fix present problem of EQI, EQR, etc from within loadAUG (time base not...

fix present problem of EQI, EQR, etc from within loadAUG (time base not consistent) with a method which should be OK when OK, taking NTIME first points

git-svn-id: https://spcsvn.epfl.ch/repos/TCV/gdat/trunk@4468 d63d8f72-b253-0410-a779-e742ad2e26cf

crpptbx/AUG/loadAUGdata.m

@@ -460,10 +460,23 @@ if size(data_type_eff,1)==2
     AUGsiglocation(1:2,end+1)=[data_type_eff(1) ; {data_type_eff_noext}];
     AUGexplocation{end+1}=shotfile_exp;
     AUGsigtimeindx(end+1)=0;
-  elseif ~strcmp(AUGkeywrdcase{index},'simplereaddata')
-    msgbox(['Problem in loadAUGdata with data_type_eff = ' char(data_type_eff(end)) ...
-          '. Full paths of nodes should only be for case simplereaddata'],'in loadAUGdata','error')
-    error('in loadAUGdata')
+    AUGkeywrdcase{index}
+  elseif length(index)>1 || ~strcmp(AUGkeywrdcase{index},'simplereaddata')
+% $$$     msgbox(['Problem in loadAUGdata with data_type_eff = ' char(data_type_eff(end)) ...
+% $$$           '. Full paths of nodes should only be for case simplereaddata'],'in loadAUGdata','error')
+% $$$     error('in loadAUGdata')
+    % chose a full path which coincides with a keyword
+    disp('the node path seems to coincide with the following keywords, which might be better to use:')
+    disp(' ')
+    disp(AUGkeywrdcase(index))
+    disp('proceed as is in any case')
+    index=length(AUGkeywrdall)+1;
+    AUGkeywrdall(end+1)={'new'};
+    AUGkeywrdcase(end+1)={'simplereaddata'};
+    AUGsiglocation(1:2,end+1)=[data_type_eff(1) ; {data_type_eff_noext}];
+    AUGexplocation{end+1}=shotfile_exp;
+    AUGsigtimeindx(end+1)=0;
+    AUGkeywrdcase{index}    
   end
 else
   index=strmatch(data_type_eff_noext,AUGkeywrdall,'exact');
@@ -1059,6 +1072,9 @@ switch AUGkeywrdcase{index}
 
   case {'equil', 'equil_fpp', 'equil_eqm', 'equil_eqr', 'equil_eqh', 'qrho', 'qrho_fpp'}
 
+    % In shotfiles time is 1st index in 2D arrays while gdat convention is to have time as last dimension
+    % so change equil.xxx to (rho,time) on the way...
+    
     shotfile_exp_eff = AUGexplocation{index};
     
