edf2csv 0.5.60 → 0.5.61
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +32 -0
- package/dist/convert/channels.js +29 -0
- package/dist/convert/channels.js.map +1 -1
- package/package.json +1 -1
package/CHANGELOG.md
CHANGED
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@@ -3,6 +3,38 @@
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3
3
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Notable changes to edf2csv. Versions follow [semantic versioning](https://semver.org); while the
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4
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major version is 0, a minor bump may contain breaking changes.
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## 0.5.61
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7
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+
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8
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### Fixed: `--channels` rejected the column name it had just printed, and called it unknown
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9
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+
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Matching is on the label. Where two channels share one, their columns gain a `_ch<index>`
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11
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suffix — so `T8-P8_ch1` is a name this tool invented. It prints it in the COLUMN column of
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`--info`, writes it into channels.csv, and puts it at the head of signals.csv. Passing it back
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got:
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14
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+
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```
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error: No channel named "T8-P8_ch1". Run with --info to list the channels in this file.
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```
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+
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which is the table it was copied out of. The reference has documented the trap for a long
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time; the message someone actually hits did not, and the advice it gave was a loop.
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+
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It says what the term is now, and gives the form that works — `#<index>`, which is also the
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only way to select one channel of a colliding pair and exactly what someone reaching for the
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suffixed column name wants:
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```
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error: "T8-P8_ch1" is a column name, not a channel name: --channels matches the label, which for this channel is "T8-P8".
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Use "#1" to select just this one, or "T8-P8" for every channel sharing that label.
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```
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+
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Only for a term that really is some channel's column name; a typo still gets "No channel
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named "ECQ". Did you mean "ECG"?". A label that merely looks like a column name still wins,
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which `label-suffix-collision.edf` pins: its third channel is genuinely called `T8_ch0`, the
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34
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same text as the first channel's column, and `--channels T8_ch0` selects the channel whose
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label it is. A channel with no label has nothing to match at all, so that case is told to use
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the position rather than offered an empty string to type.
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+
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6
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## 0.5.60
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7
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8
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### Fixed: two window messages that were false about a recording not timed from zero
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package/dist/convert/channels.js
CHANGED
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@@ -147,6 +147,35 @@ export function selectChannels(signals, terms) {
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}
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const matched = byLabel.get(term.toLowerCase());
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if (!matched || matched.length === 0) {
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/*
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The one term that is certainly not a typo: a column name.
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152
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+
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153
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Matching is on the label, and where a label collides the column gains a `_ch<index>`
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154
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suffix — so `T8-P8_ch1` is a name this tool invented, prints in the COLUMN column of
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--info, writes into channels.csv and puts at the head of signals.csv, and then
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rejects with "No channel named "T8-P8_ch1". Run with --info to list the channels in
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this file", which is where the user copied it from. The reference documents the trap;
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the message a user actually hits did not.
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Answered where it is asked instead, and with the thing that works: `#<index>` selects
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one channel of a colliding pair, which is exactly what someone reaching for the
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suffixed column name wants and the only way to get it.
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*/
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const columns = buildColumnNames(candidates);
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const owner = candidates.find((signal) => (columns.get(signal.index) ?? '').toLowerCase() === term.toLowerCase());
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if (owner) {
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// A channel with no label at all gets the column `signal_<index>`, and offering its
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// label back would be offering `""` — there is nothing to type. Position is the only
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// way to reach it, and saying so is more use than quoting an empty string twice.
