Changeset 369 for trunk

Timestamp:

02/06/05 17:40:28 (20 years ago)

Author:

vor010

Message:

SDLineFinder: bug corrections, setOption method
has been added + fitting baseline at each iterations to cope with bad
baselines

Location:

trunk

Files:

• python/asaplinefind.py (modified) (1 diff)
• src/SDLineFinder.cc (modified) (10 diffs)
• src/SDLineFinder.h (modified) (3 diffs)
• src/python_SDLineFinder.cc (modified) (1 diff)

trunk/python/asaplinefind.py

@@ -13 +13 @@
         return
 
+    def set_options(self,threshold=1.7320508075688772,min_nchan=3,
+        avg_limit=8,box_size=0.2):
+        """
+        Set the parameters of the algorithm
+        Parameters:
+             threshold    a single channel S/N ratio above which the 
+                          channel is considered to be a detection
+                          Default is sqrt(3), which together with
+                          min_nchan=3 gives a 3-sigma criterion
+             min_nchan    a minimal number of consequtive channels, 
+                          which should satisfy a threshold criterion to
+                          be a detection. Default is 3.
+             avg_limit    A number of consequtive channels not greater than
+                          this parameter can be averaged to search for
+                          broad lines. Default is 8.
+             box_size     A running mean box size specified as a fraction
+                          of the total spectrum length. Default is 1/5
+        Note:  For bad baselines threshold should be increased, 
+               and avg_limit decreased (or even switched off completely by
+               setting this parameter to 1) to avoid detecting baseline
+               undulations instead of real lines.  
+        """
+        self.finder.setoptions(threshold,min_nchan,avg_limit,box_size)
+        return
+             
     def set_scan(self,scan,mask=None,edge=(0,0)):
         """

trunk/src/SDLineFinder.cc

@@ -33 +33 @@
 // ASAP
 #include "SDLineFinder.h"
+#include "SDFitter.h"
 
 // STL
@@ -434 +435 @@
       // determine the off-line variance first
       // an assumption made: lines occupy a small part of the spectrum
-
+       
       std::vector<float> variances(edge.second-edge.first);
       DebugAssert(variances.size(),AipsError);
-
+      
       for (;running_box->haveMore();running_box->next()) 
            variances[running_box->getChannel()-edge.first]=
                                 running_box->getLinVariance();
-                                
+        
       // in the future we probably should do a proper Chi^2 estimation
       // now a simple 80% of smaller values will be used.
@@ -447 +448 @@
       // due to a bias of the Chi^2 distribution.
       stable_sort(variances.begin(),variances.end());
+      
       Float offline_variance=0;
       uInt offline_cnt=uInt(0.8*variances.size());      
@@ -459 +461 @@
       Vector<Int> signs(spectrum.nelements(),0);
 
-      ofstream os("dbg.dat");
+      //ofstream os("dbg.dat");
       for (running_box->rewind();running_box->haveMore();
                                  running_box->next()) {
@@ -471 +473 @@
            else if (buf<0) signs[ch]=-1;
            else if (buf==0) signs[ch]=0;
-           os<<ch<<" "<<spectrum[ch]<<" "<<running_box->getLinMean()<<" "<<
-                        threshold*offline_variance<<endl;
+        //   os<<ch<<" "<<spectrum[ch]<<" "<<running_box->getLinMean()<<" "<<
+          //              threshold*offline_variance<<endl;
       }
       if (lines.size())
@@ -578 +580 @@
 SDLineFinder::SDLineFinder() throw() : edge(0,0)
 {
-  // detection threshold - the minimal signal to noise ratio
-  threshold=sqrt(3.); // 3 sigma and 3 channels is a default -> sqrt(3) in
-                     // a single channel
-  box_size=1./5.; // default box size for running mean calculations is
-                  // 1/5 of the whole spectrum
-  // A minimum number of consequtive channels, which should satisfy
-  // the detection criterion, to be a detection
-  min_nchan=3;     // default is 3 channels
+  setOptions();
+}
+
+// set the parameters controlling algorithm
+// in_threshold a single channel threshold default is sqrt(3), which
+//              means together with 3 minimum channels at least 3 sigma
+//              detection criterion
+//              For bad baseline shape, in_threshold may need to be
+//              increased
+// in_min_nchan minimum number of channels above the threshold to report
+//              a detection, default is 3
+// in_avg_limit perform the averaging of no more than in_avg_limit
+//              adjacent channels to search for broad lines
+//              Default is 8, but for a bad baseline shape this 
+//              parameter should be decreased (may be even down to a
+//              minimum of 1 to disable this option) to avoid
+//              confusing of baseline undulations with a real line.
+//              Setting a very large value doesn't usually provide 
+//              valid detections. 
+// in_box_size  the box size for running mean calculation. Default is
+//              1./5. of the whole spectrum size
+void SDLineFinder::setOptions(const casa::Float &in_threshold,
+                              const casa::Int &in_min_nchan,
+                              const casa::Int &in_avg_limit,
+                              const casa::Float &in_box_size) throw()
+{
+  threshold=in_threshold;
+  min_nchan=in_min_nchan;
+  avg_limit=in_avg_limit;
+  box_size=in_box_size;
 }
 
