add IDS/IMAS to eqdsk directly

tested: gdat(131025,'eqdsk','run',43,'database_user','public','tokamak_name','ITER','machine','IMAS','time',208);

matlab/IMAS/ITERlimiter.data

+% R        Z_wall_131025run43t208ITERpublic
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matlab/IMAS/gdat_imas.m

@@ -518,6 +518,33 @@ elseif strcmp(mapping_for_imas.method,'switchcase')
       end
     end
     
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+   case {'eqdsk'}
+    % add defaults
+    if ~isfield(gdat_data.gdat_params,'time')
+      gdat_data.gdat_params.time = 1.; % default time
+    end
+    if ~isfield(gdat_data.gdat_params,'write')
+      gdat_data.gdat_params.write = 1; % default write eqdsk to /tmp/username
+    end
+    params_eff = gdat_data.gdat_params;
+    params_eff = rmfield(params_eff,'time');
+    params_eff.data_request = 'ids';
+    params_eff.source = 'equilibrium';
+    gdat_equil = gdat_imas(shot,params_eff);
+    params_eff.source = 'wall';
+    gdat_wall = gdat_imas(shot,params_eff);
+    %
+    eqdsk_filename_suffix = [num2str(gdat_data.shot) '_' num2str(gdat_data.gdat_params.run) 't' num2str(gdat_data.gdat_params.time) ...
+		    gdat_data.gdat_params.tokamak_name '_' gdat_data.gdat_params.database_user];
+    [eqdsk_out] = ids2eqdsk(gdat_equil.equilibrium,gdat_wall.wall,gdat_data.gdat_params.time,eqdsk_filename_suffix,gdat_data.gdat_params.write);
+    gdat_data.equilibrium = gdat_equil.equilibrium;
+    gdat_data.wall = gdat_wall.wall;
+    gdat_data.eqdsk = eqdsk_out;
+    if isfield(gdat_data.gdat_params,'doplot') && gdat_data.gdat_params.doplot == 1
+      plot_eqdsk(gdat_data.eqdsk)
+    end
+    
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    otherwise
     if (gdat_params.nverbose>=1); warning(['switchcase= ' data_request_eff ' not known in gdat_imas']); end

