-
Notifications
You must be signed in to change notification settings - Fork 5
/
mp_lcfind.py
1456 lines (1066 loc) · 49.7 KB
/
mp_lcfind.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
from __future__ import division
import numpy as np
import astropy
from astroquery.simbad import Simbad
from astroquery.mast import Observations
from astropy.coordinates import SkyCoord
import astropy.coordinates as coord
from astropy import units as u
import os
from astropy.io import fits as pyfits
import time
import traceback
import socket
from urllib.request import urlretrieve
import requests
from mp_tools import *
import copy
import subprocess
import shutil
#moonpydir = os.getcwd()
moonpydir = os.path.realpath(__file__)
moonpydir = moonpydir[:moonpydir.find('/mp_lcfind.py')]
curlscript_dir = moonpydir+'/tess_sector_curlscripts'
if os.path.exists(curlscript_dir) == False:
os.system('mkdir '+curlscript_dir)
#### move existing curlscripts into this directory!
os.system('mv '+moonpydir+'/*curlscript.txt '+curlscript_dir+'/')
hostname = socket.gethostname()
if ('tethys' in hostname) and ('sinica' in hostname):
#moonpydir = '/data/tethys/Documents/Software/MoonPy'
central_data_dir = '/data/tethys/Documents/Central_Data'
elif ('Alexs-MacBook') in hostname:
#moonpydir = '/Users/hal9000/Documents/Software/MoonPy'
central_data_dir = '/Users/hal9000/Documents/Central_Data'
elif 'umbriel' in hostname:
#moonpydir = '/home/cal/ateachey/Documents/MoonPy'
central_data_dir = '/home/cal/ateachey/Documents/Central_Data'
else:
#moonpydir = input('Please specify the MoonPy directory (or hard-code this into moonpy.py): ')
#central_data_dir = input("Please specify a 'central data' directory (or hard-code this into moonpy.py): ")
### store central_data within MoonPy directory
if os.path.exists(moonpydir+'/Central_Data'):
pass
else:
os.system('mkdir '+moonpydir+'/Central_Data')
central_data_dir = moonpydir+'/Central_Data'
#print('moonpydir = ', moonpydir)
#print('Light curves will be stored in '+central_data_dir)
#### THIS IS A MAJOR REWORKING OF THE ORIGINAL mp_lcfind.py (eventually mp_lcfind_deprecated.py).
#### THE KEY IS, The Kplr and k2plr packages are old, not available through conda, and cause all kinds of problems.
#### So this short_cadenceript will get around them entirely, doing it all under the hood, the way you want it.
#### (Note that you'll want to continue structuring the light curves as kplr does it.)
####
#### WILL NEED TO FOLLOW THESE INSTRUCTIONS: https://astroquery.readthedocs.io/en/latest/mast/mast.html
#####################################
# XXXXXXXXXX ALIAS FINDING XXXXXXXX #
#####################################
def Simbad_query(ra, dec, coord_format='degrees', telescope='kepler'):
print('calling mp_lcfind.py/Simbad_query().')
if 'h' in ra or ':' in ra:
coord_format == 'sexagesimal'
ra = ra.replace(' ', '') ### remove the spaces
dec = dec.replace(' ', '') ### remove the spaces
if coord_format=='degrees':
nearby_objects = Simbad.query_region(coord.SkyCoord(ra, dec, unit=(u.deg, u.deg), frame='icrs'), radius='0d0m5s')
elif coord_format=='sexagesimal':
nearby_objects = Simbad.query_region(coord.SkyCoord(str(ra)+' '+str(dec), frame='icrs'), radius='0d0m'+str(search_radius)+'s')
print(nearby_objects)
best_hit = nearby_objects[0][0].decode('UTF-8')
print("best_hit = ", best_hit)
if (telescope.lower() == 'kepler') and (best_hit.lower().startswith('koi') == False) and (best_hit.lower().startswith('kepler') == False) and (best_hit.lower().startswith("kic") == False):
### look for aliases
alias_query = Simbad.query_objectids(str(best_hit))['ID']
search_idx = 0
while search_idx < 10: ### maximum tries
try:
alias = alias_query[search_idx]
if alias.lower().startswith('koi') or alias.lower().statswith('kepler') or alias.lower().startswith("kic"):
best_hit = alias
break
else:
search_idx += 1
except:
break
print("alias = ", alias)
best_hit = alias
if best_hit.lower().startswith('koi'):
object_number = float(best_hit[4:]) ### strips off "KOI-"
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
targtype = 'koi'
object_name = "KOI-"+str(object_number)
elif best_hit.lower().startswith('kepler'):
object_number = str(int(best_hit[7:]))+'b' ### strips off "Kepler-", adds b because we don't care which planet it is.
