Changeset 2818 for trunk

Timestamp:

07/02/13 10:38:18 (11 years ago)

Author:

Malte Marquarding

Message:

Issue #291: added scantable.set_sourcename to overwrite sourcename to allow freq_align to work. Exposed 'SOURCE' averaging to python api. Added some logging to freq_align refering to the sources it aligns to

Location:

trunk

Files:

• python/__init__.py (modified) (1 diff)
• python/asapmath.py (modified) (1 diff)
• python/scantable.py (modified) (4 diffs)
• setup.py (modified) (1 diff)
• src/STMath.cpp (modified) (4 diffs)
• src/Scantable.cpp (modified) (2 diffs)
• src/Scantable.h (modified) (3 diffs)
• src/ScantableWrapper.h (modified) (1 diff)
• src/python_Scantable.cpp (modified) (1 diff)
• test/test_scantable.py (modified) (3 diffs)

trunk/python/__init__.py

@@ -59 +59 @@
 
 __date__ = '$Date$'.split()[1]
-__version__  = 'trunk'
+__version__  = '4.1.3a'
 __revision__ = get_revision()
 

trunk/python/asapmath.py

@@ -90 +90 @@
     else:
         #s = scantable(stm._average(alignedlst, mask, weight.upper(), scanav))
-        s = scantable(stm._new_average(alignedlst, compel, mask, weight.upper(), scanav))
+        s = scantable(stm._new_average(alignedlst, compel, mask, 
+                                       weight.upper(), scanav))
     s._add_history("average_time",varlist)
 

trunk/python/scantable.py

@@ -2112 +2112 @@
     #
     @asaplog_post_dec
-    def average_time(self, mask=None, scanav=False, weight='tint', align=False):
+    def average_time(self, mask=None, scanav=False, weight='tint', align=False,
+                     avmode="NONE"):
         """\
         Return the (time) weighted average of a scan. Scans will be averaged
@@ -2140 +2141 @@
             align:    align the spectra in velocity before averaging. It takes
                       the time of the first spectrum as reference time.
+            avmode:   'SOURCE' - also select by source name -  or 
+                      'NONE' (default). Not applicable for scanav=True or
+                      weight=median
 
         Example::
@@ -2150 +2154 @@
         weight = weight or 'TINT'
         mask = mask or ()
-        scanav = (scanav and 'SCAN') or 'NONE'
+        scanav = (scanav and 'SCAN') or avmode.upper()
         scan = (self, )
 
         if align:
             scan = (self.freq_align(insitu=False), )
+            asaplog.push("Note: Alignment is don on a source-by-source basis")
+            asaplog.push("Note: Averaging (by default) is not")
+            # we need to set it to SOURCE averaging here            
         s = None
         if weight.upper() == 'MEDIAN':
@@ -4246 +4253 @@
         self._add_history("set_sourcetype", varlist)
 
+
+    def set_sourcename(self, name):
+        varlist = vars()
+        self._setsourcename(name)
+        self._add_history("set_sourcename", varlist)
+
     @asaplog_post_dec
     @preserve_selection

trunk/setup.py

@@ -4 +4 @@
 
 setup(name = PKGNAME,
-      version = '4.1.0',
+      version = '4.1.3a',
       description = 'ATNF Spectral-line Analysis Package',
       author = 'Malte Marquarding',

trunk/src/STMath.cpp

@@ -2781 +2781 @@
   MVTime mvt(refEpoch.getValue());
   String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
-  os << "Aligned at reference Epoch " << epochout
+  os << "Aligning at reference Epoch " << epochout
      << " in frame " << MFrequency::showType(system) << LogIO::POST;
   // set up the iterator
@@ -2795 +2795 @@
   while ( !iter.pastEnd() ) {
     Table t = iter.table();
+    ROScalarColumn<String> snCol(t, "SRCNAME");
+    os << "Aligning to position of source '" << snCol(0) << "'" << LogIO::POST;
     MDirection::ROScalarColumn dirCol(t, "DIRECTION");
     TableIterator fiter(t, "FREQ_ID");
     // determine nchan from the first row. This should work as
-    // we are iterating over BEAMNO and IFNO    // we should have constant direction
+    // we are iterating over BEAMNO and IFNO    
+    // we should have constant direction
 
