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提取XML节点和分别在R

2013-05-29 43 views
2

属性我有一个XML数据集，看起来像这样：提取XML节点和分别在R

<protocol ID='.'> 
    <HEAD></HEAD> 
    <block ID='...'> 
     <HEAD></HEAD> 
     <trial ID='.....'> 
      <HEAD></HEAD> 
      <seq ID=''> 
       <HEAD></HEAD> 
       <calibration CLASS='affine-calibration' ID='New Calibration'> 
        <AX>.........</AX> 
        <BX>-........</BX> 
        <AY>.........</AY> 
        <BY>.........</BY> 
        <type>'por'</type> 
       </calibration> 
       <POR TIME='......'> 
        <PUPIL>.</PUPIL> 
        <BLINK>.</BLINK> 
        <V>...</V> 
        <H>...</H> 
        <PLANEINTRWV>...</PLANEINTRWV> 
        <PLANEINTRWH>...</PLANEINTRWH> 
        <PLANE>.</PLANE> 
       </POR> 
       <POR TIME='......'> 
        <PUPIL>.</PUPIL> 
        <BLINK>.</BLINK> 
        <V>...</V> 
        <H>...</H> 
        <PLANEINTRWV>...</PLANEINTRWV> 
        <PLANEINTRWH>...</PLANEINTRWH> 
        <PLANE>.</PLANE> 
       </POR> 
       <POR TIME='......'> 
        <PUPIL>.</PUPIL> 
        <BLINK>.</BLINK> 
        <V>...</V> 
        <H>...</H> 
        <PLANEINTRWV>...</PLANEINTRWV> 
        <PLANEINTRWH>...</PLANEINTRWH> 
        <PLANE>.</PLANE> 
       </POR> 
      </seq> 
     </trial> 
     <trial ID='.....'> 
      <HEAD></HEAD> 
      <seq ID=''> 
       <HEAD></HEAD> 
       <calibration CLASS='affine-calibration' ID='New Calibration'> 
        <AX>.........</AX> 
        <BX>-........</BX> 
        <AY>.........</AY> 
        <BY>.........</BY> 
        <type>'por'</type> 
       </calibration> 
       <POR TIME='......'> 
        <PUPIL>.</PUPIL> 
        <BLINK>.</BLINK> 
        <V>...</V> 
        <H>...</H> 
        <PLANEINTRWV>...</PLANEINTRWV> 
        <PLANEINTRWH>...</PLANEINTRWH> 
        <PLANE>.</PLANE> 
       </POR> 
       <POR TIME='......'> 
        <PUPIL>.</PUPIL> 
        <BLINK>.</BLINK> 
        <V>...</V> 
        <H>...</H> 
        <PLANEINTRWV>...</PLANEINTRWV> 
        <PLANEINTRWH>...</PLANEINTRWH> 
        <PLANE>.</PLANE> 
       </POR> 
      </seq> 
     </trial> 
    </block> 
</protocol>

使用XML封装，什么是提取POR标签的儿童和标签的属性，最彻底的方法？

我扔在一起这个kludge工作，但它很慢（由于xpathSApply调用最有可能），并且很难阅读。

trackToDataFrame = function(file) { 
    doc2=xmlParse(file) 
    timeStamps = t(xpathSApply(doc2, '//*[@TIME]', function(x) c(name=xmlName(x), xmlAttrs(x)))) 
    dd2 = xmlToDataFrame(getNodeSet(doc2, "//POR"), colClasses=c(rep("integer", 7))) 
    dd2 = cbind(dd2, timeStamps) 
    dd2 
}

调用数据集上的回报：

PUPIL BLINK V H PLANEINTRWV PLANEINTRWH PLANE name TIME 
1 NA NA NA NA   NA   NA NA POR ...... 
2 NA NA NA NA   NA   NA NA POR ...... 
3 NA NA NA NA   NA   NA NA POR ...... 
4 NA NA NA NA   NA   NA NA POR ...... 
5 NA NA NA NA   NA   NA NA POR ......