#object_number = object_number+'b'
targtype = 'planet'
object_name = 'Kepler-'+str(object_number)
elif best_hit.lower().startswith("kic"):
object_number = int(best_hit[4:])
targtype = 'kic'
object_name = 'KIC'+str(object_number)
print("object_number = ", object_number)
elif (telscope.lower() == 'tess') and (best_hit.lower().startswith('toi') == False) and (best_hit.lower().startswith('tic') == False):
### look for aliases if TOI or TIC number was not listed to start.
alias_query = Simbad.query_objectids(str(best_hit))['ID']
search_idx = 0
while search_idx < 10: ### maximum tries
try:
alias = alias_query[search_idx]
print('potential alias: ', alias)
if alias.lower().startswith('toi') or alias.lower().startswith('tic'):
best_hit = alias
break
else:
search_idx += 1
except:
break
print("alias = ", alias)
best_hit = alias
if best_hit.lower().startswith('toi'):
object_number = float(best_hit[4:]) ### strips off "KOI-"
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
targtype = 'toi'
object_name = "TOI-"+str(object_number)
elif best_hit.lower().startswith("tic"):
object_number = int(best_hit[4:])
targtype = 'tic'
object_name = 'TIC'+str(object_number)
try:
print("object_number = ", object_number)
except:
pass
return object_name, object_number
def find_KIC_alias(target_name):
print('calling mp_lcfind.py/find_KIC_alias().')
#### FOR USE WITH KEPLER LIGHT CURVES.
### in order to return a KIC number, you need to remove final letters and decimals.
star_number = target_name
if '.' in star_number:
star_number = star_number[:star_number.find('.')] ### this will remove the decimal and final numbers
if star_number[-1] in ['b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l']:
star_number = star_number[:-1]
target_aliases = []
alias_search_results = Simbad.query_objectids(star_number)
if type(alias_search_results) != type(None):
for alidx in np.arange(0,np.array(alias_search_results).shape[0],1):
target_alias = alias_search_results[alidx][0]
target_aliases.append(target_alias)
if target_alias.lower().startswith('kic'):
kic_number = target_alias
break
else:
kic_number = target_name
try:
return kic_number
except:
return target_aliases
def find_TIC_alias(target_name):
print('calling mp_lcfind.py/find_TIC_alias().')
#### FOR USE WITH TESS LIGHT CURVES
### in order to return a KIC number, you need to remove final letters and decimals.
star_number = target_name
if '.' in star_number:
star_number = star_number[:star_number.find('.')] ### this will remove the decimal and final numbers
if star_number[-1] in ['b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l']:
star_number = star_number[:-1]
target_aliases = []
try:
alias_search_results = Simbad.query_objectids(star_number)
print('len(alias_search_results): ', len(alias_search_results))
for alidx in np.arange(0,np.array(alias_search_results).shape[0],1):
target_alias = alias_search_results[alidx][0]
target_aliases.append(target_alias)
if target_alias.lower().startswith('tic'):
tic_number = target_alias
self.ticnum = tic_number
break
except:
print('SIMBAD WAS UNABLE TO FIND THE TARGET.')
try:
target_aliases.np.array([self.ticnum])
tic_number = self.ticnum
print("TIC# LOCATED WITHIN EXOFOP.")
except:
try:
find_planet_row()
target_aliases.np.array([self.ticnum])
tic_number = self.ticnum
print("TIC# LOCATED WITHIN EXOFOP.")
except:
try:
tic_number = 'TIC '+np.array([self.exofop_data[self.exofop_rowidx]])[0]
except:
print('TARGET ALIAS IS JUST ORIGINAL TARGET NAME INPUT.')
target_aliases = np.array([target_name])
try:
return tic_number
except:
return target_aliases
def find_EPIC_alias(target_name):
print('calling mp_lcfind.py/find_EPIC_alias().')
