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Commit c04ac62f authored by Christophe Le Bourlot's avatar Christophe Le Bourlot
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Add the option sample_shif during the 'assemble volume' step, to shift the... 

Add the option sample_shif during the 'assemble volume' step, to shift the sample of the given vector in order to have it within the field of view
parent e15ab051
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5_reconstruction/GtAssembleVol3D.m
+ 47
− 17
View file @ c04ac62f
...@@ -541,6 +541,13 @@ classdef GtAssembleVol3D < handle ...@@ -541,6 +541,13 @@ classdef GtAssembleVol3D < handle
rot = gtMathsRotationTensorComposite(rot_axes, rot_angles); rot = gtMathsRotationTensorComposite(rot_axes, rot_angles);
end end
% Sample translation
sample_shift = obj.localPar.sample_shift;
sample_shift_size = size(sample_shift);
if sample_shift_size(2)<3
sample_shift = [0, 0, 0];
end
% Adding clusters first! % Adding clusters first!
clusters = sample.phases{phase_id}.getActiveClusters(); clusters = sample.phases{phase_id}.getActiveClusters();
...@@ -579,7 +586,7 @@ classdef GtAssembleVol3D < handle ...@@ -579,7 +586,7 @@ classdef GtAssembleVol3D < handle
if (obj.localPar.solve_conflict_with_intensity) if (obj.localPar.solve_conflict_with_intensity)
[p_gids, p_int_vol, p_dm_vol] = obj.placeClusterSubVolume( ... [p_gids, p_int_vol, p_dm_vol] = obj.placeClusterSubVolume( ...
clusters(ii).included_ids(1), cl_rec.ODF6D, cl_rec.SEG, p_gids, p_int_vol, p_dm_vol); clusters(ii).included_ids(1), cl_rec.ODF6D, cl_rec.SEG, p_gids, p_int_vol, p_dm_vol, sample_shift);
else else
seg_vol = int16(cl_rec.SEG.seg); seg_vol = int16(cl_rec.SEG.seg);
seg_bb = cl_rec.SEG.segbb; seg_bb = cl_rec.SEG.segbb;
...@@ -592,15 +599,15 @@ classdef GtAssembleVol3D < handle ...@@ -592,15 +599,15 @@ classdef GtAssembleVol3D < handle
int_vol = int_vol * numel(find(seg_vol)) / sum(int_vol(:)); int_vol = int_vol * numel(find(seg_vol)) / sum(int_vol(:));
p_gids = gtPlaceSubVolume( p_gids, seg_vol, ... p_gids = gtPlaceSubVolume( p_gids, seg_vol, ...
seg_bb(1:3), ... seg_bb(1:3) + sample_shift, ...
clusters(ii).included_ids(1), ... clusters(ii).included_ids(1), ...
obj.localPar.overlaps); obj.localPar.overlaps);
p_int_vol = gtPlaceSubVolume( p_int_vol, ... p_int_vol = gtPlaceSubVolume( p_int_vol, ...
int_vol, seg_bb(1:3) ); int_vol, seg_bb(1:3) + sample_shift );
seg = struct('vol', seg_vol, 'bb', seg_bb); seg = struct('vol', seg_vol, 'bb', seg_bb);
p_dm_vol = obj.placeSubDmVol(p_dm_vol, cl_rec.ODF6D, seg); p_dm_vol = obj.placeSubDmVol(p_dm_vol, cl_rec.ODF6D, seg, sample_shift);
end end
catch mexc catch mexc
gtPrintException(mexc, sprintf('\nCluster %d (%s) failed!!\n', ii, str_ids)); gtPrintException(mexc, sprintf('\nCluster %d (%s) failed!!\n', ii, str_ids));
...@@ -685,17 +692,19 @@ classdef GtAssembleVol3D < handle ...@@ -685,17 +692,19 @@ classdef GtAssembleVol3D < handle
if (obj.localPar.deal_with_twins) if (obj.localPar.deal_with_twins)
[p_gids, obj.twinInfo{phase_id}.output{ii}] = ... [p_gids, obj.twinInfo{phase_id}.output{ii}] = ...
obj.placeTwinSubVolume(gauge, p_gids, phase_id, grain_id, seg_vol, seg_bb); obj.placeTwinSubVolume(gauge, p_gids, phase_id, grain_id, seg_vol, seg_bb, sample_shift);
elseif (obj.localPar.solve_conflict_with_intensity) elseif (obj.localPar.solve_conflict_with_intensity)
if (assemble_6D) if (assemble_6D)
[p_gids, p_int_vol, p_dm_vol] = obj.placeClusterSubVolume( ... [p_gids, p_int_vol, p_dm_vol] = obj.placeClusterSubVolume( ...
