react-cheminfo 0.9.0 → 0.10.0

package/lib/spectra/core/axisEntries.js

@@ -0,0 +1,78 @@
+import { RANGE_FIELDS, ZONE_FIELDS } from "./filterEntries.js";
+import { booleanField, enumField, formulaField, integerField, numberField, } from "./filterFields.js";
+export const AXIS_ENTRIES = {
+    xFunction: {
+        label: 'Apply a formula to x',
+        group: 'x-axis',
+        summary: 'Rewrites every x through an expression, read the same way as the y one.',
+        fields: [
+            formulaField('function', 'Expression in x', 'For instance 10000000/x, which reads nanometres as wavenumbers.'),
+        ],
+        caution: 'Every range below is then read in the new units — including the resampling range, which runs last unless you resample first.',
+    },
+    fromTo: {
+        label: 'Crop',
+        group: 'x-axis',
+        summary: 'Keeps one stretch of the spectrum and drops the rest.',
+        fields: [
+            ...RANGE_FIELDS,
+            integerField('fromIndex', 'From (point)', '0'),
+            integerField('toIndex', 'To (point)', 'the last point'),
+        ],
+        caution: 'Give x values or point numbers, not both: a point number silently wins over an x value.',
+    },
+    filterX: {
+        label: 'Keep or drop x zones',
+        group: 'x-axis',
+        summary: 'Keeps the points falling in the zones named, without resampling anything.',
+        fields: [...RANGE_FIELDS, ...ZONE_FIELDS],
+    },
+    equallySpaced: {
+        label: 'Resample on a regular grid',
+        group: 'x-axis',
+        summary: 'Interpolates onto evenly spaced x values.',
+        fields: [
+            ...RANGE_FIELDS,
+            integerField('numberOfPoints', 'Number of points', '100'),
+            ...ZONE_FIELDS,
+        ],
+        caution: 'The settings above already resample once, so this resamples twice; whichever of the two runs last sets the point count.',
+    },
+    calibrateX: {
+        label: 'Calibrate x on a peak',
+        group: 'x-axis',
+        summary: 'Finds the strongest peaks in a stretch and shifts the whole axis so their mean lands on the value asked for.',
+        fields: [
+            ...RANGE_FIELDS,
+            integerField('nbPeaks', 'Peaks to find', '1'),
+            numberField('targetX', 'Move them to', '0'),
+            booleanField('gsd.smoothY', 'Smooth before picking'),
+            booleanField('gsd.maxCriteria', 'Pick maxima', 'Off picks minima instead.'),
+            numberField('gsd.minMaxRatio', 'Smallest peak kept', '0.00025', 'As a fraction of the tallest. A step added here starts at 0.1; empty the box and this far lower default takes over.'),
+            numberField('gsd.noiseLevel', 'Noise level', 'not set'),
+            booleanField('gsd.realTopDetection', 'Refine the summit'),
+            integerField('gsd.sgOptions.windowSize', 'Peak-picking window', '9'),
+            integerField('gsd.sgOptions.polynomial', 'Peak-picking polynomial', '3'),
+            enumField('gsd.peakDetectionAlgorithm', 'Detected on', [
+                { value: 'first', label: 'The first derivative' },
+                { value: 'second', label: 'The second derivative' },
+                { value: 'auto', label: 'Whichever fits' },
+            ]),
+        ],
+        caution: 'When fewer peaks are found than asked for, the spectrum is returned untouched and nothing says so.',
+    },
+    ensureGrowing: {
+        label: 'Make x strictly increasing',
+        group: 'utility',
+        summary: 'Drops the points that repeat or go backwards, which resampling and cropping both assume never happens.',
+        fields: [],
+    },
+    reverseIfNeeded: {
+        label: 'Reverse a descending x',
+        group: 'utility',
+        summary: 'Turns a descending axis the right way round.',
+        fields: [],
+        caution: 'The chain already does this before every step, so adding it here changes nothing.',
+    },
+};
+//# sourceMappingURL=axisEntries.js.map

package/lib/spectra/core/axisEntries.js.map

@@ -0,0 +1 @@
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package/lib/spectra/core/chainProblems.d.ts

