""" This is the ATNF Single Dish Analysis package. """ import os,sys,shutil, platform # Set up AIPSPATH and first time use of asap i.e. ~/.asap/* plf = None if sys.platform == "linux2": if platform.architecture()[0] == '64bit': plf = 'linux_64b' else: plf = 'linux_gnu' elif sys.platform == 'darwin': plf = 'darwin' else: # Shouldn't happen - default to linux plf = 'linux' asapdata = __path__[-1] # Allow user defined data location if os.environ.has_key("ASAPDATA"): if os.path.exists(os.environ["ASAPDATA"]): asapdata = os.environ["ASAPDATA"] if not os.environ.has_key("AIPSPATH"): os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf) # set up user space userdir = os.environ["HOME"]+"/.asap" if not os.path.exists(userdir): print 'First time ASAP use. Setting up ~/.asap' os.mkdir(userdir) shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap") f = file(userdir+"/asapuserfuncs.py", "w") f.close() f = file(userdir+"/ipythonrc", "w") f.close() # remove from namespace del asapdata, userdir, shutil, platform def _validate_bool(b): 'Convert b to a boolean or raise' bl = b.lower() if bl in ('f', 'no', 'false', '0', 0): return False elif bl in ('t', 'yes', 'true', '1', 1): return True else: raise ValueError('Could not convert "%s" to boolean' % b) def _validate_int(s): 'convert s to int or raise' try: return int(s) except ValueError: raise ValueError('Could not convert "%s" to int' % s) def _asap_fname(): """ Return the path to the rc file Search order: * current working dir * environ var ASAPRC * HOME/.asaprc """ fname = os.path.join( os.getcwd(), '.asaprc') if os.path.exists(fname): return fname if os.environ.has_key('ASAPRC'): path = os.environ['ASAPRC'] if os.path.exists(path): fname = os.path.join(path, '.asaprc') if os.path.exists(fname): return fname if os.environ.has_key('HOME'): home = os.environ['HOME'] fname = os.path.join(home, '.asaprc') if os.path.exists(fname): return fname return None defaultParams = { # general 'verbose' : [True, _validate_bool], 'useplotter' : [True, _validate_bool], 'insitu' : [True, _validate_bool], # plotting 'plotter.gui' : [True, _validate_bool], 'plotter.stacking' : ['p', str], 'plotter.panelling' : ['s', str], 'plotter.colours' : ['', str], 'plotter.linestyles' : ['', str], 'plotter.decimate' : [False, _validate_bool], 'plotter.ganged' : [True, _validate_bool], 'plotter.histogram' : [False, _validate_bool], 'plotter.papertype' : ['A4', str], # scantable 'scantable.save' : ['ASAP', str], 'scantable.autoaverage' : [True, _validate_bool], 'scantable.freqframe' : ['LSRK', str], #default frequency frame 'scantable.verbosesummary' : [False, _validate_bool], 'scantable.storage' : ['memory', str] # fitter } def list_rcparameters(): print """ # general # print verbose output verbose : True # preload a default plotter useplotter : True # apply operations on the input scantable or return new one insitu : True # plotting # do we want a GUI or plot to a file plotter.gui : True # default mode for colour stacking plotter.stacking : Pol # default mode for panelling plotter.panelling : scan # push panels together, to share axislabels plotter.ganged : True # decimate the number of points plotted bya afactor of # nchan/1024 plotter.decimate : False # default colours/linestyles plotter.colours : plotter.linestyles : # enable/disable histogram plotting plotter.histogram : False # ps paper type plotter.papertype : A4 # scantable # default storage of scantable ('memory'/'disk') scantable.storage : memory # default ouput format when saving scantable.save : ASAP # auto averaging on read scantable.autoaverage : True # default frequency frame to set when function # scantable.set_freqframe is called scantable.freqframe : LSRK # Control the level of information printed by summary scantable.verbosesummary : False # Fitter """ def rc_params(): 'Return the default params updated from the values in the rc file' fname = _asap_fname() if fname is None or not os.path.exists(fname): message = 'could not find rc file; returning defaults' ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) #print message return ret cnt = 0 for line in file(fname): cnt +=1 line = line.strip() if not len(line): continue if line.startswith('#'): continue tup = line.split(':',1) if len(tup) !=2: print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) continue key, val = tup key = key.strip() if not defaultParams.has_key(key): print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) continue default, converter = defaultParams[key] ind = val.find('#') if ind>=0: val = val[:ind] # ignore trailing comments val = val.strip() try: cval = converter(val) # try to convert to proper type or raise except ValueError, msg: print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) continue else: # Alles Klar, update dict defaultParams[key][0] = cval # strip the conveter funcs and return ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) print ('loaded rc file %s'%fname) return ret # this is the instance used by the asap classes rcParams = rc_params() rcParamsDefault = dict(rcParams.items()) # a copy def rc(group, **kwargs): """ Set the current rc params. Group is the grouping for the rc, eg for scantable.save the group is 'scantable', for plotter.stacking, the group is 'plotter', and so on. kwargs is a list of attribute name/value pairs, eg rc('scantable', save='SDFITS') sets the current rc params and is equivalent to rcParams['scantable.save'] = 'SDFITS' Use rcdefaults to restore the default rc params after changes. """ aliases = {} for k,v in kwargs.items(): name = aliases.get(k) or k key = '%s.