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ptycho/+engines/+GPU/+PIE/apply_SVD_filter.m

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+% APPLY_SVD_FILTER The core of the variable probe (OPRP) code: 
+% find SVD decomposition and limit the probe into several orthogonal
+% modes 
+% additional prior knowledge can be also included 
+%
+% [probe, probe_evolution] = apply_SVD_filter(probe, Nmodes, mode)
+%
+% ** probe     [Nx,Ny,N] variable probe for each position 
+% ** Nmodes     (int)   number of variable modes 
+% ** mode       structure containing parameters for selected probe mode 
+% returns
+% ++ probe      [Nx,Ny,variable_modes] variable probe modes
+% ++ probe_evolution   [Npos,variable_modes] updated array containing evolution of the varaible modes for each position 
+%
+% see also: engines.GPU.PIE 
+
+function [probe, probe_evolution] = apply_SVD_filter(probe, Nmodes, mode)
+
+    import engines.GPU.shared.*
+    import engines.GPU.GPU_wrapper.*
+    import engines.GPU.shared.*
+
+    import math.*
+    import utils.* 
+    
+    
+    Np = size(probe);
+         
+    [U,S,V] = fsvd(reshape((probe),[],Np(3)) ,Nmodes);
+%      if any(diag(S.^2)/sum(diag(S.^2)) < 1e-3)  % 2e-3 is the weakest that FSVD can recover 
+%          try
+%             warning('Running full SVD (maybe use less OPR modes)  (weak modes %i/%i) ', Ggather(sum(diag(S.^2)/sum(diag(S.^2)) < 2e-3)), Nmodes)
+%             [U,S,V] = svd(reshape((probe),[],Np(3)) ,0);
+%             U = single(U(:,1:Nmodes));
+%             S = single(S(1:Nmodes,1:Nmodes));
+%             V = single(V(:,1:Nmodes));
+%          catch
+%              keyboard
+%          end            
+%      end
+
+   %Notes by YJ:
+   % U is orthonormal modes. size [Np(1)*Np(2), Nmodes]
+   % S is diagonal matrix of singular values. size [Nmodes,Nmodes]
+   % V is conjugated orthonormal evolution matrix. size [Npos,Nmodes]
+   
+   % Lower dimensional representation of the reconstructed probes = USV*
+   % probe_evolution = SV*
+   %disp('xxxx')
+   %disp(size(U))
+   U = reshape(U, Np(1),Np(2),1,[]);
+   %disp(size(U))
+   U = apply_probe_contraints(U, mode);
+   %disp('oooo')
+   
+   V(:,1) = mean(V(:,1)) + 0.99*(V(:,1) - mean(V(:,1)));
+   V(:,2:end) = mean(V(:,2:end)) + 0.99*(V(:,2:end) - mean(V(:,2:end)));
+
+    %% remove outliers 
+    aV = abs(V);
+    MAX = quantile(aV,0.99);
+    V = min(aV, MAX) .* (V ./ (aV+1e-3)); 
+    %disp(size(S*V'))
+    probe_evolution = (S*V').'; %Note by YJ: why transpose it here?
+    %disp(size(probe_evolution))
+
+    probe = U; 
+    
+    
+    avg = mean(abs(probe_evolution(:,1)),1); 
+    
+    probe = probe*avg;
+    probe_evolution = probe_evolution / avg;
+
+
+end
+