separate getting ids from TCV and writing ids to database, fix name as string...

separate getting ids from TCV and writing ids to database, fix name as string not cell in pf_active_circuit

git-svn-id: https://spcsvn.epfl.ch/repos/TCV/gdat/trunk@11411 d63d8f72-b253-0410-a779-e742ad2e26cf

crpptbx/TCV_IMAS/ids2database.m

+function [ids_put_status] = ids2database(shot,run,occurence,ids2put,varargin);
+%
+%   [ids_put_status] = ids2database(shot,run,occurence,ids2put,varargin);
+%
+% open/create shot,run and put the ids from ids2put.idsnames (names from fieldnames(ids2put) && within IDS_list)
+%
+% varargin{1}: tbd
+%
+%
+ids_put_status = 0;
+
+% initialize input parser
+p = inputParser;
+% no required inputs here so one can call with empty args and get defaults parameters
+% effectively required inputs should have defaults as empty
+p.addOptional('shot', [], @(x) (isnumeric(x) && isscalar(x) && (x == round(x)))); % integer
+p.addOptional('run', [], @(x) (isnumeric(x) && isscalar(x) && (x == round(x)))); % integer
+p.addOptional('occurence', 0, @(x) isempty(x) || (isnumeric(x) && isscalar(x) && (x == round(x)))); % integer
+p.addOptional('ids2put', struct([]), @(x) (isstruct(x)));
+
+p.parse;
+defaults_ids2database = p.Results; % to keep track of defaults
+
+if nargin==1
+  p.parse(shot);
+  params = p.Results;
+elseif nargin==2
+  p.parse(shot,run);
+  params = p.Results;
+elseif nargin==3 && ~ischar(occurence)
+  p.parse(shot,run,occurence);
+  params = p.Results;
+elseif nargin>=4
+  p.parse(shot,run,occurence,varargin{:});
+  params = p.Results;
+else
+  p.parse;
+  p.Results
+  return
+end
+
+% replace empty inputs with defaults
+names = fieldnames(params);
+mask = structfun(@isempty,params);
+if any(mask),
+  params = rmfield(params,unique([names(mask); p.UsingDefaults.']));
+end
+
+params_ids2database = params;
+
+% check ids_names
+ids_names=fieldnames(ids2put);
+ids_full_list = IDS_list;
+ids_names_notok = setdiff(ids_names,ids_full_list);
+if ~isempty(ids_names_notok)
+  disp(['these subfields are not ids names, so not used: ' sprintf('%s ',ids_names_notok{:})])
+end
+ids_names_ok = intersect(ids_full_list,ids_names);
+
+if isempty(ids_names_ok)
+  disp('no ids names available compatible with IDS_list')
+  return
+end
+
+try
+  %% Initialize the three
+  shot_is_new = 1; % seems only create is ok even if does already exist
+  mdsplustree0=getenv('MDSPLUS_TREE_BASE_0');
+  [aa,bb]=unix(['ls ' mdsplustree0 '/*' num2str(shot) num2str(run,'%4.4d') '*.tree']);
+  if aa==0
+    shot_is_new = 0;
+  end
+  if shot_is_new
+    idx  = imas_create('ids',shot,run,0,0); % 
+  else
+    idx  = imas_open('ids',shot,run); % 
+  end
+
+  %% Put the field
+  for i=1:length(ids_names_ok)
+    ids_to_get = ids_names_ok{i};
+    if occurence <= 0
+      ids_put(idx,ids_to_get,ids2put.(ids_to_get));
+    else
+      ids_put(idx,[ids_to_get '/' num2str(occurence)],ids2put.(ids_to_get));
+    end
+  end
+  
+  %% Close the file
+  imas_close(idx)
+catch ME
+  disp('problems in putting data in database:')
+  throw(ME)
+  idx
+  keyboard
+end

crpptbx/TCV_IMAS/tcv2ids.m

-function [ids_saved,varargout] = tcv2ids(shot,run,varargin);
+function [ids_from_tcv,varargout] = tcv2ids(shot,varargin);
 %
-%   [ids_saved,varargout] = tcv2ids(shot,run,varargin);
+%   [ids_from_tcv,varargout] = tcv2ids(shot,varargin);
 %
 % Assumes you have done: 
 % >> addpath ~g2osaute/public/matlab9_11_2016 (on the gateway)
@@ -10,7 +10,7 @@ function [ids_saved,varargout] = tcv2ids(shot,run,varargin);
 % addpath ~g2osaute/public/matlab9_11_2016
 % mdsconnect('localhost:5555')
 %
-% varargin{1}: ids to load, by default all defined so far
+% varargin{1}: ids to load, by default all defined so far (if empty or empty string or not given)
 %             {'equilibrium', 'magnetics', 'pf_active','wall'} or a subset
 %
 % varargout{1}: return also the ids in array of structure with the names, to allow easy use of plotallids
@@ -21,8 +21,7 @@ p = inputParser;
 % no required inputs here so one can call with empty args and get defaults parameters
 % effectively required inputs should have defaults as empty
 p.addOptional('shot', [], @(x) (isnumeric(x) && isscalar(x) && (x == round(x)))); % integer
-p.addOptional('run', [], @(x) (isnumeric(x) && isscalar(x) && (x == round(x)))); % integer
-p.addOptional('ids_names', {'equilibrium', 'magnetics', 'pf_active','wall', 'tf'}, @(x) (ischar(x) || iscell(x))); % char or cell array
+p.addOptional('ids_names', {'equilibrium', 'magnetics', 'pf_active','wall', 'tf'}, @(x) isempty(x) | (ischar(x) || iscell(x))); % char or cell array
 
