source: trunk/python/__init__.py @ 715

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[100]1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
[226]5import os,sys
6
[513]7def _validate_bool(b):
[226]8    'Convert b to a boolean or raise'
9    bl = b.lower()
10    if bl in ('f', 'no', 'false', '0', 0): return False
11    elif bl in ('t', 'yes', 'true', '1', 1): return True
12    else:
13        raise ValueError('Could not convert "%s" to boolean' % b)
14
[513]15def _validate_int(s):
[226]16    'convert s to int or raise'
17    try: return int(s)
18    except ValueError:
19        raise ValueError('Could not convert "%s" to int' % s)
20
[513]21def _asap_fname():
[226]22    """
23    Return the path to the rc file
24
25    Search order:
26
27     * current working dir
28     * environ var ASAPRC
[274]29     * HOME/.asaprc
[706]30
[226]31    """
32
33    fname = os.path.join( os.getcwd(), '.asaprc')
34    if os.path.exists(fname): return fname
35
36    if os.environ.has_key('ASAPRC'):
37        path =  os.environ['ASAPRC']
38        if os.path.exists(path):
39            fname = os.path.join(path, '.asaprc')
40            if os.path.exists(fname):
41                return fname
42
43    if os.environ.has_key('HOME'):
44        home =  os.environ['HOME']
45        fname = os.path.join(home, '.asaprc')
46        if os.path.exists(fname):
47            return fname
48    return None
49
[706]50
[226]51defaultParams = {
52    # general
[513]53    'verbose'             : [True, _validate_bool],
54    'useplotter'          : [True, _validate_bool],
[542]55    'insitu'              : [True, _validate_bool],
[706]56
[226]57    # plotting
[706]58    'plotter.gui'         : [True, _validate_bool],
[226]59    'plotter.stacking'    : ['p', str],
60    'plotter.panelling'   : ['s', str],
[700]61    'plotter.colours'     : ['', str],
62    'plotter.linestyles'  : ['', str],
[710]63    'plotter.decimate'    : [False, _validate_bool],
64    'plotter.ganged'      : [True, _validate_bool],
65
[226]66    # scantable
67    'scantable.save'      : ['ASAP', str],
[513]68    'scantable.autoaverage'      : [True, _validate_bool],
[226]69    'scantable.freqframe' : ['LSRK', str],  #default frequency frame
[513]70    'scantable.allaxes'   : [True, _validate_bool],  # apply action to all axes
71    'scantable.plotter'   : [True, _validate_bool], # use internal plotter
72    'scantable.verbosesummary'   : [False, _validate_bool]
[226]73
74    # fitter
75    }
76
[255]77def list_rcparameters():
[706]78
[255]79    print """
80    # general
81    # print verbose output
[466]82    verbose                    : True
[255]83
84    # preload a default plotter
[466]85    useplotter                 : True
[255]86
87    # apply operations on the input scantable or return new one
[542]88    insitu                     : True
[706]89
90    # plotting
[710]91
[706]92    # do we want a GUI or plot to a file
93    plotter.gui                : True
[710]94
[255]95    # default mode for colour stacking
[552]96    plotter.stacking           : Pol
[255]97
98    # default mode for panelling
[552]99    plotter.panelling          : scan
[255]100
[710]101    # push panels together, to shar axislabels
102    plotter.ganged             : True
103
[700]104    # default colours/linestyles
105    plotter.colours            :
[706]106    plotter.linestyles         :
[700]107
[255]108    # scantable
109    # default ouput format when saving
[552]110    scantable.save             : ASAP
[255]111    # auto averaging on read
[466]112    scantable.autoaverage      : True
[255]113
114    # default frequency frame to set when function
115    # scantable.set_freqfrmae is called
[552]116    scantable.freqframe        : LSRK
[255]117
118    # apply action to all axes not just the cursor location
[706]119    scantable.allaxes          : True
[255]120
121    # use internal plotter
[466]122    scantable.plotter          : True
[255]123
[381]124    # Control the level of information printed by summary
[466]125    scantable.verbosesummary   : False
[706]126
127    # Fitter
[255]128    """
[706]129
[226]130def rc_params():
131    'Return the default params updated from the values in the rc file'
[706]132
[513]133    fname = _asap_fname()
[706]134
[226]135    if fname is None or not os.path.exists(fname):
136        message = 'could not find rc file; returning defaults'
137        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
138        #print message
139        return ret
[706]140
[226]141    cnt = 0
142    for line in file(fname):
143        cnt +=1
144        line = line.strip()
145        if not len(line): continue
146        if line.startswith('#'): continue
147        tup = line.split(':',1)
148        if len(tup) !=2:
149            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
150            continue
[706]151
[226]152        key, val = tup
153        key = key.strip()
154        if not defaultParams.has_key(key):
155            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
156            continue
[706]157
[226]158        default, converter =  defaultParams[key]
159
160        ind = val.find('#')
161        if ind>=0: val = val[:ind]   # ignore trailing comments
162        val = val.strip()
163        try: cval = converter(val)   # try to convert to proper type or raise
164        except Exception, msg:
165            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
166            continue
167        else:
168            # Alles Klar, update dict
169            defaultParams[key][0] = cval
170
171    # strip the conveter funcs and return
172    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]173    print ('loaded rc file %s'%fname)
[226]174
175    return ret
176
177
178# this is the instance used by the asap classes
[706]179rcParams = rc_params()
[226]180
181rcParamsDefault = dict(rcParams.items()) # a copy
182
183def rc(group, **kwargs):
184    """
185    Set the current rc params.  Group is the grouping for the rc, eg
[379]186    for scantable.save the group is 'scantable', for plotter.stacking, the
187    group is 'plotter', and so on.  kwargs is a list of attribute
[226]188    name/value pairs, eg
189
[379]190      rc('scantable', save='SDFITS')
[226]191
192    sets the current rc params and is equivalent to
[706]193
[379]194      rcParams['scantable.save'] = 'SDFITS'
