Changeset 1232

Timestamp:

09/01/06 13:14:11 (18 years ago)

Author:

mar637

Message:

Merge from Release2.1.0b tag

Location:

trunk

Files:

• SConstruct (modified) (1 diff)
• bin/install (modified) (2 diffs)
• python/asapfit.py (modified) (2 diffs)
• python/asapfitter.py (modified) (6 diffs)
• python/asapmath.py (modified) (2 diffs)
• python/asapplotter.py (modified) (1 diff)
• src/STFitter.cpp (modified) (7 diffs)
• src/STMath.cpp (modified) (5 diffs)

trunk/SConstruct

@@ -76 +76 @@
     env = conf.Finish()
 
-env["version"] = "2.1.0b"
+env["version"] = "2.1.0b1"
 
 # general CPPFLAGS

trunk/bin/install

@@ -29 +29 @@
     for l in p.readlines():
         lsp = l.split()
-        if lsp[2] == "not":
-            unresolved.append(lsp[0])
-        else:
-            resolved.append(lsp[2])
+        # test this to avoid fails on linux_gate, which has no library
+        if len(lsp) >= 3:
+            if lsp[2] == "not":
+                unresolved.append(lsp[0])
+            else:
+                resolved.append(lsp[2])
     return resolved, unresolved
 
@@ -79 +81 @@
         print "   All required libraries are present."
 except IOError,msg:
-    print msg+" Skipping test."
+    print "Skipping test. (%s)" % msg
 
 print 'Looking for dependent python modules...'

trunk/python/asapfit.py

@@ -55 +55 @@
                   }
             comp.append(d)
+            k+=1
         out.append(comp)
         return out
+
+    def save(self, filename):
+        f = file(filename, 'w')
+        parstr = ""
+        for i in xrange(self.getcomponents()[0]):
+            pname = "P%d"% (i)
+            parstr += "%-12s " % (pname)
+        header = "#%-12s %s\n" % ("Function", parstr)
+        f.write(header)
+        i = 0
+        funcs=self.getfunctions()
+        pars=self.getparameters()
+        for c in self.getcomponents():
+            line = " %-12s " % (funcs[i])
+            for j in xrange(c):
+                line += "%3.8f " % (pars[i*c+j])
+            i+=1
+            f.write(line+"\n")
+        f.close()
 
     def _format_pars(self, pars, ftype, unit):
@@ -63 +83 @@
             i = 0
             for p in pars:
-                out += ' p%d = %3.3f %s,' % (i,p,unit)
+                out += ' p%d = %3.6f %s,' % (i,p,unit)
                 i+=1
             out = out[1:-1]
         elif ftype == 'gauss':
-            out += 'peak = %3.3f , centre = %3.3f %s, FWHM = %3.3f %s' % (pars[0],pars[1],unit,pars[2],unit)
+            out += 'peak = %3.6f , centre = %3.6f %s, FWHM = %3.6f %s' % (pars[0],pars[1],unit,pars[2],unit)
         return out

trunk/python/asapfitter.py

@@ -100 +100 @@
 
         self.fitter.setexpression(self.fitfunc,n)
+        self.fitted = False
         return
 
@@ -142 +143 @@
                 self.fitter.estimate()
         try:
+            fxdpar = list(self.fitter.getfixedparameters())
+            if len(fxdpar) and fxdpar.count(0) == 0:
+                 raise RuntimeError,"No point fitting, if all parameters are fixed."
             converged = self.fitter.fit()
             if not converged:
@@ -155 +159 @@
         return
 
-    def store_fit(self):
-        """
-        Store the fit parameters in the scantable.
+    def store_fit(self, filename=None):
+        """
+        Save the fit parameters.
+        Parameters:
+            filename:    if specified save as an ASCII file, if None (default)
+                         store it in the scnatable
         """
         if self.fitted and self.data is not None:
@@ -169 +176 @@
             fit.setcomponents(self.components)
             fit.setframeinfo(self.data._getcoordinfo())
-            self.data._addfit(fit,self._fittedrow)
+            if filename is not None:
+                import os
+                filename = os.path.expandvars(os.path.expanduser(filename))
+                if os.path.exists(filename):
+                    raise IOError("File '%s' exists." % filename)
+                fit.save(filename)
+            else:
+                self.data._addfit(fit,self._fittedrow)
 
