source: trunk/python/__init__.py @ 1190

Last change on this file since 1190 was 1190, checked in by mar637, 18 years ago

added set_feedtype (Ticket #61)

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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
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: 2006-08-28 02:47:15 +0000 (Mon, 28 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            set_feedtype    - set the feed type
403            get_fluxunit    - get the brightness flux unit
404            set_fluxunit    - set the brightness flux unit
405            create_mask     - return an mask in the current unit
406                              for the given region. The specified regions
407                              are NOT masked
408            get_restfreqs   - get the current list of rest frequencies
409            set_restfreqs   - set a list of rest frequencies
410            flag            - flag selected channels in the data
411            save            - save the scantable to disk as either 'ASAP',
412                              'SDFITS' or 'ASCII'
413            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
414            nscan           - the number of scans in the scantable
415            nrow            - te number of spectra in the scantable
416            history         - print the history of the scantable
417            get_fit         - get a fit which has been stored witnh the data
418            average_time    - return the (weighted) time average of a scan
419                              or a list of scans
420            average_pol     - average the polarisations together.
421            average_beam    - average the beams together.
422            convert_pol     - convert to a different polarisation type
423            auto_quotient   - return the on/off quotient with
424                              automatic detection of the on/off scans (closest
425                              in time off is selected)
426            mx_quotient     - Form a quotient using MX data (off beams)
427            scale, *, /     - return a scan scaled by a given factor
428            add, +, -       - return a scan with given value added
429            bin             - return a scan with binned channels
430            resample        - return a scan with resampled channels
431            smooth          - return the spectrally smoothed scan
432            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
433            auto_poly_baseline - automatically fit a polynomial baseline
434            recalc_azel     - recalculate azimuth and elevation based on
435                              the pointing
436            gain_el         - apply gain-elevation correction
437            opacity         - apply opacity correction
438            convert_flux    - convert to and from Jy and Kelvin brightness
439                              units
440            freq_align      - align spectra in frequency frame
441            invert_phase    - Invert the phase of the cross-correlation
442            swap_linears    - Swap XX and YY
443            rotate_xyphase  - rotate XY phase of cross correlation
444            rotate_linpolphase - rotate the phase of the complex
445                                 polarization O=Q+iU correlation
446            freq_switch     - perform frequency switching on the data
447            stats           - Determine the specified statistic, e.g. 'min'
448                              'max', 'rms' etc.
449            stddev          - Determine the standard deviation of the current
450                              beam/if/pol
451     [Selection]
452         selector              - a selection object to set a subset of a scantable
453            set_scans          - set (a list of) scans by index
454            set_cycles         - set (a list of) cycles by index
455            set_beams          - set (a list of) beamss by index
456            set_ifs            - set (a list of) ifs by index
457            set_polarisations  - set (a list of) polarisations by name
458                                 or by index
459            set_names          - set a selection by name (wildcards allowed)
460            set_tsys           - set a selection by tsys thresholds
461            reset              - unset all selections
462            +                  - merge to selections
463
464     [Math] Mainly functions which operate on more than one scantable
465
466            average_time    - return the (weighted) time average
467                              of a list of scans
468            quotient        - return the on/off quotient
469            simple_math     - simple mathematical operations on two scantables,
470                              'add', 'sub', 'mul', 'div'
471            quotient        - build quotient of the given on and off scans
472                              (matched pairs and 1 off/n on are valid)
473            merge           - merge a list of scantables
474
475     [Line Catalog]
476        linecatalog              - a linecatalog wrapper, taking an ASCII or
477                                   internal format table
478            summary              - print a summary of the current selection
479            set_name             - select a subset by name pattern, e.g. '*OH*'
480            set_strength_limits  - select a subset by line strength limits
481            set_frequency_limits - select a subset by frequency limits
482            reset                - unset all selections
483            save                 - save the current subset to a table (internal
484                                   format)
485            get_row              - get the name and frequency from a specific
486                                   row in the table
487     [Fitting]
488        fitter
489            auto_fit        - return a scan where the function is
490                              applied to all Beams/IFs/Pols.
491            commit          - return a new scan where the fits have been
492                              commited.
493            fit             - execute the actual fitting process
494            store_fit       - store the fit parameters in the data (scantable)
495            get_chi2        - get the Chi^2
496            set_scan        - set the scantable to be fit
497            set_function    - set the fitting function
498            set_parameters  - set the parameters for the function(s), and
499                              set if they should be held fixed during fitting
500            set_gauss_parameters - same as above but specialised for individual
501                                   gaussian components
502            get_parameters  - get the fitted parameters
503            plot            - plot the resulting fit and/or components and
504                              residual
505    [Plotter]
506        asapplotter         - a plotter for asap, default plotter is
507                              called 'plotter'
508            plot            - plot a scantable
509            plot_lines      - plot a linecatalog overlay
510            save            - save the plot to a file ('png' ,'ps' or 'eps')
511            set_mode        - set the state of the plotter, i.e.
512                              what is to be plotted 'colour stacked'
513                              and what 'panelled'
514            set_selection   - only plot a selected part of the data
515            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
516            set_legend      - specify user labels for the legend indeces
517            set_title       - specify user labels for the panel indeces
518            set_abcissa     - specify a user label for the abcissa
519            set_ordinate    - specify a user label for the ordinate
520            set_layout      - specify the multi-panel layout (rows,cols)
521            set_colors      - specify a set of colours to use
522            set_linestyles  - specify a set of linestyles to use if only
523                              using one color
524            set_font        - set general font properties, e.g. 'family'
525            set_histogram   - plot in historam style
526            set_mask        - set a plotting mask for a specific polarization
527            text            - draw text annotations either in data or relative
528                              coordinates
529            arrow           - draw arrow annotations either in data or relative
530                              coordinates
531            axhline,axvline - draw horizontal/vertical lines
532            axhspan,axvspan - draw horizontal/vertical regions
533
534        xyplotter           - matplotlib/pylab plotting functions
535
536    [Reading files]
537        reader              - access rpfits/sdfits files
538            open            - attach reader to a file
539            close           - detach reader from file
540            read            - read in integrations
541            summary         - list info about all integrations
542
543    [General]
544        commands            - this command
545        print               - print details about a variable
546        list_scans          - list all scantables created bt the user
547        list_files          - list all files readable by asap (default rpf)
548        del                 - delete the given variable from memory
549        range               - create a list of values, e.g.
550                              range(3) = [0,1,2], range(2,5) = [2,3,4]
551        help                - print help for one of the listed functions
552        execfile            - execute an asap script, e.g. execfile('myscript')
553        list_rcparameters   - print out a list of possible values to be
554                              put into $HOME/.asaprc
555        rc                  - set rc parameters from within asap
556        mask_and,mask_or,
557        mask_not            - boolean operations on masks created with
558                              scantable.create_mask
559
560    Note:
561        How to use this with help:
562                                         # function 'summary'
563        [xxx] is just a category
564        Every 'sub-level' in this list should be replaces by a '.' Period when
565        using help
566        Example:
567            ASAP> help scantable # to get info on ths scantable
568            ASAP> help scantable.summary # to get help on the scantable's
569            ASAP> help average_time
570
571            """
572        if rcParams['verbose']:
573            try:
574                from IPython.genutils import page as pager
575            except ImportError:
576                from pydoc import pager
577            pager(x)
578        else:
579            print x
580        return
581
582def welcome():
583    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
584
585Please report any bugs via:
586http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
587
588[IMPORTANT: ASAP is 0-based]
589Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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