fix pf_active, magnetics, wall, tf. Not sure yet for pf_passive if empty or not

matlab/IMAS/complete_IDS_CORSICA.m

@@ -63,12 +63,23 @@ end
 
 %% Add the data to the circuit
 tmp = data_circuits();
-Ncircuits = size(tmp,1);
+Ncircuit_eff = size(tmp,1);
+Ncircuit_in = numel(IDS_out.pf_active.circuit);
+Nsupply_in = numel(IDS_out.pf_active.supply);
 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;
-for ii=1:Ncircuits
+% 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);
+end  
+if Ncircuit_eff > Nsupply_in
+  IDS_out.pf_active.supply(Nsupply_in+1:Ncircuit_eff) = IDS_out.pf_active.supply(Nsupply_in);
+end  
+for ii=1:Ncircuit_eff
     IDS_out.pf_active.circuit{ii}.name = tmp{ii,1}{1};
     IDS_out.pf_active.supply{ii}.name = tmp{ii,1}{1};
     % Find index of the coils belonging to ii circuit
@@ -83,10 +94,10 @@ for ii=1:Ncircuits
     IDS_out.pf_active.circuit{ii}.current.data = IDS_out.pf_active.coil{index_coil(1)}.current.data/IDS_out.pf_active.coil{index_coil(1)}.element{1}.turns_with_sign;
     IDS_out.pf_active.circuit{ii}.current.time = IDS_out.pf_active.coil{index_coil(1)}.current.time;
     
-    IDS_out.pf_active.circuit{ii}.connections = zeros(2*numel(index_coil) -1 , 2*Ncircuits + 2*Ncoils);
+    IDS_out.pf_active.circuit{ii}.connections = zeros(2*numel(index_coil) -1 , 2*Ncircuit_eff + 2*Ncoils);
     for jj = 1:numel(index_coil)
-    IDS_out.pf_active.circuit{ii}.connections( jj , 2*Ncircuits + 2*(index_coil(jj)-1) +1) = 1;
-    IDS_out.pf_active.circuit{ii}.connections( jj +1 , 2*Ncircuits + 2*(index_coil(jj)-1) +2) = 1;
+    IDS_out.pf_active.circuit{ii}.connections( jj , 2*Ncircuit_eff + 2*(index_coil(jj)-1) +1) = 1;
+    IDS_out.pf_active.circuit{ii}.connections( jj +1 , 2*Ncircuit_eff + 2*(index_coil(jj)-1) +2) = 1;
     end
     
     % Add the connection to the power supply
@@ -96,111 +107,72 @@ end
 
 %% Limiter description
 tmp = data_limiter();
+IDS_out.wall.ids_properties.homogeneous_time = 0; % no times are set so just say not homogeneous
 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 = {};
+IDS_out.wall.description_ggd = {};
+
 %% Vessel description
 % Understand what I need to do for the double layer vessel
 
 %%  -------------- Synthetic diagnostics------------ Need to be recomputed from CORSICA flux map
 
+% 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;
 IDS_out.magnetics.method{1}.ip.time = LXC.t;
 IDS_out.magnetics.method{1}.ip.data = LXC.Ip;
 
-% Correct IDS magnetics
-aa = gdat([],'ids','source','magnetics');
-magnetics_default = aa.magnetics;
-mag_fluxloop_def_fields = fieldnames(magnetics_default.flux_loop{1});
-if isfield(IDS_out.magnetics,'flux_loop') && length(IDS_out.magnetics.flux_loop) > 0
-  mag_fluxloop_fields = fieldnames(IDS_out.magnetics.flux_loop{1});
-else
-  mag_fluxloop_fields = {};
-end
-fields_to_add = setdiff(mag_fluxloop_def_fields,mag_fluxloop_fields);
-
 %% Ff
 tmp = data_Ff();
-for ii=1:numel(tmp.r) 
-  if ~isempty(fields_to_add)
-    for idef=1:length(fields_to_add)
-      % add first defaults and fill in after
-      IDS_out.magnetics.flux_loop{ii}.(fields_to_add{idef}) = magnetics_default.flux_loop{1}.(fields_to_add{idef});
-    end
-    if ii==1; warning(['following fields added to magnetics.flux_loop: ' sprintf('%s ',fields_to_add{:})]); end
-  end
+% 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);
+end
+for ii=1:Nflux_loop_eff
   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};
 end
 
