Changeset 2047 for trunk/python/scantable.py

Timestamp:

03/15/11 18:31:04 (13 years ago)

Author:

WataruKawasaki

Message:

New Development: Yes

JIRA Issue: Yes CAS-2847

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: Yes

Module(s): scantable

Description: added {auto_}sinusoid_baseline() for sinusoidal baseline fitting. also minor bug fixes for asapfitter.

File:

• trunk/python/scantable.py (modified) (1 diff)

trunk/python/scantable.py

@@ -2070 +2070 @@
 
     @asaplog_post_dec
+    def sinusoid_baseline(self, insitu=None, mask=None, minnwave=None, maxnwave=None,
+                          clipthresh=None, clipniter=None, plot=None, outlog=None, blfile=None):
+        """\
+        Return a scan which has been baselined (all rows) by cubic spline function (piecewise cubic polynomial).
+        Parameters:
+            insitu:     If False a new scantable is returned.
+                        Otherwise, the scaling is done in-situ
+                        The default is taken from .asaprc (False)
+            mask:       An optional mask
+            minnwave:   Minimum wave number in spectral window (default is 0)
+            maxnwave:   Maximum wave number in spectral window (default is 3)
+            clipthresh: Clipping threshold. (default is 3.0, unit: sigma)
+            clipniter:  maximum number of iteration of 'clipthresh'-sigma clipping (default is 1)
+            plot:   *** CURRENTLY UNAVAILABLE, ALWAYS FALSE ***
+                        plot the fit and the residual. In this each
+                        indivual fit has to be approved, by typing 'y'
+                        or 'n'
+            outlog:     Output the coefficients of the best-fit
+                        function to logger (default is False)
+            blfile:     Name of a text file in which the best-fit
+                        parameter values to be written
+                        (default is "": no file/logger output)
+
+        Example:
+            # return a scan baselined by a combination of sinusoidal curves having
+            # wave numbers in spectral window from 1 to 10, 
+            # also with 3-sigma clipping, iteration up to 4 times
+            bscan = scan.sinusoid_baseline(maxnwave=10,clipthresh=3.0,clipniter=4)
+        """
+        
+        varlist = vars()
+        
+        if insitu is None: insitu = rcParams["insitu"]
+        if insitu:
+            workscan = self
+        else:
+            workscan = self.copy()
+
+        nchan = workscan.nchan()
+        
+        if mask is None: mask = [True for i in xrange(nchan)]
+        if minnwave is None: minnwave = 0
+        if maxnwave is None: maxnwave = 3
+        if clipthresh is None: clipthresh = 3.0
+        if clipniter is None: clipniter = 1
+        if plot is None: plot = False
+        if outlog is None: outlog = False
+        if blfile is None: blfile = ""
+
+        outblfile = (blfile != "") and os.path.exists(os.path.expanduser(os.path.expandvars(blfile)))
+        
+        try:
+            #CURRENTLY, PLOT=true UNAVAILABLE UNTIL cubic spline fitting is implemented as a fitter method. 
+            workscan._sinusoid_baseline(mask, minnwave, maxnwave, clipthresh, clipniter, outlog, blfile)
+            
+            workscan._add_history("sinusoid_baseline", varlist)
+            
+            if insitu:
+                self._assign(workscan)
+            else:
+                return workscan
+            
+        except RuntimeError, e:
+            msg = "The fit failed, possibly because it didn't converge."
+            if rcParams["verbose"]:
+                asaplog.push(str(e))
+                asaplog.push(str(msg))
+                return
+            else:
+                raise RuntimeError(str(e)+'\n'+msg)
+
+
+    def auto_sinusoid_baseline(self, insitu=None, mask=None, minnwave=None, maxnwave=None,
+                               clipthresh=None, clipniter=None, edge=None, threshold=None,
+                               chan_avg_limit=None, plot=None, outlog=None, blfile=None):
+        """\
+        Return a scan which has been baselined (all rows) by cubic spline
+        function (piecewise cubic polynomial).
+        Spectral lines are detected first using linefinder and masked out
+        to avoid them affecting the baseline solution.
+
+        Parameters:
+            insitu:     if False a new scantable is returned.
+                        Otherwise, the scaling is done in-situ
+                        The default is taken from .asaprc (False)
+            mask:       an optional mask retreived from scantable
+            minnwave:   Minimum wave number in spectral window (default is 0)
+            maxnwave:   Maximum wave number in spectral window (default is 3)
+            clipthresh: Clipping threshold. (default is 3.0, unit: sigma)
+            clipniter:  maximum number of iteration of 'clipthresh'-sigma clipping (default is 1)
+            edge:       an optional number of channel to drop at
