1 | from asap._asap import Scantable |
---|
2 | from asap import rcParams |
---|
3 | from asap import print_log |
---|
4 | from asap import asaplog |
---|
5 | from asap import selector |
---|
6 | from asap import linecatalog |
---|
7 | from asap import _n_bools, mask_not, mask_and, mask_or |
---|
8 | |
---|
9 | class scantable(Scantable): |
---|
10 | """ |
---|
11 | The ASAP container for scans |
---|
12 | """ |
---|
13 | |
---|
14 | def __init__(self, filename, average=None, unit=None, getpt=None): |
---|
15 | """ |
---|
16 | Create a scantable from a saved one or make a reference |
---|
17 | Parameters: |
---|
18 | filename: the name of an asap table on disk |
---|
19 | or |
---|
20 | the name of a rpfits/sdfits/ms file |
---|
21 | (integrations within scans are auto averaged |
---|
22 | and the whole file is read) |
---|
23 | or |
---|
24 | [advanced] a reference to an existing |
---|
25 | scantable |
---|
26 | average: average all integrations withinb a scan on read. |
---|
27 | The default (True) is taken from .asaprc. |
---|
28 | unit: brightness unit; must be consistent with K or Jy. |
---|
29 | Over-rides the default selected by the reader |
---|
30 | (input rpfits/sdfits/ms) or replaces the value |
---|
31 | in existing scantables |
---|
32 | getpt: for MeasurementSet input data only: |
---|
33 | If True, all pointing data are filled. |
---|
34 | The deafult is False, which makes time to load |
---|
35 | the MS data faster in some cases. |
---|
36 | """ |
---|
37 | if average is None: |
---|
38 | average = rcParams['scantable.autoaverage'] |
---|
39 | if getpt is None: |
---|
40 | getpt = False |
---|
41 | varlist = vars() |
---|
42 | from asap._asap import stmath |
---|
43 | self._math = stmath() |
---|
44 | if isinstance(filename, Scantable): |
---|
45 | Scantable.__init__(self, filename) |
---|
46 | else: |
---|
47 | if isinstance(filename, str): |
---|
48 | import os.path |
---|
49 | filename = os.path.expandvars(filename) |
---|
50 | filename = os.path.expanduser(filename) |
---|
51 | if not os.path.exists(filename): |
---|
52 | s = "File '%s' not found." % (filename) |
---|
53 | if rcParams['verbose']: |
---|
54 | asaplog.push(s) |
---|
55 | print asaplog.pop().strip() |
---|
56 | return |
---|
57 | raise IOError(s) |
---|
58 | if os.path.isdir(filename) \ |
---|
59 | and not os.path.exists(filename+'/table.f1'): |
---|
60 | # crude check if asap table |
---|
61 | if os.path.exists(filename+'/table.info'): |
---|
62 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
63 | Scantable.__init__(self, filename, ondisk) |
---|
64 | if unit is not None: |
---|
65 | self.set_fluxunit(unit) |
---|
66 | # do not reset to the default freqframe |
---|
67 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
68 | else: |
---|
69 | msg = "The given file '%s'is not a valid " \ |
---|
70 | "asap table." % (filename) |
---|
71 | if rcParams['verbose']: |
---|
72 | print msg |
---|
73 | return |
---|
74 | else: |
---|
75 | raise IOError(msg) |
---|
76 | else: |
---|
77 | self._fill([filename], unit, average, getpt) |
---|
78 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
79 | and isinstance(filename[-1], str): |
---|
80 | self._fill(filename, unit, average, getpt) |
---|
81 | self._add_history("scantable", varlist) |
---|
82 | print_log() |
---|
83 | |
---|
84 | def save(self, name=None, format=None, overwrite=False): |
---|
85 | """ |
---|
86 | Store the scantable on disk. This can be an asap (aips++) Table, |
---|
87 | SDFITS or MS2 format. |
---|
88 | Parameters: |
---|
89 | name: the name of the outputfile. For format "ASCII" |
---|
90 | this is the root file name (data in 'name'.txt |
---|
91 | and header in 'name'_header.txt) |
---|
92 | format: an optional file format. Default is ASAP. |
---|
93 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
---|
94 | 'SDFITS' (save as SDFITS file) |
---|
95 | 'ASCII' (saves as ascii text file) |
---|
96 | 'MS2' (saves as an aips++ |
---|
97 | MeasurementSet V2) |
---|
98 | overwrite: If the file should be overwritten if it exists. |
---|
99 | The default False is to return with warning |
---|
100 | without writing the output. USE WITH CARE. |
---|
101 | Example: |
---|
102 | scan.save('myscan.asap') |
---|
103 | scan.save('myscan.sdfits', 'SDFITS') |
---|
104 | """ |
---|
105 | from os import path |
---|
106 | if format is None: format = rcParams['scantable.save'] |
---|
107 | suffix = '.'+format.lower() |
---|
108 | if name is None or name == "": |
---|
109 | name = 'scantable'+suffix |
---|
110 | msg = "No filename given. Using default name %s..." % name |
---|
111 | asaplog.push(msg) |
---|
112 | name = path.expandvars(name) |
---|
113 | if path.isfile(name) or path.isdir(name): |
---|
114 | if not overwrite: |
---|
115 | msg = "File %s exists." % name |
---|
116 | if rcParams['verbose']: |
---|
117 | print msg |
---|
118 | return |
---|
119 | else: |
---|
120 | raise IOError(msg) |
---|
121 | format2 = format.upper() |
---|
122 | if format2 == 'ASAP': |
---|
123 | self._save(name) |
---|
124 | else: |
---|
125 | from asap._asap import stwriter as stw |
---|
126 | writer = stw(format2) |
---|
127 | writer.write(self, name) |
---|
128 | print_log() |
---|
129 | return |
---|
130 | |
---|
131 | def copy(self): |
---|
132 | """ |
---|
133 | Return a copy of this scantable. |
---|
134 | Note: |
---|
135 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
136 | Parameters: |
---|
137 | none |
---|
138 | Example: |
---|
139 | copiedscan = scan.copy() |
---|
140 | """ |
---|
141 | sd = scantable(Scantable._copy(self)) |
---|
142 | return sd |
---|
143 | |
---|
144 | def drop_scan(self, scanid=None): |
---|
145 | """ |
---|
146 | Return a new scantable where the specified scan number(s) has(have) |
---|
147 | been dropped. |
---|
148 | Parameters: |
---|
149 | scanid: a (list of) scan number(s) |
---|
150 | """ |
---|
151 | from asap import _is_sequence_or_number as _is_valid |
---|
152 | from asap import _to_list |
---|
153 | from asap import unique |
---|
154 | if not _is_valid(scanid): |
---|
155 | if rcParams['verbose']: |
---|
156 | print "Please specify a scanno to drop from the scantable" |
---|
157 | return |
---|
158 | else: |
---|
159 | raise RuntimeError("No scan given") |
---|
160 | try: |
---|
161 | scanid = _to_list(scanid) |
---|
162 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
163 | for sid in scanid: allscans.remove(sid) |
---|
164 | if len(allscans) == 0: |
---|
165 | raise ValueError("Can't remove all scans") |
---|
166 | except ValueError: |
---|
167 | if rcParams['verbose']: |
---|
168 | print "Couldn't find any match." |
---|
169 | return |
---|
170 | else: raise |
---|
171 | try: |
---|
172 | bsel = self.get_selection() |
---|
173 | sel = selector() |
---|
174 | sel.set_scans(allscans) |
---|
175 | self.set_selection(bsel+sel) |
---|
176 | scopy = self._copy() |
---|
177 | self.set_selection(bsel) |
---|
178 | return scantable(scopy) |
---|
179 | except RuntimeError: |
---|
180 | if rcParams['verbose']: |
---|
181 | print "Couldn't find any match." |
---|
182 | else: |
---|
183 | raise |
---|
184 | |
---|
185 | |
---|
186 | def get_scan(self, scanid=None): |
---|
187 | """ |
---|
188 | Return a specific scan (by scanno) or collection of scans (by |
---|
189 | source name) in a new scantable. |
---|
190 | Note: |
---|
191 | See scantable.drop_scan() for the inverse operation. |
---|
192 | Parameters: |
---|
193 | scanid: a (list of) scanno or a source name, unix-style |
---|
194 | patterns are accepted for source name matching, e.g. |
---|
195 | '*_R' gets all 'ref scans |
---|
196 | Example: |
---|
197 | # get all scans containing the source '323p459' |
---|
198 | newscan = scan.get_scan('323p459') |
---|
199 | # get all 'off' scans |
---|
200 | refscans = scan.get_scan('*_R') |
---|
201 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
202 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
203 | """ |
---|
204 | if scanid is None: |
---|
205 | if rcParams['verbose']: |
---|
206 | print "Please specify a scan no or name to " \ |
---|
207 | "retrieve from the scantable" |
---|
208 | return |
---|
209 | else: |
---|
210 | raise RuntimeError("No scan given") |
---|
211 | |
---|
212 | try: |
---|
213 | bsel = self.get_selection() |
---|
214 | sel = selector() |
---|
215 | if type(scanid) is str: |
---|
216 | sel.set_name(scanid) |
---|
217 | self.set_selection(bsel+sel) |
---|
218 | scopy = self._copy() |
---|
219 | self.set_selection(bsel) |
---|
220 | return scantable(scopy) |
---|
221 | elif type(scanid) is int: |
---|
222 | sel.set_scans([scanid]) |
---|
223 | self.set_selection(bsel+sel) |
---|
224 | scopy = self._copy() |
---|
225 | self.set_selection(bsel) |
---|
226 | return scantable(scopy) |
---|
227 | elif type(scanid) is list: |
---|
228 | sel.set_scans(scanid) |
---|
229 | self.set_selection(sel) |
---|
230 | scopy = self._copy() |
---|
231 | self.set_selection(bsel) |
---|
232 | return scantable(scopy) |
---|
233 | else: |
---|
234 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
235 | if rcParams['verbose']: |
---|
236 | print msg |
---|
237 | else: |
---|
238 | raise TypeError(msg) |
---|
239 | except RuntimeError: |
---|
240 | if rcParams['verbose']: print "Couldn't find any match." |
---|
241 | else: raise |
---|
242 | |
---|
243 | def __str__(self): |
---|
244 | return Scantable._summary(self, True) |
---|
245 | |
---|
246 | def summary(self, filename=None): |
---|
247 | """ |
---|
248 | Print a summary of the contents of this scantable. |
---|
249 | Parameters: |
---|
250 | filename: the name of a file to write the putput to |
---|
251 | Default - no file output |
---|
252 | verbose: print extra info such as the frequency table |
---|
253 | The default (False) is taken from .asaprc |
---|
254 | """ |
---|
