source: trunk/python/__init__.py @ 780

Last change on this file since 780 was 780, checked in by mar637, 19 years ago

merge from Release12

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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 """
[737]80# general
81# print verbose output
82verbose                    : True
[255]83
[737]84# preload a default plotter
85useplotter                 : True
[255]86
[737]87# apply operations on the input scantable or return new one
88insitu                     : True
[706]89
[737]90# plotting
[710]91
[737]92# do we want a GUI or plot to a file
93plotter.gui                : True
[710]94
[737]95# default mode for colour stacking
96plotter.stacking           : Pol
[255]97
[737]98# default mode for panelling
99plotter.panelling          : scan
[255]100
[737]101# push panels together, to share axislabels
102plotter.ganged             : True
[710]103
[737]104# decimate the number of points plotted bya afactor of
105# nchan/1024
106plotter.decimate           : False
[733]107
[737]108# default colours/linestyles
109plotter.colours            :
110plotter.linestyles         :
[700]111
[737]112# scantable
113# default ouput format when saving
114scantable.save             : ASAP
115# auto averaging on read
116scantable.autoaverage      : True
[255]117
[737]118# default frequency frame to set when function
119# scantable.set_freqfrmae is called
120scantable.freqframe        : LSRK
[255]121
[737]122# apply action to all axes not just the cursor location
123scantable.allaxes          : True
[255]124
[737]125# use internal plotter
126scantable.plotter          : True
[255]127
[737]128# Control the level of information printed by summary
129scantable.verbosesummary   : False
[706]130
[737]131# Fitter
132"""
[706]133
[226]134def rc_params():
135    'Return the default params updated from the values in the rc file'
[706]136
[513]137    fname = _asap_fname()
[706]138
[226]139    if fname is None or not os.path.exists(fname):
140        message = 'could not find rc file; returning defaults'
141        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
142        #print message
143        return ret
[706]144
[226]145    cnt = 0
146    for line in file(fname):
147        cnt +=1
148        line = line.strip()
149        if not len(line): continue
150        if line.startswith('#'): continue
151        tup = line.split(':',1)
152        if len(tup) !=2:
153            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
154            continue
[706]155
[226]156        key, val = tup
157        key = key.strip()
158        if not defaultParams.has_key(key):
159            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
160            continue
[706]161
[226]162        default, converter =  defaultParams[key]
163
164        ind = val.find('#')
165        if ind>=0: val = val[:ind]   # ignore trailing comments
166        val = val.strip()
167        try: cval = converter(val)   # try to convert to proper type or raise
168        except Exception, msg:
169            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
170            continue
171        else:
172            # Alles Klar, update dict
173            defaultParams[key][0] = cval
174
175    # strip the conveter funcs and return
176    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]177    print ('loaded rc file %s'%fname)
[226]178
179    return ret
180
181
182# this is the instance used by the asap classes
[706]183rcParams = rc_params()
[226]184
185rcParamsDefault = dict(rcParams.items()) # a copy
186
187def rc(group, **kwargs):
188    """
189    Set the current rc params.  Group is the grouping for the rc, eg
[379]190    for scantable.save the group is 'scantable', for plotter.stacking, the
191    group is 'plotter', and so on.  kwargs is a list of attribute
[226]192    name/value pairs, eg
193
[379]194      rc('scantable', save='SDFITS')
[226]195
196    sets the current rc params and is equivalent to
[706]197
[379]198      rcParams['scantable.save'] = 'SDFITS'
