source: trunk/python/__init__.py @ 1351

Last change on this file since 1351 was 1351, checked in by mar637, 17 years ago

several documentation updates for the upcoming release

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Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys,shutil, platform
6
7# Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
8plf = None
9if sys.platform == "linux2":
10    if platform.architecture()[0] == '64bit':
11        plf = 'linux_64b'
12    else:
13        plf = 'linux_gnu'
14elif sys.platform == 'darwin':
15    plf = 'darwin'
16else:
17    # Shouldn't happen - default to linux
18    plf = 'linux'
19asapdata = __path__[-1]
20# Allow user defined data location
21if os.environ.has_key("ASAPDATA"):
22    if os.path.exists(os.environ["ASAPDATA"]):
23        asapdata = os.environ["ASAPDATA"]
24if not os.environ.has_key("AIPSPATH"):
25    os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
26# set up user space
27userdir = os.environ["HOME"]+"/.asap"
28if not os.path.exists(userdir):
29    print 'First time ASAP use. Setting up ~/.asap'
30    os.mkdir(userdir)
31    shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
32    f = file(userdir+"/asapuserfuncs.py", "w")
33    f.close()
34    f = file(userdir+"/ipythonrc", "w")
35    f.close()
36# remove from namespace
37del asapdata, userdir, shutil, platform
38
39def _validate_bool(b):
40    'Convert b to a boolean or raise'
41    bl = b.lower()
42    if bl in ('f', 'no', 'false', '0', 0): return False
43    elif bl in ('t', 'yes', 'true', '1', 1): return True
44    else:
45        raise ValueError('Could not convert "%s" to boolean' % b)
46
47def _validate_int(s):
48    'convert s to int or raise'
49    try: return int(s)
50    except ValueError:
51        raise ValueError('Could not convert "%s" to int' % s)
52
53def _asap_fname():
54    """
55    Return the path to the rc file
56
57    Search order:
58
59     * current working dir
60     * environ var ASAPRC
61     * HOME/.asaprc
62
63    """
64
65    fname = os.path.join( os.getcwd(), '.asaprc')
66    if os.path.exists(fname): return fname
67
68    if os.environ.has_key('ASAPRC'):
69        path =  os.environ['ASAPRC']
70        if os.path.exists(path):
71            fname = os.path.join(path, '.asaprc')
72            if os.path.exists(fname):
73                return fname
74
75    if os.environ.has_key('HOME'):
76        home =  os.environ['HOME']
77        fname = os.path.join(home, '.asaprc')
78        if os.path.exists(fname):
79            return fname
80    return None
81
82
83defaultParams = {
84    # general
85    'verbose'             : [True, _validate_bool],
86    'useplotter'          : [True, _validate_bool],
87    'insitu'              : [True, _validate_bool],
88
89    # plotting
90    'plotter.gui'         : [True, _validate_bool],
91    'plotter.stacking'    : ['p', str],
92    'plotter.panelling'   : ['s', str],
93    'plotter.colours'     : ['', str],
94    'plotter.linestyles'  : ['', str],
95    'plotter.decimate'    : [False, _validate_bool],
96    'plotter.ganged'      : [True, _validate_bool],
97    'plotter.histogram'  : [False, _validate_bool],
98    'plotter.papertype'  : ['A4', str],
99
100    # scantable
101    'scantable.save'      : ['ASAP', str],
102    'scantable.autoaverage'      : [True, _validate_bool],
103    'scantable.freqframe' : ['LSRK', str],  #default frequency frame
104    'scantable.verbosesummary'   : [False, _validate_bool],
105    'scantable.storage'   : ['memory', str]
106    # fitter
107    }
108
109def list_rcparameters():
110
111    print """
112# general
113# print verbose output
114verbose                    : True
115
116# preload a default plotter
117useplotter                 : True
118
119# apply operations on the input scantable or return new one
120insitu                     : True
121
122# plotting
123
124# do we want a GUI or plot to a file
125plotter.gui                : True
126
127# default mode for colour stacking
128plotter.stacking           : Pol
129
130# default mode for panelling
131plotter.panelling          : scan
132
133# push panels together, to share axislabels
134plotter.ganged             : True
135
136# decimate the number of points plotted bya afactor of
137# nchan/1024
138plotter.decimate           : False
139
140# default colours/linestyles
141plotter.colours            :
142plotter.linestyles         :
143
144# enable/disable histogram plotting
145plotter.histogram          : False
