some changes to simplify cluster & extended reconstructions on OAR

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

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;

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( ...

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

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')