source: trunk/python/__init__.py @ 1471

Last change on this file since 1471 was 1471, checked in by Malte Marquarding, 15 years ago

added publich get/set_spectrum functions

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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()
[1171]40# remove from namespace
[1080]41del asapdata, userdir, shutil, platform
42
[513]43def _validate_bool(b):
[226]44    'Convert b to a boolean or raise'
45    bl = b.lower()
46    if bl in ('f', 'no', 'false', '0', 0): return False
47    elif bl in ('t', 'yes', 'true', '1', 1): return True
48    else:
49        raise ValueError('Could not convert "%s" to boolean' % b)
50
[513]51def _validate_int(s):
[226]52    'convert s to int or raise'
53    try: return int(s)
54    except ValueError:
55        raise ValueError('Could not convert "%s" to int' % s)
56
[513]57def _asap_fname():
[226]58    """
59    Return the path to the rc file
60
61    Search order:
62
63     * current working dir
64     * environ var ASAPRC
[274]65     * HOME/.asaprc
[706]66
[226]67    """
68
69    fname = os.path.join( os.getcwd(), '.asaprc')
70    if os.path.exists(fname): return fname
71
72    if os.environ.has_key('ASAPRC'):
73        path =  os.environ['ASAPRC']
74        if os.path.exists(path):
75            fname = os.path.join(path, '.asaprc')
76            if os.path.exists(fname):
77                return fname
78
79    if os.environ.has_key('HOME'):
80        home =  os.environ['HOME']
81        fname = os.path.join(home, '.asaprc')
82        if os.path.exists(fname):
83            return fname
84    return None
85
[706]86
[226]87defaultParams = {
88    # general
[513]89    'verbose'             : [True, _validate_bool],
90    'useplotter'          : [True, _validate_bool],
[542]91    'insitu'              : [True, _validate_bool],
[706]92
[226]93    # plotting
[706]94    'plotter.gui'         : [True, _validate_bool],
[226]95    'plotter.stacking'    : ['p', str],
96    'plotter.panelling'   : ['s', str],
[700]97    'plotter.colours'     : ['', str],
98    'plotter.linestyles'  : ['', str],
[710]99    'plotter.decimate'    : [False, _validate_bool],
100    'plotter.ganged'      : [True, _validate_bool],
[1022]101    'plotter.histogram'  : [False, _validate_bool],
[1097]102    'plotter.papertype'  : ['A4', str],
[710]103
[226]104    # scantable
105    'scantable.save'      : ['ASAP', str],
[513]106    'scantable.autoaverage'      : [True, _validate_bool],
[226]107    'scantable.freqframe' : ['LSRK', str],  #default frequency frame
[1076]108    'scantable.verbosesummary'   : [False, _validate_bool],
[1422]109    'scantable.storage'   : ['memory', str],
110    'scantable.history'   : [True, _validate_bool]
[226]111    # fitter
112    }
113
[255]114def list_rcparameters():
[706]115
[255]116    print """
[737]117# general
118# print verbose output
119verbose                    : True
[255]120
[737]121# preload a default plotter
122useplotter                 : True
[255]123
[737]124# apply operations on the input scantable or return new one
125insitu                     : True
[706]126
[737]127# plotting
[710]128
[737]129# do we want a GUI or plot to a file
130plotter.gui                : True
[710]131
[737]132# default mode for colour stacking
133plotter.stacking           : Pol
[255]134
[737]135# default mode for panelling
136plotter.panelling          : scan
[255]137
[737]138# push panels together, to share axislabels
139plotter.ganged             : True
[710]140
[737]141# decimate the number of points plotted bya afactor of
142# nchan/1024
143plotter.decimate           : False
[733]144
[737]145# default colours/linestyles
146plotter.colours            :
147plotter.linestyles         :
[700]148
[1022]149# enable/disable histogram plotting
150plotter.histogram          : False
151
[1097]152# ps paper type
153plotter.papertype          : A4
154
[737]155# scantable
[1076]156
[1259]157# default storage of scantable ('memory'/'disk')
[1076]158scantable.storage          : memory
[1422]159
160# write history of each call to scantable
161scantable.history          : True
162
[737]163# default ouput format when saving
164scantable.save             : ASAP
[1422]165
[737]166# auto averaging on read
167scantable.autoaverage      : True
[255]168
[737]169# default frequency frame to set when function
[1097]170# scantable.set_freqframe is called