@@ -0,0 +1,14 @@
+import type { SettingsProblem } from './problems.ts';
+import type { SpectrumFilter } from './settings.ts';
+/**
+ * Everything wrong, or probably wrong, with one chain.
+ *
+ * The order of a chain is its meaning — scaling measured before a baseline is
+ * removed measures an offset that is about to change — so the advice below is
+ * as much about where a step sits as about what it is set to.
+ * @param chain - The steps, in the order they run.
+ * @param resampleFirst - Whether the settings resample before the chain runs.
+ * @returns Every problem found, errors and advice together.
+ */
+export declare function chainProblems(chain: readonly SpectrumFilter[], resampleFirst: boolean): SettingsProblem[];
+//# sourceMappingURL=chainProblems.d.ts.map

package/lib/spectra/core/chainProblems.d.ts.map

@@ -0,0 +1 @@
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package/lib/spectra/core/chainProblems.js

@@ -0,0 +1,100 @@
+import { filterStepLabel, findFilterEntry } from "./filterCatalog.js";
+import { problem } from "./problems.js";
+import { stepProblems } from "./stepProblems.js";
+/** The steps that all say "make the y scale comparable"; only the last survives. */
+const SCALING_STEPS = new Set([
+    'divideBySD',
+    'normed',
+    'paretoNormalization',
+    'rescale',
+]);
+/** The steps that hand on plain arrays, whatever they were given. */
+const UNTYPES_X = new Set([
+    'equallySpaced',
+    'filterX',
+]);
+/** The steps that read x as a typed array and throw on a plain one. */
+const NEEDS_TYPED_X = new Set([
+    'calibrateX',
+    'fromTo',
+]);
+/**
+ * Everything wrong, or probably wrong, with one chain.
+ *
+ * The order of a chain is its meaning — scaling measured before a baseline is
+ * removed measures an offset that is about to change — so the advice below is
+ * as much about where a step sits as about what it is set to.
+ * @param chain - The steps, in the order they run.
+ * @param resampleFirst - Whether the settings resample before the chain runs.
+ * @returns Every problem found, errors and advice together.
+ */
+export function chainProblems(chain, resampleFirst) {
+    const problems = [];
+    let baselines = 0;
+    let scalings = 0;
+    let firstScaling;
+    let plainX = resampleFirst;
+    let mayBePlainX = resampleFirst;
+    for (const [index, step] of chain.entries()) {
+        const where = filterStepLabel(step.name, index);
+        const entry = findFilterEntry(step.name);
+        problems.push(...stepProblems(step, where));
+        if (entry === undefined) {
+            problems.push(problem('warning', where, `${step.name} is not one of the steps this editor knows, so its options are left as they are. The processor throws on a name it cannot dispatch.`));
+            continue;
+        }
+        if (NEEDS_TYPED_X.has(step.name)) {
+            if (plainX) {
+                problems.push(problem('error', where, TYPED_X_MESSAGE));
+            }
+            else if (mayBePlainX) {
+                problems.push(problem('warning', where, MAY_BE_PLAIN_MESSAGE));
+            }
+        }
+        if (UNTYPES_X.has(step.name)) {
+            plainX = true;
+            mayBePlainX = true;
+        }
+        if (step.name === 'ensureGrowing')
+            mayBePlainX = true;
+        const { group } = entry;
+        if (group === 'baseline') {
+            baselines++;
+            if (firstScaling !== undefined) {
+                problems.push(problem('warning', where, `Step ${String(firstScaling + 1)} scales the signal before this levels it, so the scaling is measured against an offset that then changes. Level first.`));
+                firstScaling = undefined;
+            }
+        }
+        if (SCALING_STEPS.has(step.name)) {
+            scalings++;
+            firstScaling ??= index;
+        }
+        if (step.name === 'reverseIfNeeded') {
+            problems.push(problem('warning', where, 'The chain already turns a descending axis round before every step, so this one does nothing.'));
+        }
+        if (step.name === 'equallySpaced') {
+            problems.push(problem('warning', where, resampleFirst
+                ? 'The settings resample before the chain runs, so this resamples a second time and the point count set here is the one the matrix ends up with.'
+                : 'The settings resample after the chain runs, so this resamples a second time and the point count set above is the one the matrix ends up with.'));
+        }
+        if (!resampleFirst &&
+            (step.name === 'xFunction' || step.name === 'calibrateX')) {
+            problems.push(problem('warning', where, 'This changes the x axis before the resampling runs, so the range and the exclusions above are read in the new units.'));
+        }
+        if (resampleFirst && step.name === 'filterX') {
+            problems.push(problem('warning', where, 'Cropping after the resampling can leave each spectrum on its own grid, and the matrix then lines up rows that do not match. Pin the range above, or turn resampling back to last.'));
+        }
+    }
+    if (baselines > 1) {
+        problems.push(problem('warning', 'The chain', `${String(baselines)} baselines are subtracted one after another, each estimated from what the last one left.`));
+    }
+    if (scalings > 1) {
+        problems.push(problem('warning', 'The chain', `${String(scalings)} steps set the y scale; only the last of them still shows in the result.`));
+    }
+    return problems;
+}
+/** What a step reading x as a typed array is told when it cannot be one. */
+const TYPED_X_MESSAGE = 'This step reads x as a typed array, and resampling or cropping has already turned it into a plain one, so the processor throws. Move it before them, or turn resampling back to last.';
+/** The same, when only the data can settle whether x was untyped. */
+const MAY_BE_PLAIN_MESSAGE = 'This step reads x as a typed array. An earlier step turns x into a plain one whenever it has points to drop, and the processor then throws on this step.';
+//# sourceMappingURL=chainProblems.js.map

