source: trunk/python/__init__.py @ 1171

Last change on this file since 1171 was 1171, checked in by mar637, 18 years ago

re-introduced custom ASAPDAT environment variable. Some more commands().

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File size: 21.7 KB
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"]
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
255
256def _is_sequence_or_number(param, ptype=int):
257    if isinstance(param,tuple) or isinstance(param,list):
258        if len(param) == 0: return True # empty list
259        out = True
260        for p in param:
261            out &= isinstance(p,ptype)
262        return out
263    elif isinstance(param, ptype):
264        return True
265    return False
266
267def _to_list(param, ptype=int):
268    if isinstance(param, ptype):
269        if ptype is str: return param.split()
270        else: return [param]
271    if _is_sequence_or_number(param, ptype):
272        return param
273    return None
274
275def unique(x):
276    """
277    Return the unique values in a list
278    Parameters:
279        x:      the list to reduce
280    Examples:
281        x = [1,2,3,3,4]
282        print unique(x)
283        [1,2,3,4]
284    """
285    return dict([ (val, 1) for val in x]).keys()
286
287def list_files(path=".",suffix="rpf"):
288    """
289    Return a list files readable by asap, such as rpf, sdfits, mbf, asap
290    Parameters:
291        path:     The directory to list (default '.')
292        suffix:   The file extension (default rpf)
293    Example:
294        files = list_files("data/","sdfits")
295        print files
296        ['data/2001-09-01_0332_P363.sdfits',
297        'data/2003-04-04_131152_t0002.sdfits',
298        'data/Sgr_86p262_best_SPC.sdfits']
299    """
300    import os
301    if not os.path.isdir(path):
302        return None
303    valid = "rpf sdf sdfits mbf asap".split()
304    if not suffix in valid:
305        return None
306    files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
307    return filter(lambda x: x.endswith(suffix),files)
308
309# workaround for ipython, which redirects this if banner=0 in ipythonrc
310sys.stdout = sys.__stdout__
311sys.stderr = sys.__stderr__
312
313# Logging
314from asap._asap import Log as _asaplog
315global asaplog
316asaplog=_asaplog()
317if rcParams['verbose']:
318    asaplog.enable()
319else:
320    asaplog.disable()
321
322def print_log():
323    log = asaplog.pop()
324    if len(log) and rcParams['verbose']: print log
325    return
326
327try:
328    import numpy.core as NUM
329except ImportError:
330    try:
331        import numarray as NUM
332    except ImportError:
333        raise ImportError("You need to have numpy or numarray installed")
334
335from asapfitter import fitter
336from asapreader import reader
337from selector import selector
338
339from asapmath import *
340from scantable import scantable
341from asaplinefind import linefinder
342from linecatalog import linecatalog
343
344mask_and = NUM.logical_and
345mask_or = NUM.logical_or
346mask_not = NUM.logical_not
347
348if rcParams['useplotter']:
349    from  asapplotter import asapplotter
350    gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
351    plotter = asapplotter(gui)
352    del gui
353
354__date__ = '$Date: 2006-08-22 23:45:12 +0000 (Tue, 22 Aug 2006) $'.split()[1]
355__version__  = '2.1b'
356
357if rcParams['verbose']:
358    def version(): print  "ASAP %s(%s)"% (__version__, __date__)
359    def list_scans(t = scantable):
360        import sys, types
361        globs = sys.modules['__main__'].__dict__.iteritems()
362        print "The user created scantables are:"
363        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
364        print filter(lambda x: not x.startswith('_'), sts)
365        return
366
367    def commands():
368        x = """
369    [The scan container]
370        scantable           - a container for integrations/scans
371                              (can open asap/rpfits/sdfits and ms files)
372            copy            - returns a copy of a scan
373            get_scan        - gets a specific scan out of a scantable
374                              (by name or number)
375            drop_scan       - drops a specific scan out of a scantable
376                              (by number)
377            set_selection   - set a new subselection of the data
378            get_selection   - get the current selection object
379            summary         - print info about the scantable contents
380            stats           - get specified statistic of the spectra in
381                              the scantable
382            stddev          - get the standard deviation of the spectra
383                              in the scantable
384            get_tsys        - get the TSys
385            get_time        - get the timestamps of the integrations
386            get_sourcename  - get the source names of the scans
387            get_azimuth     - get the azimuth of the scans
388            get_elevation   - get the elevation of the scans
389            get_parangle    - get the parallactic angle of the scans
390            get_unit        - get the current unit
391            set_unit        - set the abcissa unit to be used from this
392                              point on
393            get_abcissa     - get the abcissa values and name for a given
394                              row (time)
395            set_freqframe   - set the frame info for the Spectral Axis
396                              (e.g. 'LSRK')
397            set_doppler     - set the doppler to be used from this point on
