[100] | 1 | """ |
---|
| 2 | This is the ATNF Single Dish Analysis package. |
---|
| 3 | |
---|
| 4 | """ |
---|
[226] | 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/.matplotlibrc |
---|
| 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], |
---|
[255] | 55 | 'insitu' : [False, validate_bool], |
---|
[226] | 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 | |
---|
| 68 | # fitter |
---|
| 69 | } |
---|
| 70 | |
---|
[255] | 71 | def list_rcparameters(): |
---|
| 72 | |
---|
| 73 | print """ |
---|
| 74 | # general |
---|
| 75 | # print verbose output |
---|
| 76 | 'verbose' : True |
---|
| 77 | |
---|
| 78 | # preload a default plotter |
---|
| 79 | 'useplotter' : True |
---|
| 80 | |
---|
| 81 | # apply operations on the input scantable or return new one |
---|
| 82 | 'insitu' : False |
---|
| 83 | |
---|
| 84 | # plotting |
---|
| 85 | # default mode for colour stacking |
---|
| 86 | 'plotter.stacking' : 'Pol' |
---|
| 87 | |
---|
| 88 | # default mode for panelling |
---|
| 89 | 'plotter.panelling' : 'scan' |
---|
| 90 | |
---|
| 91 | # scantable |
---|
| 92 | # default ouput format when saving |
---|
| 93 | 'scantable.save' : 'ASAP' |
---|
| 94 | # auto averaging on read |
---|
| 95 | 'scantable.autoaverage' : True |
---|
| 96 | |
---|
| 97 | # default frequency frame to set when function |
---|
| 98 | # scantable.set_freqfrmae is called |
---|
| 99 | 'scantable.freqframe' : 'LSRK' |
---|
| 100 | |
---|
| 101 | # apply action to all axes not just the cursor location |
---|
| 102 | 'scantable.allaxes' : True |
---|
| 103 | |
---|
| 104 | # use internal plotter |
---|
| 105 | 'scantable.plotter' : True |
---|
| 106 | |
---|
| 107 | # Fitter |
---|
| 108 | """ |
---|
| 109 | |
---|
[226] | 110 | def rc_params(): |
---|
| 111 | 'Return the default params updated from the values in the rc file' |
---|
| 112 | |
---|
| 113 | fname = asap_fname() |
---|
| 114 | |
---|
| 115 | if fname is None or not os.path.exists(fname): |
---|
| 116 | message = 'could not find rc file; returning defaults' |
---|
| 117 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
---|
| 118 | #print message |
---|
| 119 | return ret |
---|
| 120 | |
---|
| 121 | cnt = 0 |
---|
| 122 | for line in file(fname): |
---|
| 123 | cnt +=1 |
---|
| 124 | line = line.strip() |
---|
| 125 | if not len(line): continue |
---|
| 126 | if line.startswith('#'): continue |
---|
| 127 | tup = line.split(':',1) |
---|
| 128 | if len(tup) !=2: |
---|
| 129 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
---|
| 130 | continue |
---|
| 131 | |
---|
| 132 | key, val = tup |
---|
| 133 | key = key.strip() |
---|
| 134 | if not defaultParams.has_key(key): |
---|
| 135 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
---|
| 136 | continue |
---|
| 137 | |
---|
| 138 | default, converter = defaultParams[key] |
---|
| 139 | |
---|
| 140 | ind = val.find('#') |
---|
| 141 | if ind>=0: val = val[:ind] # ignore trailing comments |
---|
| 142 | val = val.strip() |
---|
| 143 | try: cval = converter(val) # try to convert to proper type or raise |
---|
| 144 | except Exception, msg: |
---|
| 145 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) |
---|
| 146 | continue |
---|
| 147 | else: |
---|
| 148 | # Alles Klar, update dict |
---|
| 149 | defaultParams[key][0] = cval |
---|
| 150 | |
---|
| 151 | # strip the conveter funcs and return |
---|
| 152 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
---|
[255] | 153 | print 'Using rc file %s'%fname |
---|
[226] | 154 | |
---|
| 155 | return ret |
---|
| 156 | |
---|
| 157 | |
---|
| 158 | # this is the instance used by the asap classes |
---|
| 159 | rcParams = rc_params() |
---|
| 160 | |
---|
| 161 | rcParamsDefault = dict(rcParams.items()) # a copy |
---|
| 162 | |
---|
| 163 | def rc(group, **kwargs): |
---|
| 164 | """ |
---|
| 165 | Set the current rc params. Group is the grouping for the rc, eg |
---|
| 166 | for lines.linewidth the group is 'lines', for axes.facecolor, the |
---|
| 167 | group is 'axes', and so on. kwargs is a list of attribute |
---|
| 168 | name/value pairs, eg |
---|
| 169 | |
---|
| 170 | rc('lines', linewidth=2, color='r') |
---|
| 171 | |
---|
| 172 | sets the current rc params and is equivalent to |
---|
| 173 | |
---|
