source: branches/alma/python/__init__.py@ 2313

Last change on this file since 2313 was 1757, checked in by Kana Sugimoto, 14 years ago

New Development: Yes

JIRA Issue: Yes (CAS-2211)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: ASAP 3.0.0 interface changes

Test Programs:

Put in Release Notes: Yes

Module(s): all the CASA sd tools and tasks are affected.

Description: Merged ATNF-ASAP 3.0.0 developments to CASA (alma) branch.

Note you also need to update casa/code/atnf.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 26.5 KB
Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys,shutil, platform
6try:
7 from functools import wraps as wraps_dec
8except ImportError:
9 from asap.compatibility import wraps as wraps_dec
10
11# Set up CASAPATH and first time use of asap i.e. ~/.asap/*
12plf = None
13if sys.platform == "linux2":
14 if platform.architecture()[0] == '64bit':
15 plf = 'linux_64b'
16 else:
17 plf = 'linux_gnu'
18elif sys.platform == 'darwin':
19 plf = 'darwin'
20else:
21 # Shouldn't happen - default to linux
22 plf = 'linux'
23asapdata = __path__[-1]
24# Allow user defined data location
25if os.environ.has_key("ASAPDATA"):
26 if os.path.exists(os.environ["ASAPDATA"]):
27 asapdata = os.environ["ASAPDATA"]
28# use CASAPATH if defined and "data" dir present
29if not os.environ.has_key("CASAPATH") or \
30 not os.path.exists(os.environ["CASAPATH"].split()[0]+"/data"):
31 os.environ["CASAPATH"] = "%s %s somwhere" % ( asapdata, plf)
32# set up user space
33userdir = os.environ["HOME"]+"/.asap"
34if not os.path.exists(userdir):
35 print 'First time ASAP use. Setting up ~/.asap'
36 os.mkdir(userdir)
37 #shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
38 # commented out by TT on 2009.06.23 for casapy use
39 ##shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
40 ## userdir+"/ipy_user_conf.py")
41 f = file(userdir+"/asapuserfuncs.py", "w")
42 f.close()
43 f = file(userdir+"/ipythonrc", "w")
44 f.close()
45# commented out by TT on 2009.06.23 for casapy use
46##else:
47 # upgrade to support later ipython versions
48 ##if not os.path.exists(userdir+"/ipy_user_conf.py"):
49 ## shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
50 ## userdir+"/ipy_user_conf.py")
51
52# remove from namespace
53del asapdata, userdir, shutil, platform
54
55def _validate_bool(b):
56 'Convert b to a boolean or raise'
57 bl = b.lower()
58 if bl in ('f', 'no', 'false', '0', 0): return False
59 elif bl in ('t', 'yes', 'true', '1', 1): return True
60 else:
61 raise ValueError('Could not convert "%s" to boolean' % b)
62
63def _validate_int(s):
64 'convert s to int or raise'
65 try: return int(s)
66 except ValueError:
67 raise ValueError('Could not convert "%s" to int' % s)
68
69def _asap_fname():
70 """
71 Return the path to the rc file
72
73 Search order:
74
75 * current working dir
76 * environ var ASAPRC
77 * HOME/.asaprc
78
79 """
80 fname = os.path.join( os.getcwd(), '.asaprc')
81 if os.path.exists(fname): return fname
82
83 if os.environ.has_key('ASAPRC'):
84 path = os.environ['ASAPRC']
85 if os.path.exists(path):
86 fname = os.path.join(path, '.asaprc')
87 if os.path.exists(fname):
88 return fname
89
90 if os.environ.has_key('HOME'):
91 home = os.environ['HOME']
92 fname = os.path.join(home, '.asaprc')
93 if os.path.exists(fname):
94 return fname
95 return None
96
97
98defaultParams = {
99 # general
100 'verbose' : [True, _validate_bool],
101 'useplotter' : [True, _validate_bool],
102 'insitu' : [True, _validate_bool],
103
104 # plotting
105 'plotter.gui' : [True, _validate_bool],
106 'plotter.stacking' : ['p', str],
107 'plotter.panelling' : ['s', str],
108 'plotter.colours' : ['', str],
109 'plotter.linestyles' : ['', str],
110 'plotter.decimate' : [False, _validate_bool],
111 'plotter.ganged' : [True, _validate_bool],
112 'plotter.histogram' : [False, _validate_bool],
113 'plotter.papertype' : ['A4', str],
114 ## for older Matplotlib version
115 #'plotter.axesformatting' : ['mpl', str],
116 'plotter.axesformatting' : ['asap', str],
117
118 # scantable
119 'scantable.save' : ['ASAP', str],
120 'scantable.autoaverage' : [True, _validate_bool],
121 'scantable.freqframe' : ['LSRK', str], #default frequency frame
