SCOTS-ComplexGeometry/main.m at main · nidlu/SCOTS-ComplexGeometry · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SCOTS for Deployable Telescopes
% Author: Carl Johan G Nielsen
% Université Libre de Bruxelles 2023
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%todo: flip phase imaging
%C:\Users\cjgn44\Google Drive\ULB\SCOTS-ComplexGeometry\data\06_06_2023_tipDisplacement1\tipDisplacement1\tipDisplacementPetal_RoC2.5_50um.stl

%% Paths and Imports
clc;clearvars;close all;
import matlab.net.*
import matlab.net.http.*
addpath("SCOTS");
addpath('SCOTS/natsortfiles');  %%% Externally developed dependencies
addpath("SCOTS/normal_integration-master/Toolbox");
addpath("SCOTS/phase_unwrap");  %
addpath('SCOTS/zernike');       %
addpath('SCOTS/ZWOASI');        %%%
addpath('SCOTS/Inpaint_nans');
addpath('SCOTS/zernikeExpansion');%
%% Load parameters
[geom, aqPar] = loadParamsFromJSON('parameters.json');
load('cameraParams_ASI120_T1.mat'); %%load camera calibration data
%% Flags
aqPar.applyCameraCompensation = 0;
testNames{1} = 'data/25_06_2023_tip_coarse_100um_tolerance/2mmCamZ';
zerophase = 0;
acquire = 1;
integrate = 1;
aqPar.isPetal = 1;
%% Compute global variables
aqPar.phases = 0:2*pi/4:2*pi; %0:2*pi/16:2*pi*2
%aqPar.phases = [0, pi/2, pi, 3*pi/2];
%n = 20;
%aqPar.phases = linspace(0, 2*pi, n) + rand(1,n)*0.3;  % slight random spacing
%aqPar.phases(1) = 0;
aqPar.canvasPosition_px = [2800 -170 aqPar.canvasSize_px aqPar.canvasSize_px]; %screen phase window position
aqPar.imageMirrorCenterX_px = 154;%358; %px, Location of the mirror in CAM image
aqPar.imageMirrorCenterY_px = 97; %top left, down right positive.
aqPar.measurementRadius_px = round(aqPar.measurementRadius_mm/aqPar.image_mm_per_px); %px, Masking radius of the mirror in CAM image, max
aqPar.innerRadius_px =  round(aqPar.innerRadius_mm/aqPar.image_mm_per_px);
aqPar.petalStartRadius_px = round(aqPar.petalStartRadius_mm / aqPar.image_mm_per_px);
aqPar.gapWidth_px = round(aqPar.gapWidth_mm / aqPar.image_mm_per_px);
aqPar.center = [aqPar.imageMirrorCenterX_px, aqPar.imageMirrorCenterY_px];
aqPar.imageSizeX = aqPar.rawImageSizeX*aqPar.imageResizingFactor;
aqPar.imageSizeY = aqPar.rawImageSizeY*aqPar.imageResizingFactor;

% Petal mask
if(aqPar.isPetal)
    aqPar.mask = petalMask(aqPar.measurementRadius_px, aqPar.innerRadius_px, aqPar.petalStartRadius_px,...
        aqPar.center, aqPar.gapWidth_px, aqPar.nb_petals, aqPar.imageSizeX, aqPar.imageSizeY);
else
    aqPar.mask = petalMask(aqPar.measurementRadius_px, 0, 0, aqPar.center, 0, 1,...
        aqPar.imageSizeX, aqPar.imageSizeY);
end

% Create mirror coordinate system from px to mm
x = 1:aqPar.imageSizeX;
y = 1:aqPar.imageSizeY;
[aqPar.mirrorX_px_, aqPar.mirrorY_px_] = meshgrid(x, y);
aqPar.mirrorX_px_ = aqPar.mirrorX_px_ - aqPar.center(1);
aqPar.mirrorY_px_ = aqPar.mirrorY_px_ - aqPar.center(2);
aqPar.mirrorX_mm_ = aqPar.mirrorX_px_.*aqPar.image_mm_per_px;
aqPar.mirrorY_mm_ = -aqPar.mirrorY_px_.*aqPar.image_mm_per_px;

if(zerophase); showZeroPhase(aqPar); pause; end

for i = 1:length(testNames)
    aqPar.testName=testNames{i};
    mkdir(aqPar.testName);
    mkdir([aqPar.testName '/images']);mkdir([aqPar.testName '/imagesVirtual']);
    mkdir([aqPar.testName '/darkSubtracted']); mkdir([aqPar.testName '/postprocessing']);

    if(acquire)
        %[cam.CameraNumber,cam.OutputValue,cam.Sizes] = cameraSetup();
        %imageZeroPhase(aqPar,cam,cameraParams);
        %imageDark(aqPar,cam,cameraParams);
        %showImagedArea(aqPar);
        %imagePhases(aqPar,cam,cameraParams);
        %closeCameras(cam.CameraNumber)
        %makeSTLSphereWithAstigmatism(geom, aqPar, 0, [aqPar.testName '/postprocessing/w0.stl'],'parabolic'); %
        rayTrace([aqPar.testName '/postprocessing/w0.stl'], [aqPar.testName '/imagesVirtual/imageZeroPhase.png'], 0, 'zerophase');
        imageVirtualPhases(aqPar);
    end
    if(integrate)
        %darkSubtract(aqPar);
        [deltaX, deltaY, centX0, centY0, ~, ~] = computeZeroPhaseLoc(aqPar, [aqPar.testName '/imagesVirtual/imageZeroPhase.png']);%[aqPar.testName '/darkSubtracted/ds_imageZeroPhase.png']
        %centX0 = aqPar.imageMirrorCenterX_px;
        %centY0 = aqPar.imageMirrorCenterY_px;
        %computePhaseMap(aqPar,[aqPar.testName '/darkSubtracted'],[aqPar.testName '/postprocessing']);
        computePhaseMap(aqPar,[aqPar.testName '/imagesVirtual'],[aqPar.testName '/postprocessing']);
        %plotPhaseMap(aqPar);
        unwrapPhaseMap(aqPar);
        computeSlope(aqPar,geom,centX0,centY0);
        plotSlopes(aqPar);
        integrateShape(aqPar);
        shapeAnalysis(aqPar);
        %exportSTL(aqPar);
        %phaseOffset = pi;
        %rayTrace([aqPar.testName '/postprocessing/w0.stl'],[aqPar.testName '/postprocessing/rayTrace.png'],...
        %    phaseOffset,'horizontal'); %only call if you have WSL and raySect installed
        %plotOverlayImages([aqPar.testName '/postprocessing/rayTrace.png'],...
        %                  [aqPar.testName '/images/imagePhaseH0.0000.png']);
    end
end


%       disp('Acquisition complete, press to continue');
%       beep;
        %pause;