diff --git a/crpptbx/JET/gdat_jet.m b/crpptbx/JET/gdat_jet.m
index b3caeb64aadb8e7f5da469e4563353634b0a47a7..68b3ff4d01f32a8b088a42afc7595e0286686dec 100644
--- a/crpptbx/JET/gdat_jet.m
+++ b/crpptbx/JET/gdat_jet.m
@@ -387,129 +387,6 @@ elseif strcmp(mapping_for_jet.method,'switchcase')
% First the request names valid for "all" machines:
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- case {'a_minor','rgeom'}
- % compute average minor or major radius (on z=zaxis normally)
- nodenameeff=['\results::r_max_psi' substr_liuqe];
- rmaxpsi=tdi(nodenameeff);
- ijnan = find(isnan(rmaxpsi.data));
- if isempty(rmaxpsi.data) || isempty(rmaxpsi.dim) || ischar(rmaxpsi.data) || ...
- ( ~isempty(ijnan) && prod(size(ijnan))==prod(size(rmaxpsi.data)) )
- if (gdat_params.nverbose>=1); warning(['problems loading data for ' nodenameeff ' for data_request= ' data_request_eff]); end
- if (gdat_params.nverbose>=3); disp(['rerun LIUQE?']); end
- return
- end
- nodenameeff2=['\results::r_min_psi' substr_liuqe];
- rminpsi=tdi(nodenameeff2);
- ijnan = find(isnan(rminpsi.data));
- if isempty(rminpsi.data) || isempty(rminpsi.dim) || ...
- ( ~isempty(ijnan) && prod(size(ijnan))==prod(size(rminpsi.data)) )
- if (gdat_params.nverbose>=1); warning(['problems loading data for ' nodenameeff2 ' for data_request= ' data_request_eff]); end
- if (gdat_params.nverbose>=3); disp(['rerun LIUQE?']); end
- return
- end
- ij=find(rmaxpsi.data<0.5 | rmaxpsi.data>1.2);
- if ~isempty(ij); rmaxpsi.data(ij)=NaN; end
- ij=find(rminpsi.data<0.5 | rminpsi.data>1.2);
- if ~isempty(ij); rminpsi.data(ij)=NaN; end
- if strcmp(data_request_eff,'a_minor')
- gdat_data.data=0.5.*(rmaxpsi.data(end,:) - rminpsi.data(end,:));
- gdat_data.data_fullpath=[nodenameeff ' - ' nodenameeff2 ' /2'];
- elseif strcmp(data_request_eff,'rgeom')
- gdat_data.data=0.5.*(rmaxpsi.data(end,:) + rminpsi.data(end,:));
- gdat_data.data_fullpath=[nodenameeff ' + ' nodenameeff2 ' /2'];
- else
- if (gdat_params.nverbose>=1); warning(['should not be in this case with data_request_eff = ' data_request_eff]); end
- return
- end
- gdat_data.dim = rmaxpsi.dim(2);
- gdat_data.t = gdat_data.dim{1};
- if any(strcmp(fieldnames(rmaxpsi),'units'))
- gdat_data.units = rmaxpsi.units;
- end
- gdat_data.dimunits = rmaxpsi.dimunits(2);
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- case {'zgeom'}
- % compute average minor or major radius (on z=zaxis normally)
- nodenameeff=['\results::z_contour' substr_liuqe];
- zcontour=tdi(nodenameeff);
- if isempty(zcontour.data) || isempty(zcontour.dim) % || ischar(zcontour.data) (to add?)
- if (gdat_params.nverbose>=1); warning(['problems loading data for ' nodenameeff ' for data_request= ' data_request_eff]); end
- if (gdat_params.nverbose>=3); disp(['rerun LIUQE?']); end
- return
- end
- if strcmp(data_request_eff,'zgeom')
- gdat_data.data=0.5.*(max(zcontour.data,[],1) + min(zcontour.data,[],1));
- gdat_data.data_fullpath=['(max+min)/2 of ' nodenameeff];
- gdat_data.dim{1} = zcontour.dim{2};
- gdat_data.dimunits{1} = zcontour.dimunits{2};
- else
- if (gdat_params.nverbose>=1); warning(['should not be in this case with data_request_eff = ' data_request_eff]); end
- return
- end
- gdat_data.t = gdat_data.dim{mapping_for_jet.gdat_timedim};
- if any(strcmp(fieldnames(zcontour),'units'))
- gdat_data.units = zcontour.units;
- end
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- case {'b0'}
- % B0 at R0=0.88
- R0EXP=0.88;
- if liuqe_version==-1
- nodenameeff = 'jet_eq("BZERO","FBTE")';
- tracetdi=tdi(nodenameeff);
- gdat_data.data = tracetdi.data;
- else
- nodenameeff=['\magnetics::iphi'];
- tracetdi=tdi(nodenameeff);
- gdat_data.data=192.E-07 * 0.996 *tracetdi.data/R0EXP;
- end
- if isempty(tracetdi.data) || isempty(tracetdi.dim) % || ischar(tracetdi.data) (to add?)