#### FOR USE WITH k2 LIGHT CURVES.
### in order to return a EPIC number, you need to remove final letters and decimals.
star_number = target_name
if '.' in star_number:
star_number = star_number[:star_number.find('.')] ### this will remove the decimal and final numbers
if star_number[-1] in ['b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l']:
star_number = star_number[:-1]
target_aliases = []
alias_search_results = Simbad.query_objectids(star_number)
for alidx in np.arange(0,np.array(alias_search_results).shape[0],1):
target_alias = alias_search_results[alidx][0]
target_aliases.append(target_alias)
if target_alias.lower().startswith('epic'):
kic_number = target_alias
break
try:
return kic_number
except:
return target_aliases
#####################################
# XXXXXXXXXX URL GENERATION XXXXXXXX #
#####################################
def kepler_URL_generator(KIC, short_cadence=False):
print('calling mp_lcfind.py/kepler_URL_generator()')
### this function takes in a KIC number (with or without a prefix) and produces a URL and wget script.
"""
Kepler data may be retrieved without submitting a batch request.
Both lightcurve and target pixel files are online and stored in two directory trees.
For the browser paths below KKKKKKKKK is the KIC ID and XXXX is the first 4 digits
of the KIC ID including the initial zeros.
Lightcurves
http://archive.stsci.edu/pub/kepler/lightcurves/XXXX/KKKKKKKKK
http://archive.stsci.edu/pub/kepler/lightcurves/0014/001429092/
"""
query_format_number = KIC
#### you need to take the kic number, remove kic, and add zeroes until length = 9.
if query_format_number.lower().startswith('kic'):
query_format_number = query_format_number[3:]
while (query_format_number.startswith('-')) or (query_format_number.startswith(' ')):
query_format_number = query_format_number[1:]
### now it should be just a bunch of numbers:
while len(query_format_number) < 9:
query_format_number = '0'+query_format_number
assert len(query_format_number) == 9
first_four_numbers = query_format_number[:4]
#http://archive.stsci.edu/pub/kepler/lightcurves/0047/004760478/kplr004760478-2010078095331_llc.fits
final_URL = 'http://archive.stsci.edu/pub/kepler/lightcurves/'+first_four_numbers+'/'+query_format_number+'/'
if os.path.exists(central_data_dir+'/Kepler_lightcurves') == False:
os.system('mkdir '+central_data_dir+'/Kepler_lightcurves')
download_directory = central_data_dir+'/Kepler_lightcurves/KIC'+str(query_format_number)
if os.path.exists(download_directory):
pass
else:
os.system('mkdir '+download_directory)
if short_cadence == True:
wget_command = "wget -q -nH --cut-dirs=6 -r -l0 -c -N -np -R --reject tar --accept fits 'index*' -erobots=off "+final_URL+" -P "+download_directory+"/"
else:
wget_command = "wget -q -nH --cut-dirs=6 -r -l0 -c -N -np -R --reject tar --accept llc.fits 'index*' -erobots=off "+final_URL+" -P "+download_directory+"/"
return final_URL, wget_command, download_directory
def k2_URL_generator(EPIC):
print('calling mp_lcfind.py/k2_URL_generator()')
### this function takes in a EPIC number (with or without a prefix) and produces a URL and wget script.
"""
https://archive.stsci.edu/k2/download_options.html
Lightcurves
Individual files may be downloaded via FTP or through your browser (HTTPS) to download K2 data and catalogs.
For FTP, connect to archive.stsci.edu anonymously and cd to pub/k2 You will see the available directories
using ls. For HTTP, just go to https://archive.stsci.edu/pub/k2/. Examples for the browser paths to light
curves and target pixel files are shown below, where XXXXYYZZZ is the EPIC ID and N is the campaign number.
