Creating python dataframe from nested xml

Question

this is the portion of xml the file I am interested:

</Section>
<Section id="21" name="Event Strips" itemsCount="18">
    <Event title="HR Min" start="10707646" end="10709446"/>
    <Event title="HR Max" start="1043646" end="1045446"/>
    <Event title="RR Min" start="12441170" end="12442970"/>
    <Event title="RR Max" start="14690429" end="14692229"/>
</Section>
<Section id="99" name="TimeDomainHRV" itemsCount="4">
    <Info id="100" name="RRMean" value="725.99 ms"/>
    <Info id="101" name="SDNN" value="108.01 ms"/>
</Section>

I want a dataframe like below from the xml:

Event    start    end
HR Min 10707646 10709446
HR Max 1043646  1045446 
..........................

What is wrong with the code you have written? Does it give any output? If so, what is it. Are there any errors or tracebacks? If so, add their full text. All of this should be in the question itself, not as a comment. — MattDMo
– MattDMo, Commented Oct 26, 2022 at 15:32

Andrew · Accepted Answer · 2022-10-26 15:31:24Z

1

You cat just use read_xml after install lxml libruary.

Install lxml lib

pip install lxml

Load xml data in dataframe

import pandas as pd

pd.read_xml('data.xml')

answered Oct 26, 2022 at 15:31

Andrew

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2 Comments

Shourov Over a year ago

it's not working!

Andrew Over a year ago

Show your errors

Shourov · Accepted Answer · 2022-10-28 13:55:17Z

import xml.etree.ElementTree as ET
import xmltodict
import pandas as pd
import re
import glob
import os

for file in glob.glob("test_xml\\*.xml", recursive=False):
    file_name_base = os.path.splitext(file)[-2]
    file_name = file_name_base.split('\\')[-1]
    file_name = file_name.split('.')[-2]
    with open(file) as f:
        xml = f.read()
    tree = ET.fromstring(re.sub(r"(<\?xml[^>]+\?>)", r"\1<root>", xml) + "</root>")
    root = tree

    # tree = ET.parse('xml')
    xml_data = tree
    # here you can change the encoding type to be able to set it to the one you need
    xmlstr = ET.tostring(xml_data, encoding='utf-8', method='xml')

    data_dict = dict(xmltodict.parse(xmlstr))
    store_items = []
    all_items = []

    for storeno in root.iter('Event'):
        alarms_name = storeno.attrib.get('title')
        start = storeno.attrib.get('start')
        end = storeno.attrib.get('end')

        store_items = [alarms_name, start, end]
        all_items.append(store_items)

    xmlToDf = pd.DataFrame(all_items, columns=['Alarms', 'Start', 'End'])
    print('Creating reference file for ' + file_name + '........................')
    print(xmlToDf.to_string(index=False))
    xmlToDf.to_csv(file_name + '.ref', header=False, index_label=None, sep=';', index=False)

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