255 | info = Scantable._summary(self, True) |
---|
256 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
---|
257 | if filename is not None: |
---|
258 | if filename is "": |
---|
259 | filename = 'scantable_summary.txt' |
---|
260 | from os.path import expandvars, isdir |
---|
261 | filename = expandvars(filename) |
---|
262 | if not isdir(filename): |
---|
263 | data = open(filename, 'w') |
---|
264 | data.write(info) |
---|
265 | data.close() |
---|
266 | else: |
---|
267 | msg = "Illegal file name '%s'." % (filename) |
---|
268 | if rcParams['verbose']: |
---|
269 | print msg |
---|
270 | else: |
---|
271 | raise IOError(msg) |
---|
272 | if rcParams['verbose']: |
---|
273 | try: |
---|
274 | from IPython.genutils import page as pager |
---|
275 | except ImportError: |
---|
276 | from pydoc import pager |
---|
277 | pager(info) |
---|
278 | else: |
---|
279 | return info |
---|
280 | |
---|
281 | |
---|
282 | def get_selection(self): |
---|
283 | """ |
---|
284 | Get the selection object currently set on this scantable. |
---|
285 | Parameters: |
---|
286 | none |
---|
287 | Example: |
---|
288 | sel = scan.get_selection() |
---|
289 | sel.set_ifs(0) # select IF 0 |
---|
290 | scan.set_selection(sel) # apply modified selection |
---|
291 | """ |
---|
292 | return selector(self._getselection()) |
---|
293 | |
---|
294 | def set_selection(self, selection=selector()): |
---|
295 | """ |
---|
296 | Select a subset of the data. All following operations on this scantable |
---|
297 | are only applied to thi selection. |
---|
298 | Parameters: |
---|
299 | selection: a selector object (default unset the selection) |
---|
300 | Examples: |
---|
301 | sel = selector() # create a selection object |
---|
302 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
303 | scan.set_selection(sel) # set the selection |
---|
304 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
305 | scan.set_selection() # unset the selection |
---|
306 | """ |
---|
307 | self._setselection(selection) |
---|
308 | |
---|
309 | def get_row(self, row=0, insitu=None): |
---|
310 | """ |
---|
311 | Select a row in the scantable. |
---|
312 | Return a scantable with single row. |
---|
313 | Parameters: |
---|
314 | row: row no of integration, default is 0. |
---|
315 | insitu: if False a new scantable is returned. |
---|
316 | Otherwise, the scaling is done in-situ |
---|
317 | The default is taken from .asaprc (False) |
---|
318 | """ |
---|
319 | if insitu is None: insitu = rcParams['insitu'] |
---|
320 | if not insitu: |
---|
321 | workscan = self.copy() |
---|
322 | else: |
---|
323 | workscan = self |
---|
324 | # Select a row |
---|
325 | sel=selector() |
---|
326 | sel.set_scans([workscan.getscan(row)]) |
---|
327 | sel.set_cycles([workscan.getcycle(row)]) |
---|
328 | sel.set_beams([workscan.getbeam(row)]) |
---|
329 | sel.set_ifs([workscan.getif(row)]) |
---|
330 | sel.set_polarisations([workscan.getpol(row)]) |
---|
331 | sel.set_name(workscan._getsourcename(row)) |
---|
332 | workscan.set_selection(sel) |
---|
333 | if not workscan.nrow() == 1: |
---|
334 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
---|
335 | raise RuntimeError(msg) |
---|
336 | del sel |
---|
337 | if insitu: |
---|
338 | self._assign(workscan) |
---|
339 | else: |
---|
340 | return workscan |
---|
341 | |
---|
342 | def stats(self, stat='stddev', mask=None): |
---|
343 | """ |
---|
344 | Determine the specified statistic of the current beam/if/pol |
---|
345 | Takes a 'mask' as an optional parameter to specify which |
---|
346 | channels should be excluded. |
---|
347 | Parameters: |
---|
348 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
349 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
350 | mask: an optional mask specifying where the statistic |
---|
351 | should be determined. |
---|
352 | Example: |
---|
353 | scan.set_unit('channel') |
---|
354 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
355 | scan.stats(stat='mean', mask=m) |
---|
356 | """ |
---|
357 | if mask == None: |
---|
358 | mask = [] |
---|
359 | axes = ['Beam', 'IF', 'Pol', 'Time'] |
---|
360 | if not self._check_ifs(): |
---|
361 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
362 | "number of channels. Please use setselection() " |
---|
363 | "to select individual IFs") |
---|
364 | rtnabc = False |
---|
365 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
366 | getchan = False |
---|
367 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
368 | chan = self._math._minmaxchan(self, mask, stat) |
---|
369 | getchan = True |
---|
370 | statvals = [] |
---|
371 | if not rtnabc: statvals = self._math._stats(self, mask, stat) |
---|
372 | |
---|
373 | out = '' |
---|
374 | axes = [] |
---|
375 | for i in range(self.nrow()): |
---|
376 | axis = [] |
---|
377 | axis.append(self.getscan(i)) |
---|
378 | axis.append(self.getbeam(i)) |
---|
379 | axis.append(self.getif(i)) |
---|
380 | axis.append(self.getpol(i)) |
---|
381 | axis.append(self.getcycle(i)) |
---|
382 | axes.append(axis) |
---|
383 | tm = self._gettime(i) |
---|
384 | src = self._getsourcename(i) |
---|
385 | refstr = '' |
---|
386 | statunit= '' |
---|
387 | if getchan: |
---|
388 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
389 | if rtnabc: |
---|
390 | statvals.append(qx['value']) |
---|
391 | refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])' |
---|
392 | statunit= '['+qx['unit']+']' |
---|
393 | else: |
---|
394 | refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])' |
---|
395 | #statunit= ' ['+qy['unit']+']' |
---|
396 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
397 | out += 'Time[%s]:\n' % (tm) |
---|
398 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
399 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
400 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
401 | out += '= %3.3f ' % (statvals[i]) +refstr+'\n' |
---|
402 | out += "--------------------------------------------------\n" |
---|
403 | |
---|
404 | if rcParams['verbose']: |
---|
405 | print "--------------------------------------------------" |
---|
406 | print " ", stat, statunit |
---|
407 | print "--------------------------------------------------" |
---|
408 | print out |
---|
409 | #else: |
---|
410 | #retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'], |
---|
411 | # 'axes' : axes, |
---|
412 | # 'data': statvals} |
---|
413 | return statvals |
---|
414 | |
---|
415 | def chan2data(self, rowno=0, chan=0): |
---|
416 | """ |
---|
417 | Returns channel/frequency/velocity and spectral value |
---|
418 | at an arbitrary row and channel in the scantable. |
---|
419 | Parameters: |
---|
420 | rowno: a row number in the scantable. Default is the |
---|
421 | first row, i.e. rowno=0 |
---|
422 | chan: a channel in the scantable. Default is the first |
---|
423 | channel, i.e. pos=0 |
---|
424 | """ |
---|
425 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
426 | qx = {'unit': self.get_unit(), |
---|
427 | 'value': self._getabcissa(rowno)[chan]} |
---|
428 | qy = {'unit': self.get_fluxunit(), |
---|
429 | 'value': self._getspectrum(rowno)[chan]} |
---|
430 | return qx, qy |
---|
431 | |
---|
432 | def stddev(self, mask=None): |
---|
433 | """ |
---|
434 | Determine the standard deviation of the current beam/if/pol |
---|
435 | Takes a 'mask' as an optional parameter to specify which |
---|
436 | channels should be excluded. |
---|
437 | Parameters: |
---|
438 | mask: an optional mask specifying where the standard |
---|
439 | deviation should be determined. |
---|
440 | |
---|
441 | Example: |
---|
442 | scan.set_unit('channel') |
---|
443 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
444 | scan.stddev(mask=m) |
---|
445 | """ |
---|
446 | return self.stats(stat='stddev', mask=mask); |
---|
447 | |
---|
448 | |
---|
449 | def get_column_names(self): |
---|
450 | """ |
---|
451 | Return a list of column names, which can be used for selection. |
---|
452 | """ |
---|
453 | return list(Scantable.get_column_names(self)) |
---|
454 | |
---|
455 | def get_tsys(self): |
---|
456 | """ |
---|
457 | Return the System temperatures. |
---|
458 | Returns: |
---|
459 | a list of Tsys values for the current selection |
---|
460 | """ |
---|
461 | |
---|
462 | return self._row_callback(self._gettsys, "Tsys") |
---|
463 | |
---|
464 | def _row_callback(self, callback, label): |
---|
465 | axes = [] |
---|
466 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'] |
---|
467 | out = "" |
---|
468 | outvec = [] |
---|
469 | for i in range(self.nrow()): |
---|
470 | axis = [] |
---|
471 | axis.append(self.getscan(i)) |
---|
472 | axis.append(self.getbeam(i)) |
---|
473 | axis.append(self.getif(i)) |
---|
474 | axis.append(self.getpol(i)) |
---|
475 | axis.append(self.getcycle(i)) |
---|
476 | axes.append(axis) |
---|
477 | tm = self._gettime(i) |
---|
478 | src = self._getsourcename(i) |
---|
479 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
480 | out += 'Time[%s]:\n' % (tm) |
---|
481 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
482 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
483 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
484 | outvec.append(callback(i)) |
---|
485 | out += '= %3.3f\n' % (outvec[i]) |
---|
486 | out += "--------------------------------------------------\n" |
---|
487 | if rcParams['verbose']: |
---|
488 | print "--------------------------------------------------" |
---|
489 | print " %s" % (label) |
---|
490 | print "--------------------------------------------------" |
---|
491 | print out |
---|
492 | # disabled because the vector seems more useful |
---|
493 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
---|
494 | return outvec |
---|
495 | |
---|
496 | def _get_column(self, callback, row=-1): |
---|
497 | """ |
---|
498 | """ |
---|
