readScript

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 function par=readScript(fn)

 reads the data reduction script.

  sjcm
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

0001 function par=readScript(fn)
0002 
0003 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0004 %
0005 % function par=readScript(fn)
0006 %
0007 % reads the data reduction script.
0008 %
0009 %  sjcm
0010 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0011 par=[];
0012 
0013 if (strcmp(fn(end-2:end),'.red'))
0014   disp('Improper file type.  Must have ext .red')
0015   return
0016 end
0017 
0018 fid=fopen(fn,'r');
0019 if (fid==-1)
0020   error('Script not found!')
0021 end
0022 
0023 % read all lines
0024 while(1)
0025   lin=fgets(fid);
0026   if (lin==-1)
0027     % end of file reached
0028     break;
0029   else 
0030     str=sscanf(lin,'%s');
0031     if (~checkstr(str))
0032       [par,q]=interpret(par,lin);
0033       if(~q)
0034         fclose(fid);  
0035     return
0036       end
0037     end
0038   end
0039 end
0040 
0041 % check that all parameters are accounted for
0042 names=fieldnames(par);
0043 caltype=parlist('caltype');
0044 if (length(names)==length(caltype))
0045   disp('Script read successfully!');
0046   disp(' ')
0047   fclose(fid);  
0048   return
0049 else
0050   disp('Parameter settings for some calibration step is missing')
0051   disp('Setting to default values in readScript.m');
0052   disp(['Length names',int2str(length(names)),'   Length caltype',int2str(length(caltype))]);
0053 
0054   par=setdefault(par);
0055   disp(' ')
0056 end
0057 
0058 
0059 %global_plotflag=plotflag.flag
0060 %global_plotflag=2
0061 fclose(fid);
0062 
0063 % check that if in interactive mode, we actually plot shit.
0064 if(par.interactive.flag==1)
0065   if(par.plotflag.flag==0)
0066     display('Warning:  to use interactive mode you must plot data');
0067     display('Setting your plotflag parameter to true');
0068     par.plotflag.flag = 1;
0069   end
0070 end
0071 
0072 return;
0073 
0074 
0075 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0076 function par=setdefault(par);
0077 
0078 names=fieldnames(par);
0079 caltype=parlist('caltype');
0080 
0081 disp(' ')
0082 for i=1:length(caltype)
0083   f=find(strcmp(names,caltype{i}));
0084   if (isempty(f))
0085     disp(sprintf('"%s" parameter not found!  Will use default', ...
0086     caltype{i}));
0087     list=parlist(caltype{i});
0088     def=getdefault(caltype{i});
0089     if (isstrval(list))
0090       eval(sprintf('par.%s.%s=def;',caltype{i},list{1}));
0091     else
0092       if (length(def)~=length(list))
0093     disp('Default values does not match parameter list.')
0094     disp('Parameter setting for this calibraiton step')
0095     disp('will be ignored.')
