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PureJsImage v0.11.0

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@a-r-d a-r-d released this 16 Aug 21:55
· 101 commits to main since this release
v0.11.0
dd40716

PureJsImage 0.11.0

Added

  • Added the explicit purejsimage/codecs/web entry with the frozen allWebCodecs JPEG, PNG, WebP,
    and AVIF aggregate, plus a correctness-gated common-web benchmark profile with AVIF metadata,
    full-decode, resize, conversion, and external Sharp and jSquash comparison rows. The historical
    ordinary competitor profile remains unchanged.

  • Completed the initial Milestone H interchange and detector set with explicit portable readers
    for RPL/RAW, EMSA/MAS, NRRD, MetaImage MHD/MHA, NIfTI-1/2 including bounded .nii.gz, NPY,
    NanoMegas BLO, processed Merlin MIB, and rectangular ANG/CTF orientation maps. The readers
    preserve native numeric samples and calibration evidence, provide bounded selected reads where
    their storage permits, reject recognized unsupported variants, ship as individual package
    entries, and pass generated structural, hostile-limit, packed-consumer, size, and real-Chromium
    coverage. Pinned RosettaSciIO files independently exercise RPL/RAW, ISO EMSA, BLO, and processed
    Merlin MIB without redistributing their GPL binaries. EDAX and Bruker BCF remain the roadmap's
    explicit later items.

  • Added the public purejsimage/scientific/readers/ncem-emd reader for the fixture-proven
    Berkeley/openNCEM 0.2 subset. It accepts integer or decimal-string versions, discovers numeric
    groups below /data or /signals, preserves exact labeled coordinates and bounded scalar or
    array acquisition metadata, and performs selected HDF5 hyperslab reads. Three pinned real
    RosettaSciIO application files join generated hostile and independent h5py coverage without
    redistributing their GPL binaries; Direct Electron .de5 remains explicitly unsupported.

  • Added the separate public purejsimage/scientific/readers/velox-emd E2 image reader with
    hierarchy-based probing, bounded per-frame JSON under an aggregate budget, separate detector
    datasets and frame axes, native scalar and complex data, preserved positive-half uncentered FFT
    storage, and explicit
    pruned-spectrum-image errors. Every metadata column is preserved, while calibration-critical
    conflicts fall back to index axes with a structured warning. Generated hostile fixtures and
    pinned TEM stack, DPC, and FFT files verify the reader without committing the GPL fixture
    binaries. Sparse Velox spectra remain gated on the Lab Viewer spectrum surface and explicit
    event-decoding contracts.

  • Added structured calibration provenance to scientific axes, including validated embedded,
    sidecar, derived, and format-default evidence. GSF, FITS, MRC/CCP4, OME-TIFF, and Aperio SVS
    readers now identify the exact source resource and stable metadata locator behind each available
    physical axis.

  • Added the public createImageCodecScientificReader() fallback adapter and individually
    importable PNG, JPEG, WebP, BMP, and JP2 scientific readers. They preserve codec pixels and
    component semantics, source identity, cancellation, block release ownership, and explicit reader
    registration without linking codecs into the base scientific entry.

  • Added purejsimage/scientific/readers/tiff, a native-precision ordinary TIFF reader with labeled
    page axes, incompatible-series separation, SubIFD resolution levels, bounded normalized optional
    metadata, native N-channel layouts, and lower probe priority than OME-TIFF and Aperio SVS.

  • Added bounded FEI SFEG/Helios and Zeiss SEM TIFF calibration profiles with fixture-backed physical
    axes, embedded evidence, normalized acquisition metadata, and non-fatal malformed-tag handling.

  • Added a package-private bounded DM3/DM4 tag-tree indexer with checked 32-bit and 64-bit structure,
    separate payload byte order, recursive value descriptors, deterministic duplicate-name paths,
    lazy image payload spans, and size-limited metadata projection for the upcoming scientific
    reader.

  • Added the public purejsimage/scientific/readers/digital-micrograph reader for supported DM3/DM4
    rank-2 through rank-4 scalar images and volumes, all signed/unsigned 8/16/32-bit and
    float32/float64 samples, fixture-proven packed BGRA, calibrated axes and intensity units,
    bounded namespaced Gatan metadata, and direct selected-region reads. Rank-1, complex,
    undocumented packed, encrypted, and external image content remains explicitly unsupported.

  • Added a generated scientific-reader capability section covering every public reader descriptor,
    package export, hint, resource model, dataset kind, direct-range boundary, evidence, and fixture
    source. Added a pinned, checksum-verified RosettaSciIO DigitalMicrograph compatibility corpus
    workflow without redistributing its GPL-licensed fixture binaries in the package repository.

  • Added evidence-gated DigitalMicrograph multidimensional semantics: ordinary X/Y/Z volumes,
    Gatan-tagged X/Y/energy EELS spectrum images, and C-ordered 4D-STEM exposed logically as
    scanX/scanY/kx/ky with direct kx/ky diffraction-plane reads. Ambiguous rank-4 arrays remain
    neutral. A pinned small DM4 volume and bounded HTTP-range verification of LiberTEM's 1.19 GB
    CC-BY-4.0 Zenodo 4D-STEM fixture cover the new mappings without committing the large file.

  • Added honest one-axis scientific datasets with explicit native series-read capabilities, bounded
    ScientificSeriesBlock output, strict series request normalization, and a bounded row/column
    adapter over existing plane readers. Existing plane-only descriptors and readers remain
    unchanged.

