npm - edf2csv - Versions diffs - 0.4.71 → 0.4.73 - Mend

edf2csv 0.4.71 → 0.4.73

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.

Files changed (9) hide show

package/CHANGELOG.md +30 -0
package/dist/cli/report.d.ts.map +1 -1
package/dist/cli/report.js +8 -5
package/dist/cli/report.js.map +1 -1
package/dist/convert/plan.d.ts +8 -0
package/dist/convert/plan.d.ts.map +1 -1
package/dist/convert/plan.js +1 -1
package/dist/convert/plan.js.map +1 -1
package/package.json +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -3,6 +3,36 @@
 Notable changes to edf2csv. Versions follow [semantic versioning](https://semver.org); while the
 major version is 0, a minor bump may contain breaking changes.
+## 0.4.73
+### Fixed: `--info --annotations-only --gzip` named files the run would not write
+It said "Would write annotations.csv and channels.csv"; the run wrote `annotations.csv.gz`
+and `channels.csv.gz`. Those two sentences were string literals, and the gzip test below
+them reads the group file names — of which there are none under `--annotations-only`, which
+is what makes it that branch. So the same command was described one way by `--info` and
+another by the summary of the run that followed it, and a script that opened the name it was
+given got ENOENT.
+The plan now records whether the output is compressed instead of that being inferred from
+file names that may not exist, and both sentences take their suffix from it. `--info` is
+read to find out what a run leaves behind; naming a file it will not create is the one thing
+it must not do.
+## 0.4.72
+### Fixed: the correctness page stated a sweep size the sweep had outgrown
+It said `npm run estimate` runs "192 predictions over 34 recordings". It runs 216 over 39.
+The sweep's size is the fixture count crossed with its option sets, four fixtures had been
+added since the number was written, and nothing connected the two — so the page drifted
+silently, on the one page whose subject is not drifting.
+The figures are corrected, and a test now recomputes them from the same constants the
+harnesses use: the estimate sweep's recording count against the fixture directory, the
+round-trip sweep's calibrations and cells against the three arrays it crosses. Adding a
+fixture or a sweep dimension now fails a test instead of quietly making the page wrong.
 ## 0.4.71
 ### Added: `--bom`, for the one reader that needs it

package/dist/cli/report.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"report.d.ts","sourceRoot":"","sources":["../../src/cli/report.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AACnD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAGhD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAEzD,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAuBvD;;;;;;;;;;;;;GAaG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAK9C;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,SAAK,GAAG,MAAM,CAKhE;AAED,0FAA0F;AAC1F,wBAAgB,UAAU,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,cAAc,GAAG,MAAM,CA6GtE;AAED;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,QAAQ,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,cAAc,EAAE,MAAM,GAAE,MAAM,GAAG,IAAQ,GAAG,MAAM,CAwD/F;AAED,mEAAmE;AACnE,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,SAAS,UAAU,EAAE,GAAG,MAAM,CAS5E;AAED,wBAAgB,aAAa,CAAC,MAAM,EAAE,aAAa,GAAG,MAAM,CAU3D;AAED,wBAAgB,WAAW,CAAC,MAAM,EAAE,aAAa,EAAE,MAAM,GAAE,MAAM,GAAG,IAAQ,GAAG,MAAM,CAcpF"}

package/dist/cli/report.js CHANGED Viewed

@@ -140,16 +140,19 @@ export function formatInfo(file, plan) {
       file, and that the count is not knowable this cheaply, rather than inventing a zero.
     */
     if (!plan.writeSignals) {
+        // Named as they will be written. --info is read to find out what a run leaves behind,
+        // and a script that opens the name it was given must find a file there.
+        const suffix = plan.gzip ? '.csv.gz' : '.csv';
         lines.push(file.annotationSignals.length > 0
-            ? 'Would write annotations.csv and channels.csv, and no signal data. How many events ' +
-                'there are cannot be told from the header.'
-            : 'Would write channels.csv and no signal data — and no annotations.csv either, ' +
-                'since this recording has no annotation channel.');
+            ? `Would write annotations${suffix} and channels${suffix}, and no signal data. How ` +
+                'many events there are cannot be told from the header.'
+            : `Would write channels${suffix} and no signal data — and no annotations${suffix} ` +
+                'either, since this recording has no annotation channel.');
         return lines.join('\n');
     }
     // The estimate counts the characters of the CSV, which is what --gzip then compresses.
     // Reporting it as the size on disk would overstate a compressed conversion several-fold.
-    const compressing = plan.groups.some((group) => group.fileName.endsWith('.gz'));
+    const compressing = plan.gzip;
     lines.push(`Would write ${plan.estimate.rows.toLocaleString('en-US')} rows, roughly ` +
         `${formatBytes(plan.estimate.bytes)}${compressing ? ' before compression' : ''}.`);
     return lines.join('\n');

package/dist/cli/report.js.map CHANGED Viewed

	@@ -1 +1 @@
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Human-readable output for the terminal.\n \n Everything here is plain text with no colour codes, so piping to a file or a log\n * produces exactly what appeared on screen.\n /\n\nimport type { Diagnostic } from '../edf/errors.js';\nimport type { EdfFile } from '../edf/reader.js';\nimport { describeFormat, formatRates, formatWallClock } from '../edf/header.js';\nimport { formatBytes, formatDuration } from '../format/number.js';\nimport type { ConversionPlan } from '../convert/plan.js';\nimport { withoutFileRateWarning } from '../convert/plan.js';\nimport type { ConvertResult } from '../convert/run.js';\n\nfunction table(rows: readonly (readonly string[])[], alignRight: ReadonlySet<number>): string {\n if (rows.length === 0) return '';\n const width: number[] = [];\n for (const row of rows) {\n row.forEach((cell, i) => {\n width[i] = Math.max(width[i] ?? 0, cell.length);\n });\n }\n return rows\n .map((row) =>\n row\n .map((cell, i) => {\n const w = width[i] ?? 0;\n return alignRight.has(i) ? cell.padStart(w) : cell.padEnd(w);\n })\n .join(' ')\n .trimEnd(),\n )\n .join('\\n');\n}\n\n/\n Make header text safe to print to a terminal.\n \n EDF identification fields and channel labels are free text copied verbatim out of the\n * file, and `--info` puts them straight on stdout. A header carrying ANSI escapes could\n * therefore drive the reader's terminal — `\\x1b[2J\\x1b[H` clears the screen and homes the\n * cursor, which is enough to hide the rest of the output or repaint it as something else.\n * Nobody writes an EDF header that way on purpose, which is exactly why a file that does\n * should not be trusted with the terminal.\n \n Control bytes are shown as their escape instead, so a corrupt field stays diagnosable\n * rather than being silently swallowed. This affects display only: `channels.csv` and\n * `metadata.json` still copy the field verbatim, and CSV quoting already makes that safe.\n /\nexport function printable(text: string): string {\n // eslint-disable-next-line no-control-regex\n return text.replace(/[\\u0000-\\u001f\\u007f-\\u009f]/gu, (c) =>\n `\\\\x${c.codePointAt(0)!.toString(16).padStart(2, '0')}`,\n );\n}\n\n/\n The same protection for text that is meant to span lines.\n \n `printable` escapes newlines along with everything else, which is right for a channel\n * label — one has no business containing a line break, and it would break the `--info`\n * table's alignment. It is wrong for a whole message: several are written on two lines,\n * and Node's own option errors run to three. Escaping those turned the break into text:\n \n error: No channel named \"ECQ\". Did you mean \"ECG\"?