diff --git a/zUtil_DataStructures/GtPhase.m b/zUtil_DataStructures/GtPhase.m
index 6217a7cd8a48deba4567d5a001044555aa711a4f..90e47785b706d521fef3165e88cdb387cb1b6a13 100644
--- a/zUtil_DataStructures/GtPhase.m
+++ b/zUtil_DataStructures/GtPhase.m
@@ -8,6 +8,7 @@ classdef GtPhase < handle
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] ?
+ volume = zeros(0, 1); % Volume of the segmented grain
active = true; % Boolean that enables/disables the phase
phaseName = ''; % Recognisable name for the phase
volumeFile = ''; % Path of the mat file which contains the data.
@@ -53,6 +54,7 @@ classdef GtPhase < handle
obj.R_vector = zeros(number, 3);
obj.boundingBox = zeros(number, 6);
obj.bboxExtremes = zeros(number, 6);
+ obj.volume = zeros(number, 1);
obj.orderedPositions = {};
obj.use_extended = false(number, 1);
@@ -62,6 +64,21 @@ classdef GtPhase < handle
cell(0, 1), cell(0, 1), cell(0, 1), cell(0, 1), cell(0, 1), cell(0, 1));
end
+ function dropGrain(obj)
+ obj.grains_number = obj.grains_number - 1;
+
+ obj.selectedGrains = obj.selectedGrains(1 : end-1);
+ obj.completeness = obj.completeness(1 : end-1);
+ obj.center = obj.center(1 : end-1, :);
+ obj.R_vector = obj.R_vector(1: end-1, :);
+ obj.boundingBox = obj.boundingBox(1 : end-1, :);
+ obj.bboxExtremes = obj.bboxExtremes(1: end-1, :);
+ obj.orderedPositions = {};
+
+ obj.use_extended = obj.use_extended(1:end-1);
+ obj.extended_params = obj.extended_params(1:end-1);
+ end
+
function pushGrain(obj)
% GTPHASE/PUSHGRAIN Adds a new empty grain at the end of the list
obj.grains_number = obj.grains_number + 1;
@@ -229,6 +246,13 @@ classdef GtPhase < handle
bbox = obj.bboxExtremes(grainid, :);
end
+ function volume = getGrainVolume(obj, grainid)
+ if ((~exist('grainid', 'var') || isempty(grainid)))
+ grainid = 1:obj.getNumberOfGrains();
+ end
+ volume = prod(obj.boundingBox(grainid, 4:6),2);
+ end
+
function shift = getBoundingBoxShift(obj, grainid)
if ((~exist('grainid', 'var') || isempty(grainid)))
grainid = 1:obj.getNumberOfGrains();
@@ -258,6 +282,33 @@ classdef GtPhase < handle
aclusters = obj.clusters([obj.clusters(:).active]);
end
+ function setClusterActive(obj, clusterID, state)
+ obj.clusters(clusterID).active = state;
+ end
+
+ function clusterIDs = getActiveClusterIDs(obj)
+ clusterIDs = find([obj.clusters.active]);
+ end
+
+ function cluster_table = getClusterTable(obj)
+ active_clusters = obj.getActiveClusterIDs;
+ grainIDs = [];
+ clusterIDs = [];
+ for ii = 1:numel(active_clusters)
+ grainIDs = [grainIDs, obj.clusters(active_clusters(ii)).included_ids];
+ clusterIDs = [clusterIDs, repmat(active_clusters(ii), 1, numel(obj.clusters(active_clusters(ii)).included_ids))];
+ end
+ cluster_table = cat(1,grainIDs, clusterIDs);
+ end
+
+ function clusterID = getClusterID(obj, grainID)
+ cluster_table = obj.getClusterTable();
+ if ~isempty(cluster_table)
+ clusterID = cluster_table(2, find(cluster_table(1, :) == grainID));
+ else
+ clusterID = [];
+ end
+ end
% grains fields
% function ids = getMergeIDs(obj, grainid)
% ids = obj.grains{grainid}.mergeIDs;
diff --git a/zUtil_Deformation/Gt6DReconstructionAlgorithmFactory.m b/zUtil_Deformation/Gt6DReconstructionAlgorithmFactory.m
index f089bd7e481656d9222899bdd66d9fc05729a5ae..7269b3cbb4c90f7815cd7c50726e0fcbc3bded40 100644
--- a/zUtil_Deformation/Gt6DReconstructionAlgorithmFactory.m
+++ b/zUtil_Deformation/Gt6DReconstructionAlgorithmFactory.m
@@ -526,12 +526,19 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
offsets = {};
end
+ psf = {};
if (isfield(bl, 'psf'))
- psf = arrayfun(@(x){ permute(x.psf, [1 3 2]) }, bl);
+ if ~isempty(bl.psf)
+ psf = arrayfun(@(x){ permute(x.psf, [1 3 2]) }, bl);
+ end
elseif (isfield(proj, 'psf'))
- psf = { permute(proj.psf, [1 3 2]) };
- else
- psf = {};
+ if ~isempty(proj.psf)
+ psf = { permute(proj.psf, [1 3 2]) };
+ end
+ elseif (isfield(self.parameters.rec.grains.options, 'psf'))
+ if ~isempty(self.parameters.rec.grains.options.psf)
+ psf = { permute(self.parameters.rec.grains.options.psf, [1 3 2]) };
+ end
end
algo_params = struct( ...
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m b/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
index d9d7cd123e2f48d310071b86651bb742fb89749d..f1a5e3b40f9a2ce7c834a7e5b09b47353efcd178 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
@@ -19,6 +19,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
'ospace_lims', [], ...
'include_all', false, ...
'save', false, ...
+ 'use_extended', true, ...
'psf', []);
conf = parse_pv_pairs(conf, varargin);
@@ -316,6 +317,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
sample = GtSample.loadFromFile();
sample.phases{phase_id}.extended_params(gr.id) = ...
GtPhase.makeExtendedField(estim_space_bbox_pix, estim_orient_bbox);
+ sample.phases{phase_id}.setUseExtended(gr.id, conf.use_extended);
sample.saveToFile();
fprintf('\b\b: Done.\n')
end
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m b/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
index a552ea9eb84d4e298f4cfc834c74cdb0e310122d..0be03f8cf83af352fb4e6f8424e20ab3f29dbea0 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
@@ -15,7 +15,9 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
'min_eta', 15, ...
'det_index', 1, ...
'ospace_oversize', 1.1, ...
- 'save', false );
+ 'save', true, ...
+ 'cluster_type', 0, ...
+ 'active', true);
conf = parse_pv_pairs(conf, varargin);
num_grains = numel(grs_list);
@@ -298,7 +300,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
fprintf('Saving to sample.mat..')
sample = GtSample.loadFromFile();
cl_info = GtPhase.makeCluster(grs_list, refor.R_vector, ...
- estim_space_bbox_pix, estim_orient_bbox);
+ estim_space_bbox_pix, estim_orient_bbox, conf.cluster_type, conf.active);
sample.phases{phase_id}.setClusterInfo(grs_list, cl_info);
sample.saveToFile();
fprintf('\b\b: Done.\n')