1 | from asap._asap import sdtable |
---|
2 | from numarray import ones |
---|
3 | import sys |
---|
4 | |
---|
5 | class scantable(sdtable): |
---|
6 | """ |
---|
7 | The ASAP container for scans |
---|
8 | """ |
---|
9 | |
---|
10 | def __init__(self, filename): |
---|
11 | """ |
---|
12 | Create a scantable from a saved one or make a reference |
---|
13 | Parameters: |
---|
14 | filename: the name of an asap table on disk, or |
---|
15 | [advanced] a refernce to an existing |
---|
16 | scantable |
---|
17 | """ |
---|
18 | self._vb = True |
---|
19 | self._p = None |
---|
20 | sdtable.__init__(self, filename) |
---|
21 | |
---|
22 | def save(self, name, format='ASAP'): |
---|
23 | """ |
---|
24 | Store the scantable on disk. This can be a asap file or SDFITS/MS2. |
---|
25 | Parameters: |
---|
26 | name: the name of the outputfile |
---|
27 | format: an optional file format. Default is ASAP. |
---|
28 | Alllowed are 'ASAP', 'SDFITS' and 'MS2' |
---|
29 | Example: |
---|
30 | scan.save('myscan.asap') |
---|
31 | scan.save('myscan.sdfits','SDFITS') |
---|
32 | """ |
---|
33 | if format == 'ASAP': |
---|
34 | self._save(name) |
---|
35 | else: |
---|
36 | from asap._asap import sdwriter as _sw |
---|
37 | w = _sw() |
---|
38 | if format == 'SDFITS': |
---|
39 | w.write(self, name) |
---|
40 | return |
---|
41 | |
---|
42 | def _verbose(self, *args): |
---|
43 | """ |
---|
44 | Set the verbose level True or False, to indicate if output |
---|
45 | should be printed as well as returned. |
---|
46 | """ |
---|
47 | if len(args) == 0: |
---|
48 | return self._vb |
---|
49 | elif type(args[0]) is bool: |
---|
50 | self._vb = args[0] |
---|
51 | return |
---|
52 | |
---|
53 | |
---|
54 | def copy(self): |
---|
55 | """ |
---|
56 | Return a copy of this scantable. |
---|
57 | Parameters: |
---|
58 | none |
---|
59 | Example: |
---|
60 | copiedscan = scan.copy() |
---|
61 | """ |
---|
62 | sd = scantable(sdtable._copy(self)) |
---|
63 | return sd |
---|
64 | |
---|
65 | def get_scan(self, scanid=None): |
---|
66 | """ |
---|
67 | Return a specific scan (by scanno) or collection of scans (by |
---|
68 | source name) in a new scantable. |
---|
69 | Parameters: |
---|
70 | scanid: a scanno or a source name |
---|
71 | Example: |
---|
72 | scan.get_scan('323p459') |
---|
73 | # gets all scans containing the source '323p459' |
---|
74 | """ |
---|
75 | if scanid is None: |
---|
76 | print "Please specify a scan no or name to retrieve from the scantable" |
---|
77 | try: |
---|
78 | if type(scanid) is str: |
---|
79 | s = sdtable._getsource(self,scanid) |
---|
80 | return scantable(s) |
---|
81 | elif type(scanid) is int: |
---|
82 | s = sdtable._getscan(self,scanid) |
---|
83 | return scantable(s) |
---|
84 | except RuntimeError: |
---|
85 | print "Couldn't find any match." |
---|
86 | |
---|
87 | def __str__(self): |
---|
88 | return sdtable.summary(self) |
---|
89 | |
---|
90 | def summary(self,filename=None): |
---|
91 | """ |
---|
92 | Print a summary of the contents of this scantable. |
---|
93 | Parameters: |
---|
94 | filename: the name of a file to write the putput to |
---|
95 | Default - no file output |
---|
96 | """ |
---|
97 | info = sdtable.summary(self) |
---|
98 | if filename is not None: |
---|
99 | data = open(filename, 'w') |
---|
100 | data.write(info) |
---|
101 | data.close() |
---|
102 | print info |
---|
103 | |
---|
104 | def set_selection(self, thebeam=0,theif=0,thepol=0): |
---|
105 | """ |
---|
106 | Set the spectrum for individual operations. |
---|
107 | Parameters: |
---|
108 | thebeam,theif,thepol: a number |
---|
109 | Example: |
---|
110 | scan.set_selection(0,0,1) |
---|
111 | pol1rms = scan.rms(all=False) # returns rms for beam=0 |
---|
112 | # if=0, pol=1 |
---|
113 | """ |
---|
114 | self.setbeam(thebeam) |
---|
