From 31eaed5074762f800455aea2dd0c78f6b988a831 Mon Sep 17 00:00:00 2001
From: Laura Nervo <lnervo@esrf.fr>
Date: Fri, 15 Jun 2012 14:12:02 +0000
Subject: [PATCH] sample.mat : fix bug with spot2grain and sample loading and
updating...
routine:
gtSetupForwardSimulation
gtFsimCheckMissingGrains
gtFsimRunMissingGrains
gtSetupReconstruction
gtCreateGtSample
Conflicts : update and improving the routine.
gtAnalyseForwardSimulation
gtUpdateGrainsConflicts
Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>
git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@536 4c865b51-4357-4376-afb4-474e03ccb993
---
5_reconstruction/gtAnalyseForwardSimulation.m | 9 +-
5_reconstruction/gtUpdateGrainsConflicts.m | 5 +-
zUtil_DataStructures/GtGrainAnalyser.m | 12 +-
zUtil_DataStructures/GtPhase.m | 120 ++++++++++++------
zUtil_DataStructures/GtSample.m | 2 +-
zUtil_DataStructures/gtCreateGtSample.m | 57 +++++----
6 files changed, 122 insertions(+), 83 deletions(-)
diff --git a/5_reconstruction/gtAnalyseForwardSimulation.m b/5_reconstruction/gtAnalyseForwardSimulation.m
index 628d429f..a919ac17 100644
--- a/5_reconstruction/gtAnalyseForwardSimulation.m
+++ b/5_reconstruction/gtAnalyseForwardSimulation.m
@@ -37,7 +37,6 @@ function grains_merge = gtAnalyseForwardSimulation(save_flag, maxnum)
% .idconflict = list of grain ids in conflict <double 1xnumgrain>
% .delete = logical (true: flag = 1, false: flag = 2)
% .flag = logical (1: lowest grainid, 2: higher grainid)
-% .alluniquespots = [grainid, [difspots]] <cell>
%
% .conflicts{grainid} = conflicts structure <cell numgrainx1>
% .difspots = [idconflict, [difspots]] <cell numgrainx1>
@@ -164,7 +163,8 @@ for phaseid = 1 : num_phases
grains_merge{phaseid}.summary{grainid}.totspots = totspots;
grains_merge{phaseid}.summary{grainid}.numgrain = numgrain;
grains_merge{phaseid}.summary{grainid}.idconflict = idconflict;
-
+ grains_merge{phaseid}.nofConflicts(grainid) = totspots;
+
for kk = 1 : length(idconflict)
[tmp_s, tmp_c] = sfCompareGrains(...
@@ -177,7 +177,6 @@ for phaseid = 1 : num_phases
grains_merge{phaseid}.summary{grainid} = gtAddMatFile(grains_merge{phaseid}.summary{grainid},tmp_s,1,1,1);
grains_merge{phaseid}.conflicts{grainid} = gtAddMatFile(grains_merge{phaseid}.conflicts{grainid},tmp_c,1,1,1);
- grains_merge{phaseid}.nofConflicts(grainid) = length(idconflict);
end
else % no conflicts
@@ -233,9 +232,6 @@ else
return;
end
-orig_spots = unique(grain(2,:));
-s.alluniquespots = {idgrain, orig_spots};
-
current_spots = sfGetDifspotsConflicts(grain, idconflict);
c(kk).difspots = {idconflict, current_spots};
@@ -247,6 +243,7 @@ else
c(kk).merge = [];
end
+orig_spots = unique(grain(2,:));
if isempty(setdiff(orig_spots, current_spots))
c(kk).allequals = true;
else
diff --git a/5_reconstruction/gtUpdateGrainsConflicts.m b/5_reconstruction/gtUpdateGrainsConflicts.m
index f48055a7..9a037f85 100644
--- a/5_reconstruction/gtUpdateGrainsConflicts.m
+++ b/5_reconstruction/gtUpdateGrainsConflicts.m
@@ -15,7 +15,7 @@ sample = [];
filedir = fullfile('4_grains');
load(fullfile(filedir,'grains_merge.mat'));
filename = fullfile(filedir,'sample.mat');
-load(fullfile(filedir,'sample.mat'));
+load(filename);
for phaseid = 1 : length(sample.phases)
@@ -23,13 +23,12 @@ for phaseid = 1 : length(sample.phases)
merge = grains_merge{phaseid};
for grainid = 1 : length(phase.grains)
- fprintf('\b\b\b\b\b\b\b\b\b\b')
+ fprintf('\b\b\b\b\b\b\b\b\b')
phase.setTotSpots(grainid, merge.summary{grainid}.totspots);
