[Pytom-mail] Particle information extraction

[Kanika K. <kk...@uc...>]

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
pl=PickPosition()
pl.fromXMLFile(pl.xml')

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!