matlab/IMAS/ids2eqdsk.m

+function [eqdsk_out,varargout] = ids2eqdsk(ids_equilibrium,ids_wall,time_ref,eqdsk_filename_suffix,write_opt)
+%
+% [eqdsk_out, varout] = ids2eqdsk(ids_equilibrium, ids_wall, time_ref, eqdsk_filename_suffix);
+%
+% ids_equilibrium: ids equilibrium structure to extract eqdsk related quantities
+% ids_wall:        ids wall structure to extract limiter and vessel points if provided
+% time_ref:        time to extract data
+% eqdsk_filename_suffix: string to be used for end of eqdsk filename, e.g. shot_run_text
+% write_opt:       1 (default) do write eqdsk to /tmp/username, 0: no writing
+%
+% OUTPUT
+% eqdsk_out:       eqdsk structure
+%
+if ~exist('time_ref','var') || isempty(time_ref)
+  % take 1st time point
+  if ids_equilibrium.ids_properties.homogeneous_time == 1
+    time_ref = ids_equilibrium.time(1);
+  else
+    time_ref = ids_equilibrium.time_slice{1}.time;
+  end
+end
+if ~exist('eqdsk_filename','var') || isempty(eqdsk_filename)
+  eqdsk_filename = ['t' num2str(time_ref)];
+end
+if ~exist('write_opt','var') || isempty(write_opt)
+  write_opt = 1;
+end
+
+% find time_slice for equilibrium ids
+if ids_equilibrium.ids_properties.homogeneous_time == 1
+  i_equil = iround_os(ids_equilibrium.time,time_ref);
+else
+  for j=1:numel(ids_equilibrium.time_slice{j})
+    time_array(j) = ids_equilibrium.time_slice{j}.time;
+  end
+  i_equil = iround_os(time_array,time_ref);
+end
+% find time_slice for wall ids
+if ids_wall.ids_properties.homogeneous_time == 1
+  i_wall = iround_os(ids_wall.time,time_ref);
+else
+  for j=1:numel(ids_wall.time_slice{j})
+    time_array(j) = ids_wall.time_slice{j}.time;
+  end
+  i_wall = iround_os(time_array,time_ref);
+end
+
+eqdsk_out.cocos = 11; % assume 11 within IMAS at this stage, should come from ids_equilibrium metadata
+
+% check if needed fields are present and non empty
+if ids_equilibrium.time_slice{i_equil}.global_quantities.ip ~= -9.0000e+40
+  eqdsk_out.ip = ids_equilibrium.time_slice{i_equil}.global_quantities.ip;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.global_quantities.ip not provided']);
+end
+if ids_equilibrium.vacuum_toroidal_field.b0 ~= -9.0000e+40
+  eqdsk_out.b0 = ids_equilibrium.vacuum_toroidal_field.b0;
+else
+  error(['ids_equilibrium.vacuum_toroidal_field.b0 not provided']);
+end
+if ids_equilibrium.vacuum_toroidal_field.r0 ~= -9.0000e+40
+  eqdsk_out.r0 = ids_equilibrium.vacuum_toroidal_field.r0;
+else
+  error(['ids_equilibrium.vacuum_toroidal_field.r0 not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.global_quantities.magnetic_axis.r ~= -9.0000e+40
+  eqdsk_out.raxis = ids_equilibrium.time_slice{i_equil}.global_quantities.magnetic_axis.r;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.global_quantities.magnetic_axis.r not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.global_quantities.magnetic_axis.z ~= -9.0000e+40
+  eqdsk_out.zaxis = ids_equilibrium.time_slice{i_equil}.global_quantities.magnetic_axis.z;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.global_quantities.magnetic_axis.z not provided']);
+end
+eqdsk_out.zshift = 0.; % can add an option to shift eqdsk but can use eqdsk_transform
+
+if ids_equilibrium.time_slice{i_equil}.profiles_1d.dpressure_dpsi ~= -9.0000e+40
+  dpressure_dpsi = ids_equilibrium.time_slice{i_equil}.profiles_1d.dpressure_dpsi;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.profiles_1d.dpressure_dpsi not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.profiles_1d.pressure ~= -9.0000e+40
+  pressure = ids_equilibrium.time_slice{i_equil}.profiles_1d.pressure;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.profiles_1d.pressure not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.profiles_1d.f ~= -9.0000e+40
