Changeset 1757 for branches/alma/python

Timestamp:

06/09/10 19:03:06 (14 years ago)

Author:

Kana Sugimoto

Message:

New Development: Yes

JIRA Issue: Yes (CAS-2211)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: ASAP 3.0.0 interface changes

Test Programs:

Put in Release Notes: Yes

Module(s): all the CASA sd tools and tasks are affected.

Description: Merged ATNF-ASAP 3.0.0 developments to CASA (alma) branch.

Note you also need to update casa/code/atnf.

Location:

branches/alma

Files:

• . (modified) (2 props)
• python/__init__.py (modified) (21 diffs)
• python/asapfitter.py (modified) (15 diffs)
• python/asaplinefind.py (modified) (3 diffs)
• python/asaplot.py (modified) (1 diff)
• python/asaplotbase.py (modified) (9 diffs)
• python/asaplotgui.py (modified) (1 diff)
• python/asaplotgui_gtk.py (modified) (1 diff)
• python/asaplotgui_qt4.py (modified) (1 diff)
• python/asapmath.py (modified) (9 diffs)
• python/asapplotter.py (modified) (24 diffs)
• python/asapreader.py (modified) (3 diffs)
• python/compatibility.py (added)
• python/coordinate.py (added)
• python/lagflagger.py (added)
• python/opacity.py (added)
• python/scantable.py (modified) (79 diffs)
• python/selector.py (modified) (3 diffs)
• python/simplelinefinder.py (added)

branches/alma/python/__init__.py

@@ -4 +4 @@
 """
 import os,sys,shutil, platform
+try:
+    from functools import wraps as wraps_dec
+except ImportError:
+    from asap.compatibility import wraps as wraps_dec
 
 # Set up CASAPATH and first time use of asap i.e. ~/.asap/*
@@ -33 +37 @@
     #shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
     # commented out by TT on 2009.06.23 for casapy use
-    ##shutil.copyfile(asapdata+"/data/ipy_user_conf.py", 
+    ##shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
     ##                userdir+"/ipy_user_conf.py")
     f = file(userdir+"/asapuserfuncs.py", "w")
@@ -43 +47 @@
     # upgrade to support later ipython versions
     ##if not os.path.exists(userdir+"/ipy_user_conf.py"):
-    ##    shutil.copyfile(asapdata+"/data/ipy_user_conf.py", 
+    ##    shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
     ##                    userdir+"/ipy_user_conf.py")
 
@@ -74 +78 @@
 
     """
-
     fname = os.path.join( os.getcwd(), '.asaprc')
     if os.path.exists(fname): return fname
@@ -109 +112 @@
     'plotter.histogram'  : [False, _validate_bool],
     'plotter.papertype'  : ['A4', str],
-    'plotter.xaxisformatting' : ['asap', str],
+    ## for older Matplotlib version
+    #'plotter.axesformatting' : ['mpl', str],
+    'plotter.axesformatting' : ['asap', str],
 
     # scantable
@@ -118 +123 @@
     'scantable.storage'   : ['memory', str],
     'scantable.history'   : [True, _validate_bool],
-    'scantable.reference'      : ['.*(e|w|_R)$', str]
+    'scantable.reference'      : ['.*(e|w|_R)$', str],
+    'scantable.parallactify'   : [False, _validate_bool]
     # fitter
     }
@@ -146 +152 @@
 plotter.panelling          : scan
 
-# push panels together, to share axislabels
+# push panels together, to share axis labels
 plotter.ganged             : True
 
@@ -164 +170 @@
 
 # The formatting style of the xaxis
-plotter.xaxisformatting    : 'asap' or 'mpl'
+plotter.axesformatting    : 'mpl' (default) or 'asap' (for old versions of matplotlib)
 
 # scantable
@@ -189 +195 @@
 # Control the identification of reference (off) scans
 # This is has to be a regular expression
-scantable.reference         : .*(e|w|_R)$
+scantable.reference        : .*(e|w|_R)$
+
+# Indicate whether the data was parallactified (total phase offest == 0.0)
+scantable.parallactify     : False
+
 # Fitter
 """
@@ -290 +300 @@
 
 def _n_bools(n, val):
-    return [ val for i in xrange(n) ] 
+    return [ val for i in xrange(n) ]
 
 def _is_sequence_or_number(param, ptype=int):
@@ -357 +367 @@
     asaplog.disable()
 
+
+def print_log_dec(f):
+    @wraps_dec(f)
+    def wrap_it(*args, **kw):
+        val = f(*args, **kw)
+        print_log()
+        return val
+    return wrap_it
+
 def print_log(level='INFO'):
     from taskinit import casalog
@@ -382 +401 @@
 from scantable import scantable
 from asaplinefind import linefinder
+from simplelinefinder import simplelinefinder
 from linecatalog import linecatalog
 from interactivemask import interactivemask
+from opacity import skydip
+from opacity import model as opacity_model
 
 if rcParams['useplotter']:
@@ -392 +414 @@
             import matplotlib
             if not matplotlib.sys.modules['matplotlib.backends']: matplotlib.use("TkAgg")
-        import pylab
+        from matplotlib import pylab
         xyplotter = pylab
         plotter = asapplotter(gui)
@@ -402 +424 @@
 
 __date__ = '$Date$'.split()[1]
-__version__  = '2.3.1 alma'
+__version__  = '3.0.0 alma'
 # nrao casapy specific, get revision number
 #__revision__ = ' unknown '
@@ -427 +449 @@
 
 def is_ipython():
-    return '__IP' in dir(sys.modules["__main__"])
+    return 'IPython' in sys.modules.keys()
 if is_ipython():
     def version(): print  "ASAP %s(%s)"% (__version__, __date__)
+
     def list_scans(t = scantable):
-        import types
-        globs = sys.modules['__main__'].__dict__.iteritems()
-        print "The user created scantables are:"
-        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
-        print filter(lambda x: not x.startswith('_'), sts)
-        return
+        import inspect
+        print "The user created scantables are: ",
+        globs=inspect.currentframe().f_back.f_locals.copy()
+        out = [ k for k,v in globs.iteritems() \
+                     if isinstance(v, scantable) and not k.startswith("_") ]
+        print out
+        return out
 
     def commands():
@@ -462 +486 @@
             get_elevation   - get the elevation of the scans
             get_parangle    - get the parallactic angle of the scans
+            get_coordinate  - get the spectral coordinate for the given row,
+                              which can be used for coordinate conversions
+            get_weather     - get the weather condition parameters
             get_unit        - get the current unit
             set_unit        - set the abcissa unit to be used from this
@@ -506 +533 @@
             mx_quotient     - Form a quotient using MX data (off beams)
             scale, *, /     - return a scan scaled by a given factor
-            add, +, -       - return a scan with given value added
+            add, +          - return a scan with given value added
+            sub, -          - return a scan with given value subtracted
             bin             - return a scan with binned channels
             resample        - return a scan with resampled channels
@@ -529 +557 @@
             stddev          - Determine the standard deviation of the current
                               beam/if/pol
+            get_row_selector - get the selection object for a specified row
+                               number
      [Selection]
          selector              - a selection object to set a subset of a scantable
@@ -590 +620 @@
             plot            - plot a scantable
             plot_lines      - plot a linecatalog overlay
+            plotazel        - plot azimuth and elevation versus time
+            plotpointing    - plot telescope pointings
             save            - save the plot to a file ('png' ,'ps' or 'eps')
             set_mode        - set the state of the plotter, i.e.
@@ -613 +645 @@
             axhline,axvline - draw horizontal/vertical lines
             axhspan,axvspan - draw horizontal/vertical regions
+            annotate        - draw an arrow with label
+            create_mask     - create a scnatble mask interactively
 
         xyplotter           - matplotlib/pylab plotting functions
-
-    [Reading files]
-        reader              - access rpfits/sdfits files
-            open            - attach reader to a file
-            close           - detach reader from file
-            read            - read in integrations
-            summary         - list info about all integrations
 
     [General]
         commands            - this command
         print               - print details about a variable
-        list_scans          - list all scantables created bt the user
+        list_scans          - list all scantables created by the user
         list_files          - list all files readable by asap (default rpf)
         del                 - delete the given variable from memory
@@ -639 +666 @@
         mask_not            - boolean operations on masks created with
                               scantable.create_mask
+        skydip              - gain opacity values from a sky dip observation
+        opacity_model       - compute opacities fro given frequencies based on
+                              atmospheric model
 
