From 8dcabc19cbbd41df4cdbb94c027b515dd40a0845 Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Wed, 4 Feb 2015 16:57:33 +0100
Subject: [PATCH] GtSample/GtPhase: added infrastructure for holding the
information about extended grains and clusters of grains
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
zUtil_DataStructures/GtGrain.m | 7 ---
zUtil_DataStructures/GtPhase.m | 106 ++++++++++++++++++++++++--------
zUtil_DataStructures/GtSample.m | 22 +++++--
3 files changed, 97 insertions(+), 38 deletions(-)
delete mode 100644 zUtil_DataStructures/GtGrain.m
diff --git a/zUtil_DataStructures/GtGrain.m b/zUtil_DataStructures/GtGrain.m
deleted file mode 100644
index a241a34a..00000000
--- a/zUtil_DataStructures/GtGrain.m
+++ /dev/null
@@ -1,7 +0,0 @@
-classdef GtGrain < handle % XXX - To be removed after 31/12/2014
- properties
- mergedIDs = [];
- threshold = 0;
- selectedDiffspots = [];
- end
-end
diff --git a/zUtil_DataStructures/GtPhase.m b/zUtil_DataStructures/GtPhase.m
index 031e59cc..929e84c3 100644
--- a/zUtil_DataStructures/GtPhase.m
+++ b/zUtil_DataStructures/GtPhase.m
@@ -3,20 +3,25 @@ classdef GtPhase < handle
% grains are organized in a performance oriented structure and get/set methods
% are provided, to aid the consistent use of the class.
properties
- grains = {}; % XXX - To be removed after 31/12/2014
- selectedGrains = []; % Booleans that enable/disable grains
- completeness = []; % Index of completeness of a grain [0, 1]
- center = []; % Center of mass of the grain
- R_vector = []; % Orientation (in Rodrigues space) of the grain
- boundingBox = []; % Bounding Box: [x y z lx ly lz] ?
- active = true; % Boolean that enables/disables the phase
- phaseName = ''; % Recognisable name for the phase
- volumeFile = ''; % Path of the mat file which contains the data.
- % The syntax is: 'filename:field' where field is
- % the field in the mat file which actually contains
- % the volume.
- bboxExtremes = [];
+ selectedGrains = true(0, 1); % Booleans that enable/disable grains
+ completeness = zeros(0, 1); % Index of completeness of a grain [0, 1]
+ center = zeros(0, 3); % Center of mass of the grain
+ R_vector = zeros(0, 3); % Orientation (in Rodrigues space) of the grain
+ boundingBox = zeros(0, 6); % Bounding Box: [x y z lx ly lz] ?
+ active = true; % Boolean that enables/disables the phase
+ phaseName = ''; % Recognisable name for the phase
+ volumeFile = ''; % Path of the mat file which contains the data.
+ % The syntax is: 'filename:field' where field is
+ % the field in the mat file which actually contains
+ % the volume.
+ bboxExtremes = zeros(0, 6);
orderedPositions = {};
+
+ use_extended = false(0, 1);
+ extended_params = GtPhase.makeExtendedField(cell(0, 1), cell(0, 1));
+
+ clusters = GtPhase.makeCluster( ...
+ cell(0, 1), cell(0, 1), cell(0, 1), cell(0, 1), cell(0, 1));
end
properties (Access = public, Hidden = true)
@@ -53,6 +58,12 @@ classdef GtPhase < handle
obj.boundingBox = zeros(number, 6);
obj.bboxExtremes = zeros(number, 6);
obj.orderedPositions = {};
+
+ obj.use_extended = false(number, 1);
+ temp_init_cell = cell(number, 1);
+ obj.extended_params = GtPhase.makeExtendedField(temp_init_cell, temp_init_cell);
+ obj.clusters = GtPhase.makeCluster( ...
