Reading values from xml file

I've read around a bit and cant seem to get this to work. I am trying to read out a specific value from stereotyped xml files. The xml files look like this: http://i.imgur.com/uSEQt.png and I am trying to access the second "Frame relativeTime" value from the file for use in a data analysis pack I'm writing. There are many "Frame realtive time" entrees in the xml file but I am just trying to pull the second value and save it as a variable."

Any thoughts?

Thanks

Answer 1

[Pritom Kumar Saha]

Try

S = readstruct("abcd.xml")

it works on my matlab version.

It should work on matlab 2020b or higher version.

[Adam Campos]

Holy moly that just saved me hours and hours of trying to figure this stuff out. Thank you!

[Hongyuan Zhang]

This works pretty well!

Answer 2

[Turlough Hughes]

You can now read XML files in R2021a using readtable (and readtimetable). For example:

filename = 'students.xml';
T = readtable(filename);

You can also select specific variables or attributes to read via detectImportOptions (or XMLImportOptions) - first get the opts and display the variable names:

opts = detectImportOptions(filename);
opts.VariableNames.'

then select the variable names that you want - let's say you want FirstNameAttribute, LastNameAttribute and Age, that would go as follows:

opts.SelectedVariableNames = opts.VariableNames(2:4);
T = readtable(filename,opts)

[Goncalo Gouveia]

simple and easy, worked like a charm

[Catherine]

Agreed, this is exactly what I was looking for. I was getting nowhere with xmlread. Thank you very much.

Answer 3

[Thomas]

Try this from the file exchange. I have found it to be useful

http://www.mathworks.com/matlabcentral/fileexchange/28518-xml2struct

example : here is sample.xml

<?xml version="1.0"?>

   <book id="bk101">
      <author>Gambardella, Matthew</author>
      <title>XML Developer's Guide</title>
      <genre>Computer</genre>
      <price>44.95</price>
      <publish_date>2000-10-01</publish_date>
      <description>An in-depth look at creating applications 
      with XML.</description>
   </book>
   <book id="bk102">
      <author>Ralls, Kim</author>
      <title>Midnight Rain</title>
      <genre>Fantasy</genre>
      <price>5.95</price>
      <publish_date>2000-12-16</publish_date>
      <description>A former architect battles corporate zombies, 
      an evil sorceress, and her own childhood to become queen 
      of the world.</description>
   </book>

If I have to find the price of the second book:

c=xml2struct('sample.xml')  % use function from file exchange 

>> new.catalog.book{1,2}.price

ans = 

      Text: '5.95'

[Chris]

Where does the ".new" come from?

new.catalog.book{1,2}.price

[Chris]

When I enter

c=xml2struct('sample.xml')

I get c =

PVScan: [1x1 struct]

Then when I enter new.PVScan.Sequence.PVStateShard.Frame{1,1}.relativeTime i get

Undefined variable "new" or class "new.PVScan.Sequence.PVStateShard.Frame".

[Thomas]

sorry, it should read new=xml2struct('sample.xml')

and then new.catalog.book{1,2}.price

[Chris]

Used your code: Still getting

Attempt to reference field of non-structure array.

Error in Calcium2Pextended>pushbutton1_Callback (line 96)

test_data.PVScan.Sequence.Frame{1,2}.Attributes.relativeTime

Answer 4

[Image Analyst]

Did you try xmlread()? Can you show your code and maybe upload your xml file and m-file somewhere so people can try something if they want to?

[Chris]

I've tried xmlread(), I can get it to read the file but then I don't know how to access the relativeTime value

[Image Analyst]

Did you try it with the example code they gave? You know, all the "function theStruct = parseXML(filename)" stuff. It's complicated I know but that seems like the way they recommend in the help.

Answer 5

[Chris]

<?xml version="1.0" encoding="utf-8"?>
<PVScan version="4.0.0.53" date="3/23/2012 12:30:30 PM" notes="">
  
    <Lasers>
      <Laser name="Pockels" index="0" />
    </Lasers>
  
  <Sequence type="TSeries Timed Element" cycle="1" xYStageGridDefined="False" xYStageGridNumXPositions="0" xYStageGridNumYPositions="0" xYStageGridOverlapPercentage="10" xYStageGridXOverlap="10" xYStageGridYOverlap="10">
    <Frame relativeTime="0" absoluteTime="9.104738" index="1" label="CurrentSettings">
      <File channel="1" channelName="Ch1" preAmpID="0" filename="slice1_field1_500uA_stimB(+)-001_Cycle001_CurrentSettings_Ch1_000001.tif" />
      <File channel="4" channelName="Spot" preAmpID="0" filename="slice1_field1_500uA_stimB(+)-001_Cycle001_CurrentSettings_Ch4_000001.tif" />
      <ExtraParameters validData="True" />
      
