source: trunk/python/__init__.py @ 706

Last change on this file since 706 was 706, checked in by mar637, 19 years ago

various changes to enable non-gui plotting

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 14.6 KB
RevLine 
[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],
[706]63   
[226]64    # scantable
65    'scantable.save'      : ['ASAP', str],
[513]66    'scantable.autoaverage'      : [True, _validate_bool],
[226]67    'scantable.freqframe' : ['LSRK', str],  #default frequency frame
[513]68    'scantable.allaxes'   : [True, _validate_bool],  # apply action to all axes
69    'scantable.plotter'   : [True, _validate_bool], # use internal plotter
70    'scantable.verbosesummary'   : [False, _validate_bool]
[226]71
72    # fitter
73    }
74
[255]75def list_rcparameters():
[706]76
[255]77    print """
78    # general
79    # print verbose output
[466]80    verbose                    : True
[255]81
82    # preload a default plotter
[466]83    useplotter                 : True
[255]84
85    # apply operations on the input scantable or return new one
[542]86    insitu                     : True
[706]87
88    # plotting
[700]89   
[706]90    # do we want a GUI or plot to a file
91    plotter.gui                : True
92   
[255]93    # default mode for colour stacking
[552]94    plotter.stacking           : Pol
[255]95
96    # default mode for panelling
[552]97    plotter.panelling          : scan
[255]98
[700]99    # default colours/linestyles
100    plotter.colours            :
[706]101    plotter.linestyles         :
[700]102
[255]103    # scantable
104    # default ouput format when saving
[552]105    scantable.save             : ASAP
[255]106    # auto averaging on read
[466]107    scantable.autoaverage      : True
[255]108
109    # default frequency frame to set when function
110    # scantable.set_freqfrmae is called
[552]111    scantable.freqframe        : LSRK
[255]112
113    # apply action to all axes not just the cursor location
[706]114    scantable.allaxes          : True
[255]115
116    # use internal plotter
[466]117    scantable.plotter          : True
[255]118
[381]119    # Control the level of information printed by summary
[466]120    scantable.verbosesummary   : False
[706]121
122    # Fitter
[255]123    """
[706]124
[226]125def rc_params():
126    'Return the default params updated from the values in the rc file'
[706]127
[513]128    fname = _asap_fname()
[706]129
[226]130    if fname is None or not os.path.exists(fname):
131        message = 'could not find rc file; returning defaults'
132        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
133        #print message
134        return ret
[706]135
[226]136    cnt = 0
137    for line in file(fname):
138        cnt +=1
139        line = line.strip()
140        if not len(line): continue
141        if line.startswith('#'): continue
142        tup = line.split(':',1)
143        if len(tup) !=2:
144            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
145            continue
[706]146
[226]147        key, val = tup
148        key = key.strip()
149        if not defaultParams.has_key(key):
150            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
151            continue
[706]152
[226]153        default, converter =  defaultParams[key]
154
155        ind = val.find('#')
156        if ind>=0: val = val[:ind]   # ignore trailing comments
157        val = val.strip()
158        try: cval = converter(val)   # try to convert to proper type or raise
159        except Exception, msg:
160            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
161            continue
162        else:
163            # Alles Klar, update dict
164            defaultParams[key][0] = cval
165
166    # strip the conveter funcs and return
167    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]168    print ('loaded rc file %s'%fname)
[226]169
170    return ret
171
172
173# this is the instance used by the asap classes
[706]174rcParams = rc_params()
[226]175
176rcParamsDefault = dict(rcParams.items()) # a copy
177
178def rc(group, **kwargs):
179    """
180    Set the current rc params.  Group is the grouping for the rc, eg
[379]181    for scantable.save the group is 'scantable', for plotter.stacking, the
182    group is 'plotter', and so on.  kwargs is a list of attribute
[226]183    name/value pairs, eg
184
[379]185      rc('scantable', save='SDFITS')
[226]186
187    sets the current rc params and is equivalent to
[706]188
[379]189      rcParams['scantable.save'] = 'SDFITS'