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throw new ChannelSelectionError(owner.label === ''
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? `"${term}" is a column name, not a channel name: --channels matches the label, ` +
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`and this channel has none.\n` +
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`Use "#${owner.index}" — a channel with no label can only be addressed by position.`
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: `"${term}" is a column name, not a channel name: --channels matches the label, ` +
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`which for this channel is "${owner.label}".\n` +
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`Use "#${owner.index}" to select just this one, or "${owner.label}" for every ` +
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`channel sharing that label.`);
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}
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throw new ChannelSelectionError(`No channel named "${term}".${suggest(term, candidates)}\n` +
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`Run with --info to list the channels in this file.`);
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}
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@@ -1 +1 @@
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1
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-
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* Channel naming and selection.\n *\n * Two real-world facts drive this module. EDF labels are free text that routinely\n * contain spaces and punctuation (\"EEG Fpz-Cz\"), and they are not guaranteed to be\n * unique — CHB-MIT recordings ship two channels both labelled \"T8-P8\", and some\n * carry a channel labelled \"-\". Labels are therefore preserved verbatim in output,\n * and only disambiguated when the file itself is ambiguous.\n */\n\nimport type { EdfSignal } from '../edf/header.js';\nimport { listed } from '../format/list.js';\n\nexport class ChannelSelectionError extends Error {\n constructor(message: string) {\n super(message);\n this.name = 'ChannelSelectionError';\n }\n}\n\n/**\n * Column name for a signal.\n *\n * Names are derived from the whole file, not from the current selection, so a given\n * channel always produces the same column regardless of which channels were asked\n * for. Duplicated labels get a `_ch<index>` suffix pointing at their position in\n * the file, which is the only thing that reliably tells them apart.\n */\nexport function buildColumnNames(signals: readonly EdfSignal[]): Map<number, string> {\n const counts = new Map<string, number>();\n for (const signal of signals) {\n if (signal.isAnnotations) continue;\n const base = baseName(signal);\n counts.set(base, (counts.get(base) ?? 0) + 1);\n }\n\n const names = new Map<number, string>();\n for (const signal of signals) {\n if (signal.isAnnotations) continue;\n const base = baseName(signal);\n const duplicated = (counts.get(base) ?? 0) > 1;\n names.set(signal.index, duplicated ? `${base}_ch${signal.index}` : base);\n }\n\n /*\n The suffix has to be checked against the file, not only against the label it disambiguates.\n\n Counting collisions on the raw label alone made the suffix a guess: `_ch<index>` is unique\n among the channels sharing that label, and nothing stopped it from landing on a label some\n other channel already had. A file labelled T8, T8, T8_ch0 — all three legal, since EDF\n labels are free text and nothing enforces uniqueness — produced\n\n time_s,T8_ch0,T8_ch1,T8_ch0\n\n two columns with one name, while the warning beside it said the suffix kept them\n \"distinguishable\". channels.csv listed the same name against two signal indices, so the\n join it exists for could not resolve it either, and `df[\"T8_ch0\"]` in pandas or R returns\n one of the two with nothing to say which.\n\n Anything still shared after the first pass takes its own position as well. That is unique\n by construction, so the loop settles immediately in practice; the bound is there because\n a second round could in principle land on yet another literal label.\n */\n for (let round = 0; round < 8; round++) {\n const taken = new Map<string, number>();\n for (const name of names.values()) taken.set(name, (taken.get(name) ?? 