Problem of setVoiLut

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m-ishihara
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Problem of setVoiLut

#1 Post by m-ishihara » Mon, 2009-02-02, 11:31

Hello forks,

Now I am wondering if VoiLut would be applied or not using DCMTK.
In my source code, I implemented serching and appling VoiLut source code refering to Dimoimg.cxx and Dimoimg.h, as follows,

//VoiLut 1
const unsigned long table = 1;
OFString explanation;
const OFBool ignoreDepth = OFFalse;
int bb = dcmimg->setVoiLut(table, ignoreDepth);
unsigned long aa = dcmimg->getVoiLutCount();
const char *cc = dcmimg->getVoiLutExplanation(table, explanation);

The sequence No of the VoiLut is 1, so I think the source code is complietly correct.
But, it didn't work.

Please let me know what is worng with the source code, and the right way to get and apply the VoiLut.

Best regards,
Maty

Jörg Riesmeier
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#2 Post by Jörg Riesmeier » Mon, 2009-02-02, 12:18

Now I am wondering if VoiLut would be applied or not using DCMTK.
Yes, the VOI transformation is applied to the pixel data if present and activated.
The sequence No of the VoiLut is 1, so I think the source code is complietly correct.
setVoiLut(1) activates the second VOI LUT Table in the DICOM image since the tables are counted from 0 (see documentation). Btw, what is the return value of this method?

m-ishihara
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#3 Post by m-ishihara » Tue, 2009-02-03, 07:26

Hello! Jörg,

Thank you for your quick and friendly reply.
From your suggestion, I understand that I made a mistake that the table No was wrong.
I tried again and the results are as follows;

table No -aa -bb -cc
----- 0 -----1 --1 --"E25"
----- 1 -----1 --0 --nothing

In case of table No = 0, the return code bb = 1, that means correct.

BTW, I tried to get VOI Lut data stored in DICOM file with findAndGetElement, as follows;

dataset->findAndGetElement(DCM_VOILUTSequence, element, OFFalse);
dataset->findAndGetElement(DCM_LUTDescriptor, element, OFFalse);
dataset->findAndGetElement(DCM_LUTData, element, OFFalse);

Oddly enough, I can get just DCM_VOILUTSequence element but not DCM_LUTDescriptor or DCM_LUTData elements.
If how to use setVoiLut is correct, why I can't get VOI Lut data?
I would appliciate it if you let me know the reason and how to fix it.

Thanks,
Maty

Jörg Riesmeier
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#4 Post by Jörg Riesmeier » Tue, 2009-02-03, 12:45

Oddly enough, I can get just DCM_VOILUTSequence element but not DCM_LUTDescriptor or DCM_LUTData elements.
Apparently, you did not understand what a sequence is. The LUT Descriptor and LUT Data are encapsulated by an item which is contained in the VOI LUT Sequence. So, you have to retrieve the first item of the sequence and then use findAndGetXXX() on this item (not on the main dataset) ...

I guess there are many useful examples both in this forum and in the DCMTK on how to do this.

m-ishihara
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#5 Post by m-ishihara » Wed, 2009-02-04, 10:03

Hello! Jörg,

Thank you for your explanation.
Soon after reading your reply, I tried confirming the handling of setVoiLut.
Then I understood that the return value of setVoiLut is the same as "return VoiLutData->isValid()", so I believe that the obtained VoiLut is correct.

BTW, it seems that the obtained VoiLut is not applied to the image data.
If so, I would appreciate it if you let me know how to apply the obtained VoiLut data to the DICOM image data.

Thanks,
Maty

Jörg Riesmeier
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#6 Post by Jörg Riesmeier » Wed, 2009-02-04, 11:24

BTW, it seems that the obtained VoiLut is not applied to the image data.
What does the error console show in verbose/debug mode?

I would suggest that you first try "dcm2pnm -v -d --use-voi-lut 0" on this particular image ...

m-ishihara
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Location: Japan

#7 Post by m-ishihara » Wed, 2009-02-04, 11:46

Hi Jörg,

Thank you for your quick reply.
I quickly tried to run dcm2pnm as you mentioned. and got the message of the results, as follows;

$dcmtk: dcm2pnm v3.5.4 2005-12-20 $

dcm2pnm: Convert DICOM images to PGM/PPM or BMP
error: Invalid value for option --use-voi-lut (underflow: 0)

Please tell me the cause and action of the error!!