package/lib/spectra/core/chainProblems.js.map

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package/lib/spectra/core/filterCatalog.d.ts

@@ -0,0 +1,57 @@
+import type { FilterCatalogEntry } from './filterEntries.ts';
+import type { FilterGroup } from './filterFields.ts';
+import type { SpectrumFilterName } from './settings.ts';
+/**
+ * What the editor knows about every step `filterXY` dispatches.
+ *
+ * Keyed by the name rather than listed, so the day `ml-signal-processing` adds
+ * a filter this object stops compiling and the gap is a build failure instead
+ * of a step nobody can reach.
+ */
+export declare const FILTER_CATALOG: Readonly<Record<SpectrumFilterName, FilterCatalogEntry>>;
+/** Every step name, in the order the menu offers them. */
+export declare const FILTER_NAMES: readonly SpectrumFilterName[];
+/**
+ * What the editor knows about one step.
+ * @param name - The step's name.
+ * @returns Its catalog entry.
+ */
+export declare function filterEntry(name: SpectrumFilterName): FilterCatalogEntry;
+/**
+ * What the editor knows about a step whose name it may not recognise.
+ *
+ * The settings the processor accepts are typed `{ name: string }`, and
+ * `filterXY` really does dispatch four more names than the union declares, so a
+ * chain reaching the editor can name a step the catalog has never heard of.
+ * Answering nothing lets the panel say so; throwing would take the whole page
+ * down over one row.
+ * @param name - The step's name, from settings that may come from anywhere.
+ * @returns Its catalog entry, or undefined when the name is not one of the 23.
+ */
+export declare function findFilterEntry(name: string): FilterCatalogEntry | undefined;
+/**
+ * How the panel labels one step of a chain, whether or not it knows the step.
+ * @param name - The step's name.
+ * @param position - Where it sits, counting from zero.
+ * @returns The label the row and every problem about it share.
+ */
+export declare function filterStepLabel(name: string, position: number): string;
+/**
+ * The steps of one group, in menu order.
+ * @param group - Which part of the signal the steps work on.
+ * @returns Their names.
+ */
+export declare function filterNamesInGroup(group: FilterGroup): readonly SpectrumFilterName[];
+/**
+ * The whole menu, group by group, skipping a group that holds nothing.
+ *
+ * The 23 steps are unreadable as one list, and grouping them by what they touch
+ * is the same order a chain is usually built in: level the baseline, smooth,
+ * scale, then move the axis.
+ * @returns Each group with its steps.
+ */
+export declare function filterMenu(): ReadonlyArray<{
+    group: FilterGroup;
+    names: readonly SpectrumFilterName[];
+}>;
+//# sourceMappingURL=filterCatalog.d.ts.map

package/lib/spectra/core/filterCatalog.d.ts.map

@@ -0,0 +1 @@
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package/lib/spectra/core/filterCatalog.js