499 | if row == -1: |
---|
500 | return [callback(i) for i in range(self.nrow())] |
---|
501 | else: |
---|
502 | if 0 <= row < self.nrow(): |
---|
503 | return callback(row) |
---|
504 | |
---|
505 | |
---|
506 | def get_time(self, row=-1, asdatetime=False): |
---|
507 | """ |
---|
508 | Get a list of time stamps for the observations. |
---|
509 | Return a datetime object for each integration time stamp in the scantable. |
---|
510 | Parameters: |
---|
511 | row: row no of integration. Default -1 return all rows |
---|
512 | asdatetime: return values as datetime objects rather than strings |
---|
513 | Example: |
---|
514 | none |
---|
515 | """ |
---|
516 | from time import strptime |
---|
517 | from datetime import datetime |
---|
518 | times = self._get_column(self._gettime, row) |
---|
519 | if not asdatetime: |
---|
520 | return times |
---|
521 | format = "%Y/%m/%d/%H:%M:%S" |
---|
522 | if isinstance(times, list): |
---|
523 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
524 | else: |
---|
525 | return datetime(*strptime(times, format)[:6]) |
---|
526 | |
---|
527 | |
---|
528 | def get_inttime(self, row=-1): |
---|
529 | """ |
---|
530 | Get a list of integration times for the observations. |
---|
531 | Return a time in seconds for each integration in the scantable. |
---|
532 | Parameters: |
---|
533 | row: row no of integration. Default -1 return all rows. |
---|
534 | Example: |
---|
535 | none |
---|
536 | """ |
---|
537 | return self._get_column(self._getinttime, row) |
---|
538 | |
---|
539 | |
---|
540 | def get_sourcename(self, row=-1): |
---|
541 | """ |
---|
542 | Get a list source names for the observations. |
---|
543 | Return a string for each integration in the scantable. |
---|
544 | Parameters: |
---|
545 | row: row no of integration. Default -1 return all rows. |
---|
546 | Example: |
---|
547 | none |
---|
548 | """ |
---|
549 | return self._get_column(self._getsourcename, row) |
---|
550 | |
---|
551 | def get_elevation(self, row=-1): |
---|
552 | """ |
---|
553 | Get a list of elevations for the observations. |
---|
554 | Return a float for each integration in the scantable. |
---|
555 | Parameters: |
---|
556 | row: row no of integration. Default -1 return all rows. |
---|
557 | Example: |
---|
558 | none |
---|
559 | """ |
---|
560 | return self._get_column(self._getelevation, row) |
---|
561 | |
---|
562 | def get_azimuth(self, row=-1): |
---|
563 | """ |
---|
564 | Get a list of azimuths for the observations. |
---|
565 | Return a float for each integration in the scantable. |
---|
566 | Parameters: |
---|
567 | row: row no of integration. Default -1 return all rows. |
---|
568 | Example: |
---|
569 | none |
---|
570 | """ |
---|
571 | return self._get_column(self._getazimuth, row) |
---|
572 | |
---|
573 | def get_parangle(self, row=-1): |
---|
574 | """ |
---|
575 | Get a list of parallactic angles for the observations. |
---|
576 | Return a float for each integration in the scantable. |
---|
577 | Parameters: |
---|
578 | row: row no of integration. Default -1 return all rows. |
---|
579 | Example: |
---|
580 | none |
---|
581 | """ |
---|
582 | return self._get_column(self._getparangle, row) |
---|
583 | |
---|
584 | def get_direction(self, row=-1): |
---|
585 | """ |
---|
586 | Get a list of Positions on the sky (direction) for the observations. |
---|
587 | Return a float for each integration in the scantable. |
---|
588 | Parameters: |
---|
589 | row: row no of integration. Default -1 return all rows |
---|
590 | Example: |
---|
591 | none |
---|
592 | """ |
---|
593 | return self._get_column(self._getdirection, row) |
---|
594 | |
---|
595 | def get_directionval(self, row=-1): |
---|
596 | """ |
---|
597 | Get a list of Positions on the sky (direction) for the observations. |
---|
598 | Return a float for each integration in the scantable. |
---|
599 | Parameters: |
---|
600 | row: row no of integration. Default -1 return all rows |
---|
601 | Example: |
---|
602 | none |
---|
603 | """ |
---|
604 | return self._get_column(self._getdirectionvec, row) |
---|
605 | |
---|
606 | def set_unit(self, unit='channel'): |
---|
607 | """ |
---|
608 | Set the unit for all following operations on this scantable |
---|
609 | Parameters: |
---|
610 | unit: optional unit, default is 'channel' |
---|
611 | one of '*Hz', 'km/s', 'channel', '' |
---|
612 | """ |
---|
613 | varlist = vars() |
---|
614 | if unit in ['', 'pixel', 'channel']: |
---|
615 | unit = '' |
---|
616 | inf = list(self._getcoordinfo()) |
---|
617 | inf[0] = unit |
---|
618 | self._setcoordinfo(inf) |
---|
619 | self._add_history("set_unit", varlist) |
---|
620 | |
---|
621 | def set_instrument(self, instr): |
---|
622 | """ |
---|
623 | Set the instrument for subsequent processing. |
---|
624 | Parameters: |
---|
625 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
626 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
627 | """ |
---|
628 | self._setInstrument(instr) |
---|
629 | self._add_history("set_instument", vars()) |
---|
630 | print_log() |
---|
631 | |
---|
632 | def set_feedtype(self, feedtype): |
---|
633 | """ |
---|
634 | Overwrite the feed type, which might not be set correctly. |
---|
635 | Parameters: |
---|
636 | feedtype: 'linear' or 'circular' |
---|
637 | """ |
---|
638 | self._setfeedtype(feedtype) |
---|
639 | self._add_history("set_feedtype", vars()) |
---|
640 | print_log() |
---|
641 | |
---|
642 | def set_doppler(self, doppler='RADIO'): |
---|
643 | """ |
---|
644 | Set the doppler for all following operations on this scantable. |
---|
645 | Parameters: |
---|
646 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
647 | """ |
---|
648 | varlist = vars() |
---|
649 | inf = list(self._getcoordinfo()) |
---|
650 | inf[2] = doppler |
---|
651 | self._setcoordinfo(inf) |
---|
652 | self._add_history("set_doppler", vars()) |
---|
653 | print_log() |
---|
654 | |
---|
655 | def set_freqframe(self, frame=None): |
---|
656 | """ |
---|
657 | Set the frame type of the Spectral Axis. |
---|
658 | Parameters: |
---|
659 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
660 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
661 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
662 | Examples: |
---|
663 | scan.set_freqframe('BARY') |
---|
664 | """ |
---|
665 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
666 | varlist = vars() |
---|
667 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
668 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
669 | |
---|
670 | if frame in valid: |
---|
671 | inf = list(self._getcoordinfo()) |
---|
672 | inf[1] = frame |
---|
673 | self._setcoordinfo(inf) |
---|
674 | self._add_history("set_freqframe", varlist) |
---|
675 | else: |
---|
676 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
677 | if rcParams['verbose']: |
---|
678 | print msg |
---|
679 | else: |
---|
680 | raise TypeError(msg) |
---|
681 | print_log() |
---|
682 | |
---|
683 | def set_dirframe(self, frame=""): |
---|
684 | """ |
---|
685 | Set the frame type of the Direction on the sky. |
---|
686 | Parameters: |
---|
687 | frame: an optional frame type, default ''. Valid frames are: |
---|
688 | 'J2000', 'B1950', 'GALACTIC' |
---|
689 | Examples: |
---|
690 | scan.set_dirframe('GALACTIC') |
---|
691 | """ |
---|
692 | varlist = vars() |
---|
693 | try: |
---|
694 | Scantable.set_dirframe(self, frame) |
---|
695 | except RuntimeError, msg: |
---|
696 | if rcParams['verbose']: |
---|
697 | print msg |
---|
698 | else: |
---|
699 | raise |
---|
700 | self._add_history("set_dirframe", varlist) |
---|
701 | |
---|
702 | def get_unit(self): |
---|
703 | """ |
---|
704 | Get the default unit set in this scantable |
---|
705 | Returns: |
---|
706 | A unit string |
---|
707 | """ |
---|
708 | inf = self._getcoordinfo() |
---|
709 | unit = inf[0] |
---|
710 | if unit == '': unit = 'channel' |
---|
711 | return unit |
---|
712 | |
---|
713 | def get_abcissa(self, rowno=0): |
---|
714 | """ |
---|
715 | Get the abcissa in the current coordinate setup for the currently |
---|
716 | selected Beam/IF/Pol |
---|
717 | Parameters: |
---|
718 | rowno: an optional row number in the scantable. Default is the |
---|
719 | first row, i.e. rowno=0 |
---|
720 | Returns: |
---|
721 | The abcissa values and the format string (as a dictionary) |
---|
722 | """ |
---|
723 | abc = self._getabcissa(rowno) |
---|
724 | lbl = self._getabcissalabel(rowno) |
---|
725 | print_log() |
---|
726 | return abc, lbl |
---|
727 | |
---|
728 | def flag(self, mask=None, unflag=False): |
---|
729 | """ |
---|
730 | Flag the selected data using an optional channel mask. |
---|
731 | Parameters: |
---|
732 | mask: an optional channel mask, created with create_mask. Default |
---|
733 | (no mask) is all channels. |
---|
734 | unflag: if True, unflag the data |
---|
735 | """ |
---|
736 | varlist = vars() |
---|
737 | if mask is None: |
---|
738 | mask = [] |
---|
739 | try: |
---|
740 | self._flag(mask, unflag) |
---|
741 | except RuntimeError, msg: |
---|
742 | if rcParams['verbose']: |
---|
743 | print msg |
---|
744 | return |
---|
745 | else: raise |
---|
746 | self._add_history("flag", varlist) |
---|
747 | |
---|
748 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
749 | """ |
---|
750 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
751 | Flagged data in the scantable gets set to 0.0 before the fft. |
---|
752 | No taper is applied. |
---|
753 | Parameters: |
---|
754 | frequency: the frequency (really a period within the bandwidth) |
---|
755 | to remove |
---|
756 | width: the width of the frequency to remove, to remove a |
---|
757 | range of frequencies aroung the centre. |
---|
758 | unit: the frequency unit (default "GHz") |
---|
759 | Notes: |
---|
760 | It is recommended to flag edges of the band or strong |
