source: branches/Release2.1.1/python/__init__.py @ 1301

Last change on this file since 1301 was 1301, checked in by mar637, 17 years ago

version -> 2.1.1

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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"]
24os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
25# set up user space
26userdir = os.environ["HOME"]+"/.asap"
27if not os.path.exists(userdir):
28    print 'First time ASAP use. Setting up ~/.asap'
29    os.mkdir(userdir)
30    shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
31    f = file(userdir+"/asapuserfuncs.py", "w")
32    f.close()
33    f = file(userdir+"/ipythonrc", "w")
34    f.close()
35# remove from namespace
36del asapdata, userdir, shutil, platform
37
38def _validate_bool(b):
39    'Convert b to a boolean or raise'
40    bl = b.lower()
41    if bl in ('f', 'no', 'false', '0', 0): return False
42    elif bl in ('t', 'yes', 'true', '1', 1): return True
43    else:
44        raise ValueError('Could not convert "%s" to boolean' % b)
45
46def _validate_int(s):
47    'convert s to int or raise'
48    try: return int(s)
49    except ValueError:
50        raise ValueError('Could not convert "%s" to int' % s)
51
52def _asap_fname():
53    """
54    Return the path to the rc file
55
56    Search order:
57
58     * current working dir
59     * environ var ASAPRC
60     * HOME/.asaprc
61
62    """
63
64    fname = os.path.join( os.getcwd(), '.asaprc')
65    if os.path.exists(fname): return fname
66
67    if os.environ.has_key('ASAPRC'):
68        path =  os.environ['ASAPRC']
69        if os.path.exists(path):
70            fname = os.path.join(path, '.asaprc')
71            if os.path.exists(fname):
72                return fname
73
74    if os.environ.has_key('HOME'):
75        home =  os.environ['HOME']
76        fname = os.path.join(home, '.asaprc')
77        if os.path.exists(fname):
78            return fname
79    return None
80
81
82defaultParams = {
83    # general
84    'verbose'             : [True, _validate_bool],
85    'useplotter'          : [True, _validate_bool],
86    'insitu'              : [True, _validate_bool],
87
88    # plotting
89    'plotter.gui'         : [True, _validate_bool],
90    'plotter.stacking'    : ['p', str],
91    'plotter.panelling'   : ['s', str],
92    'plotter.colours'     : ['', str],
93    'plotter.linestyles'  : ['', str],
94    'plotter.decimate'    : [False, _validate_bool],
95    'plotter.ganged'      : [True, _validate_bool],
96    'plotter.histogram'  : [False, _validate_bool],
97    'plotter.papertype'  : ['A4', str],
98
99    # scantable
100    'scantable.save'      : ['ASAP', str],
101    'scantable.autoaverage'      : [True, _validate_bool],
102    'scantable.freqframe' : ['LSRK', str],  #default frequency frame
103    'scantable.verbosesummary'   : [False, _validate_bool],
104    'scantable.storage'   : ['memory', str]
105    # fitter
106    }
107
108def list_rcparameters():
109
110    print """
111# general
112# print verbose output
113verbose                    : True
114
115# preload a default plotter
116useplotter                 : True
117
118# apply operations on the input scantable or return new one
119insitu                     : True
120
121# plotting
122
123# do we want a GUI or plot to a file
124plotter.gui                : True
125
126# default mode for colour stacking
127plotter.stacking           : Pol
128
129# default mode for panelling
130plotter.panelling          : scan
131
132# push panels together, to share axislabels
133plotter.ganged             : True
134
135# decimate the number of points plotted bya afactor of
136# nchan/1024
137plotter.decimate           : False
138
139# default colours/linestyles
140plotter.colours            :
141plotter.linestyles         :
142
143# enable/disable histogram plotting
144plotter.histogram          : False
145
146# ps paper type
147plotter.papertype          : A4
148
149# scantable
150
151# default storage of scantable ('memory'/'disk')
152scantable.storage          : memory
153# default ouput format when saving
154scantable.save             : ASAP
155# auto averaging on read
156scantable.autoaverage      : True
157
158# default frequency frame to set when function
159# scantable.set_freqframe is called
160scantable.freqframe        : LSRK
161
162# Control the level of information printed by summary
163scantable.verbosesummary   : False
164
165# Fitter
166"""
167
168def rc_params():
169    'Return the default params updated from the values in the rc file'
170
171    fname = _asap_fname()
172
173    if fname is None or not os.path.exists(fname):
174        message = 'could not find rc file; returning defaults'
175        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
176        #print message
177        return ret
178
179    cnt = 0
180    for line in file(fname):
181        cnt +=1
182        line = line.strip()
183        if not len(line): continue
184        if line.startswith('#'): continue
185        tup = line.split(':',1)
186        if len(tup) !=2:
187            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
188            continue
189
190        key, val = tup
191        key = key.strip()
192        if not defaultParams.has_key(key):
193            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
194            continue
195
196        default, converter =  defaultParams[key]
197
198        ind = val.find('#')
199        if ind>=0: val = val[:ind]   # ignore trailing comments
200        val = val.strip()
201        try: cval = converter(val)   # try to convert to proper type or raise
202        except ValueError, msg:
203            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
204            continue
205        else:
206            # Alles Klar, update dict
207            defaultParams[key][0] = cval
208
209    # strip the conveter funcs and return
210    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
211    print ('loaded rc file %s'%fname)
212
213    return ret
214
215
216# this is the instance used by the asap classes
217rcParams = rc_params()
218
219rcParamsDefault = dict(rcParams.items()) # a copy
220
221def rc(group, **kwargs):
222    """
223    Set the current rc params.  Group is the grouping for the rc, eg
224    for scantable.save the group is 'scantable', for plotter.stacking, the
225    group is 'plotter', and so on.  kwargs is a list of attribute
226    name/value pairs, eg
227
228      rc('scantable', save='SDFITS')
229
230    sets the current rc params and is equivalent to
231
232      rcParams['scantable.save'] = 'SDFITS'
