Searching nested XML in Python with elementtree

Question

I have a nested XML file I would like to be able to search and store some of the elements into an array.

I can't figure out how to do it....

The XML file looks something like this

<?xml version="1.0" encoding="ISO-8859-1"?>
<modeling>
 <generator>
  <i name="program" type="string">vasp </i>
  <i name="version" type="string">5.4.1  </i>
  <i name="subversion" type="string">24Jun15 (build Dec 17 2015 12:51:06) complex                          parallel </i>
  <i name="platform" type="string">IFC91_ompi </i>
  <i name="date" type="string">2016 04 09 </i>
  <i name="time" type="string">21:14:15 </i>
 </generator>
 <incar>
  <i type="string" name="SYSTEM"> LGPS</i>
  <i type="int" name="ISTART">     1</i>
  <i type="string" name="PREC">low (precision level)</i>
  <i type="string" name="ALGO"> Very Fast   (Elect. algorithm for MD)</i>
  <i type="logical" name="ADDGRID"> T  </i>
  <i type="int" name="ISPIN">     1</i>
  <i type="int" name="MAXMIX">    40</i>
  <i type="int" name="INIWAV">     1</i>
  <i type="int" name="NELM">    20</i>
  <i type="int" name="IBRION">    -1</i>
  <i name="EDIFF">      0.00005000</i>
  <i name="EDIFFG">     -0.01000000</i>
  <i type="int" name="NSW">     0</i>
  <i type="int" name="ISIF">     2</i>
  <i type="int" name="ISYM">     0</i>
  <i type="int" name="NBLOCK">    20</i>
  <i name="ENMAX">    400.00000000</i>
  <i name="POTIM">      2.00000000</i>
  <i name="TEBEG">   1500.00000000</i>
  <i name="TEEND">   1500.00000000</i>
  <i name="SMASS">      1.00000000</i>
  <i type="string" name="LREAL"> Auto      (Projection operators: automa</i>
  <v name="ROPT">     -0.00100000     -0.00100000     -0.00100000     -0.00100000</v>
  <i type="int" name="ISMEAR">     0</i>
  <i type="int" name="NWRITE">     2</i>
  <i type="logical" name="LCORR"> F  </i>
  <i type="int" name="LMAXMIX">     4</i>
  <i type="logical" name="LORBIT"> F  </i>
  <i type="logical" name="LASPH"> T  </i>
  <i type="int" name="ICORELEVEL">     1</i>

....... It eventually gets to this array, which I would like to extract from the XML file to a numpy array using elementtree.

<calculation>
     <varray name="forces" >
       <v>      -1.72025612       1.25780435       0.86117220 </v>
       <v>       0.28139069      -0.40806318       0.01136567 </v>
       <v>      -1.44336852       0.59811466       0.94797354 </v>
       <v>      -0.65405317      -0.20586426      -0.52529678 </v>
       <v>      -0.03741255       1.58074662       0.26915233 </v>
       <v>       1.38593804      -1.81797833       1.04331444 </v>
       <v>       0.06177848      -0.40373533       1.54406535 </v>
       <v>      -0.79191096      -0.11144535      -0.39247818 </v>
       <v>      -0.02452204       0.31078139      -0.44651888 </v>
       <v>      -2.26770774      -0.09736110       0.16802829 </v>
       <v>       0.09880357      -0.68257923       0.62500619 </v>
       <v>       0.00228472       0.62722458      -0.63621109 </v>
       <v>       1.01631395       0.06241868      -1.39029537 </v>
       <v>      -0.48273274       1.54873382      -1.95990958 </v>
       <v>       2.12761082      -1.17499249      -0.46258693 </v>
       </varray>
       <varray name="stress">
       <v>       1.01631395       0.06241868      -1.39029537 </v>
       <v>      -0.48273274       1.54873382      -1.95990958 </v>
       <v>       2.12761082      -1.17499249      -0.46258693 </v>
       </varray>
</calculation>

Any suggestions would be helpful.

Thanks!

Robᵩ · Accepted Answer · 2016-04-12 21:04:35Z

1

import xml.etree.ElementTree as ET
import numpy as np

tree = ET.parse('input.xml')
root = tree.getroot()

a = np.array(
    [
        v.text.split()
        for v in root.findall(".//calculation/varray/v")
    ],
    dtype='float'
)

print a

answered Apr 12, 2016 at 21:04

Robᵩ

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2 Comments

abinitio Over a year ago

That's great - thanks. But actually there is more than one element that has the varray tag, which I hadn't noted in the original question. This pulls them both out. I've edited the XML snippet in the question to reflect this - so if you know how to pull only one of them out that would be awesome!

Robᵩ Over a year ago

Yes, change the XPath expression passed to root.findall(). For example, root.findall('.//calculation/varray[@name="stress"]/v').

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