Losslessly recompress five HDF5 files flagged by ClamAV

#82
by wsimson - opened

Five HDF5 acquisitions are marked unsafe by ClamAV signature Win.Exploit.CVE_2016_4332_1-6028013-0. Investigation located the matching sequences inside Blosc-compressed ultrasound sample chunks, supporting false positives rather than malformed HDF5 object-header messages.

This PR losslessly recompresses only tracks/track_0/data/raw_data in those five files, switching Blosc from bitshuffle to byte shuffle. It retains Zstandard, compression level 7, original chunk dimensions, data types, dataset values, attributes, and paths. Other dataset filters are unchanged. The September 26 Vanderbilt subject-ID correction is preserved.

Validation:

  • Native zea 0.1.7: all five originals and replacements pass File.validate_spec(); all 129 raw-data frames read through file.data.raw_data match original values byte-for-byte. Strided slice reads also match. The existing Vanderbilt warning about missing time_to_next_transmit is present in originals and replacements.
  • All dataset values compared against the current source files; numeric values checked byte-for-byte after decompression.
  • All attributes, HDF5 data types, shapes, maxshapes, chunk sizes, fill values, and link kinds/destinations compared.
  • Source SHA-256 hashes verified against the Hub, then rechecked before this commit.
  • All five replacement files scan clean locally with ClamAV 1.5.4 and daily database 28139 (main 63, bytecode 339); no reported scan errors or exceeded-limit alerts.
  • Scans use --allmatch --max-filesize=1900M --max-scansize=2000M --max-scantime=0 --alert-exceeds-max=yes.

All five replacement files passed local ClamAV scans. Decompressed ultrasound values are unchanged, and beamforming tests showed no visible image degradation. Hugging Face’s scan results remain pending and should be checked before merging.

File Original bytes Replacement bytes Datasets verified Attributes verified
session_01_f0374.hdf5 130455835 135367900 77 211
729304_2_Focused_Uncoded_TX.hdf5 1061224448 994510616 24 53
126987_3_Focused_Uncoded_TX.hdf5 1171259392 1120785688 24 53
559277_2_Focused_Uncoded_TX.hdf5 1043398656 990662811 24 53
829312_1_Focused_Uncoded_TX.hdf5 1111031808 1053223871 24 53

Beamforming validation (2026-10-01):

  • Ran the unmodified Vanderbilt and UBC Module C reconstruct.py entry points from open-h/OpenH-RF commit 7862883, overriding only input/output locations and selecting CPU. A wrapper captured pipeline outputs.
  • Used the repository's frozen uv.lock environment: zea 0.1.7, JAX 0.10.2, macOS ARM64 CPU. Published image grids and reconstruction settings were retained.
  • Frame 0 of all five originals and all five replacements reconstructed successfully, twice per input (20 reconstructions). This is a first-frame image regression check, not a full-cineloop beamforming test. All 129 raw frames were separately verified byte-for-byte as described above.
  • Side-by-side visual inspection found no visible changes in sector geometry, structures, contrast, or speckle. Three pairs matched exactly; the other two differed by at most 0.00001145 dB, within observed same-file repeat variability. Nonfinite masks matched exactly; Vanderbilt's NaNs are the reference scan converter's fill outside the sector. UBC output is entirely finite.
File Max image difference (dB)
126987_3_Focused_Uncoded_TX.hdf5 0
559277_2_Focused_Uncoded_TX.hdf5 1.1444092e-05
729304_2_Focused_Uncoded_TX.hdf5 0
829312_1_Focused_Uncoded_TX.hdf5 0
session_01_f0374.hdf5 7.6293945e-06
Replacement SHA-256 hashes
  • ubc/module_C/acquisitions/session_01/session_01_f0374.hdf5: 181a4cf99946b48f3c0438a13b1ef3a5a277b8eb62480927da155db34a26fe0b
  • vanderbilt/data/Fundamental/729304_2_Focused_Uncoded_TX.hdf5: 59272767eea8cc59d9baf72b1a66204452caca2d79ee80b32a90b1e753da7b4c
  • vanderbilt/data/Fundamental/126987_3_Focused_Uncoded_TX.hdf5: bc771e0552b832080e3c53760dc48b5c23fc8070a469b41c427296cd74a0020b
  • vanderbilt/data/Fundamental/559277_2_Focused_Uncoded_TX.hdf5: 1d70d00da19d9d9742c8eabcdd5d8eaa41514a4c565572dad7817f0eaa6d4e6e
  • vanderbilt/data/Fundamental/829312_1_Focused_Uncoded_TX.hdf5: 7a4b77fbf5108f8c03f3c865817b92b4e2cae61cbcaf9b234a07fd0898240c7f
wsimson changed pull request status to closed

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