react-science 0.19.1

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

@@ -0,0 +1,137 @@
+import { parseMPR, parseMPT } from 'biologic-converter';
+import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
+import { createLogEntry } from './utility/parserLog';
+/**
+ *
+ * @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, logs) {
+    const measurements = {};
+    const entries = [];
+    for (const file of fileCollection.files) {
+        try {
+            if (/\.mpr$/i.test(file.name)) {
+                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)) {
+                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 (logs) {
+                    logs.push(createLogEntry({ error, relativePath: file.relativePath }));
+                }
+                else {
+                    throw error;
+                }
+            }
+        }
+    }
+    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

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

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

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

@@ -0,0 +1,166 @@
+// @ts-expect-error netcdfjs has no types at the moment.
+import { NetCDFReader } from 'netcdfjs';
+import { assert } from '../../components/index';
+import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
+import { createLogEntry } from './utility/parserLog';
+export async function cdfLoader(fileCollection, logs) {
+    const newMeasurements = {};
+    let kind;
+    for (const file of fileCollection) {
+        if (/\.cdf$/i.test(file.name)) {
+            try {
+                const reader = new NetCDFReader(await file.arrayBuffer(), {
+                    meta: true,
+                });
+                if (reader.dataVariableExists('mass_values') &&
+                    reader.dataVariableExists('time_values')) {
+                    kind = 'gclcms';
+                }
+                else if (reader.dataVariableExists('ordinate_values') &&
+                    reader.getAttribute('detector_name') &&
+                    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')),
+                    meta: reader.header.meta,
+                    data: kind === 'gclcms'
+                        ? chromatogramWithMassSpectra(reader)
+                        : chromatogram(reader),
+                };
+                newMeasurements[kind]?.entries.push(newMeasurement);
+            }
+            catch (error) {
+                if (error instanceof Error) {
+                    //send error to UI ?
+                    if (logs) {
+                        logs.push(createLogEntry({
+                            error,
+                            parser: 'cdfLoader',
+                            message: 'error parsing file from cdfLoader',
+                            relativePath: file.relativePath,
+                        }));
+                    }
+                    else {
+                        throw error;
+                    }
+                }
+            }
+        }
+    }
+    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);
+    }
+    let 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
+    let 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;
+    }
+    let 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) {
+    reader.header.meta = {};
+    for (const item of globalAttributes) {
+        reader.header.meta[item.name] = item.value;
+    }
+}
+//# sourceMappingURL=cdfLoader.js.map

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

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

@@ -0,0 +1,9 @@
+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

@@ -0,0 +1 @@
+{"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

@@ -0,0 +1,9 @@
+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

@@ -0,0 +1 @@
+{"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

@@ -0,0 +1,11 @@
+import type { FileCollection } from 'filelist-utils';
+import type { Measurements } from '../index';
+import { ParserLog } from './utility/parserLog';
+/**
+ *
+ * @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, logs?: ParserLog[]): Promise<Partial<Measurements>>;
+//# sourceMappingURL=jcampLoader.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"jcampLoader.d.ts","sourceRoot":"","sources":["../../../src/app-data/loaders/jcampLoader.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAC;AAIrD,OAAO,KAAK,EAAmB,YAAY,EAAE,MAAM,UAAU,CAAC;AAG9D,OAAO,EAAkB,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAEhE;;;;;GAKG;AACH,wBAAsB,WAAW,CAC/B,cAAc,EAAE,cAAc,EAC9B,IAAI,CAAC,EAAE,SAAS,EAAE,GACjB,OAAO,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAyDhC"}

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

@@ -0,0 +1,101 @@
+import { convert } from 'jcampconverter';
+import { assert } from '../../components/index';
+import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
+import { createLogEntry } from './utility/parserLog';
+/**
+ *
+ * @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, logs) {
+    const newMeasurements = {};
+    for (const file of fileCollection) {
+        if (/(?:\.jdx|\.dx)$/i.test(file.name)) {
+            try {
+                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),
+                        };
+                        Object.assign(newMeasurement.info, measurement.info);
+                        newMeasurements[kind]?.entries.push(newMeasurement);
+                    }
+                }
+            }
+            catch (error) {
+                // send error to UI ?
+                if (error instanceof Error) {
+                    if (logs) {
+                        logs.push(createLogEntry({
+                            error,
+                            parser: 'jcamp converter',
+                            relativePath: file.relativePath,
+                            message: 'error parsing jdx or dx file',
+                        }));
+                    }
+                    else {
+                        throw error;
+                    }
+                }
+            }
+        }
+    }
+    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 (let key in variables) {
+                const variable = variables[key];
+                if (variable.label)
+                    continue;
+                variable.label = variable.name || variable.symbol || key;
+                if (variable.units && !variable.label.includes(variable.units)) {
+                    variable.label += ` [${variable.units}]`;
+                }
+            }
+        }
+        data.push({ variables });
+    }
+    return data;
+}
+//# sourceMappingURL=jcampLoader.js.map

