Press n or j to go to the next uncovered block, b, p or k for the previous block.
| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 | 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 1557x 6x 6x 6x 6x 6x 6x 6x 1557x 2x 1560x 1560x 1560x 1560x 1560x 2x 1706x 1706x 1706x 1706x 1706x 2x 91x 91x 91x 2x 1714x 1714x 1714x 2x 1562x 1562x 1562x 1562x 1562x 1562x 1562x 7x 7x 7x 7x 7x 7x 7x 7x 7x 7x 1562x 1562x 1562x 2x 2x 2x 2x 2x 2x 2x 9x 9x 6x 2x 887x 887x 2x 5x 5x 5x 4x 4x 4x 4x 4x 4x 4x 5x 5x 1x 1x 1x 1x 3x 1x 1x 2x 3x 2x 2x 2x 2x 2x 2x 2x 14x 14x 14x 14x 14x 14x 14x 14x 14x 11x 14x 139x 139x 11x 2x 2x 2x 1586x 1586x 1586x 2x 3738x 3738x 3738x 3738x 3738x 3738x 3738x 266046x 266046x 266046x 266046x 266046x 266046x 3738x 3738x 3738x 2x 200x 200x 200x 200x 1380x 1380x 771x 1380x 200x 200x 2x 1534x 1534x 1534x 1534x 1534x 1534x 1532x 1532x 1532x 1534x 1534x 2x 1932x 1932x 1932x 1932x 1932x 1932x 1932x 1932x 1932x 1932x 1932x 1520x 1520x 1520x 1520x 1520x 1520x 1520x 1520x 1520x 1494x 1520x 1520x 1520x 1520x 1552x 1552x 1552x 1552x 1552x 1552x 1494x 1494x 2x 34x 34x 34x 34x 34x 34x 34x 34x 34x 34x 34x 34x 34x 43x 43x 99x 99x 99x 99x 99x 99x 99x 43x 34x 34x 2x 2131x 36x 36x 2131x 2131x 1336x 1336x 2x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 2421x 115861377x 115861377x 115861377x 115861377x 17131541x 17131541x 115861377x 16256950x 16256950x 115861377x 2421x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1550x 1545x 1545x 1668x 1545x 1543x 1545x 1540x 1540x 1545x 1545x 1545x 1545x 1545x 666x 666x 666x 666x 666x 666x 666x 666x 666x 2x 2x 2x 2x 2x 2x 664x 664x 664x 425x 239x 666x 666x 38408x 38408x 38408x 17564959x 17564959x 38408x 664x 3098x 3098x 3098x 2x 2x 2x 2x 2x 2x 2x 3096x 3096x | /**
* Bounded matrix reads and the COO → dense scatter (spec §5.3, §6.2; M2).
*
* Two things here are load-bearing and easy to get wrong:
*
* 1. **The read is bounded.** A block is one slice of `indexes/bin1_offset`
* followed by one contiguous slice of each pixel column — four reads, never
* a scan. Nothing else in the file is touched.
* 2. **Storage is upper-triangular.** `bin1_id <= bin2_id`, so an off-diagonal
* block whose column range *precedes* its row range has no stored pixels at
* all and must be queried transposed and flipped. Skipping that produces
* blank inter-genome panels — silently breaking the app's most distinctive
* feature rather than erroring.
*/
import { fmt } from '../units'
import {
DENSE_MATRIX_BIN_LIMIT,
DEVICE_MEMORY_FALLBACK_GIB,
DEVICE_MEMORY_SHARE,
MAX_DENSE_ARRAY_BYTES,
MIN_DENSE_BUDGET_BYTES,
MIN_DENSE_BUDGET_GIB,
type StorageMode,
} from '../constants'
import { yieldToEventLoop } from '../async'
import { RASTER_MAX_DIM, rasterStride } from '../render/heatmap'
import { ViewerError } from '../errors'
import type { Hdf5Handle } from '../h5/api'
import { dtypeKind } from '../h5/typed'
import type { DenseMatrix, Extent, MatrixQuery, PixelChunk } from '../types'
/**
* Hints reused verbatim from `metacooler.ops.show`, so the browser and the CLI
* refuse an over-large selection with the same sentence. Diverging wording
* here would make a support question about one unanswerable from the other.
*/
/** cooler's own name for the balancing weights; `cooler balance` writes it. */
export const DEFAULT_WEIGHT_COLUMN = 'weight'
/**
* The value column every cooler has, and the default for every read.
*
* cooler's schema fixes `/pixels` at `bin1_id`, `bin2_id`, `count`, and a file
* may carry more beside them — a second normalisation, an expected value, a
* per-pixel p-value. Those are data columns exactly as `count` is, so the
* reader takes the column *by name* rather than knowing one; see
* {@link scoreColumns} for how a file says which it has.
