source: trunk/python/__init__.py @ 1560

Last change on this file since 1560 was 1560, checked in by Malte Marquarding, 15 years ago

minor doc fixes; fixed list_scans, which seems brokrn in latest ipython; rc parameter xaxisformatting -> axesformatting; fixed font settings for matplotlib rc parameters

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[100]1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
[1080]5import os,sys,shutil, platform
[226]6
[1080]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]
[1171]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"]
[1371]24# use AIPSPATH if defined and "data" dir present
25if not os.environ.has_key("AIPSPATH") or \
26        not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
[1316]27    os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
[1171]28# set up user space
[1080]29userdir = os.environ["HOME"]+"/.asap"
30if not os.path.exists(userdir):
31    print 'First time ASAP use. Setting up ~/.asap'
32    os.mkdir(userdir)
33    shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
[1434]34    shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
35                    userdir+"/ipy_user_conf.py")
[1080]36    f = file(userdir+"/asapuserfuncs.py", "w")
37    f.close()
38    f = file(userdir+"/ipythonrc", "w")
39    f.close()
[1472]40else:
41    # upgrade to support later ipython versions
42    if not os.path.exists(userdir+"/ipy_user_conf.py"):
43        shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
44                        userdir+"/ipy_user_conf.py")
45
[1171]46# remove from namespace
[1080]47del asapdata, userdir, shutil, platform
48
[513]49def _validate_bool(b):
[226]50    'Convert b to a boolean or raise'
51    bl = b.lower()
52    if bl in ('f', 'no', 'false', '0', 0): return False
53    elif bl in ('t', 'yes', 'true', '1', 1): return True
54    else:
55        raise ValueError('Could not convert "%s" to boolean' % b)
56
[513]57def _validate_int(s):
[226]58    'convert s to int or raise'
59    try: return int(s)
60    except ValueError:
61        raise ValueError('Could not convert "%s" to int' % s)
62
[513]63def _asap_fname():
[226]64    """
65    Return the path to the rc file
66
67    Search order:
68
69     * current working dir
70     * environ var ASAPRC
[274]71     * HOME/.asaprc
[706]72
[226]73    """
74
75    fname = os.path.join( os.getcwd(), '.asaprc')
76    if os.path.exists(fname): return fname
77
78    if os.environ.has_key('ASAPRC'):
79        path =  os.environ['ASAPRC']
80        if os.path.exists(path):
81            fname = os.path.join(path, '.asaprc')
82            if os.path.exists(fname):
83                return fname
84
85    if os.environ.has_key('HOME'):
86        home =  os.environ['HOME']
87        fname = os.path.join(home, '.asaprc')
88        if os.path.exists(fname):
89            return fname
90    return None
91
[706]92
[226]93defaultParams = {
94    # general
[513]95    'verbose'             : [True, _validate_bool],
96    'useplotter'          : [True, _validate_bool],
[542]97    'insitu'              : [True, _validate_bool],
[706]98
[226]99    # plotting
[706]100    'plotter.gui'         : [True, _validate_bool],
[226]101    'plotter.stacking'    : ['p', str],
102    'plotter.panelling'   : ['s', str],
[700]103    'plotter.colours'     : ['', str],
104    'plotter.linestyles'  : ['', str],
[710]105    'plotter.decimate'    : [False, _validate_bool],
106    'plotter.ganged'      : [True, _validate_bool],
[1022]107    'plotter.histogram'  : [False, _validate_bool],
[1097]108    'plotter.papertype'  : ['A4', str],
[1560]109    'plotter.axesformatting' : ['mpl', str],
[710]110
[226]111    # scantable
112    'scantable.save'      : ['ASAP', str],
[513]113    'scantable.autoaverage'      : [True, _validate_bool],
[226]114    'scantable.freqframe' : ['LSRK', str],  #default frequency frame
[1076]115    'scantable.verbosesummary'   : [False, _validate_bool],
[1422]116    'scantable.storage'   : ['memory', str],
[1504]117    'scantable.history'   : [True, _validate_bool],
118    'scantable.reference'      : ['.*(e|w|_R)$', str]
[226]119    # fitter
120    }
121
[255]122def list_rcparameters():
[706]123
[255]124    print """
[737]125# general
126# print verbose output
127verbose                    : True