     #def set_parameters(self, params, fixed=None, component=None):
@@ -224 +238 @@
         Set the Parameters of a 'Gaussian' component, set with set_function.
         Parameters:
-            peak, centre, fhwm:  The gaussian parameters
+            peak, centre, fwhm:  The gaussian parameters
             peakfixed,
             centerfixed,
@@ -352 +366 @@
             for i in range(len(pars)):
                 fix = ""
-                if fixed[i]: fix = "(fixed)"
+                if len(fixed) and fixed[i]: fix = "(fixed)"
                 if errors :
                     out += '  p%d%s= %3.6f (%1.6f),' % (c,fix,pars[i], errors[i])

trunk/python/asapmath.py

@@ -12 +12 @@
         scanav:   True averages each scan separately.
                   False (default) averages all scans together,
-        weight:   Weighting scheme. 'none, 'var' (1/var(spec)
-                  weighted), 'tsys' (1/Tsys**2 weighted), 'tint'
-                  (integration time weighted) or 'tintsys' (Tsys
-                  and tint). The default is 'tint'
+        weight:   Weighting scheme.
+                    'none'     (mean no weight)
+                    'var'      (1/var(spec) weighted)
+                    'tsys'     (1/Tsys**2 weighted)
+                    'tint'     (integration time weighted)
+                    'tintsys'  (Tint/Tsys**2)
+                    'median'   ( median averaging)
         align:    align the spectra in velocity before averaging. It takes
                   the time of the first spectrum in the first scantable
@@ -70 +73 @@
     else:
         alignedlst = lst
-    s = scantable(stm._average(alignedlst, mask, weight.upper(), scanav))
+    if weight.upper() == 'MEDIAN':
+        # median doesn't support list of scantables - merge first
+        merged = None
+        if len(alignedlst) > 1:
+            merged = merge(alignedlst)
+        else:
+            merged = alignedlst[0]
+        s = scantable(stm._averagechannel(merged, 'MEDIAN', scanav))
+        del merged
+    else:
+        s = scantable(stm._average(alignedlst, mask, weight.upper(), scanav))
     s._add_history("average_time",varlist)
     print_log()

trunk/python/asapplotter.py

@@ -123 +123 @@
         del self._plotter.axes.patches[-1]
     axvspan. __doc__ = matplotlib.axes.Axes.axvspan.__doc__
+
     def axhspan(self, *args, **kwargs):
-        self._axes_callback("ahvspan", *args, **kwargs)
+        self._axes_callback("axhspan", *args, **kwargs)
         # hack to preventy mpl from redrawing the patch
         # it seem to convert the patch into lines on every draw.

