Enable reconstruction of twinclusters on OAR, using gtSetupReconstruction

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

4_grains/gtLoadCluster.m

-function cluster = gtLoadCluster(phase_id, grain_ids, varargin)
+function cluster = gtLoadCluster(phase_id, cl_or_gr_ids, varargin)
+% GTLOADCLUSTER load the projection input of a grain cluster
+%     cl = function cluster = gtLoadCluster(phase_id, cl_or_gr_ids, varargin)
+%     INPUT:
+%       phaseID          = <int>     phase ID
+%       cl_or_gr_ids     = <int>     either the cluster_id (->sample) or
+%                                    list of grain_ids composing the
+%                                    cluster
+%
+%     OPTIONAL INPUT (p/v pairs):
+%       fields           = <string>  only load specific  fields from
+%                                    cluster structure ('ODF6D', 'SEG')
+%       parameters       = <struct>  for security (make sure to load from right directory)                                
+%
     conf = struct('fields', {{}}, 'parameters', {[]});
     conf = parse_pv_pairs(conf, varargin);
 
@@ -8,13 +21,19 @@ function cluster = gtLoadCluster(phase_id, grain_ids, varargin)
         phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
     end
 
-    grain_ids_sorted = sort(grain_ids);
-
-    if (any(grain_ids_sorted ~= grain_ids))
-        warning('gtLoadCluster:wrong_argumet', ...
-            'Some grain IDs were no sorted: %s', sprintf(' %d', grain_ids));
+    if numel(cl_or_gr_ids) == 1  %if only one element we assume it refers to a cluster
+        sample = GtSample.loadFromFile;
+        grain_ids_sorted = sample.phases{phase_id}.clusters(cl_or_gr_ids).included_ids;
+    else
+        grain_ids_sorted = sort(cl_or_gr_ids);
+        if (any(grain_ids_sorted ~= cl_or_gr_ids))
+            warning('gtLoadCluster:wrong_argumet', ...
+            'Some grain IDs were no sorted: %s', sprintf(' %d', cl_or_gr_ids));
+        end
     end
 
+
+
     str_ids = sprintf('_%04d', grain_ids_sorted);
     cluster_file = fullfile(phase_dir, sprintf('grain_cluster%s.mat', str_ids));
 

4_grains/gtLoadClusterRec.m

-function cluster_rec = gtLoadClusterRec(phase_id, grain_ids, varargin)
+function cluster_rec = gtLoadClusterRec(phase_id, cl_or_gr_ids, varargin)
+% GTLOADCLUSTERREC load the 6D reconstruction output of a grain cluster
+%     cl = function cluster_rec = gtLoadClusterRec(phase_id, cl_or_gr_ids, varargin)
+%     INPUT:
+%       phaseID          = <int>     phase ID
+%       cl_or_gr_ids     = <int>     either the cluster_id (->sample) or
+%                                    list of grain_ids composing the
+%                                    cluster
+%
+%     OPTIONAL INPUT (p/v pairs):
+%       fields           = <string>  only load specific  fields from
+%                                    cluster structure ('ODF6D', 'SEG')
+%       parameters       = <struct>  for security (make sure to load from right directory)                               
+%
+
     conf = struct('fields', {{}}, 'parameters', {[]});
     conf = parse_pv_pairs(conf, varargin);
 
@@ -8,11 +22,15 @@ function cluster_rec = gtLoadClusterRec(phase_id, grain_ids, varargin)
         phase_dir = fullfile(conf.parameters.acq.dir, '4_grains', sprintf('phase_%02d', phase_id));
     end
 
-    grain_ids_sorted = sort(grain_ids);
-
-    if (any(grain_ids_sorted ~= grain_ids))
-        warning('gtLoadCluster:wrong_argumet', ...
-            'Some grain IDs were no sorted: %s', sprintf(' %d', grain_ids));
+    if numel(cl_or_gr_ids) == 1  %only one element - it refers to a cluster
+        sample = GtSample.loadFromFile;
+        grain_ids_sorted = sample.phases{phase_id}.clusters(cl_or_gr_ids).included_ids;
+    else
+        grain_ids_sorted = sort(cl_or_gr_ids);
+        if (any(grain_ids_sorted ~= cl_or_gr_ids))
+            warning('gtLoadCluster:wrong_argumet', ...
+            'Some grain IDs were no sorted: %s', sprintf(' %d', cl_or_gr_ids));
+        end
     end
 
     str_ids = sprintf('_%04d', grain_ids_sorted);

5_reconstruction/gtReconstructGrainTwinCluster.m

-function gtReconstructGrainTwinCluster(grain_ids, phase_id, parameters, varargin)
+function gtReconstructGrainTwinCluster(phase_id, cluster_id, workingdirectory, parameters, varargin)
 % gtReconstructGrainOrientation  6D reconstructions on a GPU machine
-%     gtAstraReconstructGrain(grainIDs, phaseID, [parameters])
+%     gtReconstructGrainTwinCluster(phase_id, cluster_id, workingdirectory, parameters, varargin)
 %     -------------------------------------------------------
+    cd(workingdirectory);
+
+    if (isdeployed)
+        global GT_DB %#ok<NUSED,TLEV>
+        global GT_MATLAB_HOME %#ok<NUSED,TLEV>
+        load('workspaceGlobal.mat');
+        phase_id   = str2double(phase_id);
+        cluster_id = str2double(cluster_id);
+    end
+
+    sample = GtSample.loadFromFile;
+    grain_ids = sample.phases{phase_id}.clusters(cluster_id).included_ids;
+
     if (~exist('parameters', 'var') || isempty(parameters))
         parameters = gtLoadParameters();
     end
@@ -150,4 +163,3 @@ function gtReconstructGrainTwinCluster(grain_ids, phase_id, parameters, varargin
         save(grain_full_details_file, 'ODF6D', '-v7.3');
     end
 end
-