0) + 1);\n\n const clashing = [...names].filter(([, name]) => (taken.get(name) ?? 0) > 1);\n if (clashing.length === 0) break;\n for (const [index, name] of clashing) names.set(index, `${name}_ch${index}`);\n }\n return names;\n}\n\nfunction baseName(signal: EdfSignal): string {\n return signal.label === '' ? `signal_${signal.index}` : signal.label;\n}\n\n/**\n * Channels whose column name was pushed off their own label to keep the header unique.\n *\n * A channel genuinely labelled `T8_ch0` loses that name when another label's disambiguating\n * suffix wants it, and the resulting column is the one thing in the output that no longer\n * matches the file. Silence there is what made the collision hard to see in the first place:\n * the only warning raised was about the *other* label.\n */\nexport function renamedByCollision(\n signals: readonly EdfSignal[],\n columnNames: ReadonlyMap<number, string>,\n): EdfSignal[] {\n const counts = new Map<string, number>();\n for (const signal of signals) {\n if (signal.isAnnotations) continue;\n const base = baseName(signal);\n counts.set(base, (counts.get(base) ?? 0) + 1);\n }\n return signals.filter(\n (signal) =>\n !signal.isAnnotations &&\n (counts.get(baseName(signal)) ?? 0) === 1 &&\n columnNames.get(signal.index) !== baseName(signal),\n );\n}\n\nexport interface ChannelSelection {\n signals: EdfSignal[];\n /** Labels that matched more than one channel, so the user knows why they got extras. */\n ambiguous: { term: string; matched: EdfSignal[] }[];\n}\n\n/**\n * Resolve a `--channels` specification against the file's signals.\n *\n * Matching is case-insensitive on the exact label, with `#<index>` available to\n * address a specific channel when labels collide. A term that matches nothing is an\n * error rather than a silent omission: quietly dropping a requested channel would\n * hand the user a CSV that is missing data they explicitly asked for.\n */\nexport function selectChannels(signals: readonly EdfSignal[], terms: readonly string[]): ChannelSelection {\n const candidates = signals.filter((s) => !s.isAnnotations);\n const byLabel = new Map<string, EdfSignal[]>();\n for (const signal of candidates) {\n const key = signal.label.toLowerCase();\n const bucket = byLabel.get(key);\n if (bucket) bucket.push(signal);\n else byLabel.set(key, [signal]);\n }\n\n const chosen = new Map<number, EdfSignal>();\n const ambiguous: { term: string; matched: EdfSignal[] }[] = [];\n\n for (const rawTerm of terms) {\n const term = rawTerm.trim();\n if (term === '') continue;\n\n // '#N' addresses a channel by position, but a label may literally be \"#5\".\n // A real label always wins, so no channel becomes unreachable.\n const literal = byLabel.get(term.toLowerCase());\n if (term.startsWith('#') && (!literal || literal.length === 0)) {\n /*\n A position must be written in plain digits.\n\n `Number()` was doing the parsing, and it accepts a great deal more than a position:\n `#0x2` reached channel 2 through hex, `#0b1` channel 1 through binary, `#1e0` and\n `#2.0` and `# 2` all landed somewhere, and `#` on its own became `Number('')`, which\n is 0. Every one of them selected a channel and exited 0, so a slip did not fail —\n it quietly converted a different channel than the one asked for, which for this tool\n is the worst way to be wrong.\n */\n const position = term.slice(1);\n if (!/^\\d+$/u.test(position)) {\n throw new ChannelSelectionError(\n `\"${term}\" is not a channel position: a position is #0, #1, #2 and so on.\\n` +\n `This file has signal channels at ${listed(candidates.map((s) => `#${s.index}`))}.`,\n );\n }\n const index = Number(position);\n const signal = candidates.find((s) => s.index === index);\n if (!signal) {\n throw new ChannelSelectionError(\n `No channel at position ${term}. This file has signal channels at ` +\n `${listed(candidates.map((s) => `#${s.index}`))}.`,\n );\n }\n chosen.set(signal.index, signal);\n continue;\n }\n\n const matched = byLabel.get(term.toLowerCase());\n if (!matched || matched.length === 0) {\n throw new ChannelSelectionError(\n `No channel named \"${term}\".${suggest(term, candidates)}\\n` +\n `Run with --info to list the channels in this file.