Question about accessing data in a nested struct

Hi all,

I am trying to get data from an xml file using xml2struct. Calling the struct using dot notation such as

Settings.CAFConfigurationSettings.numberOfTestPieces.Text

doesn't seem to work. Currently, I am calling on the data using the syntax

Settings.Children(20).Children.Data

where Dataset is my structure and x, y and z are integers referring to the index position within the nested structure. The problem is that sometimes the xml structure stores the same information in different positions meaning x, y and z will be different for these. For example, the "date" field might be the 3rd index (x=3) in one file, or the 2nd index (x=2) in another.

Is there a way to navigate around this please? I need to have a consistent way to gather this data because I loop through several xml files, so I need to get the same, consistent information from all the files with certainty.

I have tried to use "find" but to no avail. a sample of the files can be found here: https://www.dropbox.com/sh/ed5uv80s272mh4t/AAA1hROx8LvVeALHpqtTuSiGa?dl=0.

Thank you in advance

The code:

Accessing the data
close all
clear all
clc
%Asking the user to select the folder with the Images and Auto analysis in
startingFolder = pwd;               
fprintf('Select the directory containing the Images and Auto analysis \n \n');
RawImages = uigetdir(startingFolder); %Creating the variable from the user selection
addpath(RawImages); %Ensuring matlab will follow the path
files           = dir([RawImages '\AutoAnalysis\*.xml']);
numOfFiles      = numel(files); %Counting number of files in the folder for looping purposes
Settings        = xml2struct([RawImages '\settings.xml']); %Converting XML to structure then accessing the number of the samples from the Settings file
NumOfSamples    = str2double(Settings.Children(20).Children.Data);
headings = {'Time','Temperature','Height','Area','Circumference', 'Shape Factor', 'Tip Radius', 'Base Width', 'Max Width', 'Height:Base Width Ratio', 'Height:Max Width Ratio', 'Bse Centre X', 'Base Centre Y', 'LHS Difference', 'RHS Difference'};
objectRangeEnd = strcat('O', num2str(numOfFiles));
objectRange = strcat('A2:', objectRangeEnd);
for j = 1:NumOfSamples %Getting the manually named test pieces from the settings
        
    TestPieceName = Settings.Children(22).Children((2*j)).Children(4).Children.Data; %Creating a name variable to use when making file and folder names
    Sample = ['Test Piece ' num2str(j) '-' TestPieceName]; 
    TestPiece = zeros(numOfFiles,3); %Making an array to store the variables
    for k = 1:numOfFiles %Grabbing the time and file data from the save file name
        
        flds    = {'date','bytes','isdir','datenum'}; %Reading time and temp from file
        A       = rmfield(files,flds); %Remove the file information that is unnecessary 
        codes   = struct2cell(A); %Reduces the structure to only the fields required
        codes   = codes'; %Converts the labels in A to the format required
        new         = strsplit(char(codes(k)),'.'); % To remove the file type
        new2        = strsplit(char(new(1)),'-'); % Splits the experimental conditions
        time        = str2double(new2(2));
        alpha       = new2(3);
        alpha       = char(alpha);
        alpha(1)    = [];
        temp        = str2double(alpha);
        TestPiece(k,1) = time;
        TestPiece(k,2) = temp;
        
        file = [ RawImages '\AutoAnalysis\' files(k).name]; % Creating the k-th file name
        DataSet = xml2struct(file); % Converting XML files to structures 
        datasetNum= numel(DataSet.Children);         
       
        testPieceLocation = datasetNum - NumOfSamples + j; %Indexing Height, Area, and Circumference etc.
               
        TestPiece(k,3) = str2double(DataSet.Children(testPieceLocation).Children(end).Children('height').Children.Data); %Height
        TestPiece(k,4) = str2double(DataSet.Children(testPieceLocation).Children(end).Children().Children.Data); %Area
        TestPiece(k,5) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(find('circumference')).Children.Data); %Circumference
        TestPiece(k,6) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(find('shapeFactor')).Children.Data); %Shape Factor
        TestPiece(k,7) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(find('tipRadius')).Children.Data); %Tip Radius
        TestPiece(k,8) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(5).Children.Data); %Base width
        TestPiece(k,9) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(6).Children.Data); %Max Width
        TestPiece(k,10) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(find('hBwRatio')).Children.Data); %hBw Ratio
        TestPiece(k,11) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(find('hMwRatio')).Children.Data); %hMw Ratio
        TestPiece(k,12) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(1).Children.Data); %Base Centre X
        TestPiece(k,13) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(2).Children.Data); %Base Centre Y
        TestPiece(k,14) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(3).Children.Data); %LHS Diff
        TestPiece(k,15) = str2double(DataSet.Children(testPieceLocation).Children(end).Children(4).Children.Data); %RHS Diff
        