grain_id, gr_rec, gr_seg, p_gids, p_int_vol, p_dm_vol); grain_id, gr_rec, gr_seg, p_gids, p_int_vol, p_dm_vol, sample_shift);
else else
[p_gids, p_int_vol] = obj.placeClusterSubVolume( ... [p_gids, p_int_vol] = obj.placeClusterSubVolume( ...
grain_id, gr_rec, gr_seg, p_gids, p_int_vol); grain_id, gr_rec, gr_seg, p_gids, p_int_vol, sample_shift);
end end
else else
p_gids = gtPlaceSubVolume(p_gids, seg_vol, seg_bb(1:3), grain_id, obj.localPar.overlaps); %fprintf(" seg_bb(1:3): ");
p_gids = gtPlaceSubVolume(p_gids, seg_vol, seg_bb(1:3) + sample_shift, grain_id, obj.localPar.overlaps);
end end
if (assemble_6D && ~obj.localPar.solve_conflict_with_intensity) if (assemble_6D && ~obj.localPar.solve_conflict_with_intensity)
seg = struct('vol', seg_vol, 'bb', seg_bb); seg = struct('vol', seg_vol, 'bb', seg_bb);
...@@ -705,7 +714,7 @@ classdef GtAssembleVol3D < handle ...@@ -705,7 +714,7 @@ classdef GtAssembleVol3D < handle
crop_bb(1:3) = crop_bb(1:3) - gr_rec.shift + 1; crop_bb(1:3) = crop_bb(1:3) - gr_rec.shift + 1;
int_vol = gtCrop(gr_rec.intensity, crop_bb) .* logical(seg_vol); int_vol = gtCrop(gr_rec.intensity, crop_bb) .* logical(seg_vol);
int_vol = int_vol * numel(find(seg_vol)) / sum(int_vol(:)); int_vol = int_vol * numel(find(seg_vol)) / sum(int_vol(:));
p_int_vol = gtPlaceSubVolume(p_int_vol, int_vol, seg_bb(1:3)); p_int_vol = gtPlaceSubVolume(p_int_vol, int_vol, seg_bb(1:3) + sample_shift);
end end
% Trigger callback (usually used in graphical applications) % Trigger callback (usually used in graphical applications)
...@@ -730,6 +739,7 @@ classdef GtAssembleVol3D < handle ...@@ -730,6 +739,7 @@ classdef GtAssembleVol3D < handle
end end
function cluster_rec = mergeTwinClusterRec(~, cluster_rec, dilate_steps) function cluster_rec = mergeTwinClusterRec(~, cluster_rec, dilate_steps)
%sample_shift not added here...
if (exist('dilate_steps', 'var') && ~isempty(dilate_steps) ... if (exist('dilate_steps', 'var') && ~isempty(dilate_steps) ...
&& (dilate_steps > 0)) && (dilate_steps > 0))
seg_vol = single(cluster_rec.SEG(1).seg); seg_vol = single(cluster_rec.SEG(1).seg);
...@@ -763,10 +773,10 @@ classdef GtAssembleVol3D < handle ...@@ -763,10 +773,10 @@ classdef GtAssembleVol3D < handle
cluster_rec = struct('ODF6D', cl_rec, 'SEG', cl_seg); cluster_rec = struct('ODF6D', cl_rec, 'SEG', cl_seg);
end end
function [ph_gids, ph_ints, ph_dms] = placeClusterSubVolume(obj, grain_id, gr_rec, gr_seg, ph_gids, ph_ints, ph_dms) function [ph_gids, ph_ints, ph_dms] = placeClusterSubVolume(obj, grain_id, gr_rec, gr_seg, ph_gids, ph_ints, ph_dms, sample_shift)
% the bbox extremes start from 0 ad not from 1 (matlab coords). % the bbox extremes start from 0 ad not from 1 (matlab coords).
% seg_bb(1:3) is a shift (argument 3) that starts from zero! % seg_bb(1:3) is a shift (argument 3) that starts from zero!
[lims_vol, lims_gr] = gtGetVolsIntersectLimits(size(ph_gids), size(gr_seg.seg), gr_seg.segbb(1:3)); [lims_vol, lims_gr] = gtGetVolsIntersectLimits(size(ph_gids), size(gr_seg.seg), gr_seg.segbb(1:3) + sample_shift);
% Getting the subvolumes -> so we operate all the costy % Getting the subvolumes -> so we operate all the costy
% operations on smaller volumes % operations on smaller volumes
...@@ -834,12 +844,20 @@ classdef GtAssembleVol3D < handle ...@@ -834,12 +844,20 @@ classdef GtAssembleVol3D < handle
end end
end end
function [volume, g_info] = placeTwinSubVolume(obj, gauge, volume, phase_id, grain_id, seg_vol, seg_bb) function [volume, g_info] = placeTwinSubVolume(obj, gauge, volume, phase_id, grain_id, seg_vol, seg_bb, sample_shift)
sample = obj.getSample(); sample = obj.getSample();
% Sample translation
sample_shift = obj.localPar.sample_shift;
+ sample_shift_size = size(sample_shift);
+ if sample_shift_size(2)<3
+ sample_shift = [0, 0, 0];
+ end
% the bbox extremes start from 0 ad not from 1 (matlab coords). % the bbox extremes start from 0 ad not from 1 (matlab coords).
