start generic profiles fit/gui

git-svn-id: https://spcsvn.epfl.ch/repos/TCV/gdat/trunk@5864 d63d8f72-b253-0410-a779-e742ad2e26cf

crpptbx/get_profile_structure.m

+function [profile_structs_out,error_status] = get_profile_structure(profile_struct_in);
+%
+% get data from self-description in single profile_struct_in following description in get_profiles.m
+%
+% profile_struct_in, input single structure, and profile_structs_out, output array of structure
+%
+
+error_status=-1001;
+
+profile_struct_def = profile_struct_in;
+
+data_request = profile_struct_def.keyword;
+shot = profile_struct_def.shot;
+
+i_structs_out = 0;
+switch lower(data_request)
+ case {'ne_thomson','te_thomson','nete_thomson'}
+  i_underscore = findstr(data_request,'_');
+  data_request_gdat = [data_request(1:i_underscore-1) '_rho'];
+  aa=gdat(shot,data_request_gdat,'fit',1,'equil',profile_struct_def.profiles_params.equil);
+  if strcmp(data_request(1:i_underscore-1),'nete')
+    % extract ne and te parts into several profile_struct
+    to_extract = {'ne','te'};
+  else
+    to_extract = {data_request(1:i_underscore-1)};
+  end
+  for i=1:length(to_extract)
+    i_structs_out = i_structs_out + 1;
+    profile_structs_out{i_structs_out} = profile_struct_def;
+    if strcmp(profile_struct_def.profiles_params.machine,'tcv')
+      profile_structs_out{i_structs_out}.keyword = [to_extract{i} '_thomson'];
+      profile_structs_out{i_structs_out}.provenance = aa.data_fullpath;
+      profile_structs_out{i_structs_out}.gdat_params = aa.gdat_params;
+      profile_structs_out{i_structs_out}.data = aa.(to_extract{i}).data;
+      profile_structs_out{i_structs_out}.t = aa.(to_extract{i}).t;
+      profile_structs_out{i_structs_out}.error_bar = aa.(to_extract{i}).error_bar;
+      profile_structs_out{i_structs_out}.units = aa.(to_extract{i}).units;
+      profile_structs_out{i_structs_out}.label = [to_extract{i} '\_thomson'];
+      profile_structs_out{i_structs_out}.grid.rhotornorm = aa.grids_1d.rhotornorm;
+      profile_structs_out{i_structs_out}.grid.rhopolnorm = aa.grids_1d.rhopolnorm;
+      profile_structs_out{i_structs_out}.grid.rhovolnorm = aa.grids_1d.rhovolnorm;
+      profile_structs_out{i_structs_out}.grid.psi = aa.grids_1d.psi;
+    elseif strcmp(profile_struct_def.profiles_params.machine,'aug')
+    % for AUG, extract core and edge parts into separate structures
+    % core
+      profile_structs_out{i_structs_out}.keyword = [to_extract{i} '_thomson_core'];
+      profile_structs_out{i_structs_out}.provenance = aa.data_fullpath;
+      profile_structs_out{i_structs_out}.gdat_params = aa.gdat_params;
+      profile_structs_out{i_structs_out}.data = aa.(to_extract{i}).core.data;
+      profile_structs_out{i_structs_out}.t = aa.(to_extract{i}).core.t;
+      profile_structs_out{i_structs_out}.error_bar = aa.(to_extract{i}).core.error_bar;
+      profile_structs_out{i_structs_out}.units = aa.(to_extract{i}).units;
+      profile_structs_out{i_structs_out}.label = [to_extract{i} '\_thomson\_core'];
+      profile_structs_out{i_structs_out}.grid.rhotornorm = aa.(to_extract{i}).core.rhotornorm;
+      profile_structs_out{i_structs_out}.grid.rhopolnorm = aa.(to_extract{i}).core.rhopolnorm;
+      profile_structs_out{i_structs_out}.grid.rhovolnorm = aa.(to_extract{i}).core.rhovolnorm;
+      profile_structs_out{i_structs_out}.grid.psi = aa.(to_extract{i}).core.psi;
+      % edge
+      i_structs_out = i_structs_out + 1;
+      profile_structs_out{i_structs_out} = profile_struct_def;
+      profile_structs_out{i_structs_out}.keyword = [to_extract{i} '_thomson_edge'];
+      profile_structs_out{i_structs_out}.provenance = aa.data_fullpath;
+      profile_structs_out{i_structs_out}.gdat_params = aa.gdat_params;
+      profile_structs_out{i_structs_out}.data = aa.(to_extract{i}).edge.data;
+      profile_structs_out{i_structs_out}.t = aa.(to_extract{i}).edge.t;
+      profile_structs_out{i_structs_out}.error_bar = aa.(to_extract{i}).edge.error_bar;
+      profile_structs_out{i_structs_out}.units = aa.(to_extract{i}).units;
+      profile_structs_out{i_structs_out}.label = [to_extract{i} '\_thomson\_edge'];
+      profile_structs_out{i_structs_out}.grid.rhotornorm = aa.(to_extract{i}).edge.rhotornorm;
+      profile_structs_out{i_structs_out}.grid.rhopolnorm = aa.(to_extract{i}).edge.rhopolnorm;
+      profile_structs_out{i_structs_out}.grid.rhovolnorm = aa.(to_extract{i}).edge.rhovolnorm;
+      profile_structs_out{i_structs_out}.grid.psi = aa.(to_extract{i}).edge.psi;
+    else
+      disp(['In get_profile_structures: not ready yet for machine = ' profile_struct_def.profiles_params.machine]);
+    end
+  end
+ 
+ case {'ne_ida', 'te_ida'}
+
+ otherwise
+  disp(['case = ' data_request ' not defined yet in get_profile_structure, ask O. Sauter']);
+  return
+end
+