\\x0aRun with --info to list ...\n \n Each line is escaped on its own, so nothing here gains the ability to drive a terminal.\n * A carriage return is still escaped, so no line can be repainted after it is printed —\n * which is the property that mattered. A newline can only add a line, never overwrite one.\n /\nexport function printableLines(text: string, indent = ''): string {\n return text\n .split('\\n')\n .map((line, index) => (index === 0 ? '' : indent) + printable(line))\n .join('\\n');\n}\n\n/* The `--info` view: what is in this recording, and what would converting it produce. /\nexport function formatInfo(file: EdfFile, plan: ConversionPlan): string {\n const { header } = file;\n const lines: string[] = [];\n\n lines.push(`File ${file.path}`);\n lines.push(`Format ${describeFormat(header)}`);\n lines.push(\n `Recorded ${\n formatWallClock(header.startDateTime)?.replace('T', ' ') ??\n `${printable(header.startDateRaw)} ${printable(header.startTimeRaw)} (unparseable)`\n }`,\n );\n lines.push(\n `Duration ${formatDuration(file.durationSeconds)} (${file.recordCount} records of ${header.recordDuration}s)`,\n );\n const elapsedSpan = plan.range.recordingEndSeconds - plan.range.recordingStartSeconds;\n if (Math.abs(elapsedSpan - file.durationSeconds) > 1e-9) {\n lines.push(`Time span ${formatDuration(elapsedSpan)} (includes discontinuities)`);\n }\n lines.push(`Size ${formatBytes(file.fileSize)}`);\n if (header.patientId) lines.push(`Patient ${printable(header.patientId)}`);\n if (header.recordingId) lines.push(`Recording ${printable(header.recordingId)}`);\n\n const signals = file.dataSignals;\n lines.push('');\n // The signal count was pluralised but the annotation-channel count was not, so a file\n // carrying two of them read \"2 annotation channel\". EDF+ permits more than one.\n const annotationCount = file.annotationSignals.length;\n const annotationPart =\n annotationCount > 0\n ? ` + ${annotationCount} annotation channel${annotationCount === 1 ? '' : 's'}`\n : '';\n lines.push(\n `Channels ${signals.length} signal${signals.length === 1 ? '' : 's'}${annotationPart}`,\n );\n lines.push('');\n\n const rows: string[][] = [['#', 'COLUMN', 'LABEL', 'UNIT', 'RATE', 'RANGE', 'OUTPUT']];\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n // Rendered as a group so that two channels recorded at different rates never show the\n // same figure in the RATE column, which is the one thing this table is asked to settle.\n const rateText = formatRates(signals.map((signal) => signal.samplingRate));\n for (const [row, signal] of signals.entries()) {\n rows.push([\n String(signal.index),\n printable(plan.columnNames.get(signal.index) ?? ''),\n printable(signal.label),\n printable(signal.physicalDimension),\n `${rateText[row]} Hz`,\n `${signal.physicalMin} to ${signal.physicalMax}`,\n /\n A channel with no samples was reported as \"(not selected)\", which is a different\n thing and not true when it was named on --channels. `edf2csv rec.edf --info\n --channels unused` said the channel the command asked for had not been chosen, when\n what is actually the case is that the file gives it nothing to convert. The\n NO_SAMPLES warning below the table says so; the table contradicted it.\n /\n fileFor.get(signal.index) ??\n (signal.samplesPerRecord === 0 ? '(no samples)' : '(not selected)'),\n ]);\n }\n lines.push(table(rows, new Set([0])));\n\n lines.push('');\n if (plan.groups.length > 1) {\n lines.push(\n `Sampling rates differ, so channels are written to ${plan.groups.length} files, one per rate. ` +\n `No channel is resampled.`,\n );\n }\n /\n The estimate describes the signal tables, and says so when that is not what will be\n written.\n\n Under --annotations-only there are no signal tables, and the line read \"Would write 0\n rows, roughly 0 B.\" for a conversion that goes on to write annotations.csv with three\n events in it. --info exists to say what a conversion will do; asserting it will write\n nothing, when it will write a file, is the one thing it must not do.\n\n How many events there are cannot be answered from the header — the annotation channel has\n to be read record by record, which is the scan --info is for avoiding. So it says which\n file, and that the count is not knowable this cheaply, rather than inventing a zero.\n /\n if (!plan.writeSignals) {\n lines.push(\n file.annotationSignals.length > 0\n ? 'Would write annotations.csv and channels.csv, and no signal data. How many events ' +\n 'there are cannot be told from the header.'\n : 'Would write channels.csv and no signal data — and no annotations.csv either, ' +\n 'since this recording has no annotation channel.',\n );\n return lines.join('\\n');\n }\n\n // The estimate counts the characters of the CSV, which is what --gzip then compresses.\n // Reporting it as the size on disk would overstate a compressed conversion several-fold.\n const compressing = plan.groups.some((group) => group.fileName.endsWith('.gz'));\n lines.push(\n `Would write ${plan.estimate.rows.toLocaleString('en-US')} rows, roughly ` +\n `${formatBytes(plan.estimate.bytes)}${compressing ? ' before compression' : ''}.`,\n );\n\n return lines.join('\\n');\n}\n\n/\n The `--info` view as JSON, for surveying files from a script.\n \n `indent` is 2 for a single recording, matching what this has always printed, and null for\n * a batch — several pretty-printed documents run together are readable by a streaming parser\n * but not by anything that expects one record per line, and a batch is exactly where\n * line-oriented reading is wanted. null rather than undefined because a default parameter\n * takes effect when undefined is passed, which quietly restored the indentation this was\n * meant to drop; JSON.stringify itself wants undefined, so it is translated at the call.\n \n `--info` answers \"what is in this recording and what would converting it cost\", which\n * is exactly the question you want to ask across a directory of hundreds of recordings —\n * and the text table is the wrong shape for that. `--json` previously applied only to\n * conversions, so scripts had to parse the aligned columns or convert files just to learn\n * what was in them.\n \n Field names match `metadata.json` where the two describe the same thing, so a survey and\n * a conversion can be read by the same code.\n /\nexport function infoJson(file: EdfFile, plan: ConversionPlan, indent: number \| null = 2): string {\n const { header } = file;\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n\n return JSON.stringify(\n {\n path: file.path,\n bytes: file.fileSize,\n format: describeFormat(header),\n start_datetime_local: formatWallClock(header.startDateTime),\n start_date_raw: header.startDateRaw,\n start_time_raw: header.startTimeRaw,\n patient_id: header.patientId,\n recording_id: header.recordingId,\n data_records: file.recordCount,\n data_records_declared: header.declaredRecordCount,\n record_duration_seconds: header.recordDuration,\n duration_seconds: file.durationSeconds,\n // For a discontinuous file this exceeds duration_seconds by the length of the gaps.\n time_span_seconds: plan.range.recordingEndSeconds - plan.range.recordingStartSeconds,\n annotation_channels: file.annotationSignals.length,\n channels: file.dataSignals.map((signal) => ({\n signal_index: signal.index,\n column: plan.columnNames.get(signal.index) ?? '',\n label: signal.label,\n unit: signal.physicalDimension,\n sampling_rate_hz: signal.samplingRate,\n samples_per_record: signal.samplesPerRecord,\n physical_min: signal.physicalMin,\n physical_max: signal.physicalMax,\n digital_min: signal.digitalMin,\n digital_max: signal.digitalMax,\n transducer: signal.transducer,\n prefiltering: signal.prefiltering,\n output_file: fileFor.get(signal.index) ?? null,\n })),\n estimate: {\n rows: plan.estimate.rows,\n // Character count of the CSV. With --gzip the file on disk is smaller than this.