From 9c66a0dd86a87e36d8a2190dbd6dfc49e4193ff9 Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Fri, 30 Jan 2015 20:18:01 +0100
Subject: [PATCH] Assembling: Fixed R-vector assembling
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
5_reconstruction/GtAssembleVol3D.m | 4 +-
zUtil_Imaging/gtPlaceSubVolume.m | 63 ++++++++++++++++++------------
2 files changed, 40 insertions(+), 27 deletions(-)
diff --git a/5_reconstruction/GtAssembleVol3D.m b/5_reconstruction/GtAssembleVol3D.m
index d0517d52..5ae04370 100644
--- a/5_reconstruction/GtAssembleVol3D.m
+++ b/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));
diff --git a/zUtil_Imaging/gtPlaceSubVolume.m b/zUtil_Imaging/gtPlaceSubVolume.m
index 5438c750..da61035c 100644
--- a/zUtil_Imaging/gtPlaceSubVolume.m
+++ b/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
--
GitLab