---|
761 | signals beforehand. |
---|
762 | """ |
---|
763 | if insitu is None: insitu = rcParams['insitu'] |
---|
764 | self._math._setinsitu(insitu) |
---|
765 | varlist = vars() |
---|
766 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. } |
---|
767 | if not base.has_key(unit): |
---|
768 | raise ValueError("%s is not a valid unit." % unit) |
---|
769 | try: |
---|
770 | s = scantable(self._math._lag_flag(self, frequency*base[unit], |
---|
771 | width*base[unit])) |
---|
772 | except RuntimeError, msg: |
---|
773 | if rcParams['verbose']: |
---|
774 | print msg |
---|
775 | return |
---|
776 | else: raise |
---|
777 | s._add_history("lag_flag", varlist) |
---|
778 | print_log() |
---|
779 | if insitu: |
---|
780 | self._assign(s) |
---|
781 | else: |
---|
782 | return s |
---|
783 | |
---|
784 | |
---|
785 | def create_mask(self, *args, **kwargs): |
---|
786 | """ |
---|
787 | Compute and return a mask based on [min, max] windows. |
---|
788 | The specified windows are to be INCLUDED, when the mask is |
---|
789 | applied. |
---|
790 | Parameters: |
---|
791 | [min, max], [min2, max2], ... |
---|
792 | Pairs of start/end points (inclusive)specifying the regions |
---|
793 | to be masked |
---|
794 | invert: optional argument. If specified as True, |
---|
795 | return an inverted mask, i.e. the regions |
---|
796 | specified are EXCLUDED |
---|
797 | row: create the mask using the specified row for |
---|
798 | unit conversions, default is row=0 |
---|
799 | only necessary if frequency varies over rows. |
---|
800 | Example: |
---|
801 | scan.set_unit('channel') |
---|
802 | a) |
---|
803 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
804 | # masks everything outside 400 and 500 |
---|
805 | # and 800 and 900 in the unit 'channel' |
---|
806 | |
---|
807 | b) |
---|
808 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
809 | # masks the regions between 400 and 500 |
---|
810 | # and 800 and 900 in the unit 'channel' |
---|
811 | c) |
---|
812 | mask only channel 400 |
---|
813 | msk = scan.create_mask([400, 400]) |
---|
814 | """ |
---|
815 | row = 0 |
---|
816 | if kwargs.has_key("row"): |
---|
817 | row = kwargs.get("row") |
---|
818 | data = self._getabcissa(row) |
---|
819 | u = self._getcoordinfo()[0] |
---|
820 | if rcParams['verbose']: |
---|
821 | if u == "": u = "channel" |
---|
822 | msg = "The current mask window unit is %s" % u |
---|
823 | i = self._check_ifs() |
---|
824 | if not i: |
---|
825 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
826 | asaplog.push(msg) |
---|
827 | n = self.nchan() |
---|
828 | msk = _n_bools(n, False) |
---|
829 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
830 | |
---|
831 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
832 | and args or args[0] |
---|
833 | for window in ws: |
---|
834 | if (len(window) != 2 or window[0] > window[1] ): |
---|
835 | raise TypeError("A window needs to be defined as [min, max]") |
---|
836 | for i in range(n): |
---|
837 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
838 | msk[i] = True |
---|
839 | if kwargs.has_key('invert'): |
---|
840 | if kwargs.get('invert'): |
---|
841 | msk = mask_not(msk) |
---|
842 | print_log() |
---|
843 | return msk |
---|
844 | |
---|
845 | def get_masklist(self, mask=None, row=0): |
---|
846 | """ |
---|
847 | Compute and return a list of mask windows, [min, max]. |
---|
848 | Parameters: |
---|
849 | mask: channel mask, created with create_mask. |
---|
850 | row: calcutate the masklist using the specified row |
---|
851 | for unit conversions, default is row=0 |
---|
852 | only necessary if frequency varies over rows. |
---|
853 | Returns: |
---|
854 | [min, max], [min2, max2], ... |
---|
855 | Pairs of start/end points (inclusive)specifying |
---|
856 | the masked regions |
---|
857 | """ |
---|
858 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
859 | raise TypeError("The mask should be list or tuple.") |
---|
860 | if len(mask) < 2: |
---|
861 | raise TypeError("The mask elements should be > 1") |
---|
862 | if self.nchan() != len(mask): |
---|
863 | msg = "Number of channels in scantable != number of mask elements" |
---|
864 | raise TypeError(msg) |
---|
865 | data = self._getabcissa(row) |
---|
866 | u = self._getcoordinfo()[0] |
---|
867 | if rcParams['verbose']: |
---|
868 | if u == "": u = "channel" |
---|
869 | msg = "The current mask window unit is %s" % u |
---|
870 | i = self._check_ifs() |
---|
871 | if not i: |
---|
872 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
873 | asaplog.push(msg) |
---|
874 | masklist=[] |
---|
875 | ist, ien = None, None |
---|
876 | ist, ien=self.get_mask_indices(mask) |
---|
877 | if ist is not None and ien is not None: |
---|
878 | for i in xrange(len(ist)): |
---|
879 | range=[data[ist[i]],data[ien[i]]] |
---|
880 | range.sort() |
---|
881 | masklist.append([range[0],range[1]]) |
---|
882 | return masklist |
---|
883 | |
---|
884 | def get_mask_indices(self, mask=None): |
---|
885 | """ |
---|
886 | Compute and Return lists of mask start indices and mask end indices. |
---|
887 | Parameters: |
---|
888 | mask: channel mask, created with create_mask. |
---|
889 | Returns: |
---|
890 | List of mask start indices and that of mask end indices, |
---|
891 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
892 | """ |
---|
893 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
894 | raise TypeError("The mask should be list or tuple.") |
---|
895 | if len(mask) < 2: |
---|
896 | raise TypeError("The mask elements should be > 1") |
---|
897 | istart=[] |
---|
898 | iend=[] |
---|
899 | if mask[0]: istart.append(0) |
---|
900 | for i in range(len(mask)-1): |
---|
901 | if not mask[i] and mask[i+1]: |
---|
902 | istart.append(i+1) |
---|
903 | elif mask[i] and not mask[i+1]: |
---|
904 | iend.append(i) |
---|
905 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
906 | if len(istart) != len(iend): |
---|
907 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
908 | for i in range(len(istart)): |
---|
909 | if istart[i] > iend[i]: |
---|
910 | raise RuntimeError("Mask start index > mask end index") |
---|
911 | break |
---|
912 | return istart,iend |
---|
913 | |
---|
914 | # def get_restfreqs(self): |
---|
915 | # """ |
---|
916 | # Get the restfrequency(s) stored in this scantable. |
---|
917 | # The return value(s) are always of unit 'Hz' |
---|
918 | # Parameters: |
---|
919 | # none |
---|
920 | # Returns: |
---|
921 | # a list of doubles |
---|
922 | # """ |
---|
923 | # return list(self._getrestfreqs()) |
---|
924 | |
---|
925 | def get_restfreqs(self, ids=None): |
---|
926 | """ |
---|
927 | Get the restfrequency(s) stored in this scantable. |
---|
928 | The return value(s) are always of unit 'Hz' |
---|
929 | Parameters: |
---|
930 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
931 | be retrieved |
---|
932 | Returns: |
---|
933 | dictionary containing ids and a list of doubles for each id |
---|
934 | """ |
---|
935 | if ids is None: |
---|
936 | rfreqs={} |
---|
937 | idlist = self.getmolnos() |
---|
938 | for i in idlist: |
---|
939 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
940 | return rfreqs |
---|
941 | else: |
---|
942 | if type(ids)==list or type(ids)==tuple: |
---|
943 | rfreqs={} |
---|
944 | for i in ids: |
---|
945 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
946 | return rfreqs |
---|
947 | else: |
---|
948 | return list(self._getrestfreqs(ids)) |
---|
949 | #return list(self._getrestfreqs(ids)) |
---|
950 | |
---|
951 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
952 | """ |
---|
953 | ********NEED TO BE UPDATED begin************ |
---|
954 | Set or replace the restfrequency specified and |
---|
955 | If the 'freqs' argument holds a scalar, |
---|
956 | then that rest frequency will be applied to all the selected |
---|
957 | data. If the 'freqs' argument holds |
---|
958 | a vector, then it MUST be of equal or smaller length than |
---|
959 | the number of IFs (and the available restfrequencies will be |
---|
960 | replaced by this vector). In this case, *all* data have |
---|
961 | the restfrequency set per IF according |
---|
962 | to the corresponding value you give in the 'freqs' vector. |
---|
963 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
964 | IF 1 gets restfreq 2e9. |
---|
965 | ********NEED TO BE UPDATED end************ |
---|
966 | You can also specify the frequencies via a linecatalog/ |
---|
967 | |
---|
968 | Parameters: |
---|
969 | freqs: list of rest frequency values or string idenitfiers |
---|
970 | unit: unit for rest frequency (default 'Hz') |
---|
971 | |
---|
972 | Example: |
---|
973 | # set the given restfrequency for the all currently selected IFs |
---|
974 | scan.set_restfreqs(freqs=1.4e9) |
---|
975 | # set multiple restfrequencies to all the selected data |
---|
976 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
977 | # If the number of IFs in the data is >= 2 the IF0 gets the first |
---|
978 | # value IF1 the second... NOTE that freqs needs to be |
---|
979 | # specified in list of list (e.g. [[],[],...] ). |
---|
980 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]]) |
---|
981 | #set the given restfrequency for the whole table (by name) |
---|
982 | scan.set_restfreqs(freqs="OH1667") |
---|
983 | |
---|
984 | Note: |
---|
985 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
986 | source and IF basis, use scantable.set_selection() before using |
---|
987 | this function. |
---|
988 | # provide your scantable is call scan |
---|
989 | selection = selector() |
---|
990 | selection.set_name("ORION*") |
---|
991 | selection.set_ifs([1]) |
---|
992 | scan.set_selection(selection) |
---|
993 | scan.set_restfreqs(freqs=86.6e9) |
---|
994 | |
---|
995 | """ |
---|
996 | varlist = vars() |