Files are available online in subdirectories in the form:
https://archive.stsci.edu/pub/k2/lightcurves/cN/XXXX00000/YY000. For example:
https://archive.stsci.edu/pub/k2/lightcurves/c3/212200000/35000/
### THEN THE FILE IS https://archive.stsci.edu/pub/k2/lightcurves/c3/212200000/35000/ktwo212235321-c03_llc.fits
"""
query_format_number = EPIC
#### you need to take the kic number, remove kic, and add zeroes until length = 9.
if query_format_number.lower().startswith('epic'):
query_format_number = query_format_number[4:] ### take off the epic
while (query_format_number.startswith('-')) or (query_format_number.startswith(' ')):
query_format_number = query_format_number[1:] #### remove initial "-" or " "
### now it should be just a bunch of numbers:
#### THE ACTION BELOW IS UNNECCESSARY FOR K2, I THINK.
#while len(query_format_number) < 9:
# query_format_number = '0'+query_format_number
assert len(query_format_number) == 9
XXXX = str(query_format_number[:4])
YY = str(query_format_number[4:6])
#final_URL = 'http://archive.stsci.edu/pub/kepler/lightcurves/'+first_four_numbers+'/'+query_format_number+'/'
#final_URL = 'https://archive.stsci.edu/pub/k2/lightcurves/c3/212200000/35000/'
download_directory = central_data_dir+'/K2_lightcurves/EPIC'+str(query_format_number)
if os.path.exists(download_directory):
pass
else:
os.system('mkdir '+download_directory)
#### since you don't know which campaign it's in, generate a list of final_URLs, a list of wget_commands,
final_URLs = []
wget_commands = []
filepaths = []
for campaign_number in np.arange(0,19,1):
print('campaign # ', campaign_number)
if campaign_number < 10:
filename = 'ktwo'+str(query_format_number)+'-c0'+str(campaign_number)+'_llc.fits'
final_URL = 'https://archive.stsci.edu/pub/k2/lightcurves/c'+str(campaign_number)+'/'+XXXX+'00000/'+YY+'000/'+filename #ktwo'+str(query_format_number)+'-c0'+str(campaign_number)+'_llc.fits'
else:
filename = 'ktwo'+str(query_format_number)+'-c'+str(campaign_number)+'_llc.fits'
final_URL = 'https://archive.stsci.edu/pub/k2/lightcurves/c'+str(campaign_number)+'/'+XXXX+'00000/'+YY+'000/'+filename #ktwo'+str(query_format_number)+'-c'+str(campaign_number)+'_llc.fits'
final_URLs.append(final_URL)
filepath = download_directory+'/'+filename
filepaths.append(filepath)
#wget_command = "wget -q -nH --cut-dirs=6 -r -l0 -c -N -np -R 'index*' -erobots=off "+final_URL+" -P "+download_directory+"/"
#wget_command = 'wget -nH --cut-dirs=6 -r -l0 -c -N -np -R "index*" -erobots=off '+final_URL+' -P '+download_directory+'/'
#os.system('wget --tries=1 "https://exoplanetarchive.ipac.caltech.edu/cgi-bin/nstedAPI/nph-nstedAPI?table=cumulative&select=kepid,kepoi_name,kepler_name,koi_disposition,koi_period,koi_period_err1,koi_period_err2,koi_sma,koi_sma_err1,koi_sma_err2,koi_insol,koi_insol_err1,koi_insol_err2,koi_time0bk,koi_time0bk_err1,koi_time0bk_err2,koi_impact,koi_impact_err1,koi_impact_err2,koi_duration,koi_duration_err1,koi_duration_err2,koi_eccen,koi_eccen_err1,koi_eccen_err2,koi_longp,koi_longp_err1,koi_longp_err2,koi_ror,koi_ror_err1,koi_ror_err2,koi_incl,koi_incl_err1,koi_incl_err2,koi_prad,koi_prad_err1,koi_prad_err2,koi_ldm_coeff2,koi_ldm_coeff1,ra,dec&order=kepoi_name&format=ascii" -O "'+kep_mast_address+'"')
wget_command = 'wget --tries=1 -N "'+final_URL+'" -P '+download_directory+'/'
wget_commands.append(wget_command)
return final_URLs, wget_commands, download_directory, filepaths
#####################################
# XXXXXXXXXX DOWNLOADING XXXXXXXX #
#####################################
def kepler_fits_download(target_name, clobber='n'):
print('calling mp_lcfind.py/kepler_fits_downloader().')
