tiffio#
Robust readers for mesofield OME-TIFF stacks.
Single-position acquisitions are written by mesofield.data.writer.OMEWriter
as one uncompressed, contiguous (Big)TIFF, so they memory-map with zero copy. The
one failure mode is a truncated file: if an acquisition is interrupted (crash,
kill, power loss), ome-writers has already written an OME-XML header declaring the
full planned plane count, but fewer planes actually reached disk. tifffile then
sees an inconsistent OME series and memmap raises image data are not
memory-mappable (with an index ... out of range warning).
memmap_ome_stack() hides that: it memmaps normally when the file is complete
and transparently falls back to reading exactly the frames present when it isn’t.
- mesofield.data.tiffio.memmap_ome_stack(path, mode='r')[source]#
Memory-map an OME-TIFF frame stack, tolerant of truncated acquisitions.
Returns a read-only
numpy.memmap(zero-copy). For a complete file this is the normal OME series memmap (preserving its N-D shape). For a file whose acquisition was interrupted – OME-XML over-declares the plane count – it retries withis_ome=False, which memmaps the frames actually on disk as a plain contiguous(frames, H, W)stack. Page order equals acquisition order, so it is a drop-in for single-position stacks.