146
147# ps paper type
148plotter.papertype          : A4
149
150# scantable
151
152# default storage of scantable ('memory'/'disk')
153scantable.storage          : memory
154# default ouput format when saving
155scantable.save             : ASAP
156# auto averaging on read
157scantable.autoaverage      : True
158
159# default frequency frame to set when function
160# scantable.set_freqframe is called
161scantable.freqframe        : LSRK
162
163# Control the level of information printed by summary
164scantable.verbosesummary   : False
165
166# Fitter
167"""
168
169def rc_params():
170    'Return the default params updated from the values in the rc file'
171
172    fname = _asap_fname()
173
174    if fname is None or not os.path.exists(fname):
175        message = 'could not find rc file; returning defaults'
176        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
177        #print message
178        return ret
179
180    cnt = 0
181    for line in file(fname):
182        cnt +=1
183        line = line.strip()
184        if not len(line): continue
185        if line.startswith('#'): continue
186        tup = line.split(':',1)
187        if len(tup) !=2:
188            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
189            continue
190
191        key, val = tup
192        key = key.strip()
193        if not defaultParams.has_key(key):
194            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
195            continue
196
197        default, converter =  defaultParams[key]
198
199        ind = val.find('#')
200        if ind>=0: val = val[:ind]   # ignore trailing comments
201        val = val.strip()
202        try: cval = converter(val)   # try to convert to proper type or raise
203        except ValueError, msg:
204            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
205            continue
206        else:
207            # Alles Klar, update dict
208            defaultParams[key][0] = cval
209
210    # strip the conveter funcs and return
211    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
212    print ('loaded rc file %s'%fname)
213
214    return ret
215
216
217# this is the instance used by the asap classes
218rcParams = rc_params()
219
220rcParamsDefault = dict(rcParams.items()) # a copy
221
222def rc(group, **kwargs):
223    """
224    Set the current rc params.  Group is the grouping for the rc, eg
225    for scantable.save the group is 'scantable', for plotter.stacking, the
226    group is 'plotter', and so on.  kwargs is a list of attribute
227    name/value pairs, eg
228
229      rc('scantable', save='SDFITS')
230
231    sets the current rc params and is equivalent to
232
233      rcParams['scantable.save'] = 'SDFITS'
234
235    Use rcdefaults to restore the default rc params after changes.
236    """
237
238    aliases = {}
239
240    for k,v in kwargs.items():
241        name = aliases.get(k) or k
242        key = '%s.%s' % (group, name)
243        if not rcParams.has_key(key):
244            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
245
246        rcParams[key] = v
247
248
249def rcdefaults():
250    """
251    Restore the default rc params - the ones that were created at
252    asap load time
253    """
254    rcParams.update(rcParamsDefault)
255
256def _n_bools(n, val):
257    return [ val for i in xrange(n) ]
258
259def _is_sequence_or_number(param, ptype=int):
260    if isinstance(param,tuple) or isinstance(param,list):
261        if len(param) == 0: return True # empty list
262        out = True
263        for p in param:
264            out &= isinstance(p,ptype)
265        return out
266    elif isinstance(param, ptype):
267        return True
268    return False
269
270def _to_list(param, ptype=int):
271    if isinstance(param, ptype):
272        if ptype is str: return param.split()
273        else: return [param]
274    if _is_sequence_or_number(param, ptype):
275        return param
276    return None
277
278def unique(x):
279    """
280    Return the unique values in a list
281    Parameters:
282        x:      the list to reduce
283    Examples:
284        x = [1,2,3,3,4]
285        print unique(x)
286        [1,2,3,4]
287    """
288    return dict([ (val, 1) for val in x]).keys()
289
290def list_files(path=".",suffix="rpf"):
291    """
292    Return a list files readable by asap, such as rpf, sdfits, mbf, asap
293    Parameters:
294        path:     The directory to list (default '.')