*/
export const DEFAULT_COUNT_COLUMN = 'count'
/** The two `/pixels` columns that are coordinates rather than values. */
const PIXEL_COORDINATES = new Set(['bin1_id', 'bin2_id'])
/**
* The value columns a file offers, `count` first.
*
* Read from the group's own child list rather than from a fixed set, because
* "what is in this file" is a question the file answers and this code cannot.
* Coordinates are dropped; everything else is a number per pixel and therefore
* something a reader might want the map drawn from.
*/
export function scoreColumns(handle: Hdf5Handle): string[] {
const keys = handle.keys('pixels').filter((key) => !PIXEL_COORDINATES.has(key))
// `count` first wherever it is, because it is the one every file has and the
// one every other column is an alternative *to*.
return [
...keys.filter((key) => key === DEFAULT_COUNT_COLUMN),
...keys.filter((key) => key !== DEFAULT_COUNT_COLUMN).sort(),
]
}
export const DENSE_HINTS = {
/** `show --level genome` on a file with too many genomes. */
genome: 'Use a smaller file.',
/** `show --level contig`. */
contig: 'Use --level genome, --genomes/--contigs, or a smaller file.',
/** `show --range/--range2`. */
range: 'Use a narrower --range/--range2.',
/** `show --level bin` with a genome/contig selection. */
binSelection: 'Use --range to select a smaller region, or --level contig.',
} as const
/** The parts of an open map a matrix read needs. `MetaCooler` satisfies it. */
export interface MatrixSource {
readonly handle: Hdf5Handle
readonly nBins: number
readonly storageMode: StorageMode
/**
* Where the pixels come from.
*
* Typed as the minimum this module uses rather than as `PixelStore`, so that
* `metacooler/store.ts` may import this module's `ReadPlan` and
* `SpanScanOptions` without the two forming a cycle. The implementations are
* `CoolerStore` and `HicStore`.
*/
readonly store: {
forEachWindow(
rows: Extent,
cols: Extent,
plan: ReadPlan,
onChunk: (chunk: PixelChunk) => void,
options?: SpanScanOptions,
): Promise<boolean>
}
}
/**
* Refuse to materialise a dense block larger than Python's limit.
*
* A mirror of `_check_dense_size`, including its element-count formulation:
* the limit is `DENSE_MATRIX_BIN_LIMIT ** 2` *cells*, not bins per axis, so a
* rectangular selection is judged on what is actually about to be allocated.
* The message is Python's, down to the `×` and the one decimal place.
*
* @throws ViewerError `dense-too-large`.
*/
export function checkDenseSize(nRows: number, nCols: number, hint: string): void {
if (nRows * nCols > DENSE_MATRIX_BIN_LIMIT ** 2) {
const gb = (nRows * nCols * 8) / 1e9
throw new ViewerError(
'dense-too-large',
`Refusing to allocate a ${nRows}×${nCols} dense matrix (${gb.toFixed(1)} GB). ${hint}`,
{ nRows, nCols, limit: DENSE_MATRIX_BIN_LIMIT },
)
}
}
/**
* What one displayed block costs, in bytes, before it is read.
*
* Not a limit — an estimate, and now an honest one. There are exactly two
* things that scale with the selection and one that does not:
*
* - the dense values, `4 B` per cell, held for as long as the view is open;
* - the raster: pooled values, RGBA and canvas backing store, `12 B` per raster
* pixel, pooled at {@link RASTER_MAX_DIM} so it stops growing there;
* - the pixel read, one bounded window at a time
* ({@link forEachPixelSpan}), which is why there is no `nnz` term any more.
*
* The `nnz` term this used to carry was wrong in two directions at once. It
* charged `16 B` per stored pixel where the unwindowed read held `32`, and it
* measured that against `min(cells, nnz)` when what the read actually pulled in
* was every pixel of the *row band* — a population bounded by the file's `nnz`
* and unrelated to the block's cell count, so a small block on the diagonal of
* a large file could cost several times what it was charged. Reading in windows
* makes the term a constant, which is both cheaper and true.
*/
export function estimateBlockBytes(nRows: number, nCols: number): number {
const cells = nRows * nCols
const rasterPixels =
Math.ceil(nRows / rasterStride(nRows)) * Math.ceil(nCols / rasterStride(nCols))
// 12 B per raster pixel: the pooled `Float32Array`, the RGBA bytes and the
// canvas backing store are all live at once, 4 each. The auto-range buffer
// this used to charge as a fourth is not live beside them: it holds only the
// finite contacts, and it is garbage before the RGBA is allocated
// (`colorize`). Measured on yeast IV at 100 bp, 15,320² cells, the tab held
// 2.9 GB where 16 B had estimated 4.7 GB and refused it.
return cells * 4 + rasterPixels * 12 + PIXEL_CHUNK_BYTES
}
/**
* What this machine will lend one block.
