From d4c2e307f0dd3ad05b9aeaeafb3f815ad9944c19 Mon Sep 17 00:00:00 2001
From: Lorenzo Valzania <valzania@rnice7-0201.esrf.fr>
Date: Thu, 5 Feb 2015 15:24:12 +0100
Subject: [PATCH] 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 | 7 +++++--
zUtil_DataStructures/GtPhase.m | 24 +++++++-----------------
zUtil_TomoUtils/GtGrainsManager.m | 2 +-
3 files changed, 13 insertions(+), 20 deletions(-)
diff --git a/4_grains/GtThreshold.m b/4_grains/GtThreshold.m
index 00d641b1..8922ad43 100644
--- a/4_grains/GtThreshold.m
+++ b/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;
diff --git a/zUtil_DataStructures/GtPhase.m b/zUtil_DataStructures/GtPhase.m
index 929e84c3..8d8f07d2 100644
--- a/zUtil_DataStructures/GtPhase.m
+++ b/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;
diff --git a/zUtil_TomoUtils/GtGrainsManager.m b/zUtil_TomoUtils/GtGrainsManager.m
index 3fee2732..15de519f 100644
--- a/zUtil_TomoUtils/GtGrainsManager.m
+++ b/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
--
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