shift_rec2 --> shift_rec

apply_shifts.m

@@ -90,15 +90,15 @@
             Yfft = cellfun(@(x) fftn(x),Yc,'un',0);
         end
         if all(options.mot_uf == 1)
-            M_fin = shift_reconstruct2(Yfft{1},shifts_temp(ii).shifts,shifts_temp(ii).diff,options.us_fac,Nr{1},Nc{1},Np{1},'NaN',0);
+            M_fin = shift_reconstruct(Yfft{1},shifts_temp(ii).shifts,shifts_temp(ii).diff,options.us_fac,Nr{1},Nc{1},Np{1},'NaN',0);
             if nd == 2; Mf{ii} = M_fin; end
             if nd == 3; Mf{ii} = M_fin; end
         else
             shifts_up = shifts_temp(ii).shifts_up;
             for i = 1:length(xx_uf)
                 for j = 1:length(yy_uf)
                     for k = 1:length(zz_uf)                  
-                         M_fin{i,j,k} = shift_reconstruct2(Yfft{i,j,k},shifts_up(i,j,k,:),shifts(t).diff(i,j,k),options.us_fac,Nr{i,j,k},Nc{i,j,k},Np{i,j,k},'NaN',0);
+                         M_fin{i,j,k} = shift_reconstruct(Yfft{i,j,k},shifts_up(i,j,k,:),shifts(t).diff(i,j,k),options.us_fac,Nr{i,j,k},Nc{i,j,k},Np{i,j,k},'NaN',0);
                     end
                 end
             end

normcorre.m

@@ -313,7 +313,7 @@
                     for k = 1:length(zz_uf)
                         extended_grid = [max(xx_us(i)-overlap_post(1),1),min(xx_uf(i)+overlap_post(1),d1),max(yy_us(j)-overlap_post(2),1),min(yy_uf(j)+overlap_post(2),d2),max(zz_us(k)-overlap_post(3),1),min(zz_uf(k)+overlap_post(3),d3)];
                         I_temp = Yt(extended_grid(1):extended_grid(2),extended_grid(3):extended_grid(4),extended_grid(5):extended_grid(6));
-                        M_fin{i,j,k} = shift_reconstruct2(I_temp,shifts_up(i,j,k,:),diff_up(i,j,k),us_fac,Nr{i,j,k},Nc{i,j,k},Np{i,j,k},'NaN',add_value);
+                        M_fin{i,j,k} = shift_reconstruct(I_temp,shifts_up(i,j,k,:),diff_up(i,j,k),us_fac,Nr{i,j,k},Nc{i,j,k},Np{i,j,k},'NaN',add_value);
                     end
                 end
             end

normcorre_batch.m

@@ -267,7 +267,7 @@
                         for k = 1:length(zz_uf)
                             extended_grid = [max(xx_us(i)-overlap_post(1),1),min(xx_uf(i)+overlap_post(1),d1),max(yy_us(j)-overlap_post(2),1),min(yy_uf(j)+overlap_post(2),d2),max(zz_us(k)-overlap_post(3),1),min(zz_uf(k)+overlap_post(3),d3)];
                             I_temp = Yt(extended_grid(1):extended_grid(2),extended_grid(3):extended_grid(4),extended_grid(5):extended_grid(6));
-                            M_fin{i,j,k} = shift_reconstruct2(I_temp,shifts_up(i,j,k,:),diff_up(i,j,k),us_fac,Nr{i,j,k},Nc{i,j,k},Np{i,j,k},'NaN',add_value);
+                            M_fin{i,j,k} = shift_reconstruct(I_temp,shifts_up(i,j,k,:),diff_up(i,j,k),us_fac,Nr{i,j,k},Nc{i,j,k},Np{i,j,k},'NaN',add_value);
                         end
                     end
                 end

shift_reconstruct2.m → old/shift_reconstruct.m

@@ -1,10 +1,9 @@
-function I = shift_reconstruct2(Y,shifts,diffphase,us_fac,Nr,Nc,Np,method,add_value)
+function I = shift_reconstruct(Y,shifts,us_fac,Nr,Nc,Np,method,add_value)
 
