Re: [Pytom-mail] Particle information extraction

[Thomas H. <th...@gm...>]

Hi Kanika,

Code between the lines. When you try to access information from a ParticleList, you must read it first from disk. You were trying to read the wrong type - PickPosition - instead of ParticleList

Replace PickPosition with ParticleList

Hope it helps solving your problem,
Thomas

> On Sep 7, 2016, at 12:00 PM, Kanika Khanna <kk...@uc...> wrote:
> 
> Hello all, 
> 
> I have been trying to get coordinates of X,Y,Z from particle list using the function 'PickPosition' from ipytom as follows:
> ipytom
> from pytom.basic.structures import PickPosition

from pytom.basic.structures import ParticleList

> pl=PickPosition()
> pl.fromXMLFile(pl.xml’)

for i,p in enumerate(pl):
	p.getPickPosition()

	or 
	
	pl[i].getPickPosition()




> But I run into the following error: 
> UnboundLocalError                         Traceback (most recent call last)
> <ipython-input-5-71b11edb47f3> in <module>()
> ----> 1 pl.fromXMLFile ('pl.xml')
> 
> /usr/local/pytom/basic/structures.py in fromXMLFile(self, filename)
>      72         lines = readStringFile(filename)
>      73
> ---> 74         self.fromStr(lines)
>      75
>      76     def toXMLFile(self,filename):
> 
> /usr/local/pytom/basic/structures.py in fromStr(self, string)
>      45         root = etree.fromstring(string)
>      46
> ---> 47         self.fromXML(root)
>      48
>      49     def __str__(self):
> 
> /usr/local/pytom/basic/structures.py in fromXML(self, xmlObj)
>    3674             TypeError('PickPosition: You must provide a valid PickPosition XML object.')
>    3675
> -> 3676         self._x = float(shift_element.get('X'))
>    3677         self._y = float(shift_element.get('Y'))
>    3678         self._z = float(shift_element.get('Z'))
> 
> UnboundLocalError: local variable 'shift_element' referenced before assignment
> 
> 
> Am I doing it right? How can I get the X,Y,Z coordinates of particles in a matrix from particle file?
> 
> Thanks!
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