233
234    Use rcdefaults to restore the default rc params after changes.
235    """
236
237    aliases = {}
238
239    for k,v in kwargs.items():
240        name = aliases.get(k) or k
241        key = '%s.%s' % (group, name)
242        if not rcParams.has_key(key):
243            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
244
245        rcParams[key] = v
246
247
248def rcdefaults():
249    """
250    Restore the default rc params - the ones that were created at
251    asap load time
252    """
253    rcParams.update(rcParamsDefault)
254
255def _n_bools(n, val):
256    return [ val for i in xrange(n) ]
257
258def _is_sequence_or_number(param, ptype=int):
259    if isinstance(param,tuple) or isinstance(param,list):
260        if len(param) == 0: return True # empty list
261        out = True
262        for p in param:
263            out &= isinstance(p,ptype)
264        return out
265    elif isinstance(param, ptype):
266        return True
267    return False
268
269def _to_list(param, ptype=int):
270    if isinstance(param, ptype):
271        if ptype is str: return param.split()
272        else: return [param]
273    if _is_sequence_or_number(param, ptype):
274        return param
275    return None
276
277def unique(x):
278    """
279    Return the unique values in a list
280    Parameters:
281        x:      the list to reduce
282    Examples:
283        x = [1,2,3,3,4]
284        print unique(x)
285        [1,2,3,4]
286    """
287    return dict([ (val, 1) for val in x]).keys()
288
289def list_files(path=".",suffix="rpf"):
290    """
291    Return a list files readable by asap, such as rpf, sdfits, mbf, asap
292    Parameters:
293        path:     The directory to list (default '.')
294        suffix:   The file extension (default rpf)
295    Example:
296        files = list_files("data/","sdfits")
297        print files
298        ['data/2001-09-01_0332_P363.sdfits',
299        'data/2003-04-04_131152_t0002.sdfits',
300        'data/Sgr_86p262_best_SPC.sdfits']
301    """
302    if not os.path.isdir(path):
303        return None
304    valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
305    if not suffix in valid:
306        return None
307    files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
308    return filter(lambda x: x.endswith(suffix),files)
309
310# workaround for ipython, which redirects this if banner=0 in ipythonrc
311sys.stdout = sys.__stdout__
312sys.stderr = sys.__stderr__
313
314# Logging
315from asap._asap import Log as _asaplog
316global asaplog
317asaplog=_asaplog()
318if rcParams['verbose']:
319    asaplog.enable()
320else:
321    asaplog.disable()
322
323def print_log():
324    log = asaplog.pop()
325    if len(log) and rcParams['verbose']: print log
326    return
327
328def mask_and(a, b):
329    assert(len(a)==len(b))
330    return [ a[i] & b[i] for i in xrange(len(a)) ]
331
332def mask_or(a, b):
333    assert(len(a)==len(b))
334    return [ a[i] | b[i] for i in xrange(len(a)) ]
335
336def mask_not(a):
337    return [ not i for i in a ]
338
339from asapfitter import fitter
340from asapreader import reader
341from selector import selector
342
343from asapmath import *
344from scantable import scantable
345from asaplinefind import linefinder
346from linecatalog import linecatalog
347
348if rcParams['useplotter']:
349    try:
350        from  asapplotter import asapplotter
351        gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
352        if gui:
353            import pylab as xyplotter
354            plotter = asapplotter(gui)
355            del gui
356    except ImportError:
357        print "Matplotlib not installed. No plotting available"
358
359__date__ = '$Date: 2006-11-09 03:06:26 +0000 (Thu, 09 Nov 2006) $'.split()[1]
360__version__  = '2.1.1'
361
362def is_ipython():
363    return '__IP' in dir(sys.modules["__main__"])
364if is_ipython():
365    def version(): print  "ASAP %s(%s)"% (__version__, __date__)
366    def list_scans(t = scantable):
367        import types
368        globs = sys.modules['__main__'].__dict__.iteritems()
369        print "The user created scantables are:"
370        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
371        print filter(lambda x: not x.startswith('_'), sts)
372        return
373
374    def commands():
375        x = """
376    [The scan container]
377        scantable           - a container for integrations/scans
378                              (can open asap/rpfits/sdfits and ms files)
379            copy            - returns a copy of a scan
380            get_scan        - gets a specific scan out of a scantable
381                              (by name or number)
382            drop_scan       - drops a specific scan out of a scantable
383                              (by number)