 % applies 3-d sub-pixel shifts to an input image
 % INPUTS:
 % Y:            input image (double 3d tensor) in space (real) or frequency (complex) domain
 % shifts:       shifts 
-% diffphase:    phase difference
 % us_fac:       upsampling factor for subpixel shifts
 % method:       method for treating boundaries
 % add_value:    value to add when zero-ing out boundaries
@@ -14,12 +13,6 @@
 
 % Written by Eftychios A. Pnevmatikakis, Simons Foundation, 2016
 
-if isreal(Y);
-    buf2ft = fftn(Y);
-else
-    buf2ft = Y;
-end
-
 if nargin < 8 || isempty(add_value); add_value = 0; end
 if nargin < 7 || isempty(method); method = 'zero'; end
 
@@ -35,22 +28,19 @@
     col_shift = shifts(2);
     if ismatrix(Y); pln_shift = 0; else pln_shift = shifts(3); end
     shifts = [row_shift,col_shift,pln_shift];
+    buf2ft = fftn(Y);
 
     if us_fac > 0
         if isvector(Nc); [Nc,Nr,Np] = meshgrid(Nc,Nr,Np); end
         Greg = buf2ft.*exp(1i*2*pi*(-row_shift*Nr/nr-col_shift*Nc/nc-pln_shift*Np/np));
     elseif us_fac == 0
         Greg = buf2ft;
     end
-    Greg = Greg*exp(1i*diffphase);
+
     I = real(ifftn(Greg));
-    I = remove_boundaries(I,shifts,method,add_value);    
+    I = remove_boundaries(I,shifts,method,add_value);
 else
-    if isreal(Y)
-        I = Y;
-    else
-        I = real(ifftn(Y));
-    end
+    I = Y;
 end
 
 end

shift_reconstruct.m

@@ -1,9 +1,10 @@
-function I = shift_reconstruct(Y,shifts,us_fac,Nr,Nc,Np,method,add_value)
+function I = shift_reconstruct(Y,shifts,diffphase,us_fac,Nr,Nc,Np,method,add_value)
 
 % applies 3-d sub-pixel shifts to an input image
 % INPUTS:
 % Y:            input image (double 3d tensor) in space (real) or frequency (complex) domain
 % shifts:       shifts 
+% diffphase:    phase difference
 % us_fac:       upsampling factor for subpixel shifts
 % method:       method for treating boundaries
 % add_value:    value to add when zero-ing out boundaries
@@ -13,6 +14,12 @@
 
 % Written by Eftychios A. Pnevmatikakis, Simons Foundation, 2016
 
+if isreal(Y);
+    buf2ft = fftn(Y);
+else
+    buf2ft = Y;
+end
+
 if nargin < 8 || isempty(add_value); add_value = 0; end
 if nargin < 7 || isempty(method); method = 'zero'; end
 
@@ -28,19 +35,22 @@
     col_shift = shifts(2);
     if ismatrix(Y); pln_shift = 0; else pln_shift = shifts(3); end
     shifts = [row_shift,col_shift,pln_shift];
-    buf2ft = fftn(Y);
 
     if us_fac > 0
         if isvector(Nc); [Nc,Nr,Np] = meshgrid(Nc,Nr,Np); end
         Greg = buf2ft.*exp(1i*2*pi*(-row_shift*Nr/nr-col_shift*Nc/nc-pln_shift*Np/np));
     elseif us_fac == 0
         Greg = buf2ft;
     end
-
+    Greg = Greg*exp(1i*diffphase);
     I = real(ifftn(Greg));
-    I = remove_boundaries(I,shifts,method,add_value);
+    I = remove_boundaries(I,shifts,method,add_value);    
 else
-    I = Y;
+    if isreal(Y)
+        I = Y;
+    else
+        I = real(ifftn(Y));
+    end
 end
 
 end