary500Loader.d.ts.map

package/lib-esm/app-data/loaders/proprietary/agilent/cary500Loader.d.ts.map

@@ -1 +0,0 @@
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