Index: tags/asap0002/python/__init__.py
===================================================================
--- tags/asap0002/python/__init__.py	(revision 584)
+++ tags/asap0002/python/__init__.py	(revision 584)
@@ -0,0 +1,394 @@
+"""
+This is the ATNF Single Dish Analysis package.
+
+"""
+import os,sys
+
+def _validate_bool(b):
+    'Convert b to a boolean or raise'
+    bl = b.lower()
+    if bl in ('f', 'no', 'false', '0', 0): return False
+    elif bl in ('t', 'yes', 'true', '1', 1): return True
+    else:
+        raise ValueError('Could not convert "%s" to boolean' % b)
+
+def _validate_int(s):
+    'convert s to int or raise'
+    try: return int(s)
+    except ValueError:
+        raise ValueError('Could not convert "%s" to int' % s)
+
+def _asap_fname():
+    """
+    Return the path to the rc file
+
+    Search order:
+
+     * current working dir
+     * environ var ASAPRC
+     * HOME/.asaprc
+     
+    """
+
+    fname = os.path.join( os.getcwd(), '.asaprc')
+    if os.path.exists(fname): return fname
+
+    if os.environ.has_key('ASAPRC'):
+        path =  os.environ['ASAPRC']
+        if os.path.exists(path):
+            fname = os.path.join(path, '.asaprc')
+            if os.path.exists(fname):
+                return fname
+
+    if os.environ.has_key('HOME'):
+        home =  os.environ['HOME']
+        fname = os.path.join(home, '.asaprc')
+        if os.path.exists(fname):
+            return fname
+    return None
+        
+
+defaultParams = {
+    # general
+    'verbose'             : [True, _validate_bool],
+    'useplotter'          : [True, _validate_bool],
+    'insitu'              : [True, _validate_bool],
+    
+    # plotting
+    'plotter.stacking'    : ['p', str],
+    'plotter.panelling'   : ['s', str],
+    
+    # scantable
+    'scantable.save'      : ['ASAP', str],
+    'scantable.autoaverage'      : [True, _validate_bool],
+    'scantable.freqframe' : ['LSRK', str],  #default frequency frame
+    'scantable.allaxes'   : [True, _validate_bool],  # apply action to all axes
+    'scantable.plotter'   : [True, _validate_bool], # use internal plotter
+    'scantable.verbosesummary'   : [False, _validate_bool]
+
+    # fitter
+    }
+
+def list_rcparameters():
+    
+    print """
+    # general
+    # print verbose output
+    verbose                    : True
+
+    # preload a default plotter
+    useplotter                 : True
+
+    # apply operations on the input scantable or return new one
+    insitu                     : True
+    
+    # plotting
+    # default mode for colour stacking
+    plotter.stacking           : Pol
+
+    # default mode for panelling
+    plotter.panelling          : scan
+
+    # scantable
+    # default ouput format when saving
+    scantable.save             : ASAP
+    # auto averaging on read
+    scantable.autoaverage      : True
+
+    # default frequency frame to set when function
+    # scantable.set_freqfrmae is called
+    scantable.freqframe        : LSRK
+
+    # apply action to all axes not just the cursor location
+    scantable.allaxes          : True 
+
+    # use internal plotter
+    scantable.plotter          : True
+
+    # Control the level of information printed by summary
+    scantable.verbosesummary   : False
+    
+    # Fitter    
+    """
+    
+def rc_params():
+    'Return the default params updated from the values in the rc file'
+    
+    fname = _asap_fname()
+    
+    if fname is None or not os.path.exists(fname):
+        message = 'could not find rc file; returning defaults'
+        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
+        #print message
+        return ret
+        
+    cnt = 0
+    for line in file(fname):
+        cnt +=1
+        line = line.strip()
+        if not len(line): continue
+        if line.startswith('#'): continue
+        tup = line.split(':',1)
+        if len(tup) !=2:
+            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
+            continue
+        
+        key, val = tup
+        key = key.strip()
+        if not defaultParams.has_key(key):
+            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
+            continue
+        
+        default, converter =  defaultParams[key]
+
+        ind = val.find('#')
+        if ind>=0: val = val[:ind]   # ignore trailing comments
+        val = val.strip()
+        try: cval = converter(val)   # try to convert to proper type or raise
+        except Exception, msg:
+            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
+            continue
+        else:
+            # Alles Klar, update dict
+            defaultParams[key][0] = cval
+
+    # strip the conveter funcs and return
+    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
+    print ('loaded rc file %s'%fname)
+
+    return ret
+
+
+# this is the instance used by the asap classes
+rcParams = rc_params() 
+
+rcParamsDefault = dict(rcParams.items()) # a copy
+
+def rc(group, **kwargs):
+    """
+    Set the current rc params.  Group is the grouping for the rc, eg
+    for scantable.save the group is 'scantable', for plotter.stacking, the
+    group is 'plotter', and so on.  kwargs is a list of attribute
+    name/value pairs, eg
+
+      rc('scantable', save='SDFITS')
+
+    sets the current rc params and is equivalent to
+    
+      rcParams['scantable.save'] = 'SDFITS'
+
+    Use rcdefaults to restore the default rc params after changes.