[255]128
[737]129# preload a default plotter
130useplotter                 : True
[255]131
[737]132# apply operations on the input scantable or return new one
133insitu                     : True
[706]134
[737]135# plotting
[710]136
[737]137# do we want a GUI or plot to a file
138plotter.gui                : True
[710]139
[737]140# default mode for colour stacking
141plotter.stacking           : Pol
[255]142
[737]143# default mode for panelling
144plotter.panelling          : scan
[255]145
[1560]146# push panels together, to share axis labels
[737]147plotter.ganged             : True
[710]148
[1513]149# decimate the number of points plotted by a factor of
[737]150# nchan/1024
151plotter.decimate           : False
[733]152
[737]153# default colours/linestyles
154plotter.colours            :
155plotter.linestyles         :
[700]156
[1022]157# enable/disable histogram plotting
158plotter.histogram          : False
159
[1097]160# ps paper type
161plotter.papertype          : A4
162
[1513]163# The formatting style of the xaxis
[1560]164plotter.axesformatting    : 'mpl' (default) or 'asap' (for old versions of matplotlib)
[1513]165
[737]166# scantable
[1076]167
[1259]168# default storage of scantable ('memory'/'disk')
[1076]169scantable.storage          : memory
[1422]170
171# write history of each call to scantable
172scantable.history          : True
173
[737]174# default ouput format when saving
175scantable.save             : ASAP
[1422]176
[737]177# auto averaging on read
178scantable.autoaverage      : True
[255]179
[737]180# default frequency frame to set when function
[1097]181# scantable.set_freqframe is called
[737]182scantable.freqframe        : LSRK
[255]183
[737]184# Control the level of information printed by summary
185scantable.verbosesummary   : False
[706]186
[1504]187# Control the identification of reference (off) scans
188# This is has to be a regular expression
189scantable.reference         : .*(e|w|_R)$
[1560]190
[737]191# Fitter
192"""
[706]193
[226]194def rc_params():
195    'Return the default params updated from the values in the rc file'
[706]196
[513]197    fname = _asap_fname()
[706]198
[226]199    if fname is None or not os.path.exists(fname):
200        message = 'could not find rc file; returning defaults'
201        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
202        #print message
203        return ret
[706]204
[226]205    cnt = 0
206    for line in file(fname):
207        cnt +=1
208        line = line.strip()
209        if not len(line): continue
210        if line.startswith('#'): continue
211        tup = line.split(':',1)
212        if len(tup) !=2:
213            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
214            continue
[706]215
[226]216        key, val = tup
217        key = key.strip()
218        if not defaultParams.has_key(key):
219            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
220            continue
[706]221
[226]222        default, converter =  defaultParams[key]
223
224        ind = val.find('#')
225        if ind>=0: val = val[:ind]   # ignore trailing comments
226        val = val.strip()
227        try: cval = converter(val)   # try to convert to proper type or raise
[1080]228        except ValueError, msg:
[226]229            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
230            continue
231        else:
232            # Alles Klar, update dict
233            defaultParams[key][0] = cval
234
235    # strip the conveter funcs and return
236    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]237    print ('loaded rc file %s'%fname)
[226]238
239    return ret
240
241
242# this is the instance used by the asap classes
[706]243rcParams = rc_params()
[226]244
245rcParamsDefault = dict(rcParams.items()) # a copy
246
247def rc(group, **kwargs):
248    """
249    Set the current rc params.  Group is the grouping for the rc, eg
[379]250    for scantable.save the group is 'scantable', for plotter.stacking, the
251    group is 'plotter', and so on.  kwargs is a list of attribute
[226]252    name/value pairs, eg
253
[379]254      rc('scantable', save='SDFITS')
[226]255
256    sets the current rc params and is equivalent to
[706]257
[379]258      rcParams['scantable.save'] = 'SDFITS'
