source: trunk/python/__init__.py @ 1175

Last change on this file since 1175 was 1175, checked in by mar637, 18 years ago

various changes to support the pylab plotter 'xyplotter'

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File size: 21.8 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    if gui:
352        import pylab as xyplotter
353    plotter = asapplotter(gui)
354    del gui
355
356__date__ = '$Date: 2006-08-23 03:15:32 +0000 (Wed, 23 Aug 2006) $'.split()[1]
357__version__  = '2.1b'
358
359if rcParams['verbose']:
360    def version(): print  "ASAP %s(%s)"% (__version__, __date__)
361    def list_scans(t = scantable):
362        import sys, types
363        globs = sys.modules['__main__'].__dict__.iteritems()
364        print "The user created scantables are:"
365        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
366        print filter(lambda x: not x.startswith('_'), sts)
367        return
368
369    def commands():
370        x = """
371    [The scan container]
372        scantable           - a container for integrations/scans
373                              (can open asap/rpfits/sdfits and ms files)
374            copy            - returns a copy of a scan
375            get_scan        - gets a specific scan out of a scantable
376                              (by name or number)
377            drop_scan       - drops a specific scan out of a scantable
378                              (by number)
379            set_selection   - set a new subselection of the data
380            get_selection   - get the current selection object
381            summary         - print info about the scantable contents
382            stats           - get specified statistic of the spectra in
383                              the scantable
384            stddev          - get the standard deviation of the spectra
385                              in the scantable
386            get_tsys        - get the TSys
387            get_time        - get the timestamps of the integrations
388            get_sourcename  - get the source names of the scans
389            get_azimuth     - get the azimuth of the scans
390            get_elevation   - get the elevation of the scans
391            get_parangle    - get the parallactic angle of the scans
392            get_unit        - get the current unit
393            set_unit        - set the abcissa unit to be used from this
394                              point on
395            get_abcissa     - get the abcissa values and name for a given
396                              row (time)
397            set_freqframe   - set the frame info for the Spectral Axis
398                              (e.g. 'LSRK')
399            set_doppler     - set the doppler to be used from this point on
400            set_dirframe    - set the frame for the direction on the sky
401            set_instrument  - set the instrument name
402            get_fluxunit    - get the brightness flux unit
403            set_fluxunit    - set the brightness flux unit
404            create_mask     - return an mask in the current unit
405                              for the given region. The specified regions
406                              are NOT masked
407            get_restfreqs   - get the current list of rest frequencies
408            set_restfreqs   - set a list of rest frequencies
409            flag            - flag selected channels in the data
410            save            - save the scantable to disk as either 'ASAP',
411                              'SDFITS' or 'ASCII'
412            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
413            nscan           - the number of scans in the scantable
414            nrow            - te number of spectra in the scantable
415            history         - print the history of the scantable
416            get_fit         - get a fit which has been stored witnh the data
417            average_time    - return the (weighted) time average of a scan
418                              or a list of scans
419            average_pol     - average the polarisations together.
420            average_beam    - average the beams together.
421            convert_pol     - convert to a different polarisation type
422            auto_quotient   - return the on/off quotient with
423                              automatic detection of the on/off scans (closest
424                              in time off is selected)
425            mx_quotient     - Form a quotient using MX data (off beams)
426            scale, *, /     - return a scan scaled by a given factor
427            add, +, -       - return a scan with given value added
428            bin             - return a scan with binned channels
429            resample        - return a scan with resampled channels
430            smooth          - return the spectrally smoothed scan
431            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
432            auto_poly_baseline - automatically fit a polynomial baseline
433            recalc_azel     - recalculate azimuth and elevation based on
434                              the pointing
435            gain_el         - apply gain-elevation correction
436            opacity         - apply opacity correction
437            convert_flux    - convert to and from Jy and Kelvin brightness
438                              units
439            freq_align      - align spectra in frequency frame
440            invert_phase    - Invert the phase of the cross-correlation
441            swap_linears    - Swap XX and YY
442            rotate_xyphase  - rotate XY phase of cross correlation
443            rotate_linpolphase - rotate the phase of the complex
444                                 polarization O=Q+iU correlation
445            freq_switch     - perform frequency switching on the data
446            stats           - Determine the specified statistic, e.g. 'min'
447                              'max', 'rms' etc.
448            stddev          - Determine the standard deviation of the current
449                              beam/if/pol
450     [Selection]
451         selector              - a selection object to set a subset of a scantable
452            set_scans          - set (a list of) scans by index
453            set_cycles         - set (a list of) cycles by index
454            set_beams          - set (a list of) beamss by index
455            set_ifs            - set (a list of) ifs by index
456            set_polarisations  - set (a list of) polarisations by name
457                                 or by index
458            set_names          - set a selection by name (wildcards allowed)
459            set_tsys           - set a selection by tsys thresholds
460            reset              - unset all selections
