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updates ff_hedm_postprocess_PlotSpots.m
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migrated to ff_hedm_postprocess_PlotSpots2.m
ff_hedm_postprocess_PlotSpots.m is now deprecated.
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@junspark
junspark committed Sep 1, 2021
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clear all
close all
clc

addpath(genpath('/home/beams/PARKJS/matlab/matlab_tools'));
% addpath(genpath('C:\Users\parkjs\Documents\GitHub\matlab_tools'));

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% CRYSTAL SYMMETRY
wsname = 'wscub3x'; % workspace name

pfname_midas_ps = '/home/beams/S1IDUSER/mnt/orthros/faber_mar21_midas/ff/s9/faber_sam1_s9_crack_ff2_Layer81_Analysis_Time_2021_03_07_07_25_19/ps_sam1_s9.txt';

%%% NOTE LAYER NUMBER AND pfimage NEED TO MATCH
pname_grains = '/home/beams/S1IDUSER/mnt/orthros/faber_mar21_midas/ff/s9/faber_sam1_s9_crack_ff2_Layer81_Analysis_Time_2021_03_07_07_25_19';
pfimage = '/home/beams/S1IDUSER/mnt/orthros/faber_mar21_data/faber_mar21/ge3/faber_sam1_s9_crack_ff2_000133.ge3';
pfdark = '/home/beams/S1IDUSER/mnt/orthros/faber_mar21_data/faber_mar21/ge3/dark_before_000052.ge3';

%%% FIT OUTPUT
pfname_output = './hedm_HTUPS_irr_s1_MultiRing/Layer1_ring1_t150_ring2_t50_SpotFits.csv';

%%%% ff_HEDM ANALYSIS RESULT
pname_ome = 'O:\faber_mar21_midas\ff\s9\faber_sam1_s9_crack_ff2_Layer1_Analysis_Time_2021_03_07_00_17_55\Output';

%%% THRESHOLDING BY COMPLETENESS; IGNORE GRAINS WITH LOWER COMPLETENESS
Thresh_Completeness = 0.7;

%%% THRESHOLDING BY MEAN RADIUS; IGNORE GRAINS WITH SMALLER RADIUS
Thresh_MeanRadius = 100;

%%% ROI SIZE (HALF THE WINDOW)
window_size = 3; %%% PIXEL
omega_wiggle_step = 2; %%% FRAMES
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Load workspace for fundamental region.
load(wsname);
eval(['ws = ', wsname, ';']);
clear(wsname)

% LOAD MIDAS PARAMETERS
midas_params = parseMIDASparams(pfname_midas_ps, pfimage);

% LOAD GRAIN INFORMATION
%%% FOR THE FULL STACK - IGNORE
% for iii = 1:1:length(pname_grains)
% pfname_grains{iii} = fullfile(pname_grains{iii}, 'Grains.csv');
% end
% Grains = parseGrainData(pfname_grains, ws.frmesh.symmetries, ...
% 'CrdSystem', 'APS', ...
% 'LabToSample', 0, ...
% 'C_xstal', BuildElasticityMatrix([386 120 132]*1000, 'Symmetry', 'cubic'));
Grains_midas = parseGrainData_OneLayer(pname_grains, ws.frmesh.symmetries, ...
'CrdSystem', 'APS', ...
'LabToSample', 0, ...
'C_xstal', BuildElasticityMatrix([386 120 132]*1000, 'Symmetry', 'cubic'), ...
'OutputReflectionTable', true);
Grains_midas.analysis_params = midas_params;

% SOME FILTERING
idx_Completeness = [Grains_midas.grains.Completeness] >= Thresh_Completeness;
idx_MeanRadius = [Grains_midas.grains.GrainRadius] >= Thresh_MeanRadius;
idx_filtered = idx_Completeness & idx_MeanRadius;

% LOAD DARK
numframes_dark = CalcNumFramesGE(pfdark);
for iii = 1:1:numframes_dark
if iii == 1
bkgpattern = NreadGE(pfdark, iii);
else
bkgpattern = bkgpattern + NreadGE(pfdark, iii);
end
end
bkgpattern = bkgpattern./numframes_dark;

data2write = [];

com = [Grains_midas.grains.COM];
rod = [Grains_midas.grains.rod];
figure(1); clf
subplot(1,2,1)
scatter3(com(1,:), com(2,:), com(3,:), 'b', 'o')
xlabel('z : +=along beam (um)'); ylabel('x : +=OB (um)'); zlabel('y : +=UP (um)')
axis equal tight; axis([-1000 1000 -1000 1000 -200 200])
hold on

subplot(1,2,2)
PlotFRPerimeter('cubic');
scatter3(rod(1,:), rod(2,:), rod(3,:), 'b', 'o')
hold on; axis equal

for iii = 1:1:Grains_midas.nGrains
if idx_filtered(iii)
disp(sprintf('grain %d - meets filters; watching ...', Grains_midas.grains(iii).GrainID))

figure(1); subplot(1,2,1)
scatter3(com(1,iii), com(2,iii), com(3,iii), 'filled', 'r', 'o')

figure(1); subplot(1,2,2)
scatter3(rod(1,iii), rod(2,iii), rod(3,iii), 'filled', 'r', 'o')

