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Copy pathrun_the_params.m~
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run_the_params.m~
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function [ feature_results, feature_names, k_list ] = run_the_params( data )
tic;
%%%%%%%%%%%%%% Get variables from the data structure %%%%%%%%%%%%%%%%%%%%%%%%%
mat_filename = data.mat_filename;
spec_list = data.spec_list; E_list = data.E_list; th_list = data.th_list;
X_list = data.X_list; Y_list = data.Y_list;
FL_E = data.FL_E; bg_E1 = data.bg_E1; bg_E2 = data.bg_E2;
bg_th1 = data.bg_th1; bg_th2 = data.bg_th2;
bg_k1 = data.bg_k1; bg_k2 = data.bg_k2;
f_E1 = data.f_E1; f_E2 = data.f_E2;
f_th1 = data.f_th1; f_th2 = data.f_th2;
f_k1 = data.f_k1; f_k2 = data.f_k2;
fS_th1 = data.fS_th1; fS_th2 = data.fS_th2;
fS_k1 = data.fS_k1; fS_k2 = data.fS_k2;
fS_X = data.fS_X;
f2_E1 = data.f2_E1; f2_E2 = data.f2_E2;
Ism_E1 = data.Ism_E1; Ism_E2 = data.Ism_E2;
Ism_th1 = data.Ism_th1; Ism_th2 = data.Ism_th2;
Ism_k1 = data.Ism_k1; Ism_k2 = data.Ism_k2;
d_E1 = data.d_E1; d_E2 = data.d_E2;
dL_th1 = data.dL_th1; dL_th2 = data.dL_th2;
dR_th1 = data.dR_th1; dR_th2 = data.dR_th2;
show_samples = data.show_samples;
azi0 = data.azi0; pol0 = data.pol0; hv = data.hv;
WF = data.WF; EB = data.EB; innerPot = data.V0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
num_spec = size(spec_list, 3);
Eax = E_list(:,1); Estep = mean(abs(Eax(2:end)-Eax(1:end-1)));
thax = th_list(:,1); thstep = mean(abs(thax(2:end)-thax(1:end-1)));
% E, th window size to search for min/max pixel intensities for bgnd/Ism
Ewindow = round( 0.1 / Estep );
thwindow = round( 3 / thstep );
% Initialize arrays for feature maps
tInts = NaN*ones(num_spec,1);
tilts = NaN*ones(num_spec,1);
f_Es = NaN*ones(num_spec,1);
f_Ss = NaN*ones(num_spec,1);
f2_Es = NaN*ones(num_spec,1);
f2_Ss = NaN*ones(num_spec,1);
f21_rats = NaN*ones(num_spec,1);
Ibgs = NaN*ones(num_spec,1);
Isms = NaN*ones(num_spec,1);
Ism_Es = NaN*ones(num_spec,1);
% Initialize array for converted theta-
k_list = NaN*ones(size(th_list,1),num_spec);
for i = 1 : num_spec
spec = mat2gray( spec_list(:,:,i) );
if ~isnan(sum(sum(spec)))
% Total intensity
tInts(i) = sum(sum(spec));
%% Tilt from d-band peaks
[tilt0_idx, ~] = d_band_center( spec, Eax, thax, d_E1, d_E2, dL_th1, dL_th2, dR_th1, dR_th2);
try
tilts(i) = -thax(tilt0_idx);
end
tParams = [azi0, pol0, hv, WF, EB, innerPot]; % azi0, pol0, hv, WF, EB, innerPot
kax = theta2kx( thax, tParams(1), tilts(i), tParams(2), tParams(3), tParams(4), tParams(5), tParams(6) );
k_list(:,i) = kax;
%% 4f energies, widths, amplitude ratio
top_X = 0.1; % Set feature energies as center of mass energy of the top top_X fraction of EDC intensities
interpDiv = 100; % Interpolate along energy axis
% Use either raw-data theta ranges or converted-k axis ranges for taking EDCs for calculating f pk/widths
if f_k2 - f_k1 > 0
[~, ~, f_E, f_S, f2_E, f2_S, f21_ratio] = f_com_finder( spec, Eax, kax, f_E1, f_E2, f2_E1, f2_E2, f_k1, f_k2, fS_k1, fS_k2, top_X, fS_X, interpDiv);
else
[~, ~, f_E, f_S, f2_E, f2_S, f21_ratio] = f_com_finder( spec, Eax, thax, f_E1, f_E2, f2_E1, f2_E2, f_th1, f_th2, fS_th1, fS_th2, top_X, fS_X, interpDiv);
end
f_Es(i) = f_E;
f_Ss(i) = f_S;
f2_Es(i) = f2_E;
f2_Ss(i) = f2_S;
f21_rats(i) = f21_ratio;
%% Bgnd intensity
% Convert to pixel idx
bg_E_srch = find(Eax > bg_E1, 1,'first') : find(Eax <= bg_E2, 1,'last');
if bg_k2 - bg_k1 > 0
bg_k_srch = find(kax > bg_k1,1,'first') : find(kax <= bg_k2, 1,'last');
Ibg_window = spec(bg_E_srch, bg_k_srch);
else % If range not given in k, use raw-theta values
bg_th_srch = find(thax > bg_th1, 1,'first') : find(thax <= bg_th2, 1,'last');
Ibg_window = spec( bg_E_srch, bg_th_srch );
end
Ibg = mean(Ibg_window(:));
Ibgs(i) = Ibg;
%% Ism
% Convert search-window ranges to pixel idx
Ism_E_srch = find(Eax > Ism_E1, 1,'first') : find(Eax <= Ism_E2, 1,'last');
if Ism_k2 - Ism_k1 > 0
Ism_k_srch = find(kax > Ism_k1,1,'first') : find(kax <= Ism_k2, 1,'last');
Ism_window = spec(Ism_E_srch, Ism_k_srch);
else
Ism_th_srch = find(thax > Ism_th1, 1,'first') : find(thax <= Ism_th2, 1,'last');
Ism_window = spec( Ism_E_srch, Ism_th_srch );
end
Ism = mean(Ism_window(:));
% Final Ism value evaluated as fractional increase from Ibg to Ism
Isms(i) = (Ism-Ibg) / Ibg;
% Edc sum over all k to get energy of Ism feature
Ism_edc = sum(spec,2);
[~, Ism_Eidx] = max( Ism_edc(Ism_E_srch) );
Ism_Eidx = Ism_Eidx + Ism_E_srch(1) - 1;
Ism_Es(i) = Eax(Ism_Eidx);
end
end
feature_names = {'tot int', 'tilt', 'f E', 'f S', 'f2_E', 'f2 S', 'f21_rat', 'Ism', 'Ism E'};
feature_results = [ tInts, tilts, f_Es, f_Ss, f2_Es, f2_Ss, f21_rats, Isms, Ism_Es];
toc
%% Plot figure showing input parameters
if show_samples > 0
display_sample_spectra(mat_filename, show_samples, spec_list, thax, Eax, ...
FL_E, f_Es, f2_Es, bg_E1,bg_E2, bg_th1,bg_th2, Ism_E1,Ism_E2, Ism_th1,Ism_th2, f_E1,f_E2, f_th1,f_th2, f2_E1,f2_E2 )
pause(.1)
end
end