---|
997 | from asap import linecatalog |
---|
998 | # simple value |
---|
999 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
1000 | # TT mod |
---|
1001 | #self._setrestfreqs(freqs, "",unit) |
---|
1002 | self._setrestfreqs([freqs], [""],unit) |
---|
1003 | # list of values |
---|
1004 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
1005 | # list values are scalars |
---|
1006 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
1007 | self._setrestfreqs(freqs, [""],unit) |
---|
1008 | # list values are tuples, (value, name) |
---|
1009 | elif isinstance(freqs[-1], dict): |
---|
1010 | #sel = selector() |
---|
1011 | #savesel = self._getselection() |
---|
1012 | #iflist = self.getifnos() |
---|
1013 | #for i in xrange(len(freqs)): |
---|
1014 | # sel.set_ifs(iflist[i]) |
---|
1015 | # self._setselection(sel) |
---|
1016 | # self._setrestfreqs(freqs[i], "",unit) |
---|
1017 | #self._setselection(savesel) |
---|
1018 | self._setrestfreqs(freqs["value"], |
---|
1019 | freqs["name"], "MHz") |
---|
1020 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
1021 | sel = selector() |
---|
1022 | savesel = self._getselection() |
---|
1023 | iflist = self.getifnos() |
---|
1024 | if len(freqs)>len(iflist): |
---|
1025 | raise ValueError("number of elements in list of list exeeds the current IF selections") |
---|
1026 | for i in xrange(len(freqs)): |
---|
1027 | sel.set_ifs(iflist[i]) |
---|
1028 | self._setselection(sel) |
---|
1029 | self._setrestfreqs(freqs[i]["value"], |
---|
1030 | freqs[i]["name"], "MHz") |
---|
1031 | self._setselection(savesel) |
---|
1032 | # freqs are to be taken from a linecatalog |
---|
1033 | elif isinstance(freqs, linecatalog): |
---|
1034 | sel = selector() |
---|
1035 | savesel = self._getselection() |
---|
1036 | for i in xrange(freqs.nrow()): |
---|
1037 | sel.set_ifs(iflist[i]) |
---|
1038 | self._setselection(sel) |
---|
1039 | self._setrestfreqs(freqs.get_frequency(i), |
---|
1040 | freqs.get_name(i), "MHz") |
---|
1041 | # ensure that we are not iterating past nIF |
---|
1042 | if i == self.nif()-1: break |
---|
1043 | self._setselection(savesel) |
---|
1044 | else: |
---|
1045 | return |
---|
1046 | self._add_history("set_restfreqs", varlist) |
---|
1047 | |
---|
1048 | def shift_refpix(self, delta): |
---|
1049 | """ |
---|
1050 | Shift the reference pixel of the Spectra Coordinate by an |
---|
1051 | integer amount. |
---|
1052 | Parameters: |
---|
1053 | delta: the amount to shift by |
---|
1054 | Note: |
---|
1055 | Be careful using this with broadband data. |
---|
1056 | """ |
---|
1057 | Scantable.shift(self, delta) |
---|
1058 | |
---|
1059 | def history(self, filename=None): |
---|
1060 | """ |
---|
1061 | Print the history. Optionally to a file. |
---|
1062 | Parameters: |
---|
1063 | filename: The name of the file to save the history to. |
---|
1064 | """ |
---|
1065 | hist = list(self._gethistory()) |
---|
1066 | out = "-"*80 |
---|
1067 | for h in hist: |
---|
1068 | if h.startswith("---"): |
---|
1069 | out += "\n"+h |
---|
1070 | else: |
---|
1071 | items = h.split("##") |
---|
1072 | date = items[0] |
---|
1073 | func = items[1] |
---|
1074 | items = items[2:] |
---|
1075 | out += "\n"+date+"\n" |
---|
1076 | out += "Function: %s\n Parameters:" % (func) |
---|
1077 | for i in items: |
---|
1078 | s = i.split("=") |
---|
1079 | out += "\n %s = %s" % (s[0], s[1]) |
---|
1080 | out += "\n"+"-"*80 |
---|
1081 | if filename is not None: |
---|
1082 | if filename is "": |
---|
1083 | filename = 'scantable_history.txt' |
---|
1084 | import os |
---|
1085 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
1086 | if not os.path.isdir(filename): |
---|
1087 | data = open(filename, 'w') |
---|
1088 | data.write(out) |
---|
1089 | data.close() |
---|
1090 | else: |
---|
1091 | msg = "Illegal file name '%s'." % (filename) |
---|
1092 | if rcParams['verbose']: |
---|
1093 | print msg |
---|
1094 | else: |
---|
1095 | raise IOError(msg) |
---|
1096 | if rcParams['verbose']: |
---|
1097 | try: |
---|
1098 | from IPython.genutils import page as pager |
---|
1099 | except ImportError: |
---|
1100 | from pydoc import pager |
---|
1101 | pager(out) |
---|
1102 | else: |
---|
1103 | return out |
---|
1104 | return |
---|
1105 | # |
---|
1106 | # Maths business |
---|
1107 | # |
---|
1108 | |
---|
1109 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
1110 | """ |
---|
1111 | Return the (time) weighted average of a scan. |
---|
1112 | Note: |
---|
1113 | in channels only - align if necessary |
---|
1114 | Parameters: |
---|
1115 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
1116 | weighting) |
---|
1117 | scanav: True averages each scan separately |
---|
1118 | False (default) averages all scans together, |
---|
1119 | weight: Weighting scheme. |
---|
1120 | 'none' (mean no weight) |
---|
1121 | 'var' (1/var(spec) weighted) |
---|
1122 | 'tsys' (1/Tsys**2 weighted) |
---|
1123 | 'tint' (integration time weighted) |
---|
1124 | 'tintsys' (Tint/Tsys**2) |
---|
1125 | 'median' ( median averaging) |
---|
1126 | The default is 'tint' |
---|
1127 | align: align the spectra in velocity before averaging. It takes |
---|
1128 | the time of the first spectrum as reference time. |
---|
1129 | Example: |
---|
1130 | # time average the scantable without using a mask |
---|
1131 | newscan = scan.average_time() |
---|
1132 | """ |
---|
1133 | varlist = vars() |
---|
1134 | if weight is None: weight = 'TINT' |
---|
1135 | if mask is None: mask = () |
---|
1136 | if scanav: scanav = "SCAN" |
---|
1137 | else: scanav = "NONE" |
---|
1138 | scan = (self, ) |
---|
1139 | try: |
---|
1140 | if align: |
---|
1141 | scan = (self.freq_align(insitu=False), ) |
---|
1142 | s = None |
---|
1143 | if weight.upper() == 'MEDIAN': |
---|
1144 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
1145 | scanav)) |
---|
1146 | else: |
---|
1147 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
1148 | scanav)) |
---|
1149 | except RuntimeError, msg: |
---|
1150 | if rcParams['verbose']: |
---|
1151 | print msg |
---|
1152 | return |
---|
1153 | else: raise |
---|
1154 | s._add_history("average_time", varlist) |
---|
1155 | print_log() |
---|
1156 | return s |
---|
1157 | |
---|
1158 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
1159 | """ |
---|
1160 | Return a scan where all spectra are converted to either |
---|
1161 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
1162 | By default the function tries to look the values up internally. |
---|
1163 | If it can't find them (or if you want to over-ride), you must |
---|
1164 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
1165 | also if you don't set it). jyperk takes precedence if you set both. |
---|
1166 | Parameters: |
---|
1167 | jyperk: the Jy / K conversion factor |
---|
1168 | eta: the aperture efficiency |
---|
1169 | d: the geomtric diameter (metres) |
---|
1170 | insitu: if False a new scantable is returned. |
---|
1171 | Otherwise, the scaling is done in-situ |
---|
1172 | The default is taken from .asaprc (False) |
---|
1173 | """ |
---|
1174 | if insitu is None: insitu = rcParams['insitu'] |
---|
1175 | self._math._setinsitu(insitu) |
---|
1176 | varlist = vars() |
---|
1177 | if jyperk is None: jyperk = -1.0 |
---|
1178 | if d is None: d = -1.0 |
---|
1179 | if eta is None: eta = -1.0 |
---|
1180 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
1181 | s._add_history("convert_flux", varlist) |
---|
1182 | print_log() |
---|
1183 | if insitu: self._assign(s) |
---|
1184 | else: return s |
---|
1185 | |
---|
1186 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
1187 | """ |
---|
1188 | Return a scan after applying a gain-elevation correction. |
---|
1189 | The correction can be made via either a polynomial or a |
---|
1190 | table-based interpolation (and extrapolation if necessary). |
---|
1191 | You specify polynomial coefficients, an ascii table or neither. |
---|
1192 | If you specify neither, then a polynomial correction will be made |
---|
1193 | with built in coefficients known for certain telescopes (an error |
---|
1194 | will occur if the instrument is not known). |
---|
1195 | The data and Tsys are *divided* by the scaling factors. |
---|
1196 | Parameters: |
---|
1197 | poly: Polynomial coefficients (default None) to compute a |
---|
1198 | gain-elevation correction as a function of |
---|
1199 | elevation (in degrees). |
---|
1200 | filename: The name of an ascii file holding correction factors. |
---|
1201 | The first row of the ascii file must give the column |
---|
1202 | names and these MUST include columns |
---|
1203 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
1204 | by this) somewhere. |
---|
1205 | The second row must give the data type of the |
---|
1206 | column. Use 'R' for Real and 'I' for Integer. |
---|
1207 | An example file would be |
---|
1208 | (actual factors are arbitrary) : |
---|
1209 | |
---|
1210 | TIME ELEVATION FACTOR |
---|
1211 | R R R |
---|
1212 | 0.1 0 0.8 |
---|
1213 | 0.2 20 0.85 |
---|
1214 | 0.3 40 0.9 |
---|
1215 | 0.4 60 0.85 |
---|
1216 | 0.5 80 0.8 |
---|
1217 | 0.6 90 0.75 |
---|
1218 | method: Interpolation method when correcting from a table. |
---|
1219 | Values are "nearest", "linear" (default), "cubic" |
---|
1220 | and "spline" |
---|
1221 | insitu: if False a new scantable is returned. |
---|
1222 | Otherwise, the scaling is done in-situ |
---|
1223 | The default is taken from .asaprc (False) |
---|
1224 | """ |
---|
1225 | |
---|
1226 | if insitu is None: insitu = rcParams['insitu'] |
---|
1227 | self._math._setinsitu(insitu) |
---|
1228 | varlist = vars() |
---|
1229 | if poly is None: |
---|
1230 | poly = () |
---|
1231 | from os.path import expandvars |
---|
1232 | filename = expandvars(filename) |
---|
1233 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
