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Zessis OPT files(J2K) can not decoding.....

it's J2K encoded, but I can't find any way to decode it, anyone can help me?

files download: http://1drv.ms/1MelGwX

-----------------------------------------------------------

------------------ Original ------------------
From:  "eichelberg";<eichelberg@offis.de>;
Date:  Thu, Oct 8, 2015 08:37 PM
To: <fengkewei@gvchina.com>;
Subject:  Re: About J2K OPT dcm parsing problem

Dear Kewei Feng,

 > Hi, I have some opt dcm files can't parse, can you using dcmtk j2k module
 > test parsing them and send parsed(default transfer syntax) dcm files for me?
> If dcmtk j2k parsed well, we will consider using dcmtk j2k module, thanks!

No, we cannot process these files. While the files claim to be DICOM,
they contain several coding errors, and in particular the pixel data
is not a JPEG 2000 bitstream, nor is it a JP2 file. Furthermore, several
files use a SOP Class UID "1.2.840.10008.5.1.4.1.1.12.77" that seems to
be DICOM, but was never allocated by the DICOM committee.

With our DCMJP2K toolkit I can process a few of the images, but not all,
and those that are decoded cannot be displayed, because the decompressed
byte stream is too short, and is not a displayable image.

I have no idea what Zeiss has done here - but these files are not DICOM.

If you Google for the SOP Class UID, you will find one open source tool that
claims to have support for this Zeiss-specific format. I have not tried it,
but it may be worth a look: http://eyesfirst.github.io/

With best regards,
Dr. Marco Eichelberg

-- 
Dr. Marco Eichelberg
Gruppenleiter Automatisierungs- und Integrationstechnik | Manager Automation and Integration Technology Group

OFFIS
FuE Bereich Gesundheit | R&D Division Health
Escherweg 2 - 26121 Oldenburg - Germany
Phone/Fax: +49 441 9722-147/111
E-Mail: eichelberg@offis.de
URL: http://www.offis.de/
0
summy00
10/26/2015 6:56:38 AM
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On Monday, October 26, 2015 at 2:56:42 PM UTC+8, summy00 wrote:
> it's J2K encoded, but I can't find any way to decode it, anyone can help me?
> 
> files download: http://1drv.ms/1MelGwX
> 
> -----------------------------------------------------------
> 
> ------------------ Original ------------------
> From:  "eichelberg";<eichelberg@offis.de>;
> Date:  Thu, Oct 8, 2015 08:37 PM
> To: <fengkewei@gvchina.com>;
> Subject:  Re: About J2K OPT dcm parsing problem
> 
> Dear Kewei Feng,
> 
>  > Hi, I have some opt dcm files can't parse, can you using dcmtk j2k module
>  > test parsing them and send parsed(default transfer syntax) dcm files for me?
> > If dcmtk j2k parsed well, we will consider using dcmtk j2k module, thanks!
> 
> No, we cannot process these files. While the files claim to be DICOM,
> they contain several coding errors, and in particular the pixel data
> is not a JPEG 2000 bitstream, nor is it a JP2 file. Furthermore, several
> files use a SOP Class UID "1.2.840.10008.5.1.4.1.1.12.77" that seems to
> be DICOM, but was never allocated by the DICOM committee.
> 
> With our DCMJP2K toolkit I can process a few of the images, but not all,
> and those that are decoded cannot be displayed, because the decompressed
> byte stream is too short, and is not a displayable image.
> 
> I have no idea what Zeiss has done here - but these files are not DICOM.
> 
> If you Google for the SOP Class UID, you will find one open source tool that
> claims to have support for this Zeiss-specific format. I have not tried it,
> but it may be worth a look: http://eyesfirst.github.io/
> 
> With best regards,
> Dr. Marco Eichelberg
> 
> -- 
> Dr. Marco Eichelberg
> Gruppenleiter Automatisierungs- und Integrationstechnik | Manager Automation and Integration Technology Group
> 
> OFFIS
> FuE Bereich Gesundheit | R&D Division Health
> Escherweg 2 - 26121 Oldenburg - Germany
> Phone/Fax: +49 441 9722-147/111
> E-Mail: eichelberg@offis.de
> URL: http://www.offis.de/