     Note:

branches/alma/python/asapfitter.py

@@ -1 +1 @@
 import _asap
 from asap import rcParams
-from asap import print_log
+from asap import print_log, print_log_dec
 from asap import _n_bools
 from asap import mask_and
@@ -79 +79 @@
         Set the function to be fit.
         Parameters:
-            poly:    use a polynomial of the order given with nonlinear least squares fit 
+            poly:    use a polynomial of the order given with nonlinear least squares fit
             lpoly:   use polynomial of the order given with linear least squares fit
             gauss:   fit the number of gaussian specified
@@ -95 +95 @@
             n = kwargs.get('poly')
             self.components = [n]
-            self.uselinear = False 
+            self.uselinear = False
         elif kwargs.has_key('lpoly'):
             self.fitfunc = 'poly'
@@ -106 +106 @@
             self.fitfuncs = [ 'gauss' for i in range(n) ]
             self.components = [ 3 for i in range(n) ]
-            self.uselinear = False 
+            self.uselinear = False
         elif kwargs.has_key('lorentz'):
             n = kwargs.get('lorentz')
@@ -112 +112 @@
             self.fitfuncs = [ 'lorentz' for i in range(n) ]
             self.components = [ 3 for i in range(n) ]
-            self.uselinear = False 
+            self.uselinear = False
         else:
             msg = "Invalid function type."
@@ -127 +127 @@
         return
 
+    #@print_log_dec
     def fit(self, row=0, estimate=False):
         """
@@ -164 +165 @@
                                                                       self.data.getbeam(i),
                                                                       self.data.getif(i),
-                                                                      self.data.getpol(i), 
+                                                                      self.data.getpol(i),
                                                                       self.data.getcycle(i))
                 asaplog.push(out,False)
@@ -221 +222 @@
                 self.data._addfit(fit,self._fittedrow)
 
-    #def set_parameters(self, params, fixed=None, component=None):
+    #@print_log_dec
     def set_parameters(self,*args,**kwargs):
         """
@@ -543 +544 @@
         return self.fitter.getfit()
 
+    #@print_log_dec
     def commit(self):
         """
@@ -571 +573 @@
         return scan
 
-    def plot(self, residual=False, components=None, plotparms=False, filename=None):
+    #@print_log_dec
+    def plot(self, residual=False, components=None, plotparms=False,
+             filename=None):
         """
         Plot the last fit.
@@ -598 +602 @@
         xlab = 'Abcissa'
         ylab = 'Ordinate'
-        from matplotlib.numerix import ma,logical_not,logical_and,array
+        from numpy import ma,logical_not,logical_and,array
         m = self.mask
         if self.data:
@@ -606 +610 @@
                              array(self.data._getmask(self._fittedrow),
                                    copy=False))
-                             
+
             ylab = self.data._get_ordinate_label()
 
@@ -670 +674 @@
         print_log()
 
+    #@print_log_dec
     def auto_fit(self, insitu=None, plot=False):
         """
@@ -700 +705 @@
                                                                    scan.getbeam(r),
                                                                    scan.getif(r),
-                                                                   scan.getpol(r), 
+                                                                   scan.getpol(r),
                                                                    scan.getcycle(r))
             asaplog.push(out, False)
@@ -723 +728 @@
         print_log()
         return scan
-

branches/alma/python/asaplinefind.py

@@ -41 +41 @@
 
     def set_options(self,threshold=1.7320508075688772,min_nchan=3,
-        avg_limit=8,box_size=0.2):
+        avg_limit=8,box_size=0.2,noise_box='all',noise_stat='mean80'):
         """
         Set the parameters of the algorithm
@@ -55 +55 @@
                           this parameter can be averaged to search for
                           broad lines. Default is 8.
-             box_size     A running mean box size specified as a fraction
+             box_size     A running mean/median box size specified as a fraction
                           of the total spectrum length. Default is 1/5
+             noise_box    Area of the spectrum used to estimate noise stats
+                          Both string values and numbers are allowed
+                          Allowed string values:
+                             'all' use all the spectrum (default)
+                             'box' noise box is the same as running mean/median
+                                   box
+                          Numeric values are defined as a fraction from the
+                          spectrum size. Values should be positive.
+                          (noise_box == box_size has the same effect as
+                           noise_box = 'box')
+             noise_stat   Statistics used to estimate noise, allowed values:
+                              'mean80' use the 80% of the lowest deviations
+                                       in the noise box (default)
+                              'median' median of deviations in the noise box
+                             
         Note:  For bad baselines threshold should be increased,
                and avg_limit decreased (or even switched off completely by
@@ -62 +77 @@
                undulations instead of real lines.
         """
-        self.finder.setoptions(threshold,min_nchan,avg_limit,box_size)
+        if noise_stat.lower() not in ["mean80",'median']:
+           raise RuntimeError, "noise_stat argument in linefinder.set_options can only be mean80 or median"
+        nStat = (noise_stat.lower() == "median")
+        nBox = -1.
+        if isinstance(noise_box,str):
+           if noise_box.lower() not in ['all','box']:
+              raise RuntimeError, "string-valued noise_box in linefinder.set_options can only be all or box"
+           if noise_box.lower() == 'box':
+              nBox = box_size
+        else:
+           nBox = float(noise_box)
+        self.finder.setoptions(threshold,min_nchan,avg_limit,box_size,nBox,nStat)
         return
 

branches/alma/python/asaplot.py

@@ -11 +11 @@
     ASAP plotting class based on matplotlib.
     """
-    def __init__(self, rows=1, cols=0, title='', size=(8,4), buffering=False):
+    def __init__(self, rows=1, cols=0, title='', size=None, buffering=False):
         """
         Create a new instance of the ASAPlot plotting class.

branches/alma/python/asaplotbase.py

@@ -10 +10 @@
 from matplotlib.figure import Figure, Text
 from matplotlib.font_manager import FontProperties as FP
-from matplotlib.numerix import sqrt
+from numpy import sqrt
 from matplotlib import rc, rcParams
 from asap import rcParams as asaprcParams
 from matplotlib.ticker import OldScalarFormatter
-from matplotlib.ticker import NullLocator
 
 # API change in mpl >= 0.98
@@ -20 +19 @@
     from matplotlib.transforms import blended_transform_factory
 except ImportError:
-    from matplotlib.transforms import blend_xy_sep_transform  as blended_transform_factory
+    from matplotlib.transforms import blend_xy_sep_transform as blended_transform_factory
 
 from asap import asaplog
@@ -29 +28 @@
     print_log( 'WARN' )
 
-#class MyFormatter(OldScalarFormatter):
-#    def __call__(self, x, pos=None):
-#        last = len(self.locs)-2
-#        if pos==0:
-#            return ''
-#        else: return OldScalarFormatter.__call__(self, x, pos)
-
 class asaplotbase:
     """
@@ -41 +33 @@
     """
 
-    def __init__(self, rows=1, cols=0, title='', size=(8,6), buffering=False):
+    def __init__(self, rows=1, cols=0, title='', size=None, buffering=False):
         """
         Create a new instance of the ASAPlot plotting class.
@@ -157 +149 @@
         fmt is the line style as in plot().
         """
-        from matplotlib.numerix import array
-        from matplotlib.numerix.ma import MaskedArray
+        from numpy import array
+        from numpy.ma import MaskedArray
         if x is None:
             if y is None: return
@@ -289 +281 @@
         self.register('button_press', position_disable)
 
+
+#     def get_region(self):
+#         pos = []
+#         print "Please select the bottom/left point"
+#         pos.append(self.figure.ginput(n=1, show_clicks=False)[0])
+#         print "Please select the top/right point"
+#         pos.append(self.figure.ginput(n=1, show_clicks=False)[0])
+#         return pos
+
+#     def get_point(self):
+#         print "Please select the point"
+#         pt = self.figure.ginput(n=1, show_clicks=False)
+#         if pt:
+#             return pt[0]
+#         else:
+#             return None
 
     def region(self):
@@ -640 +648 @@
                     self.subplots[i]['axes'] = self.figure.add_subplot(rows,
                                                 cols, i+1)
-                    if asaprcParams['plotter.xaxisformatting'] == 'mpl':
+                    if asaprcParams['plotter.axesformatting'] != 'mpl':
                         self.subplots[i]['axes'].xaxis.set_major_formatter(OldScalarFormatter())
                 else:
@@ -646 +654 @@
                         self.subplots[i]['axes'] = self.figure.add_subplot(rows,
                                                 cols, i+1)
-                        if asaprcParams['plotter.xaxisformatting'] != 'mpl':
+                        if asaprcParams['plotter.axesformatting'] != 'mpl':
                             
