Merge pull request #20 from FranckLab/dev

Added 'm' grid point as output

Matlab Code/DVC.m

@@ -215,7 +215,7 @@
 
 %% equation 4
 
-if prod(single(sSize == 32)) || prod(single(sSize == 64)) || prod(single(sSize == 128))
+if prod(single(sSize == 32)) || prod(single(sSize == 16))
     sSize = sSize(1);
 
     x = cell(1,3);

Matlab Code/Example/exampleRunFile.m

@@ -51,6 +51,9 @@
 %         u{time}{2} = displacement in y-direction at t=time of size MxNxP
 %         u{time}{3} = displacement in z-direction at t=time of size MxNxP
 %   cc: peak values of the cross-correlation for each interrogation
+%   dm: meshgrid spacing (8 by default)
+%   m:  The grid points at which displacements are computed. The grid 
+%        points locations are in the same format as 'u'.
 % 
 % NOTES
 % -------------------------------------------------------------------------
@@ -69,7 +72,7 @@
 filename = 'vol*.mat';
 
 % Estimate displacements via IDVC
-[u, cc, dm] = funIDVC(filename, sSize, incORcum);
+[u, cc, dm, m] = funIDVC(filename, sSize, incORcum);
 
 save('resultsFIDVC.mat','u','cc','dm');
 

Matlab Code/IDVC.m

@@ -1,4 +1,4 @@
-function [u, cc, dm] = IDVC(varargin)
+function [u, cc, dm, m] = IDVC(varargin)
 % [u, cc] = IDVC(I,sSize,u0,className);
 % I = filterDisplacements(I0,filterSize,z) applies a low-pass convolution
 % filter to the displacement field to mitigate divergence based on 
@@ -25,6 +25,8 @@
 %         u{4} = magnitude
 %   cc: peak values of the cross-correlation for each interrogation
 %   dm: meshgrid spacing (8 by default)
+%   m:  The grid points at which displacements are computed. The grid 
+%       points locations are in the same format as 'u'.
 %
 % NOTES
 % -------------------------------------------------------------------------
@@ -60,14 +62,16 @@
      [converged01, SSE(i-1) , sSize(i,:), sSpacing(i,:)] = checkConvergenceSSD(I,SSE,sSize,sSpacing,convergenceCrit);
 
     if ~converged01
+        finalSize = sSize(i,:);
+
         [I, m] = parseImages(I,sSize(i,:),sSpacing(i,:));
 
         % run cross-correlation to get an estimate of the displacements
         [du, cc] = DVC(I,sSize(i,:),sSpacing(i,:),DVCPadSize,ccThreshold);
 
         % add the displacements from previous iteration to current
         waitbar(3/7,wb,'Adding displacements from previous iteration');
-        [u, ~, cc] = addDisplacements(u,du,cc,m,dm);
+        [u, ~, cc, mFinal] = addDisplacements(u,du,cc,m,dm);
 
         % filter the  displacements using a predictor filter
         waitbar(4/7,wb,'Filtering Displacements');
@@ -87,11 +91,11 @@
         disp(['Elapsed time (iteration ',num2str(i-1),'): ',num2str(toc(ti))]);
         i = i + 1;
     end
-
-end
 
-[u,cc] = parseOutputs(u,cc,dm,padSize);
+end
 
+[u,cc,m] = parseOutputs(u,cc,finalSize,padSize,mFinal);
+delete(wb);
 disp(['Convergence at iteration ',num2str(i)]);
 disp(['Title time: ',num2str(toc(t0))]);
 end
@@ -167,22 +171,27 @@
 end
 
 
-function [u,cc] = parseOutputs(u,cc,filterSpacing,padSize)
+function [u,cc,m] = parseOutputs(u,cc,finalsSize,padSize,m)
 % parses outputs and unpads the displacment field and cc.
 
