react-science 10.0.0 → 11.0.0

package/src/app-data/loaders/biologicLoader.ts

@@ -1,166 +0,0 @@
-import { parseMPR, parseMPT } from 'biologic-converter';
-import type { MeasurementVariable } from 'cheminfo-types';
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-
-import type { MeasurementBase, Measurements } from '../index.js';
-
-import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile.js';
-
-/* the MeasurementBase has got a data key,
- and inside a variable key, compatible with this type */
-type MeasurementDataVariable = Record<string, MeasurementVariable>;
-/**
- *
- * @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: FileCollection,
-  logger?: FifoLogger,
-): Promise<Partial<Measurements>> {
-  const measurements: Partial<Measurements> = {};
-  const entries: MeasurementBase[] = [];
-
-  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: ${meta.technique}`,
-        );
-        // puts the "useful" variables at x and y for default plot.
-        const variables = preferredXY(meta.technique, mpr.data.variables);
-        const result: MeasurementBase = {
-          ...info,
-          meta,
-          data: [{ variables }],
-        };
-        entries.push(result);
-      } else if (/\.mpt$/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: MeasurementBase = {
-            ...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: string | undefined,
-  variables: MeasurementDataVariable,
-) {
-  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: MeasurementDataVariable,
-  label: string,
-  storeAt: 'x' | 'y',
-) {
-  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;
-}

package/src/app-data/loaders/cdfLoader.ts

@@ -1,206 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import { NetCDFReader } from 'netcdfjs';
-
-import { assert } from '../../components/index.js';
-import type {
-  MeasurementBase,
-  MeasurementKind,
-  Measurements,
-} from '../index.js';
-
-import { getMeasurementInfoFromFile } from './utility/index.js';
-
-export async function cdfLoader(
-  fileCollection: FileCollection,
-  logger?: FifoLogger,
-): Promise<Partial<Measurements>> {
-  const newMeasurements: Partial<Measurements> = {};
-  let kind: MeasurementKind | undefined;
-  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') as string | null)?.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') as string,
-          ),
-          // @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: NetCDFReader,
-): MeasurementBase['data'] {
-  // Taken from: https://github.com/cheminfo/netcdf-gcms
-  const pointCount = reader.getDataVariable('point_count') as number[];
-  const massValues = reader.getDataVariable('mass_values') as number[];
-  const intensityValues = reader.getDataVariable(
-    'intensity_values',
-  ) as number[];
-  const times = reader.getDataVariable('scan_acquisition_time');
-  const tics = reader.getDataVariable('total_intensity');
-
-  let index = 0;
-  const allMasses: Float64Array[] = [];
-  const allIntensities: Float64Array[] = [];
-  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: MeasurementBase['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: NetCDFReader): MeasurementBase['data'] {
-  // Taken from: https://github.com/cheminfo/netcdf-gcms
-  const data: MeasurementBase['data'] = [];
-  const intensities = reader.getDataVariable('ordinate_values') as number[];
-  const numberPoints = intensities.length;
-  const detector = reader.getAttribute('detector_name') as string;
-  let channel: string;
-  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] as number;
-  const runtimeLength: number = reader.getDataVariable(
-    'actual_run_time_length',
-  )[0] as number;
-  let samplingInterval;
-  if (reader.dataVariableExists('actual_sampling_interval')) {
-    samplingInterval = reader.getDataVariable(
-      'actual_sampling_interval',
-    )[0] as number;
-
-    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: number[] = [];
-  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: NetCDFReader,
-  globalAttributes: NetCDFReader['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;
-  }
-}

package/src/app-data/loaders/index.ts

@@ -1,8 +0,0 @@
-export * from './proprietary/agilent/cary500Loader.js';
-export * from './utility/index.js';
-export * from './biologicLoader.js';
-export * from './cdfLoader.js';
-export * from './jcampLoader.js';
-export * from './loadMeasurements.js';
-export * from './spcLoader.js';
-export * from './wdfLoader.js';

package/src/app-data/loaders/jcampLoader.ts

@@ -1,105 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import { convert } from 'jcampconverter';
-
-import { assert } from '../../components/index.js';
-import type { MeasurementKind, Measurements } from '../index.js';
-
-import { getMeasurementInfoFromFile } from './utility/index.js';
-
-/**
- *
- * @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: FileCollection,
-  logger?: FifoLogger,
-): Promise<Partial<Measurements>> {
-  let count = 0;
-  const newMeasurements: Partial<Measurements> = {};
-  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: MeasurementKind | undefined;
-          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 ${count} measurements with jcampLoader`);
-  return newMeasurements;
-}
-
-function normalizeSpectra(spectra: any) {
-  const data: any[] = [];
-  for (const spectrum of spectra) {
-    let variables = spectrum.variables;
-    if (!variables) {
-      variables = {};
-      variables.x = {
-        label: spectrum.xUnits,
-        symbol: 'X',
-        data: spectrum.data.x || spectrum.data.X,
-      };
-      variables.y = {
-        label: spectrum.yUnits,
-        symbol: 'Y',
-        data: spectrum.data.y || spectrum.data.Y,
-      };
-    } else {
-      for (const key in variables) {
-        const variable = variables[key];
-        if (variable.label) continue;
-        let label: string = variable.name || variable.symbol || key;
-        if (variable.units && !label.includes(variable.units)) {
-          label += ` [${variable.units}]`;
-        }
-        variable.label = label;
-      }
-    }
-    data.push({ variables });
-  }
-  return data;
-}