### first extract the KIC number
try:
KIC_name = find_KIC_alias(target_name)
print('KIC alias = ', KIC_name)
KIC_URL, KIC_wget, KIC_download_dir = functimer(kepler_URL_generator(KIC_name))
#print("KIC wget = ", KIC_wget)
#### check if KIC_download_dir files already exist... if they do, skip it!
if (len(os.listdir(KIC_download_dir)) > 0) and (clobber == 'n'):
print('light curve files already exist, no need to re-download.')
else:
print('wgetting KIC light curves...')
os.system(KIC_wget)
print('done.')
except:
traceback.print_exc()
raise Exception("something went wrong in 'kepler_fits_download()' (see traceback).")
def k2_fits_download(target_name, clobber='n'):
print('calling mp_lcfind.py/k2_fits_download().')
try:
EPIC_name = find_EPIC_alias(target_name)
EPIC_URLs, EPIC_wgets, EPIC_download_dir, EPIC_filepaths = k2_URL_generator(EPIC_name) ### EPIC_URLs and EPIC_wgets are LISTS!!!!
if (len(os.listdir(EPIC_download_dir)) > 0) and (clobber == 'n'):
print("light curve files already exist, no need to download again.")
else:
##### build a list of the EPIC_URLs that have been tried before.
unobserved_campaigns = []
if os.path.exists(EPIC_download_dir+'/unobserved_campaigns.txt'):
#### open it
unobserved_campaigns_file = open(EPIC_download_dir+'/unobserved_campaigns.txt', mode='r')
for nline,line in enumerate(unobserved_campaigns_file):
unobserved_campaigns.append(line[:line.find('\n')]) ### make sure you have just the EPIC_URL, not those final \n's.
unobserved_campaigns_file.close()
else:
#### start a new list.
unobserved_campaigns = []
print('wgetting EPIC light curves...')
for EPIC_URL, EPIC_wget, EPIC_filepath in zip(EPIC_URLs, EPIC_wgets, EPIC_filepaths):
if EPIC_URL in unobserved_campaigns:
print('target is known to not be observed in this campaign.')
else:
print('looking for ', EPIC_URL)
os.system(EPIC_wget)
print('done.')
print('EPIC filepath: ', EPIC_filepath)
if os.path.exists(EPIC_filepath) == False:
unobserved_campaigns_file = open(EPIC_download_dir+'/unobserved_campaigns.txt', mode='a')
unobserved_campaigns_file.write(EPIC_URL+'\n')
unobserved_campaigns_file.close()
print('added to the unobserved_campaigns.txt file.')
#### check to see if the file exists -- if it doesn't... add it to the unobserved_campaigns file.
except:
traceback.print_exc()
raise Exception("something went wrong in 'k2_fits_download()' (see traceback).")
#####################################
# XXXXXXXXXX UNPACK FITS XXXXXXXX #
#####################################
def kepler_unpack_fits(target_name, short_cadence=False, long_cadence=True):
print('calling mp_lcfind.py/kepler_unpack_fits().')
#### first thing you have to do is make sure the damn thing exists!
KIC_directory = functimer(kepler_URL_generator(find_KIC_alias(target_name))[2])
try:
#### use kepler_fits_download() to grab the KIC_download_dir and unpack these fits.
#KIC_directory = kepler_fits_download(target_name, download=download)
KIC_directory_files = os.listdir(KIC_directory)
print("KIC_directory_files = '", KIC_directory_files)
### start a dictionary with quarters, times, fluxes, errors, flags
kic_quarters_dict = {}
KIC_fits_files = []