5_reconstruction/gtSetupReconstruction.m

-function gtSetupReconstruction(phaseID, list)
+function gtSetupReconstruction(phaseID, varargin)
 % GTSETUPRECONSTRUCTION  Simple helper function to launch reconstruction and segmentation of
 %                        absorption volume - as well as reconstruction and segmentation of grain volumes
 %
-%     gtSetupReconstruction(phaseID, list)
+%     gtSetupReconstruction(phaseID, varargin)
 %     ------------------------------
 %
 %     INPUT:
 %       phaseID = number of the phase <double> {1}
-%       list    = vector of grainids, default value is {[1: num_grains]}
 %
+%     OPTIONAL INPUT:
+%       grain_ids    = vector of grain_ids, default value is {[1: num_grains]}
+%       cluster_ids  = vector of cluster_ids, default value is {[1: num_clusters]}
+%       'is_cluster
+%     Version 005 12-10-2016 by W. Ludwig
+%       Add possibility to launch grain-cluster reconstructions
 %     Version 004 25-05-2016 by W. Ludwig
 %       Add possibility to specify a list of grainids - which will be
 %       handled by OAR
@@ -23,6 +28,12 @@ function gtSetupReconstruction(phaseID, list)
 %       Move gtModifyStructure to before the abs reconstruction is done.
 
 GPU_OK = gtCheckGpu();
+conf.grain_ids = [];
+conf.cluster_ids = [];
+
+if (~isempty(varargin))
+    conf = parse_pv_pairs(conf, varargin);
+end
 
 if (~GPU_OK)
     disp('Not on a GPU machine, you won''t  be able to reconstruct localy!');
@@ -57,7 +68,7 @@ gtSaveParameters(parameters);
 
 nof_phases = numel(parameters.cryst);
 
-if (nof_phases > 1)
+if (nof_phases > 1) && isempty(phaseID)
     phaseID = inputwdefaultnumeric('Enter phaseID', num2str(1));
 end
 phaseID_str = sprintf('%02d', phaseID);
@@ -128,16 +139,21 @@ else
     end
 end
 
-% If input parameter list is empty, we will use all grains by default
-first = 1;
-last  = sample.phases{phaseID}.getNumberOfGrains();
+% If input parameter grain_ids is empty, we will use all  grains by default
 
-if (~exist('list', 'var') || isempty(list))
-   list = [first : last];
+
+if ~isempty(varargin)
+    conf = parse_pv_pairs(conf, varargin);
 end
 
+if isempty(conf.grain_ids)
+    first = 1;
+    last  = sample.phases{phaseID}.getNumberOfGrains();
+    list = [first : last];
+end
 
-check = inputwdefault('Launch reconstruction? [y/n]', 'y');
+
+check = inputwdefault('Launch grain reconstruction? [y/n]', 'y');
 rec_on_OAR = false;
 if  strcmpi(check, 'y')
     if (GPU_OK)
@@ -148,13 +164,35 @@ if  strcmpi(check, 'y')
     end
     if (rec_on_OAR)
         launch_on_OAR('gtReconstructGrains', first, last, phaseID_str, ...
-            parameters, 'njobs', 8, 'walltime', 3600 * 16, ...
-            'gpu', true, 'distribute', true, 'list', list);
+                parameters, 'njobs', 8, 'walltime', 3600 * 16, ...
+                'gpu', true, 'distribute', true, 'list', list);
     else
         gtReconstructGrains(first, last, parameters.acq.dir, phaseID, parameters, 'list', list);
     end
 end
 
+if ~isempty(conf.cluster_ids)
+    list = conf.cluster_ids;
+    check = inputwdefault('Launch cluster reconstruction? [y/n]', 'y');
+    rec_on_OAR = false;
+    if  strcmpi(check, 'y')
+        if (GPU_OK)
+            check2 = inputwdefault('Launch grain reconstruction via OAR? [y/n]', 'y');
+            rec_on_OAR = strcmpi(check2, 'y');
+        else
+            rec_on_OAR = true;
+        end
+        if (rec_on_OAR)
+            launch_on_OAR('gtReconstructGrainTwinClusters', first, last, phaseID_str, ...
+                    parameters, 'njobs', 8, 'walltime', 3600 * 16, ...
+                    'gpu', true, 'distribute', true, 'list', list);
+        else
+                gtReconstructGrainTwinClusters(first, last, parameters.acq.dir, phaseID, parameters, 'list', list);
+        end
+
+    end
+end
+
 if (~rec_on_OAR)
     check = inputwdefault('Launch grain segmentation? [y/n]', 'y');
     if  strcmpi(check, 'y')

zUtil_Conf/batch-dev-conf.xml

@@ -47,6 +47,9 @@
     <function name="gtReconstructGrains">
       <path absolute="false">5_reconstruction/gtReconstructGrains.m</path>
     </function>
+    <function name="gtReconstructGrainTwinClusters">
+      <path absolute="false">5_reconstruction/gtReconstructGrainTwinClusters.m</path>
+    </function>
     <function name="gtForwardSimulate_v2">
       <path absolute="false">zUtil_ForwardSim/gtForwardSimulate_v2.m</path>
     </function>