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Commit ffc58d4a authored by Nicola Vigano's avatar Nicola Vigano
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Moving segmentation output to the details/reconstruction files 


Signed-off-by: default avatarNicola Vigano <nicola.vigano@esrf.fr>
parent 74c82e7d
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4_grains/GtThreshold.m
+ 15
− 27
View file @ ffc58d4a
......@@ -258,15 +258,15 @@ classdef GtThreshold < handle
end
methods (Access = protected)
function grain_rec = loadGrain(obj, phaseID, grainID, sample)
function grain_out = loadGrain(obj, phaseID, grainID, sample)
% GTTHRESHOLD/LOADGRAIN
% grain = loadGrain(obj, phaseID, grainID)
grain_rec = gtLoadGrain(phaseID, grainID, 'fields', {'id', 'vol', 'proj'});
grain_rec.shift = grain_rec.proj.shift;
grain_out = gtLoadGrain(phaseID, grainID, 'fields', {'id'});
grain_rec = gtLoadGrainRec(phaseID, grainID);
is_6D = isfield(obj.param.rec, 'grains') ...
&& ismember(upper(obj.param.rec.grains.algorithm), {'6DL1', '6DTV', '6DTVL1'});
&& strcmpi(obj.param.rec.grains.algorithm(1:2), '6D');
if (is_6D)
file_ext_rec_path = fullfile(obj.param.acq.dir, ...
'4_grains', sprintf('phase_%02d', phaseID), ...
......@@ -274,40 +274,27 @@ classdef GtThreshold < handle
if (sample.phases{phaseID}.getUseExtended(grainID))
grain_rec = load(file_ext_rec_path, 'ODF6D');
else
grain_rec = gtLoadGrainRec(phaseID, grainID);
end
grain_rec.vol = grain_rec.ODF6D.intensity;
grain_rec.shift = grain_rec.ODF6D.shift;
grain_out.vol = grain_rec.ODF6D.intensity;
grain_out.shift = grain_rec.ODF6D.shift;
else
grain_out.vol = grain_rec.VOL3D.intensity;
grain_out.shift = grain_rec.VOL3D.shift;
end
if (~isfield(grain_rec, 'vol') || isempty(grain_rec.vol))
if (~isfield(grain_out, 'vol') || isempty(grain_out.vol))
gtError('GtThreshold:wrong_argument', ...
'Volume to segment is empty!')
end
end
function saveGrain(obj, phaseID, grainID, grain_seg)
function saveGrain(~, phaseID, grainID, grain_seg)
% GTTHRESHOLD/SAVEGRAIN
% saveGrain(obj, phaseID, grainID, grain)
if (verLessThan('matlab', '7.14'))
phase_dir = fullfile(obj.param.acq.dir, '4_grains', ...
sprintf('phase_%02d', phaseID));
filePath = fullfile(phase_dir, sprintf('grain_%04d.mat', grainID));
seg = grain_seg.seg; %#ok<NASGU>
segbb = grain_seg.segbb; %#ok<NASGU>
threshold = grain_seg.threshold; %#ok<NASGU>
Area = grain_seg.Area; %#ok<NASGU>
seed = grain_seg.seed; %#ok<NASGU>
save(filePath, '-append', 'seg', 'segbb', 'threshold', 'Area', 'seed');
else
gtSaveGrain(phaseID, grainID, grain_seg, ...
'fields', {'seg', 'segbb', 'threshold', 'Area', 'seed'});
end
seg_struct = struct('SEG', grain_seg);
gtSaveGrainRec(phaseID, grainID, seg_struct, 'fields', {'SEG'});
end
function cluster = loadCluster(obj, phase_id, grain_ids)
......@@ -332,7 +319,8 @@ classdef GtThreshold < handle
cluster_rec.SEG = struct( ...
'seg', cluster.seg, 'segbb', cluster.segbb, ...
'threshold', cluster.threshold, 'Area', cluster.Area);
'threshold', cluster.threshold, 'Area', cluster.Area, ...
'seed', cluster.seed );
save(file_cluster_rec_path, '-struct', 'cluster_rec', '-v7.3');
end
......
4_grains/gtSaveGrainRec.m
+ 1
− 1
View file @ ffc58d4a
function gtSaveGrainRec(phase_id, grain_id, grain_det, varargin)
details_fields = {'VOL3D', 'ODF6D', 'ODFw', 'ODFuvw'};
details_fields = {'VOL3D', 'ODF6D', 'ODFw', 'ODFuvw', 'SEG'};
conf = struct( ...