                             self.subplots[i]['axes'].xaxis.set_major_formatter(OldScalarFormatter())
@@ -730 +738 @@
 
             from matplotlib.artist import setp
-            fp = FP(size=rcParams['xtick.labelsize'])
-            xts = fp.get_size_in_points()- (self.cols)/2
-            fp = FP(size=rcParams['ytick.labelsize'])
-            yts = fp.get_size_in_points() - (self.rows)/2
+            fpx = FP(size=rcParams['xtick.labelsize'])
+            xts = fpx.get_size_in_points()- (self.cols)/2
+            fpy = FP(size=rcParams['ytick.labelsize'])
+            yts = fpy.get_size_in_points() - (self.rows)/2
+            fpa = FP(size=rcParams['axes.labelsize'])
+            fpat = FP(size=rcParams['axes.titlesize'])
+            axsize =  fpa.get_size_in_points()
+            tsize =  fpat.get_size_in_points()-(self.cols)/2
             for sp in self.subplots:
                 ax = sp['axes']
-                #s = ax.title.get_size()
-                #tsize = s-(self.cols+self.rows)
-                s=FP(size=rcParams['axes.titlesize'])
-                tsize = s.get_size_in_points()-(self.cols)/2
                 ax.title.set_size(tsize)
-                fp = FP(size=rcParams['axes.labelsize'])
                 setp(ax.get_xticklabels(), fontsize=xts)
                 setp(ax.get_yticklabels(), fontsize=yts)
-                origx =  fp.get_size_in_points()
-                origy = origx
                 off = 0
                 if self.cols > 1: off = self.cols
-                xfsize = origx-off
-                ax.xaxis.label.set_size(xfsize)
+                ax.xaxis.label.set_size(axsize-off)
                 off = 0
                 if self.rows > 1: off = self.rows
-                yfsize = origy-off
-                ax.yaxis.label.set_size(yfsize)
+                ax.yaxis.label.set_size(axsize-off)
 
     def subplot(self, i=None, inc=None):

branches/alma/python/asaplotgui.py

@@ -16 +16 @@
     """
 
-    def __init__(self, rows=1, cols=0, title='', size=(8,6), buffering=False):
+    def __init__(self, rows=1, cols=0, title='', size=None, buffering=False):
         """
         Create a new instance of the ASAPlot plotting class.

branches/alma/python/asaplotgui_gtk.py

@@ -18 +18 @@
     """
 
-    def __init__(self, rows=1, cols=0, title='', size=(8,6), buffering=False):
+    def __init__(self, rows=1, cols=0, title='', size=None, buffering=False):
         """
         Create a new instance of the ASAPlot plotting class.

branches/alma/python/asaplotgui_qt4.py

@@ -18 +18 @@
     """
 
-    def __init__(self, rows=1, cols=0, title='', size=(8,6), buffering=False):
+    def __init__(self, rows=1, cols=0, title='', size=None, buffering=False):
         """
         Create a new instance of the ASAPlot plotting class.

branches/alma/python/asapmath.py

@@ -1 +1 @@
 from asap.scantable import scantable
 from asap import rcParams
-from asap import print_log
+from asap import print_log, print_log_dec
 from asap import selector
 from asap import asaplog
 from asap import asaplotgui
 
+#@print_log_dec
 def average_time(*args, **kwargs):
     """
@@ -29 +30 @@
         # without using a mask
         scanav = average_time(scana,scanb)
-        # or equivalent
-        # scanav = average_time([scana, scanb])
+        # or equivalent
+        # scanav = average_time([scana, scanb])
         # return the (time) averaged scan, i.e. the average of
         # all correlator cycles
@@ -122 +123 @@
     return s
 
+#@print_log_dec
 def dototalpower(calon, caloff, tcalval=0.0):
     """
@@ -140 +142 @@
     return s
 
+#@print_log_dec
 def dosigref(sig, ref, smooth, tsysval=0.0, tauval=0.0):
     """
@@ -160 +163 @@
     return s
 
+#@print_log_dec
 def calps(scantab, scannos, smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0, verify=False):
     """
@@ -442 +446 @@
     return ress
 
+#@print_log_dec
 def calnod(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0, verify=False):
     """
@@ -682 +687 @@
     return resspec
 
+#@print_log_dec
 def calfs(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0, verify=False):
     """
@@ -889 +895 @@
     return resspec
 
-def simple_math(left, right, op='add', tsys=True):
-    """
-    Apply simple mathematical binary operations to two
-    scan tables,  returning the result in a new scan table.
-    The operation is applied to both the correlations and the TSys data
-    The cursor of the output scan is set to 0
-    Parameters:
-        left:          the 'left' scan
-        right:         the 'right' scan
-        op:            the operation: 'add' (default), 'sub', 'mul', 'div'
-        tsys:          if True (default) then apply the operation to Tsys
-                       as well as the data
-    """
-    #print "simple_math is deprecated use +=/* instead."
-    asaplog.push( "simple_math is deprecated use +=/* instead." )
-    print_log('WARN')
-
+#@print_log_dec
 def merge(*args):
     """
@@ -914 +904 @@
     Example:
         myscans = [scan1, scan2]
-        allscans = merge(myscans)
-        # or equivalent
-        sameallscans = merge(scan1, scan2)
+        allscans = merge(myscans)
+        # or equivalent
+        sameallscans = merge(scan1, scan2)
     """
     varlist = vars()

branches/alma/python/asapplotter.py

@@ -1 @@
-from asap import rcParams, print_log, selector
+from asap import rcParams, print_log, print_log_dec
+from asap import selector, scantable
 from asap import asaplog
 import matplotlib.axes
+from matplotlib.font_manager import FontProperties
+from matplotlib.text import Text
+
 import re
 
@@ -13 +17 @@
         other variables.
     """
-    def __init__(self, visible=None):
+    def __init__(self, visible=None , **kwargs):
         self._visible = rcParams['plotter.gui']
         if visible is not None:
             self._visible = visible
-        self._plotter = self._newplotter()
+        self._plotter = self._newplotter(**kwargs)
         if self._visible and matplotlib.get_backend() == "TkAgg":
             from asap.casatoolbar import CustomToolbarTkAgg
@@ -42 +46 @@
         self._selection = selector()
         self._hist = rcParams['plotter.histogram']
+        self._fp = FontProperties()
         self._panellayout = self.set_panellayout(refresh=False)
 
@@ -52 +57 @@
         return None
 
-    def _newplotter(self):
+    def _newplotter(self, **kwargs):
         backend=matplotlib.get_backend()
         if not self._visible:
@@ -64 +69 @@
         else:
             from asap.asaplot import asaplot
-        return asaplot()
-
-
+        return asaplot(**kwargs)
+
+    #@print_log_dec
     def plot(self, scan=None):
         """
@@ -101 +106 @@
         return
 
+    def gca(self):
+        return self._plotter.figure.gca()
+
+    def refresh(self):
+        """Do a soft refresh"""
+        self._plotter.figure.show()
+
+    def create_mask(self, nwin=1, panel=0, color=None):
+        """
+        Interactively define a mask.It retruns a mask that is equivalent to
+        the one created manually with scantable.create_mask.
+        Parameters:
+            nwin:       The number of mask windows to create interactively
+                        default is 1.
+            panel:      Which panel to use for mask selection. This is useful
+                        if different IFs are spread over panels (default 0)
+        """
+        if self._data is None:
+            return []
+        outmask = []
+        self._plotter.subplot(panel)
+        xmin, xmax = self._plotter.axes.get_xlim()
+        marg = 0.05*(xmax-xmin)
+        self._plotter.axes.set_xlim(xmin-marg, xmax+marg)
+        self.refresh()
+
+        def cleanup(lines=False, texts=False, refresh=False):
+            if lines:
+                del self._plotter.axes.lines[-1]
+            if texts:
+                del self._plotter.axes.texts[-1]
+            if refresh:
+                self.refresh()
+
+        for w in xrange(nwin):
+            wpos = []
+            self.text(0.05,1.0, "Add start boundary",
+                      coords="relative", fontsize=10)
+            point = self._plotter.get_point()
+            cleanup(texts=True)
+            if point is None:
+                continue
+            wpos.append(point[0])
+            self.axvline(wpos[0], color=color)
+            self.text(0.05,1.0, "Add end boundary", coords="relative", fontsize=10)
+            point = self._plotter.get_point()
+            cleanup(texts=True, lines=True)
+            if point is None:
+                self.refresh()
+                continue
+            wpos.append(point[0])
+            self.axvspan(wpos[0], wpos[1], alpha=0.1,
+                         edgecolor=color, facecolor=color)
+            ymin, ymax = self._plotter.axes.get_ylim()
+            outmask.append(wpos)
+
+        self._plotter.axes.set_xlim(xmin, xmax)
+        self.refresh()
+        if len(outmask) > 0:
+            return self._data.create_mask(*outmask)
+        return []
 
