Changeset 1818 for branches/alma/src

Timestamp:

08/02/10 16:10:43 (14 years ago)

Author:

Kana Sugimoto

Message:

New Development: Yes

JIRA Issue: No (merge)

Ready for Test: Yes

Interface Changes: No

Description:

Merged changes -r1774:1817 in newfiller branch to alma branch

Location:

branches/alma

Files:

• . (modified) (1 prop)
• src/AsapLogSink.cpp (copied) (copied from branches/newfiller/src/AsapLogSink.cpp )
• src/AsapLogSink.h (copied) (copied from branches/newfiller/src/AsapLogSink.h )
• src/FillerBase.cpp (copied) (copied from branches/newfiller/src/FillerBase.cpp )
• src/FillerBase.h (copied) (copied from branches/newfiller/src/FillerBase.h )
• src/FillerWrapper.h (copied) (copied from branches/newfiller/src/FillerWrapper.h )
• src/Makefile (modified) (4 diffs)
• src/NROFiller.cpp (copied) (copied from branches/newfiller/src/NROFiller.cpp )
• src/NROFiller.h (copied) (copied from branches/newfiller/src/NROFiller.h )
• src/PKSFiller.cpp (copied) (copied from branches/newfiller/src/PKSFiller.cpp )
• src/PKSFiller.h (copied) (copied from branches/newfiller/src/PKSFiller.h )
• src/SConscript (modified) (1 prop)
• src/STFiller.cpp (modified) (18 diffs)
• src/Scantable.cpp (modified) (16 diffs)
• src/Scantable.h (modified) (6 diffs)
• src/python_Filler.cpp (copied) (copied from branches/newfiller/src/python_Filler.cpp )
• src/python_LogSink.cpp (copied) (copied from branches/newfiller/src/python_LogSink.cpp )
• src/python_asap.cpp (modified) (2 diffs)
• src/python_asap.h (modified) (2 diffs)

branches/alma/src/Makefile

@@ -130 +130 @@
              STAtmosphere.o \
              Scantable.o \
+             FillerBase.o \
+             NROFiller.o \
+             PKSFiller.o \
+             AsapLogSink.o \
              Templates.o 
+
 PYOBJECTS := python_Scantable.o \
              python_STFiller.o \
@@ -144 +149 @@
              python_STAtmosphere.o \
              python_STCoordinate.o \
+             python_Filler.o \
+             python_LogSink.o \
              python_asap.o
 
@@ -149 +156 @@
 
 HEADERS   := MathUtils.h \
+             LineCatalog.h \
              Lorentzian1D.h \
              Lorentzian1DParam.h \
@@ -183 +191 @@
              IndexedCompare.h \
              STAtmosphere.h \
-             STCoordinate.h
+             STCoordinate.h \
+             FillerBase.h \
+             NROFiller.h \
+             PKSFiller.h \
+             AsapLogSink.h
 
 STATICCCLIB := libasap.a

branches/alma/src/STFiller.cpp

@@ -82 +82 @@
   close();
 }
-  
+
 void STFiller::open( const std::string& filename, const std::string& antenna, int whichIF, int whichBeam, casa::Bool getPt )
 {
@@ -230 +230 @@
   //For MS, add the location of POINTING of the input MS so one get
   //pointing data from there, if necessary.
-  //Also find nrow in MS 
+  //Also find nrow in MS
   nInDataRow = 0;
   if (format == "MS2") {
-    Path datapath(inName); 
+    Path datapath(inName);
     String ptTabPath = datapath.absoluteName();
     Table inMS(ptTabPath);
@@ -246 +246 @@
   }
   String freqFrame = header_->freqref;
-  //translate frequency reference frame back to 
-  //MS style (as PKSMS2reader converts the original frame 
+  //translate frequency reference frame back to
+  //MS style (as PKSMS2reader converts the original frame
   //in FITS standard style)
   if (freqFrame == "TOPOCENT") {
@@ -282 +282 @@
   int status = 0;
 
-  // 
+  //
   // for NRO data
   //
@@ -326 +326 @@
     }
     fclose( fp ) ;
-  } 
+  }
   while ( status == 0 ) {
     status = reader_->read(pksrec);
@@ -389 +389 @@
     RecordFieldPtr<uInt> ifCol(rec, "IFNO");
     *ifCol = pksrec.IFno-ifOffset_- 1;
-    uInt id;
-    /// @todo this has to change when nchan isn't global anymore
-    //id = table_->frequencies().addEntry(Double(header_->nchan/2),
-    //                                    pksrec.refFreq, pksrec.freqInc);
-    if ( pksrec.nchan == 1 ) {
-      id = table_->frequencies().addEntry(Double(0),
-                                          pksrec.refFreq, pksrec.freqInc);
-    }
-    else {
-      id = table_->frequencies().addEntry(Double(pksrec.nchan/2),
-                                          pksrec.refFreq, pksrec.freqInc);
-    }
+    uInt id = table_->frequencies().addEntry(Double(pksrec.spectra.nrow()/2),
+                                             pksrec.refFreq, pksrec.freqInc);
     RecordFieldPtr<uInt> mfreqidCol(rec, "FREQ_ID");
     *mfreqidCol = id;
@@ -419 +409 @@
 