[226]199
200    Use rcdefaults to restore the default rc params after changes.
201    """
202
[379]203    aliases = {}
[706]204
[226]205    for k,v in kwargs.items():
206        name = aliases.get(k) or k
207        key = '%s.%s' % (group, name)
208        if not rcParams.has_key(key):
209            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]210
[226]211        rcParams[key] = v
212
213
214def rcdefaults():
215    """
216    Restore the default rc params - the ones that were created at
217    asap load time
218    """
219    rcParams.update(rcParamsDefault)
220
[513]221
222def _is_sequence_or_number(param, ptype=int):
223    if isinstance(param,tuple) or isinstance(param,list):
224        out = True
225        for p in param:
226            out &= isinstance(p,ptype)
227        return out
228    elif isinstance(param, ptype):
229        return True
230    return False
231
[715]232
233# workaround for ipython, which redirects this if banner=0 in ipythonrc
234sys.stdout = sys.__stdout__
235sys.stderr = sys.__stderr__
236
237# Logging
238from asap._asap import Log as _asaplog
239global asaplog
[710]240asaplog=_asaplog()
[715]241if rcParams['verbose']:
242    asaplog.enable()
243else:
244    asaplog.disable()
245
246def print_log():
247    log = asaplog.pop()
248    if len(log) and rcParams['verbose']: print log
249    return
250
[113]251from asapfitter import *
[100]252from asapreader import reader
[710]253
[100]254from asapmath import *
255from scantable import *
[297]256from asaplinefind import *
[530]257from asapfit import *
[285]258
[466]259from numarray import logical_and as mask_and
260from numarray import logical_or as mask_or
261from numarray import logical_not as mask_not
262
[226]263if rcParams['useplotter']:
[706]264    from  asapplotter import *
265    gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
266    plotter = asapplotter(gui)
[715]267    del gui
[285]268
[574]269__date__ = '$Date: 2005-12-07 03:18:09 +0000 (Wed, 07 Dec 2005) $'.split()[1]
[780]270__version__  = '1.2.1'
[100]271
[706]272if rcParams['verbose']:
273    def list_scans(t = scantable):
274        import sys, types
275        globs = sys.modules['__main__'].__dict__.iteritems()
276        print "The user created scantables are:"
277        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
278        print filter(lambda x: not x.startswith('_'), sts)
279        return
[100]280
[715]281    def commands():
282        x = """
[113]283    [The scan container]
284        scantable           - a container for integrations/scans
[182]285                              (can open asap/rpfits/sdfits and ms files)
[113]286            copy            - returns a copy of a scan
287            get_scan        - gets a specific scan out of a scantable
[733]288                              (by name or number)
[113]289            summary         - print info about the scantable contents
[255]290            set_cursor      - set a specific Beam/IF/Pol 'cursor' for
291                              further use
292            get_cursor      - print out the current cursor position
[182]293            stats           - get specified statistic of the spectra in
294                              the scantable
295            stddev          - get the standard deviation of the spectra
296                              in the scantable
[113]297            get_tsys        - get the TSys
298            get_time        - get the timestamps of the integrations
[733]299            get_sourcename  - get the source names of the scans
[255]300            get_unit        - get the currnt unit
[513]301            set_unit        - set the abcissa unit to be used from this
302                              point on
[255]303            get_abcissa     - get the abcissa values and name for a given
304                              row (time)
[113]305            set_freqframe   - set the frame info for the Spectral Axis
306                              (e.g. 'LSRK')
[276]307            set_doppler     - set the doppler to be used from this point on
[240]308            set_instrument  - set the instrument name
[255]309            get_fluxunit    - get the brightness flux unit
[240]310            set_fluxunit    - set the brightness flux unit
[188]311            create_mask     - return an mask in the current unit
312                              for the given region. The specified regions
313                              are NOT masked
[255]314            get_restfreqs   - get the current list of rest frequencies
315            set_restfreqs   - set a list of rest frequencies
[403]316            lines           - print list of known spectral lines
[113]317            flag_spectrum   - flag a whole Beam/IF/Pol
[116]318            save            - save the scantable to disk as either 'ASAP'
319                              or 'SDFITS'
[486]320            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
[733]321            nscan           - the number of scans in the scantable
322            nrow            - te number of integrations in the scantable
[486]323            history         - print the history of the scantable
[530]324            get_fit         - get a fit which has been stored witnh the data
[706]325            average_time    - return the (weighted) time average of a scan
[513]326                              or a list of scans
327            average_pol     - average the polarisations together.
[113]328                              The dimension won't be reduced and
329                              all polarisations will contain the
330                              averaged spectrum.