*
* `navigator.deviceMemory` is a coarse, capped hint rather than a measurement,
* so the share taken from it is modest and the floor is generous. Absent — Node,
* Firefox, Safari — the fallback assumes a modest laptop.
*/
export function deviceDenseBudgetBytes(): number {
const reported = (globalThis.navigator as { deviceMemory?: number } | undefined)?.deviceMemory
return denseBudgetFor(
typeof reported === 'number' && reported > 0 ? reported : DEVICE_MEMORY_FALLBACK_GIB,
)
}
/**
* The widest window, in bins a side, this machine reads unpooled.
*
* A window up to this wide is read bin for bin through the dense path, which
* {@link checkBrowserDenseSize} guards; a wider one is pooled to `POOLED_CELL_CAP`
* cells by the reader. Derived from the same budget so that the two cannot
* disagree: a window this wide always passes the guard, and the picture never
* turns into a refusal where a pooled one would have drawn. Bounded by
* {@link RASTER_MAX_DIM}, past which the raster would pool it anyway — on a
* laptop reporting 8 GiB that bound is what binds, and a whole yeast
* chromosome IV at 100 bp (15,320 bins) is read whole.
*/
export function denseCellCap(budgetBytes = deviceDenseBudgetBytes()): number {
// Square, at one raster pixel per cell: 4 B of values and 12 of raster.
const side = Math.floor(Math.sqrt(Math.max(0, budgetBytes - PIXEL_CHUNK_BYTES) / 16))
return Math.max(1, Math.min(RASTER_MAX_DIM, side))
}
/**
* The budget for a machine claiming `gib` gibibytes — the whole policy, with
* no globals in it so it can be stated as a table in a test.
*
* The floor is a correction for a *pessimistic* hint, so it applies only where
* the hint is large enough to be one. Below {@link MIN_DENSE_BUDGET_GIB} the
* device is telling us it is small, and raising its budget to a flat 1 GB —
* four times the whole machine, at the bottom of the reported scale — is not
* generosity but a killed tab.
*/
export function denseBudgetFor(gib: number): number {
const share = gib * 1024 ** 3 * DEVICE_MEMORY_SHARE
return gib >= MIN_DENSE_BUDGET_GIB ? Math.max(MIN_DENSE_BUDGET_BYTES, share) : share
}
/**
* The same question asked of a browser tab, which is a smaller room.
*
* Separate from {@link checkDenseSize} rather than folded into it, because that
* function's numbers and wording are Python's and are asserted verbatim. This
* one speaks for the renderer, and it is deliberately an *estimate against a
* budget* rather than a fixed cell count: a whole yeast genome at 1 kb is
* 12,100 bins — 1.5e8 cells, which any fixed limit round enough to state would
* refuse, and which actually costs about 600 MB and opens fine. Small genomes
* are exactly the case a cooler in this viewer is for, so the guard has to
* measure rather than guess.
*
* There is no `nnz` consultation any more, and no file read: the estimate is a
* closed form in the block's own shape ({@link estimateBlockBytes}), because
* windowing the pixel read took the one term that depended on the file out of
* it. The guard is therefore both cheaper — it never touches the handle — and
* accurate, which the version that budgeted against `min(cells, nnz)` was not.
*
* @throws ViewerError `dense-too-large`.
*/
export function checkBrowserDenseSize(
nRows: number,
nCols: number,
hint: string,
options: { budgetBytes?: number } = {},
): void {
const cells = nRows * nCols
// First, and not subject to the budget: a block whose values do not fit in
// one typed array cannot be read however much memory the machine has or the
// user offers. `budgetBytes: Infinity` is a statement about the *estimate*,
// which is a guess about this machine; this is not a guess and not about this
// machine. See MAX_DENSE_ARRAY_BYTES.
if (cells * 4 >= MAX_DENSE_ARRAY_BYTES) {
const side = Math.floor(Math.sqrt(MAX_DENSE_ARRAY_BYTES / 4))
throw new ViewerError(
'dense-too-large',
`Refusing to load a ${nRows}×${nCols} block: its ${fmtCells(cells)} values are ` +
`${fmt.bytes(cells * 4)} and a browser serves at most ${fmt.bytes(MAX_DENSE_ARRAY_BYTES)} ` +
'in a single array — a limit of the tab, not of this machine, so more memory and more ' +
`patience will not lift it. The largest square block is about ${side}×${side} bins.` +
(hint === '' ? '' : ` ${hint}`),
{ nRows, nCols, cells, bytes: cells * 4, limit: MAX_DENSE_ARRAY_BYTES, where: 'array-limit' },
)
}
const budget = options.budgetBytes ?? deviceDenseBudgetBytes()
const bytes = estimateBlockBytes(nRows, nCols)
if (bytes <= budget) return
throw new ViewerError(
'dense-too-large',
`Refusing to load a ${nRows}×${nCols} block in a browser tab: ${fmtCells(cells)} cells ` +
`needs about ${fmt.bytes(bytes)}, and this tab is budgeting ${fmt.bytes(budget)}. ${hint}`,
{ nRows, nCols, cells, bytes, budget, where: 'browser' },
)
}
/** `2.5e9` → `2.5 billion`, for a sentence rather than a table. */
function fmtCells(cells: number): string {
if (cells >= 1e9) return `${(cells / 1e9).toFixed(1)} billion`
if (cells >= 1e6) return `${(cells / 1e6).toFixed(0)} million`
return String(cells)
}
/**
* Resolve the `pixels/count` dtype **once**, at open (correction #2).
