Coverage for /wheeldirectory/casa-6.7.0-12-py3.10.el8/lib/py/lib/python3.10/site-packages/casatasks/private/task_uvcontsub_old.py: 8%
242 statements
« prev ^ index » next coverage.py v7.6.4, created at 2024-10-31 18:48 +0000
1import os
2import re
3import shutil
4import time
5import tempfile
6import numpy as np
8# shutil.copytree is useless with directories created by tempfile
9# (or any directories that already exist).
10from distutils.dir_util import copy_tree
12from casatools import calibrater, ms, table
13from casatasks import casalog, virtualconcat
15from .mstools import write_history
16from .update_spw import *
17from .parallel.parallel_data_helper import ParallelDataHelper
18from .parallel.parallel_task_helper import ParallelTaskHelper
20mytb = table( )
21mycb = calibrater( )
22myms = ms()
23_ms = ms() # task also referenced the old global ms object
25def uvcontsub_old(vis, field, fitspw, excludechans, combine, solint, fitorder, spw, want_cont):
27 if ParallelDataHelper.isMMSAndNotServer(vis):
28 helper = ParallelTaskHelper('uvcontsub_old', locals())
29 helper._consolidateOutput = False
30 retVar = helper.go()
32 # Gather the list of continuum subtraction-SubMSs
33 cont_subMS_list = []
34 contsub_subMS_list = []
35 for subMS in retVar:
36 if retVar[subMS]:
37 cont_subMS_list.append(subMS + ".cont")
38 contsub_subMS_list.append(subMS + ".contsub")
40 if len(cont_subMS_list) <= 0:
41 raise ValueError("No continuum-subtracted sub-MSs for concatenation","SEVERE")
43 # We have to sort the list because otherwise it
44 # depends on the time the engines dispatches their sub-MSs
45 cont_subMS_list.sort()
46 contsub_subMS_list.sort()
48 # deal with the pointing table
49 auxfile = "uvcontsub_aux2_"+str(time.time())
50 pnrows = 0
51 try:
52 mytb.open(vis+'/POINTING')
53 pnrows = mytb.nrows()
54 mytb.close()
55 if(pnrows>0):
56 shutil.copytree(os.path.realpath(vis+'/POINTING'), auxfile)
57 except Exception as instance:
58 raise RuntimeError("Error handling POINTING table %s: %s" %
59 (vis+'/POINTING',str(instance)))
61 if want_cont:
62 try:
63 virtualconcat(concatvis=helper._arg['vis'] + ".cont",vis=cont_subMS_list,
64 copypointing=False)
65 except Exception as instance:
66 raise RuntimeError("Error concatenating continuum sub-MSs %s: %s" %
67 (str(cont_subMS_list),str(instance)))
68 try:
69 virtualconcat(concatvis=helper._arg['vis'] + ".contsub",vis=contsub_subMS_list,
70 copypointing=False)
71 except Exception as instance:
72 raise RuntimeError("Error concatenating continuum-subtracted sub-MSs %s: %s" %
73 (str(contsub_subMS_list),str(instance)))
75 # Remove continuum subtraction-SubMSs
76 if want_cont:
77 for subMS in cont_subMS_list:
78 if (os.system("rm -rf " + subMS ) != 0):
79 casalog.post("Problem removing continuum sub-MS %s into working directory" % (subMS),'SEVERE')
80 for subMS in contsub_subMS_list:
81 if (os.system("rm -rf " + subMS ) != 0):
82 casalog.post("Problem removing continuum-subtracted sub-MS %s into working directory" % (subMS),'SEVERE')
84 if(pnrows>0): # put back the POINTING table
85 casalog.post("Restoring the POINTING table ...",'NORMAL')
86 try:
87 if want_cont:
88 theptab = os.path.realpath(helper._arg['vis'] + ".cont/POINTING")
89 os.system('rm -rf '+theptab)
90 shutil.copytree(auxfile, theptab)
91 theptab = os.path.realpath(helper._arg['vis'] + ".contsub/POINTING")
92 os.system('rm -rf '+theptab)
93 os.system('mv '+auxfile+' '+theptab)
94 except Exception as instance:
95 raise RuntimeError("Error restoring pointing table from %s: %s" %
96 (auxfile,str(instance)))
98 # Restore origin (otherwise gcwrap shows virtualconcat)
99 casalog.origin('uvcontsub_old')
101 return
103 # Run normal code
104 try:
105 casalog.origin('uvcontsub_old')
107 casalog.post('This task is deprecated and will be removed in an upcoming release.',
108 'WARN')
110 # Get these checks done and out of the way.