package/src/app-data/loaders/loadMeasurements.ts

@@ -1,53 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import { xMinMaxValues } from 'ml-spectra-processing';
-
-import type { Enhancers, MeasurementBase, Measurements } from '../index.js';
-import { enhance } from '../index.js';
-
-import type { MeasurementsLoader, ParserLog } from './utility/index.js';
-import { mergeMeasurements } from './utility/index.js';
-
-export interface LoadOptions {
-  loaders?: MeasurementsLoader[];
-  enhancers?: Partial<Enhancers>;
-  logger?: FifoLogger;
-}
-
-export async function loadMeasurements(
-  fileCollection: FileCollection,
-  options: LoadOptions,
-) {
-  const measurements: Partial<Measurements> = {};
-  const logs: ParserLog[] = [];
-  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: MeasurementBase) {
-  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;
-      }
-    }
-  }
-}

package/src/app-data/loaders/proprietary/agilent/cary500Loader.ts

@@ -1,82 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection, FileCollectionItem } from 'filelist-utils';
-
-import type { MeasurementBase, Measurements } from '../../../index.js';
-import { getMeasurementInfoFromFile } from '../../../index.js';
-
-export async function cary500Loader(
-  fileCollection: FileCollection,
-  logger?: FifoLogger,
-): Promise<Partial<Measurements>> {
-  const newMeasurements: Partial<Measurements> = {};
-  const entries: MeasurementBase[] = [];
-
-  for (const file of fileCollection) {
-    if (/\.csv$/i.test(file.name)) {
-      try {
-        // TODO: load in parallel
-        // eslint-disable-next-line no-await-in-loop
-        const experiments = await convert(file);
-        for (const experiment of experiments) {
-          entries.push(experiment);
-        }
-      } catch (error) {
-        if (error instanceof Error) {
-          if (logger) {
-            logger.error(error);
-          } else {
-            throw error;
-          }
-        }
-      }
-    }
-  }
-  logger?.debug(`Loaded ${entries.length} entries with cary500Loader`);
-  newMeasurements.uvvis = { entries };
-  return newMeasurements;
-}
-
-async function convert(file: FileCollectionItem): Promise<MeasurementBase[]> {
-  const text = await file.text();
-  // this format allows many experiments in one file
-  const lines = text.split(/\r?\n/).map((line) => line.trim());
-
-  const titles = lines[0].split(',').map((field) => field.trim());
-  const labelUnits = lines[1].split(',').map((field) => field.trim());
-
-  let lastDataIndex;
-  for (lastDataIndex = 2; lastDataIndex < lines.length; lastDataIndex++) {
-    if (!lines[lastDataIndex].match(/^[\d,.Ee-]+$/)) {
-      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: MeasurementBase[] = [];
-  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: structuredClone(meta),
-      data: [{ variables: { x: xVariable, y: yVariable } }],
-    });
-  }
-  return experiments;
-}
-
-function labelAndUnits(labelUnits: string) {
-  const groups = labelUnits.match(/(?<label>.*) \((?<units>.*)\)/)?.groups;
-  return groups
-    ? { label: groups.label, units: groups.units }
-    : { label: labelUnits, units: '' };
-}

package/src/app-data/loaders/spcLoader.ts

@@ -1,55 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import { guessSpectraType, parse } from 'spc-parser';
-
-import { assert } from '../../components/index.js';
-import type {
-  MeasurementBase,
-  MeasurementKind,
-  Measurements,
-} from '../index.js';
-
-import { getMeasurementInfoFromFile } from './utility/index.js';
-
-/**
- *
- * @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 spcLoader(
-  fileCollection: FileCollection,
-  logger?: FifoLogger,
-): Promise<Partial<Measurements>> {
-  const measurements: Partial<Measurements> = {};
-  for (const file of fileCollection) {
-    if (/\.spc$/i.test(file.name)) {
-      try {
-        // TODO: load in parallel
-        // eslint-disable-next-line no-await-in-loop
-        const parsed = parse(await file.arrayBuffer());
-        const spectraType: MeasurementKind = guessSpectraType(parsed.meta);
-        if (!measurements[spectraType]) {
-          measurements[spectraType] = { entries: [] };
-        }
-        assert(
-          measurements[spectraType],
-          'Error while loading, kind is not defined',
-        );
-        measurements[spectraType]?.entries.push({
-          meta: parsed.meta,
-          ...getMeasurementInfoFromFile(file, parsed.meta.memo),
-          data: parsed.spectra as unknown as MeasurementBase['data'],
-        });
-      } catch (error) {
-        if (error instanceof Error && logger) {
-          logger.error(error);
-        } else {
-          throw error;
-        }
-      }
-    }
-  }
-
-  return measurements;
-}

package/src/app-data/loaders/utility/getMeasurementInfoFromFile.ts

@@ -1,21 +0,0 @@
-import { v4 } from '@lukeed/uuid';
-import type { FileCollectionItem } from 'filelist-utils';
-
-/**
- * creates a template for the MeasurementBase (part)
- * generated from just the file metadata only and id
- * @param obj - file as collection item.
- * @param title
- */
-export function getMeasurementInfoFromFile(
-  { name, relativePath, lastModified, size }: FileCollectionItem,
-  title: string,
-) {
-  return {
-    id: v4(),
-    info: {
-      title,
-      file: { name, path: relativePath, lastModified, size },
-    },
-  };
-}