115 | self.setpol(thepol) |
---|
116 | self.setif(theif) |
---|
117 | return |
---|
118 | |
---|
119 | def get_selection(self): |
---|
120 | """ |
---|
121 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
---|
122 | Parameters: |
---|
123 | none |
---|
124 | Returns: |
---|
125 | a list of values (currentBeam,currentIF,currentPol) |
---|
126 | Example: |
---|
127 | none |
---|
128 | """ |
---|
129 | i = self.getbeam() |
---|
130 | j = self.getif() |
---|
131 | k = self.getpol() |
---|
132 | if self._vb: |
---|
133 | out = 'Beam=%d IF=%d Pol=%d '% (i,j,k) |
---|
134 | print out |
---|
135 | return i,j,k |
---|
136 | |
---|
137 | def rms(self,mask=None, all=True): |
---|
138 | """ |
---|
139 | Determine the root mean square of the current beam/if/pol |
---|
140 | Takes a 'mask' as an optional parameter to specify which |
---|
141 | channels should be excluded. |
---|
142 | Parameters: |
---|
143 | mask: an optional mask specifying where the rms |
---|
144 | should be determined. |
---|
145 | all: optional flag to show all or a selected |
---|
146 | spectrum of Beam/IF/Pol |
---|
147 | |
---|
148 | Example: |
---|
149 | scan.set_unit('channel') |
---|
150 | msk = scan.create_mask([100,200],[500,600]) |
---|
151 | scan.rms(mask=m) |
---|
152 | """ |
---|
153 | from asap._asap import rms as _rms |
---|
154 | if mask == None: |
---|
155 | mask = ones(self.nchan()) |
---|
156 | if all: |
---|
157 | out = '' |
---|
158 | tmp = [] |
---|
159 | for i in range(self.nbeam()): |
---|
160 | self.setbeam(i) |
---|
161 | for j in range(self.nif()): |
---|
162 | self.setif(j) |
---|
163 | for k in range(self.npol()): |
---|
164 | self.setpol(k) |
---|
165 | rmsval = _rms(self,mask) |
---|
166 | tmp.append(rmsval) |
---|
167 | out += 'Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,rmsval) |
---|
168 | if self._vb: |
---|
169 | print out |
---|
170 | return tmp |
---|
171 | |
---|
172 | else: |
---|
173 | i = self.getbeam() |
---|
174 | j = self.getif() |
---|
175 | k = self.getpol() |
---|
176 | rmsval = _rms(self,mask) |
---|
177 | out = 'Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,rmsval) |
---|
178 | if self._vb: |
---|
179 | print out |
---|
180 | return rmsval |
---|
181 | |
---|
182 | def get_tsys(self, all=True): |
---|
183 | """ |
---|
184 | Return the System temperatures. |
---|
185 | Parameters: |
---|
186 | all: optional parameter to get the Tsys values for all |
---|
187 | Beams/IFs/Pols (default) or just the one selected |
---|
188 | with scantable.set_selection() |
---|
189 | [True or False] |
---|
190 | Returns: |
---|
191 | a list of Tsys values. |
---|
192 | """ |
---|
193 | if all: |
---|
194 | tmp = [] |
---|
195 | out = '' |
---|
196 | for i in range(self.nbeam()): |
---|
197 | self.setbeam(i) |
---|
198 | for j in range(self.nif()): |
---|
199 | self.setif(j) |
---|
200 | for k in range(self.npol()): |
---|
201 | self.setpol(k) |
---|
202 | ts = self._gettsys() |
---|
203 | tmp.append(ts) |
---|
204 | out += 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,ts) |
---|
205 | if self._vb: |
---|
206 | print out |
---|
207 | return tmp |
---|
208 | else: |
---|
209 | i = self.getbeam() |
---|
210 | j = self.getif() |
---|
211 | k = self.getpol() |
---|
212 | ts = self._gettsys() |
---|
213 | out = 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,ts) |
---|
214 | if self._vb: |
---|
215 | print out |
---|
216 | return ts |
---|
217 | |
---|
218 | def get_time(self): |
---|
219 | """ |
---|
220 | Get a list of time stamps for the observations. |
---|
221 | Return a string for each intergration in the scantable. |
---|
222 | Parameters: |
---|
223 | none |
---|
224 | Example: |
---|
225 | none |
---|
226 | """ |
---|
227 | out = [] |
---|
228 | for i in range(self.nrow()): |
---|
229 | out.append(self._gettime(i)) |
---|