+ cell(0, 1), cell(0, 1), cell(0, 1), cell(0, 1), cell(0, 1));
end
function pushGrain(obj)
@@ -67,6 +78,10 @@ classdef GtPhase < handle
obj.boundingBox = [obj.boundingBox; 0 0 0 0 0 0];
obj.bboxExtremes = [obj.bboxExtremes; 0 0 0 0 0 0];
obj.orderedPositions = {};
+
+ obj.use_extended = [obj.use_extended; false];
+ obj.extended_params = [obj.extended_params; ...
+ GtPhase.makeExtendedField([], [])];
end
function copy = getCopy(obj)
@@ -84,6 +99,10 @@ classdef GtPhase < handle
copy.bboxExtremes = obj.bboxExtremes;
copy.orderedPositions = obj.orderedPositions;
+
+ copy.use_extended = obj.use_extended;
+ copy.extended_params = obj.extended_params;
+ copy.clusters = obj.clusters;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -119,7 +138,11 @@ classdef GtPhase < handle
function setMergeIDs(obj, grainid, ids)
obj.grains{grainid}.mergeIDs = ids;
end
-
+
+ function setUseExtended(obj, grainid, use_ext)
+ obj.use_extended(grainid, 1) = use_ext;
+ end
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Getter Functions
@@ -165,6 +188,14 @@ classdef GtPhase < handle
shift = obj.boundingBox(grainid, 1:3);
end
+ function use_ext = getUseExtended(obj, grainid)
+ use_ext = obj.use_extended(grainid, 1);
+ end
+
+ function aclusters = getActiveClusters(obj)
+ aclusters = obj.clusters([obj.clusters(:).active]);
+ end
+
% grains fields
function ids = getMergeIDs(obj, grainid)
ids = obj.grains{grainid}.mergeIDs;
@@ -175,7 +206,7 @@ classdef GtPhase < handle
end
function grainIDs = getGrainsWithCompletenessLessThan(obj, value)
- % GTPHASE/GETGRAINSWITHCOMPLETENESSLESSTHAN Gets grains with
+ % GTPHASE/GETGRAINSWITHCOMPLETENESSLESSTHAN Gets grains with
% (0 < completeness <= value)
grainIDs = find(obj.completeness <= value & obj.completeness > 0);
end
@@ -184,16 +215,16 @@ classdef GtPhase < handle
% GTPHASE/GETDESELECTEDGRAINS Gets deselected grains
deselected = find(obj.selectedGrains == false);
end
-
+
function selected = getSelectedGrains(obj)
% GTPHASE/GETSELECTEDGRAINS Gets selected grains
selected = find(obj.selectedGrains == true);
end
-
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Analysis Functions
-
+
function buildBBSearchList(obj)
% buildBBSearchList(obj)
for ii = 1:size(obj.bboxExtremes, 2)
@@ -203,7 +234,7 @@ classdef GtPhase < handle
function matchList = simpleSearchBBtouched(obj, point)
% matchList = simpleSearchBBtouched(obj, point)
-
+
matchList = find( obj.bboxExtremes(:,1) <= point(1) ...
& obj.bboxExtremes(:,2) <= point(2) ...
& obj.bboxExtremes(:,3) <= point(3) ...
@@ -216,7 +247,7 @@ classdef GtPhase < handle
function IDs = getNeighbours(obj, grainID, oversize)
% IDs = getNeighbours(obj, grainID, oversize)
-
+
if (~exist('oversize', 'var'))
oversize = 1;
end
@@ -234,11 +265,10 @@ classdef GtPhase < handle
IDs = setdiff(find(all(relativeCenters < (maxDistances * oversize), 2)), grainID);
end
-
-
+
function merge = checkOverlapConflict(obj, id1, id2, pixelsize)
% function merge = checkOverlapConflict(obj, id1, id2, pixelsize)
-
+
merge_value1 = false;
merge_value2 = false;
@@ -254,7 +284,7 @@ classdef GtPhase < handle
if (dist < thr_dist)
merge_value1 = true;
end
-
+
% R_vector
r1 = obj.R_vector(id1, :);
r2 = obj.R_vector(id2, :);
@@ -265,7 +295,7 @@ classdef GtPhase < handle
if (angle < thr_angle)
merge_value2 = true;
end
-
+
merge.grainID_1 = id1;
merge.grainID_2 = id2;
merge.center_1 = c1;
@@ -281,4 +311,30 @@ classdef GtPhase < handle
merge.tobemerged = merge_value1 & merge_value2;
end
end
+
+ methods (Access = public, Static)
+ function extended_grain = makeExtendedField(bb_r_space, bb_o_space)
+ extended_grain = struct( ...
