python - 无法解析 XML 并将数据导入 Pandas 数据框

Question

我正在尝试从一个 XML 文件导入数据，该文件包含来自运动测试的逐次呼吸数据。XML 结构如下(简化以显示一般结构):

<?xml version="1.0"?>
<Workbook xmlns="urn:schemas-microsoft-com:office:spreadsheet"
   xmlns:o="urn:schemas-microsoft-com:office:office"
   xmlns:x="urn:schemas-microsoft-com:office:excel"
   xmlns:ss="urn:schemas-microsoft-com:office:spreadsheet"
   xmlns:html="http://www.w3.org/TR/REC-html40">
    <Worksheet ss:Name="MetasoftStudio">
        <Table ss:ExpandedColumnCount="21" ss:ExpandedRowCount="458" x:FullColumns="1"    x:FullRows="1" ss:StyleID="s62" ss:DefaultColumnWidth="53">
            <Column ss:StyleID="s62" ss:AutoFitWidth="0" ss:Width="137"/>
            <Column ss:StyleID="s62" ss:AutoFitWidth="0" ss:Width="97"/>
            <Column ss:StyleID="s62" ss:AutoFitWidth="0" ss:Width="137"/>
            <Row ss:AutoFitHeight="0" ss:Height="26">
                <Cell ss:StyleID="Default"><Data ss:Type="String">t</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">Phase</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">Marker</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">V'O2</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">V'O2/kg</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">V'O2/HR</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">HR</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">WR</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">V'E/V'O2</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">V'E/V'CO2</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">RER</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">V'E</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">BF</Data></Cell>
            </Row>
            <Row ss:Height="15">
                <Cell ss:StyleID="Default"><Data ss:Type="String">h:mm:ss</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String"></Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String"></Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">L/min</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">ml/min/kg</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">ml</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">/min</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">W</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String"></Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String"></Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String"></Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">L/min</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">/min</Data></Cell>
            </Row>
            <Row ss:Height="15">
                <Cell ss:StyleID="Default"><Data ss:Type="String">0:00:06</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String">Rest</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="String"></Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">0.27972413565454501</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">4.3706896196022598</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">4.5856415681072953</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">61</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">0</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">27.002532271037801</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">26.4113108545688</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">1.0223851598932201</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">10.155340000000001</Data></Cell>
                <Cell ss:StyleID="Default"><Data ss:Type="Number">18.07</Data></Cell>
            </Row>
        </Table>
    </Worksheet>
</Workbook>

我使用 lxml 解析和遍历 XML 文件，然后提取每个“单元格”中的“数据”，将其附加到列表中，然后将该列表附加到父列表中(给出我是每一行的嵌套列表)使用代码:

from lxml import etree, objectify
import pandas as pd

with open('Python/cortex.xml') as infile:
    xml_file = infile.read()

    root = objectify.fromstring(xml_file)

    header = []
    data = []

    for row in root.Worksheet.Table.getchildren():
        temp_row = []
        if not row.tag == '{urn:schemas-microsoft-com:office:spreadsheet}Column':
            for cell in row.getchildren():
                temp_row.append(cell.Data)
            data.append(temp_row)
    header = data.pop(0) #remove the first 'row' and store in header list
    del data[0] #remove 2nd line of superfluous data

第一行给出标题，因此我将其pop 放入其自己的列表中，第 2 行包含每个变量的单位，因此我将其删除。到目前为止一切正常(或者看起来如此)......

现在我需要将它放入 pd 数据框中以开始使用它。如果我去 df = pd.DataFrame(data, columns=header) 并且我 print(df) 我得到:ValueError:缓冲区的维数错误(预期为 1，得到 32)

好吧，不确定那里发生了什么......如果我在没有分配标题的情况下创建 df 并打印我得到的:

              0           1       2                        3   \
0  [[[0:00:06]]]  [[[Rest]]]  [[[]]]  [[[0.279724135654545]]]   
1  [[[0:00:09]]]  [[[Rest]]]  [[[]]]  [[[0.465136232899829]]]   
2  [[[0:00:13]]]  [[[Rest]]]  [[[]]]  [[[0.357975433456662]]]   
3  [[[0:00:19]]]  [[[Rest]]]  [[[]]]  [[[0.543332419057909]]]   
4  [[[0:00:24]]]  [[[Rest]]]  [[[]]]  [[[0.374604578743889]]]

这看起来不对! lists in lists的这些lists都是从哪里来的!如果我遍历并打印嵌套列表 data，它会完美打印，但一旦我尝试将其转换为 df，就会出现问题。

任何人都可以告诉我发生了什么以及如何将数据放入 pd df 中吗？如果有比我的方法更好的方法，那么我很乐意试一试。

Answer 1

您可以创建列表列表，然后通过构造函数创建 DataFrame。使用 this solution 进行解析:

from lxml import etree

with (open('test.xml','r')) as f:
    doc = etree.parse(f)

namespaces={'o':'urn:schemas-microsoft-com:office:office',
            'x':'urn:schemas-microsoft-com:office:excel',
            'ss':'urn:schemas-microsoft-com:office:spreadsheet'}

L = []
ws = doc.xpath('/ss:Workbook/ss:Worksheet', namespaces=namespaces)
if len(ws) > 0: 
    tables = ws[0].xpath('./ss:Table', namespaces=namespaces)
    if len(tables) > 0: 
        rows = tables[0].xpath('./ss:Row', namespaces=namespaces)
        for row in rows:
            tmp = []
            cells = row.xpath('./ss:Cell/ss:Data', namespaces=namespaces)
            for cell in cells:
#                print(cell.text);
                tmp.append(cell.text)
            L.append(tmp)
print (L)

---

[['t', 'Phase', 'Marker', "V'O2", "V'O2/kg", "V'O2/HR", 'HR', 'WR', 
  "V'E/V'O2", "V'E/V'CO2", 'RER', "V'E", 'BF'], 
 ['h:mm:ss', None, None, 'L/min', 'ml/min/kg', 'ml', 
 '/min', 'W', None, None, None, 'L/min', '/min'], 
 ['0:00:06', 'Rest', None, '0.27972413565454501', '4.3706896196022598',
  '4.5856415681072953', '61', '0', '27.002532271037801', '26.4113108545688', 
  '1.0223851598932201', '10.155340000000001', '18.07']]

df = pd.DataFrame(L[2:], columns=L[0])
print (df)
         t Phase Marker                 V'O2             V'O2/kg  \
0  0:00:06  Rest   None  0.27972413565454501  4.3706896196022598   

              V'O2/HR  HR WR            V'E/V'O2         V'E/V'CO2  \
0  4.5856415681072953  61  0  27.002532271037801  26.4113108545688   

                  RER                 V'E     BF  
0  1.0223851598932201  10.155340000000001  18.07