| 1 | """ |
|---|
| 2 | This is the ATNF Single Dish Analysis package. |
|---|
| 3 | |
|---|
| 4 | """ |
|---|
| 5 | import os,sys |
|---|
| 6 | |
|---|
| 7 | def validate_bool(b): |
|---|
| 8 | 'Convert b to a boolean or raise' |
|---|
| 9 | bl = b.lower() |
|---|
| 10 | if bl in ('f', 'no', 'false', '0', 0): return False |
|---|
| 11 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
|---|
| 12 | else: |
|---|
| 13 | raise ValueError('Could not convert "%s" to boolean' % b) |
|---|
| 14 | |
|---|
| 15 | def validate_int(s): |
|---|
| 16 | 'convert s to int or raise' |
|---|
| 17 | try: return int(s) |
|---|
| 18 | except ValueError: |
|---|
| 19 | raise ValueError('Could not convert "%s" to int' % s) |
|---|
| 20 | |
|---|
| 21 | def asap_fname(): |
|---|
| 22 | """ |
|---|
| 23 | Return the path to the rc file |
|---|
| 24 | |
|---|
| 25 | Search order: |
|---|
| 26 | |
|---|
| 27 | * current working dir |
|---|
| 28 | * environ var ASAPRC |
|---|
| 29 | * HOME/.asaprc |
|---|
| 30 | |
|---|
| 31 | """ |
|---|
| 32 | |
|---|
| 33 | fname = os.path.join( os.getcwd(), '.asaprc') |
|---|
| 34 | if os.path.exists(fname): return fname |
|---|
| 35 | |
|---|
| 36 | if os.environ.has_key('ASAPRC'): |
|---|
| 37 | path = os.environ['ASAPRC'] |
|---|
| 38 | if os.path.exists(path): |
|---|
| 39 | fname = os.path.join(path, '.asaprc') |
|---|
| 40 | if os.path.exists(fname): |
|---|
| 41 | return fname |
|---|
| 42 | |
|---|
| 43 | if os.environ.has_key('HOME'): |
|---|
| 44 | home = os.environ['HOME'] |
|---|
| 45 | fname = os.path.join(home, '.asaprc') |
|---|
| 46 | if os.path.exists(fname): |
|---|
| 47 | return fname |
|---|
| 48 | return None |
|---|
| 49 | |
|---|
| 50 | |
|---|
| 51 | defaultParams = { |
|---|
| 52 | # general |
|---|
| 53 | 'verbose' : [True, validate_bool], |
|---|
| 54 | 'useplotter' : [True, validate_bool], |
|---|
| 55 | 'insitu' : [False, validate_bool], |
|---|
| 56 | |
|---|
| 57 | # plotting |
|---|
| 58 | 'plotter.stacking' : ['p', str], |
|---|
| 59 | 'plotter.panelling' : ['s', str], |
|---|
| 60 | |
|---|
| 61 | # scantable |
|---|
| 62 | 'scantable.save' : ['ASAP', str], |
|---|
| 63 | 'scantable.autoaverage' : [True, validate_bool], |
|---|
| 64 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
|---|
| 65 | 'scantable.allaxes' : [True, validate_bool], # apply action to all axes |
|---|
| 66 | 'scantable.plotter' : [True, validate_bool], # use internal plotter |
|---|
| 67 | 'scantable.verbosesummary' : [False, validate_bool] |
|---|
| 68 | |
|---|
| 69 | # fitter |
|---|
| 70 | } |
|---|
| 71 | |
|---|
| 72 | def list_rcparameters(): |
|---|
| 73 | |
|---|
| 74 | print """ |
|---|
| 75 | # general |
|---|
| 76 | # print verbose output |
|---|
| 77 | verbose : True |
|---|
| 78 | |
|---|
| 79 | # preload a default plotter |
|---|
| 80 | useplotter : True |
|---|
| 81 | |
|---|
| 82 | # apply operations on the input scantable or return new one |
|---|
| 83 | insitu : False |
|---|
| 84 | |
|---|
| 85 | # plotting |
|---|
| 86 | # default mode for colour stacking |
|---|
| 87 | plotter.stacking : 'Pol' |
|---|
| 88 | |
|---|
| 89 | # default mode for panelling |
|---|
| 90 | plotter.panelling : 'scan' |
|---|
| 91 | |
|---|
| 92 | # scantable |
|---|
| 93 | # default ouput format when saving |
|---|
| 94 | scantable.save : 'ASAP' |
|---|
| 95 | # auto averaging on read |
|---|
| 96 | scantable.autoaverage : True |
|---|
| 97 | |
|---|
| 98 | # default frequency frame to set when function |
|---|
| 99 | # scantable.set_freqfrmae is called |
|---|
| 100 | scantable.freqframe : 'LSRK' |
|---|
| 101 | |
|---|
| 102 | # apply action to all axes not just the cursor location |
|---|
| 103 | scantable.allaxes : True |
|---|
| 104 | |
|---|
| 105 | # use internal plotter |
|---|
| 106 | scantable.plotter : True |
|---|
| 107 | |
|---|
| 108 | # Control the level of information printed by summary |
|---|
| 109 | scantable.verbosesummary : False |
