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Zessis OPT files(J2K) can not decoding.....(sorry for removing private information)

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

 > 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/ 
0
summy00
10/26/2015 11:58:05 AM
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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 11:58:37 AM
On Monday, October 26, 2015 at 5:35:16 PM UTC+8, 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 hel=
p me?
> >=20
> > files download: http://1drv.ms/1MelGwX
>=20
> I've only looked at: 5MRMJPPWOZ1M3NZ0MGH6RBUKSD91663S27IOLS4X2ZU.EX.DCM
>=20
> I can see the Pixel Data Fragments ends with FF D9 (EOI/EOC) which suspic=
iously 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 J=
PEG 2000. Technically since the DICOM header states that the encoding is ir=
reversible it will be nearly impossible to craft a JPEG 2000 header before =
the (potential) SOD marker, since there so many possible parameters.
>=20
> 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 e=
rrors (private attribute without private creators...) that it does not make=
 sense to support those files at this point.
>=20
> I know Zeiss offer decent documentation for there private file formats, s=
o you should really consider this path if you want to inspect your data.
>=20
> 2cts
> -M

quote
0
summy00
10/26/2015 12:00:30 PM
On Monday, October 26, 2015 at 7:31:28 PM UTC+8, David Clunie wrote:
> Hi Kewei Feng
>=20
> 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).
>=20
> I say this because if one looks at the header of one of
> the files with the non-standard SOP Class UID, it says:
>=20
> (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 >
>=20
> 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:
>=20
> http://www.zeiss.com/meditec/en_us/products---solutions/ophthalmology-opt=
ometry/dicom/archive.html
>=20
> It says to expect:
>=20
> Implementation Class UID 1.2.276.0.75.2.5.20
> Implementation Version Name NIM-2.2.1
>=20
> That said, assuming "CZM" standards for "Carl Zeiss Meditec",
> quite a few errors in the encoding would seem to be down to
> Zeiss.
>=20
> 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.
>=20
> David
>=20
> PS. I had a quick look at the EyesFirst source code that
> Marco mentioned, particularly:
>=20
> https://github.com/EyesFirst/eyesfirst/blob/master/dori/dicom-uploader/up=
loader-core/src/main/java/org/mitre/eyesfirst/dori/Zeiss2Dcm.java
>=20
> 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).
>=20
> 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.
>=20
>=20
> 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 he=
lp 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 susp=
iciously 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 befor=
e the (potential) SOD marker, since there so many possible parameters.
> >
> > Please check with your vendor for a proper exporting tool. And or get t=
he DICOM conformance statement. But really the DICOM files contains so many=
 errors (private attribute without private creators...) that it does not ma=
ke 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 he=
lp me?
> >>
> >> files download: http://1drv.ms/1MelGwX
> >>
> >> -----------------------------------------------------------
> >>
> >> ------------------ Original ------------------
> >>=20
> >>
> >> > Hi, I have some opt dcm files can't parse, can you using dcmtk j2k m=
odule
> >> > 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, th=
anks!
> >>
> >> 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, sever=
al
> >> files use a SOP Class UID "1.2.840.10008.5.1.4.1.1.12.77" that seems t=
o
> >> be DICOM, but was never allocated by the DICOM committee.
> >>
> >> With our DCMJP2K toolkit I can process a few of the images, but not al=
l,
> >> and those that are decoded cannot be displayed, because the decompress=
ed
> >> 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 DICO=
M.
> >>
> >> If you Google for the SOP Class UID, you will find one open source too=
l that
> >> claims to have support for this Zeiss-specific format. I have not trie=
d it,
> >> but it may be worth a look: http://eyesfirst.github.io/
> >>
> >>
> >> --

> >
> > Using weasis: http://www.dcm4che.org/confluence/display/WEA/Home
> > can't decode it either, it seems dcm4che using sun's imageio library, w=
hich seems eyesfirst using(not sure).
> >

quote
0
summy00
10/26/2015 12:01:39 PM
Hi, I have found the conformance statement of this Implementation Class UID:

http://www.zeiss.com/content/dam/Meditec/downloads/pdf/DICOM/Archive/DICOM_Conformance_Statement_Cirrus_6-0.pdf
 
0
summy00
10/27/2015 6:14:48 AM
Hi,

Was anyone able to use the EyesFirst to open the supplied DCM files?
I'm trying to read the same files, but to no avail..
0
WastingBandwidth
10/24/2016 5:07:35 PM
Reply:

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