[737]171scantable.freqframe        : LSRK
[255]172
[737]173# Control the level of information printed by summary
174scantable.verbosesummary   : False
[706]175
[737]176# Fitter
177"""
[706]178
[226]179def rc_params():
180    'Return the default params updated from the values in the rc file'
[706]181
[513]182    fname = _asap_fname()
[706]183
[226]184    if fname is None or not os.path.exists(fname):
185        message = 'could not find rc file; returning defaults'
186        ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
187        #print message
188        return ret
[706]189
[226]190    cnt = 0
191    for line in file(fname):
192        cnt +=1
193        line = line.strip()
194        if not len(line): continue
195        if line.startswith('#'): continue
196        tup = line.split(':',1)
197        if len(tup) !=2:
198            print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
199            continue
[706]200
[226]201        key, val = tup
202        key = key.strip()
203        if not defaultParams.has_key(key):
204            print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
205            continue
[706]206
[226]207        default, converter =  defaultParams[key]
208
209        ind = val.find('#')
210        if ind>=0: val = val[:ind]   # ignore trailing comments
211        val = val.strip()
212        try: cval = converter(val)   # try to convert to proper type or raise
[1080]213        except ValueError, msg:
[226]214            print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
215            continue
216        else:
217            # Alles Klar, update dict
218            defaultParams[key][0] = cval
219
220    # strip the conveter funcs and return
221    ret =  dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]222    print ('loaded rc file %s'%fname)
[226]223
224    return ret
225
226
227# this is the instance used by the asap classes
[706]228rcParams = rc_params()
[226]229
230rcParamsDefault = dict(rcParams.items()) # a copy
231
232def rc(group, **kwargs):
233    """
234    Set the current rc params.  Group is the grouping for the rc, eg
[379]235    for scantable.save the group is 'scantable', for plotter.stacking, the
236    group is 'plotter', and so on.  kwargs is a list of attribute
[226]237    name/value pairs, eg
238
[379]239      rc('scantable', save='SDFITS')
[226]240
241    sets the current rc params and is equivalent to
[706]242
[379]243      rcParams['scantable.save'] = 'SDFITS'
[226]244
245    Use rcdefaults to restore the default rc params after changes.
246    """
247
[379]248    aliases = {}
[706]249
[226]250    for k,v in kwargs.items():
251        name = aliases.get(k) or k
[1422]252        if len(group):
253            key = '%s.%s' % (group, name)
254        else:
255            key = name
[226]256        if not rcParams.has_key(key):
257            raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]258
[226]259        rcParams[key] = v
260
261
262def rcdefaults():
263    """
264    Restore the default rc params - the ones that were created at
265    asap load time
266    """
267    rcParams.update(rcParamsDefault)
268
[1295]269def _n_bools(n, val):
270    return [ val for i in xrange(n) ]
[513]271
272def _is_sequence_or_number(param, ptype=int):
273    if isinstance(param,tuple) or isinstance(param,list):
[928]274        if len(param) == 0: return True # empty list
[513]275        out = True
276        for p in param:
277            out &= isinstance(p,ptype)
278        return out
279    elif isinstance(param, ptype):
280        return True
281    return False
282
[928]283def _to_list(param, ptype=int):
284    if isinstance(param, ptype):
285        if ptype is str: return param.split()
286        else: return [param]
287    if _is_sequence_or_number(param, ptype):
288        return param
289    return None
[715]290
[944]291def unique(x):
[992]292    """
293    Return the unique values in a list
294    Parameters:
295        x:      the list to reduce
296    Examples:
297        x = [1,2,3,3,4]
298        print unique(x)
299        [1,2,3,4]
300    """
[944]301    return dict([ (val, 1) for val in x]).keys()
302
[992]303def list_files(path=".",suffix="rpf"):
304    """
305    Return a list files readable by asap, such as rpf, sdfits, mbf, asap
306    Parameters:
307        path:     The directory to list (default '.')