[226]259
260    Use rcdefaults to restore the default rc params after changes.
261    """
262
[379]263    aliases = {}
[706]264
[226]265    for k,v in kwargs.items():
266        name = aliases.get(k) or k
[1422]267        if len(group):
268            key = '%s.%s' % (group, name)
269        else:
270            key = name
[226]271        if not rcParams.has_key(key):
272            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]273
[226]274        rcParams[key] = v
275
276
277def rcdefaults():
278    """
279    Restore the default rc params - the ones that were created at
280    asap load time
281    """
282    rcParams.update(rcParamsDefault)
283
[1295]284def _n_bools(n, val):
285    return [ val for i in xrange(n) ]
[513]286
287def _is_sequence_or_number(param, ptype=int):
288    if isinstance(param,tuple) or isinstance(param,list):
[928]289        if len(param) == 0: return True # empty list
[513]290        out = True
291        for p in param:
292            out &= isinstance(p,ptype)
293        return out
294    elif isinstance(param, ptype):
295        return True
296    return False
297
[928]298def _to_list(param, ptype=int):
299    if isinstance(param, ptype):
300        if ptype is str: return param.split()
301        else: return [param]
302    if _is_sequence_or_number(param, ptype):
303        return param
304    return None
[715]305
[944]306def unique(x):
[992]307    """
308    Return the unique values in a list
309    Parameters:
310        x:      the list to reduce
311    Examples:
312        x = [1,2,3,3,4]
313        print unique(x)
314        [1,2,3,4]
315    """
[944]316    return dict([ (val, 1) for val in x]).keys()
317
[992]318def list_files(path=".",suffix="rpf"):
319    """
320    Return a list files readable by asap, such as rpf, sdfits, mbf, asap
321    Parameters:
322        path:     The directory to list (default '.')
323        suffix:   The file extension (default rpf)
324    Example:
325        files = list_files("data/","sdfits")
326        print files
327        ['data/2001-09-01_0332_P363.sdfits',
328        'data/2003-04-04_131152_t0002.sdfits',
329        'data/Sgr_86p262_best_SPC.sdfits']
330    """
331    if not os.path.isdir(path):
332        return None
[1295]333    valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
[992]334    if not suffix in valid:
335        return None
336    files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
337    return filter(lambda x: x.endswith(suffix),files)
338
[715]339# workaround for ipython, which redirects this if banner=0 in ipythonrc
340sys.stdout = sys.__stdout__
341sys.stderr = sys.__stderr__
342
343# Logging
344from asap._asap import Log as _asaplog
345global asaplog
[710]346asaplog=_asaplog()
[715]347if rcParams['verbose']:
348    asaplog.enable()
349else:
350    asaplog.disable()
351
352def print_log():
353    log = asaplog.pop()
354    if len(log) and rcParams['verbose']: print log
355    return
356
[1295]357def mask_and(a, b):
358    assert(len(a)==len(b))
359    return [ a[i] & b[i] for i in xrange(len(a)) ]
[1134]360
[1295]361def mask_or(a, b):
362    assert(len(a)==len(b))
363    return [ a[i] | b[i] for i in xrange(len(a)) ]
364
365def mask_not(a):
366    return [ not i for i in a ]
367
[1117]368from asapfitter import fitter
[895]369from asapreader import reader
[944]370from selector import selector
[710]371
[100]372from asapmath import *
[1080]373from scantable import scantable
[1097]374from asaplinefind import linefinder
[1134]375from linecatalog import linecatalog
[285]376
[928]377if rcParams['useplotter']:
[1295]378    try:
[1423]379        from asapplotter import asapplotter
380        gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
381        if gui:
[1422]382            import matplotlib
383            matplotlib.use("TkAgg")
[1423]384        import pylab
[1422]385        xyplotter = pylab
[1423]386        plotter = asapplotter(gui)
387        del gui
[1295]388    except ImportError:
[1423]389        print "Matplotlib not installed. No plotting available"
[285]390
[574]391__date__ = '$Date: 2009-03-31 01:13:51 +0000 (Tue, 31 Mar 2009) $'.split()[1]
[1560]392__version__  = '$Revision: 1560 $'
[100]393
[1193]394def is_ipython():
[1259]395    return '__IP' in dir(sys.modules["__main__"])
[1193]396if is_ipython():
[1014]397    def version(): print  "ASAP %s(%s)"% (__version__, __date__)
[1422]398   
