Merge branch '48-improve-output-key-management-and-header-construction' into 'u/jct/dev'

change readOutKeyword method so that it reads a txt file with all licit output...

See merge request Galaxies/LEPHARE!59

examples/output.para

@@ -67,7 +67,6 @@ SCALE_BEST
 NBAND_USED
 CONTEXT
 ZSPEC
-STRING_INPUT
 #MAG_MOD()
 #######  Far-IR  PARAMETERS  derived from  FIR_LIB  library  ###########
 #LUM_TIR_BEST
@@ -137,4 +136,3 @@ LUM_K_BEST
 # Predicted magnitudes in a spare filter set
 # ABSMAG_PRED()
 MAG_PRED()
-

source/alloutputkeys.txt

+IDENT
+Z_BEST
+Z_BEST68_LOW
+Z_BEST68_HIGH
+Z_BEST90_LOW
+Z_BEST90_HIGH
+Z_BEST99_LOW
+Z_BEST99_HIGH
+Z_ML
+Z_ML68_LOW
+Z_ML68_HIGH
+Z_ML90_LOW
+Z_ML90_HIGH
+Z_ML99_LOW
+Z_ML99_HIGH
+MOD_BEST
+EXTLAW_BEST
+EBV_BEST
+MASS_BEST
+LDUST_BEST
+LUM_TIR_BEST
+LUM_NUV_BEST
+LUM_R_BEST
+LUM_K_BEST
+PDZ_BEST
+CHI_BEST
+SCALE_BEST
+AGE_BEST
+SFR_BEST
+SSFR_BEST
+CONTEXT
+NBAND_USED
+NBAND_ULIM
+ZSPEC
+MAG_OBS()
+ERR_MAG_OBS()
+MAG_MOD()
+MAG_PRED()
+ABSMAG_PRED()
+MOD_QSO
+MOD_STAR
+Z_QSO
+Z_ML_QSO
+Z_ML68_LOW_QSO
+Z_ML68_HIGH_QSO
+CHI_QSO
+CHI_STAR
+MOD_SEC
+EXTLAW_SEC
+Z_SEC
+EBV_SEC
+PDZ_SEC
+CHI_SEC
+SCALE_SEC
+AGE_SEC
+AGE_MED
+AGE_INF
+AGE_SUP
+LDUST_MED
+LDUST_INF
+LDUST_SUP
+LUM_TIR_MED
+LUM_TIR_INF
+LUM_TIR_SUP
+MASS_MED
+MASS_INF
+MASS_SUP
+EBV_MED
+EBV_INF
+EBV_SUP
+SFR_MED
+SFR_INF
+SFR_SUP
+SSFR_MED
+SSFR_INF
+SSFR_SUP
+COL1_MED
+COL1_INF
+COL1_SUP
+COL2_MED
+COL2_INF
+COL2_SUP
+MREF_MED
+MREF_INF
+MREF_SUP
+LIMITS_ZMAX
+LIMITS_MFAINT
+EM_FLUX_LYA
+EM_FLUX_OII
+EM_FLUX_HB
+EM_FLUX_OIIIA
+EM_FLUX_OIIIB
+EM_FLUX_HA
+EM_FLUX_SIIIA
+EM_FLUX_SIIIB
+EM_FLUX()
+EM_EW_LYA
+EM_EW_OII
+EM_EW_HB
+EM_EW_OIIIA
+EM_EW_OIIIB
+EM_EW_HA
+EM_EW_SIIIA
+EM_EW_SIIIB
+MABS_FLUX()
+MABS_FILT()
+K_COR()
+MAG_ABS()
+EMAG_ABS()
+STRING_INPUT

source/photoz_lib.cpp

@@ -359,9 +359,6 @@ PhotoZ::PhotoZ(keymap& key_analysed)
   if(filtNameAdd!="none"){
     allFiltersAdd  = read_doc_filters(filtNameAdd);
   }
-  /* Read the output parameter file */
-  outkeywords = readOutKeywords(outpara);
-
 }
 
 keymap read_keymap_from_doc(const string libName) {
@@ -532,7 +529,7 @@ void PhotoZ::read_lib(vector<SED*> & libFull, int & ind, int nummodpre[3], const
  read the keywords of the ouput parameter file
 */
 vector<string> readOutKeywords(const string outpara){
-
+  
   //first get the list of all the keys from the master file
   string lit; 
   ifstream stoutpara;
@@ -548,86 +545,53 @@ vector<string> readOutKeywords(const string outpara){
     }
   }
   stoutpara.close();
+  if(allkeys.size()==0)
+    throw runtime_error("alloutputkeys.txt reading resulted in an empty vector!");
+  
+  // if the output parameter file is not provided,
+  // default is to output all keywords
+  if (outpara == nonestring){
+    return allkeys;
+  }
   
   vector<string> vecKey;
-  int nbLines=0;
   bool inString=false;
   