+  f_rbphi = ids_equilibrium.time_slice{i_equil}.profiles_1d.f;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.profiles_1d.f not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.profiles_1d.f_df_dpsi ~= -9.0000e+40
+  f_df_dpsi = ids_equilibrium.time_slice{i_equil}.profiles_1d.f_df_dpsi;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.profiles_1d.f_df_dpsi not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.global_quantities.psi_axis ~= -9.0000e+40
+  psi_axis = ids_equilibrium.time_slice{i_equil}.global_quantities.psi_axis;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.global_quantities.psi_axis not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.global_quantities.psi_boundary ~= -9.0000e+40
+  psi_boundary = ids_equilibrium.time_slice{i_equil}.global_quantities.psi_boundary;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.global_quantities.psi_boundary not provided']);
+end
+if ids_equilibrium.time_slice{i_equil}.profiles_1d.psi ~= -9.0000e+40
+  psi = ids_equilibrium.time_slice{i_equil}.profiles_1d.psi;
+  rhopol_norm = sqrt((psi-psi(1))./(psi(end)-psi(1)));
+  rhopol_norm(1) = 0.; rhopol_norm(end) = 1.;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.profiles_1d.psi not provided, could use rho_tor_norm, not implemented yet']);
+end
+if ids_equilibrium.time_slice{i_equil}.profiles_1d.q ~= -9.0000e+40
+  q_profile = ids_equilibrium.time_slice{i_equil}.profiles_1d.q;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.profiles_1d.q not provided']);
+end
+if numel(ids_equilibrium.time_slice{i_equil}.profiles_2d) >= 1
+  i_2d = 0;
+  % find eqdsk type grid
+  for j=1:numel(ids_equilibrium.time_slice{i_equil}.profiles_2d)
+    if ids_equilibrium.time_slice{i_equil}.profiles_2d{j}.grid_type.index == 1
+      i_2d = j;
+    end
+  end
+  if i_2d > 0
+    % grid ala eqdsk so can use psi, dim1, dim2
+    rmesh = ids_equilibrium.time_slice{i_equil}.profiles_2d{i_2d}.grid.dim1;
+    zmesh = ids_equilibrium.time_slice{i_equil}.profiles_2d{i_2d}.grid.dim2;
+    if ~isempty(ids_equilibrium.time_slice{i_equil}.profiles_2d{i_2d}.psi)
+      psi_2d = ids_equilibrium.time_slice{i_equil}.profiles_2d{i_2d}.psi;
+    else
+      error('ids_equilibrium.time_slice{i_equil}.profiles_2d{i_2d}.psi not provided');
+    end
+  else
+    error([' cannot find ids_equilibrium.time_slice{i_equil}.profiles_2d{i_2d}.grid_type.index == 1']);
+  end
+end
+if ~isempty(ids_equilibrium.time_slice{i_equil}.boundary.outline.r)
+  r_lcfs = ids_equilibrium.time_slice{i_equil}.boundary.outline.r;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.boundary.outline.r not provided']);
+end
+if ~isempty(ids_equilibrium.time_slice{i_equil}.boundary.outline.z)
+  z_lcfs = ids_equilibrium.time_slice{i_equil}.boundary.outline.z;
+else
+  error(['ids_equilibrium.time_slice{i_equil}.boundary.outline.z not provided']);
+end
+
+eqdsk_out.cocos = 11;
+eqdsk_out.nr = numel(rmesh);
+eqdsk_out.nz = numel(zmesh);
+eqdsk_out.rmesh = rmesh;
+eqdsk_out.zmesh = zmesh;
+eqdsk_out.zshift = 0.;
+eqdsk_out.psi = psi_2d;
+eqdsk_out.psirz = psi_2d;
+eqdsk_out.rboxlen = eqdsk_out.rmesh(end) - eqdsk_out.rmesh(1);
+eqdsk_out.rboxleft=eqdsk_out.rmesh(1);
+eqdsk_out.zboxlen = eqdsk_out.zmesh(end) - eqdsk_out.zmesh(1);
+eqdsk_out.zmid = 0.5*(eqdsk_out.zmesh(end) + eqdsk_out.zmesh(1)) ;
+eqdsk_out.psiaxis = psi_axis
+eqdsk_out.psiedge = psi_boundary;
+if ids_equilibrium.time_slice{i_equil}.boundary_separatrix.type == 1
+  % diverted
+  % could check psi value with psi boundary
+end
+
+% need psimesh ot be equidistant and same nb of points as nr
+eqdsk_out.psimesh=linspace(0,1,eqdsk_out.nr)';
+eqdsk_out.rhopsi = sqrt(eqdsk_out.psimesh);
+% psimesh assumed from 0 on axis (so psi_edge is delta_psi) to have correct d/dpsi but to have sign(dpsi) easily
