Re: [scipion-users] Question Regarding Creating Phantom in Xmipp

[Pablo C. <pc...@cn...>]

Thanks Jose! Now I know I was missing even more things than Jagan. ;-)


On 19/04/16 08:08, Jose Miguel de la Rosa Trevin wrote:
> Pablo,
>
> I think you has pointed out to an out-of-date Xmipp page. I think the 
> new one for *xmipp_phantom_create *is:
> http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Phantom_create_v31
>
> Additional information about the input metadata format can be found here:
> http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/FileFormats
>
> Jagan, euler angles are always tricky. In Xmipp, the convention is 
> ZYZ, this means:
> - rotate first around the Z axis (this single rotation does not change 
> the case of the cylinder volume)
> - rotate around the new Y axis, and
> - rotate around the new Z axis (again, this makes no distinction in 
> the particular case of the cylinder)
>
> I think you can use for the last values: 90 90 0 and this will give 
> you a different oriented volume than 0 90 0. As I said, *in the 
> cylinder case*, if rot and tilt angles are the same, the psi (last 
> in-plane rotation around Z) will not change the volume orientation.
>
> Hope this helps,
> Jose Miguel.
>
>
>
>
> On Mon, Apr 18, 2016 at 7:43 PM, Pablo Conesa <pc...@cn... 
> <mailto:pc...@cn...>> wrote:
>
>     Hi, Jagan...I'm probably not the right person to answer since I
>     couldn't run the phanton_create last week!!
>
>     Wait I've tried today and now I can generate a volume
>
>
>     I might be missing something too but format in the wiki and in my
>     local working file looks different:
>
>     wiki: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Create_phantom
>
>     My file has (this generate a cylinder in the center (circular base):
>
>     This:
>
>     65 65 65 0
>     cyl = 1 -30 0 0 5 10 30 0 0 0
>     cyl = 1 -10 0 0 5 10 30 0 0 90
>     cyl = 1 10 0 0 5 10 30 0 90 0
>     cyl = 1 30 0 0 5 10 30 90 0 0
>
>
>      generates this (front view -z):
>
>
>
>
>     To me, what seems to be wrong th the last one, unless I'm not
>     getting it right, which it's very likely.
>
>
>     Which version are you working with?
>
>     Sorry for not being resolutive!!
>
>     All the best, Pablo.
>
>
>     On 18/04/16 11:20, Jagan Mohan wrote:
>>     Dear All,
>>
>>     I have been trying to use xmipp_phantom_create to create a
>>     cylinder using the following description file contents -
>>
>>
>>     # XMIPP_STAR_1 *
>>     # Phantom description file, (generated with phantom help)
>>     data_block1
>>      _dimensions3D  '232 232 232'
>>      _phantomBGDensity  0
>>      _scale  1
>>     data_block2
>>     loop_
>>      _featureType
>>      _featureOperation
>>      _featureDensity
>>      _featureCenter
>>      _featureSpecificVector
>>     cyl     +       1       '0 0 0' '40 40 232 0 90 0'
>>
>>
>>     However, when I change the last line to
>>
>>     cyl     +       1       '0 0 0' '40 40 232 0 90 90'
>>
>>     I get the same volume in both cases meaning that the last
>>     rotation around Z is not being applied. Am I missing something
>>     here? Is it something to do with the center of rotation?
>>
>>
>>     Regards,
>>     Jagan
>>
>>
>>
>>
>>     -- 
>>     -{[O]}-
>>
>>
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