308        suffix:   The file extension (default rpf)
309    Example:
310        files = list_files("data/","sdfits")
311        print files
312        ['data/2001-09-01_0332_P363.sdfits',
313        'data/2003-04-04_131152_t0002.sdfits',
314        'data/Sgr_86p262_best_SPC.sdfits']
315    """
316    if not os.path.isdir(path):
317        return None
[1295]318    valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
[992]319    if not suffix in valid:
320        return None
321    files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
322    return filter(lambda x: x.endswith(suffix),files)
323
[715]324# workaround for ipython, which redirects this if banner=0 in ipythonrc
325sys.stdout = sys.__stdout__
326sys.stderr = sys.__stderr__
327
328# Logging
329from asap._asap import Log as _asaplog
330global asaplog
[710]331asaplog=_asaplog()
[715]332if rcParams['verbose']:
333    asaplog.enable()
334else:
335    asaplog.disable()
336
337def print_log():
338    log = asaplog.pop()
339    if len(log) and rcParams['verbose']: print log
340    return
341
[1295]342def mask_and(a, b):
343    assert(len(a)==len(b))
344    return [ a[i] & b[i] for i in xrange(len(a)) ]
[1134]345
[1295]346def mask_or(a, b):
347    assert(len(a)==len(b))
348    return [ a[i] | b[i] for i in xrange(len(a)) ]
349
350def mask_not(a):
351    return [ not i for i in a ]
352
[1117]353from asapfitter import fitter
[895]354from asapreader import reader
[944]355from selector import selector
[710]356
[100]357from asapmath import *
[1080]358from scantable import scantable
[1097]359from asaplinefind import linefinder
[1134]360from linecatalog import linecatalog
[285]361
[928]362if rcParams['useplotter']:
[1295]363    try:
[1423]364        from asapplotter import asapplotter
365        gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
366        if gui:
[1422]367            import matplotlib
368            matplotlib.use("TkAgg")
[1423]369        import pylab
[1422]370        xyplotter = pylab
[1423]371        plotter = asapplotter(gui)
372        del gui
[1295]373    except ImportError:
[1423]374        print "Matplotlib not installed. No plotting available"
[285]375
[574]376__date__ = '$Date: 2009-01-15 01:10:40 +0000 (Thu, 15 Jan 2009) $'.split()[1]
[1371]377__version__  = 'trunk'
[100]378
[1193]379def is_ipython():
[1259]380    return '__IP' in dir(sys.modules["__main__"])
[1193]381if is_ipython():
[1014]382    def version(): print  "ASAP %s(%s)"% (__version__, __date__)
[1422]383   
[706]384    def list_scans(t = scantable):
[1295]385        import types
[706]386        globs = sys.modules['__main__'].__dict__.iteritems()
387        print "The user created scantables are:"
388        sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
389        print filter(lambda x: not x.startswith('_'), sts)
390        return
[100]391
[715]392    def commands():
393        x = """
[113]394    [The scan container]
395        scantable           - a container for integrations/scans
[182]396                              (can open asap/rpfits/sdfits and ms files)
[113]397            copy            - returns a copy of a scan
398            get_scan        - gets a specific scan out of a scantable
[984]399                              (by name or number)
[1093]400            drop_scan       - drops a specific scan out of a scantable
401                              (by number)
[984]402            set_selection   - set a new subselection of the data
403            get_selection   - get the current selection object
[113]404            summary         - print info about the scantable contents
[182]405            stats           - get specified statistic of the spectra in
406                              the scantable
407            stddev          - get the standard deviation of the spectra
408                              in the scantable
[113]409            get_tsys        - get the TSys
410            get_time        - get the timestamps of the integrations
[1351]411            get_inttime     - get the integration time
[733]412            get_sourcename  - get the source names of the scans
[794]413            get_azimuth     - get the azimuth of the scans
414            get_elevation   - get the elevation of the scans
415            get_parangle    - get the parallactic angle of the scans
[876]416            get_unit        - get the current unit
[513]417            set_unit        - set the abcissa unit to be used from this
418                              point on
[255]419            get_abcissa     - get the abcissa values and name for a given
420                              row (time)
[1259]421            get_column_names - get the names of the columns in the scantable
422                               for use with selector.set_query
[113]423            set_freqframe   - set the frame info for the Spectral Axis
424                              (e.g. 'LSRK')
[276]425            set_doppler     - set the doppler to be used from this point on
[984]426            set_dirframe    - set the frame for the direction on the sky
[240]427            set_instrument  - set the instrument name
[1190]428            set_feedtype    - set the feed type
[255]429            get_fluxunit    - get the brightness flux unit
[240]430            set_fluxunit    - set the brightness flux unit
[188]431            create_mask     - return an mask in the current unit
432                              for the given region. The specified regions
433                              are NOT masked
[255]434            get_restfreqs   - get the current list of rest frequencies
435            set_restfreqs   - set a list of rest frequencies
[1471]436            shift_refpix    - shift the reference pixel of the IFs
437            set_spectrum    - overwrite the spectrum for a given row
438            get_spectrum    - retrieve the spectrum for a given
439            get_mask        - retrieve the mask for a given
[1012]440            flag            - flag selected channels in the data
[1192]441            lag_flag        - flag specified frequency in the data
[1151]442            save            - save the scantable to disk as either 'ASAP',
443                              'SDFITS' or 'ASCII'
[486]444            nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
[733]445            nscan           - the number of scans in the scantable
[1422]446            nrow            - the number of spectra in the scantable
[486]447            history         - print the history of the scantable
[530]448            get_fit         - get a fit which has been stored witnh the data
[706]449            average_time    - return the (weighted) time average of a scan
[513]450                              or a list of scans
451            average_pol     - average the polarisations together.
