多个 XML 文件配对成单个 CSV

Question

我在一个文件夹中存在多个 XML 文件，需要检索几个标签的信息 在 Excel 中想要检索 AbstractText Label="FINDINGS"、AbstractText Label="IMPRESSION" 和 parentImage id 标签的详细信息，并将此信息从所有 XML 文件存储到一个 csv。

我想从给定的示例 XML 文件中检索 AbstractText Label="FINDINGS"、AbstractText Label="IMPRESSION" 和 parentImage id 的详细信息，并将所有 XML 文件中的这些信息存储在 Excel 工作表中。

编辑：我想知道如何获取单个文件夹中存在的所有.xml 文件的这些详细信息，并将这些信息作为列和它们各自的值从这些 xml 标记写入单个 csv。

<?xml version="1.0" encoding="utf-8"?>
<eCitation>
    <meta type="rr"/>
    <uId id="CXR49"/>
    <pmcId id="49"/>
    <docSource>CXR</docSource>
    <IUXRId id="49"/>
    <licenseType>open-access</licenseType>
    <licenseURL>http://creativecommons.org/licenses/by-nc-nd/4.0/</licenseURL>
    <ccLicense>byncnd</ccLicense>
    <articleURL/>
    <articleDate>2013-08-01</articleDate>
    <articleType>XR</articleType>
    <publisher>Indiana University</publisher>
    <title>Indiana University Chest X-ray Collection</title>
    <note>The data are drawn from multiple hospital systems.</note>
    <specialty>pulmonary diseases</specialty>
    <subset>CXR</subset>
    <MedlineCitation Owner="Indiana University" Status="supplied by publisher">
        <Article PubModel="Electronic">
            <Journal>
                <JournalIssue>
                    <PubDate>
                        <Year>2013</Year>
                        <Month>08</Month>
                        <Day>01</Day>
                    </PubDate>
                </JournalIssue>
            </Journal>
            <ArticleTitle>Indiana University Chest X-ray Collection
</ArticleTitle>
            <Abstract>
                <AbstractText Label="COMPARISON">None.
</AbstractText>
                <AbstractText Label="INDICATION">XXXX-year-old with
osteoarthritis of the hip scheduled for total hip replacement.
Preoperative evaluation.
</AbstractText>
                <AbstractText Label="FINDINGS">The heart, pulmonary XXXX and
mediastinum are within normal limits. There is no pleural
effusion or pneumothorax. There is no focal air space opacity to
suggest a pneumonia. There are degenerative changes of the
thoracic spine. There is a calcified granuloma identified in the
right suprahilar region. The aorta is mildly tortuous and
ectatic. There is asymmetric right apical smooth pleural
thickening. There are severe degenerative changes of the XXXX.
</AbstractText>
                <AbstractText Label="IMPRESSION">No acute cardiopulmonary
disease.
</AbstractText>
            </Abstract>
            <Affiliation>Indiana University</Affiliation>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Kohli</LastName>
                    <ForeName>Marc</ForeName>
                    <Initials>MD</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Rosenman</LastName>
                    <ForeName>Marc</ForeName>
                    <Initials>M</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Radiology Report</PublicationType>
            </PublicationTypeList>
            <ArticleDate>
                <Year>2013</Year>
                <Month>08</Month>
                <Day>01</Day>
            </ArticleDate>
        </Article>
        <EssieArticleTitle>Indiana University Chest X-ray                 Collection</EssieArticleTitle>
        <IMedAuthor>Marc David Kohli MD</IMedAuthor>
        <IMedAuthor>Marc Rosenman M</IMedAuthor>
    </MedlineCitation>
    <MeSH>
        <major>Thoracic Vertebrae/degenerative</major>
        <major>Calcified Granuloma/lung/hilum/right</major>
        <major>Aorta/tortuous/mild</major>
        <major>Thickening/pleura/apex/right</major>
        <automatic>calcified granuloma</automatic>
        <automatic>degenerative change</automatic>
        <automatic>pleural thickening</automatic>
    </MeSH>
    <parentImage id="CXR49_IM-2110-1001">
        <figureId>F1</figureId>
        <caption>PA and lateral chest radiographs dated XXXX at XXXX hours.
</caption>
        <panel type="single">
            <url>/hadoop/storage/radiology/extract/CXR49_IM-2110-1001.jpg</url>
            <imgModality>7</imgModality>
            <region type="panel">
                <globalImageFeatures>
                    <CEDD>f2p0k1205</CEDD>
                    <ColorLayout>f1p0k137</ColorLayout>
                    <EdgeHistogram>f0p0k184</EdgeHistogram>
                    <FCTH>f4p0k2450</FCTH>
                    <SemanticContext60>f3p0k74</SemanticContext60>
                </globalImageFeatures>
            </region>
        </panel>
    </parentImage>
    <parentImage id="CXR49_IM-2110-2001">
        <figureId>F2</figureId>
        <caption>PA and lateral chest radiographs dated XXXX at XXXX hours.            </caption>
        <panel type="single">
            <url>/hadoop/storage/radiology/extract/CXR49_IM-2110-2001.jpg</url>
            <imgModality>7</imgModality>
            <region type="panel">
                <globalImageFeatures>
                    <CEDD>f2p0k710</CEDD>
                    <ColorLayout>f1p0k83</ColorLayout>
                    <EdgeHistogram>f0p0k1200</EdgeHistogram>
                    <FCTH>f4p0k369</FCTH>
                    <SemanticContext60>f3p0k18</SemanticContext60>
                </globalImageFeatures>
            </region>
        </panel>
    </parentImage>
</eCitation>

Answer 1

假设您的 xml 存在于 xmldoc.txt 中，以下脚本将以列表的形式获取您所需的值。您可以修改代码以满足您的需要。

from lxml import etree
import pandas as pd
df = pd.DataFrame(columns=['X', 'Y', 'Z', 'W'])#change it to what you want
for f in xmlfiles: # xmlfiles is a list of strings where each one is the absolute path to your xml files
    tree = etree.parse(f)
    findings = tree.find(".//AbstractText[@Label='FINDINGS']")
    impression = tree.find(".//AbstractText[@Label='IMPRESSION']")
    parentimages = tree.findall(".//parentImage")
    x = [findings,impression]
    y = [i.text for i in x]
    z = [i.attrib['id'] for i in parentimages]
    y.extend(z)
    df.loc[len(df)] = y
df.to_csv('everything.csv',header=TRUE)