295        suffix:   The file extension (default rpf)
296    Example:
297        files = list_files("data/","sdfits")
298        print files
299        ['data/2001-09-01_0332_P363.sdfits',
300        'data/2003-04-04_131152_t0002.sdfits',
301        'data/Sgr_86p262_best_SPC.sdfits']
302    """
303    if not os.path.isdir(path):
304        return None
305    valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
306    if not suffix in valid:
307        return None
308    files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
309    return filter(lambda x: x.endswith(suffix),files)
310
311# workaround for ipython, which redirects this if banner=0 in ipythonrc
312sys.stdout = sys.__stdout__
313sys.stderr = sys.__stderr__
314
315# Logging
316from asap._asap import Log as _asaplog
317global asaplog
318asaplog=_asaplog()
319if rcParams['verbose']:
320    asaplog.enable()
321else:
322    asaplog.disable()
323
324def print_log():
325    log = asaplog.pop()
326    if len(log) and rcParams['verbose']: print log
327    return
328
329def mask_and(a, b):
330    assert(len(a)==len(b))
331    return [ a[i] & b[i] for i in xrange(len(a)) ]
332
333def mask_or(a, b):
334    assert(len(a)==len(b))
335    return [ a[i] | b[i] for i in xrange(len(a)) ]
336
337def mask_not(a):
338    return [ not i for i in a ]
339
340from asapfitter import fitter
341from asapreader import reader
342from selector import selector
343
344from asapmath import *
345from scantable import scantable
346from asaplinefind import linefinder
347from linecatalog import linecatalog
348
349if rcParams['useplotter']:
350    try:
351        from  asapplotter import asapplotter
352        gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
353        if gui:
354            import pylab as xyplotter
355            plotter = asapplotter(gui)
356            del gui
357    except ImportError:
358        print "Matplotlib not installed. No plotting available"
359
360__date__ = '$Date: 2007-04-26 04:50:36 +0000 (Thu, 26 Apr 2007) $'.split()[1]
361__version__  = 'trunk'
362
363def is_ipython():
364    return '__IP' in dir(sys.modules["__main__"])
365if is_ipython():
366    def version(): print  "ASAP %s(%s)"% (__version__, __date__)
367    def list_scans(t = scantable):
368        import types
369        globs = sys.modules['__main__'].__dict__.iteritems()
370        print "The user created scantables are:"
371        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
372        print filter(lambda x: not x.startswith('_'), sts)
373        return
374
375    def commands():
376        x = """
377    [The scan container]
378        scantable           - a container for integrations/scans
379                              (can open asap/rpfits/sdfits and ms files)
380            copy            - returns a copy of a scan
381            get_scan        - gets a specific scan out of a scantable
382                              (by name or number)
383            drop_scan       - drops a specific scan out of a scantable
384                              (by number)
385            set_selection   - set a new subselection of the data
386            get_selection   - get the current selection object
387            summary         - print info about the scantable contents
388            stats           - get specified statistic of the spectra in
389                              the scantable
390            stddev          - get the standard deviation of the spectra
391                              in the scantable
392            get_tsys        - get the TSys
393            get_time        - get the timestamps of the integrations
394            get_inttime     - get the integration time
395            get_sourcename  - get the source names of the scans
396            get_azimuth     - get the azimuth of the scans
397            get_elevation   - get the elevation of the scans
398            get_parangle    - get the parallactic angle of the scans
399            get_unit        - get the current unit
400            set_unit        - set the abcissa unit to be used from this
401                              point on
402            get_abcissa     - get the abcissa values and name for a given
403                              row (time)
404            get_column_names - get the names of the columns in the scantable
405                               for use with selector.set_query
406            set_freqframe   - set the frame info for the Spectral Axis
407                              (e.g. 'LSRK')
408            set_doppler     - set the doppler to be used from this point on
409            set_dirframe    - set the frame for the direction on the sky
410            set_instrument  - set the instrument name
411            set_feedtype    - set the feed type
412            get_fluxunit    - get the brightness flux unit
413            set_fluxunit    - set the brightness flux unit
414            create_mask     - return an mask in the current unit
415                              for the given region. The specified regions
416                              are NOT masked
417            get_restfreqs   - get the current list of rest frequencies
418            set_restfreqs   - set a list of rest frequencies
419            flag            - flag selected channels in the data
