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ngageoint / tiff-java

Tagged Image File Format Java Library
https://ngageoint.github.io/tiff-java
MIT License
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LZW decompression - Byte offset out of range #46

Closed ghost closed 2 years ago

ghost commented 2 years ago

Version Information:

Expected Results:

A tiff file that is compressed LZW should be decompressed.

Observed Results:

Output:

[error] mil.nga.tiff.util.TiffException: Byte offset out of range. Total Bytes: 13670, Byte offset: 13670
[error]     at mil.nga.tiff.io.ByteReader.setNextByte(ByteReader.java:73)
[error]     at mil.nga.tiff.FileDirectory.readRaster(FileDirectory.java:1291)
[error]     at mil.nga.tiff.FileDirectory.readRasters(FileDirectory.java:1220)
[error]     at mil.nga.tiff.FileDirectory.readRasters(FileDirectory.java:1067)
[error]     at mil.nga.tiff.FileDirectory.readRasters(FileDirectory.java:1019)
[error]     at mil.nga.tiff.FileDirectory.readRasters(FileDirectory.java:998)
[error]     at Main$.delayedEndpoint$Main$1(Main.scala:11)
[error]     at Main$delayedInit$body.apply(Main.scala:4)
[error]     at scala.Function0.apply$mcV$sp(Function0.scala:39)
[error]     at scala.Function0.apply$mcV$sp$(Function0.scala:39)
[error]     at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
[error]     at scala.App.$anonfun$main$1(App.scala:76)
[error]     at scala.App.$anonfun$main$1$adapted(App.scala:76)
[error]     at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:563)
[error]     at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561)
[error]     at scala.collection.AbstractIterable.foreach(Iterable.scala:926)
[error]     at scala.App.main(App.scala:76)
[error]     at scala.App.main$(App.scala:74)
[error]     at Main$.main(Main.scala:4)
[error]     at Main.main(Main.scala)
[error]     at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[error]     at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[error]     at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[error]     at java.base/java.lang.reflect.Method.invoke(Method.java:566)

Steps to Reproduce:

  1. Create a SBT project with IntelliJ
  2. Include libraryDependencies ++= Seq("mil.nga" % "tiff" % "3.0.0") in build.sbt
  3. Add the relavant code from below in Main
  4. sbt run

Relevant Code:

val input = new File("src/main/resources/test.ome.tif")
val tiffImage = TiffReader.readTiff(input)
val directories = tiffImage.getFileDirectories
val directory = directories.get(0)
val rasters = directory.readRasters

Test Files:

bosborn commented 2 years ago

I looked at this for awhile and can't figure out why the LZW decoding fails on this particular tif file. Attempted to trace the decompression back a bit but didn't see the cause. The decoded bytes for the first strip start to differ (from gdal_translate decompression bytes) at byte 13590. 13,864 total decoded bytes are expected but only 13,670 bytes are decoded from the 5,572 LZW encoded bytes. The difference produces an early EOI (End of information) code (257).

I did remove compression and then encode it again using gdal_translate, and the resulting tiff file works. The encoded bits usually differ by a few bytes in each strip. I'm guessing the LZW encoding done on the original file slightly differs (potentially from spec but I'm not sure). I couldn't determine a fix at the moment to handle the difference.

gdal_translate test.ome.tif out.tif
gdal_translate out.tif out2.tif -co "COMPRESS=LZW"

out2.tif.zip

First 10 test.ome.tif strips Screen Shot 2022-09-20 at 2 58 10 PM

First 10 out2.tif strips Screen Shot 2022-09-20 at 2 57 51 PM

TIFF Image: out2.tif

-- File Directory --

ImageWidth (256)
SHORT (2 bytes)
Count: 1
Values: 6932

ImageLength (257)
SHORT (2 bytes)
Count: 1
Values: 3860

BitsPerSample (258)
SHORT (2 bytes)
Count: 1
Values: [16]

Compression (259)
SHORT (2 bytes)
Count: 1
Values: 5

PhotometricInterpretation (262)
SHORT (2 bytes)
Count: 1
Values: 1

ImageDescription (270)
ASCII (1 bytes)
Count: 4394
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LONG (4 bytes)
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SamplesPerPixel (277)
SHORT (2 bytes)
Count: 1
Values: 1

RowsPerStrip (278)
SHORT (2 bytes)
Count: 1
Values: 1

StripByteCounts (279)
LONG (4 bytes)
Count: 3860
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XResolution (282)
RATIONAL (8 bytes)
Count: 1
Values: [4294967295, 91310]

YResolution (283)
RATIONAL (8 bytes)
Count: 1
Values: [4294967295, 91310]

PlanarConfiguration (284)
SHORT (2 bytes)
Count: 1
Values: 1

ResolutionUnit (296)
SHORT (2 bytes)
Count: 1
Values: 3

Software (305)
ASCII (1 bytes)
Count: 25
Values: [OME Bio-Formats 0.12.2+0]

Predictor (317)
SHORT (2 bytes)
Count: 1
Values: 1

SampleFormat (339)
SHORT (2 bytes)
Count: 1
Values: [1]
ghost commented 2 years ago

@bosborn Thank you for the time you put into the investigation. I'll close the bug. In particular, the fact that it works with the gdal_translate encoding supports the thesis that the original LZW encoding is probably somewhat different.