Changeset 331 for trunk

Timestamp:

01/31/05 15:48:36 (20 years ago)

Author:

vor010

Message:

Line searching algorithm is now in the separate
class LFRunningMean. It allows to run the same code several passes for different
masks, criteria, etc. In the future this interface may be more readily modified
to have multiple algorithms

Location:

trunk

Files:

• python/asaplinefind.py (modified) (1 diff)
• src/SDLineFinder.cc (modified) (3 diffs)
• src/SDLineFinder.h (modified) (2 diffs)

trunk/python/asaplinefind.py

@@ -53 +53 @@
               regardless on the invert option
         """
-        return self.finder._getmask(invert)
+        return self.finder.getmask(invert)
     def get_ranges(self,defunits=True):
         """

trunk/src/SDLineFinder.cc

@@ -42 +42 @@
 using namespace boost::python;
 
+namespace asap {
+
+// An auxiliary class implementing one pass of the line search algorithm,
+// which uses a running mean. We define this class here because it is
+// used in SDLineFinder only. The incapsulation of this code into a separate
+// class will provide a possibility to add new algorithms with minor changes
+class LFRunningMean {
+   // The input data to work with. Use reference symantics to avoid
+   // an unnecessary copying   
+   const casa::Vector<casa::Float>  &spectrum; // a buffer for the spectrum
+   const casa::Vector<casa::Bool>   &mask; // associated mask
+   const std::pair<int,int>         &edge; // start and stop+1 channels
+                                           // to work with
+   
+   // statistics for running mean filtering
+   casa::Float sum;       // sum of fluxes
+   casa::Float sumsq;     // sum of squares of fluxes
+   int box_chan_cntr;     // actual number of channels in the box
+   int max_box_nchan;     // maximum allowed number of channels in the box
+                          // (calculated from boxsize and actual spectrum size)
+
+   // temporary line edge channels and flag, which is True if the line
+   // was detected in the previous channels.
+   std::pair<int,int> cur_line;
+   casa::Bool is_detected_before;
+   int  min_nchan;                         // A minimum number of consequtive
+                                           // channels, which should satisfy
+                                           // the detection criterion, to be
+                                           // a detection
+   casa::Float threshold;                  // detection threshold - the 
+                                           // minimal signal to noise ratio
+public:
+   // set up the object with the references to actual data
+   // as well as the detection criterion (min_nchan and threshold, see above)
+   // and the number of channels in the running box
+   LFRunningMean(const casa::Vector<casa::Float>  &in_spectrum,
+                 const casa::Vector<casa::Bool>   &in_mask,
+                 const std::pair<int,int>         &in_edge,
+                 int in_max_box_nchan, 
+                 int in_min_nchan = 3,
+                 casa::Float in_threshold = 5);
+                 
+   // replace the detection criterion
+   void setCriterion(int in_min_nchan, casa::Float in_threshold) throw();
+
+   // find spectral lines and add them into list
+   void findLines(std::list<pair<int,int> > &lines) throw(casa::AipsError);
+   
+protected:
+   // supplementary function to control running mean calculations.
+   // It adds a specified channel to the running mean box and
+   // removes (ch-maxboxnchan+1)'th channel from there
+   // Channels, for which the mask is false or index is beyond the
+   // allowed range, are ignored
+   void advanceRunningBox(int ch) throw(casa::AipsError);
+   
+
+   // test a channel against current running mean & rms
+   // if channel specified is masked out or beyond the allowed indexes,
+   // false is returned
+   casa::Bool testChannel(int ch) const
+                     throw(std::exception, casa::AipsError);
+
+   // process a channel: update curline and is_detected before and
+   // add a new line to the list, if necessary using processCurLine()
+   void processChannel(std::list<pair<int,int> > &lines,
+                       int ch) throw(casa::AipsError);
+
+   // process the interval of channels stored in curline
+   // if it satisfies the criterion, add this interval as a new line
+   void processCurLine(std::list<pair<int,int> > &lines) throw(casa::AipsError);
+
+};
+} // namespace asap
+
+///////////////////////////////////////////////////////////////////////////////
+//
+// LFRunningMean - a running mean algorithm for line detection
+//
+//
+
+// set up the object with the references to actual data
+// as well as the detection criterion (min_nchan and threshold, see above)
+// and the number of channels in the running box
+LFRunningMean::LFRunningMean(const casa::Vector<casa::Float>  &in_spectrum,
+                             const casa::Vector<casa::Bool>   &in_mask,
+                             const std::pair<int,int>         &in_edge,
+                             int in_max_box_nchan, 
+                             int in_min_nchan, casa::Float in_threshold) :
+        spectrum(in_spectrum), mask(in_mask), edge(in_edge),
+        max_box_nchan(in_max_box_nchan),
+        min_nchan(in_min_nchan),threshold(in_threshold) {}
+
+// replace the detection criterion
