[Gate-users] Orientation of mhd file
Albert Hirtl
albert.hirtl at meduniwien.ac.at
Thu Jul 10 15:37:26 CEST 2014
Hi,
Ok thanks for your help and the clarification.
By the way, is there a method to visualize voxelized sources which are
read in from an interfile? At least I wasn't able to visualize it in
order to check whether it is located where it should be.
My workaround would be to read it in as phantom an check the position.
However, in the manual it says, that I have to shift the source by half
in -x and -y direction. Is there a better way to check the position?
Cheers,
Albert
On 10/07/14 15:28, Jérôme Suhard wrote:
> Hi,
>
> I can reproduce it.
> Technically, my OpenGL custom commands are called one first time even
> in Stored mode. At this moment, it seems that the rotation was not yet
> applied.
> But with X11 in Stored mode, there is no "refresh" of the graphical
> scene thus leading to this artifact, you can remove it by forcing it with:
> /vis/viewer/refresh
>
> Best regards,
>
>
> 2014-07-10 9:25 GMT+02:00 Albert Hirtl <albert.hirtl at meduniwien.ac.at
> <mailto:albert.hirtl at meduniwien.ac.at>>:
>
> Dear Simon,
>
> Thanks for the header. I thought it's best if I simply sent you
> some screen shots from my system (attached). I hope the names make
> clear what's in the image. Summarized one can say, that OGLIX does
> what it should, OGLSX, however, at least on my system, does not
> what I expect it to do.
>
> The command
>
> glxinfo | grep "OpenGL version"
>
> gives
>
> OpenGL version string: 2.1 Mesa 9.0-devel
>
> I am running Scientific Linux 6.0.
>
> Maybe everything is as it is expected to be? And simply I
> misunderstand the properties of OGLSX?
>
> Cheers,
> Albert
>
>
> On 09/07/14 16:59, Simon Rit wrote:
>> Thanks for sharing the data with us. I tested on my computer and
>> I have the expected behavior, i.e.,
>> - the image is upside down because Y goes from bottom to the top
>> on Gate and it's the opposite in VV,
>> - if I set
>> /gate/patient/placement/setRotationAngle 180 deg
>> then it is back to its normal position
>> - same thing if I use the enclosed mhd but it is now upside down
>> in VV
>> - if I do the last two points together, it's back to the original
>> position.
>> Is this not what you observe?
>> Simon
>>
>>
>> On Wed, Jul 9, 2014 at 3:55 PM, Albert Hirtl
>> <albert.hirtl at meduniwien.ac.at
>> <mailto:albert.hirtl at meduniwien.ac.at>> wrote:
>>
>> Hi,
>>
>> Please find attached my very basic macros and the header of
>> my image file that I used to play around with the .mhd
>> feature (as tar archive). I can not send the raw data, since
>> even if I gzip them they are larger than 11 MB and my mail is
>> rejected. Do you have a mailbox which accepts more than 11 MB?
>>
>> Thanks again and cheers,
>> Albert
>>
>>
>>
>>
>> On 09/07/14 15:32, Jérôme Suhard wrote:
>>> X stands for X11 (old static window)
>>> Qt stands for ... Qt ( GUI with mouse support)
>>>
>>> S(tored) mode: you just see a box
>>> I(mmediate) mode: you see your image with Gate7
>>>
>>> so OGLS or OGLI should not change orientation and/or rotation...
>>>
>>> If you have time to send me your CT/macro, I'm still
>>> interested by them
>>>
>>>
>>> 2014-07-09 15:24 GMT+02:00 Albert Hirtl
>>> <albert.hirtl at meduniwien.ac.at
>>> <mailto:albert.hirtl at meduniwien.ac.at>>:
>>>
>>> Hi,
>>>
>>> Thanks for the prompt answer, it was already enough to
>>> solve the problem:
>>>
>>> I initially copied the following line from the
>>> example_PHANTOM_SOURCE/Voxelized_Phantom_Source/mainMacro.mac
>>>
>>> /vis/open OGLSX
>>>
>>> Motivated by your answer I tried OGL*I*X and everything
>>> is fine... Now all orientations are correct and
>>> rotations work properly.
>>>
>>> So, could OGLSX be a typo in the example?
>>>
>>> Thanks a lot for you help!
>>>
>>> Cheers,
>>> Albert (a bit embarrassed :-[ )
>>>
>>>
>>>
>>> On 09/07/14 15:09, Jérôme Suhard wrote:
>>>> Hi,
>>>>
>>>> 2014-07-09 15:01 GMT+02:00 Albert Hirtl
>>>> <albert.hirtl at meduniwien.ac.at
>>>> <mailto:albert.hirtl at meduniwien.ac.at>>:
>>>>
>>>> If I display the CT using OGLSX it seems to be
>>>> bottom up.
>>>>
>>>>
>>>> You mean OGL*I*X, right ?
>>>>
>>>> /gate/patient/placement/setRotationAxis 0 0 1
>>>> /gate/patient/placement/setRotationAngle
>>>> XXXX deg
>>>>
>>>> it stays the same. In vv it was in the correct
>>>> orientation. The box that is plotted around the CT
>>>> seems to be rotating, however. Do I make anything
>>>> wrong? Or is just the image that I see in OGLSX not
>>>> rotating?
>>>>
>>>>
>>>> can you give the most small macro with the CT showing
>>>> this behaviour ?
>>>>
>>>> thanks
>>>>
>>>> --
>>>> Jérôme Suhard
>>>
>>>
>>> --
>>> Medizinische Universität Wien
>>> Universitätsklinik für Radiologie und Nuklearmedizin
>>> Währinger Gürtel 18-20
>>> 1090 Wien
>>> Austria
>>>
>>> Tel.:+43 (0) 1 / 40400 55450 <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
>>>
>>> Web:
>>> http://www.meduniwien.ac.at/user/albert.hirtl
>>> http://www.meduniwien.ac.at/moccamed/
>>>
>>>
>>>
>>>
>>> --
>>> Jérôme Suhard
>>
>>
>> --
>> Medizinische Universität Wien
>> Universitätsklinik für Radiologie und Nuklearmedizin
>> Währinger Gürtel 18-20
>> 1090 Wien
>> Austria
>>
>> Tel.:+43 (0) 1 / 40400 55450 <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
>>
>> Web:
>> http://www.meduniwien.ac.at/user/albert.hirtl
>> http://www.meduniwien.ac.at/moccamed/
>>
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> <mailto:Gate-users at lists.opengatecollaboration.org>
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>>
>
>
> --
> Medizinische Universität Wien
> Universitätsklinik für Radiologie und Nuklearmedizin
> Währinger Gürtel 18-20
> 1090 Wien
> Austria
>
> Tel.:+43 (0) 1 / 40400 55450 <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
>
> Web:
> http://www.meduniwien.ac.at/user/albert.hirtl
> http://www.meduniwien.ac.at/moccamed/
>
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> <mailto:Gate-users at lists.opengatecollaboration.org>
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
>
> --
> Jérôme Suhard
--
Medizinische Universität Wien
Universitätsklinik für Radiologie und Nuklearmedizin
Währinger Gürtel 18-20
1090 Wien
Austria
Tel.: +43 (0) 1 / 40400 55450
Web:
http://www.meduniwien.ac.at/user/albert.hirtl
http://www.meduniwien.ac.at/moccamed/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140710/b9bc7416/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: albert_hirtl.vcf
Type: text/x-vcard
Size: 397 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140710/b9bc7416/attachment-0001.vcf>
More information about the Gate-users
mailing list