%s' % (group, name) if not rcParams.has_key(key): raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) rcParams[key] = v def rcdefaults(): """ Restore the default rc params - the ones that were created at asap load time """ rcParams.update(rcParamsDefault) def _n_bools(n, val): return [ val for i in xrange(n) ] def _is_sequence_or_number(param, ptype=int): if isinstance(param,tuple) or isinstance(param,list): if len(param) == 0: return True # empty list out = True for p in param: out &= isinstance(p,ptype) return out elif isinstance(param, ptype): return True return False def _to_list(param, ptype=int): if isinstance(param, ptype): if ptype is str: return param.split() else: return [param] if _is_sequence_or_number(param, ptype): return param return None def unique(x): """ Return the unique values in a list Parameters: x: the list to reduce Examples: x = [1,2,3,3,4] print unique(x) [1,2,3,4] """ return dict([ (val, 1) for val in x]).keys() def list_files(path=".",suffix="rpf"): """ Return a list files readable by asap, such as rpf, sdfits, mbf, asap Parameters: path: The directory to list (default '.') suffix: The file extension (default rpf) Example: files = list_files("data/","sdfits") print files ['data/2001-09-01_0332_P363.sdfits', 'data/2003-04-04_131152_t0002.sdfits', 'data/Sgr_86p262_best_SPC.sdfits'] """ if not os.path.isdir(path): return None valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split() if not suffix in valid: return None files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)] return filter(lambda x: x.endswith(suffix),files) # workaround for ipython, which redirects this if banner=0 in ipythonrc sys.stdout = sys.__stdout__ sys.stderr = sys.__stderr__ # Logging from asap._asap import Log as _asaplog global asaplog asaplog=_asaplog() if rcParams['verbose']: asaplog.enable() else: asaplog.disable() def print_log(): log = asaplog.pop() if len(log) and rcParams['verbose']: print log return def mask_and(a, b): assert(len(a)==len(b)) return [ a[i] & b[i] for i in xrange(len(a)) ] def mask_or(a, b): assert(len(a)==len(b)) return [ a[i] | b[i] for i in xrange(len(a)) ] def mask_not(a): return [ not i for i in a ] from asapfitter import fitter from asapreader import reader from selector import selector from asapmath import * from scantable import scantable from asaplinefind import linefinder from linecatalog import linecatalog if rcParams['useplotter']: try: from asapplotter import asapplotter gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] if gui: import pylab as xyplotter plotter = asapplotter(gui) del gui except ImportError: print "Matplotlib not installed. No plotting available" __date__ = '$Date: 2007-03-02 00:02:27 +0000 (Fri, 02 Mar 2007) $'.split()[1] __version__ = '2.1.2' def is_ipython(): return '__IP' in dir(sys.modules["__main__"]) if is_ipython(): def version(): print "ASAP %s(%s)"% (__version__, __date__) def list_scans(t = scantable): import types globs = sys.modules['__main__'].__dict__.iteritems() print "The user created scantables are:" sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) print filter(lambda x: not x.startswith('_'), sts) return def commands(): x = """ [The scan container] scantable - a container for integrations/scans (can open asap/rpfits/sdfits and ms files) copy - returns a copy of a scan get_scan - gets a specific scan out of a scantable (by name or number) drop_scan - drops a specific scan out of a scantable (by number) set_selection - set a new subselection of the data get_selection - get the current selection object summary - print info about the scantable contents stats - get specified statistic of the spectra in the scantable stddev - get the standard deviation of the spectra in the scantable get_tsys - get the TSys get_time - get the timestamps of the integrations get_sourcename - get the source names of the scans get_azimuth - get the azimuth of the scans get_elevation - get the elevation of the scans get_parangle - get the parallactic angle of the scans get_unit - get the current unit set_unit - set the abcissa unit to be used from this point on get_abcissa - get the abcissa values and name for a given row (time) get_column_names - get the names of the columns in the scantable for use with selector.set_query set_freqframe - set the frame info for the Spectral Axis (e.g. 'LSRK') set_doppler - set the doppler to be used from this point on set_dirframe - set the frame for the direction on the sky set_instrument - set the instrument name set_feedtype - set the feed type get_fluxunit - get the brightness flux unit set_fluxunit - set the brightness flux unit create_mask - return an mask in the current unit for the given region. The specified regions are NOT masked get_restfreqs - get the current list of rest frequencies set_restfreqs - set a list of rest frequencies flag - flag selected channels in the data lag_flag - flag specified frequency in the data save - save the scantable to disk as either 'ASAP', 'SDFITS' or 'ASCII' nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans nscan - the number of scans in the scantable nrow - te number of spectra in the scantable history - print the history of the scantable get_fit - get a fit which has been stored witnh the data average_time - return the (weighted) time average of a scan or a list of scans average_pol - average the polarisations together. average_beam - average the beams together. convert_pol - convert to a different polarisation type auto_quotient - return the on/off quotient with automatic detection of the on/off scans (closest in time off is selected) mx_quotient - Form a quotient using MX data (off beams) scale, *, / - return a scan scaled by a given factor add, +, - - return a scan with given value added bin - return a scan with binned channels resample - return a scan with resampled channels smooth - return the spectrally smoothed scan poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols auto_poly_baseline - automatically fit a polynomial baseline recalc_azel - recalculate azimuth and elevation based on the pointing gain_el - apply gain-elevation correction opacity - apply opacity correction convert_flux - convert to and from Jy and Kelvin brightness units freq_align - align spectra in frequency frame invert_phase - Invert the phase of the cross-correlation swap_linears - Swap XX and YY rotate_xyphase - rotate XY phase of cross correlation rotate_linpolphase - rotate the phase of the complex polarization O=Q+iU correlation freq_switch - perform frequency switching on the data stats - Determine the specified statistic, e.g. 