-for ii=1:numel(tmp.r)
-    IDS_out.magnetics.flux_loop{ii}.flux.data = -LXC.Ff(ii,:)';
-    IDS_out.magnetics.flux_loop{ii}.flux.time = LXC.t;
+for ii=1:Nflux_loop_eff
+  IDS_out.magnetics.flux_loop{ii}.flux.data = -LXC.Ff(ii,:)';
+  IDS_out.magnetics.flux_loop{ii}.flux.time = LXC.t;
 end
 
 %% Bm
 % Correct IDS magnetics
-mag_bpol_probe_def_fields = fieldnames(magnetics_default.bpol_probe{1});
-if isfield(IDS_out.magnetics,'bpol_probe') && length(IDS_out.magnetics.bpol_probe) > 0
-  mag_bpol_probe_fields = fieldnames(IDS_out.magnetics.bpol_probe{1});
-else
-  mag_bpol_probe_fields = {};
-end
-fields_to_add = setdiff(mag_bpol_probe_def_fields,mag_bpol_probe_fields);
-mag_bpol_probe_def_fields = fieldnames(magnetics_default.bpol_probe{1}.position);
-if length(IDS_out.magnetics.bpol_probe) > 0 && isfield(IDS_out.magnetics.bpol_probe{1},'position')
-  mag_bpol_probe_fields = fieldnames(IDS_out.magnetics.bpol_probe{1}.position);
-else
-  mag_bpol_probe_fields = {};
-end
-fields_to_add_position = setdiff(mag_bpol_probe_def_fields,mag_bpol_probe_fields);
-
 tmp = data_Bm();
-for ii=1:numel(tmp.name)
-  if ~isempty(fields_to_add)
-    for idef=1:length(fields_to_add)
-      % add first defaults and fill in after
-      IDS_out.magnetics.bpol_probe{ii}.(fields_to_add{idef}) = magnetics_default.bpol_probe{1}.(fields_to_add{idef});
-    end
-    if ii==1; warning(['following fields added to magnetics.bpol_probe: ' sprintf('%s ',fields_to_add{:})]); end
-  end
-  if ~isempty(fields_to_add_position)
-    for idef=1:length(fields_to_add_position)
-      % add_position first defaults and fill in after
-      IDS_out.magnetics.bpol_probe{ii}.position.(fields_to_add_position{idef}) = magnetics_default.bpol_probe{1}.position.(fields_to_add_position{idef});
-    end
-    if ii==1; warning(['following fields add_positioned to magnetics.bpol_probe.position: ' sprintf('%s ',fields_to_add_position{:})]); end
-  end
+% Make sure default substructure maintained if insert new indices
+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);
+end
+for ii=1:Nbpol_probe_eff
   IDS_out.magnetics.bpol_probe{ii}.position.r = tmp.r(ii);
   IDS_out.magnetics.bpol_probe{ii}.position.z = tmp.z(ii);
   IDS_out.magnetics.bpol_probe{ii}.poloidal_angle = -tmp.am(ii); % Correct the sign to be consistent with COCOS 11
   IDS_out.magnetics.bpol_probe{ii}.name = tmp.name{ii};
 end
 
-for ii=1:numel(tmp.name)
+for ii=1:Nbpol_probe_eff
     IDS_out.magnetics.bpol_probe{ii}.field.data = LXC.Bm(ii,:)';
     IDS_out.magnetics.bpol_probe{ii}.field.time = LXC.t;
 end
 