+ 'bb_r_space', bb_r_space, 'bb_o_space', bb_o_space);
+ end
+
+ function cluster = makeCluster(included_ids, ref_r_vec, bb_r_space, bb_o_space, active)
+ if (~exist('active', 'var') || isempty(active))
+ active = false;
+ end
+ cluster = struct( ...
+ 'included_ids', included_ids, 'ref_r_vec', ref_r_vec, ...
+ 'bb_r_space', bb_r_space, 'bb_o_space', bb_o_space, ...
+ 'active', active);
+ end
+
+ function obj = loadobj(obj)
+ % Function to keep some sort of backwards compatibility
+ if (numel(obj.use_extended) == 0)
+ obj.use_extended = false(obj.grains_number, 1);
+ temp_init_cell = cell(obj.grains_number, 1);
+ obj.extended_params = GtPhase.makeExtendedField(temp_init_cell, temp_init_cell);
+ end
+ end
+ end
end
diff --git a/zUtil_DataStructures/GtSample.m b/zUtil_DataStructures/GtSample.m
index 477ea624..9711b518 100644
--- a/zUtil_DataStructures/GtSample.m
+++ b/zUtil_DataStructures/GtSample.m
@@ -5,7 +5,7 @@ classdef GtSample < handle
volumeFile = '';
dilVolFile = '';
absVolFile = '';
-
+
fileTable = '';
version;
@@ -37,6 +37,12 @@ classdef GtSample < handle
obj.version = GtSample.getCurrentVersion();
end
+ function delete(obj)
+ for ii = 1:numel(obj.phases)
+ delete(obj.phases{ii});
+ end
+ end
+
function copy = getCopy(obj)
num_phases = numel(obj.phases);
copy = GtSample(num_phases, obj.volumeFile, ...
@@ -70,6 +76,9 @@ classdef GtSample < handle
obj.mergePhaseField(other, phaseNum, 'boundingBox', 0);
% Merge bboxExtremes
obj.mergePhaseField(other, phaseNum, 'bboxExtremes', 0);
+
+ % Merge bboxExtremes
+ obj.mergePhaseField(other, phaseNum, 'use_extended', 0);
end
end
@@ -84,7 +93,7 @@ classdef GtSample < handle
if (~exist('fieldName', 'var'))
fieldName = 'sample';
end
-
+
lock = GtLockDB(fileTable, fileName);
lock.acquire();
@@ -124,7 +133,7 @@ classdef GtSample < handle
fileName = fullfile('4_grains', 'sample.mat');
end
- sample = obj;
+ sample = obj; %#ok<NASGU>
save(fileName, 'sample', '-v7.3');
end
@@ -133,8 +142,9 @@ classdef GtSample < handle
% instances to find the grains which have a lower completeness than the
% value
- grainIDs = {};
- for phaseID = 1:numel(obj.phases)
+ num_phases = numel(obj.phases);
+ grainIDs = cell(num_phases, 1);
+ for phaseID = 1:num_phases
grainIDs{phaseID} = ...
obj.phases{phaseID}.getGrainsWithCompletenessLessThan(value);
end
@@ -199,7 +209,7 @@ classdef GtSample < handle
lock.release();
end
-
+
function sample = loadFromFile(fileName, fieldName)
% GTSAMPLE/LOADFROMFILE Not synchronized loading from a file
--
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