'min' 'max', 'rms' etc. stddev - Determine the standard deviation of the current beam/if/pol [Selection] selector - a selection object to set a subset of a scantable set_scans - set (a list of) scans by index set_cycles - set (a list of) cycles by index set_beams - set (a list of) beamss by index set_ifs - set (a list of) ifs by index set_polarisations - set (a list of) polarisations by name or by index set_names - set a selection by name (wildcards allowed) set_tsys - set a selection by tsys thresholds set_query - set a selection by SQL-like query, e.g. BEAMNO==1 reset - unset all selections + - merge to selections [Math] Mainly functions which operate on more than one scantable average_time - return the (weighted) time average of a list of scans quotient - return the on/off quotient simple_math - simple mathematical operations on two scantables, 'add', 'sub', 'mul', 'div' quotient - build quotient of the given on and off scans (matched pairs and 1 off/n on are valid) merge - merge a list of scantables [Line Catalog] linecatalog - a linecatalog wrapper, taking an ASCII or internal format table summary - print a summary of the current selection set_name - select a subset by name pattern, e.g. '*OH*' set_strength_limits - select a subset by line strength limits set_frequency_limits - select a subset by frequency limits reset - unset all selections save - save the current subset to a table (internal format) get_row - get the name and frequency from a specific row in the table [Fitting] fitter auto_fit - return a scan where the function is applied to all Beams/IFs/Pols. commit - return a new scan where the fits have been commited. fit - execute the actual fitting process store_fit - store the fit parameters in the data (scantable) get_chi2 - get the Chi^2 set_scan - set the scantable to be fit set_function - set the fitting function set_parameters - set the parameters for the function(s), and set if they should be held fixed during fitting set_gauss_parameters - same as above but specialised for individual gaussian components get_parameters - get the fitted parameters plot - plot the resulting fit and/or components and residual [Plotter] asapplotter - a plotter for asap, default plotter is called 'plotter' plot - plot a scantable plot_lines - plot a linecatalog overlay save - save the plot to a file ('png' ,'ps' or 'eps') set_mode - set the state of the plotter, i.e. what is to be plotted 'colour stacked' and what 'panelled' set_selection - only plot a selected part of the data set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] set_legend - specify user labels for the legend indeces set_title - specify user labels for the panel indeces set_abcissa - specify a user label for the abcissa set_ordinate - specify a user label for the ordinate set_layout - specify the multi-panel layout (rows,cols) set_colors - specify a set of colours to use set_linestyles - specify a set of linestyles to use if only using one color set_font - set general font properties, e.g. 'family' set_histogram - plot in historam style set_mask - set a plotting mask for a specific polarization text - draw text annotations either in data or relative coordinates arrow - draw arrow annotations either in data or relative coordinates axhline,axvline - draw horizontal/vertical lines axhspan,axvspan - draw horizontal/vertical regions xyplotter - matplotlib/pylab plotting functions [Reading files] reader - access rpfits/sdfits files open - attach reader to a file close - detach reader from file read - read in integrations summary - list info about all integrations [General] commands - this command print - print details about a variable list_scans - list all scantables created bt the user list_files - list all files readable by asap (default rpf) del - delete the given variable from memory range - create a list of values, e.g. range(3) = [0,1,2], range(2,5) = [2,3,4] help - print help for one of the listed functions execfile - execute an asap script, e.g. execfile('myscript') list_rcparameters - print out a list of possible values to be put into $HOME/.asaprc rc - set rc parameters from within asap mask_and,mask_or, mask_not - boolean operations on masks created with scantable.create_mask Note: How to use this with help: # function 'summary' [xxx] is just a category Every 'sub-level' in this list should be replaces by a '.' Period when using help Example: ASAP> help scantable # to get info on ths scantable ASAP> help scantable.summary # to get help on the scantable's ASAP> help average_time """ if rcParams['verbose']: try: from IPython.genutils import page as pager except ImportError: from pydoc import pager pager(x) else: print x return def welcome(): return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package Please report any bugs via: http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket [IMPORTANT: ASAP is 0-based] Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)