     RecordFieldPtr<uInt> mfocusidCol(rec, "FOCUS_ID");
-    id = table_->focus().addEntry(pksrec.parAngle, pksrec.focusAxi, 
+    id = table_->focus().addEntry(pksrec.parAngle, pksrec.focusAxi,
                                   pksrec.focusTan, pksrec.focusRot);
     *mfocusidCol = id;
@@ -503 +493 @@
   tm *ttm = localtime( &t0 ) ;
   LogIO os( LogOrigin( "STFiller", "openNRO()", WHERE ) ) ;
-//   cout << "STFiller::openNRO()  Start time = " << t0 
-//        << " (" 
-//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-//        << " " 
-//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+//   cout << "STFiller::openNRO()  Start time = " << t0
+//        << " ("
+//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+//        << " "
+//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
 //        << ")" << endl ;
-  os << "Start time = " << t0 
-     << " (" 
-     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-     << " " 
-     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+  os << "Start time = " << t0
+     << " ("
+     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+     << " "
+     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
      << ")" << LogIO::POST ;
 
@@ -551 +541 @@
   if ( whichIF >= 0 ) {
     if ( whichIF >= 0 && whichIF < nIF_ ) {
-      for ( int i = 0 ; i < nIF_ ; i++ ) 
+      for ( int i = 0 ; i < nIF_ ; i++ )
         ifs[i] = False ;
       ifs[whichIF] = True ;
@@ -570 +560 @@
   if (whichBeam>=0) {
     if (whichBeam>=0 && whichBeam<nBeam_) {
-      for ( int i = 0 ; i < nBeam_ ; i++ ) 
+      for ( int i = 0 ; i < nBeam_ ; i++ )
         beams[i] = False ;
       beams[whichBeam] = True;
@@ -595 +585 @@
   time( &t1 ) ;
   ttm = localtime( &t1 ) ;
-//   cout << "STFiller::openNRO()  End time = " << t1 
-//        << " (" 
-//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-//        << " " 
-//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+//   cout << "STFiller::openNRO()  End time = " << t1
+//        << " ("
+//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+//        << " "
+//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
 //        << ")" << endl ;
 //   cout << "STFiller::openNRO()  Elapsed time = " << t1 - t0 << " sec" << endl ;
-  os << "End time = " << t1 
-     << " (" 
-     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-     << " " 
-     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+  os << "End time = " << t1
+     << " ("
+     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+     << " "
+     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
      << ")" << endl ;
   os << "Elapsed time = " << t1 - t0 << " sec" << endl ;
@@ -622 +612 @@
   tm *ttm = localtime( &t0 ) ;
   LogIO os( LogOrigin( "STFiller", "readNRO()", WHERE ) ) ;
-//   cout << "STFiller::readNRO()  Start time = " << t0 
-//        << " (" 
-//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-//        << " " 
-//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+//   cout << "STFiller::readNRO()  Start time = " << t0
+//        << " ("
+//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+//        << " "
+//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
 //        << ")" << endl ;
-  os << "Start time = " << t0 
-     << " (" 
-     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-     << " " 
-     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+  os << "Start time = " << t0
+     << " ("
+     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+     << " "
+     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
      << ")" << LogIO::POST ;
   //
@@ -692 +682 @@
       srcType = 3 ;
     }
- 
+
     // if srcType is 2 (ZERO scan), ignore scan
-    if ( srcType != 2 && srcType != -1 && srcType != 3 ) { 
+    if ( srcType != 2 && srcType != -1 && srcType != 3 ) {
       TableRow row( table_->table() ) ;
       TableRecord& rec = row.record();
@@ -789 +779 @@
       *srcnCol = srcname ;
       RecordFieldPtr<Int> srctCol(rec, "SRCTYPE") ;
-      *srctCol = srcType ;     
-      RecordFieldPtr<String> fieldnCol(rec, "FIELDNAME"); 
+      *srctCol = srcType ;
+      RecordFieldPtr<String> fieldnCol(rec, "FIELDNAME");
       *fieldnCol = fieldname ;
       RecordFieldPtr< Array<Float> > specCol(rec, "SPECTRA") ;
@@ -820 +810 @@
                                        windvel,
                                        winddir ) ;
-      *mweatheridCol = id ;          
+      *mweatheridCol = id ;
       RecordFieldPtr<Double> svelCol(rec, "SRCVELOCITY") ;
       *svelCol = srcvel ;
@@ -847 +837 @@
   ttm = localtime( &t1 ) ;
 //   cout << "STFiller::readNRO()  Processed " << i << " rows" << endl ;
-//   cout << "STFiller::readNRO()  Added " << i - count << " rows (ignored " 
+//   cout << "STFiller::readNRO()  Added " << i - count << " rows (ignored "
 //        << count << " \"ZERO\" scans)" << endl ;
-//   cout << "STFiller::readNRO()  End time = " << t1 
-//        << " (" 
-//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-//        << " " 
-//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+//   cout << "STFiller::readNRO()  End time = " << t1
+//        << " ("
+//        << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+//        << " "
+//        << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
 //        << ")" << endl ;
 //   cout << "STFiller::readNRO()  Elapsed time = " << t1 - t0 << " sec" << endl ;
   os << "Processed " << i << " rows" << endl ;
-  os << "Added " << i - count << " rows (ignored " 
+  os << "Added " << i - count << " rows (ignored "
      << count << " \"ZERO\" scans)" << endl ;
   os.post() ;
-  os << "End time = " << t1 
-     << " (" 
-     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday 
-     << " " 
-     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec 
+  os << "End time = " << t1
+     << " ("
+     << ttm->tm_year + 1900 << "/" << ttm->tm_mon + 1 << "/" << ttm->tm_mday
+     << " "
+     << ttm->tm_hour << ":" << ttm->tm_min << ":" << ttm->tm_sec
      << ")" << endl ;
   os << "Elapsed time = " << t1 - t0 << " sec" << endl ;
@@ -871 +861 @@
 