@@ -0,0 +1,81 @@
+import { AXIS_ENTRIES } from "./axisEntries.js";
+import { BASELINE_ENTRIES, SIGNAL_ENTRIES } from "./filterEntries.js";
+import { FILTER_GROUPS } from "./filterFields.js";
+/**
+ * What the editor knows about every step `filterXY` dispatches.
+ *
+ * Keyed by the name rather than listed, so the day `ml-signal-processing` adds
+ * a filter this object stops compiling and the gap is a build failure instead
+ * of a step nobody can reach.
+ */
+export const FILTER_CATALOG = {
+    ...BASELINE_ENTRIES,
+    ...SIGNAL_ENTRIES,
+    ...AXIS_ENTRIES,
+};
+/** Every step name, in the order the menu offers them. */
+export const FILTER_NAMES = Object.keys(FILTER_CATALOG);
+/**
+ * What the editor knows about one step.
+ * @param name - The step's name.
+ * @returns Its catalog entry.
+ */
+export function filterEntry(name) {
+    return FILTER_CATALOG[name];
+}
+/**
+ * What the editor knows about a step whose name it may not recognise.
+ *
+ * The settings the processor accepts are typed `{ name: string }`, and
+ * `filterXY` really does dispatch four more names than the union declares, so a
+ * chain reaching the editor can name a step the catalog has never heard of.
+ * Answering nothing lets the panel say so; throwing would take the whole page
+ * down over one row.
+ * @param name - The step's name, from settings that may come from anywhere.
+ * @returns Its catalog entry, or undefined when the name is not one of the 23.
+ */
+export function findFilterEntry(name) {
+    return Object.hasOwn(FILTER_CATALOG, name)
+        ? FILTER_CATALOG[name]
+        : undefined;
+}
+/**
+ * How the panel labels one step of a chain, whether or not it knows the step.
+ * @param name - The step's name.
+ * @param position - Where it sits, counting from zero.
+ * @returns The label the row and every problem about it share.
+ */
+export function filterStepLabel(name, position) {
+    return `Step ${String(position + 1)} — ${findFilterEntry(name)?.label ?? name}`;
+}
+/**
+ * The steps of one group, in menu order.
+ * @param group - Which part of the signal the steps work on.
+ * @returns Their names.
+ */
+export function filterNamesInGroup(group) {
+    const names = [];
+    for (const name of FILTER_NAMES) {
+        if (FILTER_CATALOG[name].group === group)
+            names.push(name);
+    }
+    return names;
+}
+/**
+ * The whole menu, group by group, skipping a group that holds nothing.
+ *
+ * The 23 steps are unreadable as one list, and grouping them by what they touch
+ * is the same order a chain is usually built in: level the baseline, smooth,
+ * scale, then move the axis.
+ * @returns Each group with its steps.
+ */
+export function filterMenu() {
+    const menu = [];
+    for (const group of FILTER_GROUPS) {
+        const names = filterNamesInGroup(group);
+        if (names.length > 0)
+            menu.push({ group, names });
+    }
+    return menu;
+}
+//# sourceMappingURL=filterCatalog.js.map

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package/lib/spectra/core/filterChain.d.ts

