source: trunk/python/__init__.py @ 733

"""
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.gui'         : [True, _validate_bool],
    'plotter.stacking'    : ['p', str],
    'plotter.panelling'   : ['s', str],
    'plotter.colours'     : ['', str],
    'plotter.linestyles'  : ['', str],
    'plotter.decimate'    : [False, _validate_bool],
    'plotter.ganged'      : [True, _validate_bool],

    # 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

    # do we want a GUI or plot to a file
    plotter.gui                : True

    # default mode for colour stacking
    plotter.stacking           : Pol

    # default mode for panelling
    plotter.panelling          : scan

    # push panels together, to share axislabels
    plotter.ganged             : True

    # decimate the number of points plotted bya afactor of
    # nchan/1024
    plotter.decimate           : False

    # default colours/linestyles
    plotter.colours            :
    plotter.linestyles         :

    # 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


# workaround for ipython, which redirects this if banner=0 in ipythonrc
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__

# Logging
from asap._asap import Log as _asaplog
global asaplog
asaplog=_asaplog()
if rcParams['verbose']:
    asaplog.enable()
else:
    asaplog.disable()

def print_log():
    log = asaplog.pop()
    if len(log) and rcParams['verbose']: print log
    return

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']:
    from  asapplotter import *
    gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
    plotter = asapplotter(gui)
    del gui

__date__ = '$Date: 2005-11-24 03:12:33 +0000 (Thu, 24 Nov 2005) $'.split()[1]
__version__  = '1.2'

if rcParams['verbose']:
    def list_scans(t = scantable):
        import sys, 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

    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
                              (by name or number)
            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_sourcename  - get the source names of the scans
            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
            nscan           - the number of scans in the scantable
            nrow            - te number of integrations in the scantable
            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.
            auto_quotient   - return the on/off quotient with
                              automatic detection of the on/off scans
                              (matched pairs and 1 off - n on)
            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
            freq_switch     - perform frequency switching on the data
            stats           - Determine the specified statistic, e.g. 'min'
                              'max', 'rms' etc.
            stddev          - Determine the standard deviation of the current
                              beam/if/pol

     [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 [xmin,xmax,ymin,ymax]
            set_legend      - specify user labels for the legend indeces
            set_title       - specify user labels for the panel indeces
            set_abcissa     - specify a user label for the abcissa
            set_ordinate    - specify a user label for the ordinate
            set_layout      - specify the multi-panel layout (rows,cols)
            set_colors      - specify a set of colours to use
            set_linestyles  - specify a set of linestyles to use if only
                              using one color
            set_mask        - set a plotting mask for a specific polarization

    [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

def welcome():
    return """Welcome to ASAP v%s (%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__, __date__)