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%% SWING
% An emulator for finely adjusting etch depths during the course of ion
% beam etching

%%
% *initialization*
close all; clear all; clc

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


%% Generate the etch-depth map
% Generate etch-depth map based on the following code:
%
%   [f,x,y] = rsgeng2D (N,rL,h,clx,cly)
%
% * DESCRIPTION: Random rough surface generator of two-dimensional (isotropic and non-isotropic) square surfaces with Gaussian hdf and Gaussian acf.
% * INPUT: N-number of surface points, rL-length of surface side, h-rms height, clx-correlation length in x, cly-correlation length in y
% * OUTPUT: f-surface heights, x-surface points, y-surface points
%
% Credit: <http://www.mysimlabs.com/surface_generation.html>
%
% Source code: <matlab:edit('rsgeng2D.m') rsgeng2D.m>
% 
% Example:

% [z, x, y] = rsgeng2D(400,40,0.4,20,12);
% 
% r_z = 0.1;
% z_targ = 20;
% z_max = max(z(:));
% z_min = min(z(:));
% 
% depth = z_targ * (1 - r_z/(z_max-z_min)*(z_max-z));
% 
% figure, mesh(x, y, depth)
% titleStr = sprintf('max: %d, min %d', max(depth(:)), min(depth(:)));
% title(titleStr)
% 
% save('data/ETCH_DEPTH.mat', 'depth') % save the matrix that contains designed etch depth

load('data/ETCH_DEPTH.mat', 'depth') % load designed etch depth map

figure, mesh(depth)
titleStr = sprintf('max: %d, min %d', max(depth(:)), min(depth(:)));
title(titleStr)


%% Raster scanning over the etch-depth map
% Transform the etch-depth map into the rastered etch-depth map using the
% raster scanning algorithm.
%
%   [r, dwellTime, strokeTime, maxTunableRatio, strkSet] = rascan(depth, nTiers, ionBeamWidth, leafWidth, etchRate, showImage);
%
% Source code: <matlab:edit('rascan.m') rascan.m>, <matlab:edit('rascanOpt.m') rascanOpt.m>


%%
% * *parameters optimization*

% load data/ETCH_DEPTH.mat % load etch-depth map

leafWidth = 60; % mm
etchRate = 0.75; % provided that mean etch rate is 0.75 nm/s

N = [2 4 6]; % list of number of tiers
W = [12 36 60]; % ion beam widths

% call the script for parameters optimization
useDefaultSettings = false; rascanOpt


%%
% * *run raster scanning (including calculation of dwell times)*
%
% # Layering: The scanning path is divided into a number of directional 
% line segments or vectors.
% # Reducing: The two-dimension ribbons is reduced into one-dimension 
% ribbons by averaging the data of ribbons along the minor axis.
% # Superposing: All the layers are superposed via point-to-point mapping 
% and then the rastered etch depth map is stacked up.
% # Calculation of dwell times

x1 = 0.5:399.5; % mm, 400 points in total
y1 = 0.5:399.5; % mm
z1 = depth; % in nm

figure('Name','etch depth map (mesh)')
mesh(x1, y1, z1)
axis ij
view([-32.5000, 75.0000])

nTiers = 2; % the number of tiers should be even, such as 2, 4, 6 ...
ionBeamWidth = 36; % mm
showImage = true;

[r, dwellTime, strokeTime, maxEtchDepthContrast, strkSet] = rascan(depth, nTiers, ionBeamWidth, leafWidth, etchRate, showImage);

% fileName = sprintf('data/DWELL_TIME_%d_%d_%0.6f.mat', nTiers, ionBeamWidth, now);
% save(fileName, 'dwellTime', 'strokeTime', 'maxEtchDepthContrast', 'strkSet')
% disp(['... saved as ' fileName])


