read_data.m

function [DATA, DATA_el, REFPRN] = read_data(offsetyear, offsetdoy, in_path_offset, ...
    doy, year, folder_path, op_path, sep, signal_type, signal)
%% scint
%Read and combine scint files
if strcmp(folder_path(end-7:end-1), 'ASTRArx') || strcmp(folder_path(end-16:end-10), 'ASTRArx')
    %     keyboard;
    scintfilestruct = dir([folder_path, 'txt', sep, 'scint*.log']);
    scintfilestruct0 = [];
else
    scintfilestruct = dir([folder_path, 'txt', sep, 'scint*', year, '_', doy, '_*.log']);
    scintfilestruct0 = dir([in_path_offset, 'txt', sep, 'scint*', offsetyear, '_', offsetdoy, '_*.log']);
end

if ~isempty(scintfilestruct0)
    scintfilename0 = dlmread([in_path_offset, 'txt', sep, scintfilestruct0(end).name]);
    [in_path_offset, 'txt', sep, scintfilestruct0(end).name]
else
    scintfilename0 = [];
end

if ~isempty(scintfilestruct)
    SCINT = [];
    for jj = 1:size(scintfilestruct, 1)
        scintfile = scintfilestruct(jj, :);
        scintfilename = dlmread(strcat([folder_path, 'txt', sep, scintfile.name]));
        %         st = datestr(gps2utc(scintfilename(1,1:2)),'HHMM-');
        %         se = datestr(gps2utc(scintfilename(end,1:2)),'HHMM UT');
        %         disp([scintfile.name,' actually has data for ',st,se]);
        SCINT = [SCINT; scintfilename];
    end
    SCINT = [SCINT; scintfilename0];
    
    size(find(SCINT(:, 1) > 3640));
    SCINT = SCINT(SCINT(:, 1) <= 3640, :);
    size(find(SCINT(:, 1) > 3640));
    SCINT = sortrows(SCINT, [1, 2, 3]);
    %output scintdata for the whole day
    scfile = SCINT;
    
    %Specify signal type
    SCINT = SCINT((SCINT(:, 14) == signal_type), :);
    %Remove invalid entries
    SCINT = SCINT((SCINT(:, 8) < 1) & SCINT(:, 8) > -1 & SCINT(:, 5) > -1, :);
    REFPRN = unique(SCINT((SCINT(:, 13) == 1 | SCINT(:, 13) == 2), 15));
    %Gather data
    ORTW = SCINT(:, 1);
    ORTS = SCINT(:, 2) + SCINT(:, 3);
    S4 = SCINT(:, 5);
    SIGMAPHI = SCINT(:, 8);
    TAU0 = SCINT(:, 11);
    
    % SIGMAPHI = SCINT(:,8);
    PRN = SCINT(:, 15);
    
    DATA = [ORTW, ORTS, SIGMAPHI, PRN, S4, TAU0];
    %     gps2utc(DATA(1:10   ,1:2))
    %     keyboard;
    % DATA = sortrows(DATA,4);
else
    DATA = [];
    REFPRN = [];
    scfile = [];
end
outfilename = strcat('prn_files_', signal, sep, 'scintdata.mat');
command = strcat('mkdir -p ', [' ', op_path, 'prn_files_', signal, sep]);
system(command);
save([op_path, outfilename], 'DATA', 'scfile');
% keyboard;

%% txinfo
%Read and combine txinfo files
if strcmp(folder_path(end-7:end-1), 'ASTRArx') || strcmp(folder_path(end-16:end-10), 'ASTRArx')
    azelfilestruct = dir([folder_path, 'txt', sep, 'txinfo*.log']);
    azelfilestruct0 = [];
else
    azelfilestruct = dir([folder_path, 'txt', sep, 'txinfo*', year, '_', doy, '_*.log']);
    azelfilestruct0 = dir([in_path_offset, 'txt', sep, 'txinfo*', offsetyear, '_', offsetdoy, '_*.log']);
end

if ~isempty(azelfilestruct0)
    azelfilename0 = dlmread([in_path_offset, 'txt', sep, azelfilestruct0(end).name]);
    [in_path_offset, 'txt', sep, azelfilestruct0(end).name]
else
    azelfilename0 = [];
end

if ~isempty(azelfilestruct)
    AZEL = [];
    for jj = 1:size(azelfilestruct, 1)
        azelfile = azelfilestruct(jj, :);
        azelfilename = dlmread(strcat([folder_path, 'txt', sep, azelfile.name]));
        st = datestr(gps2utc(azelfilename(1, 1:2)), 'HHMM-');
        se = datestr(gps2utc(azelfilename(end, 1:2)), 'HHMM UT');
        %         disp([azelfile.name,' actually has data for ',st,se]);
        AZEL = [AZEL; azelfilename];
    end
    AZEL = [AZEL; azelfilename0];
    
    size(find(AZEL(:, 1) > 3640))
    AZEL = AZEL(AZEL(:, 1) <= 3640, :);
    size(find(AZEL(:, 1) > 3640))
    AZEL = sortrows(AZEL, [1, 2, 3]);
    %Remove invalid entries
    AZEL = AZEL((AZEL(:, 5) > 0), :);
    AZEL_old = AZEL;
    %Low elevation threshold;
    AZEL_low = AZEL(AZEL(:, 5) > 30, :);
    % AZEL_low = sortrows(AZEL_low,8);
    
    %Gather data
    ORTW_EL = AZEL(:, 1);
    ORTS_EL = AZEL(:, 2) + AZEL(:, 3);
    AZ = AZEL(:, 4);
    EL = AZEL(:, 5);
    PRN_EL = AZEL(:, 8);
    
    DATA_el = [ORTW_EL, ORTS_EL, EL, PRN_EL, AZ];
    % DATA = sortrows(DATA,4);
else
    DATA_el = [];
end
outfilename = strcat('prn_files_', signal, sep, 'txinfodata.mat');
command = strcat('mkdir -p ', [' ', op_path, 'prn_files_', signal, sep]);
system(command);
save([op_path, outfilename], 'DATA_el');

end