[226]195
196    Use rcdefaults to restore the default rc params after changes.
197    """
198
[379]199    aliases = {}
[706]200
[226]201    for k,v in kwargs.items():
202        name = aliases.get(k) or k
203        key = '%s.%s' % (group, name)
204        if not rcParams.has_key(key):
205            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]206
[226]207        rcParams[key] = v
208
209
210def rcdefaults():
211    """
212    Restore the default rc params - the ones that were created at
213    asap load time
214    """
215    rcParams.update(rcParamsDefault)
216
[513]217
218def _is_sequence_or_number(param, ptype=int):
219    if isinstance(param,tuple) or isinstance(param,list):
220        out = True
221        for p in param:
222            out &= isinstance(p,ptype)
223        return out
224    elif isinstance(param, ptype):
225        return True
226    return False
227
[715]228
229# workaround for ipython, which redirects this if banner=0 in ipythonrc
230sys.stdout = sys.__stdout__
231sys.stderr = sys.__stderr__
232
233# Logging
234from asap._asap import Log as _asaplog
235global asaplog
[710]236asaplog=_asaplog()
[715]237if rcParams['verbose']:
238    asaplog.enable()
239else:
240    asaplog.disable()
241
242def print_log():
243    log = asaplog.pop()
244    if len(log) and rcParams['verbose']: print log
245    return
246
[113]247from asapfitter import *
[100]248from asapreader import reader
[710]249
[100]250from asapmath import *
251from scantable import *
[297]252from asaplinefind import *
[530]253from asapfit import *
[285]254
[466]255from numarray import logical_and as mask_and
256from numarray import logical_or as mask_or
257from numarray import logical_not as mask_not
258
[226]259if rcParams['useplotter']:
[706]260    from  asapplotter import *
261    gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
262    plotter = asapplotter(gui)
[715]263    del gui
[285]264
[574]265__date__ = '$Date: 2005-11-17 03:33:14 +0000 (Thu, 17 Nov 2005) $'.split()[1]
[706]266__version__  = '1.2'
[100]267
[706]268if rcParams['verbose']:
269    def list_scans(t = scantable):
270        import sys, types
271        globs = sys.modules['__main__'].__dict__.iteritems()
272        print "The user created scantables are:"
273        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
274        print filter(lambda x: not x.startswith('_'), sts)
275        return
[100]276
[715]277    def commands():
278        x = """
[113]279    [The scan container]
280        scantable           - a container for integrations/scans
[182]281                              (can open asap/rpfits/sdfits and ms files)
[113]282            copy            - returns a copy of a scan
283            get_scan        - gets a specific scan out of a scantable
284            summary         - print info about the scantable contents
[255]285            set_cursor      - set a specific Beam/IF/Pol 'cursor' for
286                              further use
287            get_cursor      - print out the current cursor position
[182]288            stats           - get specified statistic of the spectra in
289                              the scantable
290            stddev          - get the standard deviation of the spectra
291                              in the scantable
[113]292            get_tsys        - get the TSys
293            get_time        - get the timestamps of the integrations
[255]294            get_unit        - get the currnt unit
[513]295            set_unit        - set the abcissa unit to be used from this
296                              point on
[255]297            get_abcissa     - get the abcissa values and name for a given
298                              row (time)
[113]299            set_freqframe   - set the frame info for the Spectral Axis
300                              (e.g. 'LSRK')
[276]301            set_doppler     - set the doppler to be used from this point on
[240]302            set_instrument  - set the instrument name
[255]303            get_fluxunit    - get the brightness flux unit
[240]304            set_fluxunit    - set the brightness flux unit
[188]305            create_mask     - return an mask in the current unit
306                              for the given region. The specified regions
307                              are NOT masked
[255]308            get_restfreqs   - get the current list of rest frequencies
309            set_restfreqs   - set a list of rest frequencies
[403]310            lines           - print list of known spectral lines
[113]311            flag_spectrum   - flag a whole Beam/IF/Pol
[116]312            save            - save the scantable to disk as either 'ASAP'
313                              or 'SDFITS'
[486]314            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
315            history         - print the history of the scantable
[530]316            get_fit         - get a fit which has been stored witnh the data
[706]317            average_time    - return the (weighted) time average of a scan
[513]318                              or a list of scans
319            average_pol     - average the polarisations together.