|---|
| 110 | |
|---|
| 111 | # Fitter |
|---|
| 112 | """ |
|---|
| 113 | |
|---|
| 114 | def rc_params(): |
|---|
| 115 | 'Return the default params updated from the values in the rc file' |
|---|
| 116 | |
|---|
| 117 | fname = asap_fname() |
|---|
| 118 | |
|---|
| 119 | if fname is None or not os.path.exists(fname): |
|---|
| 120 | message = 'could not find rc file; returning defaults' |
|---|
| 121 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
|---|
| 122 | #print message |
|---|
| 123 | return ret |
|---|
| 124 | |
|---|
| 125 | cnt = 0 |
|---|
| 126 | for line in file(fname): |
|---|
| 127 | cnt +=1 |
|---|
| 128 | line = line.strip() |
|---|
| 129 | if not len(line): continue |
|---|
| 130 | if line.startswith('#'): continue |
|---|
| 131 | tup = line.split(':',1) |
|---|
| 132 | if len(tup) !=2: |
|---|
| 133 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
|---|
| 134 | continue |
|---|
| 135 | |
|---|
| 136 | key, val = tup |
|---|
| 137 | key = key.strip() |
|---|
| 138 | if not defaultParams.has_key(key): |
|---|
| 139 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
|---|
| 140 | continue |
|---|
| 141 | |
|---|
| 142 | default, converter = defaultParams[key] |
|---|
| 143 | |
|---|
| 144 | ind = val.find('#') |
|---|
| 145 | if ind>=0: val = val[:ind] # ignore trailing comments |
|---|
| 146 | val = val.strip() |
|---|
| 147 | try: cval = converter(val) # try to convert to proper type or raise |
|---|
| 148 | except Exception, msg: |
|---|
| 149 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) |
|---|
| 150 | continue |
|---|
| 151 | else: |
|---|
| 152 | # Alles Klar, update dict |
|---|
| 153 | defaultParams[key][0] = cval |
|---|
| 154 | |
|---|
| 155 | # strip the conveter funcs and return |
|---|
| 156 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
|---|
| 157 | print ('loaded rc file %s'%fname) |
|---|
| 158 | |
|---|
| 159 | return ret |
|---|
| 160 | |
|---|
| 161 | |
|---|
| 162 | # this is the instance used by the asap classes |
|---|
| 163 | rcParams = rc_params() |
|---|
| 164 | |
|---|
| 165 | rcParamsDefault = dict(rcParams.items()) # a copy |
|---|
| 166 | |
|---|
| 167 | def rc(group, **kwargs): |
|---|
| 168 | """ |
|---|
| 169 | Set the current rc params. Group is the grouping for the rc, eg |
|---|
| 170 | for scantable.save the group is 'scantable', for plotter.stacking, the |
|---|
| 171 | group is 'plotter', and so on. kwargs is a list of attribute |
|---|
| 172 | name/value pairs, eg |
|---|
| 173 | |
|---|
| 174 | rc('scantable', save='SDFITS') |
|---|
| 175 | |
|---|
| 176 | sets the current rc params and is equivalent to |
|---|
| 177 | |
|---|
| 178 | rcParams['scantable.save'] = 'SDFITS' |
|---|
| 179 | |
|---|
| 180 | Use rcdefaults to restore the default rc params after changes. |
|---|
| 181 | """ |
|---|
| 182 | |
|---|
| 183 | aliases = {} |
|---|
| 184 | |
|---|
| 185 | for k,v in kwargs.items(): |
|---|
| 186 | name = aliases.get(k) or k |
|---|
| 187 | key = '%s.%s' % (group, name) |
|---|
| 188 | if not rcParams.has_key(key): |
|---|
| 189 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
|---|
| 190 | |
|---|
| 191 | rcParams[key] = v |
|---|
| 192 | |
|---|
| 193 | |
|---|
| 194 | def rcdefaults(): |
|---|
| 195 | """ |
|---|
| 196 | Restore the default rc params - the ones that were created at |
|---|
| 197 | asap load time |
|---|
| 198 | """ |
|---|
| 199 | rcParams.update(rcParamsDefault) |
|---|
| 200 | |
|---|
| 201 | from asapfitter import * |
|---|
| 202 | from asapreader import reader |
|---|
| 203 | from asapmath import * |
|---|
| 204 | from scantable import * |
|---|
| 205 | from asaplinefind import * |
|---|
| 206 | |
|---|
| 207 | from numarray import logical_and as mask_and |
|---|
| 208 | from numarray import logical_or as mask_or |
|---|
| 209 | from numarray import logical_not as mask_not |
|---|
| 210 | |
|---|
| 211 | if rcParams['useplotter']: |