+                        the edge of spectrum. If only one value is
+                        specified, the same number will be dropped
+                        from both sides of the spectrum. Default
+                        is to keep all channels. Nested tuples
+                        represent individual edge selection for
+                        different IFs (a number of spectral channels
+                        can be different)
+            threshold:  the threshold used by line finder. It is
+                        better to keep it large as only strong lines
+                        affect the baseline solution.
+            chan_avg_limit:
+                        a maximum number of consequtive spectral
+                        channels to average during the search of
+                        weak and broad lines. The default is no
+                        averaging (and no search for weak lines).
+                        If such lines can affect the fitted baseline
+                        (e.g. a high order polynomial is fitted),
+                        increase this parameter (usually values up
+                        to 8 are reasonable). Most users of this
+                        method should find the default value sufficient.
+            plot:   *** CURRENTLY UNAVAILABLE, ALWAYS FALSE ***
+                        plot the fit and the residual. In this each
+                        indivual fit has to be approved, by typing 'y'
+                        or 'n'
+            outlog:     Output the coefficients of the best-fit
+                        function to logger (default is False)
+            blfile:     Name of a text file in which the best-fit
+                        parameter values to be written
+                        (default is "": no file/logger output)
+
+        Example:
+            bscan = scan.auto_sinusoid_baseline(maxnwave=10, insitu=False)
+        """
+
+        varlist = vars()
+
+        if insitu is None: insitu = rcParams['insitu']
+        if insitu:
+            workscan = self
+        else:
+            workscan = self.copy()
+
+        nchan = workscan.nchan()
+        
+        if mask is None: mask = [True for i in xrange(nchan)]
+        if minnwave is None: minnwave = 0
+        if maxnwave is None: maxnwave = 3
+        if clipthresh is None: clipthresh = 3.0
+        if clipniter is None: clipniter = 1
+        if edge is None: edge = (0, 0)
+        if threshold is None: threshold = 3
+        if chan_avg_limit is None: chan_avg_limit = 1
+        if plot is None: plot = False
+        if outlog is None: outlog = False
+        if blfile is None: blfile = ""
+
+        outblfile = (blfile != "") and os.path.exists(os.path.expanduser(os.path.expandvars(blfile)))
+        
+        from asap.asaplinefind import linefinder
+        from asap import _is_sequence_or_number as _is_valid
+
+        if not (isinstance(edge, list) or isinstance(edge, tuple)): edge = [ edge ]
+        individualedge = False;
+        if len(edge) > 1: individualedge = isinstance(edge[0], list) or isinstance(edge[0], tuple)
+
+        if individualedge:
+            for edgepar in edge:
+                if not _is_valid(edgepar, int):
+                    raise ValueError, "Each element of the 'edge' tuple has \
+                                       to be a pair of integers or an integer."
+        else:
+            if not _is_valid(edge, int):
+                raise ValueError, "Parameter 'edge' has to be an integer or a \
+                                   pair of integers specified as a tuple. \
+                                   Nested tuples are allowed \
+                                   to make individual selection for different IFs."
+
+            if len(edge) > 1:
+                curedge = edge
+            else:
+                curedge = edge + edge
+
+        try:
+            #CURRENTLY, PLOT=true UNAVAILABLE UNTIL cubic spline fitting is implemented as a fitter method. 
+            if individualedge:
+                curedge = []
+                for i in xrange(len(edge)):
+                    curedge += edge[i]
+                
+            workscan._auto_sinusoid_baseline(mask, minnwave, maxnwave, clipthresh, clipniter, curedge, threshold, chan_avg_limit, outlog, blfile)
+
+            workscan._add_history("auto_sinusoid_baseline", varlist)
+            
+            if insitu:
+                self._assign(workscan)
+            else:
+                return workscan
+            
+        except RuntimeError, e:
+            msg = "The fit failed, possibly because it didn't converge."
+            if rcParams["verbose"]:
+                asaplog.push(str(e))
+                asaplog.push(str(msg))
+                return
+            else:
+                raise RuntimeError(str(e)+'\n'+msg)
+
+
+    @asaplog_post_dec
     def cspline_baseline(self, insitu=None, mask=None, npiece=None, clipthresh=None, clipniter=None, plot=None, outlog=None, blfile=None):
         """\