%Mat file generation of intensity data for use in statistical analysis

%Author: Jordan Rolsma - University of California, Riverside

%Features:

    %Designed to work with data generated from
    %example_NucCytSeg_IntQuant_v1_JLR_20240130.m.

    %Cleans up, clarifies, and consolidates data (removes NaNs, calculates
    %averages for use in statistical analysis, etc.)

%Housekeeping    
clearvars
close all
clc

%Loads raw mat file
load 20231026_ASC_GFP_MitoLocal_MAHS_T4_DAPI_GFP_Phalloidin554_MitoView640_TS6x6_20x_JLR_data.mat

%Specifies file length
lengthtotal = length(intDataCyt);

%Extracts number of reported values in each tilescan micrograph image
for i = 1:lengthtotal
    %remove NaNs from consideration
    intDataCyt{i,1} = rmmissing(intDataCyt{i,1});
    intDataNuc{i,1} = rmmissing(intDataNuc{i,1});
    intDataRat{i,1} = rmmissing(intDataRat{i,1});

    %number of reported values minus NaNs
    nummeasure_cyt{i,1} = height(intDataCyt{i,1});
    nummeasure_nuc{i,1} = height(intDataNuc{i,1});
    nummeasure_rat{i,1} = height(intDataRat{i,1});
end

%Calculates average value for each image
for i = 1:lengthtotal
    sum_cyt{i,1} = sum(intDataCyt{i,1});
    sum_nuc{i,1} = sum(intDataNuc{i,1});
    sum_rat{i,1} = sum(intDataRat{i,1});

    avgval_cyt{i,1} = sum_cyt{i,1}/nummeasure_cyt{i,1};
    avgval_nuc{i,1} = sum_nuc{i,1}/nummeasure_nuc{i,1};
    avgval_rat{i,1} = sum_rat{i,1}/nummeasure_rat{i,1};
end

%Calculates total average cyt, nuc, and int rates for entire lif file
for i = 1:lengthtotal
    totalavg_cyt = mean(avgval_cyt{i,1});
    totalavg_nuc = mean(avgval_nuc{i,1});
    totalavg_rat = mean(avgval_rat{i,1});
end

%Clear unneeded variables
clear avgval_cyt avgval_nuc avgval_rat i intDataCyt intDataNuc intDataRat...
    lengthtotal nummeasure_cyt nummeasure_nuc nummeasure_rat Sname sum_cyt...
    sum_nuc sum_rat 

%Save new mat file
save(sprintf('20231026_ASC_GFP_MitoLocal_MAHS_T4_IntQuant_JLR_data_final.mat'))