+void LFRunningMean::setCriterion(int in_min_nchan, casa::Float in_threshold)
+                                 throw()
+{
+  min_nchan=in_min_nchan;
+  threshold=in_threshold;
+}
+
+
+// supplementary function to control running mean calculations.
+// It adds a specified channel to the running mean box and
+// removes (ch-max_box_nchan+1)'th channel from there
+// Channels, for which the mask is false or index is beyond the
+// allowed range, are ignored
+void LFRunningMean::advanceRunningBox(int ch) throw(AipsError)
+{
+  if (ch>=edge.first && ch<edge.second)
+      if (mask[ch]) { // ch is a valid channel
+          ++box_chan_cntr;
+          sum+=spectrum[ch];
+          sumsq+=square(spectrum[ch]);          
+      }
+  int ch2remove=ch-max_box_nchan;
+  if (ch2remove>=edge.first && ch2remove<edge.second)
+      if (mask[ch2remove]) { // ch2remove is a valid channel
+          --box_chan_cntr;
+          sum-=spectrum[ch2remove];
+          sumsq-=square(spectrum[ch2remove]);  
+      }
+}
+
+// test a channel against current running mean & rms
+// if channel specified is masked out or beyond the allowed indexes,
+// false is returned
+Bool LFRunningMean::testChannel(int ch) const throw(exception, AipsError)
+{
+  if (ch<edge.first || ch>=edge.second) return False;
+  if (!mask[ch]) return False;
+  DebugAssert(box_chan_cntr, AipsError);
+  Float mean=sum/Float(box_chan_cntr);
+  Float variance=sqrt(sumsq/Float(box_chan_cntr)-square(mean));
+  /*
+  if (ch>3900 && ch<4100)
+    cout<<"Tested "<<ch<<" mean="<<mean<<" variance="<<variance<<" sp-mean="<<spectrum[ch]-mean<<endl;
+  */
+  return fabs(spectrum[ch]-mean)>=threshold*variance;
+}
+
+// process a channel: update cur_line and is_detected before and
+// add a new line to the list, if necessary
+void LFRunningMean::processChannel(std::list<pair<int,int> > &lines,
+                                   int ch) throw(casa::AipsError)
+{
+  try {
+       if (testChannel(ch)) {
+           if (is_detected_before)
+               cur_line.second=ch+1;
+           else {
+               is_detected_before=True;
+               cur_line.first=ch;
+               cur_line.second=ch+1;
+           }
+       } else processCurLine(lines);   
+  }
+  catch (const AipsError &ae) {
+      throw;
+  }  
+  catch (const exception &ex) {
+      throw AipsError(String("SDLineFinder::processChannel - STL error: ")+ex.what());
+  }
+}
+
+// process the interval of channels stored in cur_line
+// if it satisfies the criterion, add this interval as a new line
+void LFRunningMean::processCurLine(std::list<pair<int,int> > &lines)
+                                   throw(casa::AipsError)
+{
+  try {
+       if (is_detected_before) {                      
+           if (cur_line.second-cur_line.first>min_nchan) {
+               // it was a detection. We need to change the list
+               Bool add_new_line=False;
+               if (lines.size()) { 
+                   for (int i=lines.back().second;i<cur_line.first;++i)
+                        if (mask[i]) { // one valid channel in between
+                                //  means that we deal with a separate line
+                            add_new_line=True;
+                            break;
+                        }
+               } else add_new_line=True; 
+               if (add_new_line) 
+                   lines.push_back(cur_line);
+               else lines.back().second=cur_line.second;                   
+           }
+           is_detected_before=False;
+       }      
+  }
+  catch (const AipsError &ae) {
+      throw;
+  }  
+  catch (const exception &ex) {
+      throw AipsError(String("SDLineFinder::processCurLine - STL error: ")+ex.what());
+  }
+}
+
+// find spectral lines and add them into list
+void LFRunningMean::findLines(std::list<pair<int,int> > &lines)
+                        throw(casa::AipsError)
+{
+  const int minboxnchan=4;
+
+  // fill statistics for initial box
+  box_chan_cntr=0; // no channels are currently in the box
+  sum=0;           // initialize statistics
+  sumsq=0;
+  int initial_box_ch=edge.first;
+  for (;initial_box_ch<edge.second && box_chan_cntr<max_box_nchan;
+        ++initial_box_ch)
+       advanceRunningBox(initial_box_ch);
+    
+  if (initial_box_ch==edge.second)       
+      throw AipsError("LFRunningMean::findLines - too much channels are masked");
+
+  // actual search algorithm
+  is_detected_before=False;
+
+  if (box_chan_cntr>=minboxnchan) 
+      // there is a minimum amount of data. We can search in the
+      // half of the initial box   
+      for (int n=edge.first;n<initial_box_ch-max_box_nchan/2;++n)
+           processChannel(lines,n);                
+  
+  // now the box can be moved. n+max_box_nchan/2 is a new index which haven't
+  // yet been included in the running mean.
+  for (int n=initial_box_ch-max_box_nchan/2;n<edge.second;++n) {
+      advanceRunningBox(n+max_box_nchan/2); // update running mean & variance
+      if (box_chan_cntr>=minboxnchan) // have enough data to process
+          processChannel(lines,n);
+      else processCurLine(lines); // just finish what was accumulated before
+  }  
+}
+
+//
+///////////////////////////////////////////////////////////////////////////////
+
+
 // SDLineFinder  -  a class for automated spectral line search
 