| 174 | rcParams['lines.linewidth'] = 2 |
---|
| 175 | rcParams['lines.color'] = 'r' |
---|
| 176 | |
---|
| 177 | |
---|
| 178 | Note you can use python's kwargs dictionary facility to store |
---|
| 179 | dictionaries of default parameters. Eg, you can customize the |
---|
| 180 | font rc as follows |
---|
| 181 | |
---|
| 182 | font = {'family' : 'monospace', |
---|
| 183 | 'weight' : 'bold', |
---|
| 184 | 'size' : 'larger', |
---|
| 185 | } |
---|
| 186 | |
---|
| 187 | rc('font', **font) # pass in the font dict as kwargs |
---|
| 188 | |
---|
| 189 | This enables you to easily switch between several configurations. |
---|
| 190 | Use rcdefaults to restore the default rc params after changes. |
---|
| 191 | """ |
---|
| 192 | |
---|
| 193 | aliases = { |
---|
| 194 | } |
---|
| 195 | |
---|
| 196 | for k,v in kwargs.items(): |
---|
| 197 | name = aliases.get(k) or k |
---|
| 198 | key = '%s.%s' % (group, name) |
---|
| 199 | if not rcParams.has_key(key): |
---|
| 200 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
---|
| 201 | |
---|
| 202 | rcParams[key] = v |
---|
| 203 | |
---|
| 204 | |
---|
| 205 | def rcdefaults(): |
---|
| 206 | """ |
---|
| 207 | Restore the default rc params - the ones that were created at |
---|
| 208 | asap load time |
---|
| 209 | """ |
---|
| 210 | rcParams.update(rcParamsDefault) |
---|
| 211 | |
---|
[113] | 212 | from asapfitter import * |
---|
[100] | 213 | from asapreader import reader |
---|
| 214 | from asapmath import * |
---|
| 215 | from scantable import * |
---|
[226] | 216 | if rcParams['useplotter']: |
---|
| 217 | print "Initialising plotter..." |
---|
[255] | 218 | import asapplotter |
---|
| 219 | plotter = asapplotter.asapplotter() |
---|
[100] | 220 | |
---|
| 221 | __date__ = '$Date: 2005-01-21 11:22:46 +0000 (Fri, 21 Jan 2005) $' |
---|
[255] | 222 | __version__ = '0.2a' |
---|
[100] | 223 | |
---|
| 224 | def list_scans(t = scantable): |
---|
| 225 | import sys, types |
---|
| 226 | #meta_t = type(t) |
---|
| 227 | #if meta_t == types.InstanceType: |
---|
| 228 | # t = t.__class__ |
---|
| 229 | #elif meta_t not in [types.ClassType, types.TypeType]: |
---|
| 230 | # t = meta_t |
---|
| 231 | globs = sys.modules['__main__'].__dict__.iteritems() |
---|
[113] | 232 | print "The user created scantables are:" |
---|
| 233 | x = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
---|
| 234 | print x |
---|
[100] | 235 | |
---|
[113] | 236 | def commands(): |
---|
[210] | 237 | x = """ |
---|
[113] | 238 | [The scan container] |
---|
| 239 | scantable - a container for integrations/scans |
---|
[182] | 240 | (can open asap/rpfits/sdfits and ms files) |
---|
[113] | 241 | copy - returns a copy of a scan |
---|
| 242 | get_scan - gets a specific scan out of a scantable |
---|
| 243 | summary - print info about the scantable contents |
---|
[255] | 244 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
---|
| 245 | further use |
---|
| 246 | get_cursor - print out the current cursor position |
---|
[182] | 247 | stats - get specified statistic of the spectra in |
---|
| 248 | the scantable |
---|
| 249 | stddev - get the standard deviation of the spectra |
---|
| 250 | in the scantable |
---|
[113] | 251 | get_tsys - get the TSys |
---|
| 252 | get_time - get the timestamps of the integrations |
---|
[255] | 253 | get_unit - get the currnt unit |
---|
| 254 | set_unit - set the unit to be used from this point on |
---|
| 255 | get_abcissa - get the abcissa values and name for a given |
---|
| 256 | row (time) |
---|
[113] | 257 | set_freqframe - set the frame info for the Spectral Axis |
---|
| 258 | (e.g. 'LSRK') |
---|
[240] | 259 | set_instrument - set the instrument name |
---|
[255] | 260 | get_fluxunit - get the brightness flux unit |
---|
[240] | 261 | set_fluxunit - set the brightness flux unit |
---|
[188] | 262 | create_mask - return an mask in the current unit |
---|
| 263 | for the given region. The specified regions |
---|
| 264 | are NOT masked |
---|
[255] | 265 | get_restfreqs - get the current list of rest frequencies |
---|
| 266 | set_restfreqs - set a list of rest frequencies |
---|
[113] | 267 | flag_spectrum - flag a whole Beam/IF/Pol |
---|
[116] | 268 | save - save the scantable to disk as either 'ASAP' |
---|