420            lag_flag        - flag specified frequency in the data
421            save            - save the scantable to disk as either 'ASAP',
422                              'SDFITS' or 'ASCII'
423            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
424            nscan           - the number of scans in the scantable
425            nrow            - te number of spectra in the scantable
426            history         - print the history of the scantable
427            get_fit         - get a fit which has been stored witnh the data
428            average_time    - return the (weighted) time average of a scan
429                              or a list of scans
430            average_pol     - average the polarisations together.
431            average_beam    - average the beams together.
432            convert_pol     - convert to a different polarisation type
433            auto_quotient   - return the on/off quotient with
434                              automatic detection of the on/off scans (closest
435                              in time off is selected)
436            mx_quotient     - Form a quotient using MX data (off beams)
437            scale, *, /     - return a scan scaled by a given factor
438            add, +, -       - return a scan with given value added
439            bin             - return a scan with binned channels
440            resample        - return a scan with resampled channels
441            smooth          - return the spectrally smoothed scan
442            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
443            auto_poly_baseline - automatically fit a polynomial baseline
444            recalc_azel     - recalculate azimuth and elevation based on
445                              the pointing
446            gain_el         - apply gain-elevation correction
447            opacity         - apply opacity correction
448            convert_flux    - convert to and from Jy and Kelvin brightness
449                              units
450            freq_align      - align spectra in frequency frame
451            invert_phase    - Invert the phase of the cross-correlation
452            swap_linears    - Swap XX and YY (or RR LL)
453            rotate_xyphase  - rotate XY phase of cross correlation
454            rotate_linpolphase - rotate the phase of the complex
455                                 polarization O=Q+iU correlation
456            freq_switch     - perform frequency switching on the data
457            stats           - Determine the specified statistic, e.g. 'min'
458                              'max', 'rms' etc.
459            stddev          - Determine the standard deviation of the current
460                              beam/if/pol
461     [Selection]
462         selector              - a selection object to set a subset of a scantable
463            set_scans          - set (a list of) scans by index
464            set_cycles         - set (a list of) cycles by index
465            set_beams          - set (a list of) beamss by index
466            set_ifs            - set (a list of) ifs by index
467            set_polarisations  - set (a list of) polarisations by name
468                                 or by index
469            set_names          - set a selection by name (wildcards allowed)
470            set_tsys           - set a selection by tsys thresholds
471            set_query          - set a selection by SQL-like query, e.g. BEAMNO==1
472            ( also  get_ functions for all these )
473            reset              - unset all selections
474            +                  - merge two selections
475
476     [Math] Mainly functions which operate on more than one scantable
477
478            average_time    - return the (weighted) time average
479                              of a list of scans
480            quotient        - return the on/off quotient
481            simple_math     - simple mathematical operations on two scantables,
482                              'add', 'sub', 'mul', 'div'
483            quotient        - build quotient of the given on and off scans
484                              (matched pairs and 1 off - n on are valid)
485            merge           - merge a list of scantables
486
487     [Line Catalog]
488        linecatalog              - a linecatalog wrapper, taking an ASCII or
489                                   internal format table
490            summary              - print a summary of the current selection
491            set_name             - select a subset by name pattern, e.g. '*OH*'
492            set_strength_limits  - select a subset by line strength limits
493            set_frequency_limits - select a subset by frequency limits
494            reset                - unset all selections
495            save                 - save the current subset to a table (internal
496                                   format)
497            get_row              - get the name and frequency from a specific
498                                   row in the table
499     [Fitting]
500        fitter
501            auto_fit        - return a scan where the function is
502                              applied to all Beams/IFs/Pols.