0096       else
0097     for m=1:length(list)
0098       eval(sprintf('par.%s.%s=%f;',caltype{i},list{m},def(m)));
0099     end
0100       end
0101     end
0102   end
0103 end
0104 
0105 
0106 
0107 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0108 function [par,q]=interpret(par,lin)
0109 
0110 
0111 % find matching cal type
0112 caltype=parlist('caltype');
0113 f=regexpi(lin,':');
0114 
0115 type=caltype{find(strcmp(lin(1:f-1),caltype))};
0116 if (isempty(type))
0117   disp('Unknown calibration type detected in script file')
0118   disp('Script will be ignored')
0119   q=0;
0120   par=[];
0121   return
0122 end
0123 
0124 % get parameter list for cal type
0125 list=parlist(type);
0126 
0127 
0128 % there two types of inputs, numerical or string
0129 q=isstrval(list);
0130 if (isstrval(list)==1)
0131   [par,q]=getstrval(par,list,type,lin(f+1:end));
0132 elseif(isstrval(list)>=2)
0133 [par,q]= getSingleStrVal(par, list, type, lin(f+1:end),q);
0134 else
0135   [par,q]=getnumval(par,list,type,lin(f+1:end));
0136 end
0137 
0138 
0139 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0140 function [par,q]=getstrval(par,list,type,str)
0141 
0142 % get each individual inputs from str
0143 str=findspaces(str);
0144 
0145 % check that string all strings in str are in key
0146 key=sort(getkey(list));
0147 isGood = zeros(size(str));
0148 for m=1:length(str)
0149   if(any(strcmp(str(m), key)))
0150     isGood(m) = 1;
0151   else
0152     isGood(m) = 0;
0153   end
0154 end
0155 
0156 
0157 if(~any(strcmp('alpha', str)))
0158   display('WARN, no alpha step detected in redScript');
0159   display('This is okay if you have loaded previous data via load_d');
0160   display('ohterwise you should run some alpha correction');
0161   display('to put the data in the correct format, otherwise doomed to fail.');
0162 %  isGood(:) = 0;
0163 end
0164 
0165 % check that all
0166 if (all(isGood))
0167   eval(sprintf('par.%s.%s=str;',type,list{1}));
0168   q=1;
0169 else
0170   disp('Parameter list values does not match those')
0171   disp('given in the script file')
0172   disp('routines listed are incorrect or mispelled');
0173   disp('SCRIPT WILL BE IGNORED');
0174   q=0;  par=[];
0175 end
0176 
0177 
0178 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0179 function [par,q]=getSingleStrVal(par,list,type,str,q)
0180 
0181 % get each individual inputs from str
0182 str=findspaces(str);
0183 
0184 % check that all
0185 
0186     if(q==3)
0187       tempw=sprintf('%s\t',str{1:end});
0188       eval(sprintf('par.%s.%s=%s;',type,list{1},['''',tempw,'''']));
0189       clear tempw
0190     q=1;
0191     else
0192         for m=1:length(list)
0193       eval(sprintf('par.%s.%s=str{m};',type,list{m}));
0194   q=1;
0195     end
0196 end
0197 
0198 return;
0199 
0200 
0201 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0202 function [par,q]=getnumval(par,list,type,val)
0203 
0204 q=1;
0205 
0206 % isolate number
0207 val=sscanf(val,'%f');
0208 
0209 % check that if the type is a bitmask, it can handle it properly
0210 if(strcmp(type, 'bitmask'))
0211   eval(sprintf('par.%s.%s = val'';', type, list{1}));
0212   return;
0213 end
0214 
0215 if(strcmp(type, 'mains'))
0216   eval(sprintf('par.%s.%s = val'';', type, list{1}));
0217   return;
0218 end
0219 
0220 % if(strcmp(type, 'rfi'))
0221 %   eval(sprintf('par.%s.%s = val(1:4)'';', type, list{1}));
0222 %   eval(sprintf('par.%s.%s = val(5:9)'';', type, list{2}));
0223 %   eval(sprintf('par.%s.%s = val(10);', type, list{3}));
0224 %   eval(sprintf('par.%s.%s = val(11);', type, list{4}));
0225 %   return;
0226 % end
0227 
0228 
0229 % check that list is same length as val
0230 if (length(val)~=length(list))
0231   disp(val)
0232   disp('Parameter list values does not match those')
0233   disp('given in the script file')
0234   disp('Script will be ignored')
0235   q=0;
0236   par=[];
0237   return
0238 end
0239 
0240 % set values
0241 for i=1:length(val)
0242   eval(sprintf('par.%s.%s=%f;',type,list{i},val(i)));
0243 end
0244 
0245 return;
0246 
0247 
0248 
0249 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0250 function list=parlist(type)
0251 
0252 list=[];
0253 
0254 % calibration types
0255 caltype={'routines', 'bitmask','deglitch', 'rfi', 'rfio', 'coord', 'mains', ...
0256     'alpha', 'tsys', 'noise', 'stokes', 'load', 'pointing', ...
0257      'tau', 'load_d','save_d','ground','astro','plotflag', 'saveplot', 'interactive', 'autorun', ...