\n bytes: plan.estimate.bytes,\n exceeds_spreadsheet_limit: plan.estimate.exceedsSpreadsheetLimit,\n },\n // The plan's mixed-rate warning replaces the header parser's, as it does everywhere\n // else. This was the one consumer left out of that when 0.3.2 made the warning follow\n // --channels, so `--info --json` carried it twice: once counting the rates being\n // converted and once counting every rate in the file, with the same code and severity.\n warnings: plan.diagnostics\n .concat(withoutFileRateWarning(file.diagnostics))\n .map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n\n/* One line per diagnostic, prefixed so warnings are greppable. */\nexport function formatDiagnostics(diagnostics: readonly Diagnostic[]): string {\n return diagnostics\n .map((d) => {\n // Diagnostics quote channel labels, which come from the file, so they need the\n // same treatment as the --info table.\n const head = `${d.severity === 'warning' ? 'warning' : 'note'}: ${printable(d.message)}`;\n return d.hint ? `${head}\\n ${printable(d.hint)}` : head;\n })\n .join('\\n');\n}\n\nexport function formatSummary(result: ConvertResult): string {\n const lines: string[] = [];\n const rows: string[][] = [];\n for (const file of result.files) {\n rows.push([` ${file.name}`, file.rows.toLocaleString('en-US'), file.name.endsWith('.csv') ? 'rows' : '']);\n }\n lines.push(`Wrote ${result.outputDir}`);\n lines.push(table(rows, new Set([1])));\n lines.push(`Done in ${(result.elapsedMs / 1000).toFixed(1)}s.`);\n return lines.join('\\n');\n}\n\nexport function summaryJson(result: ConvertResult, indent: number \| null = 2): string {\n return JSON.stringify(\n {\n output_dir: result.outputDir,\n files: result.files,\n annotations: result.annotationCount,\n duration_seconds: result.file.durationSeconds,\n records: result.file.recordCount,\n elapsed_ms: result.elapsedMs,\n warnings: result.diagnostics.map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n"]}
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Human-readable output for the terminal.\n \n Everything here is plain text with no colour codes, so piping to a file or a log\n * produces exactly what appeared on screen.\n /\n\nimport type { Diagnostic } from '../edf/errors.js';\nimport type { EdfFile } from '../edf/reader.js';\nimport { describeFormat, formatRates, formatWallClock } from '../edf/header.js';\nimport { formatBytes, formatDuration } from '../format/number.js';\nimport type { ConversionPlan } from '../convert/plan.js';\nimport { withoutFileRateWarning } from '../convert/plan.js';\nimport type { ConvertResult } from '../convert/run.js';\n\nfunction table(rows: readonly (readonly string[])[], alignRight: ReadonlySet<number>): string {\n if (rows.length === 0) return '';\n const width: number[] = [];\n for (const row of rows) {\n row.forEach((cell, i) => {\n width[i] = Math.max(width[i] ?? 0, cell.length);\n });\n }\n return rows\n .map((row) =>\n row\n .map((cell, i) => {\n const w = width[i] ?? 0;\n return alignRight.has(i) ? cell.padStart(w) : cell.padEnd(w);\n })\n .join(' ')\n .trimEnd(),\n )\n .join('\\n');\n}\n\n/\n Make header text safe to print to a terminal.\n \n EDF identification fields and channel labels are free text copied verbatim out of the\n * file, and `--info` puts them straight on stdout. A header carrying ANSI escapes could\n * therefore drive the reader's terminal — `\\x1b[2J\\x1b[H` clears the screen and homes the\n * cursor, which is enough to hide the rest of the output or repaint it as something else.\n * Nobody writes an EDF header that way on purpose, which is exactly why a file that does\n * should not be trusted with the terminal.\n \n Control bytes are shown as their escape instead, so a corrupt field stays diagnosable\n * rather than being silently swallowed. This affects display only: `channels.csv` and\n * `metadata.json` still copy the field verbatim, and CSV quoting already makes that safe.\n /\nexport function printable(text: string): string {\n // eslint-disable-next-line no-control-regex\n return text.replace(/[\\u0000-\\u001f\\u007f-\\u009f]/gu, (c) =>\n `\\\\x${c.codePointAt(0)!.toString(16).padStart(2, '0')}`,\n );\n}\n\n/\n The same protection for text that is meant to span lines.\n \n `printable` escapes newlines along with everything else, which is right for a channel\n * label — one has no business containing a line break, and it would break the `--info`\n * table's alignment. It is wrong for a whole message: several are written on two lines,\n * and Node's own option errors run to three. Escaping those turned the break into text:\n \n error: No channel named \"ECQ\". Did you mean \"ECG\"?\\x0aRun with --info to list ...\n \n Each line is escaped on its own, so nothing here gains the ability to drive a terminal.\n * A carriage return is still escaped, so no line can be repainted after it is printed —\n * which is the property that mattered. A newline can only add a line, never overwrite one.\n /\nexport function printableLines(text: string, indent = ''): string {\n return text\n .split('\\n')\n .map((line, index) => (index === 0 ? '' : indent) + printable(line))\n .join('\\n');\n}\n\n/* The `--info` view: what is in this recording, and what would converting it produce. /\nexport function formatInfo(file: EdfFile, plan: ConversionPlan): string {\n const { header } = file;\n const lines: string[] = [];\n\n lines.push(`File ${file.path}`);\n lines.push(`Format ${describeFormat(header)}`);\n lines.push(\n `Recorded ${\n formatWallClock(header.startDateTime)?.replace('T', ' ') ??\n `${printable(header.startDateRaw)} ${printable(header.startTimeRaw)} (unparseable)`\n }`,\n );\n lines.push(\n `Duration ${formatDuration(file.durationSeconds)} (${file.recordCount} records of ${header.recordDuration}s)`,\n );\n const elapsedSpan = plan.range.recordingEndSeconds - plan.range.recordingStartSeconds;\n if (Math.abs(elapsedSpan - file.durationSeconds) > 1e-9) {\n lines.push(`Time span ${formatDuration(elapsedSpan)} (includes discontinuities)`);\n }\n lines.push(`Size ${formatBytes(file.fileSize)}`);\n if (header.patientId) lines.push(`Patient ${printable(header.patientId)}`);\n if (header.recordingId) lines.push(`Recording ${printable(header.recordingId)}`);\n\n const signals = file.dataSignals;\n lines.push('');\n // The signal count was pluralised but the annotation-channel count was not, so a file\n // carrying two of them read \"2 annotation channel\". EDF+ permits more than one.\n const annotationCount = file.annotationSignals.length;\n const annotationPart =\n annotationCount > 0\n ? ` + ${annotationCount} annotation channel${annotationCount === 1 ? '' : 's'}`\n : '';\n lines.push(\n `Channels ${signals.length} signal${signals.length === 1 ? '' : 's'}${annotationPart}`,\n );\n lines.push('');\n\n const rows: string[][] = [['#', 'COLUMN', 'LABEL', 'UNIT', 'RATE', 'RANGE', 'OUTPUT']];\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n // Rendered as a group so that two channels recorded at different rates never show the\n // same figure in the RATE column, which is the one thing this table is asked to settle.\n const rateText = formatRates(signals.map((signal) => signal.samplingRate));\n for (const [row, signal] of signals.entries()) {\n rows.push([\n String(signal.index),\n printable(plan.columnNames.get(signal.index) ?? ''),\n printable(signal.label),\n printable(signal.physicalDimension),\n `${rateText[row]} Hz`,\n `${signal.physicalMin} to ${signal.physicalMax}`,\n /\n A channel with no samples was reported as \"(not selected)\", which is a different\n thing and not true when it was named on --channels. `edf2csv rec.edf --info\n --channels unused` said the channel the command asked for had not been chosen, when\n what is actually the case is that the file gives it nothing to convert. The\n NO_SAMPLES warning below the table says so; the table contradicted it.\n /\n fileFor.get(signal.index) ??