[113]320                              The dimension won't be reduced and
321                              all polarisations will contain the
322                              averaged spectrum.
[690]323            auto_quotient   - return the on/off quotient with
324                              automatic detection of the on/off scans
[513]325            quotient        - return the on/off quotient
326            scale           - return a scan scaled by a given factor
[706]327            add             - return a scan with given value added
[513]328            bin             - return a scan with binned channels
329            resample        - return a scan with resampled channels
330            smooth          - return the spectrally smoothed scan
331            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
[706]332            auto_poly_baseline - automatically fit a polynomial baseline
[513]333            gain_el         - apply gain-elevation correction
334            opacity         - apply opacity correction
335            convert_flux    - convert to and from Jy and Kelvin brightness
[255]336                              units
[513]337            freq_align      - align spectra in frequency frame
338            rotate_xyphase  - rotate XY phase of cross correlation
339            rotate_linpolphase - rotate the phase of the complex
340                                 polarization O=Q+iU correlation
341     [Math] Mainly functions which operate on more than one scantable
[100]342
[706]343            average_time    - return the (weighted) time average
[513]344                              of a list of scans
345            quotient        - return the on/off quotient
346            simple_math     - simple mathematical operations on two scantables,
347                              'add', 'sub', 'mul', 'div'
348     [Fitting]
[113]349        fitter
350            auto_fit        - return a scan where the function is
351                              applied to all Beams/IFs/Pols.
352            commit          - return a new scan where the fits have been
353                              commited.
354            fit             - execute the actual fitting process
[530]355            store_fit       - store the fit paramaters in the data (scantable)
[113]356            get_chi2        - get the Chi^2
357            set_scan        - set the scantable to be fit
358            set_function    - set the fitting function
359            set_parameters  - set the parameters for the function(s), and
360                              set if they should be held fixed during fitting
[513]361            set_gauss_parameters - same as above but specialised for individual
362                                   gaussian components
[113]363            get_parameters  - get the fitted parameters
[513]364            plot            - plot the resulting fit and/or components and
365                              residual
[210]366    [Plotter]
367        asapplotter         - a plotter for asap, default plotter is
368                              called 'plotter'
369            plot            - plot a (list of) scantable
[378]370            save            - save the plot to a file ('png' ,'ps' or 'eps')
[210]371            set_mode        - set the state of the plotter, i.e.
372                              what is to be plotted 'colour stacked'
373                              and what 'panelled'
[530]374            set_cursor      - only plot a selected part of the data
375            set_range       - set a 'zoom' window
[255]376            set_legend      - specify user labels for the legend indeces
377            set_title       - specify user labels for the panel indeces
378            set_ordinate    - specify a user label for the ordinate
379            set_abcissa     - specify a user label for the abcissa
[378]380            set_layout      - specify the multi-panel layout (rows,cols)
[706]381
[182]382    [Reading files]
383        reader              - access rpfits/sdfits files
384            read            - read in integrations
385            summary         - list info about all integrations
386
[113]387    [General]
388        commands            - this command
389        print               - print details about a variable
390        list_scans          - list all scantables created bt the user
391        del                 - delete the given variable from memory
392        range               - create a list of values, e.g.
393                              range(3) = [0,1,2], range(2,5) = [2,3,4]
394        help                - print help for one of the listed functions
395        execfile            - execute an asap script, e.g. execfile('myscript')
[255]396        list_rcparameters   - print out a list of possible values to be
[274]397                              put into $HOME/.asaprc
[466]398        mask_and,mask_or,
399        mask_not            - boolean operations on masks created with
400                              scantable.create_mask
[706]401
[210]402    Note:
403        How to use this with help:
404                                         # function 'summary'
405        [xxx] is just a category
406        Every 'sub-level' in this list should be replaces by a '.' Period when
[706]407        using help
[210]408        Example:
409            ASAP> help scantable # to get info on ths scantable
410            ASAP> help scantable.summary # to get help on the scantable's
411            ASAP> help average_time
412
[715]413            """
414        print x
415        return
[113]416
[706]417def welcome():
418    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]419
420Please report any bugs to:
[555]421asap@atnf.csiro.au
[100]422
[378]423[IMPORTANT: ASAP is 0-based]
[706]424Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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