Python 从CZI图像数据解析XML

我有以下XML文件，我想在其中提取键的值：信息|图像| S |场景|形状|名称使用python，例如ElementTree

我已经试过各种方法，但我总是被卡住。非常感谢您的帮助

塞比

以下是我已经试用过的一些代码：

from lxml import etree as etl
import javabridge as jv
import bioformats as bf


def getinfo(root, ns, nodenames):

    NSMAP = {'mw': ns}
    namespace = u'{%s}' % ns
    nsl = len(namespace)

    if len(nodenames) >= 1:
        search = './/mw:' + nodenames[0]
    if len(nodenames) >= 2:
        search = search + '/mw:' + nodenames[1]
    if len(nodenames) >= 3:
        search = search + '/mw:' + nodenames[2]

    out = root.findall(search, namespaces=NSMAP)

    dictlist = []
    for i in range(0, len(out)):

        dict = {}
        for k in range(0, len(out[i].attrib)):
            dict[out[i].keys()[k]] = out[i].values()[k]
            print out[i].attrib

        dictlist.append(dict)

    return dictlist

filename = r'c:\Users\M1SRH\Documents\Python_Projects_Testdata\CZI_XML_Test\B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi'
bfpath = r'c:\Users\M1SRH\Documents\Software\BioFormats_Package\5.1.10\bioformats_package.jar'
jars = jv.JARS + [bfpath]
jv.start_vm(class_path=jars, max_heap_size='4G')
omexml = bf.get_omexml_metadata(filename)
new_omexml = omexml.encode('utf-8')
result = getinfo(etl.fromstring(new_omexml), 'http://www.openmicroscopy.org/Schemas/SA/2015-01', ['StructuredAnnotations', 'XMLAnnotation'])

print 'Done.'

下面是XML数据集：

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01 http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd">
  <Experimenter ID="Experimenter:0" UserName="M1SRH"/>
  <Instrument ID="Instrument:0">
    <Microscope Type="Inverted"/>
    <Detector ID="Detector:Internal" Model="TestCam"/>
    <Objective ID="Objective:1" Immersion="Air" LensNA="0.35" Model="Plan-Apochromat 5x/0.35" NominalMagnification="5.0" WorkingDistance="5000.0" WorkingDistanceUnit="µm"/>
    <FilterSet ID="FilterSet:1">
      <DichroicRef ID="Dichroic:1"/>
      <EmissionFilterRef ID="Filter:1"/>
      <EmissionFilterRef ID="Filter:2"/>
      <EmissionFilterRef ID="Filter:3"/>
    </FilterSet>
    <Filter ID="Filter:1">
      <TransmittanceRange CutIn="458.0" CutInUnit="nm" CutOut="474.0" CutOutUnit="nm"/>
    </Filter>
    <Filter ID="Filter:2">
      <TransmittanceRange CutIn="546.0" CutInUnit="nm" CutOut="564.0" CutOutUnit="nm"/>
    </Filter>
    <Filter ID="Filter:3">
      <TransmittanceRange CutIn="618.0" CutInUnit="nm" CutOut="756.0" CutOutUnit="nm"/>
    </Filter>
    <Dichroic ID="Dichroic:1"/>
  </Instrument>
  <Image ID="Image:0" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #1">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:0:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="0.46000003814697266" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="30533.145" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="5.456000089645386" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="30533.145" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:1" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #2">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:1" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:1:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="0.6510000228881836" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="32466.855" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="5.6519999504089355" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="32466.855" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:2" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #3">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:2" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:2:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="0.8610000610351562" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="30533.145" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="5.859999895095825" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="30533.145" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:3" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #4">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:3" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:3:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="1.0509998798370361" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="32466.855" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="6.055000066757202" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="32466.855" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:4" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #5">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:4" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:4:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="1.2590000629425049" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="39533.145" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="6.296999931335449" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="39533.145" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:5" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #6">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:5" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:5:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="1.4500000476837158" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="41466.855" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="6.490000009536743" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="41466.855" PositionXUnit="reference frame" PositionY="16533.145" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:6" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #7">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:6" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:6:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="1.6640000343322754" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="39533.145" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="6.700000047683716" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="39533.145" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:7" Name="B4_B5_S=8_4Pos_perWell_T=2_Z=1_CH=1.czi #8">
    <AcquisitionDate>2016-07-20T11:44:16.161</AcquisitionDate>
    <ExperimenterRef ID="Experimenter:0"/>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:7" Interleaved="false" PhysicalSizeX="0.39999999999999997" PhysicalSizeXUnit="µm" PhysicalSizeY="0.39999999999999997" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="2" SizeX="640" SizeY="640" SizeZ="1" Type="uint8">
      <Channel AcquisitionMode="WideField" EmissionWavelength="465.0" EmissionWavelengthUnit="nm" ExcitationWavelength="353.0" ExcitationWavelengthUnit="nm" ID="Channel:7:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
        <DetectorSettings Binning="1x1" Gain="0.0" ID="Detector:Internal"/>
        <FilterSetRef ID="FilterSet:1"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane DeltaT="1.8569998741149902" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="41466.855" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      <Plane DeltaT="6.898000001907349" DeltaTUnit="s" ExposureTime="20.0" ExposureTimeUnit="s" PositionX="41466.855" PositionXUnit="reference frame" PositionY="18466.855" PositionYUnit="reference frame" PositionZ="111.842" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
    </Pixels>
  </Image>
  <StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2015-01">
    <XMLAnnotation ID="Annotation:0" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>Experiment|AcquisitionBlock|TimeSeriesSetup|RegionsSetup|SampleHolder|AllowedScanArea|ContourType</Key>
          <Value>[Rectangle]</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:2127" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>Information|Image|S|Scene|Shape|Name</Key>
          <Value>[B4, B4, B4, B4, B5, B5, B5, B5]</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
  </StructuredAnnotations>
</OME>

