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OpenReadout

compare

compare A B answers “is B the same data as A?”, for example a raw file and its export. It exits 0 when the files hold the same data and 1 when they differ. The JSON wrapper has ok: true in both cases.

openreadout compare [OPTIONS] <FILE> <AGAINST>

MCP: openreadout_compare with file and against.

Flags

  • --json: print the JSON wrapper instead of text.
  • --image N: only this image, in both files.
  • --select SEL: plane selection such as c=0, z=2-5, t=0,3. Repeatable.
  • --level N: pyramid level, 0 = full resolution.
  • --tolerance T: largest absolute sample difference that still counts as equal. Default: planes must be bit-identical.
  • --ignore POINTER: leave this JSON pointer out of the metadata diff (* matches one segment). Repeatable.
  • --include-extra: also diff the format-specific extra objects.
  • --no-metadata: compare data only.
  • --no-pixels: compare metadata and geometry only.

What is compared

compare diffs the two files’ info metadata, compares geometry, channel names and physical sizes per image, and hashes every selected plane of images with equal geometry. Numbers equal within a relative 1e-9 count as equal. /path, /size_bytes, /format, /format_version, /notes and /images/*/dimension_order (the order a container stores planes in; OME-Zarr is always t, c, z) are always left out of the diff.

With --select, the planes compared are narrowed to the selection. When B holds only those planes of an image, as an export made with the same --select does, B’s planes are matched to A’s selected planes in order, the metadata diff sees A narrowed the same way, and the image is reported with selected: true.

Examples

Confirm that an export holds the same data as its source:

Terminal window
$ openreadout compare doctor.tif doctor.ome.tiff
=> identical
metadata: same (0 differences)
image 0: geometry same, channel names same, physical size same
planes: 2 compared, 2 identical, 0 within tolerance, 0 mismatched

An export of one channel:

Terminal window
openreadout export a.nd2 --select c=1 -o c1.ome.tiff
openreadout compare a.nd2 c1.ome.tiff --select c=1    # identical

JSON

compare.

Run openreadout compare --help for the full help of your installed version.