[1144]452            average_beam    - average the beams together.
[992]453            convert_pol     - convert to a different polarisation type
[690]454            auto_quotient   - return the on/off quotient with
[1069]455                              automatic detection of the on/off scans (closest
456                              in time off is selected)
[1144]457            mx_quotient     - Form a quotient using MX data (off beams)
[1014]458            scale, *, /     - return a scan scaled by a given factor
459            add, +, -       - return a scan with given value added
[513]460            bin             - return a scan with binned channels
461            resample        - return a scan with resampled channels
462            smooth          - return the spectrally smoothed scan
463            poly_baseline   - fit a polynomial baseline to all Beams/IFs/Pols
[706]464            auto_poly_baseline - automatically fit a polynomial baseline
[780]465            recalc_azel     - recalculate azimuth and elevation based on
466                              the pointing
[513]467            gain_el         - apply gain-elevation correction
468            opacity         - apply opacity correction
469            convert_flux    - convert to and from Jy and Kelvin brightness
[255]470                              units
[513]471            freq_align      - align spectra in frequency frame
[1014]472            invert_phase    - Invert the phase of the cross-correlation
[1351]473            swap_linears    - Swap XX and YY (or RR LL)
[513]474            rotate_xyphase  - rotate XY phase of cross correlation
475            rotate_linpolphase - rotate the phase of the complex
476                                 polarization O=Q+iU correlation
[733]477            freq_switch     - perform frequency switching on the data
478            stats           - Determine the specified statistic, e.g. 'min'
479                              'max', 'rms' etc.
480            stddev          - Determine the standard deviation of the current
481                              beam/if/pol
[1014]482     [Selection]
483         selector              - a selection object to set a subset of a scantable
484            set_scans          - set (a list of) scans by index
485            set_cycles         - set (a list of) cycles by index
486            set_beams          - set (a list of) beamss by index
487            set_ifs            - set (a list of) ifs by index
488            set_polarisations  - set (a list of) polarisations by name
489                                 or by index
490            set_names          - set a selection by name (wildcards allowed)
491            set_tsys           - set a selection by tsys thresholds
[1259]492            set_query          - set a selection by SQL-like query, e.g. BEAMNO==1
[1351]493            ( also  get_ functions for all these )
[1014]494            reset              - unset all selections
[1351]495            +                  - merge two selections
[733]496
[513]497     [Math] Mainly functions which operate on more than one scantable
[100]498
[706]499            average_time    - return the (weighted) time average
[513]500                              of a list of scans
501            quotient        - return the on/off quotient
502            simple_math     - simple mathematical operations on two scantables,
503                              'add', 'sub', 'mul', 'div'
[1069]504            quotient        - build quotient of the given on and off scans
[1351]505                              (matched pairs and 1 off - n on are valid)
[1117]506            merge           - merge a list of scantables
[1069]507
[1151]508     [Line Catalog]
509        linecatalog              - a linecatalog wrapper, taking an ASCII or
510                                   internal format table
511            summary              - print a summary of the current selection
512            set_name             - select a subset by name pattern, e.g. '*OH*'
513            set_strength_limits  - select a subset by line strength limits
514            set_frequency_limits - select a subset by frequency limits
515            reset                - unset all selections
516            save                 - save the current subset to a table (internal
517                                   format)
518            get_row              - get the name and frequency from a specific
519                                   row in the table
[513]520     [Fitting]
[113]521        fitter
522            auto_fit        - return a scan where the function is
523                              applied to all Beams/IFs/Pols.
