TIFF: only adjust strip/tile byte counts for uncompressed data

[melissalinkert]

Fixes #4442.

Without this change, showinf on the TIFF file linked to #4442 throws:

Exception in thread "main" loci.formats.FormatException: io.airlift.compress.MalformedInputException: Invalid magic prefix: d: offset=16400
	at ome.codecs.ZstdCodec.decompress(ZstdCodec.java:106)
	at ome.codecs.ZstdCodec.decompress(ZstdCodec.java:85)
	at loci.formats.codec.WrappedCodec.decompress(WrappedCodec.java:86)
	at loci.formats.codec.ZstdCodec.decompress(ZstdCodec.java:37)
	at loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:288)
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:845)
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:1135)
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:885)
	at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:312)
	at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
	at loci.formats.FormatReader.openBytes(FormatReader.java:922)
	at loci.formats.ImageReader.openBytes(ImageReader.java:450)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:336)
	at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86)
	at loci.formats.tools.ImageInfo.readPixels(ImageInfo.java:840)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1074)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1165)
Caused by: io.airlift.compress.MalformedInputException: Invalid magic prefix: d: offset=16400
	at io.airlift.compress.zstd.ZstdFrameDecompressor.verifyMagic(ZstdFrameDecompressor.java:976)
	at io.airlift.compress.zstd.ZstdFrameDecompressor.decompress(ZstdFrameDecompressor.java:153)
	at io.airlift.compress.zstd.ZstdDecompressor.decompress(ZstdDecompressor.java:44)
	at ome.codecs.ZstdCodec.decompress(ZstdCodec.java:103)
	... 16 more

tiffdump reports:

test1.tif:
Magic: 0x4949 <little-endian> Version: 0x2b <BigTIFF>
OffsetSize: 0x8 Unused: 0
Directory 0: offset 16400 (0x4010) next 0 (0)
ImageWidth (256) LONG (4) 1<128>
ImageLength (257) LONG (4) 1<128>
BitsPerSample (258) SHORT (3) 1<16>
Compression (259) SHORT (3) 1<50000>
Photometric (262) SHORT (3) 1<1>
ImageDescription (270) ASCII (2) 94<ImageJ=1.11a\nimages=1\nsl ...>
SamplesPerPixel (277) SHORT (3) 1<1>
Software (305) ASCII (2) 13<tiffwrite_rs\0>
DateTime (306) ASCII (2) 20<2026:06:05 17:25:50\0>
TileWidth (322) SHORT (3) 1<128>
TileLength (323) SHORT (3) 1<128>
TileOffsets (324) SHORT (3) 1<16>
TileByteCounts (325) SHORT (3) 1<16384>

As I believe we do have examples of TIFF variants (Zeiss LSM?) that store uncompressed strips with byte counts that do not reflect the bytes per pixel, I did not remove the correction in line 778, but it should now be bypassed for compressed strips/tiles. With this change, showinf on the test file opens the image without error.

[sbesson]

Confirmed that using the sample file of the accompanying issue showinf fails with Bio-Formats 8.5.0 with an io.airlift.compress.MalformedInputException while decompressing the tile.

With this PR included, the reading of the metadata and pixel data works as expected

sbesson@Sebastien-GS-MacBook-Pro-2025 bioformats % ./tools/showinf ~/Downloads/test1.tif -autoscale
Checking file format [Tagged Image File Format]
Initializing reader
TiffDelegateReader initializing /Users/sbesson/Downloads/test1.tif
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
Initialization took 0.034s

Reading core metadata
filename = /Users/sbesson/Downloads/test1.tif
Series count = 1
Series #0 :
	Image count = 1
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 128
	Height = 128
	SizeZ = 1
	SizeT = 1
	SizeC = 1
	Tile size = 128 x 128
	Thumbnail size = 128 x 128
	Endianness = intel (little)
	Dimension order = XYCZT (certain)
	Pixel type = uint16
	Valid bits per pixel = 16
	Metadata complete = true
	Thumbnail series = false
	-----
	Plane #0 <=> Z 0, C 0, T 0


Reading pixel data (0-0)
	Read 1/1 planes (100%)
[done]
0.028s elapsed (28.0ms per plane)

Launching image viewer

Reading global metadata
BitsPerSample: 16
Color mode: grayscale
Compression: Zstandard
DateTime: 2026:06:05 17:25:50
ImageJ: 1.11a
ImageLength: 128
ImageWidth: 128
MetaDataPhotometricInterpretation: Monochrome
MetaMorph: no
NumberOfChannels: 1
PhotometricInterpretation: BlackIsZero
SamplesPerPixel: 1
Software: tiffwrite_rs
TileByteCounts: 16384
TileLength: 128
TileOffsets: 16
TileWidth: 128
Unit: micron
hyperstack: true
loop: false

Reading metadata

The nightly repository builds have been passing with this change - https://bf-testing-results.s3.amazonaws.com/2026/2026-06-23/build-status.log.

Before merging, we should ensure this scenario is covered either by some unit test and/or by adding a representative sample to the curated QA repository to prevent future regression.

[melissalinkert]

curated/tiff/samples/melissa/zstd-tile-size/ has a newly generated test file (see readme) which should reproduce the original issue and read successfully with this fix. I'd expect that to be included in tonight's tests.

[sbesson]

The synthetic samples was successfully included in the nightly repository builds - https://bf-testing-results.s3.amazonaws.com/2026/2026-06-24/tiff.log