\n (signal.samplesPerRecord === 0 ? '(no samples)' : '(not selected)'),\n ]);\n }\n lines.push(table(rows, new Set([0])));\n\n lines.push('');\n if (plan.groups.length > 1) {\n lines.push(\n `Sampling rates differ, so channels are written to ${plan.groups.length} files, one per rate. ` +\n `No channel is resampled.`,\n );\n }\n /\n The estimate describes the signal tables, and says so when that is not what will be\n written.\n\n Under --annotations-only there are no signal tables, and the line read \"Would write 0\n rows, roughly 0 B.\" for a conversion that goes on to write annotations.csv with three\n events in it. --info exists to say what a conversion will do; asserting it will write\n nothing, when it will write a file, is the one thing it must not do.\n\n How many events there are cannot be answered from the header — the annotation channel has\n to be read record by record, which is the scan --info is for avoiding. So it says which\n file, and that the count is not knowable this cheaply, rather than inventing a zero.\n /\n if (!plan.writeSignals) {\n // Named as they will be written. --info is read to find out what a run leaves behind,\n // and a script that opens the name it was given must find a file there.\n const suffix = plan.gzip ? '.csv.gz' : '.csv';\n lines.push(\n file.annotationSignals.length > 0\n ? `Would write annotations${suffix} and channels${suffix}, and no signal data. How ` +\n 'many events there are cannot be told from the header.'\n : `Would write channels${suffix} and no signal data — and no annotations${suffix} ` +\n 'either, since this recording has no annotation channel.',\n );\n return lines.join('\\n');\n }\n\n // The estimate counts the characters of the CSV, which is what --gzip then compresses.\n // Reporting it as the size on disk would overstate a compressed conversion several-fold.\n const compressing = plan.gzip;\n lines.push(\n `Would write ${plan.estimate.rows.toLocaleString('en-US')} rows, roughly ` +\n `${formatBytes(plan.estimate.bytes)}${compressing ? ' before compression' : ''}.`,\n );\n\n return lines.join('\\n');\n}\n\n/\n The `--info` view as JSON, for surveying files from a script.\n \n `indent` is 2 for a single recording, matching what this has always printed, and null for\n * a batch — several pretty-printed documents run together are readable by a streaming parser\n * but not by anything that expects one record per line, and a batch is exactly where\n * line-oriented reading is wanted. null rather than undefined because a default parameter\n * takes effect when undefined is passed, which quietly restored the indentation this was\n * meant to drop; JSON.stringify itself wants undefined, so it is translated at the call.\n \n `--info` answers \"what is in this recording and what would converting it cost\", which\n * is exactly the question you want to ask across a directory of hundreds of recordings —\n * and the text table is the wrong shape for that. `--json` previously applied only to\n * conversions, so scripts had to parse the aligned columns or convert files just to learn\n * what was in them.\n \n Field names match `metadata.json` where the two describe the same thing, so a survey and\n * a conversion can be read by the same code.\n /\nexport function infoJson(file: EdfFile, plan: ConversionPlan, indent: number \| null = 2): string {\n const { header } = file;\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n\n return JSON.stringify(\n {\n path: file.path,\n bytes: file.fileSize,\n format: describeFormat(header),\n start_datetime_local: formatWallClock(header.startDateTime),\n start_date_raw: header.startDateRaw,\n start_time_raw: header.startTimeRaw,\n patient_id: header.patientId,\n recording_id: header.recordingId,\n data_records: file.recordCount,\n data_records_declared: header.declaredRecordCount,\n record_duration_seconds: header.recordDuration,\n duration_seconds: file.durationSeconds,\n // For a discontinuous file this exceeds duration_seconds by the length of the gaps.\n time_span_seconds: plan.range.recordingEndSeconds - plan.range.recordingStartSeconds,\n annotation_channels: file.annotationSignals.length,\n channels: file.dataSignals.map((signal) => ({\n signal_index: signal.index,\n column: plan.columnNames.get(signal.index) ?? '',\n label: signal.label,\n unit: signal.physicalDimension,\n sampling_rate_hz: signal.samplingRate,\n samples_per_record: signal.samplesPerRecord,\n physical_min: signal.physicalMin,\n physical_max: signal.physicalMax,\n digital_min: signal.digitalMin,\n digital_max: signal.digitalMax,\n transducer: signal.transducer,\n prefiltering: signal.prefiltering,\n output_file: fileFor.get(signal.index) ?? null,\n })),\n estimate: {\n rows: plan.estimate.rows,\n // Character count of the CSV. With --gzip the file on disk is smaller than this.\n bytes: plan.estimate.bytes,\n exceeds_spreadsheet_limit: plan.estimate.exceedsSpreadsheetLimit,\n },\n // The plan's mixed-rate warning replaces the header parser's, as it does everywhere\n // else. This was the one consumer left out of that when 0.3.2 made the warning follow\n // --channels, so `--info --json` carried it twice: once counting the rates being\n // converted and once counting every rate in the file, with the same code and severity.\n warnings: plan.diagnostics\n .concat(withoutFileRateWarning(file.diagnostics))\n .map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n\n/* One line per diagnostic, prefixed so warnings are greppable. */\nexport function formatDiagnostics(diagnostics: readonly Diagnostic[]): string {\n return diagnostics\n .map((d) => {\n // Diagnostics quote channel labels, which come from the file, so they need the\n // same treatment as the --info table.\n const head = `${d.severity === 'warning' ? 'warning' : 'note'}: ${printable(d.message)}`;\n return d.hint ? `${head}\\n ${printable(d.hint)}` : head;\n })\n .join('\\n');\n}\n\nexport function formatSummary(result: ConvertResult): string {\n const lines: string[] = [];\n const rows: string[][] = [];\n for (const file of result.files) {\n rows.push([` ${file.name}`, file.rows.toLocaleString('en-US'), file.name.endsWith('.csv') ? 'rows' : '']);\n }\n lines.push(`Wrote ${result.outputDir}`);\n lines.push(table(rows, new Set([1])));\n lines.push(`Done in ${(result.elapsedMs / 1000).toFixed(1)}s.`);\n return lines.join('\\n');\n}\n\nexport function summaryJson(result: ConvertResult, indent: number \| null = 2): string {\n return JSON.stringify(\n {\n output_dir: result.outputDir,\n files: result.files,\n annotations: result.annotationCount,\n duration_seconds: result.file.durationSeconds,\n records: result.file.recordCount,\n elapsed_ms: result.elapsedMs,\n warnings: result.diagnostics.map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n"]}

package/dist/convert/plan.d.ts CHANGED Viewed

@@ -56,6 +56,14 @@ export interface PlanOptions {
 }
 export interface ConversionPlan {
     groups: RateGroup[];
+    /**
+     * Whether the CSVs will be compressed.
+     *
+     * Recorded rather than inferred from the group file names. Under `--annotations-only`
+     * there are no groups to read it off, and `--info` named `annotations.csv` for a run that
+     * wrote `annotations.csv.gz`.
+     */
+    gzip: boolean;
     range: ResolvedRange;
     columnNames: Map<number, string>;
     writeSignals: boolean;

package/dist/convert/plan.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/convert/plan.js CHANGED Viewed

@@ -131,7 +131,7 @@ export function buildPlan(input, options = {}) {
             hint: 'Use --start and --duration to convert a section, or read the file with pandas or R.',
         });
     }
-    return { groups, range, columnNames, writeSignals, diagnostics, estimate };
+    return { groups, gzip: options.gzip === true, range, columnNames, writeSignals, diagnostics, estimate };
 }
 /**
  * Partition channels by sampling rate, largest first.