 %% Ft
-mag_method_def_fields = fieldnames(magnetics_default.method{1});
-if isfield(IDS_out.magnetics,'method') && length(IDS_out.magnetics.method) > 0
-  mag_method_fields = fieldnames(IDS_out.magnetics.method{1});
-else
-  mag_method_fields = {};
-end
-fields_to_add = setdiff(mag_method_def_fields,mag_method_fields);
-if ~isempty(fields_to_add)
-  for idef=1:length(fields_to_add)
-    % add first defaults and fill in after
-    IDS_out.magnetics.method{1}.(fields_to_add{idef}) = magnetics_default.method{1}.(fields_to_add{idef});
-  end
-  warning(['following fields added to magnetics.method: ' sprintf('%s ',fields_to_add{:})]);
-end
 IDS_out.magnetics.method{1}.diamagnetic_flux.data = -LXC.Ft;
 IDS_out.magnetics.method{1}.diamagnetic_flux.time = LXC.t;
 
 %% rBt
+IDS_out.tf.ids_properties.homogeneous_time = 1;
 IDS_out.tf.time = LXC.t;
 IDS_out.tf.b_field_tor_vacuum_r.time  = LXC.t;
 IDS_out.tf.b_field_tor_vacuum_r.data  = LXC.rBt;

[Olivier Sauter]

@amerle the .time in these substructure exist but are either empty or "default value". However I get an error in the ids_put:

ual_end_action: [UALBackendException = Cannot get Time information] ual_print_context: [UALLowlevelException = Cannot find context 8 in store] problems in putting data in database: Error using ids_put internal error occured with error code -1 ... in aos description_ggd/grid_ggd ... in IDS wall

What is the rule? Or may be there is no rule ? At this stage I made the parent an empty cell then it works

[Antoine Merle]

I don't know if it's a rule or a recommendation but yes for any array that exists you have to provide its dimensions. So for a dynamic array of structure time must be filled (or if homogeneous time is selected the base time). I think for time that is a rule. In that case it triggers an error because it is used by the backend and it can't find it (it's not an error that is linked to the mex interface particularly)

Same as always, you have to remove all unused arrays of structures before doing ids_put.

This is why for the mex I provide:

• ids_gen2 which initialises every array of structures as empty
• ids_allocate which given an ids name, a path within the ids and a size will allocate the corresponding array of structures with the correct size.

This way is more similar to the FORTRAN interface if you see what I mean.

[Olivier Sauter]

Actually having empty structures in the ids_gen is a problem since we are adding just a few data like xxx.yyy.name and xxx.yyy.data. If we do not copy the expected substructure in yyy, then xxx.yyy has only the "name" and "data" fields and the ids_put fails.

So I cannot use something like ids_gen2, nor use the ids_get with your mex, but need the ids_gen, then copy the default structure with all expected fields in yyy then put the relevant data in yyy.name and yyy.data. What I do not do is to check that a field exists before modifying, which I should actually like isfield(xxx.yyy,'name');...

[Antoine Merle]

But ... that was the purpose of my second bullet with the ids_allocate part ...

[Olivier Sauter]

OK I never tried that one hence do not know, you can do sub-allocation like:

magnetics.bpol_probe(2:N) = ids_allocate('magnetics','bpol_probe',N-1);

or something like that?

OK I just checked, indeed I can do the above. But is it standard?

[Antoine Merle]

Is it shared by the other MATLAB interface? no

But the plan is to phase out the other MATLAB interface, and I think this approach has advantages over the previous one so I hope no one will truly oppose it.

Since with ids_gen2, all arrays are initially empty, you would rather do something like:

magnetics.bpol_probe = ids_allocate('magnetics','bpol_probe',N);

[Olivier Sauter]

I fixed most things. One question is pf_passive empty or not. Do you use something from the Corsica IDS.pf_passive?

(cannot ids_put because homogeneous not set, but should not set if empty altogether)

[Olivier Sauter]

@carpanes I added a ids_check_empty and it seems pf_passive is empty, so I guess you do not use it?

You can check with my shot, run=1111 in my iter database or rmfield pf_passive before running liuqe

[Francesco Carpanese]

Indeed, vessel current which are the only eventual passive structure, we still don't know how to use them in ITER. Also for the case of TCV I haven't implemented yet, nor I think we are providing them to the IDS structure at the moment.