`,\n );\n }\n if (matched.length > 1) ambiguous.push({ term, matched: [...matched] });\n for (const signal of matched) chosen.set(signal.index, signal);\n }\n\n const selected = [...chosen.values()].sort((a, b) => a.index - b.index);\n if (selected.length === 0) {\n throw new ChannelSelectionError('No channels were selected.');\n }\n return { signals: selected, ambiguous };\n}\n\nfunction suggest(term: string, candidates: readonly EdfSignal[]): string {\n // Duplicated labels would otherwise be suggested twice, which reads like two\n // different options while naming the same thing.\n const unique = [...new Set(candidates.map((s) => s.label))];\n const scored = unique\n .map((label) => ({ label, distance: editDistance(term.toLowerCase(), label.toLowerCase()) }))\n .filter((c) => c.label !== '' && c.distance <= Math.max(2, Math.floor(term.length / 3)))\n .sort((a, b) => a.distance - b.distance)\n .slice(0, 3);\n if (scored.length === 0) return '';\n return ` Did you mean ${scored.map((c) => `\"${c.label}\"`).join(', ')}?`;\n}\n\n/** Levenshtein distance, two-row variant. */\nfunction editDistance(a: string, b: string): number {\n if (a === b) return 0;\n if (a.length === 0) return b.length;\n if (b.length === 0) return a.length;\n\n let previous = Array.from({ length: b.length + 1 }, (_, i) => i);\n let current = new Array<number>(b.length + 1).fill(0);\n\n for (let i = 1; i <= a.length; i++) {\n current[0] = i;\n for (let j = 1; j <= b.length; j++) {\n const cost = a.charCodeAt(i - 1) === b.charCodeAt(j - 1) ? 0 : 1;\n current[j] = Math.min(\n (current[j - 1] ?? 0) + 1,\n (previous[j] ?? 0) + 1,\n (previous[j - 1] ?? 0) + cost,\n );\n }\n const swap = previous;\n previous = current;\n current = swap;\n }\n return previous[b.length] ?? 0;\n}\n"]}
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* Channel naming and selection.\n *\n * Two real-world facts drive this module. EDF labels are free text that routinely\n * contain spaces and punctuation (\"EEG Fpz-Cz\"), and they are not guaranteed to be\n * unique — CHB-MIT recordings ship two channels both labelled \"T8-P8\", and some\n * carry a channel labelled \"-\". Labels are therefore preserved verbatim in output,\n * and only disambiguated when the file itself is ambiguous.\n */\n\nimport type { EdfSignal } from '../edf/header.js';\nimport { listed } from '../format/list.js';\n\nexport class ChannelSelectionError extends Error {\n constructor(message: string) {\n super(message);\n this.name = 'ChannelSelectionError';\n }\n}\n\n/**\n * Column name for a signal.\n *\n * Names are derived from the whole file, not from the current selection, so a given\n * channel always produces the same column regardless of which channels were asked\n * for. Duplicated labels get a `_ch<index>` suffix pointing at their position in\n * the file, which is the only thing that reliably tells them apart.\n */\nexport function buildColumnNames(signals: readonly EdfSignal[]): Map<number, string> {\n const counts = new Map<string, number>();\n for (const signal of signals) {\n if (signal.isAnnotations) continue;\n const base = baseName(signal);\n counts.set(base, (counts.get(base) ?? 0) + 1);\n }\n\n const names = new Map<number, string>();\n for (const signal of signals) {\n if (signal.isAnnotations) continue;\n const base = baseName(signal);\n const duplicated = (counts.get(base) ?? 0) > 1;\n names.set(signal.index, duplicated ? `${base}_ch${signal.index}` : base);\n }\n\n /*\n The suffix has to be checked against the file, not only against the label it disambiguates.\n\n Counting collisions on the raw label alone made the suffix a guess: `_ch<index>` is unique\n among the channels sharing that label, and nothing stopped it from landing on a label some\n other channel already had. A file labelled T8, T8, T8_ch0 — all three legal, since EDF\n labels are free text and nothing enforces uniqueness — produced\n\n time_s,T8_ch0,T8_ch1,T8_ch0\n\n two columns with one name, while the warning beside it said the suffix kept them\n \"distinguishable\". channels.csv listed the same name against two signal indices, so the\n join it exists for could not resolve it either, and `df[\"T8_ch0\"]` in pandas or R returns\n one of the two with nothing to say which.\n\n Anything still shared after the first pass takes its own position as well. That is unique\n by construction, so the loop settles immediately in practice; the bound is there because\n a second round could in principle land on yet another literal label.