*
* Three paths are legal — int32 at base resolution, int64 wherever counts have
* been summed (`binnify`, `merge`), and float64 when the source column was
* float, because `resolve_count_dtype` preserves float sources rather than
* truncating them. `CORE_COLUMN_KINDS` accordingly permits `i`, `u` *or* `f`,
* so this tests the dtype *kind* and never an exact dtype.
*
* The decode itself is the HDF5 layer's job (`readNumeric` narrows every
* numeric column to `Number`, which is exact for float64 and for any integer
* count below 2^53). What the kind buys is the guarantee, recorded once
* instead of re-derived per pixel, that float counts are never rounded.
*
* The kind comes from `h5/typed.dtypeKind`, never from slicing the dtype
* string: h5wasm reports **C-struct** spellings, not numpy ones — int64 is
* `'<q'`, float64 `'<d'`, a fixed-length string `'A25'`. Taking `dtype[1]`
* yields `'q'` and `'d'`, neither of which is in `['i','u','f']`, so every
* `binnify`/`merge` output (int64) and every float-count file would be refused
* as "not numeric" — which is exactly what happened before this call was
* routed through the mapping table.
*
* @throws ViewerError `format` for a `count` column that is not numeric.
*/
export function resolveCountKind(dtype: string): 'i' | 'u' | 'f' {
const kind = dtypeKind(dtype)
if (kind === 'i' || kind === 'u' || kind === 'f') return kind
throw new ViewerError(
'format',
`/pixels/count is stored as ${dtype} (kind '${kind}'); expected one of the kinds ` +
`['i', 'u', 'f']. A non-numeric count column cannot be rendered.`,
{ dtype, kind },
)
}
/**
* Read every pixel whose **row** bin falls in `[lo, hi)`.
*
* One `bin1_offset` slice gives the pixel range and each pixel's row; the two
* other columns, `bin2_id` and the value, are then one contiguous span each.
* Three reads total, independent of how many pixels come back.
*/
export function readPixelSpan(h: Hdf5Handle, lo: number, hi: number): PixelChunk {
const parts: PixelChunk[] = []
let total = 0
forEachPixelSpan(h, lo, hi, (chunk) => {
parts.push({
bin1: chunk.bin1.slice(),
bin2: chunk.bin2.slice(),
count: chunk.count.slice(),
length: chunk.length,
})
total += chunk.length
})
if (parts.length === 1) return parts[0]
const bin1 = new Int32Array(total)
const bin2 = new Int32Array(total)
const count = new Float64Array(total)
let at = 0
for (const part of parts) {
bin1.set(part.bin1, at)
bin2.set(part.bin2, at)
count.set(part.count, at)
at += part.length
}
return { bin1, bin2, count, length: total }
}
/**
* Stored pixels whose row bin falls in `[lo, hi)`, without reading the file.
*
* Two entries of an index that is one number per bin — the cheapest read there
* is, and the same one `genomeDensity` makes. It is what a size guard should be
* asking: a block's cost is set by the pixels its *row band* holds, which is
* bounded by the file's `nnz` and not by the block's own cell count.
*/
export function spanPixelCount(h: Hdf5Handle, lo: number, hi: number): number {
if (hi <= lo) return 0
const start = h.readNumeric('indexes/bin1_offset', lo, lo + 1)[0]
const end = h.readNumeric('indexes/bin1_offset', hi, hi + 1)[0]
return Math.max(0, end - start)
}
/**
* Pixels per window in {@link forEachPixelSpan}; the order of magnitude the
* scan path already uses.
*/
export const PIXEL_CHUNK = 1_000_000
/**
* Peak bytes one window of {@link forEachPixelSpan} holds.
*
* Two `Int32Array`s and a `Float64Array` at the window size, plus the transient
* buffers h5wasm mints on the way (an int64 column arrives as `BigInt64Array`
* and is narrowed in one pass). Charged as a constant by
* {@link estimateBlockBytes}, which is the whole point of reading in windows.
