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  • PcInfection_test4.m 7.50 KiB
    % Developed by ASA Salgadoe (asalgado@myune.edu.au, surantha_a@yahoo.com)
    % on 29/10/2019
    % new test of choosing wl that can classify the healthy and control
    %  PLSR (diamention REduction) + LDA or QDA for classification
    % ############################################
    
    
    load('allDAI.mat');
    % col1: week, col2:trt , col3 onwards:spectral
    % for Pc infected
    wls=allDAI(1,3:end);
    dataSet=allDAI(2:end,:);
    cat=dataSet(:,1:2);
    
    % remove first few spectra (for noise removal)
    % subset the wl 400 onwards
    loc400=find(wls==400);
    wls=wls(:,loc400:end);
    
    % All sampled data col1-treeId, col2-group, col3 onwards-bands
    % RAW spectra
    spec=dataSet(:,3:end);
    spec=spec(:,loc400:end);
    dataClean=[cat,spec];
    dataClean=sortrows(dataClean,1);
    
    % % % 1st method analyse as helathy vs dis groups
    % % % 2nd method analyse as healthy vs dis per each week 
    
    % % for 1st method
    % grp_trt=dataSet(:,2:end);
    % grp_trt=sortrows(grp_trt,1);
    
    % for 2nd method
    % DAI codes 1,2,3,4,5,6,7 
    grp_trt=dataClean(find(dataSet(:,1)==7),2:end);
    grp_trt=sortrows(grp_trt,1);
    
    % % % % % for water stressed#############
    % % % % load('glassH_WS_26_9_2017_s3.mat')
    % % % % dataWS=glassH_WS_26_9_2017_s3;
    % % % % wls=dataWS(1,3:end);
    % % % % dataSetW=dataWS(2:end,:);
    % % % % catW=dataSetW(:,2);
    % % % % 
    % % % % % remove first few spectra (for noise removal)
    % % % % % subset the wl 400 onwards
    % % % % loc400=find(wls==400);
    % % % % wls=wls(:,loc400:end);
    % % % % 
    % % % % % All sampled data col1-treeId, col2-group, col3 onwards-bands
    % % % % % RAW spectra
    % % % % specW=dataSetW(:,3:end);
    % % % % specW=specW(:,loc400:end);
    % % % % dataCleanW=[catW,specW];
    % % % % dataCleanW=sortrows(dataCleanW,1);
    
    % % % % grp_trt=dataCleanW;
    % % % % grp_trt=sortrows(grp_trt,1);
    
    % #####################################
    
    
    
    % asignment of X and Y
    x=grp_trt(:,2:end); %spectra
    y=grp_trt(:,1);%categories