     if strcmp(AUGkeywrdcase{index},'equil_fpp') || strcmp(AUGkeywrdcase{index},'qrho_fpp')
@@ -1079,90 +1095,110 @@ switch AUGkeywrdcase{index}
     NTIME_par = sf2par(DIAG,shot,'NTIME','PARMV');
     NTIME = NTIME_par.value; % nb of points
     Lpf_par = rdaAUG_eff(shot,DIAG,'Lpf',shotfile_exp_eff);
+    % since June, nb of time points in EQ results is not consistent with NTIME and time
+    % It seems the first NTIME points are correct, so use this explicitely
     NTIME_Lpf = length(Lpf_par.value);
-    Lpf_tot = Lpf_par.value; % nb of points: 100000*nb_SOL points + nb_core
+    if (NTIME < NTIME_Lpf)
+      disp('WARNING: nb of times points smaller then equil results, use first NTIME points')
+    elseif (NTIME > NTIME_Lpf)
+      disp('ERROR: nb of times points LARGER then equil results')
+      disp('this is unexpected, so stop there and ask Olivier.Sauter@epfl.ch')
+      return
+    end
+    Lpf_tot = Lpf_par.value(1:NTIME); % nb of points: 100000*nb_SOL points + nb_core
     Lpf_SOL = fix(Lpf_tot/100000);
     Lpf1_t = mod(Lpf_tot,100000)+1; % nb of Lpf points
-% since Lpf depends on time, need to load all first and then loop over time for easier mapping
+    % since Lpf depends on time, need to load all first and then loop over time for easier mapping
     [qpsi,e]=rdaAUG_eff(shot,DIAG,'Qpsi',shotfile_exp_eff);
+    ndimrho = size(qpsi.data,2);
+    if ndimrho==NTIME_Lpf
+      % data seems to be transposed
+      ndimrho = size(qpsi.data,1);
+      itotransposeback = 1; % seems x,time inverted so transpose and exchange .x and .t
+    else
+      itotransposeback = 0;
+    end
+    qpsi=adapt_rda(qpsi,NTIME,ndimrho,itotransposeback);
     [psi_tree,e]=rdaAUG_eff(shot,DIAG,'PFL',shotfile_exp);
+    psi_tree=adapt_rda(psi_tree,NTIME,ndimrho,itotransposeback);
     [phi_tree,e]=rdaAUG_eff(shot,DIAG,'TFLx',shotfile_exp);
+    phi_tree=adapt_rda(phi_tree,NTIME,ndimrho,itotransposeback);
     [Vol,e]=rdaAUG_eff(shot,DIAG,'Vol',shotfile_exp);
+    Vol=adapt_rda(Vol,NTIME,2*ndimrho,itotransposeback);
     [Area,e]=rdaAUG_eff(shot,DIAG,'Area',shotfile_exp);
+    Area=adapt_rda(Area,NTIME,2*ndimrho,itotransposeback);
     [Ri,e]=rdaAUG_eff(shot,DIAG,'Ri',shotfile_exp);
+    Ri=adapt_rda(Ri,NTIME,M_Rmesh,itotransposeback);
     [Zj,e]=rdaAUG_eff(shot,DIAG,'Zj',shotfile_exp);
+    Zj=adapt_rda(Zj,NTIME,N_Zmesh,itotransposeback);
     [PFM_tree,e]=rdaAUG_eff(shot,DIAG,'PFM',shotfile_exp);
+    PFM_tree=adaptPFM_rda(PFM_tree,M_Rmesh,N_Zmesh,NTIME);
     [Pres,e]=rdaAUG_eff(shot,DIAG,'Pres',shotfile_exp);
+    Pres=adapt_rda(Pres,NTIME,2*ndimrho,itotransposeback);
     [FFP,e]=rdaAUG_eff(shot,DIAG,'FFP',shotfile_exp);
-    if isempty(FFP.value); FFP.value=NaN*ones(NTIME,max(Lpf1_t)); end
+    if ~isempty(FFP.value)
+      FFP=adapt_rda(FFP,NTIME,ndimrho,itotransposeback);
+    else
+      FFP.value=NaN*ones(NTIME,max(Lpf1_t));
+    end
     [LPFx,e]=rdaAUG_eff(shot,DIAG,'LPFx',shotfile_exp);
+    LPFx.value=LPFx.value(1:NTIME); LPFx.data=LPFx.value; LPFx.t=LPFx.t(1:NTIME);
     [PFxx,e]=rdaAUG_eff(shot,DIAG,'PFxx',shotfile_exp);
+    PFxx=adapt_rda(PFxx,NTIME,max(LPFx.value)+1,itotransposeback);
     [RPFx,e]=rdaAUG_eff(shot,DIAG,'RPFx',shotfile_exp);
+    RPFx=adapt_rda(RPFx,NTIME,max(LPFx.value)+1,itotransposeback);