phase.setNumGrain(grainid, merge.summary{grainid}.numgrain);
phase.setIdConflict(grainid, merge.summary{grainid}.idconflict);
phase.setDelete(grainid, merge.summary{grainid}.delete);
phase.setFlag(grainid, merge.summary{grainid}.flag);
- phase.setAllUniqueSpots(grainid, merge.summary{grainid}.alluniquespots);
phase.setDifspots(grainid, merge.conflicts{grainid}.difspots);
phase.setMaxNum(grainid, merge.conflicts{grainid}.maxnum);
diff --git a/zUtil_DataStructures/GtGrainAnalyser.m b/zUtil_DataStructures/GtGrainAnalyser.m
index af0e64c4..6fd3549a 100644
--- a/zUtil_DataStructures/GtGrainAnalyser.m
+++ b/zUtil_DataStructures/GtGrainAnalyser.m
@@ -1,12 +1,12 @@
classdef GtGrainAnalyser
properties
- totspots = [];
- numgrain = [];
- idconflict = [];
- delete = false;
- flag = 0;
- alluniquespots = {};
+ totspots = [];
+ numgrain = [];
+ idconflict = [];
+ delete = false;
+ flag = 0;
+ difspotID = [];
end
end
diff --git a/zUtil_DataStructures/GtPhase.m b/zUtil_DataStructures/GtPhase.m
index 1e7e9759..5b0e3bf4 100644
--- a/zUtil_DataStructures/GtPhase.m
+++ b/zUtil_DataStructures/GtPhase.m
@@ -139,8 +139,8 @@ classdef GtPhase < handle
obj.summary{grainid}.flag = f;
end
- function setAllUniqueSpots(obj, grainid, allunique)
- obj.summary{grainid}.alluniquespots = allunique;
+ function setDifspotID(obj, grainid, spots)
+ obj.summary{grainid}.difspotID = spots;
end
function setDifspots(obj, grainid, spots)
@@ -161,43 +161,24 @@ classdef GtPhase < handle
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Getter Functions
-
+
+ % phase fields
function hasC = getHasConficts(obj, grainid)
hasC = obj.hasConflicts(grainid, 1);
end
-
- function inconflict = getConflictsGrains(obj)
- inconflict = find(obj.hasConflicts == true);
- end
-
+
function nofC = getNofConficts(obj, grainid)
nofC = obj.nofConflicts(grainid, 1);
end
-
- function grainIDs = getGrainsWithNofConflictsLessThan(obj, value)
- grainIDs = find(obj.nofConflicts < value & obj.nofConflicts > 0);
- end
-
- function grainIDs = getGrainsWithNofConflictsMoreThan(obj, value)
- grainIDs = find(obj.nofConflicts > value);
- end
-
+
function sel = getSelected(obj, grainid)
sel = obj.selectedGrains(grainid, 1);
end
- function deselected = getDeselectedGrains(obj)
- deselected = find(obj.selectedGrains == false);
- end
-
function compl = getCompleteness(obj, grainid)
compl = obj.completeness(grainid, 1);
end
- function grainIDs = getGrainsWithCompletenessLessThan(obj, value)
- grainIDs = find(obj.completeness < value);
- end
-
function center = getCenter(obj, grainid)
center = obj.center(grainid, :);
end
@@ -218,6 +199,7 @@ classdef GtPhase < handle
shift = obj.boundingBox(grainid, 1:3);
end
+ % grains fields
function thr = getThreshold(obj, grainid)
thr = obj.grains{grainid}.threshold;
end
@@ -226,18 +208,11 @@ classdef GtPhase < handle
selDiffspots = obj.grains{grainid}.selectedDiffspots;
end
- function grainIDs = getGrainsWithDifspotsNumLessThan(obj, value)
- grainsArray = [obj.grains{:}];
- % Using the cell is much faster (5.6/1.2 ratio)
- % numDifSpots = arrayfun(@(x)length(x.('selectedDiffspots')), grainsArray);
- numDifSpots = cellfun(@length, {grainsArray.('selectedDiffspots')});
- grainIDs = find(numDifSpots < value);
- end
-
function grain = getGrain(obj, grainid)
grain = obj.grains{grainid};
end
-
+
+ % summary fields
function tot = getTotSpots(obj, grainid)
tot = obj.summary{grainid}.totspots;
end
@@ -258,11 +233,15 @@ classdef GtPhase < handle
f = obj.summary{grainid}.flag;
end