398            set_dirframe    - set the frame for the direction on the sky
399            set_instrument  - set the instrument name
400            get_fluxunit    - get the brightness flux unit
401            set_fluxunit    - set the brightness flux unit
402            create_mask     - return an mask in the current unit
403                              for the given region. The specified regions
404                              are NOT masked
405            get_restfreqs   - get the current list of rest frequencies
406            set_restfreqs   - set a list of rest frequencies
407            flag            - flag selected channels in the data
408            save            - save the scantable to disk as either 'ASAP',
409                              'SDFITS' or 'ASCII'
410            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
411            nscan           - the number of scans in the scantable
412            nrow            - te number of spectra in the scantable
413            history         - print the history of the scantable
414            get_fit         - get a fit which has been stored witnh the data
415            average_time    - return the (weighted) time average of a scan
416                              or a list of scans
417            average_pol     - average the polarisations together.
418            average_beam    - average the beams together.
419            convert_pol     - convert to a different polarisation type
420            auto_quotient   - return the on/off quotient with
421                              automatic detection of the on/off scans (closest
422                              in time off is selected)
423            mx_quotient     - Form a quotient using MX data (off beams)
424            scale, *, /     - return a scan scaled by a given factor
425            add, +, -       - return a scan with given value added
426            bin             - return a scan with binned channels
427            resample        - return a scan with resampled channels
428            smooth          - return the spectrally smoothed scan
429            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
430            auto_poly_baseline - automatically fit a polynomial baseline
431            recalc_azel     - recalculate azimuth and elevation based on
432                              the pointing
433            gain_el         - apply gain-elevation correction
434            opacity         - apply opacity correction
435            convert_flux    - convert to and from Jy and Kelvin brightness
436                              units
437            freq_align      - align spectra in frequency frame
438            invert_phase    - Invert the phase of the cross-correlation
439            swap_linears    - Swap XX and YY
440            rotate_xyphase  - rotate XY phase of cross correlation
441            rotate_linpolphase - rotate the phase of the complex
442                                 polarization O=Q+iU correlation
443            freq_switch     - perform frequency switching on the data
444            stats           - Determine the specified statistic, e.g. 'min'
445                              'max', 'rms' etc.
446            stddev          - Determine the standard deviation of the current
447                              beam/if/pol
448     [Selection]
449         selector              - a selection object to set a subset of a scantable
450            set_scans          - set (a list of) scans by index
451            set_cycles         - set (a list of) cycles by index
452            set_beams          - set (a list of) beamss by index
453            set_ifs            - set (a list of) ifs by index
454            set_polarisations  - set (a list of) polarisations by name
455                                 or by index
456            set_names          - set a selection by name (wildcards allowed)
457            set_tsys           - set a selection by tsys thresholds
458            reset              - unset all selections
459            +                  - merge to selections
460
461     [Math] Mainly functions which operate on more than one scantable
462
463            average_time    - return the (weighted) time average
464                              of a list of scans
465            quotient        - return the on/off quotient
466            simple_math     - simple mathematical operations on two scantables,
467                              'add', 'sub', 'mul', 'div'
468            quotient        - build quotient of the given on and off scans
469                              (matched pairs and 1 off/n on are valid)
470            merge           - merge a list of scantables
471
472     [Line Catalog]
473        linecatalog              - a linecatalog wrapper, taking an ASCII or
474                                   internal format table
475            summary              - print a summary of the current selection
476            set_name             - select a subset by name pattern, e.g. '*OH*'
477            set_strength_limits  - select a subset by line strength limits
478            set_frequency_limits - select a subset by frequency limits
479            reset                - unset all selections
480            save                 - save the current subset to a table (internal
481                                   format)
482            get_row              - get the name and frequency from a specific
483                                   row in the table
484     [Fitting]
485        fitter
486            auto_fit        - return a scan where the function is
487                              applied to all Beams/IFs/Pols.
