small fixes

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

4_grains/gtLoadGrainRec.m

 function grain_det = gtLoadGrainRec(phase_id, grain_id, varargin)
-    conf = struct('fields', {{}}, 'parameters', {[]}, 'is_extended', {false});
+    conf = struct('fields', {{}}, 'parameters', {[]}, 'is_extended', {false}, 'full_details', {false});
     conf = parse_pv_pairs(conf, varargin);
 
     if (isempty(conf.parameters))
@@ -11,6 +11,8 @@ function grain_det = gtLoadGrainRec(phase_id, grain_id, varargin)
     for ii = numel(grain_id):-1:1
         if (conf.is_extended)
             grain_file = fullfile(phase_dir, sprintf('grain_extended_details_%04d.mat', grain_id(ii)));
+        elseif (conf.full_details)
+            grain_file = fullfile(phase_dir, sprintf('grain_full_details_%04d.mat', grain_id(ii)));
         else
             grain_file = fullfile(phase_dir, sprintf('grain_details_%04d.mat', grain_id(ii)));
         end

5_reconstruction/GtAssembleVol3D.m

@@ -1306,7 +1306,7 @@ classdef GtAssembleVol3D < handle
             if (~exist('sortOrder', 'var'))
                 sortOrder = 'descend';
             end
-
+            sample=GtSample.loadFromFile;
             grainsize = zeros(grainsNum, 1);
             gauge = GtGauge(grainsNum, sprintf('Loading grains from phase %02d: ', phase_id));
             for ii = 1:grainsNum
@@ -1317,7 +1317,7 @@ classdef GtAssembleVol3D < handle
                     else
                         vol = obj.localPar.cache.get('grain_rec', {phase_id, grain_ids(ii)}, 'SEG');
                     end
-                    grainsize(ii) = length(find(vol(:)));
+                    grainsize(ii) = length(find(vol.seg(:)));
                 catch
                     % We ignore the error because it will come up again
                     % later

5_reconstruction/gtAstraCreateProjections.m

@@ -55,7 +55,7 @@ proj    = astra_mex_data3d('get', proj_id);
 
 if (exist('psf','var') && ~isempty(psf))
     psf_obj = GtPSF();
-    psf_obj.set_psf_direct(proj.psf, [hsize, vsize]);
+    psf_obj.set_psf_direct(psf, [hsize, vsize]);
     proj = psf_obj.apply_psf_direct(proj);
 end
 

5_reconstruction/gtReconstructGrainOrientation.m

@@ -8,7 +8,8 @@ function varargout = gtReconstructGrainOrientation(grain_id, phase_id, parameter
 
     conf = struct( ...
         'ospace_resolution', [], ...
-        'ospace_lims', [] );
+        'ospace_lims', [], ...
+        'extra_output', false );
     [conf, ~] = parse_pv_pairs(conf, varargin);
 
     rec_opts = gtReconstruct6DGetParamenters(parameters);
@@ -117,7 +118,7 @@ function varargout = gtReconstructGrainOrientation(grain_id, phase_id, parameter
         varargout{1} = ODF6D;
     end
 
-    if (algo.verbose)
+    if (conf.extra_output)
         [proj_blobs, proj_spots] = algo.getProjectionOfCurrentSolution();
 
         % Restoring initial volume size (depending on the rounding)

5_reconstruction/gtSetupReconstruction.m

@@ -175,9 +175,16 @@ if (~isempty(conf.grain_ids))
             check = inputwdefault('Launch grain segmentation via OAR? [y/n]', 'y');
             if (strcmpi(check, 'y'))
                 launch_on_OAR('gtChangeThreshold3D', first, last, ...
-                    phaseID_str, parameters, 'core', 4, 'distribute', false);
+                    phaseID_str, parameters, 'core', 4, 'distribute', true, 'list', conf.grain_ids);
             else
-                gtChangeThreshold3D(first, last, [], phase_id);
+                if isempty(conf.grain_ids)
+                    gtChangeThreshold3D(first, last, [], phase_id);
+                else
+                    t=GtThreshold();
+                    for i = 1 : numel(conf.grain_ids)
+                        t.singleGrainAutoThreshold(phase_id, conf.grain_ids(i));
+                    end
+                end
             end
         end
     end

zUtil_Cryst/gtDisorientation.m

@@ -41,9 +41,13 @@ par.sort       = '';
 par.latticepar = [];
 par.convention = 'X';
 par.constrain_to_sst = false;
-
+par.grain      = [];
 [par, rej_pars] = parse_pv_pairs(par, varargin);
 
+if isempty(symm)
+    p=gtLoadParameters;
+    symm = p.cryst.symm;
+end
 Symm = {symm.g3};
 
 switch par.input
@@ -59,6 +63,13 @@ switch par.input
         Ngrain1 = size(ori1, 2);
         Ngrain2 = size(ori2, 2);
         oriConversion = @(x) gtMathsEuler2OriMat(x);
+    case 'gr_id'
+        Ngrain1 = size(ori1, 1);
+        Ngrain2 = size(ori2, 1);
+        if isempty(par.grain)
+            load 4_grains/phase_01/index
+        end
+        oriConversion = @(x) gtMathsRod2OriMat(par.grain{x}.R_vector');
     otherwise
         gtError('gtDisorientation:wrong_input_type', ...
             'Allowed orientation types are ''rod'', ''orimat'', or ''euler''!');