%%% MAKE SPOT COMPOSITE & EXTRACT SPOT FIT DATA
num_spots = Grains_midas.grains(iii).ReflectionTable.num_spots;
SpotComposite = zeros(window_size * 2 + 1, (window_size * 2 + 1) * num_spots);

ReflectionTable = Grains_midas.grains(iii).ReflectionTable;
Spots_csv_DetHCrd = ReflectionTable.Spots_csv_DetHCrd;
Spots_csv_DetVCrd = ReflectionTable.Spots_csv_DetVCrd;

figure(2); clf
scatter(Spots_csv_DetHCrd, Spots_csv_DetVCrd, 'k', 'o')
hold on; axis equal; grid on
axis([0 2048 0 2048])
for jjj = 1:1:num_spots
figure(2)
scatter(Spots_csv_DetHCrd(jjj), Spots_csv_DetVCrd(jjj), 'filled', 'k', 'o')

ome_average = (ReflectionTable.RingNr_csv_ome_min(jjj) + ReflectionTable.RingNr_csv_ome_max(jjj))/2;
[~, spot_frame_number] = min(abs(midas_params.ome_grid - ome_average));

%%% PATTERN AT THE CENTER OF OMEGA RANGE
pattern_data = rot90(NreadGE(pfimage, spot_frame_number + midas_params.junk_frames) - bkgpattern, 1);

figure(3); clf
imagesc(pattern_data)
colorbar vert; colormap jet; caxis([0 50])
axis equal tight; hold on; grid on
plot(midas_params.CENX, 2048 - midas_params.CENY, 'kx') %%% OK
plot(Spots_csv_DetHCrd(jjj), 2048 - Spots_csv_DetVCrd(jjj), 'ko')

% pattern_sum_data = rot90(ReadSUM('/home/beams/S1IDUSER/mnt/orthros/faber_mar21_bc/faber_sam1_s9_crack_ff2/ge3/faber_sam1_s9_crack_ff2_000133.ge3.sum'));

% figure(4); clf
% imagesc(pattern_sum_data)
% colorbar vert; colormap jet; caxis([-500 10000])
% axis equal tight; hold on; grid on
% plot(midas_params.CENX, 2048 - midas_params.CENY, 'kx')
% plot(Spots_csv_DetHCrd(jjj), 2048 - Spots_csv_DetVCrd(jjj), 'ko')

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% GO +/- OMEGA STEPS FROM CENTROID OMEGA POSITIONS
%%% OMEGA WIGGLE IS NOT IMPLEMENTED HERE YET
%%% ONLY FITTING FOR OMEGA0 WHERE SPOT WAS FOUND
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
idxIni = spot_frame_number - omega_wiggle_step;
idxFin = spot_frame_number + omega_wiggle_step;

if idxIni < 1
idxIni = 1;
end

if idxFin > midas_params.num_frames
idxFin = midas_params.num_frames;
end
idxGrid = idxIni:1:idxFin;

SpotStack = zeros(window_size*2 + 1, window_size*2 + 1, length(idxGrid));
detX = Spots_csv_DetHCrd(jjj);
detY = 2048 - Spots_csv_DetVCrd(jjj);
for kkk = 1:1:length(idxGrid)
pattern_data = rot90(NreadGE(pfimage, idxGrid(kkk) + midas_params.junk_frames) - bkgpattern, 1);

ri = round(detY - window_size);
rf = round(detY + window_size);

ci = round(detX - window_size);
cf = round(detX + window_size);

if ri < 0
ri = 1;
end
if ci < 0
ci = 1;
end
if rf > 2048
rf = 2048;
end
if cf > 2048
cf = 2048;
end