        initialheight  = TestPiece(1,3);
        initialarea    = TestPiece(1,4);
        initialcirc    = TestPiece(1,5);
        initialSFactor = TestPiece(1,6);
        initialTRad    = TestPiece(1,7);
        initialBW      = TestPiece(1,8);
        initialMWidth  = TestPiece(1,9);
        initialHBW     = TestPiece(1,10);
        initialHMW     = TestPiece(1,11);
        initialBaseCX  = TestPiece(1,12);
        initialBaseCY  = TestPiece(1,13);
        initialLHSDiff = TestPiece(1,14);
        initialRHSDiff = TestPiece(1,15);
        
        TestPiece(k,3) = TestPiece(k,3)/initialheight;
        TestPiece(k,4) = TestPiece(k,4)/initialarea;
        TestPiece(k,5) = TestPiece(k,5)/initialcirc;     
        TestPiece(k,6) = TestPiece(k,6)/initialSFactor;  
        TestPiece(k,7) = TestPiece(k,7)/initialTRad;
        TestPiece(k,8) = TestPiece(k,8)/initialBW;
        TestPiece(k,9) = TestPiece(k,9)/initialMWidth;
        TestPiece(k,10) = TestPiece(k,10)/initialHBW;
        TestPiece(k,11) = TestPiece(k,11)/initialHMW;
        TestPiece(k,12) = TestPiece(k,12)/initialBaseCX;
        TestPiece(k,13) = TestPiece(k,13)/initialBaseCY;
        TestPiece(k,14) = TestPiece(k,14)/initialLHSDiff;
        TestPiece(k,15) = TestPiece(k,15)/initialRHSDiff;
    end
        
    sampleDirectory = fullfile(RawImages); %file creation
    filename = fullfile(sampleDirectory, ['Results.xls']); %Creating the filename to put the excel file in the appropriate folder
    writecell(headings, filename, 'Sheet', Sample, 'Range', 'A1:O1');
    writematrix(TestPiece, filename, 'Sheet', Sample, 'Range', objectRange);
    
end

[per isakson]

In the identical question, which you deleted, I proposed that you should try xml_read in xml_io_tools by Jaroslaw Tuszynski. xml2struct produces an overly complicated structure. There are more than one xml2struct around. I assumed that you use the one in the demo-folder of the "bioinfo" toolbox. You never confirmed.

[Teshan Rezel]

hi @per isakson, I tried it but again I got an error that dot indexing wasn't allowed...I tried working with the "find" function too but to no avail. I'm sure I'm doing something wrong but I'm not sure what.

path = 'mypath...\settings.xml';
settings = xml_read(path);
numTestPieces = settings.activeTestPiece;

[Teshan Rezel]

nevermind @per isakson, I was being stupid! thank you for your help, it's worked! can you type an answer please so I can accept yours?

Answer 1

[per isakson]

It is impossible (for me) to help based on the little information that you provide. Here (R2018b) it works fine.

>> sas = xml_read( '..\settings.xml') % the xml-file is in the parent folder 
sas = 
  struct with fields:
                    version: '1.3.6213.31983'
                       date: '2020-03-18T13:44:48.0887698+00:00'
          testStandardIndex: 'CoalAsh'
    startCaptureTemperature: 400
      endCaptureTemperature: 1550
            temperatureRamp: 7
        temperatureInterval: 1
         standbyTemperature: 30
    backlightOffTemperature: 710
         numberOfTestPieces: 6
                  testPiece: [1×1 struct]
                        cal: [1×1 struct]
          gridDisplayEnable: 1
            activeTestPiece: 1
                  ATTRIBUTE: [1×1 struct]
>> sas.activeTestPiece
ans =
     1

where xml_read is part of xml_io_tools by Jaroslaw Tuszynski.

I propose that you use XML Notepad (free, Windows) to inspect the structure of the xml-files. Be sure not to reference non-existing fields.