122 'scantable.verbosesummary' : [False, _validate_bool],
123 'scantable.storage' : ['memory', str],
124 'scantable.history' : [True, _validate_bool],
125 'scantable.reference' : ['.*(e|w|_R)$', str],
126 'scantable.parallactify' : [False, _validate_bool]
127 # fitter
128 }
129
130def list_rcparameters():
131
132 print """
133# general
134# print verbose output
135verbose : True
136
137# preload a default plotter
138useplotter : True
139
140# apply operations on the input scantable or return new one
141insitu : True
142
143# plotting
144
145# do we want a GUI or plot to a file
146plotter.gui : True
147
148# default mode for colour stacking
149plotter.stacking : Pol
150
151# default mode for panelling
152plotter.panelling : scan
153
154# push panels together, to share axis labels
155plotter.ganged : True
156
157# decimate the number of points plotted by a factor of
158# nchan/1024
159plotter.decimate : False
160
161# default colours/linestyles
162plotter.colours :
163plotter.linestyles :
164
165# enable/disable histogram plotting
166plotter.histogram : False
167
168# ps paper type
169plotter.papertype : A4
170
171# The formatting style of the xaxis
172plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib)
173
174# scantable
175
176# default storage of scantable ('memory'/'disk')
177scantable.storage : memory
178
179# write history of each call to scantable
180scantable.history : True
181
182# default ouput format when saving
183scantable.save : ASAP
184
185# auto averaging on read
186scantable.autoaverage : True
187
188# default frequency frame to set when function
189# scantable.set_freqframe is called
190scantable.freqframe : LSRK
191
192# Control the level of information printed by summary
193scantable.verbosesummary : False
194
195# Control the identification of reference (off) scans
196# This is has to be a regular expression
197scantable.reference : .*(e|w|_R)$
198
199# Indicate whether the data was parallactified (total phase offest == 0.0)
200scantable.parallactify : False
201
202# Fitter
203"""
204
205def rc_params():
206 'Return the default params updated from the values in the rc file'
207
208 fname = _asap_fname()
209
210 if fname is None or not os.path.exists(fname):
211 message = 'could not find rc file; returning defaults'
212 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
213 #print message
214 return ret
215
216 cnt = 0
217 for line in file(fname):
218 cnt +=1
219 line = line.strip()
220 if not len(line): continue
221 if line.startswith('#'): continue
222 tup = line.split(':',1)
223 if len(tup) !=2:
224 #print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
225 asaplog.push('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
226 print_log('WARN')
227 continue
228
229 key, val = tup
230 key = key.strip()
231 if not defaultParams.has_key(key):
232 #print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
233 asaplog.push('Bad key "%s" on line %d in %s' % (key, cnt, fname))
234 print_log('WARN')
235 continue
236
237 default, converter = defaultParams[key]
238
239 ind = val.find('#')
240 if ind>=0: val = val[:ind] # ignore trailing comments
241 val = val.strip()
242 try: cval = converter(val) # try to convert to proper type or raise
243 except ValueError, msg:
244 #print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
245 asaplog.push('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, str(msg)))
246 print_log('WARN')
247 continue
248 else:
249 # Alles Klar, update dict
250 defaultParams[key][0] = cval
251
252 # strip the conveter funcs and return
253 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
254 print ('loaded rc file %s'%fname)
255
256 return ret
257
258
259# this is the instance used by the asap classes
260rcParams = rc_params()
261
262rcParamsDefault = dict(rcParams.items()) # a copy
263
264def rc(group, **kwargs):
265 """
266 Set the current rc params. Group is the grouping for the rc, eg
267 for scantable.save the group is 'scantable', for plotter.stacking, the
268 group is 'plotter', and so on. kwargs is a list of attribute
269 name/value pairs, eg
270
271 rc('scantable', save='SDFITS')
272
273 sets the current rc params and is equivalent to
274
275 rcParams['scantable.save'] = 'SDFITS'