\n */\n for (let round = 0; round < 8; round++) {\n const taken = new Map<string, number>();\n for (const name of names.values()) taken.set(name, (taken.get(name) ?? 0) + 1);\n\n const clashing = [...names].filter(([, name]) => (taken.get(name) ?? 0) > 1);\n if (clashing.length === 0) break;\n for (const [index, name] of clashing) names.set(index, `${name}_ch${index}`);\n }\n return names;\n}\n\nfunction baseName(signal: EdfSignal): string {\n return signal.label === '' ? `signal_${signal.index}` : signal.label;\n}\n\n/**\n * Channels whose column name was pushed off their own label to keep the header unique.\n *\n * A channel genuinely labelled `T8_ch0` loses that name when another label's disambiguating\n * suffix wants it, and the resulting column is the one thing in the output that no longer\n * matches the file. Silence there is what made the collision hard to see in the first place:\n * the only warning raised was about the *other* label.\n */\nexport function renamedByCollision(\n signals: readonly EdfSignal[],\n columnNames: ReadonlyMap<number, string>,\n): EdfSignal[] {\n const counts = new Map<string, number>();\n for (const signal of signals) {\n if (signal.isAnnotations) continue;\n const base = baseName(signal);\n counts.set(base, (counts.get(base) ?? 0) + 1);\n }\n return signals.filter(\n (signal) =>\n !signal.isAnnotations &&\n (counts.get(baseName(signal)) ?? 0) === 1 &&\n columnNames.get(signal.index) !== baseName(signal),\n );\n}\n\nexport interface ChannelSelection {\n signals: EdfSignal[];\n /** Labels that matched more than one channel, so the user knows why they got extras. */\n ambiguous: { term: string; matched: EdfSignal[] }[];\n}\n\n/**\n * Resolve a `--channels` specification against the file's signals.\n *\n * Matching is case-insensitive on the exact label, with `#<index>` available to\n * address a specific channel when labels collide. A term that matches nothing is an\n * error rather than a silent omission: quietly dropping a requested channel would\n * hand the user a CSV that is missing data they explicitly asked for.\n */\nexport function selectChannels(signals: readonly EdfSignal[], terms: readonly string[]): ChannelSelection {\n const candidates = signals.filter((s) => !s.isAnnotations);\n const byLabel = new Map<string, EdfSignal[]>();\n for (const signal of candidates) {\n const key = signal.label.toLowerCase();\n const bucket = byLabel.get(key);\n if (bucket) bucket.push(signal);\n else byLabel.set(key, [signal]);\n }\n\n const chosen = new Map<number, EdfSignal>();\n const ambiguous: { term: string; matched: EdfSignal[] }[] = [];\n\n for (const rawTerm of terms) {\n const term = rawTerm.trim();\n if (term === '') continue;\n\n // '#N' addresses a channel by position, but a label may literally be \"#5\".\n // A real label always wins, so no channel becomes unreachable.\n const literal = byLabel.get(term.toLowerCase());\n if (term.startsWith('#') && (!literal || literal.length === 0)) {\n /*\n A position must be written in plain digits.\n\n `Number()` was doing the parsing, and it accepts a great deal more than a position:\n `#0x2` reached channel 2 through hex, `#0b1` channel 1 through binary, `#1e0` and\n `#2.0` and `# 2` all landed somewhere, and `#` on its own became `Number('')`, which\n is 0. Every one of them selected a channel and exited 0, so a slip did not fail —\n it quietly converted a different channel than the one asked for, which for this tool\n is the worst way to be wrong.\n */\n const position = term.slice(1);\n if (!/^\\d+$/u.test(position)) {\n throw new ChannelSelectionError(\n `\"${term}\" is not a channel position: a position is #0, #1, #2 and so on.\\n` +\n `This file has signal channels at ${listed(candidates.map((s) => `#${s.index}`))}.`,\n );\n }\n const index = Number(position);\n const signal = candidates.find((s) => s.index === index);\n if (!signal) {\n throw new ChannelSelectionError(\n `No channel at position ${term}. This file has signal channels at ` +\n `${listed(candidates.map((s) => `#${s.index}`))}.`,\n );\n }\n chosen.set(signal.index, signal);\n continue;\n }\n\n const matched = byLabel.get(term.toLowerCase());\n if (!matched || matched.length === 0) {\n /*\n The one term that is certainly not a typo: a column name.