@@ -0,0 +1,69 @@
+import type { SpectrumFilter, SpectrumFilterName } from './settings.ts';
+/** What a step's options are, before any one filter's shape is assumed. */
+type OptionsRecord = Record<string, unknown>;
+/**
+ * A new chain step, carrying only the options upstream cannot default safely.
+ * @param name - Which step to add.
+ * @returns The step.
+ */
+export declare function defaultFilter(name: SpectrumFilterName): SpectrumFilter;
+/**
+ * The chain with one more step at the end.
+ * @param chain - The steps, in the order they run.
+ * @param name - Which step to add.
+ * @returns A new chain.
+ */
+export declare function addFilter(chain: readonly SpectrumFilter[], name: SpectrumFilterName): SpectrumFilter[];
+/**
+ * The chain without the step at that position.
+ * @param chain - The steps, in the order they run.
+ * @param index - Which step to drop.
+ * @returns A new chain.
+ */
+export declare function removeFilter(chain: readonly SpectrumFilter[], index: number): SpectrumFilter[];
+/**
+ * The chain with the step at that position repeated just after it.
+ * @param chain - The steps, in the order they run.
+ * @param index - Which step to repeat.
+ * @returns A new chain.
+ */
+export declare function duplicateFilter(chain: readonly SpectrumFilter[], index: number): SpectrumFilter[];
+/**
+ * The chain with one step moved.
+ *
+ * Order is the whole meaning of a chain — scaling before a baseline correction
+ * measures an offset that is about to change — so moving a step is a first-class
+ * edit rather than something to be done by deleting and adding again.
+ * @param chain - The steps, in the order they run.
+ * @param index - Which step to move.
+ * @param offset - How far, negative towards the start.
+ * @returns A new chain, unchanged when the move would fall off either end.
+ */
+export declare function moveFilter(chain: readonly SpectrumFilter[], index: number, offset: number): SpectrumFilter[];
+/**
+ * What one option of a step is set to.
+ * @param filter - The step.
+ * @param key - Where the value sits, dotted for a nested one.
+ * @returns The value, or undefined when the step leaves it to upstream.
+ */
+export declare function readFilterOption(filter: SpectrumFilter, key: string): unknown;
+/**
+ * The step with one option set, or dropped when the value is undefined.
+ *
+ * Dropping rather than writing `undefined` is what lets a cleared field mean
+ * "whatever upstream does", which is the only way a reader can get back to the
+ * default once they have typed over it.
+ * @param filter - The step.
+ * @param key - Where the value sits, dotted for a nested one.
+ * @param value - What to set it to, or undefined to clear it.
+ * @returns A new step.
+ */
+export declare function setFilterOption(filter: SpectrumFilter, key: string, value: unknown): SpectrumFilter;
+/**
+ * The step's options as a plain record, for a form that walks the catalog.
+ * @param filter - The step.
+ * @returns Its options, empty when it carries none.
+ */
+export declare function filterOptions(filter: SpectrumFilter): Readonly<OptionsRecord>;
+export {};
+//# sourceMappingURL=filterChain.d.ts.map

package/lib/spectra/core/filterChain.d.ts.map

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package/lib/spectra/core/filterChain.js