|---|
| 212 | if os.environ.has_key('DISPLAY'): |
|---|
| 213 | print "Initialising asapplotter with the name 'plotter' ..." |
|---|
| 214 | import asapplotter |
|---|
| 215 | plotter = asapplotter.asapplotter() |
|---|
| 216 | else: |
|---|
| 217 | print "No $DISPLAY set. Disabling plotter.\n" |
|---|
| 218 | |
|---|
| 219 | #from numarray ones,zeros |
|---|
| 220 | |
|---|
| 221 | |
|---|
| 222 | __date__ = '$Date: 2005-02-23 04:01:41 +0000 (Wed, 23 Feb 2005) $' |
|---|
| 223 | __version__ = '0.2' |
|---|
| 224 | |
|---|
| 225 | def list_scans(t = scantable): |
|---|
| 226 | import sys, types |
|---|
| 227 | #meta_t = type(t) |
|---|
| 228 | #if meta_t == types.InstanceType: |
|---|
| 229 | # t = t.__class__ |
|---|
| 230 | #elif meta_t not in [types.ClassType, types.TypeType]: |
|---|
| 231 | # t = meta_t |
|---|
| 232 | globs = sys.modules['__main__'].__dict__.iteritems() |
|---|
| 233 | print "The user created scantables are:" |
|---|
| 234 | x = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
|---|
| 235 | print x |
|---|
| 236 | |
|---|
| 237 | def commands(): |
|---|
| 238 | x = """ |
|---|
| 239 | [The scan container] |
|---|
| 240 | scantable - a container for integrations/scans |
|---|
| 241 | (can open asap/rpfits/sdfits and ms files) |
|---|
| 242 | copy - returns a copy of a scan |
|---|
| 243 | get_scan - gets a specific scan out of a scantable |
|---|
| 244 | summary - print info about the scantable contents |
|---|
| 245 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
|---|
| 246 | further use |
|---|
| 247 | get_cursor - print out the current cursor position |
|---|
| 248 | stats - get specified statistic of the spectra in |
|---|
| 249 | the scantable |
|---|
| 250 | stddev - get the standard deviation of the spectra |
|---|
| 251 | in the scantable |
|---|
| 252 | get_tsys - get the TSys |
|---|
| 253 | get_time - get the timestamps of the integrations |
|---|
| 254 | get_unit - get the currnt unit |
|---|
| 255 | set_unit - set the abcissa unit to be used from this point on |
|---|
| 256 | get_abcissa - get the abcissa values and name for a given |
|---|
| 257 | row (time) |
|---|
| 258 | set_freqframe - set the frame info for the Spectral Axis |
|---|
| 259 | (e.g. 'LSRK') |
|---|
| 260 | set_doppler - set the doppler to be used from this point on |
|---|
| 261 | set_instrument - set the instrument name |
|---|
| 262 | get_fluxunit - get the brightness flux unit |
|---|
| 263 | set_fluxunit - set the brightness flux unit |
|---|
| 264 | create_mask - return an mask in the current unit |
|---|
| 265 | for the given region. The specified regions |
|---|
| 266 | are NOT masked |
|---|
| 267 | get_restfreqs - get the current list of rest frequencies |
|---|
| 268 | set_restfreqs - set a list of rest frequencies |
|---|
| 269 | lines - print list of known spectral lines |
|---|
| 270 | flag_spectrum - flag a whole Beam/IF/Pol |
|---|
| 271 | save - save the scantable to disk as either 'ASAP' |
|---|
| 272 | or 'SDFITS' |
|---|
| 273 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
|---|
| 274 | history - print the history of the scantable |
|---|
| 275 | [Math] |
|---|
| 276 | average_time - return the (weighted) time average of a scan |
|---|
| 277 | or a list of scans |
|---|
| 278 | average_pol - average the polarisations together. |
|---|
| 279 | The dimension won't be reduced and |
|---|
| 280 | all polarisations will contain the |
|---|
| 281 | averaged spectrum. |
|---|
| 282 | quotient - return the on/off quotient |
|---|
| 283 | simple_math - simple mathematical operations on two scantables, |
|---|
| 284 | 'add', 'sub', 'mul', 'div' |
|---|
| 285 | scale - return a scan scaled by a given factor |
|---|
| 286 | add - return a scan with given value added |
|---|
| 287 | bin - return a scan with binned channels |
|---|
| 288 | resample - return a scan with resampled channels |
|---|
| 289 | smooth - return the spectrally smoothed scan |