111 # This one is redundant - it is already checked at the XML level.
112 if not os.path.isdir(vis):
113 raise ValueError('Visibility data set not found - please verify the name')
115 #
116 if excludechans:
117 locfitspw=_quantityRangesToChannels(vis,field,fitspw,excludechans)
118 casalog.post("Exclude channels in fitspw: spws:channels will be used in the fit are:%s" % locfitspw)
119 elif fitspw.count('Hz'):
120 locfitspw=_quantityRangesToChannels(vis,field,fitspw,excludechans)
121 else:
122 locfitspw=fitspw
123 # casalog.post("locfitspw=",locfitspw)
124 mytb.open(vis + '/SPECTRAL_WINDOW')
125 allspw = '0~' + str(mytb.nrows() - 1)
126 mytb.close()
128 # Verify fitspw and spw as plausible
129 if len(locfitspw)>0:
130 fitspwerr=subtract_spws(locfitspw,allspw)
131 if fitspwerr:
132 badfitspw=''
133 for ispw in range(len(fitspwerr)):
134 badfitspw+=str(fitspwerr.pop())
135 raise ValueError("fitspw contains non-existent spw(s): "+badfitspw)
136 if len(spw)>0:
137 spwerr=subtract_spws(spw,allspw)
138 if spwerr:
139 badspw=''
140 for ispw in range(len(spwerr)):
141 badspw+=str(spwerr.pop())
142 raise ValueError("spw contains non-existent spw(s): "+badspw)
144 if 'spw' not in combine:
145 #spwmfitspw = subtract_spws(spw, fitspw)
146 spwmfitspw = subtract_spws(spw, locfitspw)
147 if spwmfitspw == 'UNKNOWN':
148 #spwmfitspw = subtract_spws(allspw, fitspw)
149 spwmfitspw = subtract_spws(allspw, locfitspw)
150 if spwmfitspw:
151 raise ValueError("combine must include 'spw' when the fit is being applied to spws outside fitspw.")
153 # cb will put the continuum-subtracted data in CORRECTED_DATA, so
154 # protect vis by splitting out its relevant parts to a working copy.
155 csvis = vis.rstrip('/') + '.contsub'
157 # The working copy will need all of the channels in fitspw + spw, so we
158 # may or may not need to filter it down to spw at the end.
159 #myfitspw = fitspw
160 myfitspw = locfitspw
161 myspw = spw
163 # We only need the spws in the union of fitspw and spw, but keep all
164 # the channels or the weights (as used by calibrater) will be messed up.
165 #tempspw = re.sub(r':[^,]+', '', join_spws(fitspw, spw))
166 tempspw = re.sub(r':[^,]+', '', join_spws(locfitspw, spw))
167 if tempspw == allspw:
168 tempspw = ''
169 if tempspw:
170 # The split will reindex the spws. Update spw and fitspw.
171 # Do fitspw first because the spws in spw are supposed to be
172 # a subset of the ones in fitspw.
173 casalog.post('split is being run internally, and the selected spws')
174 casalog.post('will be renumbered to start from 0 in the output!')
176 # Now get myfitspw.
177 #myfitspw = update_spwchan(vis, tempspw, fitspw)
178 myfitspw = update_spwchan(vis, tempspw, locfitspw)
179 myspw = update_spwchan(vis, tempspw, spw)
181 final_csvis = csvis
182 workingdir = os.path.abspath(os.path.dirname(vis.rstrip('/')))
183 csvis = tempfile.mkdtemp(prefix=csvis.split('/')[-1], dir=workingdir)
185 # ms does not have a colnames method, so open vis with tb even though
186 # it is already open with myms. Note that both use nomodify=True,
187 # however, and no problem was revealed in testing.