     # forwards to matplotlib axes
     def text(self, *args, **kwargs):
+        if kwargs.has_key("interactive"):
+            #if kwargs.pop("interactive"):
+            #    pos = self._plotter.get_point()
+            #    args = tuple(pos)+args
+            kwargs.pop("interactive")
         self._axes_callback("text", *args, **kwargs)
+
     text.__doc__ = matplotlib.axes.Axes.text.__doc__
+
     def arrow(self, *args, **kwargs):
+        if kwargs.has_key("interactive"):
+            #if kwargs.pop("interactive"):
+            #    pos = self._plotter.get_region()
+            #    dpos = (pos[0][0], pos[0][1],
+            #            pos[1][0]-pos[0][0],
+            #            pos[1][1] - pos[0][1])
+            #    args = dpos + args
+            kwargs.pop("interactive")
         self._axes_callback("arrow", *args, **kwargs)
+
     arrow.__doc__ = matplotlib.axes.Axes.arrow.__doc__
+
+    def annotate(self, text, xy=None, xytext=None, **kwargs):
+        if kwargs.has_key("interactive"):
+            #if kwargs.pop("interactive"):
+            #    xy = self._plotter.get_point()
+            #    xytext = self._plotter.get_point()
+            kwargs.pop("interactive")
+        if not kwargs.has_key("arrowprops"):
+            kwargs["arrowprops"] = dict(arrowstyle="->")
+        self._axes_callback("annotate", text, xy, xytext, **kwargs)
+
+    annotate.__doc__ = matplotlib.axes.Axes.annotate.__doc__
+
     def axvline(self, *args, **kwargs):
+        if kwargs.has_key("interactive"):
+            #if kwargs.pop("interactive"):
+            #    pos = self._plotter.get_point()
+            #    args = (pos[0],)+args
+            kwargs.pop("interactive")
         self._axes_callback("axvline", *args, **kwargs)
+
     axvline.__doc__ = matplotlib.axes.Axes.axvline.__doc__
+
     def axhline(self, *args, **kwargs):
+        if kwargs.has_key("interactive"):
+            #if kwargs.pop("interactive"):
+            #    pos = self._plotter.get_point()
+            #    args = (pos[1],)+args
+            kwargs.pop("interactive")
         self._axes_callback("axhline", *args, **kwargs)
+
     axhline.__doc__ = matplotlib.axes.Axes.axhline.__doc__
+
     def axvspan(self, *args, **kwargs):
+        if kwargs.has_key("interactive"):
+            #if kwargs.pop("interactive"):
+            #    pos = self._plotter.get_region()
+            #    dpos = (pos[0][0], pos[1][0])
+            #    args = dpos + args
+            kwargs.pop("interactive")
         self._axes_callback("axvspan", *args, **kwargs)
         # hack to preventy mpl from redrawing the patch
         # it seem to convert the patch into lines on every draw.
         # This doesn't happen in a test script???
-        del self._plotter.axes.patches[-1]
+        #del self._plotter.axes.patches[-1]
+
     axvspan.__doc__ = matplotlib.axes.Axes.axvspan.__doc__
 
     def axhspan(self, *args, **kwargs):
+        if kwargs.has_key("interactive"):
+            #if kwargs.pop("interactive"):
+            #    pos = self._plotter.get_region()
+            #    dpos = (pos[0][1], pos[1][1])
+            #    args = dpos + args
+            kwargs.pop("interactive")
         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.
         # This doesn't happen in a test script???
-        del self._plotter.axes.patches[-1]
+        #del self._plotter.axes.patches[-1]
+
     axhspan.__doc__ = matplotlib.axes.Axes.axhspan.__doc__
 
@@ -465 +588 @@
         if refresh and self._data: self.plot(self._data)
 
-    def set_font(self, family=None, style=None, weight=None, size=None, refresh=True):
+    def set_font(self, refresh=True,**kwargs):
         """
         Set font properties.
@@ -479 +602 @@
         """
         from matplotlib import rc as rcp
-        if isinstance(family, str):
-            rcp('font', family=family)
-        if isinstance(style, str):
-            rcp('font', style=style)
-        if isinstance(weight, str):
-            rcp('font', weight=weight)
-        if isinstance(size, float) or isinstance(size, int):
-            rcp('font', size=size)
+        fdict = {}
+        for k,v in kwargs.iteritems():
+            if v:
+                fdict[k] = v
+        self._fp = FontProperties(**fdict)
         if refresh and self._data: self.plot(self._data)
 
@@ -540 +660 @@
         if not self._data.get_unit().endswith("Hz"):
             raise RuntimeError("Can only overlay linecatalogs when data is in frequency.")
-        from matplotlib.numerix import ma
+        from numpy import ma
         for j in range(len(self._plotter.subplots)):
             self._plotter.subplot(j)
@@ -716 +836 @@
         if isinstance(nstack0, int): nstack = nstack0
         else: nstack = len(nstack0)
-        maxpanel, maxstack = 16,8
+        maxpanel, maxstack = 16,16
         if n > maxpanel or nstack > maxstack:
             maxn = 0
@@ -761 +881 @@
                 ylab = self._ordinate and self._ordinate[panelcount] \
                        or scan._get_ordinate_label()
-                self._plotter.set_axes('xlabel',xlab)
-                self._plotter.set_axes('ylabel',ylab)
+                self._plotter.set_axes('xlabel', xlab)
+                self._plotter.set_axes('ylabel', ylab)
                 lbl = self._get_label(scan, r, self._panelling, self._title)
                 if isinstance(lbl, list) or isinstance(lbl, tuple):
@@ -781 +901 @@
                     y = scan._getspectrum(r)
                 m = scan._getmask(r)
-                from matplotlib.numerix import logical_not, logical_and
+                from numpy import logical_not, logical_and
                 if self._maskselection and len(self._usermask) == len(m):
                     if d[self._stacking](r) in self._maskselection[self._stacking]:
                         m = logical_and(m, self._usermask)
                 x = scan._getabcissa(r)
-                from matplotlib.numerix import ma, array
+                from numpy import ma, array
                 y = ma.masked_array(y,mask=logical_not(array(m,copy=False)))
                 if self._minmaxx is not None:
@@ -839 +959 @@
         #reset the selector to the scantable's original
         scan.set_selection(savesel)
-
-    def set_selection(self, selection=None, refresh=True):
+        
+        #temporary switch-off for older matplotlib
+        #if self._fp is not None:
+        if self._fp is not None and getattr(self._plotter.figure,'findobj',False):
+            for o in self._plotter.figure.findobj(Text):
+                o.set_fontproperties(self._fp)
+
+    def set_selection(self, selection=None, refresh=True, **kw):
         """
         Parameters:
@@ -848 +974 @@
                         Otherwise,the parameter(s) are set without replotting.
         """
-        self._selection = isinstance(selection,selector) and selection or selector()
+        if selection is None:
+            # reset
+            if len(kw) == 0:
+                self._selection = selector()
+            else:
+                # try keywords
+                for k in kw:
+                    if k not in selector.fields:
+                        raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields))
+                self._selection = selector(**kw)
+        elif isinstance(selection, selector):
+            self._selection = selection
+        else:
+            raise TypeError("'selection' is not of type selector")
+
         d0 = {'s': 'SCANNO', 'b': 'BEAMNO', 'i':'IFNO',
               'p': 'POLNO', 'c': 'CYCLENO', 't' : 'TIME' }
@@ -885 +1025 @@
 
     def plotazel(self, scan=None, outfile=None):
-        """
-        plot azimuth and elevation  versus time of a scantable
-        """
-        import pylab as PL
-        from matplotlib.dates import DateFormatter, timezone, HourLocator, MinuteLocator, DayLocator
+    #def plotazel(self):
+        """
+        plot azimuth and elevation versus time of a scantable
+        """
+        from matplotlib import pylab as PL
+        from matplotlib.dates import DateFormatter, timezone
+        from matplotlib.dates import HourLocator, MinuteLocator,SecondLocator, DayLocator
         from matplotlib.ticker import MultipleLocator
-        from matplotlib.numerix import array, pi
+        from numpy import array, pi
         self._data = scan
         self._outfile = outfile
@@ -898 +1040 @@
         tz = timezone('UTC')
         PL.cla()
-        #PL.ioff()
+        PL.ioff()
         PL.clf()
         # Adjust subplot layouts
@@ -917 +1059 @@
             minloc = HourLocator(range(0,23,12))
             timefmt = DateFormatter("%b%d")
+        elif tdel > 24./60.:
+            timefmt = DateFormatter('%H:%M')
+            majloc = HourLocator()
+            minloc = MinuteLocator(30)
         else:
-            timefmt = DateFormatter('%H')
-            majloc = HourLocator()
-            minloc = MinuteLocator(20)
+            timefmt = DateFormatter('%H:%M')
+            majloc = MinuteLocator(interval=5)
+            minloc = SecondLocator(30)
+
         PL.title(dstr)
-
         if tdel == 0.0:
             th = (t - PL.floor(t))*24.0
@@ -947 +1093 @@
                 if az[irow] < 0: az[irow] += 360.0
 
-        ax = PL.subplot(2,1,2)
+        ax2 = PL.subplot(2,1,2)
         #PL.xlabel('Time (UT [hour])')
         PL.ylabel('Az [deg.]')
@@ -954 +1100 @@
         else:
             PL.plot_date(t,az,'o', markersize=2,markeredgecolor='b',markerfacecolor='b',tz=tz)
-            ax.xaxis.set_major_formatter(timefmt)
-            ax.xaxis.set_major_locator(majloc)
-            ax.xaxis.set_minor_locator(minloc)
-        #ax.grid(True)
-        ax.set_ylim(0,360)
-        ax.yaxis.grid(True)
+            ax2.xaxis.set_major_formatter(timefmt)
+            ax2.xaxis.set_major_locator(majloc)
+            ax2.xaxis.set_minor_locator(minloc)
+        #ax2.grid(True)
+        ax2.set_ylim(0,360)
+        ax2.yaxis.grid(True)
         #hfmt = DateFormatter('%H')
         #hloc = HourLocator()
         yloc = MultipleLocator(60)
-        ax.yaxis.set_major_locator(yloc)
+        ax2.yaxis.set_major_locator(yloc)
         if tdel > 1.0:
-            labels = ax.get_xticklabels()
+            labels = ax2.get_xticklabels()
             PL.setp(labels, fontsize=10)
             PL.xlabel('Time (UT [day])')
@@ -971 +1117 @@
             PL.xlabel('Time (UT [hour])')
 