- if (gdat_params.nverbose>=1); warning(['problems loading data for ' nodenameeff ' for data_request= ' data_request_eff]); end
- return
- end
- gdat_data.data_fullpath=[nodenameeff];
- gdat_data.dim = tracetdi.dim;
- gdat_data.t = gdat_data.dim{1};
- if any(strcmp(fieldnames(tracetdi),'units'))
- gdat_data.units = tracetdi.units;
- end
- gdat_data.dimunits = tracetdi.dimunits;
- gdat_data.request_description = ['vacuum magnetic field at R0=' num2str(R0EXP) 'm; COCOS=17'];
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- case {'betan'}
- % 100*beta / |Ip[MA] * B0[T]| * a[m]
- % get B0 from gdat_jet, without re-opening the shot and using the same parameters except data_request
- % easily done thanks to structure call for options
- params_eff = gdat_data.gdat_params;
- params_eff.data_request='b0';
- b0=gdat_jet([],params_eff); % note: no need to set .doplot=0 since gdat_jet does not call gdat_plot in any case
- params_eff.data_request='ip';
- ip=gdat_jet([],params_eff);
- params_eff.data_request='beta';
- beta=gdat_jet([],params_eff);
- params_eff.data_request='a_minor';
- a_minor=gdat_jet([],params_eff);
- % use beta as time base
- if isempty(b0.data) || isempty(b0.dim) || isempty(ip.data) || isempty(ip.dim) || isempty(a_minor.data) || isempty(a_minor.dim) || isempty(beta.data) || isempty(beta.dim)
- if (gdat_params.nverbose>=1); warning(['problems loading data for data_request= ' data_request_eff]); end
- return
- end
- gdat_data.dim = beta.dim;
- gdat_data.t = beta.dim{1};
- gdat_data.data = beta.data;
- ij=find(~isnan(ip.data));
- ip_t = interp1(ip.dim{1}(ij),ip.data(ij),gdat_data.t);
- ij=find(~isnan(b0.data));
- b0_t = interp1(b0.dim{1}(ij),b0.data(ij),gdat_data.t);
- ij=find(~isnan(a_minor.data));
- a_minor_t = interp1(a_minor.dim{1}(ij),a_minor.data(ij),gdat_data.t);
- gdat_data.data = 100.*beta.data ./ abs(ip_t).*1.e6 .* abs(b0_t) .* a_minor_t;
- gdat_data.data_fullpath='100*beta/ip*1e6*b0*a_minor, each from gdat_jet';
- gdat_data.units = '';
- gdat_data.dimunits{1} = 's';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'cxrs'}
@@ -747,11 +624,18 @@ elseif strcmp(mapping_for_jet.method,'switchcase')
end
if strcmp(lower(gdat_data.gdat_params.source),'hrt2')
nodenameeff_rho = []; % profiles already on rho
+ gdat_data.gdat_params.fit = 0; % no need, chain2 is already a fit on rhopol
end
else
gdat_data.gdat_params.source = 'hrts';
end
- params_eff = gdat_data.gdat_params;
+ if ~isfield(gdat_data.gdat_params,'fit_ne_edge') || isempty(gdat_data.gdat_params.fit_ne_edge) || ~isnumeric(gdat_data.gdat_params.fit_ne_edge)
+ gdat_data.gdat_params.fit_ne_edge = 1e18; % default edge ne value (-1 to let free)
+ end
+ if ~isfield(gdat_data.gdat_params,'fit_te_edge') || isempty(gdat_data.gdat_params.fit_te_edge) || ~isnumeric(gdat_data.gdat_params.fit_te_edge)
+ gdat_data.gdat_params.fit_te_edge = 50; % default edge te value (-1 to let free)
+ end
+ params_eff = gdat_data.gdat_params;
params_eff.doplot = 0;
% ne or Te from Thomson data on raw z mesh vs (z,t)
params_eff.data_request = {'ppf',params_eff.source,data_request_eff};
@@ -795,9 +679,15 @@ elseif strcmp(mapping_for_jet.method,'switchcase')