     [zPFx,e]=rdaAUG_eff(shot,DIAG,'zPFx',shotfile_exp);
+    zPFx=adapt_rda(zPFx,NTIME,max(LPFx.value)+1,itotransposeback);
     % seems "LCFS" q-value is far too large, limit to some max (when diverted)
-    max_qValue = 40; % Note could just put a NaN on LCFS value since ill-defined when diverted
-    % check NTIME ok with qvalue
-    if NTIME== size(qpsi.value,2)
-      for it=1:NTIME
-	Lpf1 = Lpf1_t(it);
-	% Qpsi and similar data is on (time,radius) with radius being: LCFS..Lpf_points dummy LCFS..SOL part
-	% change it to (radial,time) and use only Lpf+1 points up to LCFS
-	if qpsi.value(1,2)<0
-	  equil.qvalue(:,it) = max(qpsi.value(it,Lpf1:-1:1)',-max_qValue);
+    max_qValue = 40.0; % Note could just put a NaN on LCFS value since ill-defined when diverted
+    for it=1:NTIME
+      Lpf1 = Lpf1_t(it);
+      % Qpsi and similar data is on (time,radius) with radius being: LCFS..Lpf_points dummy LCFS..SOL part
+      % change it to (radial,time) and use only Lpf+1 points up to LCFS
+      if qpsi.value(1,2)<0
+	equil.qvalue(:,it) = max(qpsi.value(it,Lpf1:-1:1)',-max_qValue);
+      else
+	equil.qvalue(:,it) = min(qpsi.value(it,Lpf1:-1:1)',max_qValue);
+      end
+      % get x values
+      equil.psi(:,it)=psi_tree.value(it,Lpf1:-1:1)';
+      equil.psi_axis(it)= equil.psi(1,it);
+      equil.psi_lcfs(it)= equil.psi(end,it);
+      equil.rhopolnorm(:,it) = sqrt(abs((equil.psi(:,it)-equil.psi_axis(it)) ./(equil.psi_lcfs(it)-equil.psi_axis(it))));
+      if strcmp(DIAG,'EQR');
+	% q value has only a few values and from center to edge, assume they are from central rhopol values on
+	% But they are every other point starting from 3rd
+	ijk=find(equil.qvalue(:,it)~=0);
+	qeff=equil.qvalue(ijk(end:-1:1),it);
+	rhoeff=equil.rhopolnorm(3:2:2*length(ijk)+1,it);
+	if length(ijk)>2
+	  ij_nonan=find(~isnan(equil.rhopolnorm(:,it)));
+	  qfit = zeros(size(equil.rhopolnorm(:,it)));
+	  qfit(ij_nonan)=interpos([0.; rhoeff],[qeff(1) ;qeff],equil.rhopolnorm(ij_nonan,it),-0.01,[1 0],[0 0],[300; ones(size(qeff))]);
 	else
-	  equil.qvalue(:,it) = min(qpsi.value(it,Lpf1:-1:1)',max_qValue);
+	  qfit = zeros(size(equil.rhopolnorm(:,it)));
 	end
-	% get x values
-	equil.psi(:,it)=psi_tree.value(it,Lpf1:-1:1)';
-	equil.psi_axis(it)= equil.psi(1,it);
-	equil.psi_lcfs(it)= equil.psi(end,it);
-	equil.rhopolnorm(:,it) = sqrt(abs((equil.psi(:,it)-equil.psi_axis(it)) ./(equil.psi_lcfs(it)-equil.psi_axis(it))));
-	if strcmp(DIAG,'EQR');
-	  % q value has only a few values and from center to edge, assume they are from central rhopol values on
-	  % But they are every other point starting from 3rd
-	  ijk=find(equil.qvalue(:,it)~=0);
-	  qeff=equil.qvalue(ijk(end:-1:1),it);
-	  rhoeff=equil.rhopolnorm(3:2:2*length(ijk)+1,it);
-	  if length(ijk)>2
-	    ij_nonan=find(~isnan(equil.rhopolnorm(:,it)));
-	    qfit = zeros(size(equil.rhopolnorm(:,it)));
-	    qfit(ij_nonan)=interpos([0.; rhoeff],[qeff(1) ;qeff],equil.rhopolnorm(ij_nonan,it),-0.01,[1 0],[0 0],[300; ones(size(qeff))]);
-	  else
-	    qfit = zeros(size(equil.rhopolnorm(:,it)));
-	  end
-	  equil.qvalue(:,it) = qfit;
-	end    
-	% get rhotor values
-	equil.phi(:,it) = phi_tree.value(it,Lpf1:-1:1)';
-	equil.rhotornorm(:,it) = sqrt(abs(equil.phi(:,it) ./ equil.phi(end,it)));