+    """
+
+    aliases = {}
+    
+    for k,v in kwargs.items():
+        name = aliases.get(k) or k
+        key = '%s.%s' % (group, name)
+        if not rcParams.has_key(key):
+            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
+        
+        rcParams[key] = v
+
+
+def rcdefaults():
+    """
+    Restore the default rc params - the ones that were created at
+    asap load time
+    """
+    rcParams.update(rcParamsDefault)
+
+
+def _is_sequence_or_number(param, ptype=int):
+    if isinstance(param,tuple) or isinstance(param,list):
+        out = True
+        for p in param:
+            out &= isinstance(p,ptype)
+        return out
+    elif isinstance(param, ptype):
+        return True
+    return False
+
+from asapfitter import *
+from asapreader import reader
+from asapmath import *
+from scantable import *
+from asaplinefind import *
+from asapfit import *
+
+from numarray import logical_and as mask_and
+from numarray import logical_or as mask_or
+from numarray import logical_not as mask_not
+
+if rcParams['useplotter']:
+    if os.environ.has_key('DISPLAY'):
+        print "Initialising asapplotter with the name 'plotter' ..."
+        import asapplotter 
+        plotter = asapplotter.asapplotter()
+    else:
+        print "No $DISPLAY set. Disabling plotter.\n"
+
+#from numarray ones,zeros
+
+
+__date__ = '$Date$'
+__version__  = '1.0'
+
+def list_scans(t = scantable):
+    import sys, types
+    #meta_t = type(t)
+    #if meta_t == types.InstanceType:
+    #    t = t.__class__
+    #elif meta_t not in [types.ClassType, types.TypeType]:
+    #    t = meta_t
+    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)
+
+def commands():
+    x = """    
+    [The scan container]
+        scantable           - a container for integrations/scans
+                              (can open asap/rpfits/sdfits and ms files)
+            copy            - returns a copy of a scan
+            get_scan        - gets a specific scan out of a scantable
+            summary         - print info about the scantable contents
+            set_cursor      - set a specific Beam/IF/Pol 'cursor' for
+                              further use
+            get_cursor      - print out the current cursor position
+            stats           - get specified statistic of the spectra in
+                              the scantable
+            stddev          - get the standard deviation of the spectra
+                              in the scantable
+            get_tsys        - get the TSys
+            get_time        - get the timestamps of the integrations
+            get_unit        - get the currnt unit
+            set_unit        - set the abcissa unit to be used from this
+                              point on
+            get_abcissa     - get the abcissa values and name for a given
+                              row (time)
+            set_freqframe   - set the frame info for the Spectral Axis
+                              (e.g. 'LSRK')
+            set_doppler     - set the doppler to be used from this point on
+            set_instrument  - set the instrument name
+            get_fluxunit    - get the brightness flux unit
+            set_fluxunit    - set the brightness flux unit
+            create_mask     - return an mask in the current unit
+                              for the given region. The specified regions
+                              are NOT masked
+            get_restfreqs   - get the current list of rest frequencies
+            set_restfreqs   - set a list of rest frequencies
+            lines           - print list of known spectral lines
+            flag_spectrum   - flag a whole Beam/IF/Pol
+            save            - save the scantable to disk as either 'ASAP'
+                              or 'SDFITS'
+            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
+            history         - print the history of the scantable
+            get_fit         - get a fit which has been stored witnh the data
+            average_time    - return the (weighted) time average of a scan 
+                              or a list of scans
+            average_pol     - average the polarisations together.