*/
export const PIXEL_CHUNK_BYTES = PIXEL_CHUNK * 36
/**
* Read the pixels whose **row** bin falls in `[lo, hi)`, in bounded windows.
*
* One `bin1_offset` slice gives the pixel range; `bin2_id` and the value column
* are then read a window at a time and handed to `onChunk` before the next
* window is fetched, each pixel's row taken from the slice ({@link RowIndex}).
*
* **The windowing is not an optimisation, it is the correctness fix.** The span
* of a whole-genome block is the whole file, and reading it in one shot put
* `32 B` per stored pixel on the JS heap simultaneously — 3.2 GB at 100 M
* pixels — while the estimator that had waved the block through charged 16.
* It also staged each column whole inside h5wasm's linear memory, which is hard
* capped at 2 GiB whatever the machine has, so a span past ~2.7e8 pixels failed
* outright with an error carrying no code and no advice. A window is 36 MB and
* neither problem exists at any file size.
*
* The buffers handed to `onChunk` are **not** retained between calls; a callback
* that needs them past its own return must copy.
*/
export function forEachPixelSpan(
h: Hdf5Handle,
lo: number,
hi: number,
onChunk: (chunk: PixelChunk) => void,
chunkSize: number = PIXEL_CHUNK,
value: string = DEFAULT_COUNT_COLUMN,
): void {
const span = pixelSpanOf(h, lo, hi)
if (span === null) return
const width = Math.max(1, Math.trunc(chunkSize))
for (let at = span.p0; at < span.p1; at += width) {
onChunk(readPixelWindow(h, at, Math.min(at + width, span.p1), value, span.rows))
}
}
/**
* Which row each stored pixel is in, answered from `bin1_offset` rather than
* read from `pixels/bin1_id`.
*
* The index *is* that column, run-length encoded: row `r` holds the pixels
* `[offsets[r], offsets[r + 1])`, and a cooler is valid only where the two agree
* (`MetaCooler.validateDeep` checks exactly that). So the column is not read.
* It was two-fifths of the bytes every row band inflated — eight of the twenty
* a pixel takes in an int64/int64/int32 table — for numbers already in hand,
* and cooler's own range query (`CSRReader`) has never read it either: it fills
* each row's pixels with the row from the same index. What is handed on is the
* same `Int32Array` of the same values; only where it came from has changed.
*
* Built over a slice of the index — rows `[firstBin, firstBin + offsets.length −
* 1)` — and asked in pixel order, which is how every walk asks, so finding the
* row is a cursor that only moves forward; a jump back or ahead is a binary
* search ({@link seek}).
*/
export class RowIndex {
private row = 0
constructor(
/** `bin1_offset` for the rows covered, and one past the last: `rows + 1` long. */
private readonly offsets: ArrayLike<number>,
/** The bin of the first entry of `offsets`. */
private readonly firstBin: number,
) {}
/** The row of every pixel in `[at, end)`, as `pixels/bin1_id` stores it. */
bin1(at: number, end: number): Int32Array {
const out = new Int32Array(Math.max(0, end - at))
const offsets = this.offsets
const lastRow = offsets.length - 2
if (lastRow < 0) return out
if (at < offsets[this.row]) this.seek(at)
let r = this.row
for (let k = at; k < end; ) {
// The row that holds pixel `k`: the first whose end is past it. Empty rows
// are stepped over here, which is all an empty row ever is.
while (r < lastRow && offsets[r + 1] <= k) r++
// Never short of `end` on an index that brackets the walk; where one does
// not, the remainder is given to the last row rather than looped on.
const stop = r < lastRow ? Math.min(end, offsets[r + 1]) : end
const to = stop > k ? stop : end
out.fill(this.firstBin + r, k - at, to - at)
k = to
}
this.row = r
return out
}
/** Put the cursor on the row that holds pixel `at`. */
seek(at: number): void {
const offsets = this.offsets
// The last row whose start is at or before `at`, empty rows before it skipped
// by the forward walk in {@link bin1}.
let lo = 0
let hi = Math.max(0, offsets.length - 2)
while (lo < hi) {
const mid = (lo + hi + 1) >> 1
if (offsets[mid] <= at) lo = mid
else hi = mid - 1
}
this.row = lo
}
}
/** What a span asks for: its pixel range and the rows over it, or `null` when it holds none. */
function pixelSpanOf(
h: Hdf5Handle,
lo: number,
hi: number,
): { p0: number; p1: number; rows: RowIndex } | null {
if (hi <= lo) return null
// hi + 1 is safe: bin1_offset has one entry per bin plus a terminator.
const offsets = h.readNumeric('indexes/bin1_offset', lo, hi + 1)
const p0 = offsets[0]
const p1 = offsets[offsets.length - 1]
return p1 <= p0 ? null : { p0, p1, rows: new RowIndex(offsets, lo) }
}
/**
* One window of stored pixels, `[at, end)` of the table.