   return 0 ;
-} 
+}
 
 Bool STFiller::fileCheck()
@@ -881 +871 @@
   if ( inFile.isDirectory() )
     return bval ;
-  
+
   // if beginning of header data is "RW", return true
-  // otherwise, return false ; 
+  // otherwise, return false ;
   FILE *fp = fopen( filename_.c_str(), "r" ) ;
   char buf[9] ;

branches/alma/src/Scantable.cpp

@@ -224 +224 @@
   td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
   td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
-  td.addColumn(ScalarColumnDesc<Int>("REFBEAMNO"));
-
-  td.addColumn(ScalarColumnDesc<uInt>("FLAGROW"));
+
+  ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
+  refbeamnoColumn.setDefault(Int(-1));
+  td.addColumn(refbeamnoColumn);
+
+  ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
+  flagrowColumn.setDefault(uInt(0));
+  td.addColumn(flagrowColumn);
 
   td.addColumn(ScalarColumnDesc<Double>("TIME"));
@@ -361 +366 @@
       for (int i = 0; i < size; ++i)
         arr[i] = static_cast<T>(defValue[i]);
-      
+
       col.fillColumn(arr);
     } else {
@@ -949 +954 @@
           Vector<Double> vec(moleculeTable_.getRestFrequency(i));
           if (vec.nelements() > 0) {
-               if (firstline) { 
+               if (firstline) {
                    oss << setprecision(10) << vec << " [Hz]" << endl;
                    firstline=False;
                }
-               else{ 
+               else{
                    oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
-               } 
+               }
           } else {
               oss << "none" << endl;
@@ -1167 +1172 @@
   //Quantum<Double> urf(rf, u);
   Quantum<Vector<Double> >urf(rf, u);
-  Vector<String> formattedname(0); 
+  Vector<String> formattedname(0);
   //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
-  
+
   //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
   uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
@@ -1241 +1246 @@
 }
 
-std::string Scantable::getAntennaName() const
+String Scantable::getAntennaName() const
 {
   String out;
@@ -1347 +1352 @@
   Vector<Float> arr = specCol_( 0 ) ;
   int nChan = arr.nelements() ;
-  
+
   // if nmin < 0 or nmax < 0, nothing to do
   if (  nmin < 0 ) {
@@ -1355 +1360 @@
     throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
   }
-  
+
   // if nmin > nmax, exchange values
   if ( nmin > nmax ) {
@@ -1362 +1367 @@
     nmin = tmp ;
     LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
-    os << "Swap values. Applied range is [" 
+    os << "Swap values. Applied range is ["
        << nmin << ", " << nmax << "]" << LogIO::POST ;
   }
-  
+
   // if nmin exceeds nChan, nothing to do
   if ( nmin >= nChan ) {
     throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
   }
-  
+
   // if nmax exceeds nChan, reset nmax to nChan
   if ( nmax >= nChan ) {
@@ -1386 +1391 @@
     }
   }
-  
+
   // reshape specCol_ and flagCol_
   for ( int irow = 0 ; irow < nrow() ; irow++ ) {
@@ -1406 +1411 @@
      ***/
     refval = refval - ( refpix - nmin ) * increment ;
-    refpix = 0 ;  
+    refpix = 0 ;
     freqTable_.setEntry( refpix, refval, increment, irow ) ;
   }
-  
+
   // update nchan
   int newsize = nmax - nmin + 1 ;
   table_.rwKeywordSet().define( "nChan", newsize ) ;
-  
+
   // update bandwidth
   // assumed all spectra in the scantable have same bandwidth
   table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
-  
+
   return ;
 }
 