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

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

@@ -0,0 +1,14 @@
+import type { FileCollection } from 'filelist-utils';
+import { Measurements, Enhancers } from '../index';
+import { MeasurementsLoader } from './utility/measurementLoader';
+import type { ParserLog } from './utility/parserLog';
+export interface LoadOptions {
+    loaders?: MeasurementsLoader[];
+    enhancers?: Partial<Enhancers>;
+    logger?: boolean;
+}
+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

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

@@ -0,0 +1,36 @@
+import { xMinMaxValues } from 'ml-spectra-processing';
+import { enhance } from '../index';
+import { mergeMeasurements, } from './utility/measurementLoader';
+export async function loadMeasurements(fileCollection, options = {}) {
+    const measurements = {};
+    let logs = [];
+    const { loaders = [], enhancers = {}, logger = true } = options;
+    for (const loader of loaders) {
+        const loaderData = await loader(fileCollection, logger ? logs : undefined);
+        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 (typeof variable.min === 'undefined' ||
+                typeof 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

@@ -0,0 +1,4 @@
+import type { FileCollection } from 'filelist-utils';
+import { Measurements, ParserLog } from '../../../index';
+export declare function cary500Loader(fileCollection: FileCollection, logs?: ParserLog[]): Promise<Partial<Measurements>>;
+//# sourceMappingURL=cary500Loader.d.ts.map

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

@@ -0,0 +1 @@
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package/lib-esm/app-data/loaders/proprietary/agilent/cary500Loader.js

@@ -0,0 +1,74 @@
+import { getMeasurementInfoFromFile, createLogEntry, } from '../../../index';
+export async function cary500Loader(fileCollection, logs) {
+    const newMeasurements = {};
+    const entries = [];
+    for (const file of fileCollection) {
+        if (/\.csv$/i.test(file.name)) {
+            try {
+                const experiments = await convert(file);
+                for (const experiment of experiments) {
+                    entries.push(experiment);
+                }
+            }
+            catch (error) {
+                if (error instanceof Error) {
+                    if (logs) {
+                        logs.push(createLogEntry({
+                            kind: 'error',
+                            parser: 'cary500Loader',
+                            message: 'Error parsing cary500 experiment.',
+                            error,
+                            relativePath: file.relativePath,
+                        }));
+                    }
+                    else {
+                        throw error;
+                    }
+                }
+            }
+        }
+    }
+    newMeasurements.uvvis = { entries };
+    return newMeasurements;
+}
+async function convert(file) {
+    const text = await file.text();
+    // this format allows many experiments in one file
+    const lines = text.split(/\r?\n/).map((line) => line.trim());
+    const titles = lines[0].split(',').map((field) => field.trim());
+    const labelUnits = lines[1].split(',').map((field) => field.trim());
+    let lastDataIndex;
+    for (lastDataIndex = 2; lastDataIndex < lines.length; lastDataIndex++) {
+        if (!lines[lastDataIndex].match(/^[\d,.Ee-]+$/)) {
+            break;
+        }
+    }
+    const data = lines.slice(2, lastDataIndex).map((line) => line.split(','));
+    const meta = lines.slice(lastDataIndex);
+    const nbExperiments = Math.floor(labelUnits.length / 2);
+    const experiments = [];
+    for (let i = 0; i < nbExperiments; i++) {
+        const column = i * 2;
+        const xVariable = {
+            ...labelAndUnits(labelUnits[column]),
+            data: data.map((row) => Number(row[column])),
+        };
+        const yVariable = {
+            ...labelAndUnits(labelUnits[column + 1]),
+            data: data.map((row) => Number(row[column + 1])),
+        };
+        experiments.push({
+            ...getMeasurementInfoFromFile(file, titles[column]),
+            meta: JSON.parse(JSON.stringify(meta)),
+            data: [{ variables: { x: xVariable, y: yVariable } }],
+        });
+    }
+    return experiments;
+}
+function labelAndUnits(labelUnits) {
+    const groups = labelUnits.match(/(?<label>.*) \((?<units>.*)\)/)?.groups;
+    return groups
+        ? { label: groups.label, units: groups.units }
+        : { label: labelUnits, units: '' };
+}
+//# sourceMappingURL=cary500Loader.js.map

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

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