% seg_bb(1:3) is a shift (argument 3) that starts from zero! % seg_bb(1:3) is a shift (argument 3) that starts from zero!
[limsVolume, limsGrain] = gtGetVolsIntersectLimits(size(volume), size(seg_vol), seg_bb(1:3)); [limsVolume, limsGrain] = gtGetVolsIntersectLimits(size(volume), size(seg_vol), seg_bb(1:3) + sample_shift);
% Getting the subvolumes -> so we operate all the costy % Getting the subvolumes -> so we operate all the costy
% operations on smaller volumes % operations on smaller volumes
...@@ -945,12 +963,12 @@ classdef GtAssembleVol3D < handle ...@@ -945,12 +963,12 @@ classdef GtAssembleVol3D < handle
% because the might have cropped the volumes, due to grains % because the might have cropped the volumes, due to grains
% falling out of the volume % falling out of the volume
volume = gtPlaceSubVolume(volume, sub_phase_vol, ... volume = gtPlaceSubVolume(volume, sub_phase_vol, ...
(limsVolume(1, :) - 1), 0, 'assign'); (limsVolume(1, :) - 1) + sample_shift, 0, 'assign');
else else
g_info = {}; g_info = {};
% Ok, no conflict or no twin case -> let's treat it as % Ok, no conflict or no twin case -> let's treat it as
% normal case % normal case
volume = gtPlaceSubVolume(volume, seg_vol, seg_bb(1:3), ... volume = gtPlaceSubVolume(volume, seg_vol, seg_bb(1:3) + sample_shift, ...
grain_id, obj.localPar.overlaps); grain_id, obj.localPar.overlaps);
end end
end end
...@@ -1317,8 +1335,12 @@ classdef GtAssembleVol3D < handle ...@@ -1317,8 +1335,12 @@ classdef GtAssembleVol3D < handle
conf.force_only_indexed = false; conf.force_only_indexed = false;
conf.solve_conflict_with_intensity = false; conf.solve_conflict_with_intensity = false;
conf.rotation_axes = zeros(0, 3); conf.rotation_axes = zeros(0, 3);
conf.rotation_angles = zeros(0, 1); conf.rotation_angles = zeros(0, 1);
% add a sample shift after assembling to have it in the field of view
conf.sample_shift = zeros(0, 3);
end end
function [newVol, offset] = convertCombinedVolumeToUIDs(phaseIDs, grainIDs, offset) function [newVol, offset] = convertCombinedVolumeToUIDs(phaseIDs, grainIDs, offset)
...@@ -1352,8 +1374,16 @@ classdef GtAssembleVol3D < handle ...@@ -1352,8 +1374,16 @@ classdef GtAssembleVol3D < handle
phaseIDs(grainIDs == 0) = 0; phaseIDs(grainIDs == 0) = 0;
end end
function dmvol = placeSubDmVol(dmvol, vol6D, seg) function dmvol = placeSubDmVol(dmvol, vol6D, seg, sample_shift)
% GTASSEMBLEVOL3D/placeSubDmVol % GTASSEMBLEVOL3D/placeSubDmVol
if nargin < 4
sample_shift = [0, 0, 0];
end
sample_shift_size = size(sample_shift);
if sample_shift_size(2)<3
sample_shift = [0, 0, 0];
end
seg_bb = [seg.bb(1:3) - vol6D.shift + 1, seg.bb(4:6)]; seg_bb = [seg.bb(1:3) - vol6D.shift + 1, seg.bb(4:6)];
for ii_dim = 1:3 for ii_dim = 1:3
single_dim_dmvol = vol6D.voxels_avg_R_vectors(:, :, :, ii_dim); single_dim_dmvol = vol6D.voxels_avg_R_vectors(:, :, :, ii_dim);
...@@ -1361,7 +1391,7 @@ classdef GtAssembleVol3D < handle ...@@ -1361,7 +1391,7 @@ classdef GtAssembleVol3D < handle
single_dim_dmvol(~seg.vol) = 0; single_dim_dmvol(~seg.vol) = 0;
dmvol = gtPlaceSubVolume( dmvol, single_dim_dmvol, ... dmvol = gtPlaceSubVolume( dmvol, single_dim_dmvol, ...
[seg.bb(1:3), ii_dim-1], [], 'assign'); [seg.bb(1:3), ii_dim-1] + [sample_shift, 0], [], 'assign');
end end
end end
......
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