Re: [Pytom-mail] pytom.basic.transformations.project numpy error

[Friedrich F. <foe...@bi...>]

dear dustin,

the project function is still experimental and not used anywhere else.
nevertheless, your fix should be fine - if you look at the volume in
chimera you probably will end up with many z-layers showing the same 2d
data.
this and other functions will have more support when we have hired a
full-time developer for pytom.

cheers

friedrich



On Fri, Feb 26, 2016 at 9:54 PM, Dustin Morado <dus...@gm...>
wrote:

> Hi all,
>
> When I try to project a subvolume I get the following error:
>
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call last)
> <ipython-input-9-c7d5e1885a02> in <module>()
> ----> 1 sv2d = project(sv, r)
>
> /opt/pytom/basic/transformations.py in project(v, rot, verbose)
>     611     npprojection = ndarray([v.sizeX(), v.sizeY(), 1],
> dtype=float32, buffer=None, offset=0, strides=npvol.strides,
>     612                            order='F')
> --> 613     proj(npvol, axis=2, dtype=float32, out=npprojection)
>     614     projection = npy2vol(npprojection,3)
>     615     return projection
>
> /usr/lib/python2.7/dist-packages/numpy/core/fromnumeric.pyc in sum(a,
> axis, dtype, out, keepdims)
>    1712     else:
>    1713         return _methods._sum(a, axis=axis, dtype=dtype,
> -> 1714                             out=out, keepdims=keepdims)
>    1715
>    1716 def product (a, axis=None, dtype=None, out=None, keepdims=False):
>
> /usr/lib/python2.7/dist-packages/numpy/core/_methods.pyc in _sum(a, axis,
> dtype, out, keepdims)
>      23 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
>      24     return um.add.reduce(a, axis=axis, dtype=dtype,
> ---> 25                             out=out, keepdims=keepdims)
>      26
>      27 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
>
> ValueError: output parameter for reduction operation add has too many
> dimensions
>
> If I add ‘keepdims=True’ to the sum call I get a projection, but is this
> OK to do?
>
> —
> Cheers,
> Dustin
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>



-- 
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2632
Fax: +49 89 8578 2641

www.biochem.mpg.de/foerster