230 | return out |
---|
231 | |
---|
232 | def set_unit(self, unit='channel'): |
---|
233 | """ |
---|
234 | Set the unit for all following operations on this scantable |
---|
235 | Parameters: |
---|
236 | unit: optional unit, default is 'channel' |
---|
237 | one of '*Hz','km/s','channel', '' |
---|
238 | """ |
---|
239 | |
---|
240 | if unit in ['','pixel', 'channel']: |
---|
241 | unit = '' |
---|
242 | inf = list(self._getcoordinfo()) |
---|
243 | inf[0] = unit |
---|
244 | self._setcoordinfo(inf) |
---|
245 | if self._p: self.plot() |
---|
246 | |
---|
247 | def set_freqframe(self, frame='LSRK'): |
---|
248 | """ |
---|
249 | Set the frame type of the Spectral Axis. |
---|
250 | Parameters: |
---|
251 | frame: an optional frame type, default 'LSRK'. |
---|
252 | Examples: |
---|
253 | scan.set_freqframe('BARY') |
---|
254 | """ |
---|
255 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
256 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
257 | if frame in valid: |
---|
258 | inf = list(self._getcoordinfo()) |
---|
259 | inf[1] = frame |
---|
260 | self._setcoordinfo(inf) |
---|
261 | else: |
---|
262 | print "Please specify a valid freq type. Valid types are:\n",valid |
---|
263 | |
---|
264 | def get_unit(self): |
---|
265 | """ |
---|
266 | Get the default unit set in this scantable |
---|
267 | Parameters: |
---|
268 | Returns: |
---|
269 | A unit string |
---|
270 | """ |
---|
271 | inf = self._getcoordinfo() |
---|
272 | unit = inf[0] |
---|
273 | if unit == '': unit = 'channel' |
---|
274 | return unit |
---|
275 | |
---|
276 | def get_abscissa(self, rowno=0): |
---|
277 | """ |
---|
278 | Get the abscissa in the current coordinate setup for the currently |
---|
279 | selected Beam/IF/Pol |
---|
280 | Parameters: |
---|
281 | none |
---|
282 | Returns: |
---|
283 | The abscissa values and it's format string. |
---|
284 | """ |
---|
285 | absc = self.getabscissa(rowno) |
---|
286 | lbl = self.getabscissalabel(rowno) |
---|
287 | return absc, lbl |
---|
288 | |
---|
289 | def create_mask(self, *args, **kwargs): |
---|
290 | """ |
---|
291 | Compute and return a mask based on [min,max] windows. |
---|
292 | The specified windows are to be EXCLUDED, when the mask is |
---|
293 | applied. |
---|
294 | Parameters: |
---|
295 | [min,max],[min2,max2],... |
---|
296 | Pairs of start/end points specifying the regions |
---|
297 | to be masked |
---|
298 | invert: return an inverted mask, i.e. the regions |
---|
299 | specified are not masked (INCLUDED) |
---|
300 | Example: |
---|
301 | scan.set_unit('channel') |
---|
302 | |
---|
303 | a) |
---|
304 | msk = scan.set_mask([400,500],[800,900]) |
---|
305 | # masks the regions between 400 and 500 |
---|
306 | # and 800 and 900 in the unit 'channel' |
---|
307 | |
---|
308 | b) |
---|
309 | msk = scan.set_mask([400,500],[800,900], invert=True) |
---|
310 | # masks the regions outside 400 and 500 |
---|
311 | # and 800 and 900 in the unit 'channel' |
---|
312 | |
---|
313 | """ |
---|
314 | u = self._getcoordinfo()[0] |
---|
315 | if self._vb: |
---|
316 | if u == "": u = "channel" |
---|
317 | print "The current mask window unit is", u |
---|
318 | n = self.nchan() |
---|
319 | data = self.getabscissa() |
---|
320 | msk = ones(n) |
---|
321 | for window in args: |
---|
322 | if (len(window) != 2 or window[0] > window[1] ): |
---|
323 | print "A window needs to be defined as [min,max]" |
---|
324 | return |
---|
325 | for i in range(n): |
---|
326 | if data[i] >= window[0] and data[i] < window[1]: |
---|
327 | msk[i] = 0 |
---|
328 | if kwargs.has_key('invert'): |
---|
329 | if kwargs.get('invert'): |
---|
330 | from numarray import logical_not |
---|
331 | msk = logical_not(msk) |
---|
332 | return msk |
---|
333 | |
---|
334 | def set_restfreqs(self, freqs, unit='Hz'): |
---|
335 | """ |