@@ -0,0 +1,163 @@
+/**
+ * The peak-picking `calibrateX` tunes for itself.
+ *
+ * Upstream reads these off the whole `gsd` object, so the moment the settings
+ * carry a `gsd` at all — even an empty one — every value here is replaced by
+ * ml-gsd's own, which pick peaks a four-hundredth as tall. The editor therefore
+ * writes them out in full rather than ever emitting a partial one.
+ */
+const CALIBRATE_PEAK_PICKING = {
+    maxCriteria: true,
+    minMaxRatio: 0.1,
+    realTopDetection: true,
+    smoothY: true,
+    sgOptions: { windowSize: 7, polynomial: 3 },
+};
+/**
+ * A new chain step, carrying only the options upstream cannot default safely.
+ * @param name - Which step to add.
+ * @returns The step.
+ */
+export function defaultFilter(name) {
+    if (name === 'calibrateX') {
+        return { name, options: { gsd: { ...CALIBRATE_PEAK_PICKING } } };
+    }
+    return { name };
+}
+/**
+ * The chain with one more step at the end.
+ * @param chain - The steps, in the order they run.
+ * @param name - Which step to add.
+ * @returns A new chain.
+ */
+export function addFilter(chain, name) {
+    return [...chain, defaultFilter(name)];
+}
+/**
+ * The chain without the step at that position.
+ * @param chain - The steps, in the order they run.
+ * @param index - Which step to drop.
+ * @returns A new chain.
+ */
+export function removeFilter(chain, index) {
+    return chain.filter((_, position) => position !== index);
+}
+/**
+ * The chain with the step at that position repeated just after it.
+ * @param chain - The steps, in the order they run.
+ * @param index - Which step to repeat.
+ * @returns A new chain.
+ */
+export function duplicateFilter(chain, index) {
+    const step = chain[index];
+    if (step === undefined)
+        return [...chain];
+    return [
+        ...chain.slice(0, index + 1),
+        structuredClone(step),
+        ...chain.slice(index + 1),
+    ];
+}
+/**
+ * The chain with one step moved.
+ *
+ * Order is the whole meaning of a chain — scaling before a baseline correction
+ * measures an offset that is about to change — so moving a step is a first-class
+ * edit rather than something to be done by deleting and adding again.
+ * @param chain - The steps, in the order they run.
+ * @param index - Which step to move.
+ * @param offset - How far, negative towards the start.
+ * @returns A new chain, unchanged when the move would fall off either end.
+ */
+export function moveFilter(chain, index, offset) {
+    const target = index + offset;
+    const step = chain[index];
+    if (step === undefined || target < 0 || target >= chain.length) {
+        return [...chain];
+    }
+    const moved = [...chain];
+    moved.splice(index, 1);
+    moved.splice(target, 0, step);
+    return moved;
+}
+/**
+ * What one option of a step is set to.
+ * @param filter - The step.
+ * @param key - Where the value sits, dotted for a nested one.
+ * @returns The value, or undefined when the step leaves it to upstream.
+ */
+export function readFilterOption(filter, key) {
+    let current = 'options' in filter ? filter.options : undefined;
+    for (const segment of key.split('.')) {
+        if (typeof current !== 'object' || current === null)
+            return undefined;
+        current = current[segment];
+    }
+    return current;
+}
+/**
+ * The step with one option set, or dropped when the value is undefined.
+ *
+ * Dropping rather than writing `undefined` is what lets a cleared field mean
+ * "whatever upstream does", which is the only way a reader can get back to the
+ * default once they have typed over it.
+ * @param filter - The step.
+ * @param key - Where the value sits, dotted for a nested one.
+ * @param value - What to set it to, or undefined to clear it.
+ * @returns A new step.
+ */
+export function setFilterOption(filter, key, value) {
+    const written = writePath(filterOptions(filter), key.split('.'), value);
+    if (Object.keys(written).length === 0)
+        return { name: filter.name };
+    return { name: filter.name, options: written };
+}
+/**
+ * The step's options as a plain record, for a form that walks the catalog.
+ * @param filter - The step.
+ * @returns Its options, empty when it carries none.
+ */
+export function filterOptions(filter) {
+    const options = 'options' in filter ? filter.options : undefined;
+    if (typeof options !== 'object' || options === null)
+        return {};
+    // An interface carries no index signature, so a form that walks the catalog
+    // has to read it as the record the catalog's keys describe.
+    return options;
+}
+/**
+ * A copy of the record with one path written, creating what it passes through.
+ * @param record - What to copy.
+ * @param path - The remaining segments.
+ * @param value - What to set, or undefined to drop the key.
+ * @returns A new record.
+ */
+function writePath(record, path, value) {
+    const [head, ...rest] = path;
+    if (head === undefined)
+        return { ...record };
+    if (rest.length === 0 && value === undefined) {
+        const kept = {};
+        for (const [name, held] of Object.entries(record)) {
+            if (name !== head)
+                kept[name] = held;
+        }
+        return kept;
+    }
+    const next = { ...record };
+    if (rest.length === 0) {
+        next[head] = value;
+        return next;
+    }
+    const child = next[head];
+    const childRecord = typeof child === 'object' && child !== null ? child : {};
+    const written = writePath(childRecord, rest, value);
+    // An emptied nested object is not the same as an absent one: upstream reads a
+    // present `gsd` as "options were given" and drops its own tuned defaults.
+    if (Object.keys(written).length === 0) {
+        return writePath(record, [head], undefined);
+    }
+    next[head] = written;
+    return next;
+}
+//# sourceMappingURL=filterChain.js.map

package/lib/spectra/core/filterChain.js.map

@@ -0,0 +1 @@
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