[226]190
191    Use rcdefaults to restore the default rc params after changes.
192    """
193
[379]194    aliases = {}
[706]195
[226]196    for k,v in kwargs.items():
197        name = aliases.get(k) or k
198        key = '%s.%s' % (group, name)
199        if not rcParams.has_key(key):
200            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]201
[226]202        rcParams[key] = v
203
204
205def rcdefaults():
206    """
207    Restore the default rc params - the ones that were created at
208    asap load time
209    """
210    rcParams.update(rcParamsDefault)
211
[513]212
213def _is_sequence_or_number(param, ptype=int):
214    if isinstance(param,tuple) or isinstance(param,list):
215        out = True
216        for p in param:
217            out &= isinstance(p,ptype)
218        return out
219    elif isinstance(param, ptype):
220        return True
221    return False
222
[113]223from asapfitter import *
[100]224from asapreader import reader
225from asapmath import *
226from scantable import *
[297]227from asaplinefind import *
[530]228from asapfit import *
[285]229
[466]230from numarray import logical_and as mask_and
231from numarray import logical_or as mask_or
232from numarray import logical_not as mask_not
233
[226]234if rcParams['useplotter']:
[706]235    from  asapplotter import *
236    if rcParams['verbose']:
237        print "Initialising GUI asapplotter with the name 'plotter' ..."
238    gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
239    plotter = asapplotter(gui)
[285]240
[574]241__date__ = '$Date: 2005-11-02 02:17:39 +0000 (Wed, 02 Nov 2005) $'.split()[1]
[706]242__version__  = '1.2'
[100]243
[706]244if rcParams['verbose']:
245    def list_scans(t = scantable):
246        import sys, types
247        globs = sys.modules['__main__'].__dict__.iteritems()
248        print "The user created scantables are:"
249        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
250        print filter(lambda x: not x.startswith('_'), sts)
251        return
252else:
253    pass
[100]254
[113]255def commands():
[706]256    x = """
[113]257    [The scan container]
258        scantable           - a container for integrations/scans
[182]259                              (can open asap/rpfits/sdfits and ms files)
[113]260            copy            - returns a copy of a scan
261            get_scan        - gets a specific scan out of a scantable
262            summary         - print info about the scantable contents
[255]263            set_cursor      - set a specific Beam/IF/Pol 'cursor' for
264                              further use
265            get_cursor      - print out the current cursor position
[182]266            stats           - get specified statistic of the spectra in
267                              the scantable
268            stddev          - get the standard deviation of the spectra
269                              in the scantable
[113]270            get_tsys        - get the TSys
271            get_time        - get the timestamps of the integrations
[255]272            get_unit        - get the currnt unit
[513]273            set_unit        - set the abcissa unit to be used from this
274                              point on
[255]275            get_abcissa     - get the abcissa values and name for a given
276                              row (time)
[113]277            set_freqframe   - set the frame info for the Spectral Axis
278                              (e.g. 'LSRK')
[276]279            set_doppler     - set the doppler to be used from this point on
[240]280            set_instrument  - set the instrument name
[255]281            get_fluxunit    - get the brightness flux unit
[240]282            set_fluxunit    - set the brightness flux unit
[188]283            create_mask     - return an mask in the current unit
284                              for the given region. The specified regions
285                              are NOT masked
[255]286            get_restfreqs   - get the current list of rest frequencies
287            set_restfreqs   - set a list of rest frequencies
[403]288            lines           - print list of known spectral lines
[113]289            flag_spectrum   - flag a whole Beam/IF/Pol
[116]290            save            - save the scantable to disk as either 'ASAP'
291                              or 'SDFITS'
[486]292            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
293            history         - print the history of the scantable
[530]294            get_fit         - get a fit which has been stored witnh the data
[706]295            average_time    - return the (weighted) time average of a scan
[513]296                              or a list of scans
297            average_pol     - average the polarisations together.
[113]298                              The dimension won't be reduced and
299                              all polarisations will contain the
300                              averaged spectrum.
