Twins forward Simulation : try to improve the functionalities

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@996 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_Twins/gtTwinForwardSimulate.m

-function grain = gtTwinForwardSimulate(first, last, workingdirectory, phaseID, grain, varargin)
+function grain = gtTwinForwardSimulate(phaseID, grain, varargin)
 % GTTWINFORWARDSIMULATE  Finds diffraction spots in the database relative to the twin variant
-%     grain = gtTwinForwardSimulate(first, last, workingdirectory, phaseID, grain, varargin)
+%     grain = gtTwinForwardSimulate(phaseID, grain, varargin)
 %     --------------------------------------------------------------------------------------
 %
 %     INPUT:
-%       first            = <int>    first grainid
-%       last             = <int>    last grainid
-%       workingdirectory = <string> working directory
 %       phaseID          = <int>    phase number {1}
-%       grain            = <struct> grain structure with fields
+%       grain            = <struct> grain structure of interest
 %
 %     OPTIONAL INPUT (varargin):
-%       bb_size         = <int>     size of search area  ([] will use default projection size)
-%       assemble_figure = <logical> collects all difspots and assembles them into a fullimage
-%       save_grain      = <logical> flag to save or not the twins_####_##.mat
+%       save_grain      = <logical> flag to save or not the twins_####.mat
+%       variantIDs      = <double>  array of ID for variants {all}
 %
 %     OUTPUT:
 %       grain  = cell structure with fields for each variant:
@@ -39,7 +35,6 @@ if isdeployed
   load('workspaceGlobal.mat');
 end
 
-cd(workingdirectory);
 gtDBConnect();
 
 parameters = [];
@@ -56,11 +51,13 @@ end
 if isdeployed
   phaseID = str2double(phaseID);
   fsim.display_figure = false;
-else
-  % in interactive mode we can modify parameters
-  fsim = parse_pv_pairs(fsim, varargin);
 end
 
+app.save_grain = false;
+app.variantIDs = 1:length(grain.g_twins);
+app = parse_pv_pairs(app, varargin);
+
+
 difspotfile = '2_difspot/difspot00001.edf';
 if exist(difspotfile, 'file');
   info = edf_info(difspotfile);
@@ -98,15 +95,15 @@ mymcmd = sprintf(['SELECT difspotID, CentroidX, CentroidY, CentroidImage, '...
   allspots.BoundingBoxYsizes, allspots.BoundingBoxXorigins, allspots.BoundingBoxYorigins] = mym(mymcmd);
 
 
-gr = grain;
 % loop over the variants
 
-for kk=1:length(gr.g_twins)
+
+for kk=app.variantIDs
     fprintf('\nRunning forward simulation for variant %d ...\n',kk);
 
-    variant = gr.g_twins(kk);
+    variant = grain.g_twins(kk);
     % assume same center for parent and twin
-    graincenter = gr.center ./ pixelsize;    % graincenter contains COM coordinates in pixels
+    graincenter = grain.center ./ pixelsize;    % graincenter contains COM coordinates in pixels
     out.g        = variant.g;
     out.R_vector = variant.R_vector;
 
@@ -114,15 +111,11 @@ for kk=1:length(gr.g_twins)
     %  define theshold values which will be used during the database search later
 
     dif_Xsize    = mean(allspots.BoundingBoxXsizes);
-    %dif_Xsize    = gr.stat.bbxsmean; % average X Size of difspots
     dif_Ysize    = mean(allspots.BoundingBoxYsizes);
-    %dif_Ysize    = gr.stat.bbysmean; % average Y Size of difspots
 
     % take the biggest spot and add a relative extra margin (multiplicative factor oversize)
-    %hsize = round(max(gr.bbxs)*fsim.oversize);
     hsize = round(max(allspots.BoundingBoxXsizes)*fsim.oversize);
     % ...same for vertical direction
-    %vsize = round(max(gr.bbys)*fsim.oversize);
     vsize = round(max(allspots.BoundingBoxYsizes)*fsim.oversize);
 
     u = variant.allblobs.uv(:, 1);
@@ -370,12 +363,12 @@ for kk=1:length(gr.g_twins)
 
     out.included  = flag(included) == 3;
     out.selected  = flag(included) == 4;%>= fsim.selected;  % vector of logicals with pre-selected spots active
-    out.id        = gr.id;
-    out.parent_R_vector  = gr.R_vector;
+    out.id        = grain.id;
+    out.parent_R_vector  = grain.R_vector;
     out.phaseid   = phaseID;
     out.center    = graincenter*pixelsize;
     out.ondet     = ondet;
-    out.allblobs  = gr.allblobs;
+    out.allblobs  = grain.allblobs;
     out.full      = full;
     out.flag      = flag;
     out.status    = status;
@@ -384,7 +377,7 @@ for kk=1:length(gr.g_twins)
     out.difspotID = spotid(included);
     out.omega     = omega(included);
     out.hklsp     = hklsp(included,:);
-    out.uvw       = gr.allblobs.uvw(ondet(included),:);
+    out.uvw       = grain.allblobs.uvw(ondet(included),:);
     out.uv_exp    = [U(included), V(included)];
     out.bb        = bb(included,:);
     out.r_th      = r_th(included,:);
@@ -412,16 +405,13 @@ for kk=1:length(gr.g_twins)
       gtShowFsim(out,fsim.Grayscale)
     end
     
-    gr.g_twins(kk).out = out;
-    
-    
+    grain.g_twins(kk).out = out;
 
 end % loop over the variants
 
-grain = gr;
-if fsim.save_grain
+if app.save_grain
     filename = fullfile(acq.dir, '4_grains', sprintf('phase_%02d',phaseID), ...
-    sprintf('twins_%04d.mat', gr.id));
+    sprintf('twins_%04d.mat', grain.id));
     save(filename, 'grain');
 end