        <Key key="objectiveLens" permissions="Read, Write, Save" value="10X" />
        <Key key="objectiveLensNA" permissions="Read, Write, Save" value="0.3" />
        <Key key="objectiveLensMag" permissions="Read, Write, Save" value="10" />
        <Key key="pixelsPerLine" permissions="Read, Write, Save" value="200" />
        <Key key="linesPerFrame" permissions="Read, Write, Save" value="88" />
        <Key key="systemType" permissions="Write, Save" value="0" />
        <Key key="binningMode" permissions="Read, Write, Save" value="0" />
        <Key key="frameAveraging" permissions="Read, Write, Save" value="0" />
        <Key key="framePeriod" permissions="Read, Write, Save" value="0.191488" />
        <Key key="scanlinePeriod" permissions="Read, Write, Save" value="0.002176" />
        <Key key="dwellTime" permissions="Read, Write, Save" value="8" />
        <Key key="bitDepth" permissions="Read, Write, Save" value="12" />
        <Key key="positionCurrent_XAxis" permissions="Write, Save" value="19401.38671875" />
        <Key key="positionCurrent_YAxis" permissions="Write, Save" value="-20993.3203125" />
        <Key key="positionCurrent_ZAxis" permissions="Write, Save" value="15902.42" />
        <Key key="zDevice" permissions="Write, Save" value="0" />
        <Key key="rotation" permissions="Read, Write, Save" value="20" />
        <Key key="opticalZoom" permissions="Read, Write, Save" value="1" />
        <Key key="micronsPerPixel_XAxis" permissions="Read, Write, Save" value="0.219298245614035" />
        <Key key="micronsPerPixel_YAxis" permissions="Read, Write, Save" value="0.219298245614035" />
        <Key key="pmtGain_0" permissions="Write, Save" value="786.290322580645" />
        <Key key="pmtGain_1" permissions="Write, Save" value="0" />
        <Key key="pmtOffset_0" permissions="Write, Save" value="0" />
        <Key key="pmtOffset_1" permissions="Write, Save" value="0" />
        <Key key="laserPower_0" permissions="Write, Save" value="18" />
        <Key key="laserPowerCalibrated_0" permissions="Write, Save" value="0" />
        <Key key="laserPowerAttenuation_0" permissions="Write, Save" value="0" />
        <Key key="twophotonLaserPower_0" permissions="Write, Save" value="2926.17" />
        <Key key="minVoltage_XAxis" permissions="Write, Save" value="-0.205995077821132" />
        <Key key="minVoltage_YAxis" permissions="Write, Save" value="-0.855391548993729" />
        <Key key="maxVoltage_XAxis" permissions="Write, Save" value="0.722359696628628" />
        <Key key="maxVoltage_YAxis" permissions="Write, Save" value="0.0375257076868368" />
        <Key key="imagingDevice" permissions="Write, Save" value="Ultima" />
      
    </Frame>
    <Frame relativeTime="0.191488" absoluteTime="9.296226" index="2" label="CurrentSettings">
      <File channel="1" channelName="Ch1" preAmpID="0" filename="slice1_field1_500uA_stimB(+)-001_Cycle001_CurrentSettings_Ch1_000002.tif" />
      <File channel="4" channelName="Spot" preAmpID="0" filename="slice1_field1_500uA_stimB(+)-001_Cycle001_CurrentSettings_Ch4_000002.tif" />
      <ExtraParameters validData="True" />
      