0258      'autosave', 'rev', 'field', 'fits','dataselect','dataselect_name'};
0259 
0260 
0261 if (strcmp(type,'caltype'))
0262   list=caltype;
0263   return
0264 end
0265 
0266 switch type
0267   case 'rev'
0268     list={'version'};
0269   
0270   case 'routines'
0271     list={'order'};
0272     
0273   case 'bitmask'
0274     list={'bitVals'};
0275     
0276   case 'deglitch'
0277     list={'chan1', 'chan2'};
0278 
0279   case 'rfio'
0280     list={'aggressive'};
0281   
0282   case 'rfi'
0283     list={'fast', 'polarization', 'intensity'};
0284     
0285   case 'coord'
0286     list={'hemisphere'};
0287  
0288   case 'fits'
0289   list={'domapflag','frame','projection','hdf','source','ini','pyplot'}; 
0290 
0291   case 'dataselect'
0292   list={'dflags'};
0293   
0294   case 'dataselect_name'
0295   list={'fname'};
0296 
0297   case 'mains'
0298     list={'tukey'};
0299     
0300   case 'alpha'
0301     list={'type', 'solve', 'jump', 'flat'};
0302     
0303   case 'stokes'
0304     list={'maxVal', 'slope', 'smooth'};
0305 
0306   case 'pointing'
0307     list={'method'};
0308     
0309   case 'tsys'
0310     list={'valuehi', 'valuelo'};
0311     
0312   case 'noise'
0313     list={'valuehi', 'valuelo', 'primary'};
0314     
0315 %  case 'gain'
0316 %    list={'min', 'max', 'sigma'};
0317 
0318   case 'load'
0319     list={'scaleType'};
0320     
0321   case 'tau'
0322     list={'sigma'};
0323   
0324   case 'load_d'
0325       list={'filename'};
0326 
0327   case 'save_d'
0328       list={'filename'};
0329 
0330   case 'ground'
0331     list={'template_filename_stub'};
0332     
0333   case 'astro'
0334     list={'noflag'};
0335    
0336   case 'plotflag'    
0337     list={'flag'};
0338   
0339   case 'saveplot'
0340   list={'flag','web'};
0341 
0342   case 'interactive'
0343     list={'flag'};
0344 
0345   case 'autorun'
0346     list={'flag'};
0347 
0348   case 'autosave'
0349     list={'flag'};
0350     
0351   case 'field'
0352     list={'name'};
0353 
0354 end    
0355 
0356 
0357 
0358 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0359 function val=getdefault(type)
0360 
0361 val=[];
0362 
0363 switch type
0364   case 'routines'
0365     val = { 'pointing', 'deglitch', 'rfi', 'rfio', 'mains', 'alpha', 'load', ...
0366         'tsys', 'noise', 'tau', 'load_d', 'save_d','ground','astro', 'stokes', 'power', ...
0367         'overf', 'rms', 'summary', 'fits','dataselect','dataselect_name'}; 
0368     
0369   
0370   case 'bitmask'
0371     val = [0 1 5 6 7 8 10 12 15];
0372   
0373   case 'deglitch'
0374     % tolerance Intensity Chan 1
0375     val(1) = 5;
0376     % tolerance Intensity Chan 2
0377     val(2) = 2;
0378 
0379   case 'rfi'
0380     % moderately aggressive.
0381     val(1) = 4;
0382     val(2) = 3;
0383     val(3) = 5;
0384     
0385   case 'rfio'
0386     % moderately aggressive.
