GtSample/GtPhase: fixed a few bugs introduced by removing the GtGrain class

Signed-off-by: Lorenzo Valzania <valzania@rnice7-0201.esrf.fr>

4_grains/GtThreshold.m

@@ -100,7 +100,7 @@ classdef GtThreshold < handle
                 gauge.incrementAndDisplay();
 
                 try
-                    grain = obj.loadGrain(phaseID, grainID);
+                    grain = obj.loadGrain(phaseID, grainID, sample);
 
                     % Actually threshold now!
                     if (obj.checkIsIterative())
@@ -144,8 +144,11 @@ classdef GtThreshold < handle
         % GTTHRESHOLD/singleGrainThresholdInFile
         % grain = singleGrainThresholdInFile(obj, phaseID, grainID, threshold, center)
 
+            samplefile  = fullfile(obj.param.acq.dir, '4_grains', 'sample.mat');
+            sample = GtSample.loadFromFile(samplefile);
+
             fprintf('Segmenting Grain %d, from phase %d.. ', grainID, phaseID);
-            grain = obj.loadGrain(phaseID, grainID);
+            grain = obj.loadGrain(phaseID, grainID, sample);
 
             if (exist('center', 'var'))
                 do_morpho = true;

zUtil_DataStructures/GtPhase.m

@@ -47,10 +47,6 @@ classdef GtPhase < handle
         % grains
             obj.grains_number    = number;
 
-            obj.grains           = cell(number,1);
-            for ii = 1:number
-                obj.grains{ii}   = GtGrain();
-            end
             obj.selectedGrains   = true(number, 1);
             obj.completeness     = ones(number, 1);
             obj.center           = zeros(number, 3);
@@ -70,7 +66,6 @@ classdef GtPhase < handle
         % GTPHASE/PUSHGRAIN Adds a new empty grain at the end of the list
             obj.grains_number    = obj.grains_number + 1;
 
-            obj.grains{end+1}    = GtGrain();
             obj.selectedGrains   = [obj.selectedGrains; true];
             obj.completeness     = [obj.completeness; 1];
             obj.center           = [obj.center; 0 0 0];
@@ -90,7 +85,6 @@ classdef GtPhase < handle
             copy.active           = obj.active;
             copy.volumeFile       = obj.volumeFile;
 
-            copy.grains           = obj.grains;
             copy.selectedGrains   = obj.selectedGrains;
             copy.completeness     = obj.completeness;
             copy.center           = obj.center;
@@ -135,9 +129,9 @@ classdef GtPhase < handle
         end
 
         % grains fields
-        function setMergeIDs(obj, grainid, ids)
-            obj.grains{grainid}.mergeIDs = ids;
-        end
+%         function setMergeIDs(obj, grainid, ids)
+%             obj.grains{grainid}.mergeIDs = ids;
+%         end
 
         function setUseExtended(obj, grainid, use_ext)
             obj.use_extended(grainid, 1) = use_ext;
@@ -197,13 +191,9 @@ classdef GtPhase < handle
         end
 
         % grains fields
-        function ids = getMergeIDs(obj, grainid)
-            ids = obj.grains{grainid}.mergeIDs;
-        end
-
-        function grain = getGrain(obj, grainid)
-            grain = obj.grains{grainid};
-        end
+%         function ids = getMergeIDs(obj, grainid)
+%             ids = obj.grains{grainid}.mergeIDs;
+%         end
 
         function grainIDs = getGrainsWithCompletenessLessThan(obj, value)
         % GTPHASE/GETGRAINSWITHCOMPLETENESSLESSTHAN  Gets grains with
@@ -251,7 +241,7 @@ classdef GtPhase < handle
             if (~exist('oversize', 'var'))
                 oversize = 1;
             end
-            numGrains = length(obj.grains);
+            numGrains = obj.getNumberOfGrains();
             replOnes = ones(numGrains, 1);
 
             halfLengths = obj.boundingBox(:, 4:6) / 2;

zUtil_TomoUtils/GtGrainsManager.m

@@ -1712,7 +1712,7 @@ classdef GtGrainsManager < GtVolView
             filePath = fullfile(obj.dataDir, '4_grains', ...
                                 sprintf('phase_%02d', phaseID), 'grain_*.mat');
             fileInfo = dir(filePath);
-            numGrains = length(phase.grains);
+            numGrains = phase.getNumberOfGrains();
             if (length(fileInfo) < numGrains)
                 upToDate = false;
                 return