SpotStack(:,:,kkk) = pattern_data(ri:rf, ci:cf);
end

for kkk = 1:1:length(idxGrid)
figure(100+kkk); clf
imagesc(SpotStack(:,:,kkk))
colorbar vert; colormap jet; caxis([0 max(SpotStack(:))])
axis equal tight; grid on
title(sprintf('measured spot at omega = %2.1f deg', midas_params.ome_grid(idxGrid(kkk))))
end
pause
end
return
else
disp(sprintf('grain %d - does not meet filters; skipping ...', Grains_midas.grains(iii).GrainID))
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
return



for i = 1:1:num_grains










for j = 1:1:num_spots
detX = Spots.data(j,8)/200;
detY = Spots.data(j,9)/200;
detX = -detX + CENX;
detY = -detY + (2048 - CENY);

ome = Spots.data(j,10);

[~, idx] = min(abs(ome_grid - ome));

pattern_data = rot90(NreadGE(pfimage{im_stack_number(idx)}, frame_number(idx)) - bkgpattern, 1);

figure(2); clf
imagesc(double(pattern_data), [0 200])
axis square tight
hold on
colorbar vert
plot(CENX, 2048 - CENY, 'k.')
plot(detX, detY, 'ro')

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% GO +/- OMEGA STEPS FROM CENTROID OMEGA POSITIONS
%%% OMEGA WIGGLE IS NOT IMPLEMENTED HERE YET
%%% ONLY FITTING FOR OMEGA0 WHERE SPOT WAS FOUND
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
idxIni = idx - omega_wiggle_step;
idxFin = idx + omega_wiggle_step;

if idxIni < 1
idxIni = 1;
end

if idxFin > num_ome_steps
idxFin = num_ome_steps;
end
idxGrid = idxIni:1:idxFin;

SpotStack = zeros(window_size*2 + 1, window_size*2 + 1, length(idxGrid));
for k = 1:1:length(idxGrid)
pattern_data = rot90(NreadGE(pfimage{im_stack_number(idxGrid(k))}, frame_number(idxGrid(k))) - bkgpattern, 1);

ri = round(detY - window_size);
rf = round(detY + window_size);

ci = round(detX - window_size);
cf = round(detX + window_size);

if ri < 0
ri = 1;
end
if ci < 0
ci = 1;
end
if rf > 2048
rf = 2048;
end
if cf > 2048
cf = 2048;
end

xWindow = (ci:cf) - CENX;
yWindow = (ri:rf) - (2048 - CENY);

[xWindow, yWindow] = meshgrid(xWindow, yWindow);
xWindow = xWindow(:);
yWindow = yWindow(:);

num_window_pixels = length(yWindow);

rWindow = sqrt(xWindow(:).*xWindow + yWindow.*yWindow);
etaWindow = rad2deg(atan2(yWindow, xWindow)) + 180;

if abs(sum(sign(yWindow))) ~= num_window_pixels && (sum(xWindow < 0) == num_window_pixels)
idx_eta = yWindow < 0;
etaShifted = 360 + etaWindow(idx_eta);
etaWindow(idx_eta) = etaShifted;
end

Ipk = pattern_data(ri:rf, ci:cf);
Ipk = double(Ipk(:));

[maxIpk, idxMaxIpk] = max(Ipk);
p0 = [max(Ipk); 1.75; 0.5; rWindow(idxMaxIpk); etaWindow(idxMaxIpk); 10];
[p, resnorm] = lsqcurvefit(@pkGaussian2, p0, [rWindow etaWindow], Ipk);

Ipk_fit0 = pkGaussian2(p0, [rWindow etaWindow]);
Ipk_fit = pkGaussian2(p, [rWindow etaWindow]);

tthMean = atand(p(4)*200./Dsam);
etaMean = p(5);

SpotStack(:,:,k) = pattern_data(ri:rf, ci:cf);

figure(2)
subplot(2,2,1); cla
imagesc(SpotStack(:,:,k))
hold on
axis square tight
title('measured peak profile ')

subplot(2,2,2); cla
imagesc(reshape(Ipk_fit0, window_size*2+1, window_size*2+1))
hold on
axis square tight
title('peak profile from initial guess')

subplot(2,2,3); cla
imagesc(reshape(Ipk_fit, window_size*2+1, window_size*2+1))
hold on
axis square tight
title('peak profile from fit')

subplot(2,2,4); cla
imagesc(SpotStack(:,:,k) - reshape(Ipk_fit, window_size*2+1, window_size*2+1))
hold on
axis square tight
title('fit - measured peak')

if idxGrid(k) == idx
ci = 1 + (window_size * 2 + 1) * (j - 1);
cf = (window_size * 2 + 1) * j;
SpotComposite(:, ci:cf) = SpotStack(:,:,k);
%%% grain# spot# tth eta Amp gamma_r gamma_eta r_fit eta_fit bck grain radius
data2write = [data2write; i j tthMean etaMean p' resnorm grains(i,23)];
end
end
end
end

csvwrite(pfname_output, data2write)

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