- function allunique = getAllUniqueSpots(obj, grainid)
- allunique = obj.summary{grainid}.alluniquespots;
+ function ids = getDifspotID(obj, grainid)
+ ids = obj.summary{grainid}.difspotID;
end
-
+ function summary = getSummary(obj, grainid)
+ summary = obj.summary{grainid};
+ end
+
+ % conflicts fields
function spots = getDifspots(obj, grainid)
spots = obj.conflicts{grainid}.difspots;
end
@@ -279,14 +258,73 @@ classdef GtPhase < handle
alleq = obj.conflicts{grainid}.allequals;
end
- function summary = getSummary(obj, grainid)
- summary = obj.summary{grainid};
- end
-
function conflicts = getConflicts(obj, grainid)
conflicts = obj.conflicts{grainid};
end
+ % get all values from grains
+ function allvalues = getAllValuesFromGrainsField(obj, field)
+ grainsArray = [obj.grains{:}];
+ allvalues = cellfun(@(name) name, {grainsArray.(field)});
+ end
+
+ % get all values from summary
+ function allvalues = getAllValuesFromSummaryField(obj, field)
+ summaryArray = [obj.summary{:}];
+ allvalues = cellfun(@(name) name, {summaryArray.(field)});
+ end
+
+ % get all values from conflicts
+ function allvalues = getAllValuesFromConflictsField(obj, field)
+ conflictsArray = [obj.conflicts{:}];
+ allvalues = cellfun(@(name) name, {conflictsArray.(field)});
+ end
+
+ % less than
+ function grainIDs = getGrainsWithThresholdLessThan(obj, value)
+ allvalues = getAllValuesFromGrainsField(obj, 'threshold');
+ grainIDs = find(allvalues < value);
+ end
+
+ function grainIDs = getSummaryWithFieldValueLessThan(obj, field, value)
+ allvalues = getAllValuesFromSummaryField(obj, field);
+ grainIDs = find(allvalues < value);
+ end
+
+ function grainIDs = getConflictsWithFieldValueLessThan(obj, field, value)
+ allvalues = getAllValuesFromConflictsField(obj, field);
+ grainIDs = find(allvalues < value);
+ end
+
+ % between 0 and value
+ function grainIDs = getGrainsWithNofConflictsLessThan(obj, value)
+ grainIDs = find(obj.nofConflicts < value & obj.nofConflicts > 0);
+ end
+
+ function grainIDs = getGrainsWithCompletenessLessThan(obj, value)
+ grainIDs = find(obj.completeness < value & obj.completeness > 0);
+ end
+
+ function grainIDs = getGrainsWithDiffspotsNumLessThan(obj, value)
+ grainsArray = [obj.grains{:}];
+ numDiffSpots = cellfun(@length, {grainsArray.('selectedDiffspots')});
+ grainIDs = find(numDiffSpots < value & numDiffSpots > 0);
+ end
+
+ % more than value
+ function grainIDs = getGrainsWithNofConflictsMoreThan(obj, value)
+ grainIDs = find(obj.nofConflicts > value);
+ end
+
+ % logical values
+ function inconflict = getConflictsGrains(obj)
+ inconflict = find(obj.hasConflicts == true);
+ end
+
+ function deselected = getDeselectedGrains(obj)
+ deselected = find(obj.selectedGrains == false);
+ end
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Analysis Functions
function buildBBSearchList(obj)
diff --git a/zUtil_DataStructures/GtSample.m b/zUtil_DataStructures/GtSample.m
index b7bf93de..e754d7b2 100644
--- a/zUtil_DataStructures/GtSample.m
+++ b/zUtil_DataStructures/GtSample.m
@@ -51,7 +51,7 @@ classdef GtSample < handle
obj.mergeSummaryField(other, phaseNum, grainNum, 'idconflict', []);
obj.mergeSummaryField(other, phaseNum, grainNum, 'numgrain', []);
obj.mergeSummaryField(other, phaseNum, grainNum, 'totspots', []);
- obj.mergeSummaryField(other, phaseNum, grainNum, 'alluniquespots', {});
+ obj.mergeSummaryField(other, phaseNum, grainNum, 'difspotID', []);
end
for grainNum = 1:length(other.phases{phaseNum}.conflicts)
obj.mergeConflictsField(other, phaseNum, grainNum, 'difspots', {});