package/dist/convert/plan.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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Turning a request into a concrete conversion plan.\n \n The plan is where the tool's central promise is enforced: channels recorded at\n * different sampling rates are never merged into one table. A single wide CSV can\n * only hold mixed rates by inventing samples for the slow channels — MNE, for\n * instance, expands three genuine 1 Hz temperature readings into 768 interpolated\n * values without warning. Instead each distinct rate gets its own file, so every\n * number in every output file is a number that was actually recorded.\n /\n\nimport type { Diagnostic } from '../edf/errors.js';\nimport type { EdfSignal } from '../edf/header.js';\nimport { formatRate, formatRates } from '../edf/header.js';\nimport { decimalsForSignal } from '../edf/scale.js';\nimport { UTF8_BOM, csvRow } from '../format/csv.js';\nimport { listed } from '../format/list.js';\nimport { timeDecimals } from '../format/number.js';\nimport { buildColumnNames, renamedByCollision, selectChannels } from './channels.js';\nimport { assertOptions } from './options.js';\nimport { countSamplesInRange, resolveRange } from './time-range.js';\nimport type { ResolvedRange } from './time-range.js';\n\nexport interface PlannedChannel {\n signal: EdfSignal;\n column: string;\n decimals: number;\n}\n\nexport interface RateGroup {\n /* Sampling rate in Hz shared by every channel in this group. /\n rate: number;\n samplesPerRecord: number;\n fileName: string;\n timeDecimals: number;\n channels: PlannedChannel[];\n}\n\nexport interface PlanInput {\n signals: readonly EdfSignal[];\n recordDuration: number;\n recordCount: number;\n hasAnnotationChannel: boolean;\n /\n True start time of each data record, supplied for discontinuous files. The\n * requested time window is resolved against these rather than against\n * `recordCount * recordDuration`, which for a file with gaps is the amount of\n * data rather than the span of time it covers.\n /\n recordStarts?: Float64Array \| null \| undefined;\n}\n\nexport interface PlanOptions {\n channels?: readonly string[] \| undefined;\n start?: number \| undefined;\n /* The `--start` value exactly as typed, for error messages. /\n startText?: string \| undefined;\n duration?: number \| undefined;\n end?: number \| undefined;\n /* The `--end` value exactly as typed, for error messages. /\n endText?: string \| undefined;\n annotationsOnly?: boolean \| undefined;\n /* Force a fixed number of decimals instead of deriving it per channel. /\n decimals?: number \| undefined;\n /* Compress each CSV with gzip, giving every one of them a `.gz` name. /\n gzip?: boolean \| undefined;\n /* Start each CSV with a UTF-8 byte order mark, so Excel reads it as UTF-8. /\n bom?: boolean \| undefined;\n}\n\nexport interface ConversionPlan {\n groups: RateGroup[];\n range: ResolvedRange;\n columnNames: Map<number, string>;\n writeSignals: boolean;\n diagnostics: Diagnostic[];\n estimate: OutputEstimate;\n}\n\nexport interface OutputEstimate {\n /* Total data rows across every signal file. /\n rows: number;\n /* Approximate size of the signal CSVs on disk. /\n bytes: number;\n /* True when any single file would exceed Excel's row limit. /\n exceedsSpreadsheetLimit: boolean;\n}\n\nconst BOM_BYTES = Buffer.byteLength(UTF8_BOM);\n\n/* Excel and most spreadsheet tools stop at 1,048,576 rows including the header. /\nexport const SPREADSHEET_ROW_LIMIT = 1_048_576;\n\nexport function buildPlan(input: PlanInput, options: PlanOptions = {}): ConversionPlan {\n // First, and before a directory is created or a stream opened, so a rejected option\n // leaves nothing behind. See assertOptions for what used to get through.\n assertOptions(options);\n\n const diagnostics: Diagnostic[] = [];\n const columnNames = buildColumnNames(input.signals);\n\n // A channel whose own label was taken by another channel's disambiguating suffix. The\n // duplicate-label warning is about the labels that collided; this is about the channel\n // that lost its name to them, which is the one whose column no longer matches the file.\n for (const signal of renamedByCollision(input.signals, columnNames)) {\n diagnostics.push({\n code: 'DUPLICATE_LABEL',\n severity: 'warning',\n message:\n `Signal ${signal.index} is labelled \"${signal.label}\", which is also the column name ` +\n `another channel's \"_ch\" suffix produces, so its column is \"${columnNames.get(signal.index)}\".`,\n hint: 'Column names are unique; look this channel up in channels.csv by its signal_index.',\n });\n }\n\n const range = resolveRange({\n start: options.start,\n startText: options.startText,\n duration: options.duration,\n end: options.end,\n endText: options.endText,\n recordDuration: input.recordDuration,\n recordCount: input.recordCount,\n recordStarts: input.recordStarts,\n });\n\n const writeSignals = options.annotationsOnly !== true;\n\n let chosen: EdfSignal[] = input.signals.filter((s) => !s.isAnnotations);\n\n /\n Channel names are checked even under --annotations-only, where the selection is not\n otherwise used.\n\n Skipping the check meant `--channels TYPO --annotations-only` exited 0 in silence while\n the same typo without the flag was a usage error, and `--channels \"\"` stayed an error\n in both — so a mistyped name was the one form of bad input the tool accepted quietly.\n Everywhere else a term matching nothing is reported rather than ignored; a flag that\n happens not to apply is a poor reason to make an exception.\n /\n if (options.channels && options.channels.length > 0) {\n const selection = selectChannels(input.signals, options.channels);\n if (writeSignals) chosen = selection.signals;\n for (const { term, matched } of selection.ambiguous) {\n diagnostics.push({\n code: 'DUPLICATE_LABEL',\n severity: 'warning',\n message:\n `\"${term}\" matches ${matched.length} channels (positions ` +\n `${listed(matched.map((s) => `#${s.index}`))}); all of them were selected.`,\n hint: `Use --channels \"#${matched[0]?.index ?? 0}\" to pick just one.`,\n });\n }\n }\n\n const groups = writeSignals\n ? groupByRate(chosen, columnNames, options.decimals, options.gzip === true)\n : [];\n const estimate = estimateOutput(\n groups,\n range,\n input.recordDuration,\n input.recordStarts,\n options.bom === true,\n );\n\n /\n The mixed-rate warning describes what this conversion does, not what the file holds.\n\n The header parser raises its own, which is right for `parseHeader` — but it sees every\n channel and knows nothing about `--channels`. Converting one channel out of a three-rate\n recording therefore announced \"3 different sampling rates ... written to one file per\n rate\" over a run that wrote one file, in the same output where `--info` had already\n marked the other two \"(not selected)\". Selecting two of the three was wrong the other\n way: still \"3\".\n\n Callers combining these with a file's own diagnostics drop that copy in favour of this\n one; see `withoutFileRateWarning`.\n /\n if (groups.length > 1) {\n diagnostics.push({\n code: 'MIXED_SAMPLING_RATES',\n severity: 'warning',\n message:\n `Channels use ${groups.length} different sampling rates ` +\n `(${listed(formatRates(groups.map((g) => g.rate)).map((r) => `${r} Hz`))}).`,\n hint: 'They are written to one file per rate so no channel is resampled.',\n });\n }\n\n /\n A time column that cannot tell two samples apart.\n\n Sample times are written to at most nine decimal places, which separates everything up to\n a gigahertz. Below that the column repeats: a recording of 1 ns records holding ten\n samples each writes twenty rows carrying three distinct times, so joining or plotting on\n `time_s` silently collapses them. Nothing is lost from the file — every sample is there,\n in order — but the column stops being an identifier, and that is worth saying rather than\n leaving to be discovered.\n /\n for (const group of groups) {\n const step = group.rate > 0 ? 1 / group.rate : 0;\n if (step > 0 && step < 10 * -group.timeDecimals) {\n diagnostics.push({\n code: 'TIME_RESOLUTION',\n severity: 'warning',\n message:\n `Channels at ${formatRate(group.rate)} Hz sample faster than the time column can ` +\n `distinguish, so consecutive rows in ${group.fileName} carry the same time_s value.`,\n hint:\n 'Every sample is written, in order. Use the row number rather than time_s to tell ' +\n 'them apart, or convert one rate at a time with --channels.',\n });\n }\n }\n\n if (estimate.exceedsSpreadsheetLimit) {\n diagnostics.push({\n code: 'LARGE_OUTPUT',\n severity: 'warning',\n message:\n `At least one output file will have more than ${SPREADSHEET_ROW_LIMIT.toLocaleString('en-US')} ` +\n `rows, which is more than Excel or Numbers can open.