我搞清楚整个事情可以用一个xmlToDataFrame调用来完成，但我不是用XML封装以获得足够的熟悉它工作。

我真正感兴趣的是'TIME'列以及从xmlToDataFrame调用中提取的所有列。

来源

2013-05-29 Clayton Stanley

回答

13 
require(XML) 
Fun1 <- function(xdata){ 
    dum <- xmlParse(xdata) 
    xDf <- xmlToDataFrame(nodes = getNodeSet(dum, "//*/POR"), stringsAsFactors = FALSE) 
    xattrs <- xpathSApply(dum, "//*/POR/@TIME") 
    xDf$name <- "POR" 
    xDf$TIME <- xattrs 
    xDf 
} 

Fun2 <-function(xdata){ 
    dumFun <- function(x){ 
    xname <- xmlName(x) 
    xattrs <- xmlAttrs(x) 
    c(sapply(xmlChildren(x), xmlValue), name = xname, xattrs) 
    } 
    dum <- xmlParse(xdata) 
    as.data.frame(t(xpathSApply(dum, "//*/POR", dumFun)), stringsAsFactors = FALSE) 
} 

> identical(Fun1(xdata), Fun2(xdata)) 
[1] TRUE 

library(rbenchmark) 

benchmark(Fun1(xdata), Fun2(xdata)) 

     test replications elapsed relative user.self sys.self user.child 
1 Fun1(xdata)   100 1.047 2.069  1.044  0   0 
2 Fun2(xdata)   100 0.506 1.000  0.504  0   0 
    sys.child 
1   0 
2   0

来源

2013-05-29 03:56:20 user1609452

+1

第二方法的两倍快。 – user1609452

0

user1609452的修改版本：

extractXML <-function(xdata, expr, transpo = T){ 

    # expr should be "//*/Array" 
    # cat("[INFO] - expr is an expression of the path usually something like '//*/Array'.") 
    # cat("\n[INFO] - Use Transpo = F is you do not want to transpose the output. Just try it out.\n\n") 

    dumFun <- function(x){ 
    xname <- xmlName(x) 
    xattrs <- xmlAttrs(x) 
    c(sapply(xmlChildren(x), xmlValue), name = xname, xattrs) 
    } 

    dum <- xmlParse(xdata) 
    listxml <- xpathSApply(dum, expr, dumFun) 

    if(transpo == T) { 
    data <- as.data.table(t(listxml), stringsAsFactors = FALSE) 
    } else { 
    data <- as.data.table(rbind.fill(lapply(listxml,function(y){as.data.frame(y,stringsAsFactors=F)}))) 
    } 

    return(data) 
}

的目标是在这里得到的属性时，有没有儿童（TRANSPO = F），但你想要得到的属性。下面

实施例：

<Arrays> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam1" Type="Image"/> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam2" Type="Image"/> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam1" Type="Image"/> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam2" Type="Image"/> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam1" Type="Image"/> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam2" Type="Image"/> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam1" Type="Image"/> 
    <Array Factor="1.000000" CompressionRate="" CompressionType="" BitsPerPixel="16" Height="515" Width="682" Name="Exp1Cam2" Type="Image" Description=""/> 
</Arrays> 


extractXML(xdata, "//*/Array", T) 

     V1  V2  V3  V4  V5  V6  V7  V8 
1: <list> <list> <list> <list> <list> <list> <list> <list> 

extractXML(xdata, "//*/Array", F) 

    name Factor CompressionRate CompressionType BitsPerPixel Height Width  Name Type Description 
1: Array 1.000000           16 515 682 Exp1Cam1 Image   NA 
2: Array 1.000000           16 515 682 Exp1Cam2 Image   NA 
3: Array 1.000000           16 515 682 Exp1Cam1 Image   NA 
4: Array 1.000000           16 515 682 Exp1Cam2 Image   NA 
5: Array 1.000000           16 515 682 Exp1Cam1 Image   NA 
6: Array 1.000000           16 515 682 Exp1Cam2 Image   NA 
7: Array 1.000000           16 515 682 Exp1Cam1 Image   NA 
8: Array 1.000000           16 515 682 Exp1Cam2 Image

来源

2017-07-01 11:26:52

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