scipion-users

[scipion-users] Question Regarding Creating Phantom in Xmipp

[Jagan M. <o....@gm...>]

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]}-

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

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

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]}-
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

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]}-
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

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]}-
>>
>>
>>     ------------------------------------------------------------------------------
>>     Find and fix application performance issues faster with Applications Manager
>>     Applications Manager provides deep performance insights into multiple tiers of
>>     your business applications. It resolves application problems quickly and
>>     reduces your MTTR. Get your free trial!
>>     https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>
>>
>>     _______________________________________________
>>     scipion-users mailing list
>>     sci...@li...
>>     <mailto:sci...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>     ------------------------------------------------------------------------------
>     Find and fix application performance issues faster with
>     Applications Manager
>     Applications Manager provides deep performance insights into
>     multiple tiers of
>     your business applications. It resolves application problems
>     quickly and
>     reduces your MTTR. Get your free trial!
>     https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>     _______________________________________________
>     scipion-users mailing list
>     sci...@li...
>     <mailto:sci...@li...>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>