0387     val(1) = 3;
0388         
0389   case 'coord'
0390     % hemisphere
0391     val = 1;
0392   
0393   case 'mains'
0394     % no flagging
0395     val = [0];
0396     
0397   case 'tsys'
0398     % no flagging
0399     val(1) = 100;
0400     val(2) = 10;
0401     
0402   case 'pointing'
0403     % default to Mel method
0404     val(1) = 1;
0405   
0406   case 'noise'
0407     val(1) = 4.0;
0408     val(2) = 1;
0409     val(3) = 8;
0410 %  case 'gain'
0411 %    % no flagging
0412 %    val(1) = 100;
0413 %    val(2) = 200;
0414 %    val(3) = 5;
0415 
0416   case 'alpha'
0417     % type of correction to run
0418     val(1) = 1;
0419     % default to not solve for alpha from data
0420     val(2) = 0;
0421     % tolerance for noise diode jump
0422     val(3) = 2;
0423     % tolerance for stable channels
0424     val(4) = 0.2;
0425     
0426   case 'stokes'
0427     % slope improvement
0428     val(1) = 2;
0429     val(2) = 30;
0430     val(3) = 10;
0431     
0432   case 'load'
0433     % defalt scale type
0434     val = 0;
0435     
0436   case 'tau'
0437     % outlier significance
0438     val = 3;
0439     
0440   case 'load_d'
0441     % unused at the moment
0442     val = 'default';
0443   
0444    case 'save_d'
0445     % unused at the moment
0446     val = 'default'; 
0447 
0448   case 'ground'
0449     % unused at the moment
0450     val = 'default_';
0451   
0452   case 'astro'
0453     % no flagging yet
0454     val = 0;
0455     
0456   case 'galactic'
0457      % switches co-ordiante system for healpix maps
0458     val = 1;
0459   
0460   case 'plotflag'
0461     % set default to plot
0462     val=1;
0463     
0464   case 'saveplot'
0465     % set default to not save and not to publish to web
0466   val(1)=0;
0467  val(2)=0;  
0468     
0469   case 'interactive'
0470     % set default for automated
0471     val=0;
0472     
0473   case 'field'
0474     % set default to other
0475     val = 'other';
0476     
0477   case 'autorun'
0478     % turn auto run off
0479     val=0;
0480     
0481   case 'autosave'
0482     % turn auto save off
0483     val=0;
0484     
0485   case 'rev'
0486     % rev number is NaN
0487     val=NaN;
0488     
0489   case 'dataselect'
0490   % Default to flags: -zkg and name: BASIC
0491   val='-zkg';
0492   
0493   case 'dataselect_name'
0494   val='BASIC'; 
0495 end
0496 
0497 
0498 
0499 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0500 function q=isstrval(list)
0501 
0502 if (~strmatch(list{1}, 'order', 'exact') | ~strmatch(list{1}, 'name', ...
0503 'exact') | ~strmatch(list{1}, 'domapflag', 'exact') | ~strmatch(list{1}, 'dflags', ...
0504 'exact') | ~strmatch(list{1}, 'template_filename_stub', 'exact')  | ~strmatch(list{1}, 'filename', 'exact') | ~strmatch(list{1}, 'fname','exact') )
0505   q=0;
0506   return
0507 end
0508 
0509 switch list{1}
0510   case 'order'
0511     q = 1;
0512     
0513   case 'name' 
0514     q = 2;
0515 
0516   case 'domapflag'
0517      q=2;
0518  
0519  case 'dflags'
0520   q=3;
0521  
0522  case 'fname'
0523   q=2;
0524  
0525     case 'template_filename_stub'
0526   q=2;
0527 
0528  case 'filename'
0529   q=2;
0530    
0531   otherwise
0532     q=0;
0533 end
0534 
0535 
0536 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0537 function q=checkstr(str)
0538 
0539 if (isempty(str))
0540   q=1;
0541 else
0542   if (str(1)=='#')
0543     q=1;
0544   else
0545     q=0;
0546   end
0547 end
0548 
0549 
0550 
0551 
0552 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0553 function key=getkey(list)
0554 
0555 switch list{1}
0556   case 'order'
0557     key= {'pointing', 'deglitch', 'rfi', 'rfio', 'mains', 'alpha', 'load', 'tsys', ...
0558       'noise', 'tau','load_d','save_d','ground','astro','stokes', 'power', 'overf', ...
0559       'rms', 'summary', 'fits','dataselect','dataselect_name'};
0560 
0561  end
0562          
0563          
0564 
0565 
0566 
0567 
0568 
0569 
0570 
0571 
0572 
0573