diff --git a/zUtil_DataStructures/gtCreateGtSample.m b/zUtil_DataStructures/gtCreateGtSample.m
index 3d00853b..d1acd808 100644
--- a/zUtil_DataStructures/gtCreateGtSample.m
+++ b/zUtil_DataStructures/gtCreateGtSample.m
@@ -1,6 +1,8 @@
function sample = gtCreateGtSample()
-% GTCREATEGTSAMPLE Loads the grain.mat file and generates the GtSample data
-% structure
+% GTCREATEGTSAMPLE Loads the grain.mat file and generates the GtSample data
+% structure
+% sample = gtCreateGtSample()
+% ---------------------------
parameters = [];
load('parameters.mat');
@@ -18,50 +20,53 @@ difspot_num = mym(['SELECT count(*) FROM ' parameters.acq.name 'difspot']); % n
spot2grain = cell(difspot_num, 1); % cell array linking difspots with grainids
spot2phase = cell(difspot_num, 1);
-for jj = 1:phaseNum
- sprintf('Collecting information for phase %d', jj)
+for phaseid = 1 : phaseNum
+ sprintf('Collecting information for phase %d', phaseid)
phaseName = parameters.cryst(phaseNum).name;
- index = fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', jj), 'index.mat');
- load(index);
-
+ indexterFile = fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', phaseid), 'index.mat');
+ grain = [];
+ load(indexterFile,'grain');
+
% Preallocate the space for the grains
grainsNum = length(grain);
phase = GtPhase(phaseName, grainsNum);
-
- phaseDir = sprintf('phase_%02d', jj);
- fprintf('Phase %02d: ', jj);
- for ii = 1:grainsNum
- fprintf('%04d/%04d', ii, grainsNum);
-
- grainFile = sprintf('grain_%04d.mat', ii);
+
+ phaseDir = sprintf('phase_%02d', phaseid);
+ fprintf('Phase %02d: ', phaseid);
+ for grainid = 1 : grainsNum
+ fprintf('%04d/%04d', grainid, grainsNum);
+
+ grainFile = sprintf('grain_%04d.mat', grainid);
grainPath = fullfile('4_grains', phaseDir, grainFile);
- grainInfo = load(grainPath, 'vol', 'shift', 'difspotID', 'completeness', 'selected', 'segbb', 'threshold');
-
- phase.setR_vector(ii, grain{ii}.R_vector);
- phase.setCenter(ii, grain{ii}.center);
+ grainInfo = load(grainPath, 'shift', 'vol', 'segbb', 'selected', 'threshold', 'completeness', 'difspotID');
+
+ phase.setR_vector(grainid, grain{grainid}.R_vector);
+ phase.setCenter(grainid, grain{grainid}.center);
if (~isfield(grainInfo, 'segbb'))
- phase.setBoundingBox(ii, [grainInfo.shift, size(grainInfo.vol)]);
+ phase.setBoundingBox(grainid, [grainInfo.shift, size(grainInfo.vol)]);
else
- phase.setBoundingBox(ii, grainInfo.segbb);
+ phase.setBoundingBox(grainid, grainInfo.segbb);
end
- phase.setThreshold(ii, grainInfo.threshold);
selected = zeros(length(grainInfo.difspotID),1);
selected(grainInfo.selected) = 1;
- phase.setSelectedDiffspots(ii, selected);
+ phase.setSelectedDiffspots(grainid, selected);
+
+ phase.setThreshold(grainid, grainInfo.threshold);
+ phase.setCompleteness(grainid, grainInfo.completeness);
+ phase.setDifspotID(grainid, grainInfo.difspotID);
- phase.setCompleteness(ii, grainInfo.completeness);
difspotID = grainInfo.difspotID;
for kk = 1 : length(grainInfo.selected)
if grainInfo.selected(kk)
- spot2grain{difspotID(kk)} = [spot2grain{difspotID(kk)}, ii];
- spot2phase{difspotID(kk)} = [spot2phase{difspotID(kk)}, jj];
+ spot2grain{difspotID(kk)} = [spot2grain{difspotID(kk)}, grainid];
+ spot2phase{difspotID(kk)} = [spot2phase{difspotID(kk)}, phaseid];
end
end
fprintf('\b\b\b\b\b\b\b\b\b');
end
- sample.phases{jj} = phase;
+ sample.phases{phaseid} = phase;
fprintf('(%04d) Done.\n', grainsNum);
end
--
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