gdat_data.(data_request_eff).rhopol = gdat_data.x;
gdat_data.dimunits{1} = 'rhopol';
end
-keyboard
- gdat_data = get_grids_1d(gdat_data,1,1,gdat_params.nverbose);
-
+ if length(gdat_data.x) == numel(gdat_data.rhopol)
+ % gdat_data.x is already rhopol and 1D
+ gdat_data = get_grids_1d(gdat_data,1,1,gdat_params.nverbose);
+ else
+ aa=gdat_data; aa.x = aa.rhopol;
+ gdat_data2 = get_grids_1d(aa,2,1,gdat_params.nverbose);
+ gdat_data.grids_1d = gdat_data2.grids_1d;
+ clear aa gdat_data2
+ end
% defaults for fits, so user always gets std structure
gdat_data.fit.rhotornorm = []; % same for both ne and te
gdat_data.fit.rhopolnorm = [];
@@ -810,7 +700,7 @@ keyboard
gdat_data.fit.raw.te.rhotornorm = [];
gdat_data.fit.raw.ne.data = [];
gdat_data.fit.raw.ne.rhotornorm = [];
- fit_tension_default = -0.1;
+ fit_tension_default = -1;
if isfield(gdat_data.gdat_params,'fit_tension')
fit_tension = gdat_data.gdat_params.fit_tension;
else
@@ -853,17 +743,17 @@ keyboard
gdat_data.fit.ne.drhotornorm = gdat_data.fit.rhotornorm;
end
for it=1:length(gdat_data.t)
- % make rhotor->rhopol transformation for each time since equilibrium might have changed
- irhook=find(gdat_data.grids_1d.rhotornorm(:,it)>0 & gdat_data.grids_1d.rhotornorm(:,it)<1); % no need for ~isnan
- [rhoeff isort]=sort(gdat_data.grids_1d.rhotornorm(irhook,it));
- gdat_data.fit.rhopolnorm(:,it)=interpos([0; rhoeff; 1],[0; gdat_data.grids_1d.rhopolnorm(irhook(isort),it); 1],rhopolfit,-0.1,[2 2],[0 1]);
+ % make rhopol->rhotor transformation for each time since equilibrium might have changed
+ irhook=find(gdat_data.grids_1d.rhopolnorm(:,it)>0 & gdat_data.grids_1d.rhopolnorm(:,it)<1); % no need for ~isnan
+ [rhoeff isort]=sort(gdat_data.grids_1d.rhopolnorm(irhook,it));
+ gdat_data.fit.rhotornorm(:,it)=interpos([0; rhoeff; 1],[0; gdat_data.grids_1d.rhotornorm(irhook(isort),it); 1],rhopolfit,-0.1,[2 2],[0 1]);
if any(strfind(data_request_eff,'te'))
- idatate = find(gdat_data.te.data(:,it)>0 & gdat_data.grids_1d.rhotornorm(:,it)<=1.05);
+ idatate = find(gdat_data.te.data(:,it)>1 & gdat_data.grids_1d.rhopolnorm(:,it)<=1.05);
if length(idatate)>0
- gdat_data.fit.raw.te.rhotornorm(idatate,it) = gdat_data.grids_1d.rhotornorm(idatate,it);
+ gdat_data.fit.raw.te.rhopolnorm(idatate,it) = gdat_data.grids_1d.rhopolnorm(idatate,it);
gdat_data.fit.raw.te.data(idatate,it) = gdat_data.te.data(idatate,it);
gdat_data.fit.raw.te.error_bar(idatate,it) = gdat_data.te.error_bar(idatate,it);
- [rhoeff,irhoeff] = sort(gdat_data.grids_1d.rhotornorm(idatate,it));
+ [rhoeff,irhoeff] = sort(gdat_data.grids_1d.rhopolnorm(idatate,it));
rhoeff = [0; rhoeff];
teeff = gdat_data.te.data(idatate(irhoeff),it);
te_err_eff = gdat_data.te.error_bar(idatate(irhoeff),it);
@@ -873,16 +763,22 @@ keyboard
%
teeff = [teeff(1); teeff];
te_err_eff = [1e4; te_err_eff];
- [gdat_data.fit.te.data(:,it), gdat_data.fit.te.drhotornorm(:,it)] = interpos(rhoeff,teeff,rhopolfit,fit_tension.te,[1 0],[0 0],te_err_eff);
+ if gdat_data.gdat_params.fit_te_edge < 0
+ [gdat_data.fit.te.data(:,it), gdat_data.fit.te.drhopolnorm(:,it)] = interpos(rhoeff,teeff,rhopolfit,fit_tension.te,[1 0],[0 ...