Using weasis: http://www.dcm4che.org/confluence/display/WEA/Home
can't decode it either, it seems dcm4che using sun's imageio library, which seems eyesfirst using(not sure).
0
summy00
10/26/2015 7:11:12 AM
On Monday, October 26, 2015 at 7:56:42 AM UTC+1, summy00 wrote:
> it's J2K encoded, but I can't find any way to decode it, anyone can help =
me?
>=20
> files download: http://1drv.ms/1MelGwX

I've only looked at: 5MRMJPPWOZ1M3NZ0MGH6RBUKSD91663S27IOLS4X2ZU.EX.DCM

I can see the Pixel Data Fragments ends with FF D9 (EOI/EOC) which suspicio=
usly looks like a JPEG encoded stream. However since there is no header, th=
ere is no way to know if this is JPEG (ITU 81), JPEG-LS, JPEG-XR and/or JPE=
G 2000. Technically since the DICOM header states that the encoding is irre=
versible it will be nearly impossible to craft a JPEG 2000 header before th=
e (potential) SOD marker, since there so many possible parameters.

Please check with your vendor for a proper exporting tool. And or get the D=
ICOM conformance statement. But really the DICOM files contains so many err=
ors (private attribute without private creators...) that it does not make s=
ense to support those files at this point.

I know Zeiss offer decent documentation for there private file formats, so =
you should really consider this path if you want to inspect your data.

2cts
-M
0
Mathieu
10/26/2015 9:35:12 AM
Hi Kewei Feng

The first question I would ask would be whether or not these
are actually the images directly off the Zeiss device, or
whether they have been passed through some other software
that has messed them up (or made them even worse).

I say this because if one looks at the header of one of
the files with the non-standard SOP Class UID, it says:

(0x0002,0x0012) UI Implementation Class UID <1.2.721.2233.11>
(0x0002,0x0013) SH Implementation Version Name <Baycor DICOM>
(0x0008,0x0070) LO Manufacturer <Carl Zeiss Meditec>
(0x0008,0x1070) PN Operators' Name <Operator^Cirrus^^^>
(0x0008,0x1090) LO Manufacturer's Model Name <4000>
(0x0018,0x1020) LO Software Version(s) <6.0.0.599 >

But if you look at the Zeiss conformance statement for
Cirrus HD-OCT 4000 and 400 Instrument and Review Software
Version 6.0.1 at:

http://www.zeiss.com/meditec/en_us/products---solutions/ophthalmology-optometry/dicom/archive.html

It says to expect:

Implementation Class UID 1.2.276.0.75.2.5.20
Implementation Version Name NIM-2.2.1

That said, assuming "CZM" standards for "Carl Zeiss Meditec",
quite a few errors in the encoding would seem to be down to
Zeiss.

So, even though the DICOM encoding of both the standard DICOM
SOP Class instances, and the illegal non-standard one, seem to
rank among the worst I have seen in a while, I would be reluctant
to attribute all the errors to Zeiss without more information.

David

PS. I had a quick look at the EyesFirst source code that
Marco mentioned, particularly:

https://github.com/EyesFirst/eyesfirst/blob/master/dori/dicom-uploader/uploader-core/src/main/java/org/mitre/eyesfirst/dori/Zeiss2Dcm.java

which appears to read the "DICOM like" Zeiss OPT files
that are written with the (illegal non-standard) SOP Class
UID "1.2.840.10008.5.1.4.1.1.12.77", and seems to decipher
whatever is buried in the delimited fragments Pixel Data
(which though the Transfer Syntax in the samples you sent
claims is JPEG 2000, but doesn't appear to contain any J2K
marker segments as Mathieu and Marco describe).