@@ -123 +362 @@
                       " use set_scan");
   DebugAssert(mask.nelements()==scan->nChan(), AipsError);
-  lines.resize(0); // search from the scratch
-  
-  max_box_nchan=int(scan->nChan()*box_size); // number of channels in running
-                                              // box
-
+  int max_box_nchan=int(scan->nChan()*box_size); // number of channels in running
+                                                 // box
   if (max_box_nchan<2)
       throw AipsError("SDLineFinder::findLines - box_size is too small");
 
   scan->getSpectrum(spectrum);
-  
-  // fill statistics for initial box
-  box_chan_cntr=0; // no channels are currently in the box
-  sum=0;           // initialize statistics
-  sumsq=0;
-  int initial_box_ch=edge.first;
-  for (;initial_box_ch<edge.second && box_chan_cntr<max_box_nchan;
-        ++initial_box_ch)
-       advanceRunningBox(initial_box_ch);
-    
-  if (initial_box_ch==edge.second)       
-      throw AipsError("SDLineFinder::findLines - too much channels are masked");
-
-  // actual search algorithm
-  is_detected_before=False;
-
-  if (box_chan_cntr>=minboxnchan) 
-      // there is a minimum amount of data. We can search in the
-      // half of the initial box   
-      for (int n=edge.first;n<initial_box_ch-max_box_nchan/2;++n)
-           processChannel(n);                      
-  
-  // now the box can be moved. n+max_box_nchan/2 is a new index which haven't
-  // yet been included in the running mean.
-  for (int n=initial_box_ch-max_box_nchan/2;n<edge.second;++n) {
-      advanceRunningBox(n+max_box_nchan/2); // update running mean & variance
-      if (box_chan_cntr>=minboxnchan) // have enough data to process
-          processChannel(n);
-      else processCurLine(); // just finish what was accumulated before
-  }
+
+  lines.resize(0); // search from the scratch
+  Vector<Bool> temp_mask(mask);
+  size_t cursz;
+  do {
+     cursz=lines.size();
+     // line find algorithm
+     LFRunningMean lfalg(spectrum,temp_mask,edge,max_box_nchan,min_nchan,threshold);
+     lfalg.findLines(lines);
+     temp_mask=getMask();
+  } while (cursz!=lines.size());
   return int(lines.size());
 }
 