| 269 | or 'SDFITS' |
---|
[113] | 270 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
| 271 | [Math] |
---|
[142] | 272 | average_time - return the (weighted) time average of a scan |
---|
| 273 | or a list of scans |
---|
[128] | 274 | average_pol - average the polarisations together. |
---|
[113] | 275 | The dimension won't be reduced and |
---|
| 276 | all polarisations will contain the |
---|
| 277 | averaged spectrum. |
---|
| 278 | quotient - return the on/off quotient |
---|
[255] | 279 | simple_math - simple mathematical operations on two scantables, |
---|
| 280 | 'add', 'sub', 'mul', 'div' |
---|
[113] | 281 | scale - returns a scan scaled by a given factor |
---|
[149] | 282 | add - returns a scan with given value added |
---|
[113] | 283 | bin - return a scan with binned channels |
---|
[179] | 284 | smooth - return the spectrally smoothed scan |
---|
[113] | 285 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
[240] | 286 | gain_el - apply gain-elevation correction |
---|
| 287 | opacity - apply opacity correction |
---|
[255] | 288 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
| 289 | units |
---|
[100] | 290 | |
---|
[113] | 291 | fitter |
---|
| 292 | auto_fit - return a scan where the function is |
---|
| 293 | applied to all Beams/IFs/Pols. |
---|
| 294 | commit - return a new scan where the fits have been |
---|
| 295 | commited. |
---|
| 296 | fit - execute the actual fitting process |
---|
| 297 | get_chi2 - get the Chi^2 |
---|
| 298 | set_scan - set the scantable to be fit |
---|
| 299 | set_function - set the fitting function |
---|
| 300 | set_parameters - set the parameters for the function(s), and |
---|
| 301 | set if they should be held fixed during fitting |
---|
| 302 | get_parameters - get the fitted parameters |
---|
[210] | 303 | [Plotter] |
---|
| 304 | asapplotter - a plotter for asap, default plotter is |
---|
| 305 | called 'plotter' |
---|
| 306 | plot - plot a (list of) scantable |
---|
| 307 | set_mode - set the state of the plotter, i.e. |
---|
| 308 | what is to be plotted 'colour stacked' |
---|
| 309 | and what 'panelled' |
---|
| 310 | set_range - set the abcissa 'zoom' range |
---|
[255] | 311 | set_legend - specify user labels for the legend indeces |
---|
| 312 | set_title - specify user labels for the panel indeces |
---|
| 313 | set_ordinate - specify a user label for the ordinate |
---|
| 314 | set_abcissa - specify a user label for the abcissa |
---|
[210] | 315 | |
---|
[182] | 316 | [Reading files] |
---|
| 317 | reader - access rpfits/sdfits files |
---|
| 318 | read - read in integrations |
---|
| 319 | summary - list info about all integrations |
---|
| 320 | |
---|
[113] | 321 | [General] |
---|
| 322 | commands - this command |
---|
| 323 | print - print details about a variable |
---|
| 324 | list_scans - list all scantables created bt the user |
---|
| 325 | del - delete the given variable from memory |
---|
| 326 | range - create a list of values, e.g. |
---|
| 327 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
| 328 | help - print help for one of the listed functions |
---|
| 329 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
[255] | 330 | list_rcparameters - print out a list of possible values to be |
---|
| 331 | put into .asaprc |
---|
[210] | 332 | Note: |
---|
| 333 | How to use this with help: |
---|
| 334 | # function 'summary' |
---|
| 335 | [xxx] is just a category |
---|
| 336 | Every 'sub-level' in this list should be replaces by a '.' Period when |
---|
| 337 | using help |
---|
| 338 | Example: |
---|
| 339 | ASAP> help scantable # to get info on ths scantable |
---|
| 340 | ASAP> help scantable.summary # to get help on the scantable's |
---|
| 341 | ASAP> help average_time |
---|
| 342 | |
---|
[113] | 343 | """ |
---|
| 344 | print x |
---|
| 345 | return |
---|
| 346 | |
---|
| 347 | print """Welcome to ASAP - the ATNF Single Dish Analysis Package |
---|
[100] | 348 | This is a testing pre-release v0.1a |
---|
| 349 | |
---|
| 350 | Please report any bugs to: |
---|
[128] | 351 | Malte.Marquarding@csiro.au |
---|
[100] | 352 | |
---|
[113] | 353 | [NOTE: ASAP is 0-based] |
---|
| 354 | Type commands() to get a list of all available ASAP commands. |
---|
[100] | 355 | """ |
---|