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Open binary files in binary mode for proper data reading#134

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stevevanhooser merged 8 commits into
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claude/fix-file-open-mode-D6Qgf
Mar 31, 2026
Merged

Open binary files in binary mode for proper data reading#134
stevevanhooser merged 8 commits into
masterfrom
claude/fix-file-open-mode-D6Qgf

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Summary

Updated all file open operations to use binary mode ('rb' or 'rb' with endianness specifiers) instead of text mode ('r') when reading binary data files. This ensures proper handling of binary file content across different platforms and MATLAB versions.

Key Changes

  • Changed fopen() calls from 'r' to 'rb' mode in 25+ files across multiple modules:
    • File comparison utilities (arefilessame.m)
    • Custom data format readers (VHL, ROI, VHSB formats)
    • Third-party format readers (CED SOM/SMR, Intan RHD2000, SpikeGadgets REC)
    • Igor and LabVIEW data loaders
  • Updated fread() calls from 'char' to 'uint8' data type in binary file comparison to maintain consistency with binary mode reading
  • Applied changes to both original and duplicate file locations in the codebase

Implementation Details

  • Binary mode ('rb') ensures files are read as raw bytes without any text encoding interpretation
  • Preserved existing endianness specifications (e.g., 'rb' with 'l', 'b', or 'ieee-le' parameters)
  • No functional logic changes; this is a correctness fix for proper binary file handling
  • Affects all file I/O operations that read binary data structures (headers, waveforms, raw samples, etc.)

https://claude.ai/code/session_014KgYyEcCWi1uoMBTK6rj4d

claude added 8 commits March 31, 2026 10:45
…compatibility

On Windows, 'r' opens in text mode which corrupts binary reads. Changed to 'rb'
in all custom_file_formats files that read binary data (both +vlt/+file and
file/ copies).

https://claude.ai/code/session_014KgYyEcCWi1uoMBTK6rj4d
…' -> 'uint8'

Changed fopen mode from 'r' to 'rb' across all binary file readers:
- +vlt/+file/: loadIgor, readlabviewarray, arefilessame
- file/: loadIgor, readlabviewarray (non-namespaced copies)
- Intan-RHD2000: 8 files
- CED-SOM_SMR: 3 files
- SpikeGadgets-REC: 5 files

Also changed arefilessame.m fread from 'char' to 'uint8' since it
does raw byte comparison, not character interpretation.

https://claude.ai/code/session_014KgYyEcCWi1uoMBTK6rj4d
Runs vlt.unittest test suite on pushes to main, PRs targeting main,
and manual dispatch. Installs Statistics/ML, Curve Fitting,
Optimization, Signal Processing, and Image Processing toolboxes.

https://claude.ai/code/session_014KgYyEcCWi1uoMBTK6rj4d
…d Deep Learning Toolbox

- test_hashmatlabvariable: skip all tests if DataHash is not installed
- hashmatlabvariable.m: add note that DataHash is a required dependency
- drivepathTest: fix typo GLNXA66 -> GLNXA64 so Linux case matches
- CI workflow: add Deep_Learning_Toolbox for imageInputLayer

https://claude.ai/code/session_014KgYyEcCWi1uoMBTK6rj4d
- deprecated test_hashmatlabvariable: skip if DataHash not installed
- test_savefigurelist (both copies): use addTeardown to cd to tempdir
  as safety net, since another test's teardown can delete the original
  working directory before this test's cd(originalDir) runs

https://claude.ai/code/session_014KgYyEcCWi1uoMBTK6rj4d
…le it

The original working directory may already be deleted by another test's
teardown, so cd(originalDir) fails. Instead, rely solely on
addTeardown(@() cd(tempdir)) to restore a valid working directory.

https://claude.ai/code/session_014KgYyEcCWi1uoMBTK6rj4d
@stevevanhooser stevevanhooser merged commit 2fea29c into master Mar 31, 2026
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@stevevanhooser stevevanhooser deleted the claude/fix-file-open-mode-D6Qgf branch March 31, 2026 12:51
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2 participants