`,\n hint: 'Use --start and --duration to convert a section, or read the file with pandas or R.',\n });\n }\n\n return { groups, range, columnNames, writeSignals, diagnostics, estimate };\n}\n\n/*\n Partition channels by sampling rate, largest first.\n \n The common case — every channel at one rate — collapses to a single group and a\n * single `signals.csv`, so the honest behaviour costs nothing when there is nothing\n * to be honest about.\n /\nfunction groupByRate(\n signals: readonly EdfSignal[],\n columnNames: Map<number, string>,\n forcedDecimals: number \| undefined,\n gzip: boolean,\n): RateGroup[] {\n const byRate = new Map<number, EdfSignal[]>();\n for (const signal of signals) {\n // A channel with no samples has no sampling rate to group by, and would\n // otherwise produce an empty \"0hz\" file. The header parser already warned.\n if (signal.samplesPerRecord === 0) continue;\n const bucket = byRate.get(signal.samplingRate);\n if (bucket) bucket.push(signal);\n else byRate.set(signal.samplingRate, [signal]);\n }\n\n const rates = [...byRate.keys()].sort((a, b) => b - a);\n const single = rates.length === 1;\n\n /\n Two distinct rates can produce the same slug, because the slug rounds to six decimal\n places. Rates come from samplesPerRecord / recordDuration and every channel shares the\n record duration, so the closest two rates can be is 1 / recordDuration — which drops\n below 1e-6 once a record is longer than about eleven days. Absurd, but the header\n permits it, and the failure was silent and destructive: both groups opened a write\n stream on the same path, so the file ended up holding interleaved rows from both\n channels under a header naming only one of them.\n\n Distinct rates therefore get distinct files, always. The suffix is only ever reached by\n a collision, so ordinary recordings keep the names they have always had.\n\n Naming from the whole set of rates at once removes most of those collisions before the\n suffix has to. Rounding each rate on its own gave 1e-6 Hz and 1.25e-6 Hz the same slug,\n and the numbering below then produced signals_0_000001hz.csv and signals_0_000001hz_2.csv\n — two files that no longer overwrite each other, but of which only one is named for the\n rate it holds. The suffix stays as the backstop for anything this still cannot separate.\n /\n const suffix = gzip ? '.csv.gz' : '.csv';\n const slugs = formatRates(rates).map((text) => `${text.replace('.', '_')}hz`);\n const used = new Set<string>();\n const uniqueName = (index: number): string => {\n const base = `signals_${slugs[index]}`;\n let name = `${base}${suffix}`;\n for (let n = 2; used.has(name); n++) name = `${base}_${n}${suffix}`;\n used.add(name);\n return name;\n };\n\n return rates.map((rate, index) => {\n const members = byRate.get(rate) ?? [];\n const first = members[0];\n return {\n rate,\n samplesPerRecord: first ? first.samplesPerRecord : 0,\n fileName: single ? `signals${suffix}` : uniqueName(index),\n timeDecimals: timeDecimals(rate),\n channels: members.map((signal) => ({\n signal,\n column: columnNames.get(signal.index) ?? `signal_${signal.index}`,\n decimals: forcedDecimals ?? decimalsForSignal(signal),\n })),\n };\n });\n}\n\n/\n A file's diagnostics with the header's mixed-rate warning removed.\n \n `buildPlan` raises that warning for the channels actually being converted, so keeping both\n * would either duplicate it or contradict it. The header parser's copy stays where it is, for\n * callers reading a header without planning a conversion.\n /\nexport function withoutFileRateWarning(diagnostics: readonly Diagnostic[]): Diagnostic[] {\n return diagnostics.filter((d) => d.code !== 'MIXED_SAMPLING_RATES');\n}\n\n/* `256hz`, `12_5hz` — safe in a filename on every platform. /\nexport function rateSlug(rate: number): string {\n return `${formatRate(rate).replace('.', '_')}hz`;\n}\n\n/* Characters a fixed-decimal number of this magnitude occupies, sign included. /\nfunction widthOf(magnitude: number, decimals: number, signed = false): number {\n const size = Math.abs(magnitude);\n const sign = signed ? 1 : 0;\n const fraction = decimals > 0 ? 1 + decimals : 0;\n\n /\n Cells are written with toFixed, which rounds. Taking the integer digits from the floor of\n the bound therefore under-counted whenever rounding carried into a new digit: a channel\n bounded at 9999.999 and written to zero decimals produces \"10000\", five characters where\n the floor of 9999.999 suggests four. Every cell on such a channel was a byte short, and\n `--info` reported 127 KB for a file that came out 131 KB.\n\n Measuring the bound as rendered removes that. toFixed switches to exponential notation\n past 1e21, so the arithmetic form still covers magnitudes beyond it.\n /\n if (!Number.isFinite(size)) return sign + 1 + fraction;\n if (size < 1e21) return sign + size.toFixed(Math.min(decimals, 100)).length;\n return sign + (Math.floor(Math.log10(size)) + 1) + fraction;\n}\n\nfunction estimateOutput(\n groups: readonly RateGroup[],\n range: ResolvedRange,\n recordDuration: number,\n recordStarts: Float64Array \| null \| undefined,\n bom: boolean,\n): OutputEstimate {\n let rows = 0;\n let bytes = 0;\n let exceeds = false;\n\n for (const group of groups) {\n let groupRows = 0;\n for (let record = range.startRecord; record < range.endRecord; record++) {\n const recordStart = recordStarts\n ? (recordStarts[record] ?? record recordDuration)\n : record * recordDuration;\n groupRows += countSamplesInRange({\n recordStart,\n rate: group.rate,\n samplesPerRecord: group.samplesPerRecord,\n startSeconds: range.startSeconds,\n endSeconds: range.endSeconds,\n });\n }\n rows += groupRows;\n if (groupRows + 1 > SPREADSHEET_ROW_LIMIT) exceeds = true;\n\n /\n Width per cell, from the channel's own calibration rather than a flat allowance.\n\n The old `decimals + 6` budgeted six characters for the sign, integer part and decimal\n point on every channel, whatever it actually held. That over-counted a millivolt\n channel spanning ±5 by four characters a cell and ran 30-55% high across the fixture\n set — on a number people use to decide whether a conversion is worth starting.\n\n The channel's declared physical range is what bounds a cell, so that bound is what is\n used. Most samples sit below it, so this still reads high, which is the direction a\n size estimate should err in.\n\n One case is outside the bound rather than under it: nothing obliges a recording to keep\n its samples inside the digital range it declares, and one that does not maps outside the\n physical range too. Such a file can convert larger than the estimate. Clamping the data\n to make the estimate true is not a trade worth making — the samples are what they are.\n /\n const timeWidth = widthOf(range.endSeconds, group.timeDecimals);\n const cellWidth = group.channels.reduce(\n (sum, c) =>\n sum +\n widthOf(\n Math.max(Math.abs(c.signal.physicalMin), Math.abs(c.signal.physicalMax)),\n c.decimals,\n c.signal.physicalMin < 0 \|\| c.signal.physicalMax < 0,\n ),\n 0,\n );\n // One comma per channel, plus the newline.\n bytes += groupRows * (timeWidth + cellWidth + group.channels.length + 1);\n /\n The header row, measured as it will be written rather than as the labels are stored.\n\n A column name is quoted when it contains a comma, a quote, a newline or a leading or\n trailing space, and every quote inside it is doubled. Counting the raw label under-counted\n that row: three channels labelled `a,b,c,d,e`, `x\"y` and `plain` write a 32-byte header\n and were budgeted 27. EDF labels are free text, so commas in them are ordinary — a montage\n written as `EEG Fpz-Cz, ref` is exactly the kind of thing this is for.\n\n csvRow is the function that writes it, so it is the function that measures it. Nothing\n else is in a position to stay correct when the quoting rules change.\n /\n bytes += Buffer.byteLength(csvRow(['time_s', ...group.channels.map((c) => c.column)])) + 1;\n // Three bytes per file under --bom. Small, but the estimate promises never to read\n // under what gets written, and a one-row conversion is small enough for it to matter.\n if (bom) bytes += BOM_BYTES;\n }\n\n return { rows, bytes, exceedsSpreadsheetLimit: exceeds };\n}\n"]}