Thanks,
Maty

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#8 Post by Jörg Riesmeier » Wed, 2009-02-04, 11:58

Sorry, this was my mistake: For dcm2pnm, the LUTs are counted from 1. So "--use-voi-lut 1" will select the first VOI LUT stored in the DICOM image.

m-ishihara
Posts: 40
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#9 Post by m-ishihara » Wed, 2009-02-04, 12:13

Thank you for your reply.
The result is as follows;

reading DICOM file: voi_in.dcm
preparing pixel data.
activating VOI LUT 1
WARNING: invalid value for 'NumberOfTableEntries' (2119) ... assuming 1 !
WARNING: unsuitable value for 'BitsPerTableEntry' (16) ... assuming 8 !
writing frame 1 to aaa
cleaning up memory.

Please let me know your analysis.

Thanks.
Maty

Jörg Riesmeier
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#10 Post by Jörg Riesmeier » Wed, 2009-02-04, 12:16

Could you please post the dump of the VOILUTSequence using "dcmdump +P VOILUTSequence +L voi_in.dcm".

m-ishihara
Posts: 40
Joined: Thu, 2008-09-18, 09:20
Location: Japan

#11 Post by m-ishihara » Wed, 2009-02-04, 12:28

The result is as follows;

(0028,3010) SQ (Sequence with undefined length #=1) # u/l, 1 VOILUTSequence
(fffe,e000) na (Item with undefined length #=4) # u/l, 1 Item
(0028,0000) UL 4272 # 4, 1 ImagePresentationGroupLength
(0028,3002) xs 2119\1438\16 # 6, 3 LUTDescriptor
(0028,3003) LO [E25] # 4, 1 LUTExplanation
(0028,3006) lt 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0db8\0dbd\0dc1\0dc6\0dca\0dcf\0dd4\0dd8\0ddd\0de2\0de6\0deb\0def\0df4\0df9\0dfd\0e02\0e07\0e0b\0e10\0e15\0e19\0e1e\0e23\0e28\0e2c\0e31\0e36\0e3a\0e3f\0e44\0e49\0e4d\0e52\0e57\0e5c\0e60\0e65\0e6a\0e6f\0e74\0e79\0e7e\0e83\0e88\0e8c\0e91\0e96\0e9b\0ea0\0ea5\0eaa\0eaf\0eb4\0eb9\0ebe\0ec3\0ec8\0ecd\0ed2\0ed7\0edc\0ee1\0ee6\0eeb\0ef0\0ef5\0efa\0eff\0f04\0f09\0f0e\0f13\0f18\0f1d\0f22\0f27\0f2c\0f31\0f36\0f3b\0f40\0f46\0f4b\0f50\0f55\0f5a\0f5f\0f64\0f69\0f6e\0f73\0f78\0f7d\0f82\0f87\0f8d\0f92\0f97\0f9c\0fa1\0fa6\0fab\0fb0\0fb6\0fbb\0fc0\0fc5\0fcb\0fd0\0fd5\0fda\0fe0\0fe5\0fea\0fef\0ff5\0ffa\0fff # 4238, 1 LUTData
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
Maty

Jörg Riesmeier
ICSMED DICOM Services
ICSMED DICOM Services
Posts: 2217
Joined: Fri, 2004-10-29, 21:38
Location: Oldenburg, Germany

#12 Post by Jörg Riesmeier » Wed, 2009-02-04, 12:35

Thanks. Would it also be possible to send the complete DICOM image to us by email (dicom/at/offis/dot/de)? This would facilitate the analysis significantly ...

m-ishihara
Posts: 40
Joined: Thu, 2008-09-18, 09:20
Location: Japan

#13 Post by m-ishihara » Wed, 2009-02-04, 12:45

I am sending DICOM image attached to e-mail, to 'dicom@offis.de'.
Please tell me the results.

Thanks,
Maty
Maty

Jörg Riesmeier
ICSMED DICOM Services
ICSMED DICOM Services
Posts: 2217
Joined: Fri, 2004-10-29, 21:38
Location: Oldenburg, Germany

#14 Post by Jörg Riesmeier » Wed, 2009-02-04, 12:53

Thank you for the image. The two dcm2pnm warning message are apparently caused by a bug in DCMTK 3.5.4 which have already been fixed in the current snapshot.

Using the current development version of dcm2pnm I could render the image without any errors or warnings. However, the third value of the LUT descriptor is not really appropriate for the image. Using dcm2pnm's new option +Mv (--ignore-vlut-depth) the correct depth (12 instead of 16) is used and the image looks good to me :-)

m-ishihara
Posts: 40
Joined: Thu, 2008-09-18, 09:20
Location: Japan

#15 Post by m-ishihara » Mon, 2009-02-16, 09:29

Hi Jörg,

Thank you for your help.
BTW, we need to apply VOI Lut stored in DICOM image to rendered data using mainstream DCMTK.
I would appriciate it if you modify it.
Or, please tell me how to modify.

Thanks,
Maty

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