276
277 Use rcdefaults to restore the default rc params after changes.
278 """
279
280 aliases = {}
281
282 for k,v in kwargs.items():
283 name = aliases.get(k) or k
284 if len(group):
285 key = '%s.%s' % (group, name)
286 else:
287 key = name
288 if not rcParams.has_key(key):
289 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
290
291 rcParams[key] = v
292
293
294def rcdefaults():
295 """
296 Restore the default rc params - the ones that were created at
297 asap load time
298 """
299 rcParams.update(rcParamsDefault)
300
301def _n_bools(n, val):
302 return [ val for i in xrange(n) ]
303
304def _is_sequence_or_number(param, ptype=int):
305 if isinstance(param,tuple) or isinstance(param,list):
306 if len(param) == 0: return True # empty list
307 out = True
308 for p in param:
309 out &= isinstance(p,ptype)
310 return out
311 elif isinstance(param, ptype):
312 return True
313 return False
314
315def _to_list(param, ptype=int):
316 if isinstance(param, ptype):
317 if ptype is str: return param.split()
318 else: return [param]
319 if _is_sequence_or_number(param, ptype):
320 return param
321 return None
322
323def unique(x):
324 """
325 Return the unique values in a list
326 Parameters:
327 x: the list to reduce
328 Examples:
329 x = [1,2,3,3,4]
330 print unique(x)
331 [1,2,3,4]
332 """
333 return dict([ (val, 1) for val in x]).keys()
334
335def list_files(path=".",suffix="rpf"):
336 """
337 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
338 Parameters:
339 path: The directory to list (default '.')
340 suffix: The file extension (default rpf)
341 Example:
342 files = list_files("data/","sdfits")
343 print files
344 ['data/2001-09-01_0332_P363.sdfits',
345 'data/2003-04-04_131152_t0002.sdfits',
346 'data/Sgr_86p262_best_SPC.sdfits']
347 """
348 if not os.path.isdir(path):
349 return None
350 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
351 if not suffix in valid:
352 return None
353 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
354 return filter(lambda x: x.endswith(suffix),files)
355
356# workaround for ipython, which redirects this if banner=0 in ipythonrc
357sys.stdout = sys.__stdout__
358sys.stderr = sys.__stderr__
359
360# Logging
361from asap._asap import Log as _asaplog
362global asaplog
363asaplog=_asaplog()
364if rcParams['verbose']:
365 asaplog.enable()
366else:
367 asaplog.disable()
368
369
370def print_log_dec(f):
371 @wraps_dec(f)
372 def wrap_it(*args, **kw):
373 val = f(*args, **kw)
374 print_log()
375 return val
376 return wrap_it
377
378def print_log(level='INFO'):
379 from taskinit import casalog
380 log = asaplog.pop()
381 #if len(log) and rcParams['verbose']: print log
382 if len(log) and rcParams['verbose']: casalog.post( log, priority=level )
383 return
384
385def mask_and(a, b):
386 assert(len(a)==len(b))
387 return [ a[i] & b[i] for i in xrange(len(a)) ]
388
389def mask_or(a, b):
390 assert(len(a)==len(b))
391 return [ a[i] | b[i] for i in xrange(len(a)) ]
392
393def mask_not(a):
394 return [ not i for i in a ]
395
396from asapfitter import fitter
397from asapreader import reader
398from selector import selector
399
400from asapmath import *
401from scantable import scantable
402from asaplinefind import linefinder
403from simplelinefinder import simplelinefinder
404from linecatalog import linecatalog
405from interactivemask import interactivemask
406from opacity import skydip
407from opacity import model as opacity_model
408
409if rcParams['useplotter']:
410 try:
411 from asapplotter import asapplotter
412 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
413 if gui:
414 import matplotlib
415 if not matplotlib.sys.modules['matplotlib.backends']: matplotlib.use("TkAgg")
416 from matplotlib import pylab
417 xyplotter = pylab
418 plotter = asapplotter(gui)
419 del gui
420 except ImportError:
421 #print "Matplotlib not installed. No plotting available"
422 asaplog.post( "Matplotlib not installed. No plotting available")
423 print_log('WARN')
424
425__date__ = '$Date: 2010-06-09 09:03:06 +0000 (Wed, 09 Jun 2010) $'.split()[1]
426__version__ = '3.0.0 alma'
427# nrao casapy specific, get revision number
428#__revision__ = ' unknown '
429casapath=os.environ["CASAPATH"].split()
430#svninfo.txt path
431if os.path.isdir(casapath[0]+'/'+casapath[1]+'/python/2.5/asap'):
432 # for casa developer environment (linux or darwin)
433 revinfo=casapath[0]+'/'+casapath[1]+'/python/2.5/asap/svninfo.txt'
434else:
435 # for end-user environments
436 if casapath[1]=='darwin':
437 revinfo=casapath[0]+'/Resources/python/asap/svninfo.txt'
438 else:
439 revinfo=casapath[0]+'/lib/python2.5/asap/svninfo.txt'
440if os.path.isfile(revinfo):
441 f = file(revinfo)
442 f.readline()
443 revsionno=f.readline()
444 f.close()
445 del f
446 __revision__ = revsionno.rstrip()
447else:
448 __revision__ = ' unknown '
449
450def is_ipython():
451 return 'IPython' in sys.modules.keys()
452if is_ipython():
453 def version(): print "ASAP %s(%s)"% (__version__, __date__)
454
455 def list_scans(t = scantable):
456 import inspect
457 print "The user created scantables are: ",
458 globs=inspect.currentframe().f_back.f_locals.copy()
459 out = [ k for k,v in globs.iteritems() \
460 if isinstance(v, scantable) and not k.startswith("_") ]
461 print out
462 return out
463
464 def commands():
465 x = """
466 [The scan container]
467 scantable - a container for integrations/scans
468 (can open asap/rpfits/sdfits and ms files)
469 copy - returns a copy of a scan
470 get_scan - gets a specific scan out of a scantable
471 (by name or number)
472 drop_scan - drops a specific scan out of a scantable
473 (by number)
474 set_selection - set a new subselection of the data
475 get_selection - get the current selection object
476 summary - print info about the scantable contents
477 stats - get specified statistic of the spectra in
478 the scantable
479 stddev - get the standard deviation of the spectra
480 in the scantable
481 get_tsys - get the TSys
482 get_time - get the timestamps of the integrations
483 get_inttime - get the integration time
484 get_sourcename - get the source names of the scans
485 get_azimuth - get the azimuth of the scans
486 get_elevation - get the elevation of the scans
487 get_parangle - get the parallactic angle of the scans
488 get_coordinate - get the spectral coordinate for the given row,
489 which can be used for coordinate conversions
490 get_weather - get the weather condition parameters
491 get_unit - get the current unit
492 set_unit - set the abcissa unit to be used from this
493 point on
494 get_abcissa - get the abcissa values and name for a given
495 row (time)
496 get_column_names - get the names of the columns in the scantable
497 for use with selector.set_query
498 set_freqframe - set the frame info for the Spectral Axis
499 (e.g. 'LSRK')
500 set_doppler - set the doppler to be used from this point on
501 set_dirframe - set the frame for the direction on the sky
502 set_instrument - set the instrument name
503 set_feedtype - set the feed type
504 get_fluxunit - get the brightness flux unit
505 set_fluxunit - set the brightness flux unit
506 set_sourcetype - set the type of the source - source or reference
507 create_mask - return an mask in the current unit
508 for the given region. The specified regions
509 are NOT masked
510 get_restfreqs - get the current list of rest frequencies
511 set_restfreqs - set a list of rest frequencies
512 shift_refpix - shift the reference pixel of the IFs
513 set_spectrum - overwrite the spectrum for a given row
514 get_spectrum - retrieve the spectrum for a given
515 get_mask - retrieve the mask for a given
516 flag - flag selected channels in the data