'fields', {details_fields}, ...
'parameters', {[]}, ...
......
5_reconstruction/GtAssembleVol3D.m
+ 24
− 18
View file @ ffc58d4a
......@@ -124,13 +124,13 @@ classdef GtAssembleVol3D < handle
grainDirsModel = fullfile('4_grains', 'phase_%02d', 'grain_%04d.mat');
obj.localPar.cache.createModel(grainDirsModel, 'grain');
end
if (~obj.localPar.cache.isModel('grain_details'))
if (~obj.localPar.cache.isModel('grain_rec'))
grainDirsModel = fullfile('4_grains', 'phase_%02d', 'grain_details_%04d.mat');
obj.localPar.cache.createModel(grainDirsModel, 'grain_details');
obj.localPar.cache.createModel(grainDirsModel, 'grain_rec');
end
if (~obj.localPar.cache.isModel('grain_extended_details'))
if (~obj.localPar.cache.isModel('grain_ext_rec'))
grainDirsModel = fullfile('4_grains', 'phase_%02d', 'grain_extended_details_%04d.mat');
obj.localPar.cache.createModel(grainDirsModel, 'grain_extended_details');
obj.localPar.cache.createModel(grainDirsModel, 'grain_ext_rec');
end
if (obj.localPar.deal_with_twins)
......@@ -391,7 +391,7 @@ classdef GtAssembleVol3D < handle
fprintf(' Applying Absorption Mask.\n')
% Let's cut of the things out of the mask
newUidVol = zeros(size(uidVol), class(uidVol));
newUidVol = zeros(size(uidVol), 'like', uidVol);
indexes = (maskVol ~= 0);
newUidVol(indexes) = uidVol(indexes);
uidVol = newUidVol;
......@@ -609,11 +609,12 @@ classdef GtAssembleVol3D < handle
try
if (assemble_6D)
if (sample.phases{phase_id}.getUseExtended(grain_id))
vol6D = obj.localPar.cache.get('grain_extended_details', {phase_id, grain_id}, 'ODF6D');
vol6D = obj.localPar.cache.get('grain_ext_rec', {phase_id, grain_id}, 'ODF6D');
else
vol6D = obj.localPar.cache.get('grain_details', {phase_id, grain_id}, 'ODF6D');
vol6D = obj.localPar.cache.get('grain_rec', {phase_id, grain_id}, 'ODF6D');
end
end
gr_seg = obj.localPar.cache.get('grain_rec', {phase_id, grain_id}, 'SEG');
if (rotate_vols)
gr_proj = obj.localPar.cache.get('grain', {phase_id, grain_id}, 'proj');
......@@ -632,21 +633,26 @@ classdef GtAssembleVol3D < handle
vol6D.shift = gtFwdSimComputeVolumeShifts(...
gr_proj, obj.parameters, size(int_vol));
else
int_vol = obj.localPar.cache.get('grain', {phase_id, grain_id}, 'vol');
int_vol = gtRotateVolume(int_vol, rot);
vol3D = obj.localPar.cache.get('grain_rec', {phase_id, grain_id}, 'VOL3D');
int_vol = gtRotateVolume(vol3D.intensity, rot);
vol3D.shift = gtFwdSimComputeVolumeShifts(...
gr_proj, obj.parameters, size(int_vol));
end
thr = obj.localPar.cache.get('grain', {phase_id, grain_id}, 'threshold');
gr_rec_center = round(size(int_vol) / 2);
gr_seg = t.volumeThreshold(int_vol, thr, gr_rec_center);
seg_vol = int16(gr_seg.seg);
seg_bb = gr_seg.segbb;
seg_bb(1:3) = seg_bb(1:3) + vol6D.shift;
else
seg_vol = obj.localPar.cache.get('grain', {phase_id, grain_id}, 'seg');
seg_vol = int16(seg_vol);
seg_bb = obj.localPar.cache.get('grain', {phase_id, grain_id}, 'segbb');
gr_seg = t.volumeThreshold(int_vol, gr_seg.threshold, gr_rec_center);
if (assemble_6D)
gr_seg.segbb(1:3) = gr_seg.segbb(1:3) + vol6D.shift;
else
gr_seg.segbb(1:3) = gr_seg.segbb(1:3) + vol3D.shift;
end
end
seg_vol = int16(gr_seg.seg);
seg_bb = gr_seg.segbb;
catch mexc
gtPrintException(mexc, sprintf('\nGrain %d failed!!\n', grain_id));
gauge.rePrint();
......
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