### if short_cadence=True, you need to check whether there is a slc version!
### if short_cadence=False, reject slcs!
reject_wrong_cadence_files = []
for i,ki in enumerate(KIC_directory_files):
if ('slc.fits' in ki) and (short_cadence == False):
reject_wrong_cadence_files.append(ki)
if ('llc.fits' in ki) and (long_cadence == False):
reject_wrong_cadence_files.append(ki)
elif (short_cadence == True) and (long_cadence == True):
##### now we need to give preference for short_cadence over long_cadence
if 'llc.fits' in ki:
filename_before_suffix = ki[:ki.find('_llc.fits')]
continue
elif 'slc.fits' in ki:
filename_before_suffix = ki[:ki.find('_slc.fits')]
reject_wrong_cadence_files.append(filename_before_suffix+'_llc.fits')
print('reject wrong cadence files: ', reject_wrong_cadence_files)
for Kdf in KIC_directory_files:
if Kdf in reject_wrong_cadence_files:
continue
if ('.fits' in Kdf) and (Kdf not in reject_wrong_cadence_files):
print('reading ', Kdf)
KIC_fits_files.append(Kdf)
kdf_path = KIC_directory+'/'+Kdf
kdf_file = pyfits.open(kdf_path)
header = kdf_file[0].header
data = kdf_file[1].data
quarter = header['QUARTER']
kic_times = data['TIME']
kic_sap_flux = data['SAP_FLUX']
kic_sap_err = data['SAP_FLUX_ERR']
kic_pdc_flux = data['PDCSAP_FLUX']
kic_pdc_err = data['PDCSAP_FLUX_ERR']
kic_sap_qual = data['SAP_QUALITY']
#### create a dictionary JUST FOR THIS QUARTER
kic_quarter_dict = {}
kic_quarter_dict['TIME'] = kic_times
kic_quarter_dict['SAP_FLUX'] = kic_sap_flux
kic_quarter_dict['SAP_FLUX_ERR'] = kic_sap_err
kic_quarter_dict['PDCSAP_FLUX'] = kic_pdc_flux
kic_quarter_dict['PDCSAP_FLUX_ERR'] = kic_pdc_err
kic_quarter_dict['SAP_QUALITY'] = kic_sap_qual
### now add this dictionary to the kic_quarter_dict
kic_quarters_dict[quarter] = kic_quarter_dict
### output the kic_quarters_dict
return kic_quarters_dict
except:
traceback.print_exc()
raise Exception("Something went wrong in 'kepler_unpack_fits()' (see traceback).")
def k2_unpack_fits(target_name):
print('calling mp_lcfind.py/k2_unpack_fits()')
#### first thing you have to do is make sure the damn thing exists!
EPIC_directory = k2_URL_generator(find_EPIC_alias(target_name))[2]
try:
#### use kepler_fits_download() to grab the KIC_download_dir and unpack these fits.
#KIC_directory = kepler_fits_download(target_name, download=download)
EPIC_directory_files = os.listdir(EPIC_directory)
### start a dictionary with quarters, times, fluxes, errors, flags
epic_quarters_dict = {}
epic_fits_files = []
for Edf in EPIC_directory_files:
if '.fits' in Edf:
epic_fits_files.append(Edf)
edf_path = EPIC_directory+'/'+Edf
edf_file = pyfits.open(edf_path)
header = edf_file[0].header
data = edf_file[1].data
quarter = header['CAMPAIGN']
epic_times = data['TIME']
epic_sap_flux = data['SAP_FLUX']
epic_sap_err = data['SAP_FLUX_ERR']
epic_pdc_flux = data['PDCSAP_FLUX']
epic_pdc_err = data['PDCSAP_FLUX_ERR']
epic_sap_qual = data['SAP_QUALITY']
#### create a dictionary JUST FOR THIS QUARTER
epic_quarter_dict = {}
epic_quarter_dict['TIME'] = epic_times
epic_quarter_dict['SAP_FLUX'] = epic_sap_flux
epic_quarter_dict['SAP_FLUX_ERR'] = epic_sap_err
epic_quarter_dict['PDCSAP_FLUX'] = epic_pdc_flux
epic_quarter_dict['PDCSAP_FLUX_ERR'] = epic_pdc_err
epic_quarter_dict['SAP_QUALITY'] = epic_sap_qual
### now add this dictionary to the kic_quarter_dict
epic_quarters_dict[quarter] = epic_quarter_dict
### output the kic_quarters_dict
return epic_quarters_dict
except:
traceback.print_exc()
raise Exception("Something went wrong in 'k2_unpack_fits()' (see traceback).")
def kplr_target_download(targID, targtype='koi', quarters='all', lc_format='pdc', telescope='kepler', clobber='n', short_cadence=False):
print('calling mp_lcfind.py/kplr_target_download().')