-        #PL.ion()
+        PL.ion()
         PL.draw()
         if (self._outfile is not None):
@@ -977 +1123 @@
 
     def plotpointing(self, scan=None, outfile=None):
+    #def plotpointing(self):
         """
         plot telescope pointings
         """
-        import pylab as PL
-        from matplotlib.dates import DateFormatter, timezone
-        from matplotlib.ticker import MultipleLocator
-        from matplotlib.numerix import array, pi, zeros
+        from matplotlib import pylab as PL
+        from numpy import array, pi
         self._data = scan
         self._outfile = outfile
@@ -1001 +1146 @@
         #ax = PL.axes([0.1,0.1,0.8,0.8])
         ax.set_aspect('equal')
-        PL.plot(ra,dec, 'b,')
+        PL.plot(ra, dec, 'b,')
         PL.xlabel('RA [deg.]')
         PL.ylabel('Declination [deg.]')
@@ -1135 +1280 @@
         # Print Observation header to the upper-left corner of plot
         if plot:
-            srest=ssum[ssum.find('Rest Freqs:'):ssum.find('Abcissa:')]
-            shead=ssum[ssum.find('Beams:'):ssum.find('Flux Unit:')]
-            headstr=shead.split('\n\n')
-            if extrastr != '': headstr[1]=extrastr+'\n'+headstr[1]
+            headstr=[ssum[ssum.find('Observer:'):ssum.find('Flux Unit:')]]
+            headstr.append(ssum[ssum.find('Beams:'):ssum.find('Observer:')]
+                         +ssum[ssum.find('Rest Freqs:'):ssum.find('Abcissa:')])
+            if extrastr != '': headstr[0]=extrastr+'\n'+headstr[0]
             #headstr[1]='Data File:     '+(filestr or 'unknown')+'\n'+headstr[1]
-            headstr[0]=headstr[0]+'\n'+srest
-            headstr.reverse()
             ssel='***Selections***\n'+(selstr+self._data.get_selection().__str__() or 'none')
             headstr.append(ssel)
@@ -1159 +1302 @@
                             verticalalignment='bottom',fontsize=8)
             self._plotter.release()
-            del srest, shead, headstr, ssel
+            del headstr, ssel
         if logger:
             asaplog.push("----------------\n  Plot Summary\n----------------")

branches/alma/python/asapreader.py

@@ -1 +1 @@
 from asap._asap import stfiller
-from asap import print_log
+from asap import print_log, print_log_dec
 
 class reader(stfiller):
@@ -25 +25 @@
                rpfits ONLY.
     """
-
+    #@print_log_dec
     def __init__(self, filename, unit=None, theif=None, thebeam=None):
         self.unit = unit
@@ -48 +48 @@
         print_log()
 
+    #@print_log_dec
     def read(self):
         """

branches/alma/python/scantable.py

@@ +1 @@
+import os
+try:
+    from functools import wraps as wraps_dec
+except ImportError:
+    from asap.compatibility import wraps as wraps_dec
+
 from asap._asap import Scantable
 from asap import rcParams
-from asap import print_log
+from asap import print_log, print_log_dec
 from asap import asaplog
 from asap import selector
 from asap import linecatalog
+from asap.coordinate import coordinate
 from asap import _n_bools, mask_not, mask_and, mask_or
+
+
+def preserve_selection(func):
+    @wraps_dec(func)
+    def wrap(obj, *args, **kw):
+        basesel = obj.get_selection()
+        val = func(obj, *args, **kw)
+        obj.set_selection(basesel)
+        return val
+    return wrap
+
+
+def is_scantable(filename):
+    return (os.path.isdir(filename)
+            and not os.path.exists(filename+'/table.f1')
+            and os.path.exists(filename+'/table.info'))
+
 
 class scantable(Scantable):
@@ -12 +36 @@
     """
 
-    def __init__(self, filename, average=None, unit=None, getpt=None, antenna=None):
+    #@print_log_dec
+    def __init__(self, filename, average=None, unit=None, getpt=None, antenna=None, parallactify=None):
         """
         Create a scantable from a saved one or make a reference
@@ -36 +61 @@
             antenna:     Antenna selection. integer (id) or string (name
                          or id).
+            parallactify: Indcicate that the data had been parallatified.
+                          Default is taken form rc file.
         """
         if average is None:
@@ -57 +84 @@
                     return 
             antenna = tmpstr.rstrip(',')
+        parallactify = parallactify or rcParams['scantable.parallactify']
         varlist = vars()
         from asap._asap import stmath
@@ -63 +91 @@
             Scantable.__init__(self, filename)
         else:
-            if isinstance(filename, str):# or \
-#                (isinstance(filename, list) or isinstance(filename, tuple)) \
-#                  and isinstance(filename[-1], str):
-                import os.path
+            if isinstance(filename, str):
                 filename = os.path.expandvars(filename)
                 filename = os.path.expanduser(filename)
@@ -73 +98 @@
                     if rcParams['verbose']:
                         asaplog.push(s)
-                        #print asaplog.pop().strip()
                         print_log('ERROR')
                         return
                     raise IOError(s)
-                if os.path.isdir(filename) \
-                    and not os.path.exists(filename+'/table.f1'):
-                    # crude check if asap table
-                    if os.path.exists(filename+'/table.info'):
-                        ondisk = rcParams['scantable.storage'] == 'disk'
-                        Scantable.__init__(self, filename, ondisk)
-                        if unit is not None:
-                            self.set_fluxunit(unit)
-                        # do not reset to the default freqframe
-                        #self.set_freqframe(rcParams['scantable.freqframe'])
+                if is_scantable(filename):
+                    ondisk = rcParams['scantable.storage'] == 'disk'
+                    Scantable.__init__(self, filename, ondisk)
+                    if unit is not None:
+                        self.set_fluxunit(unit)
+                    # do not reset to the default freqframe
+                    #self.set_freqframe(rcParams['scantable.freqframe'])
+                elif os.path.isdir(filename) \
+                         and not os.path.exists(filename+'/table.f1'):
+                    msg = "The given file '%s'is not a valid " \
+                          "asap table." % (filename)
+                    if rcParams['verbose']:
+                        #print msg
+                        asaplog.push( msg )
+                        print_log( 'ERROR' )
+                        return
                     else:
-                        msg = "The given file '%s'is not a valid " \
-                              "asap table." % (filename)
-                        if rcParams['verbose']:
-                            #print msg
-                            asaplog.push( msg )
-                            print_log( 'ERROR' )
-                            return
-                        else:
-                            raise IOError(msg)
+                        raise IOError(msg)
                 else:
                     self._fill([filename], unit, average, getpt, antenna)
@@ -102 +124 @@
                   and isinstance(filename[-1], str):
                 self._fill(filename, unit, average, getpt, antenna)
+        self.parallactify(parallactify)
         self._add_history("scantable", varlist)
         print_log()
 
+    #@print_log_dec
     def save(self, name=None, format=None, overwrite=False):
         """
@@ -119 +143 @@
                                        'MS2' (saves as an aips++
                                               MeasurementSet V2)
-                                       'FITS' (save as image FITS - not 
+                                       'FITS' (save as image FITS - not
                                                readable by class)
                                        'CLASS' (save as FITS readable by CLASS)
@@ -130 +154 @@
         """
         from os import path
-        if format is None: format = rcParams['scantable.save']
+        format = format or rcParams['scantable.save']
         suffix = '.'+format.lower()
         if name is None or name == "":
@@ -203 +227 @@
             else: raise
         try:
-            bsel = self.get_selection()
-            sel = selector()
-            sel.set_scans(allscans)
-            self.set_selection(bsel+sel)
-            scopy = self._copy()
-            self.set_selection(bsel)
-            return scantable(scopy)
+            sel = selector(scans=allscans)
+            return self._select_copy(sel)
         except RuntimeError:
             if rcParams['verbose']:
@@ -219 +238 @@
                 raise
 
