JPEG 2000 / JP2K compression broken if verification is enabled

[bjoernalbers]

Hello,

at first I was surprised by the excellent compression ratio of 30:1 :-)
But then I've noticed that all images where empty when JPEG 2000 compression is selected:

However, JPEG-LS does work.

Snipped from server.log:

2017-01-26 16:11:37,088 INFO  [org.dcm4che3.net.Dimse] (EE-ManagedExecutorService-default-Thread-5) DCM4CHEE<-albers(1) >> 1:C-STORE-RQ[pcid=41, prior=2
  cuid=1.2.840.10008.5.1.4.1.1.2 - CT Image Storage
  iuid=1.2.392.200036.9116.2.6.1.3268.2060189428.1481864242.64849 - ?
  tsuid=1.2.840.10008.1.2.1 - Explicit VR Little Endian
2017-01-26 16:11:37,112 DEBUG [org.dcm4che3.net.Dimse] (EE-ManagedExecutorService-default-Thread-5) Command:
(0000,0002) UI [1.2.840.10008.5.1.4.1.1.2] AffectedSOPClassUID
(0000,0100) US [1] CommandField
(0000,0110) US [1] MessageID
(0000,0700) US [2] Priority
(0000,0800) US [1] CommandDataSetType
(0000,1000) UI [1.2.392.200036.9116.2.6.1.3268.2060189428.1481864242.64849] Af

2017-01-26 16:11:37,148 DEBUG [org.dcm4che3.imageio.codec.Transcoder] (EE-ManagedExecutorService-default-Thread-5) Compressor: com.sun.media.imageioimpl.plugins.jpeg2000.J2KImage
WriterCodecLib
2017-01-26 16:11:37,152 DEBUG [org.dcm4che3.imageio.codec.Transcoder] (EE-ManagedExecutorService-default-Thread-5) Verifier: com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderCodecLib
2017-01-26 16:11:42,272 DEBUG [org.dcm4che3.imageio.codec.Transcoder] (EE-ManagedExecutorService-default-Thread-5) Compressed frame #1 30.826:1 in 85 ms
2017-01-26 16:11:42,353 DEBUG [org.dcm4che3.imageio.codec.Transcoder] (EE-ManagedExecutorService-default-Thread-5) Verified compressed frame #1 in 81 ms - max pixel value error: 0

Image-Metadata:

$ gdcminfo D0DD6998 
MediaStorage is 1.2.840.10008.5.1.4.1.1.2 [CT Image Storage]
TransferSyntax is 1.2.840.10008.1.2.4.90 [JPEG 2000 Image Compression (Lossless Only)]
NumberOfDimensions: 2
Dimensions: (1256,1256,1)
SamplesPerPixel    :1
BitsAllocated      :16
BitsStored         :16
HighBit            :15
PixelRepresentation:1
ScalarType found   :INT16
PhotometricInterpretation: MONOCHROME2 
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.4.90
Origin: (-76.4545,35.7079,-820.2)
Spacing: (0.12,0.12,1)
DirectionCosines: (1,0,0,0,0,-1)
Rescale Intercept/Slope: (0,1)
Orientation Label: CORONAL

$ du -h D0DD6998 
4,0K    D0DD6998

The archive runs on Ubuntu 16.04 following the official installation instructions.

$ uname -a
Linux gandalf 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

$ md5sum /opt/wildfly/modules/com/sun/media/imageio/main/* 2>/dev/null
a427c487f4a0f18a7aead09d5162b1ef  /opt/wildfly/modules/com/sun/media/imageio/main/clibwrapper_jiio-1.2-pre-dr-b04.jar
c9b9b705c5c95af91d8effcfaff8b13e  /opt/wildfly/modules/com/sun/media/imageio/main/jai_imageio-1.2-pre-dr-b04.jar
b4d4e731930dd774d4437274d0275a69  /opt/wildfly/modules/com/sun/media/imageio/main/module.xml

$ md5sum /opt/wildfly/modules/com/sun/media/imageio/main/lib/linux-x86_64/libclib_jiio.so 
8fb2ddb06382fb02beb1b0a11a5acd43  /opt/wildfly/modules/com/sun/media/imageio/main/lib/linux-x86_64/libclib_jiio.so

Björn

[gunterze]

The used J2K codec is not maintained by dcm4che - anyway I will try to reproduce the issue, if you provide a test image which compression/decompression failed.

[bjoernalbers]

Thanks, I'll send some images.
Basically all images are affected so far.

[bjoernalbers]

@gunterze Here are the images... https://dl.dropboxusercontent.com/u/150292/dcm4chee-arc-light-issue533.tgz

PS: I didn't test this with the dcm4che's official docker image but it might also be affected. So far each image is "empty" when I select JPEG2000-compression.

[gunterze]

The error only occurs if verification is enabled by dcmImageWriteParam: maxPixelValueError=0.0. It's caused by an unbalanced ImageInputStream.mark() in the setInput(Object input,..) method of com.sun.media.imageioimpl.plugins.jpeg2000/J2KImageReaderCodecLib, so a client cannot rely to restore previously marked stream position by ImageInputStream.reset(). Fixed by commit 51499c9