It wasn't obvious from the code how this was data was
being extracted, since what I read seemed to describe
the extraction of raw bytes per frame, rather than
decompressing them with J2K, but I didn't spend much
time on it or test it with your bad image samples.


On 10/26/15 5:35 AM, Mathieu Malaterre wrote:
> On Monday, October 26, 2015 at 7:56:42 AM UTC+1, summy00 wrote:
>> it's J2K encoded, but I can't find any way to decode it, anyone can help me?
>>
>> files download: http://1drv.ms/1MelGwX
>
> I've only looked at: 5MRMJPPWOZ1M3NZ0MGH6RBUKSD91663S27IOLS4X2ZU.EX.DCM
>
> I can see the Pixel Data Fragments ends with FF D9 (EOI/EOC) which suspiciously looks like a JPEG encoded stream. However since there is no header, there is no way to know if this is JPEG (ITU 81), JPEG-LS, JPEG-XR and/or JPEG 2000. Technically since the DICOM header states that the encoding is irreversible it will be nearly impossible to craft a JPEG 2000 header before the (potential) SOD marker, since there so many possible parameters.
>
> Please check with your vendor for a proper exporting tool. And or get the DICOM conformance statement. But really the DICOM files contains so many errors (private attribute without private creators...) that it does not make sense to support those files at this point.
>
> I know Zeiss offer decent documentation for there private file formats, so you should really consider this path if you want to inspect your data.
>
> 2cts
> -M
>
On 10/26/15 3:11 AM, summy00 wrote:
> On Monday, October 26, 2015 at 2:56:42 PM UTC+8, summy00 wrote:
>> it's J2K encoded, but I can't find any way to decode it, anyone can help me?
>>
>> files download: http://1drv.ms/1MelGwX
>>
>> -----------------------------------------------------------
>>
>> ------------------ Original ------------------
>> From: "eichelberg";<eichelberg@offis.de>;
>> Date: Thu, Oct 8, 2015 08:37 PM
>> To: <fengkewei@gvchina.com>;
>> Subject: Re: About J2K OPT dcm parsing problem
>>
>> Dear Kewei Feng,
>>
>> > Hi, I have some opt dcm files can't parse, can you using dcmtk j2k module
>> > test parsing them and send parsed(default transfer syntax) dcm files for me?
>>> If dcmtk j2k parsed well, we will consider using dcmtk j2k module, thanks!
>>
>> No, we cannot process these files. While the files claim to be DICOM,
>> they contain several coding errors, and in particular the pixel data
>> is not a JPEG 2000 bitstream, nor is it a JP2 file. Furthermore, several
>> files use a SOP Class UID "1.2.840.10008.5.1.4.1.1.12.77" that seems to
>> be DICOM, but was never allocated by the DICOM committee.
>>
>> With our DCMJP2K toolkit I can process a few of the images, but not all,
>> and those that are decoded cannot be displayed, because the decompressed
>> byte stream is too short, and is not a displayable image.
>>
>> I have no idea what Zeiss has done here - but these files are not DICOM.
>>
>> If you Google for the SOP Class UID, you will find one open source tool that
>> claims to have support for this Zeiss-specific format. I have not tried it,
>> but it may be worth a look: http://eyesfirst.github.io/
>>
>> With best regards,
>> Dr. Marco Eichelberg
>>
>> --
>> Dr. Marco Eichelberg
>> Gruppenleiter Automatisierungs- und Integrationstechnik | Manager Automation and Integration Technology Group
>>
>> OFFIS
>> FuE Bereich Gesundheit | R&D Division Health
>> Escherweg 2 - 26121 Oldenburg - Germany
>> Phone/Fax: +49 441 9722-147/111
>> E-Mail: eichelberg@offis.de
>> URL: http://www.offis.de/
>
> Using weasis: http://www.dcm4che.org/confluence/display/WEA/Home
> can't decode it either, it seems dcm4che using sun's imageio library, which seems eyesfirst using(not sure).
>
0
David
10/26/2015 11:31:23 AM
Reply:

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