+    def _select_copy(self, selection):
+        orig = self.get_selection()
+        self.set_selection(orig+selection)
+        cp = self.copy()
+        self.set_selection(orig)
+        return cp
 
     def get_scan(self, scanid=None):
@@ -253 +278 @@
             if type(scanid) is str:
                 sel.set_name(scanid)
-                self.set_selection(bsel+sel)
-                scopy = self._copy()
-                self.set_selection(bsel)
-                return scantable(scopy)
+                return self._select_copy(sel)
             elif type(scanid) is int:
                 sel.set_scans([scanid])
-                self.set_selection(bsel+sel)
-                scopy = self._copy()
-                self.set_selection(bsel)
-                return scantable(scopy)
+                return self._select_copy(sel)
             elif type(scanid) is list:
                 sel.set_scans(scanid)
-                self.set_selection(sel)
-                scopy = self._copy()
-                self.set_selection(bsel)
-                return scantable(scopy)
+                return self._select_copy(sel)
             else:
                 msg = "Illegal scanid type, use 'int' or 'list' if ints."
@@ -294 +310 @@
             filename:    the name of a file to write the putput to
                          Default - no file output
-            verbose:     print extra info such as the frequency table
-                         The default (False) is taken from .asaprc
         """
         info = Scantable._summary(self, True)
-        #if verbose is None: verbose = rcParams['scantable.verbosesummary']
         if filename is not None:
             if filename is "":
@@ -328 +341 @@
         """Return the spectrum for the current row in the scantable as a list.
         Parameters:
-             rowno:   the row number to retrieve the spectrum from        
+             rowno:   the row number to retrieve the spectrum from
         """
         return self._getspectrum(rowno)
@@ -335 +348 @@
         """Return the mask for the current row in the scantable as a list.
         Parameters:
-             rowno:   the row number to retrieve the mask from        
+             rowno:   the row number to retrieve the mask from
         """
         return self._getmask(rowno)
@@ -343 +356 @@
         Parameters:
              spec:   the spectrum
-             rowno:    the row number to set the spectrum for        
+             rowno:    the row number to set the spectrum for
         """
         assert(len(spec) == self.nchan())
         return self._setspectrum(spec, rowno)
+
+    def get_coordinate(self, rowno):
+        """Return the (spectral) coordinate for a a given 'rowno'.
+        NOTE:
+            * This coordinate is only valid until a scantable method modifies
+              the frequency axis.
+            * This coordinate does contain the original frequency set-up
+              NOT the new frame. The conversions however are done using the user
+              specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate,
+              use scantable.freq_align first. Without it there is no closure,
+              i.e.
+              c = myscan.get_coordinate(0)
+              c.to_frequency(c.get_reference_pixel()) != c.get_reference_value()
+
+        Parameters:
+             rowno:    the row number for the spectral coordinate
+
+        """
+        return coordinate(Scantable.get_coordinate(self, rowno))
 
     def get_selection(self):
@@ -360 +392 @@
         return selector(self._getselection())
 
-    def set_selection(self, selection=selector()):
+    def set_selection(self, selection=None, **kw):
         """
         Select a subset of the data. All following operations on this scantable
         are only applied to thi selection.
         Parameters:
-            selection:    a selector object (default unset the selection)
+            selection:    a selector object (default unset the selection),
+
+            or
+
+            any combination of
+            "pols", "ifs", "beams", "scans", "cycles", "name", "query"
+
         Examples:
             sel = selector()         # create a selection object
@@ -372 +410 @@
             scan.summary()           # will only print summary of scanno 0 an 3
             scan.set_selection()     # unset the selection
-        """
+            # or the equivalent
+            scan.set_selection(scans=[0,3])
+            scan.summary()           # will only print summary of scanno 0 an 3
+            scan.set_selection()     # unset the selection
+        """
+        if selection is None:
+            # reset
+            if len(kw) == 0:
+                selection = selector()
+            else:
+                # try keywords
+                for k in kw:
+                    if k not in selector.fields:
+                        raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields))
+                selection = selector(**kw)
         self._setselection(selection)
 
@@ -425 +477 @@
             scan.stats(stat='mean', mask=m)
         """
-        if mask == None:
-            mask = []
-        axes = ['Beam', 'IF', 'Pol', 'Time']
+        mask = mask or []
         if not self._check_ifs():
             raise ValueError("Cannot apply mask as the IFs have different "
@@ -441 +491 @@
         if not rtnabc: statvals = self._math._stats(self, mask, stat)
 
-        out = ''
-        axes = []
+        #def cb(i):
+        #    return statvals[i]
+
+        #return self._row_callback(cb, stat)
+
+        label=stat
+        #callback=cb
+        out = ""
+        #outvec = []
+        sep = '-'*50
         for i in range(self.nrow()):
-            axis = []
-            axis.append(self.getscan(i))
-            axis.append(self.getbeam(i))
-            axis.append(self.getif(i))
-            axis.append(self.getpol(i))
-            axis.append(self.getcycle(i))
-            axes.append(axis)
-            tm = self._gettime(i)
-            src = self._getsourcename(i)
             refstr = ''
             statunit= ''
@@ -459 +508 @@
                 if rtnabc:
                     statvals.append(qx['value'])
-                    #refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])'
                     refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])'
                     statunit= '['+qx['unit']+']'
                 else:
-                    #refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])'
                     refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])'
-                    #statunit= ' ['+qy['unit']+']'
-            out += 'Scan[%d] (%s) ' % (axis[0], src)
+
+            tm = self._gettime(i)
+            src = self._getsourcename(i)
+            out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
             out += 'Time[%s]:\n' % (tm)
-            if self.nbeam(-1) > 1: out +=  ' Beam[%d] ' % (axis[1])
-            if self.nif(-1) > 1: out +=  ' IF[%d] ' % (axis[2])
-            if self.npol(-1) > 1: out +=  ' Pol[%d] ' % (axis[3])
-            #out += '= %3.3f   ' % (statvals[i]) +refstr+'\n' 
+            if self.nbeam(-1) > 1:
+                out +=  ' Beam[%d] ' % (self.getbeam(i))
+            if self.nif(-1) > 1: out +=  ' IF[%d] ' % (self.getif(i))
+            if self.npol(-1) > 1: out +=  ' Pol[%d] ' % (self.getpol(i))
+            #outvec.append(callback(i))
+            #out += ('= %'+form) % (outvec[i]) +'   '+refstr+'\n' 
             out += ('= %'+form) % (statvals[i]) +'   '+refstr+'\n' 
-            out +=  "--------------------------------------------------\n"
+            out +=  sep+"\n"
 
         if rcParams['verbose']:
@@ -484 +535 @@
             tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats'
             f=open(tmpfile,'w')
-            print >> f, "--------------------------------------------------"
-            print >> f, " ", stat, statunit
-            print >> f, "--------------------------------------------------"
+            print >> f, sep
+            print >> f, ' %s %s' % (label, statunit)
+            print >> f, sep
             print >> f, out
             f.close()
@@ -492 +543 @@
             x=f.readlines()
             f.close()
-            for xx in x:
-                asaplog.push( xx, False )
+            blanc=''
+            asaplog.push(blanc.join(x), False)
+            #for xx in x:
+            #    asaplog.push( xx, False )
             print_log()
-        #else:
-            #retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
-            #           'axes' : axes,
-            #           'data': statvals}
         return statvals
 
@@ -541 +590 @@
         return list(Scantable.get_column_names(self))
 
-    def get_tsys(self):
+    def get_tsys(self, row=-1):
         """
         Return the System temperatures.
@@ -547 +596 @@
             a list of Tsys values for the current selection
         """
-
+        if row > -1:
+            return self._get_column(self._gettsys, row)
         return self._row_callback(self._gettsys, "Tsys")
 
+
+    def get_weather(self, row=-1):
+        values = self._get_column(self._get_weather, row)
+        if row > -1:
+            return {'temperature': values[0],
+                    'pressure': values[1], 'humidity' : values[2],
+                    'windspeed' : values[3], 'windaz' : values[4]
+                    }
+        else:
+            out = []
+            for r in values:
+
+                out.append({'temperature': r[0],
+                            'pressure': r[1], 'humidity' : r[2],
+                            'windspeed' : r[3], 'windaz' : r[4]
+                    })
+            return out
+
     def _row_callback(self, callback, label):
-        axes = []
-        axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
         out = ""
         outvec = []
+        sep = '-'*50
         for i in range(self.nrow()):
-            axis = []
-            axis.append(self.getscan(i))
-            axis.append(self.getbeam(i))
-            axis.append(self.getif(i))
-            axis.append(self.getpol(i))
-            axis.append(self.getcycle(i))
-            axes.append(axis)
             tm = self._gettime(i)
             src = self._getsourcename(i)
-            out += 'Scan[%d] (%s) ' % (axis[0], src)
+            out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
             out += 'Time[%s]:\n' % (tm)
-            if self.nbeam(-1) > 1: out +=  ' Beam[%d] ' % (axis[1])
-            if self.nif(-1) > 1: out +=  ' IF[%d] ' % (axis[2])
-            if self.npol(-1) > 1: out +=  ' Pol[%d] ' % (axis[3])
+            if self.nbeam(-1) > 1:
+                out +=  ' Beam[%d] ' % (self.getbeam(i))
+            if self.nif(-1) > 1: out +=  ' IF[%d] ' % (self.getif(i))
+            if self.npol(-1) > 1: out +=  ' Pol[%d] ' % (self.getpol(i))
             outvec.append(callback(i))
             out += '= %3.3f\n' % (outvec[i])
-            out +=  "--------------------------------------------------\n"
+            out +=  sep+'\n'
         if rcParams['verbose']:
-            asaplog.push("--------------------------------------------------")
+            asaplog.push(sep)
             asaplog.push(" %s" % (label))
-            asaplog.push("--------------------------------------------------")
+            asaplog.push(sep)
             asaplog.push(out)
             print_log()
-        # disabled because the vector seems more useful
-        #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
         return outvec
 