*
* `rows` answers each pixel's row from the index ({@link RowIndex}); without one
* `pixels/bin1_id` is read, which is what a check of the file against its own
* index has to do (`CoolerStore.scanAll`'s `storedRows`).
*/
export function readPixelWindow(
h: Hdf5Handle,
at: number,
end: number,
value: string = DEFAULT_COUNT_COLUMN,
rows: RowIndex | null = null,
): PixelChunk {
const bin2 = h.readInt32('pixels/bin2_id', at, end)
const count = h.readNumeric(`pixels/${value}`, at, end)
const bin1 = rows === null ? h.readInt32('pixels/bin1_id', at, end) : rows.bin1(at, at + count.length)
return { bin1, bin2, count, length: count.length }
}
/** How a caller watches, and interrupts, a walk over a span of pixels. */
export interface SpanScanOptions {
chunkSize?: number
/** Polled between windows; `true` abandons the walk where it stands. */
cancelled?: () => boolean
/** Pixels read so far, and how many there are in this span. */
onProgress?: (done: number, total: number) => void
/**
* Which `/pixels` column the values come from; `count` when absent.
*
* The same choice {@link MatrixQuery.value} makes for the dense path, and it
* belongs here for the same reason it belongs there: it is a property of the
* *read*, not of what the caller does with what comes back.
*
* It was missing, and the omission was not cosmetic. `forEachPixelSpan` has
* always taken a column and the dense path has always threaded it, so a file
* with an `expected` column drew `expected` — right up to the size at which
* the reader pools instead, at which point the same view silently drew
* `count`. One picture, two quantities, no tell. That the resolution now moves
* with the zoom is what made it urgent: a quantity that changes as you
* magnify is not a picture of anything.
*/
value?: string
}
/**
* The same walk, watched — and therefore interruptible.
*
* Identical to {@link forEachPixelSpan} in what it reads and in what order; the
* difference is the `await` between windows. That is not politeness, it is the
* whole of what makes a cancel work: the cancel arrives as a message, and a
* synchronous loop never lets the message queue run however many microtasks it
* awaits (`../async`). A read that can take twenty seconds has to be one a
* person can call off, and cannot report how far along it is unless it stops
* between windows to say so.
*
* @returns `false` when it stopped early because the caller said so.
*/
export async function forEachPixelSpanAsync(
h: Hdf5Handle,
lo: number,
hi: number,
onChunk: (chunk: PixelChunk) => void,
options: SpanScanOptions = {},
): Promise<boolean> {
const span = pixelSpanOf(h, lo, hi)
if (span === null) return true
const { p0, p1, rows } = span
const width = Math.max(1, Math.trunc(options.chunkSize ?? PIXEL_CHUNK))
const total = p1 - p0
const value = options.value ?? DEFAULT_COUNT_COLUMN
for (let at = p0; at < p1; at += width) {
if (options.cancelled?.() === true) return false
const end = Math.min(at + width, p1)
onChunk(readPixelWindow(h, at, end, value, rows))
options.onProgress?.(end - p0, total)
await yieldToEventLoop()
}
return true
}
/**
* Stored pixels' worth of gap that is cheaper to read across than to seek over.
*
* The byte sources read in 1 MiB chunks, and a stored pixel is 16 bytes on the
* wire, so anything under about 65,000 pixels is inside a chunk that is being
* fetched regardless. Merging below it turns a thousand small bands into a few
* large ones without reading a byte more than the source already would.
*/
export const PIXEL_BAND_GAP = 65_536
/**
* The same walk over **several** pixel ranges, as one operation.
*
* A selection of four MAGs out of two thousand used to cost the whole file: the
* pixels it wants are scattered, so the read walked `[0, nBins)` and threw away
* everything that was not on either axis. But the pixels are sorted by `bin1`,
* so every pixel a selection wants is inside the *row band* of one of its own
* sequences — a pair with both ends selected is stored under the lower of them,
* which is selected — and `bin1_offset` says where each band is in two lookups.
*
* So the caller hands in the bands, already merged, and this walks them in
* order with one progress count across the lot. Cancellation is checked between
* windows exactly as it is for a single range, because it is the same loop.
*
* `offsets` is the whole of `bin1_offset`, where the caller holds it — a
* `CoolerStore` does, having built the bands from it — and is what each pixel's
* row is then taken from ({@link RowIndex}); without it `pixels/bin1_id` is
* read.