1234 | s._add_history("gain_el", varlist) |
---|
1235 | print_log() |
---|
1236 | if insitu: self._assign(s) |
---|
1237 | else: return s |
---|
1238 | |
---|
1239 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
1240 | """ |
---|
1241 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
1242 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
1243 | set_freqframe. |
---|
1244 | Parameters: |
---|
1245 | reftime: reference time to align at. By default, the time of |
---|
1246 | the first row of data is used. |
---|
1247 | method: Interpolation method for regridding the spectra. |
---|
1248 | Choose from "nearest", "linear", "cubic" (default) |
---|
1249 | and "spline" |
---|
1250 | insitu: if False a new scantable is returned. |
---|
1251 | Otherwise, the scaling is done in-situ |
---|
1252 | The default is taken from .asaprc (False) |
---|
1253 | """ |
---|
1254 | if insitu is None: insitu = rcParams["insitu"] |
---|
1255 | self._math._setinsitu(insitu) |
---|
1256 | varlist = vars() |
---|
1257 | if reftime is None: reftime = "" |
---|
1258 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
1259 | s._add_history("freq_align", varlist) |
---|
1260 | print_log() |
---|
1261 | if insitu: self._assign(s) |
---|
1262 | else: return s |
---|
1263 | |
---|
1264 | def opacity(self, tau, insitu=None): |
---|
1265 | """ |
---|
1266 | Apply an opacity correction. The data |
---|
1267 | and Tsys are multiplied by the correction factor. |
---|
1268 | Parameters: |
---|
1269 | tau: Opacity from which the correction factor is |
---|
1270 | exp(tau*ZD) |
---|
1271 | where ZD is the zenith-distance |
---|
1272 | insitu: if False a new scantable is returned. |
---|
1273 | Otherwise, the scaling is done in-situ |
---|
1274 | The default is taken from .asaprc (False) |
---|
1275 | """ |
---|
1276 | if insitu is None: insitu = rcParams['insitu'] |
---|
1277 | self._math._setinsitu(insitu) |
---|
1278 | varlist = vars() |
---|
1279 | s = scantable(self._math._opacity(self, tau)) |
---|
1280 | s._add_history("opacity", varlist) |
---|
1281 | print_log() |
---|
1282 | if insitu: self._assign(s) |
---|
1283 | else: return s |
---|
1284 | |
---|
1285 | def bin(self, width=5, insitu=None): |
---|
1286 | """ |
---|
1287 | Return a scan where all spectra have been binned up. |
---|
1288 | Parameters: |
---|
1289 | width: The bin width (default=5) in pixels |
---|
1290 | insitu: if False a new scantable is returned. |
---|
1291 | Otherwise, the scaling is done in-situ |
---|
1292 | The default is taken from .asaprc (False) |
---|
1293 | """ |
---|
1294 | if insitu is None: insitu = rcParams['insitu'] |
---|
1295 | self._math._setinsitu(insitu) |
---|
1296 | varlist = vars() |
---|
1297 | s = scantable(self._math._bin(self, width)) |
---|
1298 | s._add_history("bin", varlist) |
---|
1299 | print_log() |
---|
1300 | if insitu: self._assign(s) |
---|
1301 | else: return s |
---|
1302 | |
---|
1303 | |
---|
1304 | def resample(self, width=5, method='cubic', insitu=None): |
---|
1305 | """ |
---|
1306 | Return a scan where all spectra have been binned up. |
---|
1307 | |
---|
1308 | Parameters: |
---|
1309 | width: The bin width (default=5) in pixels |
---|
1310 | method: Interpolation method when correcting from a table. |
---|
1311 | Values are "nearest", "linear", "cubic" (default) |
---|
1312 | and "spline" |
---|
1313 | insitu: if False a new scantable is returned. |
---|
1314 | Otherwise, the scaling is done in-situ |
---|
1315 | The default is taken from .asaprc (False) |
---|
1316 | """ |
---|
1317 | if insitu is None: insitu = rcParams['insitu'] |
---|
1318 | self._math._setinsitu(insitu) |
---|
1319 | varlist = vars() |
---|
1320 | s = scantable(self._math._resample(self, method, width)) |
---|
1321 | s._add_history("resample", varlist) |
---|
1322 | print_log() |
---|
1323 | if insitu: self._assign(s) |
---|
1324 | else: return s |
---|
1325 | |
---|
1326 | |
---|
1327 | def average_pol(self, mask=None, weight='none'): |
---|
1328 | """ |
---|
1329 | Average the Polarisations together. |
---|
1330 | Parameters: |
---|
1331 | mask: An optional mask defining the region, where the |
---|
1332 | averaging will be applied. The output will have all |
---|
1333 | specified points masked. |
---|
1334 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
1335 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
1336 | """ |
---|
1337 | varlist = vars() |
---|
1338 | if mask is None: |
---|
1339 | mask = () |
---|
1340 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
1341 | s._add_history("average_pol", varlist) |
---|
1342 | print_log() |
---|
1343 | return s |
---|
1344 | |
---|
1345 | def average_beam(self, mask=None, weight='none'): |
---|
1346 | """ |
---|
1347 | Average the Beams together. |
---|
1348 | Parameters: |
---|
1349 | mask: An optional mask defining the region, where the |
---|
1350 | averaging will be applied. The output will have all |
---|
1351 | specified points masked. |
---|
1352 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
1353 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
1354 | """ |
---|
1355 | varlist = vars() |
---|
1356 | if mask is None: |
---|
1357 | mask = () |
---|
1358 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
1359 | s._add_history("average_beam", varlist) |
---|
1360 | print_log() |
---|
1361 | return s |
---|
1362 | |
---|
1363 | def convert_pol(self, poltype=None): |
---|
1364 | """ |
---|
1365 | Convert the data to a different polarisation type. |
---|
1366 | Parameters: |
---|
1367 | poltype: The new polarisation type. Valid types are: |
---|
1368 | "linear", "stokes" and "circular" |
---|
1369 | """ |
---|
1370 | varlist = vars() |
---|
1371 | try: |
---|
1372 | s = scantable(self._math._convertpol(self, poltype)) |
---|
1373 | except RuntimeError, msg: |
---|
1374 | if rcParams['verbose']: |
---|
1375 | print msg |
---|
1376 | return |
---|
1377 | else: |
---|
1378 | raise |
---|
1379 | s._add_history("convert_pol", varlist) |
---|
1380 | print_log() |
---|
1381 | return s |
---|
1382 | |
---|
1383 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
1384 | """ |
---|
1385 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
1386 | Parameters: |
---|
1387 | kernel: The type of smoothing kernel. Select from |
---|
1388 | 'hanning' (default), 'gaussian', 'boxcar' and |
---|
1389 | 'rmedian' |
---|
1390 | width: The width of the kernel in pixels. For hanning this is |
---|
1391 | ignored otherwise it defauls to 5 pixels. |
---|
1392 | For 'gaussian' it is the Full Width Half |
---|
1393 | Maximum. For 'boxcar' it is the full width. |
---|
1394 | For 'rmedian' it is the half width. |
---|
1395 | insitu: if False a new scantable is returned. |
---|
1396 | Otherwise, the scaling is done in-situ |
---|
1397 | The default is taken from .asaprc (False) |
---|
1398 | Example: |
---|
1399 | none |
---|
1400 | """ |
---|
1401 | if insitu is None: insitu = rcParams['insitu'] |
---|
1402 | self._math._setinsitu(insitu) |
---|
1403 | varlist = vars() |
---|
1404 | s = scantable(self._math._smooth(self, kernel.lower(), width)) |
---|
1405 | s._add_history("smooth", varlist) |
---|
1406 | print_log() |
---|
1407 | if insitu: self._assign(s) |
---|
1408 | else: return s |
---|
1409 | |
---|
1410 | |
---|
1411 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None): |
---|
1412 | """ |
---|
1413 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1414 | Parameters: |
---|
1415 | mask: an optional mask |
---|
1416 | order: the order of the polynomial (default is 0) |
---|
1417 | plot: plot the fit and the residual. In this each |
---|
1418 | indivual fit has to be approved, by typing 'y' |
---|
1419 | or 'n' |
---|
1420 | uselin: use linear polynomial fit |
---|
1421 | insitu: if False a new scantable is returned. |
---|
1422 | Otherwise, the scaling is done in-situ |
---|
1423 | The default is taken from .asaprc (False) |
---|
1424 | Example: |
---|
1425 | # return a scan baselined by a third order polynomial, |
---|
1426 | # not using a mask |
---|
1427 | bscan = scan.poly_baseline(order=3) |
---|
1428 | """ |
---|
1429 | if insitu is None: insitu = rcParams['insitu'] |
---|
1430 | varlist = vars() |
---|
1431 | if mask is None: |
---|
1432 | mask = [True for i in xrange(self.nchan(-1))] |
---|
1433 | from asap.asapfitter import fitter |
---|
1434 | try: |
---|
1435 | f = fitter() |
---|
1436 | f.set_scan(self, mask) |
---|
1437 | if uselin: |
---|
1438 | f.set_function(lpoly=order) |
---|
1439 | else: |
---|
1440 | f.set_function(poly=order) |
---|
1441 | s = f.auto_fit(insitu, plot=plot) |
---|
1442 | # Save parameters of baseline fits as a class attribute. |
---|
1443 | # NOTICE: It does not reflect changes in scantable! |
---|
1444 | self.blpars = f.blpars |
---|
1445 | s._add_history("poly_baseline", varlist) |
---|
1446 | print_log() |
---|
1447 | if insitu: self._assign(s) |
---|
1448 | else: return s |
---|
1449 | except RuntimeError: |
---|
1450 | msg = "The fit failed, possibly because it didn't converge." |
---|
1451 | if rcParams['verbose']: |
---|
1452 | print msg |
---|
1453 | return |
---|
1454 | else: |
---|
1455 | raise RuntimeError(msg) |
---|
1456 | |
---|
1457 | |
---|
1458 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
1459 | threshold=3, chan_avg_limit=1, plot=False, |
---|
1460 | insitu=None): |
---|
1461 | """ |
---|
1462 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1463 | Spectral lines are detected first using linefinder and masked out |
---|
1464 | to avoid them affecting the baseline solution. |
---|
1465 | |
---|
1466 | Parameters: |
---|
1467 | mask: an optional mask retreived from scantable |
---|
1468 | edge: an optional number of channel to drop at |
---|
1469 | the edge of spectrum. If only one value is |
---|