488            commit          - return a new scan where the fits have been
489                              commited.
490            fit             - execute the actual fitting process
491            store_fit       - store the fit parameters in the data (scantable)
492            get_chi2        - get the Chi^2
493            set_scan        - set the scantable to be fit
494            set_function    - set the fitting function
495            set_parameters  - set the parameters for the function(s), and
496                              set if they should be held fixed during fitting
497            set_gauss_parameters - same as above but specialised for individual
498                                   gaussian components
499            get_parameters  - get the fitted parameters
500            plot            - plot the resulting fit and/or components and
501                              residual
502    [Plotter]
503        asapplotter         - a plotter for asap, default plotter is
504                              called 'plotter'
505            plot            - plot a scantable
506            plot_lines      - plot a linecatalog overlay
507            save            - save the plot to a file ('png' ,'ps' or 'eps')
508            set_mode        - set the state of the plotter, i.e.
509                              what is to be plotted 'colour stacked'
510                              and what 'panelled'
511            set_selection   - only plot a selected part of the data
512            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
513            set_legend      - specify user labels for the legend indeces
514            set_title       - specify user labels for the panel indeces
515            set_abcissa     - specify a user label for the abcissa
516            set_ordinate    - specify a user label for the ordinate
517            set_layout      - specify the multi-panel layout (rows,cols)
518            set_colors      - specify a set of colours to use
519            set_linestyles  - specify a set of linestyles to use if only
520                              using one color
521            set_font        - set general font properties, e.g. 'family'
522            set_histogram   - plot in historam style
523            set_mask        - set a plotting mask for a specific polarization
524            text            - draw text annotations either in data or relative
525                              coordinates
526            arrow           - draw arrow annotations either in data or relative
527                              coordinates
528            axhline,axvline - draw horizontal/vertical lines
529            axhspan,axvspan - draw horizontal/vertical regions
530           
531    [Reading files]
532        reader              - access rpfits/sdfits files
533            open            - attach reader to a file
534            close           - detach reader from file
535            read            - read in integrations
536            summary         - list info about all integrations
537
538    [General]
539        commands            - this command
540        print               - print details about a variable
541        list_scans          - list all scantables created bt the user
542        list_files          - list all files readable by asap (default rpf)
543        del                 - delete the given variable from memory
544        range               - create a list of values, e.g.
545                              range(3) = [0,1,2], range(2,5) = [2,3,4]
546        help                - print help for one of the listed functions
547        execfile            - execute an asap script, e.g. execfile('myscript')
548        list_rcparameters   - print out a list of possible values to be
549                              put into $HOME/.asaprc
550        rc                  - set rc parameters from within asap
551        mask_and,mask_or,
552        mask_not            - boolean operations on masks created with
553                              scantable.create_mask
554
555    Note:
556        How to use this with help:
557                                         # function 'summary'
558        [xxx] is just a category
559        Every 'sub-level' in this list should be replaces by a '.' Period when
560        using help
561        Example:
562            ASAP> help scantable # to get info on ths scantable
563            ASAP> help scantable.summary # to get help on the scantable's
564            ASAP> help average_time
565
566            """
567        if rcParams['verbose']:
568            try:
569                from IPython.genutils import page as pager
570            except ImportError:
571                from pydoc import pager
572            pager(x)
573        else:
574            print x
575        return
576
577def welcome():
578    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
579
580Please report any bugs via:
581http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
582
583[IMPORTANT: ASAP is 0-based]
584Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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