@@ -624 +683 @@
             none
         """
-        return self._get_column(self._getinttime, row)        
-        
+        return self._get_column(self._getinttime, row)
+
 
     def get_sourcename(self, row=-1):
@@ -674 +733 @@
         """
         Get a list of Positions on the sky (direction) for the observations.
-        Return a float for each integration in the scantable.
+        Return a string for each integration in the scantable.
         Parameters:
             row:    row no of integration. Default -1 return all rows
@@ -693 +752 @@
         return self._get_column(self._getdirectionvec, row)
 
+    #@print_log_dec
     def set_unit(self, unit='channel'):
         """
@@ -708 +768 @@
         self._add_history("set_unit", varlist)
 
+    #@print_log_dec
     def set_instrument(self, instr):
         """
@@ -719 +780 @@
         print_log()
 
+    #@print_log_dec
     def set_feedtype(self, feedtype):
         """
@@ -729 +791 @@
         print_log()
 
+    #@print_log_dec
     def set_doppler(self, doppler='RADIO'):
         """
@@ -742 +805 @@
         print_log()
 
+    #@print_log_dec
     def set_freqframe(self, frame=None):
         """
@@ -747 +811 @@
         Parameters:
             frame:   an optional frame type, default 'LSRK'. Valid frames are:
-                     'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
+                     'TOPO', 'LSRD', 'LSRK', 'BARY',
                      'GEO', 'GALACTO', 'LGROUP', 'CMB'
         Examples:
             scan.set_freqframe('BARY')
         """
-        if frame is None: frame = rcParams['scantable.freqframe']
-        varlist = vars()
-        valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
+        frame = frame or rcParams['scantable.freqframe']
+        varlist = vars()
+        # "REST" is not implemented in casacore
+        #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
+        #           'GEO', 'GALACTO', 'LGROUP', 'CMB']
+        valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \
                    'GEO', 'GALACTO', 'LGROUP', 'CMB']
 
@@ -829 +896 @@
         """
         varlist = vars()
-        if mask is None:
-            mask = []
+        mask = mask or []
         try:
             self._flag(mask, unflag)
@@ -883 +949 @@
             else: raise
         self._add_history("clip", varlist)
-        
-    def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
+
+    #@print_log_dec
+    def lag_flag(self, start, end, unit="MHz", insitu=None):
+    #def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
         """
         Flag the data in 'lag' space by providing a frequency to remove.
-        Flagged data in the scantable gets set to 0.0 before the fft.
+        Flagged data in the scantable gets interpolated over the region.
         No taper is applied.
         Parameters:
-            frequency:    the frequency (really a period within the bandwidth) 
-                          to remove
-            width:        the width of the frequency to remove, to remove a 
-                          range of frequencies around the centre.
-            unit:         the frequency unit (default "GHz")
+            start:    the start frequency (really a period within the
+                      bandwidth)  or period to remove
+            end:      the end frequency or period to remove
+            unit:     the frequency unit (default "MHz") or "" for
+                      explicit lag channels
         Notes:
-            It is recommended to flag edges of the band or strong 
+            It is recommended to flag edges of the band or strong
             signals beforehand.
         """
@@ -902 +970 @@
         self._math._setinsitu(insitu)
         varlist = vars()
-        base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
-        if not base.has_key(unit):
+        base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.}
+        if not (unit == "" or base.has_key(unit)):
             raise ValueError("%s is not a valid unit." % unit)
         try:
-            s = scantable(self._math._lag_flag(self, frequency*base[unit],
-                                               width*base[unit]))
+            if unit == "":
+                s = scantable(self._math._lag_flag(self, start, end, "lags"))
+            else:
+                s = scantable(self._math._lag_flag(self, start*base[unit],
+                                                   end*base[unit], "frequency"))
         except RuntimeError, msg:
             if rcParams['verbose']:
@@ -923 +994 @@
             return s
 
-
+    #@print_log_dec
     def create_mask(self, *args, **kwargs):
         """
@@ -952 +1023 @@
             c)
             mask only channel 400
-            msk =  scan.create_mask([400, 400])
-        """
-        row = 0
-        if kwargs.has_key("row"):
-            row = kwargs.get("row")
+            msk =  scan.create_mask([400])
+        """
+        row = kwargs.get("row", 0)
         data = self._getabcissa(row)
         u = self._getcoordinfo()[0]
@@ -973 +1042 @@
              and args or args[0]
         for window in ws:
-            if (len(window) != 2 or window[0] > window[1] ):
-                raise TypeError("A window needs to be defined as [min, max]")
+            if len(window) == 1:
+                window = [window[0], window[0]]
+            if len(window) == 0 or  len(window) > 2:
+                raise ValueError("A window needs to be defined as [start(, end)]")
+            if window[0] > window[1]:
+                tmp = window[0]
+                window[0] = window[1]
+                window[1] = tmp
             for i in range(n):
                 if data[i] >= window[0] and data[i] <= window[1]:
@@ -1127 +1202 @@
             source and IF basis, use scantable.set_selection() before using
             this function.
-            # provide your scantable is call scan
+            # provide your scantable is called scan
             selection = selector()
             selection.set_name("ORION*")
@@ -1188 +1263 @@
 
     def shift_refpix(self, delta):
-        """
-        Shift the reference pixel of the Spectra Coordinate by an 
-        integer amount.
-        Parameters:
-            delta:   the amount to shift by
+        """
+        Shift the reference pixel of the Spectra Coordinate by an
+        integer amount.
+        Parameters:
+            delta:   the amount to shift by
         Note:
-            Be careful using this with broadband data.
-        """
-        Scantable.shift(self, delta)
+            Be careful using this with broadband data.
+        """
+        Scantable.shift_refpix(self, delta)
 
     def history(self, filename=None):
@@ -1249 +1324 @@
     # Maths business
     #
-
+    #@print_log_dec
     def average_time(self, mask=None, scanav=False, weight='tint', align=False):
         """
@@ -1275 +1350 @@
         """
         varlist = vars()
-        if weight is None: weight = 'TINT'
-        if mask is None: mask = ()
-        if scanav: scanav = "SCAN"
-        else: scanav = "NONE"
+        weight = weight or 'TINT'
+        mask = mask or ()
+        scanav = (scanav and 'SCAN') or 'NONE'
         scan = (self, )
         try:
@@ -1302 +1376 @@
         return s
 
+    #@print_log_dec
     def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
         """
@@ -1321 +1396 @@
         self._math._setinsitu(insitu)
         varlist = vars()
-        if jyperk is None: jyperk = -1.0
-        if d is None: d = -1.0
-        if eta is None: eta = -1.0
+        jyperk = jyperk or -1.0
+        d = d or -1.0
+        eta = eta or -1.0
         s = scantable(self._math._convertflux(self, d, eta, jyperk))
         s._add_history("convert_flux", varlist)
@@ -1330 +1405 @@
         else: return s
 
+    #@print_log_dec
     def gain_el(self, poly=None, filename="", method="linear", insitu=None):
         """
@@ -1373 +1449 @@
         self._math._setinsitu(insitu)
         varlist = vars()
-        if poly is None:
-            poly = ()
+        poly = poly or ()
         from os.path import expandvars
         filename = expandvars(filename)
@@ -1380 +1455 @@
         s._add_history("gain_el", varlist)
         print_log()
-        if insitu: self._assign(s)
-        else: return s
-
+        if insitu:
+            self._assign(s)
+        else:
+            return s
+
+    #@print_log_dec
     def freq_align(self, reftime=None, method='cubic', insitu=None):
         """
@@ -1401 +1479 @@
         self._math._setinsitu(insitu)
         varlist = vars()
-        if reftime is None: reftime = ""
+        reftime = reftime or ""
         s = scantable(self._math._freq_align(self, reftime, method))
         s._add_history("freq_align", varlist)
@@ -1408 +1486 @@
         else: return s
 
-    def opacity(self, tau, insitu=None):
+    #@print_log_dec
+    def opacity(self, tau=None, insitu=None):
         """
         Apply an opacity correction. The data
         and Tsys are multiplied by the correction factor.
         Parameters:
-            tau:         Opacity from which the correction factor is
+            tau:         (list of) opacity from which the correction factor is
                          exp(tau*ZD)
-                         where ZD is the zenith-distance
+                         where ZD is the zenith-distance.
+                         If a list is provided, it has to be of length nIF,
+                         nIF*nPol or 1 and in order of IF/POL, e.g.
+                         [opif0pol0, opif0pol1, opif1pol0 ...]
+                         if tau is `None` the opacities are determined from a
+                         model.
             insitu:      if False a new scantable is returned.
                          Otherwise, the scaling is done in-situ
@@ -1423 +1507 @@
         self._math._setinsitu(insitu)
         varlist = vars()
+        if not hasattr(tau, "__len__"):
+            tau = [tau]
         s = scantable(self._math._opacity(self, tau))
         s._add_history("opacity", varlist)
@@ -1429 +1515 @@
         else: return s
 