  • Added the public purejsimage/scientific/readers/tia-ser reader for FEI/Thermo TIA SER v528 and
    v544 scalar spectra, spectrum images, and image series. It indexes calibrated elements and valid
    counts without eager payload reads, preserves incomplete elements as bounded document metadata,
    provides direct canonical sample reads, and is verified against pinned real RosettaSciIO files
    without redistributing their GPL-licensed binaries.

  • Added the public purejsimage/scientific/readers/tia-emi companion reader for portable embedded
    ObjectInfo XML, numbered SER resource composition, acquisition metadata, stable identities,
    and evidence-preserving reciprocal-space reinterpretation. Contradictory SER coordinates remain
    authoritative and are reported rather than overwritten.

  • Added a package-private HDF5 file and address layer with legal user-block signature discovery,
    superblock versions 0 through 3, 2/4/8/16-byte integers, relocation-aware bigint addresses,
    lookup3 superblock checksum verification, and a bounded source-identity-aware metadata page
    cache. Legacy family, multi-file, and unknown drivers plus modern superblock extensions remain
    explicit unsupported boundaries while the object graph is implemented separately.

  • Added the first package-private HDF5 object-graph slice with version 1 and 2 object headers,
    checksummed continuation chunks, compact hard and soft links, link-info storage descriptors,
    bounded legacy symbol-table groups with local heaps and B-tree v1, and configurable
    hostile-metadata limits. A revision- and SHA-256-pinned HDF Group fixture verifies the real legacy
    group path without adding its binary to the repository.

  • Continued the package-private HDF5 object graph with checksummed fractal-heap headers, root direct
    and recursive indirect managed blocks, seven-byte managed heap IDs, and type-5 B-tree v2 leaf and
    internal nodes for modern dense groups. Generated hostile fixtures cover hard, soft, ASCII, UTF-8,
    creation-order, bounds, cycles, ordering, and corruption behavior. A second pinned HDF Group file
    verifies a real 40-record dense index and the explicit external-link boundary. Huge and tiny heap
    objects, filtered heaps, and the secondary creation-order index remain explicit deferred
    variants; bounded graph traversal, attributes, dataset layouts, chunk indexes, required filters,
    and exact selected reads are implemented by the later package-private D2-D6 layers. General
    public HDF5 reader claims remain intentionally absent.

  • Completed the fixture-proven package-private HDF5 D3-D6 substrate: bounded datatypes,
    dataspaces, attributes, compact/contiguous/chunked layouts, every required classic and modern
    chunk index, raw/Deflate/Shuffle/Fletcher32 filters, exact fill handling, local/HTTP parity, and
    cancellable selected dataset blocks. Contiguous rank-2 strided selections now batch many rows
    under independent input-span, output, and read-operation caps.

  • Added public Nanonis SXM, Igor Binary Wave v5, Digital Surf SUR/PRO, and ISO 5436-2 X3P surface
    readers plus a bounded ZIP/ZIP64 container. Committed test-only surface binaries now have a
    machine-readable per-file manifest with exact source revision/path/URL, license, attribution,
    redistribution rationale, SHA-256, and oracle.

Changed

  • Documentation pages keep wide tables, code samples, comparison matrices, and chip navigation
    inside named mobile scroll regions. The homepage comparison now leads with a compact six-dimension
    summary on narrow screens and keeps the full TIFF matrix in an expandable, prerendered section.
  • The README now leads with measured whole-slide, scientific explorer, and web codec memory visuals,
    and the generated scientific reader block is a family summary that links to the format reference.
  • Hardened scientific probing and metadata semantics after review: HDF5 dialect probes use exact
    eight-byte signature reads and pass the verified user-block offset into dialect opening; shared
    HDF5 loads isolate caller cancellation, preserve late-waiter coalescing, coalesce graph accounting,
    and cannot repopulate after close; Velox enforces its JSON budget across the complete document;
    NIfTI ignores scl_inter when scl_slope is zero, classifies affine columns relative to their
    own scale, and rejects non-finite header fields explicitly; and DM, TIA SER, Velox, and NIfTI
    omit physical units/evidence when numeric calibration is incomplete while retaining raw values
    and structured warnings.
  • Run the codec test library against hostile one-byte buffered image sources by default, preserving
    the strict source-buffer lifetime coverage while removing the duplicate full-suite test pass from
    npm run check.
  • Coalesced sequential packed-row reads in NPY, NIfTI, and NRRD so a full-plane block issues one
    source request per output block instead of one request per row. In the isolated 9-run scaling
    harness, the 256 MiB NPY and NIfTI full-plane rows fell from 16,387 and 8,195 source reads to 515
    and 259, and from 2,918.8 ms and 2,009.2 ms to 720.2 ms and 766.4 ms. The Node competitor
    scorecard's matching 64 MiB NPY, NIfTI, and NRRD full-plane medians fell from 830.9 ms, 609.8 ms,
    and 540.5 ms to 194.9 ms, 192.1 ms, and 176.4 ms.
  • Reduced DigitalMicrograph tag-walk, packed MRC, and tiled TIFF window source reads without
    changing decode hashes. The DigitalMicrograph 2D range row at 100 ms of injected latency went
    from 702 reads / 70,354 ms to 125 reads / 12,534 ms. The competitor-scorecard MRC full-plane
    median fell from 928.8 ms to 383.2 ms, and the selected TIFF window returned 68 KiB instead of
    128 KiB.
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