-	% get rhovol values
-	equil.vol(:,it)=Vol.value(it,2*Lpf1-1:-2:1)'; 
-	equil.dvoldpsi(:,it)=Vol.value(it,2*Lpf1:-2:2)'; % 2nd index are dV/dpsi
-	equil.rhovolnorm(:,it) = sqrt(abs(equil.vol(:,it) ./ equil.vol(end,it)));
-	equil.area(:,it)=Area.value(it,2*Lpf1-1:-2:1)'; 
-	equil.dareadpsi(:,it)=Area.value(it,2*Lpf1:-2:2)'; % 2nd index are dV/dpsi
-	equil.Rmesh(:,it) = Ri.value(it,1:M_Rmesh);
-	equil.Zmesh(:,it) = Zj.value(it,1:N_Zmesh);
-	equil.psi2D(1:M_Rmesh,1:N_Zmesh,it) = PFM_tree.value(1:M_Rmesh,1:N_Zmesh,it);
-	equil.pressure(:,it)=Pres.value(it,2*Lpf1-1:-2:1)'; 
-	equil.dpressuredpsi(:,it)=Pres.value(it,2*Lpf1:-2:2)'; % 2nd index are dV/dpsi
-	equil.ffprime(:,it) = FFP.value(it,Lpf1:-1:1)';
-	equil.Xpoints.psi(1:LPFx.value(it)+1,it) = PFxx.value(it,1:LPFx.value(it)+1);
-	equil.Xpoints.Rvalue(1:LPFx.value(it)+1,it) = RPFx.value(it,1:LPFx.value(it)+1);
-	equil.Xpoints.Zvalue(1:LPFx.value(it)+1,it) = zPFx.value(it,1:LPFx.value(it)+1);
-	%
-      end
-    else
-      disp('***********************************************************************')
-      disp('***********************************************************************')
-      disp(['problem with nb of time points: NTIME for parameter is: ' num2str(NTIME) ' while qpsi dim= ' num2str(size(qpsi.value))])
-      disp('***********************************************************************')
-      disp('***********************************************************************')
-      equil.qvalue = [];
-      equil.qpsi=qpsi;
-      equil.PFL=psi_tree;
-      equil.TFLx=phi_tree;
-      equil.rhopolnorm=[];
+	equil.qvalue(:,it) = qfit;
+      end    
+      % get rhotor values
+      equil.phi(:,it) = phi_tree.value(it,Lpf1:-1:1)';
+      equil.rhotornorm(:,it) = sqrt(abs(equil.phi(:,it) ./ equil.phi(end,it)));
+      % get rhovol values
+      equil.vol(:,it)=Vol.value(it,2*Lpf1-1:-2:1)'; 
+      equil.dvoldpsi(:,it)=Vol.value(it,2*Lpf1:-2:2)'; % 2nd index are dV/dpsi
+      equil.rhovolnorm(:,it) = sqrt(abs(equil.vol(:,it) ./ equil.vol(end,it)));
+      equil.area(:,it)=Area.value(it,2*Lpf1-1:-2:1)'; 
+      equil.dareadpsi(:,it)=Area.value(it,2*Lpf1:-2:2)'; % 2nd index are dV/dpsi
+      equil.Rmesh(:,it) = Ri.value(it,1:M_Rmesh);
+      equil.Zmesh(:,it) = Zj.value(it,1:N_Zmesh);
+      equil.psi2D(1:M_Rmesh,1:N_Zmesh,it) = PFM_tree.value(1:M_Rmesh,1:N_Zmesh,it);
+      equil.pressure(:,it)=Pres.value(it,2*Lpf1-1:-2:1)'; 
+      equil.dpressuredpsi(:,it)=Pres.value(it,2*Lpf1:-2:2)'; % 2nd index are dV/dpsi
+      equil.ffprime(:,it) = FFP.value(it,Lpf1:-1:1)';
+      equil.Xpoints.psi(1:LPFx.value(it)+1,it) = PFxx.value(it,1:LPFx.value(it)+1);
+      equil.Xpoints.Rvalue(1:LPFx.value(it)+1,it) = RPFx.value(it,1:LPFx.value(it)+1);
+      equil.Xpoints.Zvalue(1:LPFx.value(it)+1,it) = zPFx.value(it,1:LPFx.value(it)+1);
+      %
     end
     equil.x = equil.rhopolnorm;
     %
@@ -1175,7 +1211,7 @@ switch AUGkeywrdcase{index}
     equil.t = equil_time.value(1:NTIME);
     %
     [IpiPSI,e]=rdaAUG_eff(shot,DIAG,'IpiPSI',shotfile_exp);
-    equil.Ip = IpiPSI.value';
+    equil.Ip = IpiPSI.value(1:NTIME);
     %
     equil.data = equil.qvalue; % put q in data
     equil.unit=[]; % not applicable