2016-07-20T11:44:16.161
2016-07-20T11:44:16.161
2016-07-20T11:44:16.161
2016-07-20T11:44:16.161
2016-07-20T11:44:16.161
2016-07-20T11:44:16.161
2016-07-20T11:44:16.161
2016-07-20T11:44:16.161
实验|采集块|时间体验设置|区域设置|样本架|允许扫描区域|轮廓类型
[矩形]
信息|图像| S |场景|形状|名称
[B4，B4，B4，B4，B5，B5，B5，B5]

假设您没有使用名称空间来查找元素。 我试图从OriginalMetadata获取键和值

import xml.etree.ElementTree as ET

tree = ET.fromstring(initial_string)
# Define NameSpace
name_space = "{http://www.openmicroscopy.org/Schemas/SA/2015-01}"
origin_meta_datas = tree.findall(".//{}OriginalMetadata".format(name_space))
# Iterate in founded origins
for origin in origin_meta_datas:
    key = origin.find("{}Key".format(name_space)).text
    if key == "Information|Image|S|Scene|Shape|Name":
        value = origin.find("{}Value".format(name_space)).text
        print("Value: {}".format(value))

---

假设您没有使用名称空间来查找元素。 我试图从OriginalMetadata获取键和值

import xml.etree.ElementTree as ET

tree = ET.fromstring(initial_string)
# Define NameSpace
name_space = "{http://www.openmicroscopy.org/Schemas/SA/2015-01}"
origin_meta_datas = tree.findall(".//{}OriginalMetadata".format(name_space))
# Iterate in founded origins
for origin in origin_meta_datas:
    key = origin.find("{}Key".format(name_space)).text
    if key == "Information|Image|S|Scene|Shape|Name":
        value = origin.find("{}Value".format(name_space)).text
        print("Value: {}".format(value))

---

展示你已经尝试过的，并告诉你在哪里卡住了。对不起，你是对的。这里有一个我到目前为止尝试过的简短例子：展示你已经尝试过的东西，并说出你的困境。对不起，你是对的。这里有一个我到目前为止尝试过的简短例子：哇。这正是我们要找的。我差一点就知道了，但我只知道最后的步骤。非常感谢。哇。这正是我们要找的。我差一点就知道了，但我只知道最后的步骤。谢谢。