fix cases getting empty substructure when ids_get with mex is used

matlab/IMAS/complete_IDS_CORSICA.m

@@ -44,13 +44,18 @@ L = liuc(Pliuqe,G);
 
 %%  -------------------- ADD the missing information on the existing IDS_out CORSICA -----------------------
 
+% Make sure default substructure maintained if insert new indices
+pf_active_default = gdat([],'ids','source','pf_active');
+pf_active_default = pf_active_default.pf_active;
 %% Consider each circuit to be composed by only one coil
 tmp = data_coils();
+if isempty(IDS_out.pf_active.coil); IDS_out.pf_active.coil(1:numel(tmp.names)) = pf_active_default.coil(1); end
 for ii = 1:numel(tmp.names)
     for jj=1:numel(IDS_out.pf_active.coil)
         % Remove strange character in coil names
         IDS_out.pf_active.coil{jj}.name = regexprep(IDS_out.pf_active.coil{jj}.name,'[\n\r]+','');
         if strcmp(tmp.names{ii},IDS_out.pf_active.coil{jj}.name)
+	  if isempty(IDS_out.pf_active.coil{jj}.element); IDS_out.pf_active.coil{jj}.element(1) = pf_active_default.coil{1}.element(1); end
             IDS_out.pf_active.coil{jj}.element{1}.geometry.geometry_type = 2; % Rectangle description
             IDS_out.pf_active.coil{jj}.element{1}.geometry.rectangle.r = tmp.R(ii);
             IDS_out.pf_active.coil{jj}.element{1}.geometry.rectangle.z = tmp.Z(ii);
@@ -70,14 +75,11 @@ Ncoils = numel(IDS_out.pf_active.coil);
 % time will be set in circuit.current.time so should not put it at top and set homogeneous to 0?
 IDS_out.pf_active.time = [];
 IDS_out.pf_active.ids_properties.homogeneous_time = 0;
-% Make sure default substructure maintained if insert new indices
-pf_active_default = gdat([],'ids','source','pf_active');
-pf_active_default = pf_active_default.pf_active;
 if Ncircuit_eff > Ncircuit_in
-  IDS_out.pf_active.circuit(Ncircuit_in+1:Ncircuit_eff) = pf_active_default.circuit(1);
+  IDS_out.pf_active.circuit(Ncircuit_in+1:Ncircuit_eff,1) = pf_active_default.circuit(1);
 end  
 if Ncircuit_eff > Nsupply_in
-  IDS_out.pf_active.supply(Nsupply_in+1:Ncircuit_eff) = pf_active_default.supply(Nsupply_in);
+  IDS_out.pf_active.supply(Nsupply_in+1:Ncircuit_eff,1) = pf_active_default.supply(1);
 end  
 for ii=1:Ncircuit_eff
     IDS_out.pf_active.circuit{ii}.name = tmp{ii,1}{1};
@@ -107,12 +109,19 @@ end
 
 %% Limiter description
 tmp = data_limiter();
+% Make sure default substructure maintained if insert new indices
+wall_default = gdat([],'ids','source','wall');
+wall_default = wall_default.wall;
 IDS_out.wall.ids_properties.homogeneous_time = 0; % no times are set so just say not homogeneous
+if isempty(IDS_out.wall.description_2d); IDS_out.wall.description_2d(1) = wall_default.description_2d(1); end
+if isempty(IDS_out.wall.description_2d{1}.limiter.unit); IDS_out.wall.description_2d{1}.limiter.unit(1) = wall_default.description_2d{1}.limiter.unit(1); end
 IDS_out.wall.description_2d{1}.limiter.unit{1}.outline.r = tmp.r;
 IDS_out.wall.description_2d{1}.limiter.unit{1}.outline.z = tmp.z;
 
 % problem with mex ids_put when time default or empty, make outline  and ggd empty
-IDS_out.wall.description_2d{1}.mobile.unit{1}.outline = {};
+if ~isempty(IDS_out.wall.description_2d{1}.mobile.unit)
+  IDS_out.wall.description_2d{1}.mobile.unit{1}.outline = {};
+end
 IDS_out.wall.description_ggd = {};
 
 %% Vessel description
@@ -120,22 +129,24 @@ IDS_out.wall.description_ggd = {};
 
 %%  -------------- Synthetic diagnostics------------ Need to be recomputed from CORSICA flux map
 
+% Make sure default substructure maintained if insert new indices
+magnetics_default = gdat([],'ids','source','magnetics');
+magnetics_default = magnetics_default.magnetics;
 % since time set in subnode method{1}.ip.time, set homogeneous to 0 (magnetics.time already empty)
 IDS_out.magnetics.ids_properties.homogeneous_time = 0;
+if isempty(IDS_out.magnetics.method); IDS_out.magnetics.method(1) = magnetics_default.method(1); end
 IDS_out.magnetics.method{1}.ip.time = LXC.t;
 IDS_out.magnetics.method{1}.ip.data = LXC.Ip;
 
 %% Ff
 tmp = data_Ff();
-% Make sure default substructure maintained if insert new indices
-magnetics_default = gdat([],'ids','source','magnetics');
-magnetics_default = magnetics_default.magnetics;
 Nflux_loop_in = numel(IDS_out.magnetics.flux_loop);
 Nflux_loop_eff = numel(tmp.r);
 if Nflux_loop_eff > Nflux_loop_in
-  IDS_out.magnetics.flux_loop(Nflux_loop_in+1:Nflux_loop_eff) = magnetics_default.flux_loop(1);
+  IDS_out.magnetics.flux_loop(Nflux_loop_in+1:Nflux_loop_eff,1) = magnetics_default.flux_loop(1);
 end
 for ii=1:Nflux_loop_eff
+  if isempty(IDS_out.magnetics.flux_loop{ii}.position); IDS_out.magnetics.flux_loop{ii}.position(1) = magnetics_default.flux_loop{ii}.position(1); end
   IDS_out.magnetics.flux_loop{ii}.position{1}.r = tmp.r(ii);
   IDS_out.magnetics.flux_loop{ii}.position{1}.z = tmp.z(ii);
   IDS_out.magnetics.flux_loop{ii}.name = tmp.name{ii};
@@ -153,7 +164,7 @@ tmp = data_Bm();
 Nbpol_probe_in = numel(IDS_out.magnetics.bpol_probe);
 Nbpol_probe_eff = numel(tmp.name);
 if Nbpol_probe_eff > Nbpol_probe_in
-  IDS_out.magnetics.bpol_probe(Nbpol_probe_in+1:Nbpol_probe_eff) = magnetics_default.bpol_probe(1);
+  IDS_out.magnetics.bpol_probe(Nbpol_probe_in+1:Nbpol_probe_eff,1) = magnetics_default.bpol_probe(1);
 end
 for ii=1:Nbpol_probe_eff
   IDS_out.magnetics.bpol_probe{ii}.position.r = tmp.r(ii);
@@ -181,6 +192,7 @@ IDS_out.tf.b_field_tor_vacuum_r.data  = LXC.rBt;
 cocos_in = 17;
 cocos_out = 11;
 to_transform = {'pf_active','pf_passive','magnetics','tf','wall','equilibrium'};
+to_transform = {'pf_active','magnetics','tf','wall','equilibrium'}; % at this stage pf_passive is empty and not used
 for i=1:length(to_transform)
   IDS_out.(to_transform{i}) = ids_generic_cocos_nodes_transformation_symbolic(IDS_out.(to_transform{i}), to_transform{i}, cocos_in, cocos_out,[],[],[],[],[],3);
 end