384            set_selection   - set a new subselection of the data
385            get_selection   - get the current selection object
386            summary         - print info about the scantable contents
387            stats           - get specified statistic of the spectra in
388                              the scantable
389            stddev          - get the standard deviation of the spectra
390                              in the scantable
391            get_tsys        - get the TSys
392            get_time        - get the timestamps of the integrations
393            get_sourcename  - get the source names of the scans
394            get_azimuth     - get the azimuth of the scans
395            get_elevation   - get the elevation of the scans
396            get_parangle    - get the parallactic angle of the scans
397            get_unit        - get the current unit
398            set_unit        - set the abcissa unit to be used from this
399                              point on
400            get_abcissa     - get the abcissa values and name for a given
401                              row (time)
402            get_column_names - get the names of the columns in the scantable
403                               for use with selector.set_query
404            set_freqframe   - set the frame info for the Spectral Axis
405                              (e.g. 'LSRK')
406            set_doppler     - set the doppler to be used from this point on
407            set_dirframe    - set the frame for the direction on the sky
408            set_instrument  - set the instrument name
409            set_feedtype    - set the feed type
410            get_fluxunit    - get the brightness flux unit
411            set_fluxunit    - set the brightness flux unit
412            create_mask     - return an mask in the current unit
413                              for the given region. The specified regions
414                              are NOT masked
415            get_restfreqs   - get the current list of rest frequencies
416            set_restfreqs   - set a list of rest frequencies
417            flag            - flag selected channels in the data
418            lag_flag        - flag specified frequency in the data
419            save            - save the scantable to disk as either 'ASAP',
420                              'SDFITS' or 'ASCII'
421            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
422            nscan           - the number of scans in the scantable
423            nrow            - te number of spectra in the scantable
424            history         - print the history of the scantable
425            get_fit         - get a fit which has been stored witnh the data
426            average_time    - return the (weighted) time average of a scan
427                              or a list of scans
428            average_pol     - average the polarisations together.
429            average_beam    - average the beams together.
430            convert_pol     - convert to a different polarisation type
431            auto_quotient   - return the on/off quotient with
432                              automatic detection of the on/off scans (closest
433                              in time off is selected)
434            mx_quotient     - Form a quotient using MX data (off beams)
435            scale, *, /     - return a scan scaled by a given factor
436            add, +, -       - return a scan with given value added
437            bin             - return a scan with binned channels
438            resample        - return a scan with resampled channels
439            smooth          - return the spectrally smoothed scan
440            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
441            auto_poly_baseline - automatically fit a polynomial baseline
442            recalc_azel     - recalculate azimuth and elevation based on
443                              the pointing
444            gain_el         - apply gain-elevation correction
445            opacity         - apply opacity correction
446            convert_flux    - convert to and from Jy and Kelvin brightness
447                              units
448            freq_align      - align spectra in frequency frame
449            invert_phase    - Invert the phase of the cross-correlation
450            swap_linears    - Swap XX and YY
451            rotate_xyphase  - rotate XY phase of cross correlation
452            rotate_linpolphase - rotate the phase of the complex
453                                 polarization O=Q+iU correlation
454            freq_switch     - perform frequency switching on the data
455            stats           - Determine the specified statistic, e.g. 'min'
456                              'max', 'rms' etc.