+                              The dimension won't be reduced and
+                              all polarisations will contain the
+                              averaged spectrum.
+            quotient        - return the on/off quotient
+            scale           - return a scan scaled by a given factor
+            add             - return a scan with given value added 
+            bin             - return a scan with binned channels
+            resample        - return a scan with resampled channels
+            smooth          - return the spectrally smoothed scan
+            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
+            auto_poly_baseline - automatically fit a polynomial baseline 
+            gain_el         - apply gain-elevation correction
+            opacity         - apply opacity correction
+            convert_flux    - convert to and from Jy and Kelvin brightness
+                              units
+            freq_align      - align spectra in frequency frame
+            rotate_xyphase  - rotate XY phase of cross correlation
+            rotate_linpolphase - rotate the phase of the complex
+                                 polarization O=Q+iU correlation
+     [Math] Mainly functions which operate on more than one scantable
+
+            average_time    - return the (weighted) time average 
+                              of a list of scans
+            quotient        - return the on/off quotient
+            simple_math     - simple mathematical operations on two scantables,
+                              'add', 'sub', 'mul', 'div'
+     [Fitting]
+        fitter
+            auto_fit        - return a scan where the function is
+                              applied to all Beams/IFs/Pols.
+            commit          - return a new scan where the fits have been
+                              commited.
+            fit             - execute the actual fitting process
+            store_fit       - store the fit paramaters in the data (scantable)
+            get_chi2        - get the Chi^2
+            set_scan        - set the scantable to be fit
+            set_function    - set the fitting function
+            set_parameters  - set the parameters for the function(s), and
+                              set if they should be held fixed during fitting
+            set_gauss_parameters - same as above but specialised for individual
+                                   gaussian components
+            get_parameters  - get the fitted parameters
+            plot            - plot the resulting fit and/or components and
+                              residual
+    [Plotter]
+        asapplotter         - a plotter for asap, default plotter is
+                              called 'plotter'
+            plot            - plot a (list of) scantable
+            save            - save the plot to a file ('png' ,'ps' or 'eps')
+            set_mode        - set the state of the plotter, i.e.
+                              what is to be plotted 'colour stacked'
+                              and what 'panelled'
+            set_cursor      - only plot a selected part of the data
+            set_range       - set a 'zoom' window
+            set_legend      - specify user labels for the legend indeces
+            set_title       - specify user labels for the panel indeces
+            set_ordinate    - specify a user label for the ordinate
+            set_abcissa     - specify a user label for the abcissa
+            set_layout      - specify the multi-panel layout (rows,cols)
+            
+    [Reading files]
+        reader              - access rpfits/sdfits files
+            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
+        del                 - delete the given variable from memory
+        range               - create a list of values, e.g.
+                              range(3) = [0,1,2], range(2,5) = [2,3,4]
+        help                - print help for one of the listed functions
+        execfile            - execute an asap script, e.g. execfile('myscript')
+        list_rcparameters   - print out a list of possible values to be
+                              put into $HOME/.asaprc
+        mask_and,mask_or,
+        mask_not            - boolean operations on masks created with
+                              scantable.create_mask
+        
+    Note:
+        How to use this with help:
+                                         # function 'summary'
+        [xxx] is just a category
+        Every 'sub-level' in this list should be replaces by a '.' Period when
+        using help 
+        Example:
+            ASAP> help scantable # to get info on ths scantable
+            ASAP> help scantable.summary # to get help on the scantable's
+            ASAP> help average_time
+
+    """
+    print x
+    return
+
+print """Welcome to ASAP v%s - the ATNF Spectral Analysis Package
+
+Please report any bugs to:
+asap@atnf.csiro.au
+
+[IMPORTANT: ASAP is 0-based]
+Type commands() to get a list of all available ASAP commands.
+""" % (__version__)