[690]301            auto_quotient   - return the on/off quotient with
302                              automatic detection of the on/off scans
[513]303            quotient        - return the on/off quotient
304            scale           - return a scan scaled by a given factor
[706]305            add             - return a scan with given value added
[513]306            bin             - return a scan with binned channels
307            resample        - return a scan with resampled channels
308            smooth          - return the spectrally smoothed scan
309            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
[706]310            auto_poly_baseline - automatically fit a polynomial baseline
[513]311            gain_el         - apply gain-elevation correction
312            opacity         - apply opacity correction
313            convert_flux    - convert to and from Jy and Kelvin brightness
[255]314                              units
[513]315            freq_align      - align spectra in frequency frame
316            rotate_xyphase  - rotate XY phase of cross correlation
317            rotate_linpolphase - rotate the phase of the complex
318                                 polarization O=Q+iU correlation
319     [Math] Mainly functions which operate on more than one scantable
[100]320
[706]321            average_time    - return the (weighted) time average
[513]322                              of a list of scans
323            quotient        - return the on/off quotient
324            simple_math     - simple mathematical operations on two scantables,
325                              'add', 'sub', 'mul', 'div'
326     [Fitting]
[113]327        fitter
328            auto_fit        - return a scan where the function is
329                              applied to all Beams/IFs/Pols.
330            commit          - return a new scan where the fits have been
331                              commited.
332            fit             - execute the actual fitting process
[530]333            store_fit       - store the fit paramaters in the data (scantable)
[113]334            get_chi2        - get the Chi^2
335            set_scan        - set the scantable to be fit
336            set_function    - set the fitting function
337            set_parameters  - set the parameters for the function(s), and
338                              set if they should be held fixed during fitting
[513]339            set_gauss_parameters - same as above but specialised for individual
340                                   gaussian components
[113]341            get_parameters  - get the fitted parameters
[513]342            plot            - plot the resulting fit and/or components and
343                              residual
[210]344    [Plotter]
345        asapplotter         - a plotter for asap, default plotter is
346                              called 'plotter'
347            plot            - plot a (list of) scantable
[378]348            save            - save the plot to a file ('png' ,'ps' or 'eps')
[210]349            set_mode        - set the state of the plotter, i.e.
350                              what is to be plotted 'colour stacked'
351                              and what 'panelled'
[530]352            set_cursor      - only plot a selected part of the data
353            set_range       - set a 'zoom' window
[255]354            set_legend      - specify user labels for the legend indeces
355            set_title       - specify user labels for the panel indeces
356            set_ordinate    - specify a user label for the ordinate
357            set_abcissa     - specify a user label for the abcissa
[378]358            set_layout      - specify the multi-panel layout (rows,cols)
[706]359
[182]360    [Reading files]
361        reader              - access rpfits/sdfits files
362            read            - read in integrations
363            summary         - list info about all integrations
364
[113]365    [General]
366        commands            - this command
367        print               - print details about a variable
368        list_scans          - list all scantables created bt the user
369        del                 - delete the given variable from memory
370        range               - create a list of values, e.g.
371                              range(3) = [0,1,2], range(2,5) = [2,3,4]
372        help                - print help for one of the listed functions
373        execfile            - execute an asap script, e.g. execfile('myscript')
[255]374        list_rcparameters   - print out a list of possible values to be
[274]375                              put into $HOME/.asaprc
[466]376        mask_and,mask_or,
377        mask_not            - boolean operations on masks created with
378                              scantable.create_mask
[706]379
[210]380    Note:
381        How to use this with help:
382                                         # function 'summary'
383        [xxx] is just a category
384        Every 'sub-level' in this list should be replaces by a '.' Period when
[706]385        using help
[210]386        Example:
387            ASAP> help scantable # to get info on ths scantable
388            ASAP> help scantable.summary # to get help on the scantable's
389            ASAP> help average_time
390
[113]391    """
392    print x
393    return
394
[706]395def welcome():
396    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]397
398Please report any bugs to:
[555]399asap@atnf.csiro.au
[100]400
[378]401[IMPORTANT: ASAP is 0-based]
[706]402Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
Note: See TracBrowser for help on using the repository browser.