\n\n Matching is on the label, and where a label collides the column gains a `_ch<index>`\n suffix — so `T8-P8_ch1` is a name this tool invented, prints in the COLUMN column of\n --info, writes into channels.csv and puts at the head of signals.csv, and then\n rejects with \"No channel named \"T8-P8_ch1\". Run with --info to list the channels in\n this file\", which is where the user copied it from. The reference documents the trap;\n the message a user actually hits did not.\n\n Answered where it is asked instead, and with the thing that works: `#<index>` selects\n one channel of a colliding pair, which is exactly what someone reaching for the\n suffixed column name wants and the only way to get it.\n */\n const columns = buildColumnNames(candidates);\n const owner = candidates.find(\n (signal) => (columns.get(signal.index) ?? '').toLowerCase() === term.toLowerCase(),\n );\n if (owner) {\n // A channel with no label at all gets the column `signal_<index>`, and offering its\n // label back would be offering `\"\"` — there is nothing to type. Position is the only\n // way to reach it, and saying so is more use than quoting an empty string twice.\n throw new ChannelSelectionError(\n owner.label === ''\n ? `\"${term}\" is a column name, not a channel name: --channels matches the label, ` +\n `and this channel has none.\\n` +\n `Use \"#${owner.index}\" — a channel with no label can only be addressed by position.`\n : `\"${term}\" is a column name, not a channel name: --channels matches the label, ` +\n `which for this channel is \"${owner.label}\".\\n` +\n `Use \"#${owner.index}\" to select just this one, or \"${owner.label}\" for every ` +\n `channel sharing that label.`,\n );\n }\n throw new ChannelSelectionError(\n `No channel named \"${term}\".${suggest(term, candidates)}\\n` +\n `Run with --info to list the channels in this file.`,\n );\n }\n if (matched.length > 1) ambiguous.push({ term, matched: [...matched] });\n for (const signal of matched) chosen.set(signal.index, signal);\n }\n\n const selected = [...chosen.values()].sort((a, b) => a.index - b.index);\n if (selected.length === 0) {\n throw new ChannelSelectionError('No channels were selected.');\n }\n return { signals: selected, ambiguous };\n}\n\nfunction suggest(term: string, candidates: readonly EdfSignal[]): string {\n // Duplicated labels would otherwise be suggested twice, which reads like two\n // different options while naming the same thing.\n const unique = [...new Set(candidates.map((s) => s.label))];\n const scored = unique\n .map((label) => ({ label, distance: editDistance(term.toLowerCase(), label.toLowerCase()) }))\n .filter((c) => c.label !== '' && c.distance <= Math.max(2, Math.floor(term.length / 3)))\n .sort((a, b) => a.distance - b.distance)\n .slice(0, 3);\n if (scored.length === 0) return '';\n return ` Did you mean ${scored.map((c) => `\"${c.label}\"`).join(', ')}?`;\n}\n\n/** Levenshtein distance, two-row variant. */\nfunction editDistance(a: string, b: string): number {\n if (a === b) return 0;\n if (a.length === 0) return b.length;\n if (b.length === 0) return a.length;\n\n let previous = Array.from({ length: b.length + 1 }, (_, i) => i);\n let current = new Array<number>(b.length + 1).fill(0);\n\n for (let i = 1; i <= a.length; i++) {\n current[0] = i;\n for (let j = 1; j <= b.length; j++) {\n const cost = a.charCodeAt(i - 1) === b.charCodeAt(j - 1) ? 0 : 1;\n current[j] = Math.min(\n (current[j - 1] ?? 0) + 1,\n (previous[j] ?? 0) + 1,\n (previous[j - 1] ?? 0) + cost,\n );\n }\n const swap = previous;\n previous = current;\n current = swap;\n }\n return previous[b.length] ?? 0;\n}\n"]}
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package/package.json
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@@ -1,6 +1,6 @@
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{
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"name": "edf2csv",
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-
"version": "0.5.
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+
"version": "0.5.61",
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"description": "Convert EDF, EDF+ and BDF biosignal recordings (European Data Format) to CSV from the command line. Local, streaming, and never resamples or alters units.",
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"keywords": [
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"edf",
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