|---|
| 290 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
|---|
| 291 | auto_poly_baseline - automatically fit a polynomial baseline |
|---|
| 292 | gain_el - apply gain-elevation correction |
|---|
| 293 | opacity - apply opacity correction |
|---|
| 294 | convert_flux - convert to and from Jy and Kelvin brightness |
|---|
| 295 | units |
|---|
| 296 | freq_align - align spectra in frequency frame |
|---|
| 297 | rotate_xyphase - rotate XY phase of cross correlation |
|---|
| 298 | |
|---|
| 299 | fitter |
|---|
| 300 | auto_fit - return a scan where the function is |
|---|
| 301 | applied to all Beams/IFs/Pols. |
|---|
| 302 | commit - return a new scan where the fits have been |
|---|
| 303 | commited. |
|---|
| 304 | fit - execute the actual fitting process |
|---|
| 305 | get_chi2 - get the Chi^2 |
|---|
| 306 | set_scan - set the scantable to be fit |
|---|
| 307 | set_function - set the fitting function |
|---|
| 308 | set_parameters - set the parameters for the function(s), and |
|---|
| 309 | set if they should be held fixed during fitting |
|---|
| 310 | get_parameters - get the fitted parameters |
|---|
| 311 | [Plotter] |
|---|
| 312 | asapplotter - a plotter for asap, default plotter is |
|---|
| 313 | called 'plotter' |
|---|
| 314 | plot - plot a (list of) scantable |
|---|
| 315 | save - save the plot to a file ('png' ,'ps' or 'eps') |
|---|
| 316 | set_mode - set the state of the plotter, i.e. |
|---|
| 317 | what is to be plotted 'colour stacked' |
|---|
| 318 | and what 'panelled' |
|---|
| 319 | set_range - set the abcissa 'zoom' range |
|---|
| 320 | set_legend - specify user labels for the legend indeces |
|---|
| 321 | set_title - specify user labels for the panel indeces |
|---|
| 322 | set_ordinate - specify a user label for the ordinate |
|---|
| 323 | set_abcissa - specify a user label for the abcissa |
|---|
| 324 | set_layout - specify the multi-panel layout (rows,cols) |
|---|
| 325 | |
|---|
| 326 | [Reading files] |
|---|
| 327 | reader - access rpfits/sdfits files |
|---|
| 328 | read - read in integrations |
|---|
| 329 | summary - list info about all integrations |
|---|
| 330 | |
|---|
| 331 | [General] |
|---|
| 332 | commands - this command |
|---|
| 333 | print - print details about a variable |
|---|
| 334 | list_scans - list all scantables created bt the user |
|---|
| 335 | del - delete the given variable from memory |
|---|
| 336 | range - create a list of values, e.g. |
|---|
| 337 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
|---|
| 338 | help - print help for one of the listed functions |
|---|
| 339 | execfile - execute an asap script, e.g. execfile('myscript') |
|---|
| 340 | list_rcparameters - print out a list of possible values to be |
|---|
| 341 | put into $HOME/.asaprc |
|---|
| 342 | mask_and,mask_or, |
|---|
| 343 | mask_not - boolean operations on masks created with |
|---|
| 344 | scantable.create_mask |
|---|
| 345 | |
|---|
| 346 | Note: |
|---|
| 347 | How to use this with help: |
|---|
| 348 | # function 'summary' |
|---|
| 349 | [xxx] is just a category |
|---|
| 350 | Every 'sub-level' in this list should be replaces by a '.' Period when |
|---|
| 351 | using help |
|---|
| 352 | Example: |
|---|
| 353 | ASAP> help scantable # to get info on ths scantable |
|---|
| 354 | ASAP> help scantable.summary # to get help on the scantable's |
|---|
| 355 | ASAP> help average_time |
|---|
| 356 | |
|---|
| 357 | """ |
|---|
| 358 | print x |
|---|
| 359 | return |
|---|
| 360 | |
|---|
| 361 | print """Welcome to ASAP - the ATNF Single Dish Analysis Package |
|---|
| 362 | This is a testing pre-release %s |
|---|
| 363 | |
|---|
| 364 | Please report any bugs to: |
|---|
| 365 | Malte.Marquarding@csiro.au |
|---|
| 366 | |
|---|
| 367 | [IMPORTANT: ASAP is 0-based] |
|---|
| 368 | Type commands() to get a list of all available ASAP commands. |
|---|
| 369 | """ % (__version__) |
|---|