+ 0],te_err_eff);
+ else
+ [gdat_data.fit.te.data(:,it), gdat_data.fit.te.drhopolnorm(:,it)] = ...
+ interpos(rhoeff,teeff,rhopolfit,fit_tension.te,[1 2],[0 gdat_data.gdat_params.fit_te_edge],te_err_eff);
+ end
end
end
if any(strfind(data_request_eff,'ne'))
- idatane = find(gdat_data.ne.data(:,it)>0 & gdat_data.grids_1d.rhotornorm(:,it)<=1.05);
+ idatane = find(gdat_data.ne.data(:,it)>1 & gdat_data.grids_1d.rhopolnorm(:,it)<=1.05);
if length(idatane)>0
- gdat_data.fit.raw.ne.rhotornorm(idatane,it) = gdat_data.grids_1d.rhotornorm(idatane,it);
+ gdat_data.fit.raw.ne.rhopolnorm(idatane,it) = gdat_data.grids_1d.rhopolnorm(idatane,it);
gdat_data.fit.raw.ne.data(idatane,it) = gdat_data.ne.data(idatane,it);
gdat_data.fit.raw.ne.error_bar(idatane,it) = gdat_data.ne.error_bar(idatane,it);
- [rhoeff,irhoeff] = sort(gdat_data.grids_1d.rhotornorm(idatane,it));
+ [rhoeff,irhoeff] = sort(gdat_data.grids_1d.rhopolnorm(idatane,it));
rhoeff = [0; rhoeff];
% they are some strange low error_bars, so remove these by max(Te/error_bar)<=10; and changing it to large error bar
neeff = gdat_data.ne.data(idatane(irhoeff),it);
@@ -892,7 +788,15 @@ keyboard
%
neeff = [neeff(1); neeff];
ne_err_eff = [1e21; ne_err_eff];
- [gdat_data.fit.ne.data(:,it), gdat_data.fit.ne.drhotornorm(:,it)] = interpos(rhoeff,neeff,rhopolfit,fit_tension.ne,[1 0],[0 0],ne_err_eff);
+ if gdat_data.gdat_params.fit_ne_edge < 0
+ [gdat_data.fit.ne.data(:,it), gdat_data.fit.ne.drhopolnorm(:,it)] = interpos(rhoeff,neeff,rhopolfit,fit_tension.ne,[1 0],[0 ...
+ 0],ne_err_eff);
+ else
+ ij_in_1 = find(rhoeff<1);
+ [gdat_data.fit.ne.data(:,it), gdat_data.fit.ne.drhopolnorm(:,it)] = ...
+ interpos([rhoeff(ij_in_1); 1.],[neeff(ij_in_1); gdat_data.gdat_params.fit_ne_edge], ...
+ rhopolfit,fit_tension.ne,[1 2],[0 gdat_data.gdat_params.fit_ne_edge],[ne_err_eff(ij_in_1);ne_err_eff(1)]);
+ end
end
end
end
@@ -1364,6 +1268,7 @@ keyboard
rad_bulk2=gdat_jet(shot,params_eff);
gdat_data.rad_bulk_u = rad_bulk2.data;
gdat_data.rad_bulk_avg = 0.5.*(rad_bulk1.data+rad_bulk2.data);
+ gdat_data.rad_bulk_t = rad_bulk1.t;
end
gdat_data.t = rad.t;
gdat_data.dim{1} = gdat_data.t;
@@ -1396,6 +1301,7 @@ keyboard
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'q_rho'}
% q profile on psi from liuqe
+ nodenameeff=[{'ppf'},{'EFTM'},{'Q'}];
nodenameeff=[{'ppf'},{'EFIT'},{'Q'}];
ppftype = nodenameeff{1};
tracename = [nodenameeff{2} '/' nodenameeff{3}];
diff --git a/crpptbx/JET/get_grids_1d.m b/crpptbx/JET/get_grids_1d.m
index 783436477bdd8c5e14195cec6e35dabfa5c5eebe..497eb6c51db33606e8584715d7ce1666d9a1cfe2 100644
--- a/crpptbx/JET/get_grids_1d.m
+++ b/crpptbx/JET/get_grids_1d.m
@@ -27,7 +27,7 @@ end
params_eff = gdat_data.gdat_params;params_eff.doplot=0;
params_eff.data_request='rhotor_norm';
-rhotor_norm = gdat(gdat_data.shot,params_eff)
+rhotor_norm = gdat(gdat_data.shot,params_eff);
params_eff.data_request='rhovol';
rhovol = gdat(gdat_data.shot,params_eff);
params_eff.data_request='psi_axis';
diff --git a/crpptbx/JET/jet_help_parameters.m b/crpptbx/JET/jet_help_parameters.m
index ee75d00d39b8332c95f07cd56136d6c09579f164..0635755a3be8c0195bbc7384644d3f411683e4d5 100644
--- a/crpptbx/JET/jet_help_parameters.m
+++ b/crpptbx/JET/jet_help_parameters.m
@@ -27,15 +27,17 @@ help_struct_all = struct(...