517 lag_flag - flag specified frequency in the data
518 save - save the scantable to disk as either 'ASAP',
519 'SDFITS' or 'ASCII'
520 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
521 nscan - the number of scans in the scantable
522 nrow - the number of spectra in the scantable
523 history - print the history of the scantable
524 get_fit - get a fit which has been stored witnh the data
525 average_time - return the (weighted) time average of a scan
526 or a list of scans
527 average_pol - average the polarisations together.
528 average_beam - average the beams together.
529 convert_pol - convert to a different polarisation type
530 auto_quotient - return the on/off quotient with
531 automatic detection of the on/off scans (closest
532 in time off is selected)
533 mx_quotient - Form a quotient using MX data (off beams)
534 scale, *, / - return a scan scaled by a given factor
535 add, + - return a scan with given value added
536 sub, - - return a scan with given value subtracted
537 bin - return a scan with binned channels
538 resample - return a scan with resampled channels
539 smooth - return the spectrally smoothed scan
540 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
541 auto_poly_baseline - automatically fit a polynomial baseline
542 recalc_azel - recalculate azimuth and elevation based on
543 the pointing
544 gain_el - apply gain-elevation correction
545 opacity - apply opacity correction
546 convert_flux - convert to and from Jy and Kelvin brightness
547 units
548 freq_align - align spectra in frequency frame
549 invert_phase - Invert the phase of the cross-correlation
550 swap_linears - Swap XX and YY (or RR LL)
551 rotate_xyphase - rotate XY phase of cross correlation
552 rotate_linpolphase - rotate the phase of the complex
553 polarization O=Q+iU correlation
554 freq_switch - perform frequency switching on the data
555 stats - Determine the specified statistic, e.g. 'min'
556 'max', 'rms' etc.
557 stddev - Determine the standard deviation of the current
558 beam/if/pol
559 get_row_selector - get the selection object for a specified row
560 number
561 [Selection]
562 selector - a selection object to set a subset of a scantable
563 set_scans - set (a list of) scans by index
564 set_cycles - set (a list of) cycles by index
565 set_beams - set (a list of) beamss by index
566 set_ifs - set (a list of) ifs by index
567 set_polarisations - set (a list of) polarisations by name
568 or by index
569 set_names - set a selection by name (wildcards allowed)
570 set_tsys - set a selection by tsys thresholds
571 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
572 ( also get_ functions for all these )
573 reset - unset all selections
574 + - merge two selections
575
576 [Math] Mainly functions which operate on more than one scantable
577
578 average_time - return the (weighted) time average
579 of a list of scans
580 quotient - return the on/off quotient
581 simple_math - simple mathematical operations on two scantables,
582 'add', 'sub', 'mul', 'div'
583 quotient - build quotient of the given on and off scans
584 (matched pairs and 1 off - n on are valid)
585 merge - merge a list of scantables
586
587 [Line Catalog]
588 linecatalog - a linecatalog wrapper, taking an ASCII or
589 internal format table
590 summary - print a summary of the current selection
591 set_name - select a subset by name pattern, e.g. '*OH*'
592 set_strength_limits - select a subset by line strength limits
593 set_frequency_limits - select a subset by frequency limits
594 reset - unset all selections
595 save - save the current subset to a table (internal
596 format)
597 get_row - get the name and frequency from a specific
598 row in the table
599 [Fitting]
600 fitter
601 auto_fit - return a scan where the function is
602 applied to all Beams/IFs/Pols.