*/
export async function forEachPixelRangesAsync(
h: Hdf5Handle,
ranges: ReadonlyArray<Extent>,
onChunk: (chunk: PixelChunk) => void,
options: SpanScanOptions = {},
offsets: ArrayLike<number> | null = null,
): Promise<boolean> {
const width = Math.max(1, Math.trunc(options.chunkSize ?? PIXEL_CHUNK))
const total = ranges.reduce((sum, [p0, p1]) => sum + Math.max(0, p1 - p0), 0)
const value = options.value ?? DEFAULT_COUNT_COLUMN
const rows = offsets === null ? null : new RowIndex(offsets, 0)
let done = 0
for (const [p0, p1] of ranges) {
rows?.seek(p0)
for (let at = p0; at < p1; at += width) {
if (options.cancelled?.() === true) return false
const end = Math.min(at + width, p1)
onChunk(readPixelWindow(h, at, end, value, rows))
done += end - at
options.onProgress?.(done, total)
await yieldToEventLoop()
}
}
return true
}
/**
* Where each stored pixel lands in the output block.
*
* - `direct` — `(bin1 → row, bin2 → col)` only.
* - `transpose` — `(bin2 → row, bin1 → col)` only; the stored pixel is the
* flip of the cell being drawn.
* - `symmetric` — both, with the diagonal placed once.
*/
export type PlacementMode = 'direct' | 'transpose' | 'symmetric'
/** How a block must be fetched and placed, given the storage mode. */
export interface ReadPlan {
/** Row-bin span to slice out of `bin1_offset`. */
span: Extent
mode: PlacementMode
}
/**
* Decide the bounded read for a block, and how its pixels map into it.
*
* Under `symmetric-upper` there are three shapes:
*
* - **column range strictly before the row range** — every relevant pixel is
* stored with `bin1` in the *columns*, so the span is the column range and
* every pixel is placed transposed. This is the case §5.3 warns about.
* - **row range strictly before the column range** — pixels are stored the way
* they will be displayed; read the row band and filter on `bin2`.
* - **overlapping (including the on-diagonal case)** — read from the lower of
* the two starts to the lower of the two ends, place directly, and mirror
* across the diagonal without doubling the diagonal itself.
*
* The overlapping read stops at the lower end, not the higher, because no row
* past it can hold a cell of the block: a stored pixel has `bin1 ≤ bin2`, and
* one with `bin1` at or past `min(r1, c1)` has both its bins past the end of
* one axis, so it is in the block neither as stored nor mirrored. Reading to the
* union's end fetched those rows and threw every pixel of them away, which a
* block on the diagonal never notices and a band (rows `[a, b)` against columns
* `[a, b + hi)`, `analysis/run/blocks.ts`) paid for on every strip: `hi` rows
* read twice.
*
* Under `square` both triangles are stored, so mirroring is skipped entirely
* and the row band alone is always correct.
*/
export function planRead(rows: Extent, cols: Extent, storageMode: StorageMode): ReadPlan {
if (storageMode !== 'symmetric-upper') {
return { span: rows, mode: 'direct' }
}
if (cols[1] <= rows[0]) return { span: cols, mode: 'transpose' }
if (rows[1] <= cols[0]) return { span: rows, mode: 'direct' }
return { span: [Math.min(rows[0], cols[0]), Math.min(rows[1], cols[1])], mode: 'symmetric' }
}
/**
* Scatter a COO chunk into a dense row-major block.
*
* Counts are added, never assigned, and never rounded: a float `count` column
* survives to the canvas exactly as stored.
*/
export function scatterDense(
chunk: PixelChunk,
rows: Extent,
cols: Extent,
plan: ReadPlan,
values: Float32Array,
): void {
const [r0, r1] = rows
const [c0, c1] = cols
const nCols = c1 - c0
const { bin1, bin2, count, length } = chunk
const placeDirect = plan.mode !== 'transpose'
const placeFlipped = plan.mode !== 'direct'
// Under 'symmetric' the two placements are the same cell when b1 === b2, and
// that guard is the whole reason the diagonal is not counted twice. Under
// 'transpose' the ranges are disjoint, so b1 === b2 cannot occur anyway.
const skipDiagonal = plan.mode === 'symmetric'
for (let i = 0; i < length; i++) {
const b1 = bin1[i]
const b2 = bin2[i]
const v = count[i]
if (placeDirect && b1 >= r0 && b1 < r1 && b2 >= c0 && b2 < c1) {
values[(b1 - r0) * nCols + (b2 - c0)] += v
}
if (placeFlipped && !(skipDiagonal && b1 === b2) && b2 >= r0 && b2 < r1 && b1 >= c0 && b1 < c1) {
values[(b2 - r0) * nCols + (b1 - c0)] += v
}
}
}
/**
* Read one dense block: the single entry point every view goes through.
*
* @param src The open map (its handle, bin count and storage mode).
* @param q Row range, optional column range (defaults to the rows), balancing.
* @param hint Sentence appended to a size refusal — pick one of
* {@link DENSE_HINTS} so the wording matches the CLI's for that situation.