188 mytb.open(vis, nomodify=True)
189 if 'CORRECTED_DATA' in mytb.colnames():
190 whichcol = 'CORRECTED_DATA'
191 else:
192 # DON'T remind the user that split before uvcontsub wastes time -
193 # scratch columns will eventually go away.
194 whichcol = 'DATA'
195 mytb.close()
197 casalog.post('Preparing to add scratch columns.')
198 myfield = field
199 if field == '':
200 myfield = '*'
201 if myfield != '*' and set(_ms.msseltoindex(vis,
202 field=myfield)['field']) == set(_ms.msseltoindex(vis,
203 field='*')['field']):
204 myfield = '*'
205 if whichcol != 'DATA' or tempspw != '' or myfield != '*':
206 casalog.post('splitting to ' + csvis + ' with spw="'
207 + tempspw + '"')
208 myms.open(vis, nomodify=True)
209 split_result = myms.split(csvis, spw=tempspw, field=myfield, whichcol=whichcol)
210 myms.close()
211 # jagonzal (CAS-4113): Take care of the trivial parallelization
212 if not split_result:
213 msg = "MSSelectionNullSelection: %s does not have data for spw=%s, field=%s, bailing out!" % (vis,tempspw,field)
214 shutil.rmtree(csvis)
215 raise RuntimeError(msg)
216 else:
217 # This takes almost 30s/GB. (lustre, 8/2011)
218 casalog.post('Copying ' + vis + ' to ' + csvis + ' with cp.')
219 copy_tree(vis, csvis, preserve_symlinks=True)
221 # It is less confusing if we write the history now that the "root" MS
222 # is made, but before cb adds its messages.
223 #
224 param_names = uvcontsub_old.__code__.co_varnames[:uvcontsub_old.__code__.co_argcount]
225 local_vars = locals( )
226 param_vals = [local_vars[p] for p in param_names]
228 write_history(myms, csvis, 'uvcontsub_old', param_names, param_vals,
229 casalog)
231 if (type(csvis) == str) and os.path.isdir(csvis):
232 mycb.setvi(old=True,quiet=False); # old VI, for now
233 mycb.open(csvis)
234 else:
235 raise RuntimeError('Visibility data set not found - please verify the name')
237 # select the data for continuum subtraction
238 mycb.reset()
239 mycb.selectvis(spw=myfitspw)
241 # Set up the solve
242 amuellertab = tempfile.mkdtemp(prefix='Temp_contsub.tab',
243 dir=workingdir)
245 mycb.setsolve(type='A', t=solint, table=amuellertab, combine=combine,
246 fitorder=fitorder)
248 # solve for the continuum
249 mycb.solve()
251 # subtract the continuum
252 mycb.selectvis(spw=myspw)
253 aspwmap=-1
254 # if we combined on spw in solve, fanout the result with spwmap=-999;
255 if 'spw' in combine:
256 aspwmap = -999
257 mycb.setapply(table=amuellertab, spwmap=aspwmap)
259 # Generate CORRECTED_DATA without continuum
260 mycb.correct()
262 if want_cont:
263 # Generate MODEL_DATA with only the continuum model
264 mycb.corrupt()
266 mycb.close()
268 # Delete the temporary caltable
269 shutil.rmtree(amuellertab)
271 # Move the line data from CORRECTED_DATA to DATA, and do any
272 # final filtering by spw.
273 myms.open(csvis)
274 # Using ^ in spw is untested here!
275 myms.split(final_csvis, spw=myspw, whichcol='corrected')
276 myms.close()
278 #casalog.post("\"want_cont\" = \"%s\"" % want_cont, 'WARN')
279 #casalog.post("\"csvis\" = \"%s\"" % csvis, 'WARN')
280 if want_cont:
281 myms.open(csvis)
282 # No channel averaging (== skipping for fitorder == 0) is done
283 # here, but it would be a reasonable option. The user can always
284 # do it by running split again.
