Assembling: Fixed R-vector assembling

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

5_reconstruction/GtAssembleVol3D.m

@@ -547,10 +547,8 @@ classdef GtAssembleVol3D < handle
                         single_dim_dmvol = gtCrop(single_dim_dmvol, segbb);
                         single_dim_dmvol(~seg_vol) = 0;
 
-                        % Turning the C functions off is way slower, but
-                        % for some reason they don't work in this case
                         dmvol = gtPlaceSubVolume( dmvol, single_dim_dmvol, ...
-                            [volBBox(1:3), ii_dim-1], [], obj.localPar.overlaps, false);
+                            [volBBox(1:3), ii_dim-1], [], 'assign');
                     end
                 catch mexc
                     gtPrintException(mexc, sprintf('\nGrain %d failed!!\n', ii));

zUtil_Imaging/gtPlaceSubVolume.m

@@ -14,6 +14,11 @@ function output = gtPlaceSubVolume(output, input, shift, index, assign_op, use_c
 %     shift=[2 -2 0] means that voxel (a, b, c) will be at (a+2, b-2, c) in
 %     output.
 %
+%     if the output volume has more than 3 dimensions, the shifts have to
+%     be extended in order to select the position in the next dimensions.
+%     Otherwhise ones will be placed
+%     However, the placing will still happen in the first 3 dimensions
+%
 %     Note - this is used to add on volume to another one, rather than
 %     placing one image in the other.
 %     I have modified so it no longer adds it. I hope this doesn't break
@@ -32,6 +37,10 @@ function output = gtPlaceSubVolume(output, input, shift, index, assign_op, use_c
         assign_op = 'assign';
     end
 
+    if (index ~= 0)
+        input = index .* input;
+    end
+
     inputSize = size(input);
     outputSize = size(output);
     num_input_dims = numel(inputSize);
@@ -49,28 +58,17 @@ function output = gtPlaceSubVolume(output, input, shift, index, assign_op, use_c
     inputSize((num_input_dims+1):3) = 1;
     outputSize((num_output_dims+1):3) = 1;
 
-    shift((numel(shift)+1):max(num_output_dims, 3)) = 0;
-
-    % We add one because the shifting is done in matlab code!
-    extra_dims_shift = arrayfun(@(x){x+1}, shift(4:num_output_dims));
-
-    full_output = output;
-    if (~isempty(extra_dims_shift))
-        output = full_output(:, :, :, extra_dims_shift{:});
-    end
+    shift((numel(shift)+1):num_output_dims) = 0;
 
     % output and input volume limits
     [outLims, inLims] = gtGetVolsIntersectLimits(outputSize(1:3), inputSize, shift(1:3));
 
-    input = input(  inLims(1, 1):inLims(2, 1), ...
-                    inLims(1, 2):inLims(2, 2), ...
-                    inLims(1, 3):inLims(2, 3)  );
-    lims = [  outLims(1, 1) outLims(2, 1) ...
-              outLims(1, 2) outLims(2, 2) ...
-              outLims(1, 3) outLims(2, 3)  ];
-
     if (use_c_functions)
-        % Logicals are not handled in he C++ classes
+        shifts_op = [outLims(1, :) - 1, shift(4:end)];
+        shifts_ip = inLims(1, :) - 1;
+        dims = outLims(2, :) - outLims(1, :) + 1;
+
+        % Logicals are not handled in the C++ function
         is_out_logical = islogical(output);
         if (is_out_logical)
             output = uint8(output);
@@ -90,11 +88,11 @@ function output = gtPlaceSubVolume(output, input, shift, index, assign_op, use_c
 
         switch (assign_op)
             case {'zero', 'conflict', 'adaptive'} % Mark overlapping...
-                output = internal_gtAssignGrainToVol_interf( output, input, index, lims );
+                gtCxxPlaceSubVolumeInterf(output, input, shifts_op, shifts_ip, dims);
             case 'summed'
-                output = internal_gtAssignGrainToVol_sum( output, input, index, lims );
+                gtCxxPlaceSubVolumeSum(output, input, shifts_op, shifts_ip, dims);
             case {'assign', 'parent'}
-                output = internal_gtAssignGrainToVol( output, input, index, lims );
+                gtCxxPlaceSubVolumeAssign(output, input, shifts_op, shifts_ip, dims);
             otherwise
                 error('PLACE:wrong_argument', 'No option for "%s"', assign_op);
         end
@@ -103,6 +101,23 @@ function output = gtPlaceSubVolume(output, input, shift, index, assign_op, use_c
             output = logical(output);
         end
     else
+        input = input( ...
+            inLims(1, 1):inLims(2, 1), ...
+            inLims(1, 2):inLims(2, 2), ...
+            inLims(1, 3):inLims(2, 3) );
+        lims = [ ...
+            outLims(1, 1), outLims(2, 1), ...
+            outLims(1, 2), outLims(2, 2), ...
+            outLims(1, 3), outLims(2, 3) ];
+
+        % We add one because the shifting is done in matlab code!
+        extra_dims_shift = arrayfun(@(x){x+1}, shift(4:num_output_dims));
+
+        full_output = output;
+        if (~isempty(extra_dims_shift))
+            output = full_output(:, :, :, extra_dims_shift{:});
+        end
+
         switch (assign_op)
             case {'zero', 'conflict', 'adaptive'}
                 % Matlab sugars to do the same that 'internal_gtAssignGrainToVol_interf'
@@ -128,10 +143,10 @@ function output = gtPlaceSubVolume(output, input, shift, index, assign_op, use_c
             otherwise
                 error('PLACE:wrong_argument', 'No option for "%s"', assign_op);
         end
-    end
 
-    if (~isempty(extra_dims_shift))
-        full_output(:, :, :, extra_dims_shift{:}) = output;
-        output = full_output;
+        if (~isempty(extra_dims_shift))
+            full_output(:, :, :, extra_dims_shift{:}) = output;
+            output = full_output;
+        end
     end
 end