---|
336 | Set the restfrequency(s) for this scantable. |
---|
337 | Parameters: |
---|
338 | freqs: one or more frequencies |
---|
339 | unit: optional 'unit', default 'Hz' |
---|
340 | Example: |
---|
341 | scan.set_restfreqs([1000000000.0]) |
---|
342 | """ |
---|
343 | if type(freqs) is float or int: |
---|
344 | freqs = (freqs) |
---|
345 | sdtable._setrestfreqs(self,freqs, unit) |
---|
346 | return |
---|
347 | |
---|
348 | def flag_spectrum(self, thebeam, theif, thepol): |
---|
349 | """ |
---|
350 | This flags a selected spectrum in the scan 'for good'. |
---|
351 | USE WITH CARE - not reversible. |
---|
352 | Use masks for non-permanent exclusion of channels. |
---|
353 | Parameters: |
---|
354 | thebeam,theif,thepol: all have to be explicitly |
---|
355 | specified |
---|
356 | Example: |
---|
357 | scan.flag_spectrum(0,0,1) |
---|
358 | flags the spectrum for Beam=0, IF=0, Pol=1 |
---|
359 | """ |
---|
360 | if (thebeam < self.nbeam() and theif < self.nif() and thepol < self.npol()): |
---|
361 | stable.setbeam(thebeam) |
---|
362 | stable.setif(theif) |
---|
363 | stable.setpol(thepol) |
---|
364 | stable._flag(self) |
---|
365 | else: |
---|
366 | print "Please specify a valid (Beam/IF/Pol)" |
---|
367 | return |
---|
368 | |
---|
369 | def plot(self, what='spectrum',col='Pol', panel=None): |
---|
370 | """ |
---|
371 | Plot the spectra contained in the scan. Alternatively you can also |
---|
372 | Plot Tsys vs Time |
---|
373 | Parameters: |
---|
374 | what: a choice of 'spectrum' (default) or 'tsys' |
---|
375 | col: which out of Beams, IFs, Pols (default) |
---|
376 | should be colour stacked |
---|
377 | panel: set up multiple panels, currently not working. |
---|
378 | """ |
---|
379 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} |
---|
380 | |
---|
381 | validyax = ['spectrum','tsys'] |
---|
382 | if not self._p: |
---|
383 | from asap.asaplot import ASAPlot |
---|
384 | self._p = ASAPlot() |
---|
385 | # print "Plotting not enabled" |
---|
386 | # return |
---|
387 | npan = 1 |
---|
388 | x = None |
---|
389 | if what == 'tsys': |
---|
390 | n = self.nrow() |
---|
391 | if n < 2: |
---|
392 | print "Only one integration. Can't plot." |
---|
393 | return |
---|
394 | self._p.hold() |
---|
395 | self._p.clear() |
---|
396 | if panel == 'Time': |
---|
397 | npan = self.nrow() |
---|
398 | self._p.set_panels(rows=npan) |
---|
399 | xlab,ylab,tlab = None,None,None |
---|
400 | vb = self._verbose() |
---|
401 | self._verbose(False) |
---|
402 | sel = self.get_selection() |
---|
403 | for i in range(npan): |
---|
404 | self._p.subplot(i) |
---|
405 | for j in range(validcol[col]): |
---|
406 | x = None |
---|
407 | y = None |
---|
408 | m = None |
---|
409 | tlab = self._getsourcename(i) |
---|
410 | import re |
---|
411 | tlab = re.sub('_S','',tlab) |
---|
412 | if col == 'Beam': |
---|
413 | self.setbeam(j) |
---|
414 | elif col == 'IF': |
---|
415 | self.setif(j) |
---|
416 | elif col == 'Pol': |
---|
417 | self.setpol(j) |
---|
418 | if what == 'tsys': |
---|
419 | x = range(self.nrow()) |
---|
420 | xlab = 'Time [pixel]' |
---|
421 | m = list(ones(len(x))) |
---|
422 | y = [] |
---|
423 | ylab = r'$T_{sys}$' |
---|
424 | for k in range(len(x)): |
---|
425 | y.append(self._gettsys(k)) |
---|
426 | else: |
---|
427 | x,xlab = self.get_abscissa(i) |
---|
428 | y = self.getspectrum(i) |
---|
429 | ylab = r'Flux' |
---|
430 | m = self.getmask(i) |
---|
431 | llab = col+' '+str(j) |
---|
432 | self._p.set_line(label=llab) |
---|
433 | self._p.plot(x,y,m) |
---|
434 | self._p.set_axes('xlabel',xlab) |
---|
435 | self._p.set_axes('ylabel',ylab) |
---|
436 | self._p.set_axes('title',tlab) |
---|
437 | self._p.release() |
---|
438 | self.set_selection(sel[0],sel[1],sel[2]) |
---|
439 | self._verbose(vb) |
---|
440 | return |
---|