1470 | specified, the same number will be dropped from |
---|
1471 | both sides of the spectrum. Default is to keep |
---|
1472 | all channels. Nested tuples represent individual |
---|
1473 | edge selection for different IFs (a number of spectral |
---|
1474 | channels can be different) |
---|
1475 | order: the order of the polynomial (default is 0) |
---|
1476 | threshold: the threshold used by line finder. It is better to |
---|
1477 | keep it large as only strong lines affect the |
---|
1478 | baseline solution. |
---|
1479 | chan_avg_limit: |
---|
1480 | a maximum number of consequtive spectral channels to |
---|
1481 | average during the search of weak and broad lines. |
---|
1482 | The default is no averaging (and no search for weak |
---|
1483 | lines). If such lines can affect the fitted baseline |
---|
1484 | (e.g. a high order polynomial is fitted), increase this |
---|
1485 | parameter (usually values up to 8 are reasonable). Most |
---|
1486 | users of this method should find the default value |
---|
1487 | sufficient. |
---|
1488 | plot: plot the fit and the residual. In this each |
---|
1489 | indivual fit has to be approved, by typing 'y' |
---|
1490 | or 'n' |
---|
1491 | insitu: if False a new scantable is returned. |
---|
1492 | Otherwise, the scaling is done in-situ |
---|
1493 | The default is taken from .asaprc (False) |
---|
1494 | |
---|
1495 | Example: |
---|
1496 | scan2=scan.auto_poly_baseline(order=7) |
---|
1497 | """ |
---|
1498 | if insitu is None: insitu = rcParams['insitu'] |
---|
1499 | varlist = vars() |
---|
1500 | from asap.asapfitter import fitter |
---|
1501 | from asap.asaplinefind import linefinder |
---|
1502 | from asap import _is_sequence_or_number as _is_valid |
---|
1503 | |
---|
1504 | # check whether edge is set up for each IF individually |
---|
1505 | individualedge = False; |
---|
1506 | if len(edge) > 1: |
---|
1507 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
1508 | individualedge = True; |
---|
1509 | |
---|
1510 | if not _is_valid(edge, int) and not individualedge: |
---|
1511 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
1512 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
1513 | to make individual selection for different IFs." |
---|
1514 | |
---|
1515 | curedge = (0, 0) |
---|
1516 | if individualedge: |
---|
1517 | for edgepar in edge: |
---|
1518 | if not _is_valid(edgepar, int): |
---|
1519 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
1520 | to be a pair of integers or an integer." |
---|
1521 | else: |
---|
1522 | curedge = edge; |
---|
1523 | |
---|
1524 | # setup fitter |
---|
1525 | f = fitter() |
---|
1526 | f.set_function(poly=order) |
---|
1527 | |
---|
1528 | # setup line finder |
---|
1529 | fl = linefinder() |
---|
1530 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
1531 | |
---|
1532 | if not insitu: |
---|
1533 | workscan = self.copy() |
---|
1534 | else: |
---|
1535 | workscan = self |
---|
1536 | |
---|
1537 | fl.set_scan(workscan) |
---|
1538 | |
---|
1539 | rows = range(workscan.nrow()) |
---|
1540 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
1541 | # NOTICE: It does not reflect changes in scantable! |
---|
1542 | if len(rows) > 0: |
---|
1543 | self.blpars=[] |
---|
1544 | self.masklists=[] |
---|
1545 | asaplog.push("Processing:") |
---|
1546 | for r in rows: |
---|
1547 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
1548 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
1549 | workscan.getpol(r), workscan.getcycle(r)) |
---|
1550 | asaplog.push(msg, False) |
---|
1551 | |
---|
1552 | # figure out edge parameter |
---|
1553 | if individualedge: |
---|
1554 | if len(edge) >= workscan.getif(r): |
---|
1555 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
1556 | "be less than the number of IFs" |
---|
1557 | curedge = edge[workscan.getif(r)] |
---|
1558 | |
---|
1559 | # setup line finder |
---|
1560 | fl.find_lines(r, mask, curedge) |
---|
1561 | outmask=fl.get_mask() |
---|
1562 | f.set_scan(workscan, fl.get_mask()) |
---|
1563 | f.x = workscan._getabcissa(r) |
---|
1564 | f.y = workscan._getspectrum(r) |
---|
1565 | f.data = None |
---|
1566 | f.fit() |
---|
1567 | |
---|
1568 | # Show mask list |
---|
1569 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
1570 | msg = "mask range: "+str(masklist) |
---|
1571 | asaplog.push(msg, False) |
---|
1572 | |
---|
1573 | fpar = f.get_parameters() |
---|
1574 | if plot: |
---|
1575 | f.plot(residual=True) |
---|
1576 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
1577 | if x.upper() == 'N': |
---|
1578 | self.blpars.append(None) |
---|
1579 | self.masklists.append(None) |
---|
1580 | continue |
---|
1581 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
1582 | self.blpars.append(fpar) |
---|
1583 | self.masklists.append(masklist) |
---|
1584 | if plot: |
---|
1585 | f._p.unmap() |
---|
1586 | f._p = None |
---|
1587 | workscan._add_history("auto_poly_baseline", varlist) |
---|
1588 | if insitu: |
---|
1589 | self._assign(workscan) |
---|
1590 | else: |
---|
1591 | return workscan |
---|
1592 | |
---|
1593 | def rotate_linpolphase(self, angle): |
---|
1594 | """ |
---|
1595 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
1596 | This is always done in situ in the raw data. So if you call this |
---|
1597 | function more than once then each call rotates the phase further. |
---|
1598 | Parameters: |
---|
1599 | angle: The angle (degrees) to rotate (add) by. |
---|
1600 | Examples: |
---|
1601 | scan.rotate_linpolphase(2.3) |
---|
1602 | """ |
---|
1603 | varlist = vars() |
---|
1604 | self._math._rotate_linpolphase(self, angle) |
---|
1605 | self._add_history("rotate_linpolphase", varlist) |
---|
1606 | print_log() |
---|
1607 | return |
---|
1608 | |
---|
1609 | |
---|
1610 | def rotate_xyphase(self, angle): |
---|
1611 | """ |
---|
1612 | Rotate the phase of the XY correlation. This is always done in situ |
---|
1613 | in the data. So if you call this function more than once |
---|
1614 | then each call rotates the phase further. |
---|
1615 | Parameters: |
---|
1616 | angle: The angle (degrees) to rotate (add) by. |
---|
1617 | Examples: |
---|
1618 | scan.rotate_xyphase(2.3) |
---|
1619 | """ |
---|
1620 | varlist = vars() |
---|
1621 | self._math._rotate_xyphase(self, angle) |
---|
1622 | self._add_history("rotate_xyphase", varlist) |
---|
1623 | print_log() |
---|
1624 | return |
---|
1625 | |
---|
1626 | def swap_linears(self): |
---|
1627 | """ |
---|
1628 | Swap the linear polarisations XX and YY, or better the first two |
---|
1629 | polarisations as this also works for ciculars. |
---|
1630 | """ |
---|
1631 | varlist = vars() |
---|
1632 | self._math._swap_linears(self) |
---|
1633 | self._add_history("swap_linears", varlist) |
---|
1634 | print_log() |
---|
1635 | return |
---|
1636 | |
---|
1637 | def invert_phase(self): |
---|
1638 | """ |
---|
1639 | Invert the phase of the complex polarisation |
---|
1640 | """ |
---|
1641 | varlist = vars() |
---|
1642 | self._math._invert_phase(self) |
---|
1643 | self._add_history("invert_phase", varlist) |
---|
1644 | print_log() |
---|
1645 | return |
---|
1646 | |
---|
1647 | def add(self, offset, insitu=None): |
---|
1648 | """ |
---|
1649 | Return a scan where all spectra have the offset added |
---|
1650 | Parameters: |
---|
1651 | offset: the offset |
---|
1652 | insitu: if False a new scantable is returned. |
---|
1653 | Otherwise, the scaling is done in-situ |
---|
1654 | The default is taken from .asaprc (False) |
---|
1655 | """ |
---|
1656 | if insitu is None: insitu = rcParams['insitu'] |
---|
1657 | self._math._setinsitu(insitu) |
---|
1658 | varlist = vars() |
---|
1659 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
1660 | s._add_history("add", varlist) |
---|
1661 | print_log() |
---|
1662 | if insitu: |
---|
1663 | self._assign(s) |
---|
1664 | else: |
---|
1665 | return s |
---|
1666 | |
---|
1667 | def scale(self, factor, tsys=True, insitu=None): |
---|
1668 | """ |
---|
1669 | Return a scan where all spectra are scaled by the give 'factor' |
---|
1670 | Parameters: |
---|
1671 | factor: the scaling factor |
---|
1672 | insitu: if False a new scantable is returned. |
---|
1673 | Otherwise, the scaling is done in-situ |
---|
1674 | The default is taken from .asaprc (False) |
---|
1675 | tsys: if True (default) then apply the operation to Tsys |
---|
1676 | as well as the data |
---|
1677 | """ |
---|
1678 | if insitu is None: insitu = rcParams['insitu'] |
---|
1679 | self._math._setinsitu(insitu) |
---|
1680 | varlist = vars() |
---|
1681 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
1682 | s._add_history("scale", varlist) |
---|
1683 | print_log() |
---|
1684 | if insitu: |
---|
1685 | self._assign(s) |
---|
1686 | else: |
---|
1687 | return s |
---|
1688 | |
---|
1689 | def auto_quotient(self, preserve=True, mode='paired'): |
---|
1690 | """ |
---|
1691 | This function allows to build quotients automatically. |
---|
1692 | It assumes the observation to have the same numer of |
---|
1693 | "ons" and "offs" |
---|
1694 | Parameters: |
---|
1695 | preserve: you can preserve (default) the continuum or |
---|
1696 | remove it. The equations used are |
---|
1697 | preserve: Output = Toff * (on/off) - Toff |
---|
1698 | remove: Output = Toff * (on/off) - Ton |
---|
1699 | mode: the on/off detection mode |
---|
1700 | 'paired' (default) |
---|
1701 | identifies 'off' scans by the |
---|
1702 | trailing '_R' (Mopra/Parkes) or |
---|
1703 | '_e'/'_w' (Tid) and matches |
---|
1704 | on/off pairs from the observing pattern |
---|
1705 | 'time' |
---|
1706 | finds the closest off in time |
---|
1707 | |
---|
1708 | """ |
---|
1709 | modes = ["time", "paired"] |
---|
1710 | if not mode in modes: |
---|
1711 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