        <Key key="objectiveLens" permissions="Read, Write, Save" value="10X" />
        <Key key="objectiveLensNA" permissions="Read, Write, Save" value="0.3" />
        <Key key="objectiveLensMag" permissions="Read, Write, Save" value="10" />
        <Key key="pixelsPerLine" permissions="Read, Write, Save" value="200" />
        <Key key="linesPerFrame" permissions="Read, Write, Save" value="88" />
        <Key key="systemType" permissions="Write, Save" value="0" />
        <Key key="binningMode" permissions="Read, Write, Save" value="0" />
        <Key key="frameAveraging" permissions="Read, Write, Save" value="0" />
        <Key key="framePeriod" permissions="Read, Write, Save" value="0.191488" />
        <Key key="scanlinePeriod" permissions="Read, Write, Save" value="0.002176" />
        <Key key="dwellTime" permissions="Read, Write, Save" value="8" />
        <Key key="bitDepth" permissions="Read, Write, Save" value="12" />
        <Key key="positionCurrent_XAxis" permissions="Write, Save" value="19401.38671875" />
        <Key key="positionCurrent_YAxis" permissions="Write, Save" value="-20993.3203125" />
        <Key key="positionCurrent_ZAxis" permissions="Write, Save" value="15902.42" />
        <Key key="zDevice" permissions="Write, Save" value="0" />
        <Key key="rotation" permissions="Read, Write, Save" value="20" />
        <Key key="opticalZoom" permissions="Read, Write, Save" value="1" />
        <Key key="micronsPerPixel_XAxis" permissions="Read, Write, Save" value="0.219298245614035" />
        <Key key="micronsPerPixel_YAxis" permissions="Read, Write, Save" value="0.219298245614035" />
        <Key key="pmtGain_0" permissions="Write, Save" value="786.290322580645" />
        <Key key="pmtGain_1" permissions="Write, Save" value="0" />
        <Key key="pmtOffset_0" permissions="Write, Save" value="0" />
        <Key key="pmtOffset_1" permissions="Write, Save" value="0" />
        <Key key="laserPower_0" permissions="Write, Save" value="18" />
        <Key key="laserPowerCalibrated_0" permissions="Write, Save" value="0" />
        <Key key="laserPowerAttenuation_0" permissions="Write, Save" value="0" />
        <Key key="twophotonLaserPower_0" permissions="Write, Save" value="2926.17" />
        <Key key="minVoltage_XAxis" permissions="Write, Save" value="-0.205995077821132" />
        <Key key="minVoltage_YAxis" permissions="Write, Save" value="-0.855391548993729" />
        <Key key="maxVoltage_XAxis" permissions="Write, Save" value="0.722359696628628" />
        <Key key="maxVoltage_YAxis" permissions="Write, Save" value="0.0375257076868368" />
        <Key key="imagingDevice" permissions="Write, Save" value="Ultima" />
      
      </Frame>
   </Sequence>
</PVScan>

[Geoff]

Could you please format that as code? Edit, highlight all, hit the '{} code' button, save. Cheers.

[Chris]

Sorry bout that, fixed.

[Thomas]

Chris I saved your xml file as test.xml

>>test_data=xml2struct('test.xml')

to get the second relativeTime

>> test_data.PVScan.Sequence.Frame{1,2}.Attributes.relativeTime

ans =

0.191488

[Chris]

I keep getting this:

test_data =

PVScan: [1x1 struct]

Attempt to reference field of non-structure array.

Here's a link to a full xml file. http://dl.dropbox.com/u/91186/test.xml

Does this still work for you?

[Chris]

I think it may have to do with the 655K filesize. I can get the proper return value when I only include a few frames in the xml file...

[Chris]

Figured it out.

Had to use xpath, but could jump right to the node I wanted without mapping from the file (which was too big). Explanation here http://blogs.mathworks.com/desktop/2010/11/01/xml-and-matlab-navigating-a-tree/

[xmlfilename,pathname]=uigetfile('*.xml');

openxmlfilename = fullfile(pathname,xmlfilename);

xDoc=xmlread(openxmlfilename)

import javax.xml.xpath.*

factory = XPathFactory.newInstance;

xpath = factory.newXPath;

expression = xpath.compile('PVScan/Sequence/Frame[2]/@relativeTime');

relativeTime = expression.evaluate(xDoc, XPathConstants.NUMBER)

Answer 6

[Jeffrey Warner]

Hello,

I am trying to read this xml file to return the current filter position (<FilterPosition>) which is 4, and the Position name and position ID under the <Position Defined> node. I have not dealt with xm; files before. I tried xmlread and that returned a null result. Any healp is greatly appreciated.

DOMnode = xmlread(flName).

DOMnode = [#document: null]

I could not upload the xml file. Here is the contents of the file.

<FW102CProfileModel xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" Pcount="6">

<SpeedMode>HighSpeed</SpeedMode>

<TriggerMode>Input</TriggerMode>

<SensorMode>TurnOff</SensorMode>

<FilterPosition>4</FilterPosition>

<PositionDefined>

<FW102CFilterConfigMode>

<PositionName>OD0</PositionName>

<PositionID>1</PositionID>

</FW102CFilterConfigMode>

<FW102CFilterConfigMode>

<PositionName>OD0.2 (5232)</PositionName>

<PositionID>2</PositionID>

</FW102CFilterConfigMode>

<FW102CFilterConfigMode>

<PositionName>OD0.5 (5235)</PositionName>

<PositionID>3</PositionID>

</FW102CFilterConfigMode>

<FW102CFilterConfigMode>

<PositionName>OD1 (5240)</PositionName>

<PositionID>4</PositionID>

</FW102CFilterConfigMode>

<FW102CFilterConfigMode>

<PositionName>OD2 (5242)</PositionName>

<PositionID>5</PositionID>

</FW102CFilterConfigMode>

<FW102CFilterConfigMode>

<PositionName>OD2.5 (5243)</PositionName>

<PositionID>6</PositionID>

</FW102CFilterConfigMode>

</PositionDefined>

<SequenceDefined/>

</FW102CProfileModel>