@@ -635 +659 @@
                edge.second=scan->nChan()-edge.second;
            } else edge.second=scan->nChan()-edge.first;
-           if (edge.second<0 || (edge.second+edge.first)>scan->nChan())
+           if (edge.second<0 || (edge.first>=edge.second))
                throw AipsError("SDLineFinder::setScan - all channels are rejected by the in_edge parameter");
        }       
@@ -674 +698 @@
      // a buffer for new lines found at this iteration
      std::list<pair<int,int> > new_lines;     
-     // line find algorithm
-     LFAboveThreshold lfalg(new_lines,avg_factor*min_nchan, threshold);
 
      try {
+         // line find algorithm
+         LFAboveThreshold lfalg(new_lines,avg_factor*min_nchan, threshold);
          lfalg.findLines(spectrum,temp_mask,edge,max_box_nchan);
          first_pass=False;
@@ -688 +712 @@
          // nothing new - proceed to the next step of averaging, if any
          // (to search for broad lines)
+         if (avg_factor>avg_limit) break; // averaging up to avg_limit
+                                          // adjacent channels,
+                                          // stop after that
          avg_factor*=2; // twice as more averaging
+         subtractBaseline(temp_mask,9);
          averageAdjacentChannels(temp_mask,avg_factor);
-         if (avg_factor>8) break; // averaging up to 8 adjacent channels,
-                                  // stop after that
          continue; 
      }
@@ -701 +727 @@
   }
   return int(lines.size());
+}
+
+// auxiliary function to fit and subtract a polynomial from the current
+// spectrum. It uses the SDFitter class. This action is required before
+// reducing the spectral resolution if the baseline shape is bad
+void SDLineFinder::subtractBaseline(const casa::Vector<casa::Bool> &temp_mask,
+                      const casa::Int &order) throw(casa::AipsError)
+{
+  AlwaysAssert(spectrum.nelements(),AipsError);
+  // use the fact that temp_mask excludes channels rejected at the edge
+  SDFitter sdf;
+  std::vector<float> absc(spectrum.nelements());
+  for (Int i=0;i<absc.size();++i)
+       absc[i]=float(i)/float(spectrum.nelements());
+  std::vector<float> spec;
+  spectrum.tovector(spec);
+  std::vector<bool> std_mask;
+  temp_mask.tovector(std_mask);
+  sdf.setData(absc,spec,std_mask);
+  sdf.setExpression("poly",order);
+  if (!sdf.fit()) return; // fit failed, use old spectrum
+  spectrum=casa::Vector<casa::Float>(sdf.getResidual());    
 }
 

trunk/src/SDLineFinder.h

@@ -135 +135 @@
    virtual ~SDLineFinder() throw(casa::AipsError);
 
+   // set the parameters controlling algorithm
+   // in_threshold a single channel threshold default is sqrt(3), which
+   //              means together with 3 minimum channels at least 3 sigma
+   //              detection criterion
+   //              For bad baseline shape, in_threshold may need to be
+   //              increased
+   // in_min_nchan minimum number of channels above the threshold to report
+   //              a detection, default is 3
+   // in_avg_limit perform the averaging of no more than in_avg_limit
+   //              adjacent channels to search for broad lines
+   //              Default is 8, but for a bad baseline shape this 
+   //              parameter should be decreased (may be even down to a
+   //              minimum of 1 to disable this option) to avoid
+   //              confusing of baseline undulations with a real line.
+   //              Setting a very large value doesn't usually provide 
+   //              valid detections. 
+   // in_box_size  the box size for running mean calculation. Default is
+   //              1./5. of the whole spectrum size
+   void setOptions(const casa::Float &in_threshold=sqrt(3.),
+                   const casa::Int &in_min_nchan=3,
+                   const casa::Int &in_avg_limit=8,
+                   const casa::Float &in_box_size=0.2) throw();
+
    // set the scan to work with (in_scan parameter), associated mask (in_mask
    // parameter) and the edge channel rejection (in_edge parameter)
@@ -171 +194 @@
                                const casa::Int &boxsize)
                                throw(casa::AipsError);
+
+   // auxiliary function to fit and subtract a polynomial from the current
+   // spectrum. It uses the SDFitter class. This action is required before
+   // reducing the spectral resolution if the baseline shape is bad
+   void subtractBaseline(const casa::Vector<casa::Bool> &temp_mask,
+                         const casa::Int &order) throw(casa::AipsError);
    
    // an auxiliary function to remove all lines from the list, except the
@@ -203 +232 @@
                                            // the detection criterion, to be
                                            // a detection
+   casa::Int   avg_limit;                  // perform the averaging of no
+                                           // more than in_avg_limit
+                                           // adjacent channels to search
+                                           // for broad lines. see setOptions
    std::list<std::pair<int, int> > lines;  // container of start and stop+1
                                            // channels of the spectral lines

trunk/src/python_SDLineFinder.cc

@@ -40 +40 @@
        class_<SDLineFinder>("linefinder")
          .def( init <> () )
+         .def("setoptions",&SDLineFinder::setOptions)
          .def("setscan",&SDLineFinder::setScan)
          .def("findlines",&SDLineFinder::findLines)