524            commit          - return a new scan where the fits have been
525                              commited.
526            fit             - execute the actual fitting process
[984]527            store_fit       - store the fit parameters in the data (scantable)
[113]528            get_chi2        - get the Chi^2
529            set_scan        - set the scantable to be fit
530            set_function    - set the fitting function
531            set_parameters  - set the parameters for the function(s), and
532                              set if they should be held fixed during fitting
[513]533            set_gauss_parameters - same as above but specialised for individual
534                                   gaussian components
[113]535            get_parameters  - get the fitted parameters
[513]536            plot            - plot the resulting fit and/or components and
537                              residual
[210]538    [Plotter]
539        asapplotter         - a plotter for asap, default plotter is
540                              called 'plotter'
[984]541            plot            - plot a scantable
[1151]542            plot_lines      - plot a linecatalog overlay
[378]543            save            - save the plot to a file ('png' ,'ps' or 'eps')
[210]544            set_mode        - set the state of the plotter, i.e.
545                              what is to be plotted 'colour stacked'
546                              and what 'panelled'
[984]547            set_selection   - only plot a selected part of the data
[733]548            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
[255]549            set_legend      - specify user labels for the legend indeces
550            set_title       - specify user labels for the panel indeces
[733]551            set_abcissa     - specify a user label for the abcissa
[255]552            set_ordinate    - specify a user label for the ordinate
[378]553            set_layout      - specify the multi-panel layout (rows,cols)
[733]554            set_colors      - specify a set of colours to use
555            set_linestyles  - specify a set of linestyles to use if only
556                              using one color
[1151]557            set_font        - set general font properties, e.g. 'family'
[1054]558            set_histogram   - plot in historam style
[733]559            set_mask        - set a plotting mask for a specific polarization
[1171]560            text            - draw text annotations either in data or relative
561                              coordinates
562            arrow           - draw arrow annotations either in data or relative
563                              coordinates
564            axhline,axvline - draw horizontal/vertical lines
565            axhspan,axvspan - draw horizontal/vertical regions
[1175]566
567        xyplotter           - matplotlib/pylab plotting functions
568
[182]569    [Reading files]
570        reader              - access rpfits/sdfits files
[984]571            open            - attach reader to a file
572            close           - detach reader from file
[182]573            read            - read in integrations
574            summary         - list info about all integrations
575
[113]576    [General]
577        commands            - this command
578        print               - print details about a variable
579        list_scans          - list all scantables created bt the user
[992]580        list_files          - list all files readable by asap (default rpf)
[113]581        del                 - delete the given variable from memory
582        range               - create a list of values, e.g.
583                              range(3) = [0,1,2], range(2,5) = [2,3,4]
584        help                - print help for one of the listed functions
585        execfile            - execute an asap script, e.g. execfile('myscript')
[255]586        list_rcparameters   - print out a list of possible values to be
[274]587                              put into $HOME/.asaprc
[1171]588        rc                  - set rc parameters from within asap
[466]589        mask_and,mask_or,
590        mask_not            - boolean operations on masks created with
591                              scantable.create_mask
[706]592
[210]593    Note:
594        How to use this with help:
595                                         # function 'summary'
596        [xxx] is just a category
597        Every 'sub-level' in this list should be replaces by a '.' Period when
[706]598        using help
[210]599        Example:
600            ASAP> help scantable # to get info on ths scantable
601            ASAP> help scantable.summary # to get help on the scantable's
602            ASAP> help average_time
603
[715]604            """
[1151]605        if rcParams['verbose']:
606            try:
607                from IPython.genutils import page as pager
608            except ImportError:
609                from pydoc import pager
610            pager(x)
611        else:
612            print x
[715]613        return
[113]614
[706]615def welcome():
616    return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]617
[1035]618Please report any bugs via:
[1378]619http://svn.atnf.csiro.au/trac/asap/simpleticket
[100]620
[378]621[IMPORTANT: ASAP is 0-based]
[706]622Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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