*/
export async function readDenseMatrix(
src: MatrixSource,
q: MatrixQuery,
hint: string,
): Promise<DenseMatrix> {
const rows = checkExtent(q.rows, src.nBins, 'rows')
const cols = checkExtent(q.cols ?? q.rows, src.nBins, 'cols')
const nRows = rows[1] - rows[0]
const nCols = cols[1] - cols[0]
checkDenseSize(nRows, nCols, hint)
checkBrowserDenseSize(nRows, nCols, hint, {
...(q.budgetBytes === undefined ? {} : { budgetBytes: q.budgetBytes }),
})
const values = allocateDense(nRows, nCols, hint)
if (nRows > 0 && nCols > 0) {
const plan = planRead(rows, cols, src.storageMode)
// Scattered chunk by chunk: `scatterDense` is additive and per-pixel, so it
// needs no knowledge that the read arrived in pieces, and the peak COO
// footprint is one chunk rather than the whole row band.
//
// Asynchronous because one of the two containers has to decompress a block
// to answer, and there is no synchronous inflate in a browser that does not
// cost a bundle. Every caller was already inside an `async` method.
await src.store.forEachWindow(rows, cols, plan, (chunk) => {
scatterDense(chunk, rows, cols, plan, values)
}, { chunkSize: PIXEL_CHUNK, value: q.value ?? DEFAULT_COUNT_COLUMN })
if (q.balance === true) applyWeights(src.handle, rows, cols, values)
}
return { nrows: nRows, ncols: nCols, values, rowExtent: rows, colExtent: cols }
}
/**
* The dense block, or a refusal carrying the same code as the estimate's.
*
* The estimate is a prediction; this is the machine answering. A typed array
* the runtime cannot serve throws a catchable `RangeError`, which is a
* *measurement* of what is available in the only unit that matters and is free
* to take — where guessing from `navigator.deviceMemory`, a value two of the
* three major engines do not implement, is neither. Translating it here is what
* lets the estimate above be generous without the failure being a raw stack
* trace on an error screen.
*/
function allocateDense(nRows: number, nCols: number, hint: string): Float32Array {
try {
return new Float32Array(nRows * nCols)
} catch (cause) {
const cells = nRows * nCols
throw new ViewerError(
'dense-too-large',
`This machine could not allocate the ${nRows}×${nCols} block: ${fmtCells(cells)} cells ` +
`is ${fmt.bytes(cells * 4)} in one array, and the request was refused. ${hint}`,
{ nRows, nCols, cells, bytes: cells * 4, where: 'allocation', cause: String(cause) },
)
}
}
/**
* Multiply a block by its bin weights, which is what "balanced" means.
*
* `balanced[i][j] = raw[i][j] * w[i] * w[j]` — cooler's own definition, and the
* only normalisation a cooler ships. A `NaN` weight marks a bin the balancer
* threw out (low coverage, repeat-dense); the product is then `NaN`, which the
* renderer draws as transparent, so a filtered row reads as absent rather than
* as empty. That is matplotlib's "bad" colour and it is the diagnostically
* correct answer.
*
* **This is the one read of `/bins` in the reader**, and it is bounded: two
* slices of the weight column, one per axis, for the bins actually on screen —
* never the whole column, never `/bins/chrom`, and never at all unless the user
* asked for balanced counts. Spec §3.3's rule is that *coordinates* never come
* from `/bins`; they still do not.
*/
function applyWeights(
handle: Hdf5Handle,
rows: Extent,
cols: Extent,
values: Float32Array,
): void {
const column = DEFAULT_WEIGHT_COLUMN
const path = `bins/${column}`
if (!handle.has(path)) {
throw new ViewerError(
'unsupported',
`This file has no /bins/${column} column, so there are no weights to balance with. ` +
'Run `cooler balance` on it, or view the raw counts.',
{ column },
)
}
const rowWeights = handle.readNumeric(path, rows[0], rows[1])
const colWeights =
cols[0] === rows[0] && cols[1] === rows[1]
? rowWeights
: handle.readNumeric(path, cols[0], cols[1])
const nCols = cols[1] - cols[0]
for (let r = 0; r < rows[1] - rows[0]; r++) {
const wr = rowWeights[r]
const base = r * nCols
for (let c = 0; c < nCols; c++) {
values[base + c] = values[base + c] * wr * colWeights[c]
}
}
}
/** Bin ranges, validated against the file's bin count. */
function checkExtent(extent: Extent, nBins: number, which: string): Extent {
const [lo, hi] = extent
if (!Number.isInteger(lo) || !Number.isInteger(hi) || lo < 0 || hi < lo || hi > nBins) {
throw new ViewerError(
'bad-range',
`Bin range for ${which} is [${lo}, ${hi}); it must be a half-open integer interval ` +
`inside [0, ${nBins}).`,
{ extent, nBins, which },
)
}
return [lo, hi]
}
|