-unpadSize(1,:) = ceil(padSize(1,:)/filterSpacing);
-unpadSize(2,:) = floor((padSize(2,:)+1)/filterSpacing); 
-% +1 from the extra meshgrid point during the meshing of the DVC algorithm. EBK (10-23-2013)
-
+% % % % unpadSize(1,:) = ceil(padSize(1,:)/filterSpacing);
+% % % % unpadSize(2,:) = floor((padSize(2,:)+1)/filterSpacing); 
+% % % % % +1 from the extra meshgrid point during the meshing of the DVC algorithm. EBK (10-23-2013)
+% % % % 
+% % % % for i = 1:3
+% % % %     u{i} = u{i}(1+unpadSize(1,1):end-unpadSize(2,1),...
+% % % %         1+unpadSize(1,2):end-unpadSize(2,2),...
+% % % %         1+unpadSize(1,3):end-unpadSize(2,3));
+% % % % end
+% % % % u{4} = sqrt(u{1}.^2 + u{2}.^2 + u{3}.^2);
+% % % % 
+% % % % cc = cc(1+unpadSize(1,1):end-unpadSize(2,1),...
+% % % %     1+unpadSize(1,2):end-unpadSize(2,2),...
+% % % %     1+unpadSize(1,3):end-unpadSize(2,3));
+filterSpacing = finalsSize/2;
+u{4} = sqrt(u{1}.^2 + u{2}.^2 + u{3}.^2);
 for i = 1:3
-    u{i} = u{i}(1+unpadSize(1,1):end-unpadSize(2,1),...
-        1+unpadSize(1,2):end-unpadSize(2,2),...
-        1+unpadSize(1,3):end-unpadSize(2,3));
+    m{i} = m{i}-padSize(1,i)-filterSpacing(i);
 end
-u{4} = sqrt(u{1}.^2 + u{2}.^2 + u{3}.^2);
-
-cc = cc(1+unpadSize(1,1):end-unpadSize(2,1),...
-    1+unpadSize(1,2):end-unpadSize(2,2),...
-    1+unpadSize(1,3):end-unpadSize(2,3));
 
 end

Matlab Code/addDisplacements.m

@@ -1,4 +1,4 @@
-function [u, du, cc] = addDisplacements(u0,du0,cc0,m0,dm)
+function [u, du, cc, m] = addDisplacements(u0,du0,cc0,m0,dm)
 % u = addDisplacements(u,thr,epsilon) removes outliers using the universal
 % outlier test based on
 %

Matlab Code/funIDVC.m

@@ -1,4 +1,4 @@
-function [u, cc, dm] = funIDVC(varargin)
+function [u, cc, dm, m] = funIDVC(varargin)
 % u = funIDVC(filename, sSize, incORcum) is the main function that performs
 % IDVC on a time increment of volumetric images.  
 % 
@@ -40,6 +40,8 @@
 %         u{time}{4} = magnitude
 %   cc: peak values of the cross-correlation for each interrogation point
 %   dm: meshgrid spacing (8 by default)
+%   m:  The grid points at which displacements are computed. The grid 
+%       points locations are in the same format as 'u'.
 % 
 % NOTES
 % -------------------------------------------------------------------------
@@ -62,7 +64,7 @@
 
     %Start DVC
     disp(['Current file: ' fileInfo.filename{i}])
-    [u_, cc{i-1}, dm] = IDVC(I,sSize0,u_);
+    [u_, cc{i-1}, dm, m] = IDVC(I,sSize0,u_);
 
     % Saving iterations of the DVC
     u{i-1}{1} = -u_{1};  u{i-1}{2} = -u_{2};  u{i-1}{3} = -u_{3}; u{i-1}{4} = u_{4};

README.md

@@ -1,7 +1,7 @@
 The Fast Iterative Digital Volume Correlation Algorithm (FIDVC) is the next generation DVC algorithm providing significantly improved signal-to-noise, and large (finite) deformation (incl. large rotations and image stretches) capture capability at low computational cost (please see [Bar-Kochba, Toyjanova et al., Exp. Mechanics, 2014](http://link.springer.com/article/10.1007/s11340-014-9874-2?sa_campaign=email/event/articleAuthor/onlineFirst) for more details).
 
 ### Important pages
-* [Download latest version v1.2.3!](https://github.com/FranckLab/FIDVC/releases)
+* [Download latest version v1.2.4!](https://github.com/FranckLab/FIDVC/releases)
 * [Example data](https://drive.google.com/folderview?id=0ByhZqlrbo5srSmU2ZW1TOXpfVkE&usp=sharing)
 * [FAQ](https://github.com/FranckLab/FIDVC#faq)
 * [Questions/Issues](https://github.com/FranckLab/FIDVC/issues)