1	+ 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Turning a request into a concrete conversion plan.\n \n The plan is where the tool's central promise is enforced: channels recorded at\n * different sampling rates are never merged into one table. A single wide CSV can\n * only hold mixed rates by inventing samples for the slow channels — MNE, for\n * instance, expands three genuine 1 Hz temperature readings into 768 interpolated\n * values without warning. Instead each distinct rate gets its own file, so every\n * number in every output file is a number that was actually recorded.\n /\n\nimport type { Diagnostic } from '../edf/errors.js';\nimport type { EdfSignal } from '../edf/header.js';\nimport { formatRate, formatRates } from '../edf/header.js';\nimport { decimalsForSignal } from '../edf/scale.js';\nimport { UTF8_BOM, csvRow } from '../format/csv.js';\nimport { listed } from '../format/list.js';\nimport { timeDecimals } from '../format/number.js';\nimport { buildColumnNames, renamedByCollision, selectChannels } from './channels.js';\nimport { assertOptions } from './options.js';\nimport { countSamplesInRange, resolveRange } from './time-range.js';\nimport type { ResolvedRange } from './time-range.js';\n\nexport interface PlannedChannel {\n signal: EdfSignal;\n column: string;\n decimals: number;\n}\n\nexport interface RateGroup {\n /* Sampling rate in Hz shared by every channel in this group. /\n rate: number;\n samplesPerRecord: number;\n fileName: string;\n timeDecimals: number;\n channels: PlannedChannel[];\n}\n\nexport interface PlanInput {\n signals: readonly EdfSignal[];\n recordDuration: number;\n recordCount: number;\n hasAnnotationChannel: boolean;\n /\n True start time of each data record, supplied for discontinuous files. The\n * requested time window is resolved against these rather than against\n * `recordCount * recordDuration`, which for a file with gaps is the amount of\n * data rather than the span of time it covers.\n /\n recordStarts?: Float64Array \| null \| undefined;\n}\n\nexport interface PlanOptions {\n channels?: readonly string[] \| undefined;\n start?: number \| undefined;\n /* The `--start` value exactly as typed, for error messages. /\n startText?: string \| undefined;\n duration?: number \| undefined;\n end?: number \| undefined;\n /* The `--end` value exactly as typed, for error messages. /\n endText?: string \| undefined;\n annotationsOnly?: boolean \| undefined;\n /* Force a fixed number of decimals instead of deriving it per channel. /\n decimals?: number \| undefined;\n /* Compress each CSV with gzip, giving every one of them a `.gz` name. /\n gzip?: boolean \| undefined;\n /* Start each CSV with a UTF-8 byte order mark, so Excel reads it as UTF-8. /\n bom?: boolean \| undefined;\n}\n\nexport interface ConversionPlan {\n groups: RateGroup[];\n /\n Whether the CSVs will be compressed.\n \n Recorded rather than inferred from the group file names. Under `--annotations-only`\n * there are no groups to read it off, and `--info` named `annotations.csv` for a run that\n * wrote `annotations.csv.gz`.\n /\n gzip: boolean;\n range: ResolvedRange;\n columnNames: Map<number, string>;\n writeSignals: boolean;\n diagnostics: Diagnostic[];\n estimate: OutputEstimate;\n}\n\nexport interface OutputEstimate {\n /* Total data rows across every signal file. /\n rows: number;\n /* Approximate size of the signal CSVs on disk. /\n bytes: number;\n /* True when any single file would exceed Excel's row limit. /\n exceedsSpreadsheetLimit: boolean;\n}\n\nconst BOM_BYTES = Buffer.byteLength(UTF8_BOM);\n\n/* Excel and most spreadsheet tools stop at 1,048,576 rows including the header. /\nexport const SPREADSHEET_ROW_LIMIT = 1_048_576;\n\nexport function buildPlan(input: PlanInput, options: PlanOptions = {}): ConversionPlan {\n // First, and before a directory is created or a stream opened, so a rejected option\n // leaves nothing behind. See assertOptions for what used to get through.\n assertOptions(options);\n\n const diagnostics: Diagnostic[] = [];\n const columnNames = buildColumnNames(input.signals);\n\n // A channel whose own label was taken by another channel's disambiguating suffix. The\n // duplicate-label warning is about the labels that collided; this is about the channel\n // that lost its name to them, which is the one whose column no longer matches the file.\n for (const signal of renamedByCollision(input.signals, columnNames)) {\n diagnostics.push({\n code: 'DUPLICATE_LABEL',\n severity: 'warning',\n message:\n `Signal ${signal.index} is labelled \"${signal.label}\", which is also the column name ` +\n `another channel's \"_ch\" suffix produces, so its column is \"${columnNames.get(signal.index)}\".`,\n hint: 'Column names are unique; look this channel up in channels.csv by its signal_index.',\n });\n }\n\n const range = resolveRange({\n start: options.start,\n startText: options.startText,\n duration: options.duration,\n end: options.end,\n endText: options.endText,\n recordDuration: input.recordDuration,\n recordCount: input.recordCount,\n recordStarts: input.recordStarts,\n });\n\n const writeSignals = options.annotationsOnly !== true;\n\n let chosen: EdfSignal[] = input.signals.filter((s) => !s.isAnnotations);\n\n /\n Channel names are checked even under --annotations-only, where the selection is not\n otherwise used.\n\n Skipping the check meant `--channels TYPO --annotations-only` exited 0 in silence while\n the same typo without the flag was a usage error, and `--channels \"\"` stayed an error\n in both — so a mistyped name was the one form of bad input the tool accepted quietly.\n Everywhere else a term matching nothing is reported rather than ignored; a flag that\n happens not to apply is a poor reason to make an exception.\n /\n if (options.channels && options.channels.length > 0) {\n const selection = selectChannels(input.signals, options.channels);\n if (writeSignals) chosen = selection.signals;\n for (const { term, matched } of selection.ambiguous) {\n diagnostics.push({\n code: 'DUPLICATE_LABEL',\n severity: 'warning',\n message:\n `\"${term}\" matches ${matched.length} channels (positions ` +\n `${listed(matched.map((s) => `#${s.index}`))}); all of them were selected.`,\n hint: `Use --channels \"#${matched[0]?.index ?? 0}\" to pick just one.`,\n });\n }\n }\n\n const groups = writeSignals\n ? groupByRate(chosen, columnNames, options.decimals, options.gzip === true)\n : [];\n const estimate = estimateOutput(\n groups,\n range,\n input.recordDuration,\n input.recordStarts,\n options.bom === true,\n );\n\n /\n The mixed-rate warning describes what this conversion does, not what the file holds.\n\n The header parser raises its own, which is right for `parseHeader` — but it sees every\n channel and knows nothing about `--channels`. Converting one channel out of a three-rate\n recording therefore announced \"3 different sampling rates ... written to one file per\n rate\" over a run that wrote one file, in the same output where `--info` had already\n marked the other two \"(not selected)\". Selecting two of the three was wrong the other\n way: still \"3\".\n\n Callers combining these with a file's own diagnostics drop that copy in favour of this\n one; see `withoutFileRateWarning`.\n /\n if (groups.length > 1) {\n diagnostics.push({\n code: 'MIXED_SAMPLING_RATES',\n severity: 'warning',\n message:\n `Channels use ${groups.length} different sampling rates ` +\n `(${listed(formatRates(groups.map((g) => g.rate)).map((r) => `${r} Hz`))}).`,\n hint: 'They are written to one file per rate so no channel is resampled.',\n });\n }\n\n /\n A time column that cannot tell two samples apart.\n\n Sample times are written to at most nine decimal places, which separates everything up to\n a gigahertz. Below that the column repeats: a recording of 1 ns records holding ten\n samples each writes twenty rows carrying three distinct times, so joining or plotting on\n `time_s` silently collapses them. Nothing is lost from the file — every sample is there,\n in order — but the column stops being an identifier, and that is worth saying rather than\n leaving to be discovered.\n /\n for (const group of groups) {\n const step = group.rate > 0 ? 1 / group.rate : 0;\n if (step > 0 && step < 10 * -group.timeDecimals) {\n diagnostics.push({\n code: 'TIME_RESOLUTION',\n severity: 'warning',\n message:\n `Channels at ${formatRate(group.rate)} Hz sample faster than the time column can ` +\n `distinguish, so consecutive rows in ${group.fileName} carry the same time_s value.`,\n hint:\n 'Every sample is written, in order. Use the row number rather than time_s to tell ' +\n 'them apart, or convert one rate at a time with --channels.',\n });\n }\n }\n\n if (estimate.exceedsSpreadsheetLimit) {\n diagnostics.push({\n code: 'LARGE_OUTPUT',\n severity: 'warning',\n message:\n `At least one output file will have more than ${SPREADSHEET_ROW_LIMIT.toLocaleString('en-US')} ` +\n `rows, which is more than Excel or Numbers can open.