%% ==========================================================
% MASTER_RUNUP.m
% Master script for CIRN video-based run-up processing.
%
% The script:
%   1. Checks for existing GCP and camera solutions
%   2. Generates the rectification grid if required
%   3. Generates image products if required
%   4. Extracts pixel-instrument data if required
%   5. Performs run-up analysis if required
%
% Existing processing products are detected automatically and
% are not regenerated unless the corresponding output is missing.
%
%% ==========================================================

clear
close all
clc

%% Select run
% Specify the experiment/run to process.
runName = "C7a";
% Options:
% "C3"
% "C3a"
% "C7"
% "C7a"
% "C11"
% "C11a"

%% User-configurable paths
%% Root folders
% videoRoot contains one folder per experimental run.
% dataRoot contains calibration files shared between runs.

videoRoot = "PATH_TO_MAIN_VIDEOS";
dataRoot  = "PATH_TO_MAIN_DATA";
scriptFolder = "PATH_TO_FINAL_SCRIPTS";

%% Common calibration files

intrinsicsFile = fullfile(dataRoot,"FORALL_IO.mat");
gcpWorldFile   = fullfile(dataRoot,"GCP Real Cords.txt");

%% Run folder

runFolder = fullfile(videoRoot, runName);

video = dir(fullfile(runFolder,"*.mp4"));
bed = [ ...
    dir(fullfile(runFolder,"*bed*.csv")); ...
    dir(fullfile(runFolder,"*bed*.xlsx")) ...
    ];

if isempty(bed)
    error("No bed file found in %s", runFolder);
end

bedFile = fullfile(bed(1).folder, bed(1).name);
lidar = dir(fullfile(runFolder,"*lidar.*"));

videoFile = fullfile(video.folder,video.name);
lidarFile = fullfile(runFolder, lidar.name);

outputFolder = fullfile(runFolder,"Outputs");

%% Standard folders

framesFolder = fullfile(outputFolder,"Frames");

rectifiedFolder  = fullfile(outputFolder,"Rectified");
instrumentFolder = fullfile(outputFolder,"Instruments");
resultsFolder    = fullfile(outputFolder,"Results");

folders = {framesFolder, rectifiedFolder, instrumentFolder, resultsFolder};

for i = 1:length(folders)
    if ~exist(folders{i},'dir')
        mkdir(folders{i});
    end
end

qcFolder = fullfile(outputFolder,"QC");

if ~exist(qcFolder,'dir')
    mkdir(qcFolder)
end

%% Display

disp("Current run:")
disp(runName)

disp("Video:")
disp(videoFile)

disp("Output:")
disp(outputFolder)

%% Standard filenames

gridFile      = fullfile(runFolder, sprintf("GRID_%s.mat",runName));
pixInstFile   = fullfile(instrumentFolder, sprintf("%s_pixInst.mat",runName));
runupCSV      = fullfile(resultsFolder, sprintf("%s_runup.csv",runName));
metricsCSV    = fullfile(resultsFolder, sprintf("%s_metrics.csv",runName));
ioeoFile = fullfile(outputFolder, runName + "_IOEOInitial.mat");
gridMetaFile = fullfile(rectifiedFolder, ...
    sprintf("%s_gridMeta.mat",runName));
shorelineFile = fullfile(resultsFolder,...
    sprintf("%s_shoreline_timeseries.mat",runName));

%% Required run inputs
%
% Each run folder should contain:
%   - Run video (*.mp4)
%   - Bed/topographic survey (*bed*.csv or *bed*.xlsx)
%   - LiDAR data (*lidar.*)
%
% Shared calibration data are stored in dataRoot.

addpath(scriptFolder)
addpath(genpath(fullfile(scriptFolder,"X_CoreFunctions")))
rehash

% ---------- B ----------

gcpFile = fullfile(outputFolder, runName + "_gcpUVdInitial.mat");

if exist(gcpFile,'file')
    disp("✓ Existing GCP file found.")
else
    disp("No GCP file found - launching GCP selection.")
    run('B_gcpSelection.m')
end

% ---------- C ----------

if exist(ioeoFile,'file')
    disp("✓ Existing IOEO solution found.")
else
    disp("No IOEO solution found - solving camera.")
    run('C_singleExtrinsicSolution.m')
end

% ---------- D ----------
if exist(gridFile,'file')
    disp("Existing grid found.")
else
    run('D_gridGenExampleRect.m')
end


% ---------- G1 ----------
if exist(gridMetaFile,'file')
    disp("✓ Existing image products found.")
else
    disp("Running image products...")
    run('G1_imageProducts.m')
end

% ---------- G2 ----------
% G2 is only rerun if the pixel-instrument MAT file does not
% contain the expected pixInst variable.
needG2 = true;

if exist(pixInstFile,'file')

    try
        vars = who('-file', pixInstFile);

        if any(strcmp(vars,'pixInst'))
            needG2 = false;
            disp("✓ Existing pixel instruments found.")
        else
            disp("Pixel instrument file is incomplete - rebuilding.")
        end

    catch
        disp("Pixel instrument file is corrupted - rebuilding.")
    end

end

if needG2
    disp("Running pixel instruments...")
    run('G2_pixelInstruments.m')
end

% ---------- J: Run-up analysis ----------
% Detect shoreline position, calculate run-up elevation,
% compare with LiDAR, and save run-up/validation products.

if exist(shorelineFile,'file')
    disp("✓ Existing run-up analysis found.")
else
    disp("Running run-up analysis...")
    run('J_runup_variance.m')
end

disp(" ")
disp("===================================")
disp("Processing complete!")
disp("===================================")