461            +                  - merge to selections
462
463     [Math] Mainly functions which operate on more than one scantable
464
465            average_time    - return the (weighted) time average
466                              of a list of scans
467            quotient        - return the on/off quotient
468            simple_math     - simple mathematical operations on two scantables,
469                              'add', 'sub', 'mul', 'div'
470            quotient        - build quotient of the given on and off scans
471                              (matched pairs and 1 off/n on are valid)
472            merge           - merge a list of scantables
473
474     [Line Catalog]
475        linecatalog              - a linecatalog wrapper, taking an ASCII or
476                                   internal format table
477            summary              - print a summary of the current selection
478            set_name             - select a subset by name pattern, e.g. '*OH*'
479            set_strength_limits  - select a subset by line strength limits
480            set_frequency_limits - select a subset by frequency limits
481            reset                - unset all selections
482            save                 - save the current subset to a table (internal
483                                   format)
484            get_row              - get the name and frequency from a specific
485                                   row in the table
486     [Fitting]
487        fitter
488            auto_fit        - return a scan where the function is
489                              applied to all Beams/IFs/Pols.
490            commit          - return a new scan where the fits have been
491                              commited.
492            fit             - execute the actual fitting process
493            store_fit       - store the fit parameters in the data (scantable)
494            get_chi2        - get the Chi^2
495            set_scan        - set the scantable to be fit
496            set_function    - set the fitting function
497            set_parameters  - set the parameters for the function(s), and
498                              set if they should be held fixed during fitting
499            set_gauss_parameters - same as above but specialised for individual
500                                   gaussian components
501            get_parameters  - get the fitted parameters
502            plot            - plot the resulting fit and/or components and
503                              residual
504    [Plotter]
505        asapplotter         - a plotter for asap, default plotter is
506                              called 'plotter'
507            plot            - plot a scantable
508            plot_lines      - plot a linecatalog overlay
509            save            - save the plot to a file ('png' ,'ps' or 'eps')
510            set_mode        - set the state of the plotter, i.e.
511                              what is to be plotted 'colour stacked'
512                              and what 'panelled'
513            set_selection   - only plot a selected part of the data
514            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
515            set_legend      - specify user labels for the legend indeces
516            set_title       - specify user labels for the panel indeces
517            set_abcissa     - specify a user label for the abcissa
518            set_ordinate    - specify a user label for the ordinate
519            set_layout      - specify the multi-panel layout (rows,cols)
520            set_colors      - specify a set of colours to use
521            set_linestyles  - specify a set of linestyles to use if only
522                              using one color
523            set_font        - set general font properties, e.g. 'family'
524            set_histogram   - plot in historam style
525            set_mask        - set a plotting mask for a specific polarization
526            text            - draw text annotations either in data or relative
527                              coordinates
528            arrow           - draw arrow annotations either in data or relative
529                              coordinates
530            axhline,axvline - draw horizontal/vertical lines
531            axhspan,axvspan - draw horizontal/vertical regions
532
533        xyplotter           - matplotlib/pylab plotting functions
534
535    [Reading files]
536        reader              - access rpfits/sdfits files
537            open            - attach reader to a file
538            close           - detach reader from file
539            read            - read in integrations
540            summary         - list info about all integrations
541
542    [General]
543        commands            - this command
544        print               - print details about a variable
545        list_scans          - list all scantables created bt the user
546        list_files          - list all files readable by asap (default rpf)
547        del                 - delete the given variable from memory
548        range               - create a list of values, e.g.
549                              range(3) = [0,1,2], range(2,5) = [2,3,4]
550        help                - print help for one of the listed functions
551        execfile            - execute an asap script, e.g. execfile('myscript')
552        list_rcparameters   - print out a list of possible values to be
553                              put into $HOME/.asaprc
554        rc                  - set rc parameters from within asap
555        mask_and,mask_or,
556        mask_not            - boolean operations on masks created with
557                              scantable.create_mask
558
559    Note:
560        How to use this with help:
561                                         # function 'summary'
562        [xxx] is just a category
563        Every 'sub-level' in this list should be replaces by a '.' Period when
564        using help
565        Example:
566            ASAP> help scantable # to get info on ths scantable
567            ASAP> help scantable.summary # to get help on the scantable's
568            ASAP> help average_time
569
570            """
571        if rcParams['verbose']:
572            try:
573                from IPython.genutils import page as pager
574            except ImportError:
575                from pydoc import pager
576            pager(x)
577        else:
578            print x
579        return
580
581def welcome():
582    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
583
584Please report any bugs via:
585http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
586
587[IMPORTANT: ASAP is 0-based]
588Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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