`,\n hint: 'Use --start and --duration to convert a section, or read the file with pandas or R.',\n });\n }\n\n return { groups, gzip: options.gzip === true, range, columnNames, writeSignals, diagnostics, estimate };\n}\n\n/*\n Partition channels by sampling rate, largest first.\n \n The common case — every channel at one rate — collapses to a single group and a\n * single `signals.csv`, so the honest behaviour costs nothing when there is nothing\n * to be honest about.\n /\nfunction groupByRate(\n signals: readonly EdfSignal[],\n columnNames: Map<number, string>,\n forcedDecimals: number \| undefined,\n gzip: boolean,\n): RateGroup[] {\n const byRate = new Map<number, EdfSignal[]>();\n for (const signal of signals) {\n // A channel with no samples has no sampling rate to group by, and would\n // otherwise produce an empty \"0hz\" file. The header parser already warned.\n if (signal.samplesPerRecord === 0) continue;\n const bucket = byRate.get(signal.samplingRate);\n if (bucket) bucket.push(signal);\n else byRate.set(signal.samplingRate, [signal]);\n }\n\n const rates = [...byRate.keys()].sort((a, b) => b - a);\n const single = rates.length === 1;\n\n /\n Two distinct rates can produce the same slug, because the slug rounds to six decimal\n places. Rates come from samplesPerRecord / recordDuration and every channel shares the\n record duration, so the closest two rates can be is 1 / recordDuration — which drops\n below 1e-6 once a record is longer than about eleven days. Absurd, but the header\n permits it, and the failure was silent and destructive: both groups opened a write\n stream on the same path, so the file ended up holding interleaved rows from both\n channels under a header naming only one of them.\n\n Distinct rates therefore get distinct files, always. The suffix is only ever reached by\n a collision, so ordinary recordings keep the names they have always had.\n\n Naming from the whole set of rates at once removes most of those collisions before the\n suffix has to. Rounding each rate on its own gave 1e-6 Hz and 1.25e-6 Hz the same slug,\n and the numbering below then produced signals_0_000001hz.csv and signals_0_000001hz_2.csv\n — two files that no longer overwrite each other, but of which only one is named for the\n rate it holds. The suffix stays as the backstop for anything this still cannot separate.\n /\n const suffix = gzip ? '.csv.gz' : '.csv';\n const slugs = formatRates(rates).map((text) => `${text.replace('.', '_')}hz`);\n const used = new Set<string>();\n const uniqueName = (index: number): string => {\n const base = `signals_${slugs[index]}`;\n let name = `${base}${suffix}`;\n for (let n = 2; used.has(name); n++) name = `${base}_${n}${suffix}`;\n used.add(name);\n return name;\n };\n\n return rates.map((rate, index) => {\n const members = byRate.get(rate) ?? [];\n const first = members[0];\n return {\n rate,\n samplesPerRecord: first ? first.samplesPerRecord : 0,\n fileName: single ? `signals${suffix}` : uniqueName(index),\n timeDecimals: timeDecimals(rate),\n channels: members.map((signal) => ({\n signal,\n column: columnNames.get(signal.index) ?? `signal_${signal.index}`,\n decimals: forcedDecimals ?? decimalsForSignal(signal),\n })),\n };\n });\n}\n\n/\n A file's diagnostics with the header's mixed-rate warning removed.\n \n `buildPlan` raises that warning for the channels actually being converted, so keeping both\n * would either duplicate it or contradict it. The header parser's copy stays where it is, for\n * callers reading a header without planning a conversion.\n /\nexport function withoutFileRateWarning(diagnostics: readonly Diagnostic[]): Diagnostic[] {\n return diagnostics.filter((d) => d.code !== 'MIXED_SAMPLING_RATES');\n}\n\n/* `256hz`, `12_5hz` — safe in a filename on every platform. /\nexport function rateSlug(rate: number): string {\n return `${formatRate(rate).replace('.', '_')}hz`;\n}\n\n/* Characters a fixed-decimal number of this magnitude occupies, sign included. /\nfunction widthOf(magnitude: number, decimals: number, signed = false): number {\n const size = Math.abs(magnitude);\n const sign = signed ? 1 : 0;\n const fraction = decimals > 0 ? 1 + decimals : 0;\n\n /\n Cells are written with toFixed, which rounds. Taking the integer digits from the floor of\n the bound therefore under-counted whenever rounding carried into a new digit: a channel\n bounded at 9999.999 and written to zero decimals produces \"10000\", five characters where\n the floor of 9999.999 suggests four. Every cell on such a channel was a byte short, and\n `--info` reported 127 KB for a file that came out 131 KB.\n\n Measuring the bound as rendered removes that. toFixed switches to exponential notation\n past 1e21, so the arithmetic form still covers magnitudes beyond it.\n /\n if (!Number.isFinite(size)) return sign + 1 + fraction;\n if (size < 1e21) return sign + size.toFixed(Math.min(decimals, 100)).length;\n return sign + (Math.floor(Math.log10(size)) + 1) + fraction;\n}\n\nfunction estimateOutput(\n groups: readonly RateGroup[],\n range: ResolvedRange,\n recordDuration: number,\n recordStarts: Float64Array \| null \| undefined,\n bom: boolean,\n): OutputEstimate {\n let rows = 0;\n let bytes = 0;\n let exceeds = false;\n\n for (const group of groups) {\n let groupRows = 0;\n for (let record = range.startRecord; record < range.endRecord; record++) {\n const recordStart = recordStarts\n ? (recordStarts[record] ?? record recordDuration)\n : record * recordDuration;\n groupRows += countSamplesInRange({\n recordStart,\n rate: group.rate,\n samplesPerRecord: group.samplesPerRecord,\n startSeconds: range.startSeconds,\n endSeconds: range.endSeconds,\n });\n }\n rows += groupRows;\n if (groupRows + 1 > SPREADSHEET_ROW_LIMIT) exceeds = true;\n\n /\n Width per cell, from the channel's own calibration rather than a flat allowance.\n\n The old `decimals + 6` budgeted six characters for the sign, integer part and decimal\n point on every channel, whatever it actually held. That over-counted a millivolt\n channel spanning ±5 by four characters a cell and ran 30-55% high across the fixture\n set — on a number people use to decide whether a conversion is worth starting.\n\n The channel's declared physical range is what bounds a cell, so that bound is what is\n used. Most samples sit below it, so this still reads high, which is the direction a\n size estimate should err in.\n\n One case is outside the bound rather than under it: nothing obliges a recording to keep\n its samples inside the digital range it declares, and one that does not maps outside the\n physical range too. Such a file can convert larger than the estimate. Clamping the data\n to make the estimate true is not a trade worth making — the samples are what they are.\n /\n const timeWidth = widthOf(range.endSeconds, group.timeDecimals);\n const cellWidth = group.channels.reduce(\n (sum, c) =>\n sum +\n widthOf(\n Math.max(Math.abs(c.signal.physicalMin), Math.abs(c.signal.physicalMax)),\n c.decimals,\n c.signal.physicalMin < 0 \|\| c.signal.physicalMax < 0,\n ),\n 0,\n );\n // One comma per channel, plus the newline.\n bytes += groupRows * (timeWidth + cellWidth + group.channels.length + 1);\n /\n The header row, measured as it will be written rather than as the labels are stored.\n\n A column name is quoted when it contains a comma, a quote, a newline or a leading or\n trailing space, and every quote inside it is doubled. Counting the raw label under-counted\n that row: three channels labelled `a,b,c,d,e`, `x\"y` and `plain` write a 32-byte header\n and were budgeted 27. EDF labels are free text, so commas in them are ordinary — a montage\n written as `EEG Fpz-Cz, ref` is exactly the kind of thing this is for.\n\n csvRow is the function that writes it, so it is the function that measures it. Nothing\n else is in a position to stay correct when the quoting rules change.\n /\n bytes += Buffer.byteLength(csvRow(['time_s', ...group.channels.map((c) => c.column)])) + 1;\n // Three bytes per file under --bom. Small, but the estimate promises never to read\n // under what gets written, and a one-row conversion is small enough for it to matter.\n if (bom) bytes += BOM_BYTES;\n }\n\n return { rows, bytes, exceedsSpreadsheetLimit: exceeds };\n}\n"]}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "edf2csv",
-  "version": "0.4.71",
+  "version": "0.4.73",
   "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.",
   "keywords": [
     "edf",