-void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) 
+void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
 {
   // reshape specCol_ and flagCol_
@@ -1462 +1467 @@
   for ( int irow = 0 ; irow < nrow() ; irow++ ) {
     regridChannel( nChan, dnu, irow ) ;
-  } 
+  }
   coordinfo[0] = oldinfo ;
   setCoordInfo( coordinfo ) ;
 
 
-  // NOTE: this method does not update metadata such as 
+  // NOTE: this method does not update metadata such as
   //       FREQUENCIES subtable, nChan, Bandwidth, etc.
 
-  return ; 
-}
-
-void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) 
+  return ;
+}
+
+void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
 {
   // logging
@@ -1483 +1488 @@
   Vector<Float> newspec( nChan, 0 ) ;
   Vector<uChar> newflag( nChan, false ) ;
-  
+
   // regrid
   vector<double> abcissa = getAbcissa( irow ) ;
@@ -1502 +1507 @@
   zi[0] = z[0] - 0.5 * dnu ;
   zi[1] = z[0] + 0.5 * dnu ;
-  for ( int ii = 2 ; ii < nChan ; ii++ ) 
+  for ( int ii = 2 ; ii < nChan ; ii++ )
     zi[ii] = zi[ii-1] + dnu ;
   zi[nChan] = z[nChan-1] + 0.5 * dnu ;
@@ -1509 +1514 @@
   for ( int ii = 2 ; ii < oldsize ; ii++ )
     yi[ii] = abcissa[ii-1] + olddnu ;
-  yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ; 
+  yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ;
   if ( dnu > 0.0 ) {
     for ( int ii = 0 ; ii < nChan ; ii++ ) {
@@ -1664 +1669 @@
 //    ***/
 //   // NOTE: Assumed that all spectra have the same bandwidth
-//   pile += dnu ; 
+//   pile += dnu ;
 //   newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
 //   newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
@@ -1683 +1688 @@
 //   newspec[nChan-1] /= wsum ;
 //   //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
-  
+
 //   specCol_.put( irow, newspec ) ;
 //   flagsCol_.put( irow, newflag ) ;

branches/alma/src/Scantable.h

@@ -237 +237 @@
 
   /**
-   * Get flagRow info at the specified row. If true, the whole data 
+   * Get flagRow info at the specified row. If true, the whole data
    * at the row should be flagged.
    */
@@ -250 +250 @@
 
   /**
-   * Return a list of booleans with the size of nchan for a specified row, to get info 
+   * Return a list of booleans with the size of nchan for a specified row, to get info
    * about which channel is clipped.
    */
   std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
-  void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag, 
+  void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
                           casa::Vector<casa::uChar> flgs);
 
@@ -441 +441 @@
    * @return antenna name string
    */
-  std::string getAntennaName() const;
+  casa::String getAntennaName() const;
 
   /**
@@ -470 +470 @@
    * @param[in] nmin, nmax minimum and maximum channel
    * @param[in] irow       row number
-   * 
-   * 30/07/2008 Takeshi Nakazato  
+   *
+   * 30/07/2008 Takeshi Nakazato
    **/
   void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
@@ -486 +486 @@
   void regridChannel( int nchan, double dnu, int irow ) ;
 
- 
+
 private:
 
@@ -583 +583 @@
 
   /**
-   * Add an auxiliary column to the main table and attach it to a 
+   * Add an auxiliary column to the main table and attach it to a
    * cached column. Use for adding new columns that the original asap2
-   * tables do not have. 
+   * tables do not have.
    * @param[in] col      reference to the cached column to be attached
    * @param[in] colName  column name in asap table

branches/alma/src/python_asap.cpp

@@ -67 +67 @@
   asap::python::python_Scantable();
   asap::python::python_STFiller();
+  asap::python::python_Filler();
   asap::python::python_STSelector();
   asap::python::python_STMath();
@@ -75 +76 @@
   asap::python::python_LineCatalog();
   asap::python::python_Logger();
+  asap::python::python_LogSink();
   asap::python::python_STCoordinate();
   asap::python::python_STAtmosphere();

branches/alma/src/python_asap.h

@@ -39 +39 @@
     void python_Scantable();
     void python_STFiller();
+    void python_Filler();
     void python_STSelector();
     void python_STMath();
@@ -47 +48 @@
     void python_LineCatalog();
     void python_Logger();
+    void python_LogSink();
     void python_STCoordinate();
     void python_STAtmosphere();