gtForwardSimulate: fixed case for no blobs in files

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

5_reconstruction/gtForwardSimulate_v2.m

@@ -305,30 +305,30 @@ for n = first : last
         difstack(:, ii, :) = spot';
     end
 
-    %%% We now build the diffraction blob stack
-    for ii = reshape(matched, [1 numel(matched)])
-        [blob_vol, blob_bb] = buildBlob(spotid(ii), parameters, spotsCommProps);
-%         blob_vol = permute(blob_vol, [2 1 3]);
-
-%         if (fsim.assemble_figure)
-%             full = gtPlaceSubImage2(sum(blob_vol, 3), full, bb(ii, 1), bb(ii, 2), 'summed');
-%         end
-
-        % Essentially zero pads the blob to make it fit into ASTRA's
-        % diffraction stack
-        shifts_blob = getBlobStackShifts(spotsCommProps, blob_bb);
-        shifts = [shifts_blob.v + 1, shifts_blob.h + 1, 1];
-
-        bl(ii).intm = gtPlaceSubVolume( ...
-            zeros(spotsCommProps.stackVSize, spotsCommProps.stackHSize, blob_bb(6)), ...
-            blob_vol, shifts);
-        bl(ii).intm = permute(bl(ii).intm, [2 1 3]);
-
-        bl(ii).bbuim = [blob_bb(2), (blob_bb(2)+blob_bb(5)-1)];
-        bl(ii).bbvim = [blob_bb(1), (blob_bb(1)+blob_bb(4)-1)];
-        bl(ii).bbwim = [blob_bb(3), (blob_bb(3)+blob_bb(6)-1)];
-
-        bl(ii).bbsize = [blob_bb(5), blob_bb(4), blob_bb(6)];
+    if (isfield(parameters.seg, 'writehdf5') && parameters.seg.writehdf5)
+        %%% We now build the diffraction blob stack
+        for ii = reshape(matched, [1 numel(matched)])
+            [blob_vol, blob_bb] = buildBlob(spotid(ii), parameters, spotsCommProps);
+
+            % Essentially zero pads the blob to make it fit into ASTRA's
+            % diffraction stack
+            shifts_blob = getBlobStackShifts(spotsCommProps, blob_bb);
+            shifts = [shifts_blob.v, shifts_blob.h, 1];
+
+            % We are applying a padding of one slice (perside) on the w
+            % diretion
+            bl(ii).intm = gtPlaceSubVolume( ...
+                zeros(spotsCommProps.stackVSize, spotsCommProps.stackHSize, blob_bb(6)+2), ...
+                blob_vol, shifts);
+            bl(ii).intm = permute(bl(ii).intm, [2 1 3]);
+            blob_bb = blob_bb([2 1 3 5 4 6]);
+
+            bl(ii).bbsize = size(bl(ii).intm);
+
+            bl(ii).bbuim = [(blob_bb(1) - shifts_blob.h), (blob_bb(1) - shifts_blob.h + bl(ii).bbsize(1) - 1)];
+            bl(ii).bbvim = [(blob_bb(2) - shifts_blob.v), (blob_bb(2) - shifts_blob.v + bl(ii).bbsize(2) - 1)];
+            bl(ii).bbwim = [blob_bb(3)-1, (blob_bb(3) + blob_bb(6))];
+        end
     end
 
     %%% We now Build ASTRA's geometry