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

[Jose M. de la R. T. <del...@gm...>]

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I think you has pointed out to an out-of-date Xmipp page.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...> 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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