[690]331            auto_quotient   - return the on/off quotient with
332                              automatic detection of the on/off scans
[733]333                              (matched pairs and 1 off - n on)
[513]334            quotient        - return the on/off quotient
335            scale           - return a scan scaled by a given factor
[706]336            add             - return a scan with given value added
[513]337            bin             - return a scan with binned channels
338            resample        - return a scan with resampled channels
339            smooth          - return the spectrally smoothed scan
340            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
[706]341            auto_poly_baseline - automatically fit a polynomial baseline
[780]342            recalc_azel     - recalculate azimuth and elevation based on
343                              the pointing
[513]344            gain_el         - apply gain-elevation correction
345            opacity         - apply opacity correction
346            convert_flux    - convert to and from Jy and Kelvin brightness
[255]347                              units
[513]348            freq_align      - align spectra in frequency frame
349            rotate_xyphase  - rotate XY phase of cross correlation
350            rotate_linpolphase - rotate the phase of the complex
351                                 polarization O=Q+iU correlation
[733]352            freq_switch     - perform frequency switching on the data
353            stats           - Determine the specified statistic, e.g. 'min'
354                              'max', 'rms' etc.
355            stddev          - Determine the standard deviation of the current
356                              beam/if/pol
357
[513]358     [Math] Mainly functions which operate on more than one scantable
[100]359
[706]360            average_time    - return the (weighted) time average
[513]361                              of a list of scans
362            quotient        - return the on/off quotient
363            simple_math     - simple mathematical operations on two scantables,
364                              'add', 'sub', 'mul', 'div'
365     [Fitting]
[113]366        fitter
367            auto_fit        - return a scan where the function is
368                              applied to all Beams/IFs/Pols.
369            commit          - return a new scan where the fits have been
370                              commited.
371            fit             - execute the actual fitting process
[530]372            store_fit       - store the fit paramaters in the data (scantable)
[113]373            get_chi2        - get the Chi^2
374            set_scan        - set the scantable to be fit
375            set_function    - set the fitting function
376            set_parameters  - set the parameters for the function(s), and
377                              set if they should be held fixed during fitting
[513]378            set_gauss_parameters - same as above but specialised for individual
379                                   gaussian components
[113]380            get_parameters  - get the fitted parameters
[513]381            plot            - plot the resulting fit and/or components and
382                              residual
[210]383    [Plotter]
384        asapplotter         - a plotter for asap, default plotter is
385                              called 'plotter'
386            plot            - plot a (list of) scantable
[378]387            save            - save the plot to a file ('png' ,'ps' or 'eps')
[210]388            set_mode        - set the state of the plotter, i.e.
389                              what is to be plotted 'colour stacked'
390                              and what 'panelled'
[530]391            set_cursor      - only plot a selected part of the data
[733]392            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
[255]393            set_legend      - specify user labels for the legend indeces
394            set_title       - specify user labels for the panel indeces
[733]395            set_abcissa     - specify a user label for the abcissa
[255]396            set_ordinate    - specify a user label for the ordinate
[378]397            set_layout      - specify the multi-panel layout (rows,cols)
[733]398            set_colors      - specify a set of colours to use
399            set_linestyles  - specify a set of linestyles to use if only
400                              using one color
401            set_mask        - set a plotting mask for a specific polarization
[706]402
[182]403    [Reading files]
404        reader              - access rpfits/sdfits files
405            read            - read in integrations
406            summary         - list info about all integrations
407
[113]408    [General]
409        commands            - this command
410        print               - print details about a variable
411        list_scans          - list all scantables created bt the user
412        del                 - delete the given variable from memory
413        range               - create a list of values, e.g.
414                              range(3) = [0,1,2], range(2,5) = [2,3,4]
415        help                - print help for one of the listed functions
416        execfile            - execute an asap script, e.g. execfile('myscript')
[255]417        list_rcparameters   - print out a list of possible values to be
[274]418                              put into $HOME/.asaprc
[466]419        mask_and,mask_or,
420        mask_not            - boolean operations on masks created with
421                              scantable.create_mask
[706]422
[210]423    Note:
424        How to use this with help:
425                                         # function 'summary'
426        [xxx] is just a category
427        Every 'sub-level' in this list should be replaces by a '.' Period when
[706]428        using help
[210]429        Example:
430            ASAP> help scantable # to get info on ths scantable
431            ASAP> help scantable.summary # to get help on the scantable's
432            ASAP> help average_time
433
[715]434            """
435        print x
436        return
[113]437
[706]438def welcome():
439    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]440
441Please report any bugs to:
[555]442asap@atnf.csiro.au
[100]443
[378]444[IMPORTANT: ASAP is 0-based]
[706]445Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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