Allow Diondo helical scans

Author: AnderBiguri

MATLAB/Utilities/IO/Diondo/loadDiondoProjections.m

@@ -74,7 +74,9 @@
     proj(:,:,ii)=-log(proj(:,:,ii)/single(2^16));
 end
 geo=rmfield(geo,'whitelevel');
-%%
+if isfield(geo,'offOrigin')
+    geo.offOrigin = geo.offOrigin(:,index);
+end
 angles=angles_to_load;
 end
 

MATLAB/Utilities/IO/Diondo/readDiondoGeometry.m

@@ -14,13 +14,15 @@
 
     s = readstruct([file.folder,'\',file.name]);
 
-    if ~strcmp(s.ScanParameter.HelixMode,'false')
-        error("Helix mode reading not implemented")
-    end
+
     if ~strcmp(s.ScanParameter.Laminography, 'false')
         error("Laminography mode reading not implemented")
     end
 
+   
+    geo.offOrigin = [0;0;0];
+    geo.offDetector = [0;0];
+
     geo.nDetector = [s.Recon.ProjectionDimX; s.Recon.ProjectionDimY];
     geo.dDetector = [s.Recon.ProjectionPixelSizeX; s.Recon.ProjectionPixelSizeY];
     geo.sDetector = geo.nDetector.*geo.dDetector;
@@ -31,14 +33,20 @@
 
     geo.DSD = s.Geometrie.SourceDetectorDist;
     geo.DSO = s.Geometrie.SourceObjectDist;
-    geo.COR = s.Recon.ProjectionCenterOffsetX;
+    geo.COR = -s.Recon.ProjectionCenterOffsetX*s.Recon.ProjectionPixelSizeX;
 
     if s.Recon.ProjectionCount ~= s.Recon.ProjectionCountPer360deg
         warning("Never tested with angles not in 360deg. If it doesnt work please contact tigre.toolbox@gmail.com to help improve this loader");
     end
     angles=linspace(0,2*pi,s.Recon.ProjectionCount);
     angles=-angles(1:end-1);
 
+    if ~strcmp(s.ScanParameter.HelixMode,'True')
+         z_step = -s.ScanParameter.HelixPerStepDistanceZ;
+         offsetz=linspace(0,z_step*length(angles)-z_step,length(angles));
+         offsetz = offsetz-offsetz(end)/2;
+         geo.offOrigin=[zeros(1,length(angles));zeros(1,length(angles));offsetz];
+    end
 
     height = char(s.Geometrie.Slices.string());
     height  = height(1:strfind(s.Geometrie.Slices.string,"mm")-2);