[1560]399    def list_scans(t = scantable):       
400        import inspect
401        print "The user created scantables are: ",
402        globs=inspect.currentframe().f_back.f_locals.copy()
403        out = [ k for k,v in globs.iteritems() \
404                     if isinstance(v, scantable) and not k.startswith("_") ]
405        print out
406        return out
[100]407
[715]408    def commands():
409        x = """
[113]410    [The scan container]
411        scantable           - a container for integrations/scans
[182]412                              (can open asap/rpfits/sdfits and ms files)
[113]413            copy            - returns a copy of a scan
414            get_scan        - gets a specific scan out of a scantable
[984]415                              (by name or number)
[1093]416            drop_scan       - drops a specific scan out of a scantable
417                              (by number)
[984]418            set_selection   - set a new subselection of the data
419            get_selection   - get the current selection object
[113]420            summary         - print info about the scantable contents
[182]421            stats           - get specified statistic of the spectra in
422                              the scantable
423            stddev          - get the standard deviation of the spectra
424                              in the scantable
[113]425            get_tsys        - get the TSys
426            get_time        - get the timestamps of the integrations
[1351]427            get_inttime     - get the integration time
[733]428            get_sourcename  - get the source names of the scans
[794]429            get_azimuth     - get the azimuth of the scans
430            get_elevation   - get the elevation of the scans
431            get_parangle    - get the parallactic angle of the scans
[876]432            get_unit        - get the current unit
[513]433            set_unit        - set the abcissa unit to be used from this
434                              point on
[255]435            get_abcissa     - get the abcissa values and name for a given
436                              row (time)
[1259]437            get_column_names - get the names of the columns in the scantable
438                               for use with selector.set_query
[113]439            set_freqframe   - set the frame info for the Spectral Axis
440                              (e.g. 'LSRK')
[276]441            set_doppler     - set the doppler to be used from this point on
[984]442            set_dirframe    - set the frame for the direction on the sky
[240]443            set_instrument  - set the instrument name
[1190]444            set_feedtype    - set the feed type
[255]445            get_fluxunit    - get the brightness flux unit
[240]446            set_fluxunit    - set the brightness flux unit
[1508]447            set_sourcetype  - set the type of the source - source or reference
[188]448            create_mask     - return an mask in the current unit
449                              for the given region. The specified regions
450                              are NOT masked
[255]451            get_restfreqs   - get the current list of rest frequencies
452            set_restfreqs   - set a list of rest frequencies
[1471]453            shift_refpix    - shift the reference pixel of the IFs
454            set_spectrum    - overwrite the spectrum for a given row
455            get_spectrum    - retrieve the spectrum for a given
456            get_mask        - retrieve the mask for a given
[1012]457            flag            - flag selected channels in the data
[1192]458            lag_flag        - flag specified frequency in the data
[1151]459            save            - save the scantable to disk as either 'ASAP',
460                              'SDFITS' or 'ASCII'
[486]461            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
[733]462            nscan           - the number of scans in the scantable
[1422]463            nrow            - the number of spectra in the scantable
[486]464            history         - print the history of the scantable
[530]465            get_fit         - get a fit which has been stored witnh the data
[706]466            average_time    - return the (weighted) time average of a scan
[513]467                              or a list of scans
468            average_pol     - average the polarisations together.