% $$$ help_struct_all.time_interval = ['if provided sets a specific time interval [tstart tend].' ...
% $$$ char(10) 'cxrs: (time_interval can have several nbs) take data and average over time interval(s) only, plots from CXRS_get_profiles are then provided' ...
% $$$ ' as well'];
-% $$$ help_struct_all.fit_tension = ['smoothing value used in interpos fitting routine, -30 means ''30 times default value'', thus -1 often a' ...
-% $$$ ' good value' char(10) ...
-% $$$ 'cxrs: if numeric, default for all cases, if structure, default for non given fields'];
+help_struct_all.fit_tension = ['smoothing value used in interpos fitting routine, -30 means ''30 times default value'', thus -1 often a' ...
+ ' good value' char(10) ...
+ ];
help_struct_all.time = 'time(s) value(s) if relevant, for example eqdsk is provided by default only for time=1.0s';
help_struct_all.zshift = 'vertical shift of equilibrium, either for eqdsk (1 or -99 to shift to zaxis=0) or for mapping measurements on to rho surfaces [m]';
help_struct_all.cocos = ['cocos value desired in output, uses eqdsk_cocos_transform. Note should use latter if a specific Ip and/or B0 sign' ...
'is wanted. See O. Sauter et al Comput. Phys. Commun. 184 (2013) 293'];
% $$$ help_struct_all.edge = '0 (default), 1 to get edge Thomson values';
-% $$$ help_struct_all.fit = '0, no fit profiles, 1 (default) if fit profiles desired as well, relevant for _rho profiles. See also fit_type';
+help_struct_all.fit = '0, no fit profiles, 1 (default) if fit profiles desired as well, relevant for _rho profiles. See also fit_type';
+help_struct_all.fit_ne_edge = '-1, no edge value imposed, >0, value at boundary for all times';
+help_struct_all.fit_te_edge = '-1, no edge value imposed, >0, value at boundary for all times';
% $$$ help_struct_all.fit_type = 'provenance of fitted profiles ''conf'' (default) from conf nodes, ''avg'' or ''local'' for resp. proffit: nodes';
help_struct_all.source = 'sxr: ''H'' (default), camera name ''T'', ''V'' ; for Vloop: ''ppf''(default),''jpf''';
help_struct_all.camera = ['[] (default, all), [i1 i2 ...] chord nbs ([1 3 5] if only chords 1, 3 and 5 are desired), ''central'' uses H10'];
diff --git a/crpptbx/JET/jet_requests_mapping.m b/crpptbx/JET/jet_requests_mapping.m
index 3b579e5ece405661fa3c3044bae5a59d9003f845..f76d7674fa910e4597fc01aaa58ff44c93466ea7 100644
--- a/crpptbx/JET/jet_requests_mapping.m
+++ b/crpptbx/JET/jet_requests_mapping.m
@@ -126,6 +126,11 @@ switch lower(data_request)
mapping.label = 'l_i_3';
mapping.method = 'signal';
mapping.expression = [{'ppf'},{'EFIT'},{'LI3M'}];
+ case {'locked', 'locked_mode'}
+ mapping.timedim = 1;
+ mapping.label = 'locked mode';
+ mapping.method = 'signal';
+ mapping.expression = [{'jpf'},{'DA'},{'C2-LOCA'}];
case 'mhd'
mapping.timedim = 1;
mapping.label = 'n=1 and n=2 amplitude';