 p.parse;
 defaults_tcv2ids = p.Results; % to keep track of defaults
@@ -30,11 +29,8 @@ defaults_tcv2ids = p.Results; % to keep track of defaults
 if nargin==1
   p.parse(shot);
   params = p.Results;
-elseif nargin==2
-  p.parse(shot,run);
-  params = p.Results;
-elseif nargin>=3
-  p.parse('shot',shot,'run',run,varargin{:});
+elseif nargin>=2
+  p.parse(shot,varargin{:});
   params = p.Results;
 else
   p.parse;
@@ -47,12 +43,18 @@ names = fieldnames(params);
 mask = structfun(@isempty,params);
 if any(mask),
   params = rmfield(params,unique([names(mask); p.UsingDefaults.']));
+  if ~isfield(params, 'shot') || isnan(params.shot)
+    warning('No shot entered');
+    return
+  end
+  p.parse(params.shot,rmfield(params,'shot'));
+  params = p.Results;
 end
 
 % check ids_names
 if ~isfield(params,'ids_names')
   disp(['do not provide any ids_names or choose from : '])
-  ids_saved.ids_names_available = defaults_tcv2ids.ids_names;
+  ids_from_tcv.ids_names_available = defaults_tcv2ids.ids_names;
   defaults_tcv2ids.ids_names
   return
 end
@@ -80,32 +82,20 @@ for i=1:length(params_tcv2ids.ids_names)
   ids_to_get = params_tcv2ids.ids_names{i};
   ids_empty=ids_gen(ids_to_get);
   tmp = gdat(shot,'ids','source',ids_to_get,'machine','tcv');
-  ids_saved.(ids_to_get) = tmp.(ids_to_get);
-  ids_saved.([ids_to_get '_description']) = tmp.([ids_to_get '_description']);
-end
-
-%% Initialize the three
-shot_is_new = 1; % seems only create is ok even if does already exist
-if shot_is_new
-  idx  = imas_create('ids',shot,run,run,run); % 
-else
-  idx  = imas_open('ids',shot,run); % 
+  ids_from_tcv.(ids_to_get) = tmp.(ids_to_get);
+  ids_from_tcv.([ids_to_get '_description']) = tmp.([ids_to_get '_description']);
 end
 
-%% Put the field
-for i=1:length(params_tcv2ids.ids_names)
-  ids_to_get = params_tcv2ids.ids_names{i};
-  ids_put(idx,ids_to_get,ids_saved.(ids_to_get));
-end
-
-%% Close the file
-imas_close(idx)
-
 if nargout>=2
-  for i=1:length(params_tcv2ids.ids_names)
-    ids_to_get = params_tcv2ids.ids_names{i};
-    varargout{1}.ids{i} = ids_saved.(ids_to_get);
-    varargout{1}.idsname{i} = ids_to_get;
-    varargout{1}.ids{i}.idsname = ids_to_get;
+  try
+    for i=1:length(params_tcv2ids.ids_names)
+      ids_to_get = params_tcv2ids.ids_names{i};
+      varargout{1}.ids{i} = ids_from_tcv.(ids_to_get);
+      varargout{1}.idsname{i} = ids_to_get;
+      varargout{1}.ids{i}.idsname = ids_to_get;
+    end
+  catch
+    varargout{1} = [];
+    disp('problems to fill in varargout')
   end
 end

crpptbx/TCV_IMAS/tcv2ids2database.m

+% 
+% script to get TCV data as ids and then write them on the database
+%
+
+shot=40000;
+run_out=999;
+occurence=0;
+
+ids2get = []; % default will load all defined so far
+[ids_from_tcv,idsok] = tcv2ids(shot,ids2get);
+
+% can plot with: [plotids_H] = plotids([],idsok.ids{1},idsok.ids{2});
+[ids_put_status] = ids2database(shot,run_out,occurence,ids_from_tcv);
+

crpptbx/TCV_IMAS/tcv_get_ids_circuit.m

@@ -11,10 +11,6 @@ for ii=1:tcv_circuit_info.ntotcircuits
     ids_struct_out{ii}.current.data = tmpdata.data;
     ids_struct_out{ii}.current.time = tmpdata.dim{1};
     ids_struct_out{ii}.connections = tcv_circuit_info.connection_matrix{ii};
-    ids_struct_out{ii}.name = tcv_circuit_info.circuit_names{ii};
+    ids_struct_out{ii}.name = tcv_circuit_info.circuit_names{ii}{1};
 end
 
-
-end
-
-