[1144]469            average_beam    - average the beams together.
[992]470            convert_pol     - convert to a different polarisation type
[690]471            auto_quotient   - return the on/off quotient with
[1069]472                              automatic detection of the on/off scans (closest
473                              in time off is selected)
[1144]474            mx_quotient     - Form a quotient using MX data (off beams)
[1014]475            scale, *, /     - return a scan scaled by a given factor
[1560]476            add, +          - return a scan with given value added
477            sub, -          - return a scan with given value subtracted
[513]478            bin             - return a scan with binned channels
479            resample        - return a scan with resampled channels
480            smooth          - return the spectrally smoothed scan
481            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
[706]482            auto_poly_baseline - automatically fit a polynomial baseline
[780]483            recalc_azel     - recalculate azimuth and elevation based on
484                              the pointing
[513]485            gain_el         - apply gain-elevation correction
486            opacity         - apply opacity correction
487            convert_flux    - convert to and from Jy and Kelvin brightness
[255]488                              units
[513]489            freq_align      - align spectra in frequency frame
[1014]490            invert_phase    - Invert the phase of the cross-correlation
[1351]491            swap_linears    - Swap XX and YY (or RR LL)
[513]492            rotate_xyphase  - rotate XY phase of cross correlation
493            rotate_linpolphase - rotate the phase of the complex
494                                 polarization O=Q+iU correlation
[733]495            freq_switch     - perform frequency switching on the data
496            stats           - Determine the specified statistic, e.g. 'min'
497                              'max', 'rms' etc.
498            stddev          - Determine the standard deviation of the current
499                              beam/if/pol
[1014]500     [Selection]
501         selector              - a selection object to set a subset of a scantable
502            set_scans          - set (a list of) scans by index
503            set_cycles         - set (a list of) cycles by index
504            set_beams          - set (a list of) beamss by index
505            set_ifs            - set (a list of) ifs by index
506            set_polarisations  - set (a list of) polarisations by name
507                                 or by index
508            set_names          - set a selection by name (wildcards allowed)
509            set_tsys           - set a selection by tsys thresholds
[1259]510            set_query          - set a selection by SQL-like query, e.g. BEAMNO==1
[1351]511            ( also  get_ functions for all these )
[1014]512            reset              - unset all selections
[1351]513            +                  - merge two selections
[733]514
[513]515     [Math] Mainly functions which operate on more than one scantable
[100]516
[706]517            average_time    - return the (weighted) time average
[513]518                              of a list of scans
519            quotient        - return the on/off quotient
520            simple_math     - simple mathematical operations on two scantables,
521                              'add', 'sub', 'mul', 'div'
[1069]522            quotient        - build quotient of the given on and off scans
[1351]523                              (matched pairs and 1 off - n on are valid)
[1117]524            merge           - merge a list of scantables
[1069]525
[1151]526     [Line Catalog]
527        linecatalog              - a linecatalog wrapper, taking an ASCII or
528                                   internal format table
529            summary              - print a summary of the current selection
530            set_name             - select a subset by name pattern, e.g. '*OH*'
531            set_strength_limits  - select a subset by line strength limits
532            set_frequency_limits - select a subset by frequency limits
533            reset                - unset all selections
534            save                 - save the current subset to a table (internal
535                                   format)
536            get_row              - get the name and frequency from a specific
537                                   row in the table
[513]538     [Fitting]
[113]539        fitter
540            auto_fit        - return a scan where the function is
541                              applied to all Beams/IFs/Pols.
542            commit          - return a new scan where the fits have been
543                              commited.