-  // check that an output parameter file exists
-  if (outpara.compare(nonestring) != 0){
-    
-    // open the output parameter file into a stream
-    stoutpara.open(outpara.c_str());
-    if(!stoutpara){
-      cerr << "Can't open output parameter file " << outpara << endl;
-      exit(1);
-    }
-    
-    //Take the stream line by line
-    while(getline( stoutpara, lit)){
-      
-      //If the first character of the line is not #
-      if(test_first_char(lit)) {
-	
-	//put the line into the stream ss again 
-	stringstream ss(lit);
-	
-	ss >> fakeString ;
-	// Check that the string is not a deprecated keyword
-	//check_deprecated(fakeString) ;
-	// Check that the string is not "STRING_INPUT"
-	if (fakeString.compare("STRING_INPUT") != 0){
-	  vecKey.push_back(fakeString);
-	}else{
-	  inString=true;
-	}
-	
-	//Count lines
-	nbLines++;
+  // open the output parameter file into a stream
+  stoutpara.open(outpara.c_str());
+  if(!stoutpara)
+    throw invalid_argument("Cannot open output parameter file "+ outpara);
+  
+  //Take the stream line by line
+  while(getline( stoutpara, lit)){
+    if(test_first_char(lit)) {
+      stringstream ss(lit);
+      ss >> fakeString ;
+      // "STRING_INPUT" if present needs to be put at the end of the vector
+      if (fakeString != "STRING_INPUT"){
+	vecKey.push_back(fakeString);
+      }else{
+	inString=true;
       }
     }
   }
+  stoutpara.close();
   
-  if(nbLines == 0 )cout << "No keyword for the output parameter file " << endl;
+  if( vecKey.size()==0 )
+    throw runtime_error("No keyword read from "+outpara);
   
   // Put "STRING_INPUT" at the end
-  if(inString)vecKey.push_back("STRING_INPUT");
-  //Close the stream
-  stoutpara.close();
-  
-  for(vector<string>::iterator it=allkeys.begin(); it!=allkeys.end(); ){
-    if(find(vecKey.begin(), vecKey.end(), *it) == vecKey.end()){
-      //cout<<*it<<" not found"<<endl;
-	it = allkeys.erase(it);
-    } else{
-      ++it;
-      //cout<<*it<<" found"<<endl;
+  if(inString)
+    vecKey.push_back("STRING_INPUT");
+
+  //check that all user output parameters are licit
+  for(vector<string>::iterator it=vecKey.begin(); it!=vecKey.end(); it++){
+    if(find(allkeys.begin(), allkeys.end(), *it) == allkeys.end()){
+      throw invalid_argument(*it+" is not a licit output parameter. Check licit parameters in source/alloutputkeys.txt.");
     }
   }
   
-  return allkeys;
-}
-
-/*
-check that the keyword is not deprecated and replace if necessary
-*/
-void check_deprecated(string& checkString){
-
-  // List of the keywords which changed
-  string oldkey[] = {"Z_ML","Z_ML68_LOW","Z_ML68_HIGH","Z_ML90_LOW","Z_ML90_HIGH","Z_ML99_LOW","Z_ML99_HIGH","AGE_MED","AGE_INF","AGE_SUP","LDUST_MED","LDUST_INF","LDUST_SUP","LUM_TIR_MED","LUM_TIR_INF","LUM_TIR_SUP","MASS_MED","MASS_INF","MASS_SUP","EBV_MED","EBV_INF","EBV_SUP","SFR_MED","SFR_INF","SFR_SUP","SSFR_MED","SSFR_INF","SSFR_SUP","COL1_MED","COL1_INF","COL1_SUP","COL2_MED","COL2_INF","COL2_SUP","MREF_MED","MREF_INF","MREF_SUP","Z_ML_QSO","Z_ML68_LOW_QSO","Z_ML68_HIGH_QSO"};
-  string newkey[] = {"Z_MOD","Z_MOD68_LOW","Z_MOD68_HIGH","Z_MOD90_LOW","Z_MOD90_HIGH","Z_MOD99_LOW","Z_MOD99_HIGH","AGE_MOD","AGE_LOW","AGE_HIGH","LDUST_MOD","LDUST_LOW","LDUST_HIGH","LUM_TIR_MOD","LUM_TIR_LOW","LUM_TIR_HIGH","MASS_MOD","MASS_LOW","MASS_HIGH","EBV_MOD","EBV_LOW","EBV_HIGH","SFR_MOD","SFR_LOW","SFR_HIGH","SSFR_MOD","SSFR_LOW","SSFR_HIGH","COL1_MOD","COL1_LOW","COL1_HIGH","COL2_MOD","COL2_LOW","COL2_HIGH","MREF_MOD","MREF_LOW","MREF_HIGH","Z_MOD_QSO","Z_MOD68_LOW_QSO","Z_MOD68_HIGH_QSO"};
-  
-  // List on the keywords which need to be changed
-  for (int k=0;k<int(sizeof(oldkey)/sizeof(oldkey[0])); k++){
-    // Test if it is a deprecated keyword
-   if (checkString.compare(oldkey[k]) == 0){
-     cout << "Output keyword " << oldkey[k] << " deprecated. Replaced by " << newkey[k] << endl;
-     // replace
-     checkString = newkey[k];
-     break;
-   }
-  }
-  return;
+  return vecKey;
 }
 