trunk/src/STFitter.cpp

@@ -64 +64 @@
   funcs_.resize(0,True);
   parameters_.resize();
+  fixedpar_.resize();
   error_.resize();
   thefit_.resize();
@@ -205 +206 @@
     if (parameters_.nelements() > 0 && tmppar.nelements() != parameters_.nelements())
         throw (AipsError("Number of parameters inconsistent with function."));
-    if (parameters_.nelements() == 0)
+    if (parameters_.nelements() == 0) {
         parameters_.resize(tmppar.nelements());
-        fixedpar_.resize(tmppar.nelements());
-        fixedpar_ = False;
+        if (tmppar.nelements() != fixedpar_.nelements()) {
+            fixedpar_.resize(tmppar.nelements());
+            fixedpar_ = False;
+        }
+    }
     if (dynamic_cast<Gaussian1D<Float>* >(funcs_[0]) != 0) {
         uInt count = 0;
@@ -224 +228 @@
         }
     }
+    // reset
+    if (params.size() == 0) {
+        parameters_.resize();
+        fixedpar_.resize();
+    }
     return true;
 }
@@ -229 +238 @@
 bool Fitter::setFixedParameters(std::vector<bool> fixed)
 {
-    Vector<Bool> tmp(fixed);
     if (funcs_.nelements() == 0)
         throw (AipsError("Function not yet set."));
-    if (fixedpar_.nelements() > 0 && tmp.nelements() != fixedpar_.nelements())
+    if (fixedpar_.nelements() > 0 && fixed.size() != fixedpar_.nelements())
         throw (AipsError("Number of mask elements inconsistent with function."));
+    if (fixedpar_.nelements() == 0) {
+        fixedpar_.resize(parameters_.nelements());
+        fixedpar_ = False;
+    }
     if (dynamic_cast<Gaussian1D<Float>* >(funcs_[0]) != 0) {
         uInt count = 0;
         for (uInt j=0; j < funcs_.nelements(); ++j) {
             for (uInt i=0; i < funcs_[j]->nparameters(); ++i) {
-                funcs_[j]->mask(i) = !tmp[count];
-                fixedpar_[count] = !tmp[count];
+                funcs_[j]->mask(i) = !fixed[count];
+                fixedpar_[count] = fixed[count];
                 ++count;
             }
@@ -245 +257 @@
     } else if (dynamic_cast<Polynomial<Float>* >(funcs_[0]) != 0) {
         for (uInt i=0; i < funcs_[0]->nparameters(); ++i) {
-            fixedpar_[i] = tmp[i];
-            funcs_[0]->mask(i) =  tmp[i];
-        }
-    }
-    //fixedpar_ = !tmpmsk;
+            fixedpar_[i] = fixed[i];
+            funcs_[0]->mask(i) =  !fixed[i];
+        }
+    }
     return true;
 }
@@ -263 +274 @@
   Vector<Bool> out(parameters_.nelements());
   if (fixedpar_.nelements() == 0) {
-    out = False;
+    return std::vector<bool>();
     //throw (AipsError("No parameter mask set."));
   } else {
@@ -312 +323 @@
   residual_ =  y_;
   fitter.residual(residual_,x_);
-
   // use fitter.residual(model=True) to get the model
   thefit_.resize(x_.nelements());

trunk/src/STMath.cpp

@@ -211 +211 @@
   ArrayColumn<Float> tsysColOut(tout,"TSYS");
   ScalarColumn<uInt> scanColOut(tout,"SCANNO");
+  ScalarColumn<Double> intColOut(tout, "INTERVAL");
   Table tmp = in->table().sort("BEAMNO");
   Block<String> cols(3);
@@ -227 +228 @@
     ROArrayColumn<Float> specCol, tsysCol;
     ROArrayColumn<uChar> flagCol;
+    ROScalarColumn<Double> intCol(subt, "INTERVAL");
     specCol.attach(subt,"SPECTRA");
     flagCol.attach(subt,"FLAGTRA");
@@ -255 +257 @@
     flagColOut.put(outrowCount, outflag);
     tsysColOut.put(outrowCount, outtsys);
-
+    Double intsum = sum(intCol.getColumn());
+    intColOut.put(outrowCount, intsum);
     ++outrowCount;
     ++iter;
@@ -1126 +1129 @@
                                 const std::string& weight )
 {
-  if (in->getPolType() != "linear"  || in->npol() != 2 )
-    throw(AipsError("averagePolarisations can only be applied to two linear polarisations."));
+  if (in->npol() < 2 )
+    throw(AipsError("averagePolarisations can only be applied to two or more"
+                    "polarisations"));
   bool insitu = insitu_;
   setInsitu(false);
-  CountedPtr< Scantable > pols = getScantable(in, false);
+  CountedPtr< Scantable > pols = getScantable(in, true);
   setInsitu(insitu);
   Table& tout = pols->table();
-  // give all rows the same POLNO
+  std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
+  Table tab = tableCommand(taql, in->table());
+  if (tab.nrow() == 0 )
+    throw(AipsError("Could not find  any rows with POLNO==0 and POLNO==1"));
+  TableCopy::copyRows(tout, tab);
   TableVector<uInt> vec(tout, "POLNO");
   vec = 0;
   pols->table_.rwKeywordSet().define("nPol", Int(1));
+  pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
   std::vector<CountedPtr<Scantable> > vpols;
   vpols.push_back(pols);
-  CountedPtr< Scantable > out = average(vpols, mask, weight, "NONE");
+  CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
   return out;
 }
@@ -1159 +1168 @@
   std::vector<CountedPtr<Scantable> > vbeams;
   vbeams.push_back(beams);
-  CountedPtr< Scantable > out = average(vbeams, mask, weight, "NONE");
+  CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
   return out;
 }