%%
% * *Considering the non-uniformity of etch rate*
% Simulation of the ion beam current density distribution
%
%   [exErrMap, errMap, mus] = beamdist(nMajor, nMinor, nMajorRands, nMinorSamps, lambda, nsig)
%
% Source code: <matlab:edit('beamdist.m') beamdist.m>, <matlab:edit('beamdistRun.m') beamdistRun.m>

vStroke = 460; % vertical stroke (mm)
% ionBeamWidth = 36; % mm
nMajorRands = 12;
nMinorSamps = 8;
lambda = 8/100; % +/-4% deviations
nSig = 0.6 * ionBeamWidth/60;

% call the script for generating the ion beam current density distribution
useDefaultSettings = false; beamdistRun

k_e = 0.6157; % etch rate over ion current density
etchRateVector =  etchRate + k_e * (yy - mean(yy)); % yy is the ion current density
[r, dwellTime, strokeTime, maxEtchDepthContrast, strkSet] = rascan(depth, nTiers, ionBeamWidth, leafWidth, etchRateVector, showImage);

% fileName = sprintf('data/_DWELL_TIME_%d_%d_%0.6f.mat', nTiers, ionBeamWidth, now);
% save(fileName, 'dwellTime', 'strokeTime', 'maxEtchDepthContrast', 'strkSet')
% disp(['... saved as ' fileName])


%% Trajectory optimization using pattern search
%
% See <readme1.html trajectory optimization> in a new page.


%% Generate data table for PLC
%
% Generate the data table containing pulse frequencies and pulse numbers.
%
%   [pulseFreqs, pulseNums, nRamps, crtSteps] = dataopt(wa, wd, wf, w1, w2, crt, strokeTime);
%
% Source code: <matlab:edit('dataopt.m') dataopt.m>, <matlab:edit('dataoptRun.m') dataoptRun.m>

% load stroke time
latestDwellFile = selatest('data', 'DWELL_TIME_*.mat');
load(latestDwellFile, 'strokeTime');

% load optimization results
latestOptFile = selatest('data', 'OPT_RESULT_*.mat');
load(latestOptFile, 'C', 'params');

% call the script for generating the data table
useDefaultSettings = false; dataoptRun

% save results
fileName = ['data/DATA_TABLE_' num2str(now, 12) '.mat'];
save(fileName, 'DataTable', 'DataTable2');
disp(['... saved as ' fileName])


%%
% convert data table into CSV format
% See <matlab:edit('data2csvTest.m') data2csvTest.m> for details.

data2csvTest


%% Error model for feasibility analysis
%
% Evaluate the errors introduced by all the processes
%
% outDwellTime = data2dwell(strokeTime, strkSet, C, DataTable, leafWidth,
% stepAngleDeg, timeStep);
%
% outEtchDepth = dwell2depth(strkSet, inDwellTime, strokeTime, etchRate,
% ionBeamWidth);
%
% Source code: 
% <matlab:edit('errormodelRun.m') errormodelRun.m>, 
% <matlab:edit('data2dwell.m') data2dwell.m>,
% <matlab:edit('dwell2depth.m') dwell2depth.m>


% load caculated data
% load('data/ETCH_DEPTH.mat', 'depth');
load(selatest('data', 'DWELL_TIME_*.mat'), 'strokeTime',  'strkSet', 'dwellTime');
load(selatest('data', 'OPT_RESULT_*.mat'), 'C', 'optDwellTime', 'rmsds');
load(selatest('data', 'DATA_TABLE_*.mat'), 'DataTable');

% leafWidth = 60; % 60 mm
stepAngleDeg = 1.8 / 8;
timeStep = 0.001; % 1 ms

% ionBeamWidth = 36; % mm
% etchRate = 0.75;

% call the script for the feasibility analysis
useDefaultSettings = false; errormodelRun

% considering the non-uniformity of etch rate
etchRate = etchRateVector';
% call the script for the feasibility analysis
useDefaultSettings = false; errormodelRun