285 myms.split(final_csvis[:-3], # .contsub -> .cont
286 whichcol='MODEL_DATA',
287 spw=myspw)
288 myms.close()
290 #casalog.post("rming \"%s\"" % csvis, 'WARN')
291 shutil.rmtree(csvis)
293 finally:
294 mycb.close() # Harmless if cb is closed.
297def _quantityRangesToChannels(vis,field,infitspw,excludechans):
298 """
299 private function to convert frequnecy (in the future, velocity
300 as well) ranges in fitspw to channel indexes.
301 For excludeechans=True, it will select channels outside given by infitspw
302 returns: list containing new channel ranges
303 """
304 mytb.open(vis+'/SPECTRAL_WINDOW')
305 nspw=mytb.nrows()
306 mytb.close()
308 fullspwids=str(list(range(nspw))).strip('[,]')
309 tql={'field':field,'spw':fullspwids}
310 myms.open(vis)
311 myms.msselect(tql,True)
312 allsels=myms.msselectedindices()
313 myms.reset()
314 # input fitspw selection
315 tql['spw']=infitspw
316 myms.msselect(tql,True)
317 usersels=myms.msselectedindices()['channel']
318 myms.close()
319 # sort the arrays so that chan ranges are
320 # in order
321 usersels=usersels[np.lexsort((usersels[:,1],usersels[:,0]))]
322 spwsels=''
323 spwid=-1
324 prevspwid=None
325 newchanlist=[]
326 nsels=len(usersels)
327 # casalog.post("Usersels=",usersels)
328 if excludechans:
329 for isel in range(nsels):
330 prevspwid = spwid
331 spwid=usersels[isel][0]
332 lochan=usersels[isel][1]
333 hichan=usersels[isel][2]
334 stp=usersels[isel][3]
335 maxchanid=allsels['channel'][spwid][2]
336 # find left and right side ranges of the selected range
337 if spwid != prevspwid:
338 # first line in the selected spw
339 if lochan > 0:
340 outloL=0
341 outhiL=lochan-1
342 outloR= (0 if hichan+1>=maxchanid else hichan+1)
343 if outloR:
344 if isel<nsels-1 and usersels[isel+1][0]==spwid:
345 outhiR=usersels[isel+1][1]-1
346 else:
347 outhiR=maxchanid
348 else:
349 outhiR=0 # higher end of the user selected range reaches maxchanid
350 # so no right hand side range
351 # casalog.post("outloL,outhiL,outloR,outhiR==", outloL,outhiL,outloR,outhiR)
352 else:
353 # no left hand side range
354 outloL=0
355 outhiL=0
356 outloR=hichan+1
357 if isel<nsels-1 and usersels[isel+1][0]==spwid:
358 outhiR=usersels[isel+1][1]-1
359 else:
360 outhiR=maxchanid
361 else:
362 #expect the left side range is already taken care of
363 outloL=0
364 outhiL=0
365 outloR=hichan+1
366 if outloR>=maxchanid:
367 #No more boundaries to consider
368 outloR=0
369 outhiR=0
370 else:
371 if isel<nsels-1 and usersels[isel+1][0]==spwid:
372 outhiR=min(usersels[isel+1][1]-1,maxchanid)
373 else:
374 outhiR=maxchanid
375 if outloR > outhiR:
376 outloR = 0
377 outhiR = 0
379 #
380 if (not(outloL == 0 and outhiL == 0)) and outloL <= outhiL:
381 newchanlist.append([spwid,outloL,outhiL,stp])
382 if (not(outloR == 0 and outhiR == 0)) and outloR <= outhiR:
383 newchanlist.append([spwid,outloR,outhiR,stp])
384 # casalog.post("newchanlist=",newchanlist)
385 else:
386 # excludechans=False
387 newchanlist=usersels
389 #return newchanlist
390 # create spw selection string from newchanlist
391 spwstr=''
392 for irange in range(len(newchanlist)):
393 chanrange=newchanlist[irange]
394 spwstr+=str(chanrange[0])+':'+str(chanrange[1])+'~'+str(chanrange[2])
395 if irange != len(newchanlist)-1:
396 spwstr+=','
397 return spwstr