     ROArrayColumn<Float> sCol(t, "SPECTRA");
@@ -2813 +2816 @@
     ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
     // get the SpectralCoordinate for the freqid, which we are iterating over
-    SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
+    SpectralCoordinate sC = \
+      in->frequencies().getSpectralCoordinate(freqidCol(0));
     FrequencyAligner<Float> fa( sC, nchan, refEpoch,
                                 direction, refPos, system );
@@ -2826 +2830 @@
                                                 sc2.increment()[0]);
     while ( !fiter.pastEnd() ) {
+      
       ftab = fiter.table();
       // spectral coordinate for the current FREQ_ID

trunk/src/Scantable.cpp

@@ -180 +180 @@
         table_ = TableCopy::makeEmptyMemoryTable(newname,
                                                  other.table_, True);
-      } else
+      } else {
         table_ = other.table_.copyToMemoryTable(newname);
+      }
   } else {
       other.table_.deepCopy(newname, Table::New, False,
@@ -450 +451 @@
   TableVector<Int> tabvec(table_, "SRCTYPE");
   tabvec = Int(stype);
+}
+
+void Scantable::setSourceName( const std::string& name )
+{
+  TableVector<String> tabvec(table_, "SRCNAME");
+  tabvec = name;
 }
 

trunk/src/Scantable.h

@@ -155 +155 @@
   void setSourceType(int stype);
 
+  /**
+   *
+   * @param stype The name of the source
+   */
+  void setSourceName(const std::string& name);
+
 
   /**
@@ -387 +393 @@
 
   //std::string getTime(int whichrow=-1, bool showdate=true) const;
-  std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
+  std::string getTime(int whichrow=-1, bool showdate=true, 
+                      casa::uInt prec=0) const;
   double getIntTime(int whichrow) const { return integrCol_(whichrow); }
 
@@ -668 +675 @@
 
   std::string formatTime(const casa::MEpoch& me, bool showdate)const;
-  std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
+  std::string formatTime(const casa::MEpoch& me, bool showdate, 
+                         casa::uInt prec)const;
 
   /**

trunk/src/ScantableWrapper.h

@@ -188 +188 @@
     { table_->setSourceType(stype); }
 
+  void setSourceName(const std::string& name)
+    { table_->setSourceName(name); }
+
   void shift(int npix)
   { table_->shift(npix); }

trunk/src/python_Scantable.cpp

@@ -137 +137 @@
     .def("_recalcazel", &ScantableWrapper::calculateAZEL)
     .def("_setsourcetype", &ScantableWrapper::setSourceType)
+    .def("_setsourcename", &ScantableWrapper::setSourceName)
     .def("_getdirectionvec", &ScantableWrapper::getDirectionVector)
     .def("_parallactify", &ScantableWrapper::parallactify)

trunk/test/test_scantable.py

@@ -149 +149 @@
                           'Orion_SiO', 'Orion_SiO'])
 
+    def test_set_sourcename(self):
+        s = self.st.copy()
+        newname = "TEST"
+        s.set_sourcename(newname)
+        assert_equal(s.get_sourcename(), [newname]*4)
+
     def test_get_azimuth(self):
         assert_almost_equal(self.st.get_azimuth()[0], 5.628767013)
@@ -194 +200 @@
         assert_almost_equal(q1.stats(stat='max')[0], 2.66563416)
 
+
+    def test_average_time_weight(self):
+        weights = {'none': 236.61423,
+                   'var' : 232.98752,
+                   'tsys' : 236.37482,
+                   'tint' : 236.61423,
+                   'tintsys' : 236.37485,
+                   'median' : 236.61423,
+                   }
+
+        for k,v in weights.items():
+            yield self.av_weight, k, v
+
+    def av_weight(self, weight, result):
+        out = self.st.average_time(weight=weight)
+        assert_almost_equals(max(out.get_spectrum(0)), result, 5)
+
     @with_setup(tempdir_setup, tempdir_teardown)
     def test_save(self):
@@ -203 +226 @@
                    (fname % 'txt', 'ASCII', False),
                    ]
-        for format in formats:
-            yield self.save, format
+        for fmt in formats:
+            yield self.save, fmt
 
     def save(self, args):