-// supplementary function to control running mean calculations.
-// It adds a specified channel to the running mean box and
-// removes (ch-max_box_nchan+1)'th channel from there
-// Channels, for which the mask is false or index is beyond the
-// allowed range, are ignored
-void SDLineFinder::advanceRunningBox(int ch) throw(AipsError)
-{
-  if (ch>=edge.first && ch<edge.second)
-      if (mask[ch]) { // ch is a valid channel
-          ++box_chan_cntr;
-          sum+=spectrum[ch];
-          sumsq+=square(spectrum[ch]);          
-      }
-  int ch2remove=ch-max_box_nchan;
-  if (ch2remove>=edge.first && ch2remove<edge.second)
-      if (mask[ch2remove]) { // ch2remove is a valid channel
-          --box_chan_cntr;
-          sum-=spectrum[ch2remove];
-          sumsq-=square(spectrum[ch2remove]);  
-      }
-}
-
-// test a channel against current running mean & rms
-// if channel specified is masked out or beyond the allowed indexes,
-// false is returned
-Bool SDLineFinder::testChannel(int ch) throw(exception, AipsError)
-{
-  if (ch<edge.first || ch>=edge.second) return False;
-  if (!mask[ch]) return False;
-  DebugAssert(box_chan_cntr, AipsError);
-  Float mean=sum/Float(box_chan_cntr);
-  Float variance=sqrt(sumsq/Float(box_chan_cntr)-square(mean));
-  /*
-  if (ch>3900 && ch<4100)
-    cout<<"Tested "<<ch<<" mean="<<mean<<" variance="<<variance<<" sp-mean="<<spectrum[ch]-mean<<endl;
-  */
-  return fabs(spectrum[ch]-mean)>=threshold*variance;
-}
-
-// process a channel: update cur_line and is_detected before and
-// add a new line to the list, if necessary
-void SDLineFinder::processChannel(int ch) throw(casa::AipsError)
-{
-  try {
-       if (testChannel(ch)) {
-           if (is_detected_before)
-               cur_line.second=ch+1;
-           else {
-               is_detected_before=True;
-               cur_line.first=ch;
-               cur_line.second=ch+1;
-           }
-       } else processCurLine();   
-  }
-  catch (const AipsError &ae) {
-      throw;
-  }  
-  catch (const exception &ex) {
-      throw AipsError(String("SDLineFinder::processChannel - STL error: ")+ex.what());
-  }
-}
-
-// process the interval of channels stored in cur_line
-// if it satisfies the criterion, add this interval as a new line
-void SDLineFinder::processCurLine() throw(casa::AipsError)
-{
-  try {
-       if (is_detected_before) {                      
-           if (cur_line.second-cur_line.first>min_nchan) {
-               // it was a detection. We need to change the list
-               Bool add_new_line=False;
-               if (lines.size()) { 
-                   for (int i=lines.back().second;i<cur_line.first;++i)
-                        if (mask[i]) { // one valid channel in between
-                                //  means that we deal with a separate line
-                            add_new_line=True;
-                            break;
-                        }
-               } else add_new_line=True; 
-               if (add_new_line) 
-                   lines.push_back(cur_line);
-               else lines.back().second=cur_line.second;                   
-           }
-           is_detected_before=False;
-       }      
-  }
-  catch (const AipsError &ae) {
-      throw;
-  }  
-  catch (const exception &ex) {
-      throw AipsError(String("SDLineFinder::processCurLine - STL error: ")+ex.what());
-  }
-}
 
 // get the mask to mask out all lines that have been found (default)
@@ -341 +465 @@
   }
 }
+
+// concatenate two lists preserving the order. If two lines appear to
+// be adjacent, they are joined into the new one
+void SDLineFinder::addNewSearchResult(const std::list<pair<int, int> > &newlines)
+                        throw(AipsError)
+{
+  try {
+      for (std::list<pair<int,int> >::const_iterator cli=newlines.begin();
+           cli!=newlines.end();++cli) {
+           // search for a right place for the new line
+           //TODO
+      }
+  }
+  catch (const AipsError &ae) {
+      throw;
+  }  
+  catch (const exception &ex) {
+      throw AipsError(String("SDLineFinder::addNewSearchResult - STL error: ")+ex.what());
+  }
+
+}

trunk/src/SDLineFinder.h

@@ -85 +85 @@
    std::vector<int>   getLineRanges(bool defunits=true)
                                 const throw(casa::AipsError);
-   
 protected:
-   // supplementary function to control running mean calculations.
-   // It adds a specified channel to the running mean box and
-   // removes (ch-maxboxnchan+1)'th channel from there
-   // Channels, for which the mask is false or index is beyond the
-   // allowed range, are ignored
-   void advanceRunningBox(int ch) throw(casa::AipsError);
-   
-
-   // test a channel against current running mean & rms
-   // if channel specified is masked out or beyond the allowed indexes,
-   // false is returned
-   casa::Bool testChannel(int ch) throw(std::exception, casa::AipsError);
-
-   // process a channel: update curline and is_detected before and
-   // add a new line to the list, if necessary using processCurLine()
-   void processChannel(int ch) throw(casa::AipsError);
-
-   // process the interval of channels stored in curline
-   // if it satisfies the criterion, add this interval as a new line
-   void processCurLine() throw(casa::AipsError);
-   
+   // concatenate two lists preserving the order. If two lines appear to
+   // be adjacent, they are joined into the new one
+   void addNewSearchResult(const std::list<std::pair<int, int> > &newlines)
+                           throw(casa::AipsError);
 private:
    casa::CountedConstPtr<SDMemTable> scan; // the scan to work with
@@ -124 +106 @@
    std::list<std::pair<int, int> > lines;  // container of start and stop+1
                                            // channels of the spectral lines
-   // statistics for running mean filtering
-   casa::Float sum;       // sum of fluxes
-   casa::Float sumsq;     // sum of squares of fluxes
-   int box_chan_cntr;     // actual number of channels in the box
-   int max_box_nchan;     // maximum allowed number of channels in the box
-                          // (calculated from boxsize and actual spectrum size)
    // a buffer for the spectrum
    mutable casa::Vector<casa::Float>  spectrum;
 
-   // temporary line edge channels and flag, which is True if the line
-   // was detected in the previous channels.
-   std::pair<int,int> cur_line;
-   casa::Bool is_detected_before;
 };
 } // namespace asap