crpptbx/get_profiles.m

+function [profile_struct,varargout] = get_profiles(shot,data_request_in,varargin);
+%
+% data_request_in: 1 or several of the optional keywords related to the machine options for profiles
+%               for example: 'te_thomson', or {'te_thomson','te_ece'}, or {'ne_thomson','te_thomson'}
+%               (case insensitive)
+%
+% varargin in pairs:
+%      'equil',equil_source: equilibrium source: EQI(default), EQH, etc for AUG or LIUQE1 (default), LIUQE2, etc for TCV
+%      'machine', machine_name: 'TCV', 'AUG' (default is the default in gdat, thus local machine)
+%
+% output profile_struct is an array of structure for each requested keyword:
+%
+% profile_struct{i}.data, .t, .error_bar, .label, .shot, .keyword, .provenance, .comment, .q (q profile)
+% profile_struct{i}.grid.rhotornorm, .rhopolnorm, .rhovolnorm, .rovera, .psi, .phi, .vol, .provenance
+%
+% profile_struct = get_profiles; % returns the list of possible keywords in profile_struct{i}.keyword
+%
+
+error_status = -1;
+% default output structure
+i_init=1;
+profile_struct{i_init}.data = [];
+profile_struct{i_init}.t = [];
+profile_struct{i_init}.error_bar = [];
+profile_struct{i_init}.label = [];
+profile_struct{i_init}.shot = [];
+profile_struct{i_init}.keyword = [];
+profile_struct{i_init}.provenance = [];
+profile_struct{i_init}.comment = [];
+profile_struct{i_init}.q = [];
+profile_struct{i_init}.grid.rhotornorm = [];
+profile_struct{i_init}.grid.rhopolnorm = [];
+profile_struct{i_init}.grid.rhovolnorm = [];
+profile_struct{i_init}.grid.rovera = [];
+profile_struct{i_init}.grid.psi = [];
+profile_struct{i_init}.grid.phi = [];
+profile_struct{i_init}.grid.vol = [];
+profile_struct{i_init}.grid.provenance = [];
+% default param
+get_profiles_params.machine = [];
+get_profiles_params.equil = [];
+get_profiles_params.nverbose = [];
+get_profiles_params.help.machine = 'machine to get data, aug or tcv at this stage';
+get_profiles_params.help.equil = 'equilibrium source, use default of gdat as default';
+get_profiles_params.help.nverbose = ...
+    'level of information written during the call to get_profiles, default=1, up to warnings but no details';
+profile_struct{i_init}.profiles_params = get_profiles_params;
+
+
+% defaults:
+shot_eff = [];
+if exist('shot') && ~isempty(shot); shot_eff = shot; end
+data_request_eff = [];
+if exist('data_request_in') && ~isempty(data_request_in)
+  if ischar(data_request_in)
+    data_request_eff{1} = data_request_in;
+  else
+    data_request_eff = data_request_in;
+  end
+  if ~iscell(data_request_eff)
+    disp('problem with data_request_in, expects string or cell of strings')
+    error_status=-2;
+    return
+  end
+end
+
+% get default machine
+aa=gdat;
+get_profiles_params.machine = aa.gdat_params.machine;
+get_profiles_params.equil = aa.gdat_params.equil;
+get_profiles_params.nverbose=1;
+
+% extract parameters from pairs of varargin:
+if nargin>=3
+  if mod(nargin-2,2)==0
+    for i=1:2:length(varargin)-1
+      if ischar(varargin{i})
+        % enforce lower case for any character driven input
+        if ischar(varargin{i+1})
+          get_profiles_params.(lower(varargin{i})) = lower(varargin{i+1});
+        else
+          get_profiles_params.(lower(varargin{i})) = varargin{i+1};
+        end
+      else
+        if get_profiles_params.nverbose>=1; warning(['varargin input argument nb: ' num2str(i) ...
+		    ' (nargin=' num2str(i+2) ') is incorrect, expects a character string']); 
+	end
+	error_status=-11;
+	return
+      end
+    end
+  else
+    if get_profiles_params.nverbose>=1; ...
+	  warning('number of varargin input arguments incorrect, cannot make pairs of parameters');
+    end
+    error_status=-12;
+    return
+  end
+end
+profile_struct{i_init}.profiles_params = get_profiles_params;
+
+% list of keywords
+keywords={'te_thomson','ne_thomson','vrot_cxrs','ni_cxrs','ti_cxrs','vpol_cxrs'};
+keywords_tcv_only = [];
+keywords_aug_only = {'te_ece','te_ida','ne_ida'};
+if strcmp(get_profiles_params.machine,'tcv')
+  if ~isempty(keywords_tcv_only); keywords(end+1:end+length(keywords_tcv_only)) = keywords_tcv_only; end
+elseif strcmp(get_profiles_params.machine,'aug')
+  if ~isempty(keywords_aug_only); keywords(end+1:end+length(keywords_aug_only)) = keywords_aug_only; end
+else
+  if get_profiles_params.nverbose>=1
+    disp(['warning machine = ' get_profiles_params.machine ' is not known'])
+    return
+  end
+end
+keywords = sort(keywords);
+
+if isempty(data_request_eff)
+  profile_struct{i_init}.keyword = keywords;
+  return
+end
+
+% fill in default structure for each data_requested keyword, ignore unexpected keywords
+ieff = 0;
+data_request_eff = sort(data_request_eff);
+for i=1:length(data_request_eff)
+  if ~isempty(strmatch(data_request_eff{i},keywords,'exact'))
+    ieff = ieff + 1;
+    if ieff>1
+      profile_struct{ieff} = profile_struct{1};
+    end
+    profile_struct{ieff}.keyword = data_request_eff{i};
+    profile_struct{ieff}.shot = shot_eff;
+  else
+    if get_profiles_params.nverbose>=1
+      disp(['warning data_request = ' data_request_eff{i} ' is not available and ignored, ask O. Sauter'])
+    end
+  end
+end
+
+if ieff==0
+  profile_struct{i_init}.keyword = keywords;
+  return
+end
+
+% Now can fill in data using gdat calls (meaning that gdat calls should be more and more standardized as well to this structure)
+% should use only profile_struct{ieff} to determine what to get, in order to make sure it is self-consistent and fully described
+
+for i=1:length(profile_struct)
+  try
+    profile_struct{i} = get_profile_structure(profile_struct{i});
+  catch
+    if get_profiles_params.nverbose>=1
+      disp(['could not get_profile_structure for ' profile_struct{i}.keyword ', shot = ' num2str(profile_struct{i}.shot)]);
+    end
+  end
+end
+