544            fit             - execute the actual fitting process
[984]545            store_fit       - store the fit parameters in the data (scantable)
[113]546            get_chi2        - get the Chi^2
547            set_scan        - set the scantable to be fit
548            set_function    - set the fitting function
549            set_parameters  - set the parameters for the function(s), and
550                              set if they should be held fixed during fitting
[513]551            set_gauss_parameters - same as above but specialised for individual
552                                   gaussian components
[113]553            get_parameters  - get the fitted parameters
[513]554            plot            - plot the resulting fit and/or components and
555                              residual
[210]556    [Plotter]
557        asapplotter         - a plotter for asap, default plotter is
558                              called 'plotter'
[984]559            plot            - plot a scantable
[1151]560            plot_lines      - plot a linecatalog overlay
[378]561            save            - save the plot to a file ('png' ,'ps' or 'eps')
[210]562            set_mode        - set the state of the plotter, i.e.
563                              what is to be plotted 'colour stacked'
564                              and what 'panelled'
[984]565            set_selection   - only plot a selected part of the data
[733]566            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
[255]567            set_legend      - specify user labels for the legend indeces
568            set_title       - specify user labels for the panel indeces
[733]569            set_abcissa     - specify a user label for the abcissa
[255]570            set_ordinate    - specify a user label for the ordinate
[378]571            set_layout      - specify the multi-panel layout (rows,cols)
[733]572            set_colors      - specify a set of colours to use
573            set_linestyles  - specify a set of linestyles to use if only
574                              using one color
[1151]575            set_font        - set general font properties, e.g. 'family'
[1054]576            set_histogram   - plot in historam style
[733]577            set_mask        - set a plotting mask for a specific polarization
[1171]578            text            - draw text annotations either in data or relative
579                              coordinates
580            arrow           - draw arrow annotations either in data or relative
581                              coordinates
582            axhline,axvline - draw horizontal/vertical lines
583            axhspan,axvspan - draw horizontal/vertical regions
[1560]584            annotate        - draw an arrow with label
585            create_mask     - create a scnatble mask interactively
[1175]586
587        xyplotter           - matplotlib/pylab plotting functions
588
[182]589    [Reading files]
590        reader              - access rpfits/sdfits files
[984]591            open            - attach reader to a file
592            close           - detach reader from file
[182]593            read            - read in integrations
594            summary         - list info about all integrations
595
[113]596    [General]
597        commands            - this command
598        print               - print details about a variable
[1560]599        list_scans          - list all scantables created by the user
[992]600        list_files          - list all files readable by asap (default rpf)
[113]601        del                 - delete the given variable from memory
602        range               - create a list of values, e.g.
603                              range(3) = [0,1,2], range(2,5) = [2,3,4]
604        help                - print help for one of the listed functions
605        execfile            - execute an asap script, e.g. execfile('myscript')
[255]606        list_rcparameters   - print out a list of possible values to be
[274]607                              put into $HOME/.asaprc
[1171]608        rc                  - set rc parameters from within asap
[466]609        mask_and,mask_or,
610        mask_not            - boolean operations on masks created with
611                              scantable.create_mask
[706]612
[210]613    Note:
614        How to use this with help:
615                                         # function 'summary'
616        [xxx] is just a category
617        Every 'sub-level' in this list should be replaces by a '.' Period when
[706]618        using help
[210]619        Example:
620            ASAP> help scantable # to get info on ths scantable
621            ASAP> help scantable.summary # to get help on the scantable's
622            ASAP> help average_time
623
[715]624            """
[1151]625        if rcParams['verbose']:
626            try:
627                from IPython.genutils import page as pager
628            except ImportError:
629                from pydoc import pager
630            pager(x)
631        else:
632            print x
[715]633        return
[113]634
[706]635def welcome():
636    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]637
[1035]638Please report any bugs via:
[1378]639http://svn.atnf.csiro.au/trac/asap/simpleticket
[100]640
[378]641[IMPORTANT: ASAP is 0-based]
[706]642Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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