503            commit          - return a new scan where the fits have been
504                              commited.
505            fit             - execute the actual fitting process
506            store_fit       - store the fit parameters in the data (scantable)
507            get_chi2        - get the Chi^2
508            set_scan        - set the scantable to be fit
509            set_function    - set the fitting function
510            set_parameters  - set the parameters for the function(s), and
511                              set if they should be held fixed during fitting
512            set_gauss_parameters - same as above but specialised for individual
513                                   gaussian components
514            get_parameters  - get the fitted parameters
515            plot            - plot the resulting fit and/or components and
516                              residual
517    [Plotter]
518        asapplotter         - a plotter for asap, default plotter is
519                              called 'plotter'
520            plot            - plot a scantable
521            plot_lines      - plot a linecatalog overlay
522            save            - save the plot to a file ('png' ,'ps' or 'eps')
523            set_mode        - set the state of the plotter, i.e.
524                              what is to be plotted 'colour stacked'
525                              and what 'panelled'
526            set_selection   - only plot a selected part of the data
527            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
528            set_legend      - specify user labels for the legend indeces
529            set_title       - specify user labels for the panel indeces
530            set_abcissa     - specify a user label for the abcissa
531            set_ordinate    - specify a user label for the ordinate
532            set_layout      - specify the multi-panel layout (rows,cols)
533            set_colors      - specify a set of colours to use
534            set_linestyles  - specify a set of linestyles to use if only
535                              using one color
536            set_font        - set general font properties, e.g. 'family'
537            set_histogram   - plot in historam style
538            set_mask        - set a plotting mask for a specific polarization
539            text            - draw text annotations either in data or relative
540                              coordinates
541            arrow           - draw arrow annotations either in data or relative
542                              coordinates
543            axhline,axvline - draw horizontal/vertical lines
544            axhspan,axvspan - draw horizontal/vertical regions
545
546        xyplotter           - matplotlib/pylab plotting functions
547
548    [Reading files]
549        reader              - access rpfits/sdfits files
550            open            - attach reader to a file
551            close           - detach reader from file
552            read            - read in integrations
553            summary         - list info about all integrations
554
555    [General]
556        commands            - this command
557        print               - print details about a variable
558        list_scans          - list all scantables created bt the user
559        list_files          - list all files readable by asap (default rpf)
560        del                 - delete the given variable from memory
561        range               - create a list of values, e.g.
562                              range(3) = [0,1,2], range(2,5) = [2,3,4]
563        help                - print help for one of the listed functions
564        execfile            - execute an asap script, e.g. execfile('myscript')
565        list_rcparameters   - print out a list of possible values to be
566                              put into $HOME/.asaprc
567        rc                  - set rc parameters from within asap
568        mask_and,mask_or,
569        mask_not            - boolean operations on masks created with
570                              scantable.create_mask
571
572    Note:
573        How to use this with help:
574                                         # function 'summary'
575        [xxx] is just a category
576        Every 'sub-level' in this list should be replaces by a '.' Period when
577        using help
578        Example:
579            ASAP> help scantable # to get info on ths scantable
580            ASAP> help scantable.summary # to get help on the scantable's
581            ASAP> help average_time
582
583            """
584        if rcParams['verbose']:
585            try:
586                from IPython.genutils import page as pager
587            except ImportError:
588                from pydoc import pager
589            pager(x)
590        else:
591            print x
592        return
593
594def welcome():
595    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
596
597Please report any bugs via:
598http://svn.atnf.csiro.au/trac/asap/newticket
599
600[IMPORTANT: ASAP is 0-based]
601Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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