1712 | raise ValueError(msg) |
---|
1713 | varlist = vars() |
---|
1714 | s = None |
---|
1715 | if mode.lower() == "paired": |
---|
1716 | basesel = self.get_selection() |
---|
1717 | sel = selector()+basesel |
---|
1718 | sel.set_query("SRCTYPE==1") |
---|
1719 | self.set_selection(sel) |
---|
1720 | offs = self.copy() |
---|
1721 | sel.set_query("SRCTYPE==0") |
---|
1722 | self.set_selection(sel) |
---|
1723 | ons = self.copy() |
---|
1724 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
1725 | self.set_selection(basesel) |
---|
1726 | elif mode.lower() == "time": |
---|
1727 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
1728 | s._add_history("auto_quotient", varlist) |
---|
1729 | print_log() |
---|
1730 | return s |
---|
1731 | |
---|
1732 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
1733 | """ |
---|
1734 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
1735 | Parameters: |
---|
1736 | mask: an optional mask to be used when weight == 'stddev' |
---|
1737 | weight: How to average the off beams. Default is 'median'. |
---|
1738 | preserve: you can preserve (default) the continuum or |
---|
1739 | remove it. The equations used are |
---|
1740 | preserve: Output = Toff * (on/off) - Toff |
---|
1741 | remove: Output = Toff * (on/off) - Ton |
---|
1742 | """ |
---|
1743 | if mask is None: mask = () |
---|
1744 | varlist = vars() |
---|
1745 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
1746 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
1747 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
1748 | from asapmath import quotient |
---|
1749 | q = quotient(on, off, preserve) |
---|
1750 | q._add_history("mx_quotient", varlist) |
---|
1751 | print_log() |
---|
1752 | return q |
---|
1753 | |
---|
1754 | def freq_switch(self, insitu=None): |
---|
1755 | """ |
---|
1756 | Apply frequency switching to the data. |
---|
1757 | Parameters: |
---|
1758 | insitu: if False a new scantable is returned. |
---|
1759 | Otherwise, the swictching is done in-situ |
---|
1760 | The default is taken from .asaprc (False) |
---|
1761 | Example: |
---|
1762 | none |
---|
1763 | """ |
---|
1764 | if insitu is None: insitu = rcParams['insitu'] |
---|
1765 | self._math._setinsitu(insitu) |
---|
1766 | varlist = vars() |
---|
1767 | s = scantable(self._math._freqswitch(self)) |
---|
1768 | s._add_history("freq_switch", varlist) |
---|
1769 | print_log() |
---|
1770 | if insitu: self._assign(s) |
---|
1771 | else: return s |
---|
1772 | |
---|
1773 | def recalc_azel(self): |
---|
1774 | """ |
---|
1775 | Recalculate the azimuth and elevation for each position. |
---|
1776 | Parameters: |
---|
1777 | none |
---|
1778 | Example: |
---|
1779 | """ |
---|
1780 | varlist = vars() |
---|
1781 | self._recalcazel() |
---|
1782 | self._add_history("recalc_azel", varlist) |
---|
1783 | print_log() |
---|
1784 | return |
---|
1785 | |
---|
1786 | def __add__(self, other): |
---|
1787 | varlist = vars() |
---|
1788 | s = None |
---|
1789 | if isinstance(other, scantable): |
---|
1790 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
1791 | elif isinstance(other, float): |
---|
1792 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
1793 | else: |
---|
1794 | raise TypeError("Other input is not a scantable or float value") |
---|
1795 | s._add_history("operator +", varlist) |
---|
1796 | print_log() |
---|
1797 | return s |
---|
1798 | |
---|
1799 | def __sub__(self, other): |
---|
1800 | """ |
---|
1801 | implicit on all axes and on Tsys |
---|
1802 | """ |
---|
1803 | varlist = vars() |
---|
1804 | s = None |
---|
1805 | if isinstance(other, scantable): |
---|
1806 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
1807 | elif isinstance(other, float): |
---|
1808 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
1809 | else: |
---|
1810 | raise TypeError("Other input is not a scantable or float value") |
---|
1811 | s._add_history("operator -", varlist) |
---|
1812 | print_log() |
---|
1813 | return s |
---|
1814 | |
---|
1815 | def __mul__(self, other): |
---|
1816 | """ |
---|
1817 | implicit on all axes and on Tsys |
---|
1818 | """ |
---|
1819 | varlist = vars() |
---|
1820 | s = None |
---|
1821 | if isinstance(other, scantable): |
---|
1822 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
1823 | elif isinstance(other, float): |
---|
1824 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
1825 | else: |
---|
1826 | raise TypeError("Other input is not a scantable or float value") |
---|
1827 | s._add_history("operator *", varlist) |
---|
1828 | print_log() |
---|
1829 | return s |
---|
1830 | |
---|
1831 | |
---|
1832 | def __div__(self, other): |
---|
1833 | """ |
---|
1834 | implicit on all axes and on Tsys |
---|
1835 | """ |
---|
1836 | varlist = vars() |
---|
1837 | s = None |
---|
1838 | if isinstance(other, scantable): |
---|
1839 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
1840 | elif isinstance(other, float): |
---|
1841 | if other == 0.0: |
---|
1842 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
1843 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
1844 | else: |
---|
1845 | raise TypeError("Other input is not a scantable or float value") |
---|
1846 | s._add_history("operator /", varlist) |
---|
1847 | print_log() |
---|
1848 | return s |
---|
1849 | |
---|
1850 | def get_fit(self, row=0): |
---|
1851 | """ |
---|
1852 | Print or return the stored fits for a row in the scantable |
---|
1853 | Parameters: |
---|
1854 | row: the row which the fit has been applied to. |
---|
1855 | """ |
---|
1856 | if row > self.nrow(): |
---|
1857 | return |
---|
1858 | from asap.asapfit import asapfit |
---|
1859 | fit = asapfit(self._getfit(row)) |
---|
1860 | if rcParams['verbose']: |
---|
1861 | print fit |
---|
1862 | return |
---|
1863 | else: |
---|
1864 | return fit.as_dict() |
---|
1865 | |
---|
1866 | def _add_history(self, funcname, parameters): |
---|
1867 | # create date |
---|
1868 | sep = "##" |
---|
1869 | from datetime import datetime |
---|
1870 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
1871 | hist = dstr+sep |
---|
1872 | hist += funcname+sep#cdate+sep |
---|
1873 | if parameters.has_key('self'): del parameters['self'] |
---|
1874 | for k, v in parameters.iteritems(): |
---|
1875 | if type(v) is dict: |
---|
1876 | for k2, v2 in v.iteritems(): |
---|
1877 | hist += k2 |
---|
1878 | hist += "=" |
---|
1879 | if isinstance(v2, scantable): |
---|
1880 | hist += 'scantable' |
---|
1881 | elif k2 == 'mask': |
---|
1882 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
1883 | hist += str(self._zip_mask(v2)) |
---|
1884 | else: |
---|
1885 | hist += str(v2) |
---|
1886 | else: |
---|
1887 | hist += str(v2) |
---|
1888 | else: |
---|
1889 | hist += k |
---|
1890 | hist += "=" |
---|
1891 | if isinstance(v, scantable): |
---|
1892 | hist += 'scantable' |
---|
1893 | elif k == 'mask': |
---|
1894 | if isinstance(v, list) or isinstance(v, tuple): |
---|
1895 | hist += str(self._zip_mask(v)) |
---|
1896 | else: |
---|
1897 | hist += str(v) |
---|
1898 | else: |
---|
1899 | hist += str(v) |
---|
1900 | hist += sep |
---|
1901 | hist = hist[:-2] # remove trailing '##' |
---|
1902 | self._addhistory(hist) |
---|
1903 | |
---|
1904 | |
---|
1905 | def _zip_mask(self, mask): |
---|
1906 | mask = list(mask) |
---|
1907 | i = 0 |
---|
1908 | segments = [] |
---|
1909 | while mask[i:].count(1): |
---|
1910 | i += mask[i:].index(1) |
---|
1911 | if mask[i:].count(0): |
---|
1912 | j = i + mask[i:].index(0) |
---|
1913 | else: |
---|
1914 | j = len(mask) |
---|
1915 | segments.append([i, j]) |
---|
1916 | i = j |
---|
1917 | return segments |
---|
1918 | |
---|
1919 | def _get_ordinate_label(self): |
---|
1920 | fu = "("+self.get_fluxunit()+")" |
---|
1921 | import re |
---|
1922 | lbl = "Intensity" |
---|
1923 | if re.match(".K.", fu): |
---|
1924 | lbl = "Brightness Temperature "+ fu |
---|
1925 | elif re.match(".Jy.", fu): |
---|
1926 | lbl = "Flux density "+ fu |
---|
1927 | return lbl |
---|
1928 | |
---|
1929 | def _check_ifs(self): |
---|
1930 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
1931 | nchans = filter(lambda t: t > 0, nchans) |
---|
1932 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
1933 | |
---|
1934 | def _fill(self, names, unit, average, getpt): |
---|
1935 | import os |
---|
1936 | from asap._asap import stfiller |
---|
1937 | first = True |
---|
1938 | fullnames = [] |
---|
1939 | for name in names: |
---|
1940 | name = os.path.expandvars(name) |
---|
1941 | name = os.path.expanduser(name) |
---|
1942 | if not os.path.exists(name): |
---|
1943 | msg = "File '%s' does not exists" % (name) |
---|
1944 | if rcParams['verbose']: |
---|
1945 | asaplog.push(msg) |
---|
1946 | print asaplog.pop().strip() |
---|
1947 | return |
---|
1948 | raise IOError(msg) |
---|
1949 | fullnames.append(name) |
---|
1950 | if average: |
---|
1951 | asaplog.push('Auto averaging integrations') |
---|
1952 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
1953 | for name in fullnames: |
---|
1954 | tbl = Scantable(stype) |
---|
1955 | r = stfiller(tbl) |
---|
1956 | msg = "Importing %s..." % (name) |
---|
1957 | asaplog.push(msg, False) |
---|
1958 | print_log() |
---|
1959 | r._open(name, -1, -1, getpt) |
---|
1960 | r._read() |
---|
1961 | #tbl = r._getdata() |
---|
1962 | if average: |
---|
1963 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
1964 | #tbl = tbl2 |
---|
1965 | if not first: |
---|
1966 | tbl = self._math._merge([self, tbl]) |
---|
1967 | #tbl = tbl2 |
---|
1968 | Scantable.__init__(self, tbl) |
---|
1969 | r._close() |
---|
1970 | del r, tbl |
---|
1971 | first = False |
---|
1972 | if unit is not None: |
---|
1973 | self.set_fluxunit(unit) |
---|
1974 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
1975 | |
---|