+    #@print_log_dec
     def bin(self, width=5, insitu=None):
         """
@@ -1444 +1531 @@
         s._add_history("bin", varlist)
         print_log()
-        if insitu: self._assign(s)
-        else: return s
-
-
+        if insitu:
+            self._assign(s)
+        else:
+            return s
+
+    #@print_log_dec
     def resample(self, width=5, method='cubic', insitu=None):
         """
@@ -1470 +1559 @@
         else: return s
 
-
+    #@print_log_dec
     def average_pol(self, mask=None, weight='none'):
         """
@@ -1482 +1571 @@
         """
         varlist = vars()
-        if mask is None:
-            mask = ()
+        mask = mask or ()
         s = scantable(self._math._averagepol(self, mask, weight.upper()))
         s._add_history("average_pol", varlist)
@@ -1489 +1577 @@
         return s
 
+    #@print_log_dec
     def average_beam(self, mask=None, weight='none'):
         """
@@ -1500 +1589 @@
         """
         varlist = vars()
-        if mask is None:
-            mask = ()
+        mask = mask or ()
         s = scantable(self._math._averagebeams(self, mask, weight.upper()))
         s._add_history("average_beam", varlist)
@@ -1507 +1595 @@
         return s
 
+    def parallactify(self, pflag):
+        """
+        Set a flag to inidcate whether this data should be treated as having
+        been 'parallactified' (total phase == 0.0)
+        Parameters:
+            pflag:  Bool inidcating whether to turn this on (True) or
+                    off (False)
+        """
+        varlist = vars()
+        self._parallactify(pflag)
+        self._add_history("parallactify", varlist)
+
+    #@print_log_dec
     def convert_pol(self, poltype=None):
         """
         Convert the data to a different polarisation type.
+        Note that you will need cross-polarisation terms for most conversions.
         Parameters:
             poltype:    The new polarisation type. Valid types are:
-                        "linear", "stokes" and "circular"
+                        "linear", "circular", "stokes" and "linpol"
         """
         varlist = vars()
@@ -1530 +1632 @@
         return s
 
-    #def smooth(self, kernel="hanning", width=5.0, insitu=None):
-    def smooth(self, kernel="hanning", width=5.0, plot=False, insitu=None):
+    #@print_log_dec
+    def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None):
         """
         Smooth the spectrum by the specified kernel (conserving flux).
         Parameters:
             kernel:     The type of smoothing kernel. Select from
-                        'hanning' (default), 'gaussian', 'boxcar' and
-                        'rmedian'
+                        'hanning' (default), 'gaussian', 'boxcar', 'rmedian'
+                        or 'poly'
             width:      The width of the kernel in pixels. For hanning this is
                         ignored otherwise it defauls to 5 pixels.
                         For 'gaussian' it is the Full Width Half
                         Maximum. For 'boxcar' it is the full width.
-                        For 'rmedian' it is the half width.
+                        For 'rmedian' and 'poly' it is the half width.
+            order:      Optional parameter for 'poly' kernel (default is 2), to
+                        specify the order of the polnomial. Ignored by all other
+                        kernels.
             plot:       plot the original and the smoothed spectra.
                         In this each indivual fit has to be approved, by
@@ -1558 +1663 @@
         if plot: orgscan = self.copy()
 
-        s = scantable(self._math._smooth(self, kernel.lower(), width))
+        s = scantable(self._math._smooth(self, kernel.lower(), width, order))
         s._add_history("smooth", varlist)
 
@@ -1601 +1706 @@
         else: return s
 
-
-    def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
+    #@print_log_dec
+    def poly_baseline(self, mask=None, order=0, plot=False, uselin=False,
+                      insitu=None):
         """
         Return a scan which has been baselined (all rows) by a polynomial.
@@ -1833 +1939 @@
             return workscan
 
+    #@print_log_dec
     def rotate_linpolphase(self, angle):
         """
@@ -1849 +1956 @@
         return
 
-
+    #@print_log_dec
     def rotate_xyphase(self, angle):
         """
@@ -1866 +1973 @@
         return
 
+    #@print_log_dec
     def swap_linears(self):
         """
-        Swap the linear polarisations XX and YY, or better the first two 
+        Swap the linear polarisations XX and YY, or better the first two
         polarisations as this also works for ciculars.
         """
@@ -1877 +1985 @@
         return
 
+    #@print_log_dec
     def invert_phase(self):
         """
@@ -1887 +1996 @@
         return
 
+    #@print_log_dec
     def add(self, offset, insitu=None):
         """
@@ -1907 +2017 @@
             return s
 
+    #@print_log_dec
     def scale(self, factor, tsys=True, insitu=None):
         """
@@ -1972 +2083 @@
         self._setsourcetype(stype)
         self.set_selection(basesel)
-        s._add_history("set_sourcetype", varlist)
-
+        self._add_history("set_sourcetype", varlist)
+
+    #@print_log_dec
     def auto_quotient(self, preserve=True, mode='paired', verify=False):
         """
@@ -1984 +2096 @@
                             preserve: Output = Toff * (on/off) - Toff
                             remove:   Output = Toff * (on/off) - Ton
-            mode:           the on/off detection mode 
+            mode:           the on/off detection mode
                             'paired' (default)
                             identifies 'off' scans by the
@@ -2017 +2129 @@
         return s
 
+    #@print_log_dec
     def mx_quotient(self, mask = None, weight='median', preserve=True):
         """
@@ -2028 +2141 @@
                             remove:   Output = Toff * (on/off) - Ton
         """
-        if mask is None: mask = ()
+        mask = mask or ()
         varlist = vars()
         on = scantable(self._math._mx_extract(self, 'on'))
@@ -2039 +2152 @@
         return q
 
+    #@print_log_dec
     def freq_switch(self, insitu=None):
         """
@@ -2058 +2172 @@
         else: return s
 
+    #@print_log_dec
     def recalc_azel(self):
         """
@@ -2071 +2186 @@
         return
 
+    #@print_log_dec
     def __add__(self, other):
         """
@@ -2077 +2193 @@
         return self._operation( other, "ADD" )
 
+    #@print_log_dec
     def __sub__(self, other):
         """
@@ -2083 +2200 @@
         return self._operation( other, 'SUB' )
 
+    #@print_log_dec
     def __mul__(self, other):
         """
@@ -2089 +2207 @@
         return self._operation( other, 'MUL' )
 
+    #@print_log_dec
     def __div__(self, other):
         """
@@ -2120 +2239 @@
         basesel = self.get_selection()
         for i in range(self.nrow()):
-            sel = selector()+basesel
-            sel.set_scans(self.getscan(i))
-            sel.set_beams(self.getbeam(i))
-            sel.set_ifs(self.getif(i))
-            sel.set_polarisations(self.getpol(i))
-            self.set_selection(sel)
+            sel = self.get_row_selector(i)
+            self.set_selection(basesel+sel)
             nans = numpy.isnan(self._getspectrum(0))
         if numpy.any(nans):
@@ -2131 +2246 @@
             self.flag(bnans)
         self.set_selection(basesel)
-        
+
+    def get_row_selector(self, rowno):
+        return selector(beams=self.getbeam(rowno),
+                        ifs=self.getif(rowno),
+                        pols=self.getpol(rowno),
+                        scans=self.getscan(rowno),
+                        cycles=self.getcycle(rowno))
 
     def _add_history(self, funcname, parameters):

branches/alma/python/selector.py

@@ -7 +7 @@
     scantables to specific rows.
     """
-    def __init(self):
-        _selector.__init__(self)
+    fields = ["pols", "ifs", "beams", "scans", "cycles", "name", "query"]
+
+    def __init__(self, *args, **kw):
+        if len(args) == 1:
+            if isinstance(args[0], self.__class__) \
+               or isinstance(args[0], _selector):
+                _selector.__init__(self, args[0])
+            else:
+                raise TypeError("Argument can only be a selector object")
+        else:
+            _selector.__init__(self)
+            for k,v  in kw.items():
+                if k in self.fields:
+                    func = getattr(self, "set_%s" % k)
+                    func(v)
 
     def reset(self):
@@ -45 +58 @@
         else:
             raise TypeError('Unknown pol type. Please use [0,1...] or ["XX","YY"...]')
-    
+
     # for the americans
     set_polarizations = set_polarisations
@@ -220 +233 @@
         Merge two selections.
         """
+        if self.is_empty():
+            return other
+        elif other.is_empty():
+            return self
         union = selector()
         gets = [[self._getscans(), other._getscans(), union._setscans],