457            stddev          - Determine the standard deviation of the current
458                              beam/if/pol
459     [Selection]
460         selector              - a selection object to set a subset of a scantable
461            set_scans          - set (a list of) scans by index
462            set_cycles         - set (a list of) cycles by index
463            set_beams          - set (a list of) beamss by index
464            set_ifs            - set (a list of) ifs by index
465            set_polarisations  - set (a list of) polarisations by name
466                                 or by index
467            set_names          - set a selection by name (wildcards allowed)
468            set_tsys           - set a selection by tsys thresholds
469            set_query          - set a selection by SQL-like query, e.g. BEAMNO==1
470            reset              - unset all selections
471            +                  - merge to selections
472
473     [Math] Mainly functions which operate on more than one scantable
474
475            average_time    - return the (weighted) time average
476                              of a list of scans
477            quotient        - return the on/off quotient
478            simple_math     - simple mathematical operations on two scantables,
479                              'add', 'sub', 'mul', 'div'
480            quotient        - build quotient of the given on and off scans
481                              (matched pairs and 1 off/n on are valid)
482            merge           - merge a list of scantables
483
484     [Line Catalog]
485        linecatalog              - a linecatalog wrapper, taking an ASCII or
486                                   internal format table
487            summary              - print a summary of the current selection
488            set_name             - select a subset by name pattern, e.g. '*OH*'
489            set_strength_limits  - select a subset by line strength limits
490            set_frequency_limits - select a subset by frequency limits
491            reset                - unset all selections
492            save                 - save the current subset to a table (internal
493                                   format)
494            get_row              - get the name and frequency from a specific
495                                   row in the table
496     [Fitting]
497        fitter
498            auto_fit        - return a scan where the function is
499                              applied to all Beams/IFs/Pols.
500            commit          - return a new scan where the fits have been
501                              commited.
502            fit             - execute the actual fitting process
503            store_fit       - store the fit parameters in the data (scantable)
504            get_chi2        - get the Chi^2
505            set_scan        - set the scantable to be fit
506            set_function    - set the fitting function
507            set_parameters  - set the parameters for the function(s), and
508                              set if they should be held fixed during fitting
509            set_gauss_parameters - same as above but specialised for individual
510                                   gaussian components
511            get_parameters  - get the fitted parameters
512            plot            - plot the resulting fit and/or components and
513                              residual
514    [Plotter]
515        asapplotter         - a plotter for asap, default plotter is
516                              called 'plotter'
517            plot            - plot a scantable
518            plot_lines      - plot a linecatalog overlay
519            save            - save the plot to a file ('png' ,'ps' or 'eps')
520            set_mode        - set the state of the plotter, i.e.
521                              what is to be plotted 'colour stacked'
522                              and what 'panelled'
523            set_selection   - only plot a selected part of the data
524            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
525            set_legend      - specify user labels for the legend indeces
526            set_title       - specify user labels for the panel indeces
527            set_abcissa     - specify a user label for the abcissa
528            set_ordinate    - specify a user label for the ordinate
529            set_layout      - specify the multi-panel layout (rows,cols)
530            set_colors      - specify a set of colours to use
531            set_linestyles  - specify a set of linestyles to use if only
532                              using one color
533            set_font        - set general font properties, e.g. 'family'
534            set_histogram   - plot in historam style
535            set_mask        - set a plotting mask for a specific polarization
536            text            - draw text annotations either in data or relative
537                              coordinates
538            arrow           - draw arrow annotations either in data or relative
539                              coordinates
540            axhline,axvline - draw horizontal/vertical lines
541            axhspan,axvspan - draw horizontal/vertical regions
542
543        xyplotter           - matplotlib/pylab plotting functions
544
545    [Reading files]
546        reader              - access rpfits/sdfits files
547            open            - attach reader to a file
548            close           - detach reader from file
549            read            - read in integrations
550            summary         - list info about all integrations
551
552    [General]
553        commands            - this command
554        print               - print details about a variable
555        list_scans          - list all scantables created bt the user
556        list_files          - list all files readable by asap (default rpf)
557        del                 - delete the given variable from memory
558        range               - create a list of values, e.g.
559                              range(3) = [0,1,2], range(2,5) = [2,3,4]
560        help                - print help for one of the listed functions
561        execfile            - execute an asap script, e.g. execfile('myscript')
562        list_rcparameters   - print out a list of possible values to be
563                              put into $HOME/.asaprc
564        rc                  - set rc parameters from within asap
565        mask_and,mask_or,
566        mask_not            - boolean operations on masks created with
567                              scantable.create_mask
568
569    Note:
570        How to use this with help:
571                                         # function 'summary'
572        [xxx] is just a category
573        Every 'sub-level' in this list should be replaces by a '.' Period when
574        using help
575        Example:
576            ASAP> help scantable # to get info on ths scantable
577            ASAP> help scantable.summary # to get help on the scantable's
578            ASAP> help average_time
579
580            """
581        if rcParams['verbose']:
582            try:
583                from IPython.genutils import page as pager
584            except ImportError:
585                from pydoc import pager
586            pager(x)
587        else:
588            print x
589        return
590
591def welcome():
592    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
593
594Please report any bugs via:
595http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
596
597[IMPORTANT: ASAP is 0-based]
598Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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