+% (psimesh from 0 to 1) eqdsk_out.psimesh = (eqdsk_out.psiedge-eqdsk_out.psiaxis) .* eqdsk_out.psimesh;
+nrho = size(pressure,1);
+eqdsk_out.p = interpos(rhopol_norm,pressure,eqdsk_out.rhopsi,-0.01,[1 2],[0 pressure(end)]);
+eqdsk_out.pprime = interpos(rhopol_norm,dpressure_dpsi,eqdsk_out.rhopsi,-0.01,[1 2],[0 dpressure_dpsi(end)]);
+eqdsk_out.F = interpos(rhopol_norm,f_rbphi,eqdsk_out.rhopsi,-0.01,[1 2],[0 f_rbphi(end)]);
+eqdsk_out.FFprime = interpos(rhopol_norm,f_df_dpsi,eqdsk_out.rhopsi,-0.01,[1 2],[0 f_df_dpsi(end)]);
+eqdsk_out.q = interpos(rhopol_norm,q_profile,eqdsk_out.rhopsi,-0.01,[1 2],[0 q_profile(end)]);
+
+eqdsk_out.stitle = [eqdsk_filename_suffix ' tref=' num2str(time_ref)];
+
+eqdsk_out.nbbound = numel(ids_equilibrium.time_slice{i_equil}.boundary.outline.r);
+if ~isempty(ids_equilibrium.time_slice{i_equil}.boundary.outline.r) && eqdsk_out.nbbound > 1 && ...
+      eqdsk_out.nbbound == numel(ids_equilibrium.time_slice{i_equil}.boundary.outline.z)
+  eqdsk_out.rplas = ids_equilibrium.time_slice{i_equil}.boundary.outline.r;
+  eqdsk_out.zplas = ids_equilibrium.time_slice{i_equil}.boundary.outline.z;
+else
+  error('Plasma boundary not provided in time_slice{i_equil}.boundary.outline.r');
+end
+
+% extract limiter + double ids_wall if available
+if numel(ids_wall.description_2d)>0 && numel(ids_wall.description_2d{1}.limiter.unit)>0 && ...
+      ~isempty(ids_wall.description_2d{1}.limiter.unit{1}.outline.r) && ...
+      numel(ids_wall.description_2d{1}.vessel.unit)>=2 && ...
+      ~isempty(ids_wall.description_2d{1}.vessel.unit{1}.annular.centreline.r) && ...
+      ~isempty(ids_wall.description_2d{1}.vessel.unit{2}.annular.centreline.r)
+  Rlimiter = ids_wall.description_2d{1}.limiter.unit{1}.outline.r;
+  Zlimiter = ids_wall.description_2d{1}.limiter.unit{1}.outline.z;
+  if numel(ids_wall.description_2d{1}.limiter.unit)>=2 && ~isempty(ids_wall.description_2d{1}.limiter.unit{2}.outline.r)
+    nbpts2 = numel(ids_wall.description_2d{1}.limiter.unit{2}.outline.r);
+    Rlimiter(end+1:end+nbpts2) = ids_wall.description_2d{1}.limiter.unit{2}.outline.r(nbpts2:-1:1);
+    Zlimiter(end+1:end+nbpts2) = ids_wall.description_2d{1}.limiter.unit{2}.outline.z(nbpts2:-1:1);
+  end
+  Rlimiter(end+1) = Rlimiter(1);
+  Zlimiter(end+1) = Zlimiter(1);
+  
+  % vessel
+  Rvessel_1 = ids_wall.description_2d{1}.vessel.unit{1}.annular.centreline.r;
+  Zvessel_1 = ids_wall.description_2d{1}.vessel.unit{1}.annular.centreline.z;
+  Rvessel_2 = ids_wall.description_2d{1}.vessel.unit{2}.annular.centreline.r;
+  Zvessel_2 = ids_wall.description_2d{1}.vessel.unit{2}.annular.centreline.z;
+  
+  aa = [Rlimiter Zlimiter];
+  nlim = size(aa,1);
+  nvessel_1 = numel(Rvessel_1);
+  nvessel_2 = numel(Rvessel_2);
+
+  d_lim_vessel_1 = sqrt((Rvessel_1-Rlimiter(end)).^2 + (Zvessel_1-Zlimiter(end)).^2);
+  [zzz,idmin] = min(d_lim_vessel_1);
+  aa(nlim+1:nlim+(nvessel_1-idmin+1),1) = Rvessel_1(idmin:end);
+  aa(nlim+(nvessel_1-idmin+1)+1:nlim+nvessel_1+1,1) = Rvessel_1(1:idmin); % end return point
+  aa(nlim+1:nlim+(nvessel_1-idmin+1),2) = Zvessel_1(idmin:end);
+  aa(nlim+(nvessel_1-idmin+1)+1:nlim+nvessel_1+1,2) = Zvessel_1(1:idmin);
+  
+  d_lim_vessel_2 = sqrt((Rvessel_2-Rlimiter(end)).^2 + (Zvessel_2-Zlimiter(end)).^2);
+  [zzz,idmin] = min(d_lim_vessel_2);
+  aa(nlim+nvessel_1+1+1:nlim+nvessel_1+1+(nvessel_2-idmin+1),1) = Rvessel_2(idmin:end);
+  aa(nlim+nvessel_1+1+(nvessel_2-idmin+1)+1:nlim+nvessel_1+1+nvessel_2+1,1) = Rvessel_2(1:idmin);
+  aa(nlim+nvessel_1+1+1:nlim+nvessel_1+1+(nvessel_2-idmin+1),2) = Zvessel_2(idmin:end);
+  aa(nlim+nvessel_1+1+(nvessel_2-idmin+1)+1:nlim+nvessel_1+1+nvessel_2+1,2) = Zvessel_2(1:idmin);
+  
+else