 
@@ -662,25 +626,24 @@ string prep_header(vector<string> outkeywords, const int & imagm, const int & im
   form += "# Format topcat: \n#";
 
   // Loop over each keyword
-for(auto& key : outkeywords){
-  if(key.find("()") == string::npos ) {
+  for(auto& key : outkeywords){
+    if(key.find("()") == string::npos ) {
     form +=  " "+key+" ";
-  } else {
-    key = key.substr(0, key.size()-2);//remove ()
-    for(const auto& key2 : {"MAG_OBS", "MAG_MOD", "K_COR", "MABS_FILT", "MAG_ABS"} ){
-      if(key.find(key2) != string::npos)
-	{for (int l=0; l<imagm; l++)form +=  " "+ key +  to_string(l)+" ";}
+    } else {
+      key = key.substr(0, key.size()-2);//remove ()
+      for(const auto& key2 : {"MAG_OBS", "MAG_MOD", "K_COR", "MABS_FILT", "MAG_ABS"} ){
+	if(key.find(key2) != string::npos)
+	  {for (int l=0; l<imagm; l++)form +=  " "+ key +  to_string(l)+" ";}
+      }
+      if(key.find("MAG_PRED()") != string::npos)
+	{for (int l=0; l<imagmAdd; l++)form +=  " "+ key +  to_string(l)+" ";}
+
+      if(key == "EM_FLUX()")
+	{for (int l=0; l<65; l++)form +=  " "+ key +  to_string(l)+" ";}
     }
-    
-    if(key.find("MAG_PRED()") != string::npos)
-      {for (int l=0; l<imagmAdd; l++)form +=  " "+ key +  to_string(l)+" ";}
-    
-    if(key == "EM_FLUX()")
-      {for (int l=0; l<65; l++)form +=  " "+ key +  to_string(l)+" ";}
-  }
- } 
- form += '\n';
- return form; 
+  } 
+  form += '\n';
+  return form; 
 }
 
 /*

tests/test_suite.sh

@@ -31,6 +31,7 @@ $LEPHAREDIR/bin/mag_gal  -c $LEPHAREDIR/examples/COSMOS.para -t G --GAL_LIB_IN L
 
 cat_out=zphot_short.out
 
-$LEPHAREDIR/bin/zphota -c $LEPHAREDIR/examples/COSMOS.para --CAT_IN $LEPHAREDIR/examples/COSMOS.in --CAT_OUT $cat_out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS  --ADD_EMLINES 0,100 --AUTO_ADAPT YES --CAT_LINES 1,100 --SPEC_OUT YES --PARA_OUT $LEPHAREDIR/examples/output.para --VERBOSE NO --ZFIX YES
+$LEPHAREDIR/bin/zphota -c $LEPHAREDIR/examples/COSMOS.para --CAT_IN $LEPHAREDIR/examples/COSMOS.in --CAT_OUT $cat_out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS  --ADD_EMLINES 0,100 --AUTO_ADAPT NO --CAT_LINES 1,10 --SPEC_OUT NO --PARA_OUT $LEPHAREDIR/examples/output.para --VERBOSE NO --ZFIX NO
 
 mv $cat_out Id*.spec $LEPHAREWORK/zphota/
+