Redefine origin of recgeo.orig(3) (z) to match with center of detector

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

zUtil_ForwardSim/gtSetupForwardSimulation.m

-function gtSetupForwardSimulation(varargin)
+function gtSetupForwardSimulation(phaseID, varargin)
 % GTSETUPFORWARDSIMULATION  Simple helper function to run gtForwardSimulate_v2
 %     gtSetupForwardSimulation()
 %     --------------------------
@@ -8,11 +8,14 @@ conf = struct( ...
     'reset_sample', true, ...
     'reset_spot2grain', [], ...
     'reset_difspot_table', [], ...
-    'reset_grains', [] );
-conf = parse_pv_pairs(conf, varargin);
-
+    'reset_grains', [], ...
+    'list', []);
+[conf, rej_conf_pars] = parse_pv_pairs(conf, varargin);
 parameters = gtLoadParameters();
 
+[parameters.fsim, rej_pars] = parse_pv_pairs(parameters.fsim, rej_conf_pars);
+conf.mode = parameters.fsim.mode
+
 % Let's check every field is in, and in case let's update it!
 parameters = gtCheckParameters(parameters, 'fsim', 'verbose', true);
 parameters = gtCheckParameters(parameters, 'recgeo', 'verbose', true);
@@ -22,8 +25,9 @@ end
 if (~isfield(parameters.labgeo, 'omstep') || isempty(parameters.labgeo.omstep))
     parameters.labgeo.omstep = gtAcqGetOmegaStep(parameters);
 end
+
 % Updating recgeo with a consistent set of parameters
-parameters.recgeo = gtGeoRecDefaultParameters(parameters.detgeo, parameters.samgeo);
+parameters.recgeo = gtGeoRecDefaultParameters(parameters.detgeo, parameters.samgeo, parameters.acq);
 gtSaveParameters(parameters);
 
 gtDBConnect();
@@ -58,6 +62,7 @@ for ii = 1:nof_phases
     ngrains(ii) = length(grain);
 end
 
+
 if (isempty(conf.reset_difspot_table))
     check = inputwdefault('Do you want to reset grainID/flag/phaseID in the difspot table? [y/n]', 'y');
     conf.reset_difspot_table = strcmpi(check, 'y');
@@ -151,6 +156,12 @@ if (~strcmpi(check, 'y'))
     save(fullfile(parameters.acq.dir, 'parameters.mat'), 'parameters');
 end
 
+% If list is provided, the grain_ids are distributed over the cluster
+if isempty(conf.list)
+    conf.list = 1 : ngrains(phaseID)
+end
+
+
 % launch forward simulation process to OAR - split to two jobs
 check = inputwdefault([ ...
     'Launch Forward Simulation with OAR (o), here on the command line ' ...
@@ -172,7 +183,7 @@ switch(lower(check))
         OARh   = (OARtmp - OARm) / 60; % hours
 
         OAR_parameters.walltime = sprintf('%02d:%02d:00', OARh, OARm);
-
+        OAR_parameters.otherparameters = sprintf('mode %s ', conf.mode);
         disp('Using OAR parameters:')
         disp(OAR_parameters)
         disp(['Using ' num2str(OAR_parameters.njobs) ' OAR jobs']);
@@ -186,8 +197,8 @@ switch(lower(check))
                 'walltime', OAR_parameters.walltime, 'mem', OAR_parameters.mem);
         else
             OAR_make('gtForwardSimulate_v2', 1, ngrains(phaseID), OAR_parameters.njobs, ...
-                [parameters.acq.dir ' ' phaseID_str], true, ...
-                'walltime', OAR_parameters.walltime, 'mem', OAR_parameters.mem);
+                sprintf('%s %s %s ', parameters.acq.dir, phaseID_str, OAR_parameters.otherparameters), true, ...
+                'walltime', OAR_parameters.walltime, 'mem', OAR_parameters.mem, 'distribute', true, 'list', conf.list);
         end
     case 'c'
         disp('Launching forward simulation...')
@@ -196,7 +207,7 @@ switch(lower(check))
         if (isfield(parameters.labgeo, 'sourcepoint') && ~isempty(parameters.labgeo.sourcepoint))
             gtForwardSimulatePoly(1, ngrains(phaseID), parameters.acq.dir, phaseID);
         else
-            gtForwardSimulate_v2(1, ngrains(phaseID), parameters.acq.dir, phaseID, 'display_figure', false);
+            gtForwardSimulate_v2(1, ngrains(phaseID), parameters.acq.dir, phaseID, 'display_figure', false, 'list', conf.list);
         end
     otherwise
         disp('Quitting forward simulation...')