603 commit - return a new scan where the fits have been
604 commited.
605 fit - execute the actual fitting process
606 store_fit - store the fit parameters in the data (scantable)
607 get_chi2 - get the Chi^2
608 set_scan - set the scantable to be fit
609 set_function - set the fitting function
610 set_parameters - set the parameters for the function(s), and
611 set if they should be held fixed during fitting
612 set_gauss_parameters - same as above but specialised for individual
613 gaussian components
614 get_parameters - get the fitted parameters
615 plot - plot the resulting fit and/or components and
616 residual
617 [Plotter]
618 asapplotter - a plotter for asap, default plotter is
619 called 'plotter'
620 plot - plot a scantable
621 plot_lines - plot a linecatalog overlay
622 plotazel - plot azimuth and elevation versus time
623 plotpointing - plot telescope pointings
624 save - save the plot to a file ('png' ,'ps' or 'eps')
625 set_mode - set the state of the plotter, i.e.
626 what is to be plotted 'colour stacked'
627 and what 'panelled'
628 set_selection - only plot a selected part of the data
629 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
630 set_legend - specify user labels for the legend indeces
631 set_title - specify user labels for the panel indeces
632 set_abcissa - specify a user label for the abcissa
633 set_ordinate - specify a user label for the ordinate
634 set_layout - specify the multi-panel layout (rows,cols)
635 set_colors - specify a set of colours to use
636 set_linestyles - specify a set of linestyles to use if only
637 using one color
638 set_font - set general font properties, e.g. 'family'
639 set_histogram - plot in historam style
640 set_mask - set a plotting mask for a specific polarization
641 text - draw text annotations either in data or relative
642 coordinates
643 arrow - draw arrow annotations either in data or relative
644 coordinates
645 axhline,axvline - draw horizontal/vertical lines
646 axhspan,axvspan - draw horizontal/vertical regions
647 annotate - draw an arrow with label
648 create_mask - create a scnatble mask interactively
649
650 xyplotter - matplotlib/pylab plotting functions
651
652 [General]
653 commands - this command
654 print - print details about a variable
655 list_scans - list all scantables created by the user
656 list_files - list all files readable by asap (default rpf)
657 del - delete the given variable from memory
658 range - create a list of values, e.g.
659 range(3) = [0,1,2], range(2,5) = [2,3,4]
660 help - print help for one of the listed functions
661 execfile - execute an asap script, e.g. execfile('myscript')
662 list_rcparameters - print out a list of possible values to be
663 put into $HOME/.asaprc
664 rc - set rc parameters from within asap
665 mask_and,mask_or,
666 mask_not - boolean operations on masks created with
667 scantable.create_mask
668 skydip - gain opacity values from a sky dip observation
669 opacity_model - compute opacities fro given frequencies based on
670 atmospheric model
671
672 Note:
673 How to use this with help:
674 # function 'summary'
675 [xxx] is just a category
676 Every 'sub-level' in this list should be replaces by a '.' Period when
677 using help
678 Example:
679 ASAP> help scantable # to get info on ths scantable
680 ASAP> help scantable.summary # to get help on the scantable's
681 ASAP> help average_time
682
683 """
684 if rcParams['verbose']:
685 try:
686 from IPython.genutils import page as pager
687 except ImportError:
688 from pydoc import pager
689 pager(x)
690 else:
691 print x
692 return
693
694def welcome():
695 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
696
697Please report any bugs via:
698http://svn.atnf.csiro.au/trac/asap/simpleticket
699
700[IMPORTANT: ASAP is 0-based]
701Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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