minor fixes

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m

@@ -18,7 +18,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
         'rspace_oversize', 1.1, ...
         'ospace_lims', [], ...
         'include_all', false, ...
-        'save', false );
+        'save', false, ...
+        'psf', []);
     conf = parse_pv_pairs(conf, varargin);
 
     if (~isstruct(gr_id))
@@ -299,7 +300,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
     proj.vol_size_x = vol_size(2);
     proj.vol_size_y = vol_size(1);
     proj.vol_size_z = vol_size(3);
-
+    proj.psf = conf.psf;
     refor.proj(conf.det_index) = proj;
     refor.bb_ors = ors;
 

zUtil_EDF/edf_read.m

@@ -30,7 +30,7 @@ function [img, varargout] = edf_read(filename, GT_bb, dispmes, info, varargin)
         dispmes = ~strcmp(dispmes, 'nodisp');
     end
 
-    conf = struct('verbose', dispmes, 'convert', true);
+    conf = struct('verbose', dispmes, 'convert', true, 'permute', true);
     conf = parse_pv_pairs(conf, varargin);
 
     % Check file
@@ -102,11 +102,12 @@ function [img, varargout] = edf_read(filename, GT_bb, dispmes, info, varargin)
 
     %%% Let's reshape to the real format of the matrix
     img = reshape(img, dim_1, dim_2, info.dim_3);
-
-    if (info.dim_3 > 1) % 3D volume
-        img = permute(img, [2 1 3]); % reorganise dimensions
-    else % 2D image
-        img = transpose(img);
+    if conf.permute
+        if (info.dim_3 > 1) % 3D volume
+            img = permute(img, [2 1 3]); % reorganise dimensions
+        else % 2D image
+            img = transpose(img);
+        end
     end
 
     if (~isa(img, 'double') && conf.convert)

zUtil_ForwardSim/gtFwdSimBuildDifstackBlobs.m

@@ -27,9 +27,9 @@ function bl = gtFwdSimBuildDifstackBlobs(blobids, parameters, stackUSize, stackV
         blob_bb = blob_bb([2 1 3 5 4 6]);
 
         bl(ii).mbbsize = blob_bb(4:6);
-        bl(ii).mbbu = [blob_bb(1), blob_bb(1) + blob_bb(4) + 1];
-        bl(ii).mbbv = [blob_bb(2), blob_bb(2) + blob_bb(5) + 1];
-        bl(ii).mbbw = [blob_bb(3), blob_bb(3) + blob_bb(6) + 1];
+        bl(ii).mbbu = [blob_bb(1), blob_bb(1) + blob_bb(4) - 1];
+        bl(ii).mbbv = [blob_bb(2), blob_bb(2) + blob_bb(5) - 1];
+        bl(ii).mbbw = [blob_bb(3), blob_bb(3) + blob_bb(6) - 1];
 
         % Essentially zero pads the blob to make it fit into ASTRA's
         % diffraction stack

zUtil_ForwardSim/gtFwdSimCheckSpotInRawImages.m

@@ -16,8 +16,8 @@ function [found_intensity, spotInfo] = gtFwdSimCheckSpotInRawImages(uvw, spotsCo
     % completeness) is empty, use the same size as the difspot average size +
     % 5 percent
     if isempty(parameters.fsim.bb_size)
-        bbhsize = floor(spotsCommProps.Xsize*1.05);
-        bbvsize = floor(spotsCommProps.Ysize*1.05);
+        bbhsize = spotsCommProps.stackUSize;
+        bbvsize = spotsCommProps.stackVSize;
     else
         bbhsize = parameters.fsim.bb_size(1);
         bbvsize = parameters.fsim.bb_size(2);