#### using the functions developed above
### first, try unpacking without downloading.
### FOR MOONPY COMPATIBILITY, THIS REQUIRES SUPPORT FOR BOTH KEPLER AND K2 LIGHT CURVES.
if telescope.lower() == 'kepler':
kepler_fits_download(targID, clobber=clobber)
try:
kepler_lc_dictionary = kepler_unpack_fits(targID, short_cadence=short_cadence)
except:
print('first except triggered.')
time.sleep(2)
try:
print('lc may not have been downloaded. Attempting to download...')
kepler_fits_download(targID, clobber=clobber)
### after it's been downloaded, you can try to unpack again.
kepler_lc_dictionary = kepler_unpack_fits(targID, short_cadence=short_cadence)
except:
print('second except triggered.')
time.sleep(2)
traceback.print_exc()
raise Exception("Something went wrong in 'kplr_target_download()' (see traceback).")
elif telescope.lower() == 'k2':
k2_fits_download(targID, clobber=clobber)
try:
kepler_lc_dictionary = k2_unpack_fits(targID)
except:
print('first except triggered.')
time.sleep(2)
try:
print('lc may not have been downloaded. Attempting to download...')
k2_fits_download(targID, clobber=clobber)
### after it's been downloaded, you can try to unpack again.
kepler_lc_dictionary = k2_unpack_fits(targID)
except:
print('second except triggered.')
time.sleep(2)
traceback.print_exc()
raise Exception("Something went wrong in 'kplr_target_download()' (see traceback).")
### now you should have kepler_lc_dictionary, that's ready to return to spit out in the original format.
### first, sort the quarters
sorted_quarters = np.sort(list(kepler_lc_dictionary.keys()))
if quarters == 'all':
output_quarters = np.array(sorted_quarters)
else:
output_quarters = quarters
### make a bunch of lists -- this kinda sucks, but it's backwards compatible with the old kplr output.
kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, kobj_sap_fluxes, kobj_sap_errors = [], [], [], [], [], [], []
for oq in output_quarters:
quarter_entry = kepler_lc_dictionary[int(oq)]
#### need to find finite_idxs
times_finite = np.where(np.isfinite(quarter_entry['TIME']))[0]
pdc_flux_finite = np.where(np.isfinite(quarter_entry['PDCSAP_FLUX']))[0]
pdc_fluxerr_finite = np.where(np.isfinite(quarter_entry['PDCSAP_FLUX_ERR']))[0]
pdc_flags_finite = np.where(np.isfinite(quarter_entry['SAP_QUALITY']))[0]
sap_flux_finite = np.where(np.isfinite(quarter_entry['SAP_FLUX']))[0]
sap_fluxerr_finite = np.where(np.isfinite(quarter_entry['SAP_FLUX_ERR']))[0]
finite_idxs, finite_idx_counts = np.unique(np.concatenate((times_finite, pdc_flux_finite, pdc_fluxerr_finite, pdc_flags_finite, sap_flux_finite, sap_fluxerr_finite)), return_counts=True)
#### there are six arrays being concatenated... therefore, you only want the indices finite_idx_counts == 6.
finite_idxs = finite_idxs[finite_idx_counts == 6]
#print('len(finite_idxs) = ', len(finite_idxs))
#raise Exception("Look what you've done!")
kobj_times.append(quarter_entry['TIME'][finite_idxs])
kobj_pdc_fluxes.append(quarter_entry['PDCSAP_FLUX'][finite_idxs])
kobj_pdc_errors.append(quarter_entry['PDCSAP_FLUX_ERR'][finite_idxs])
kobj_flags.append(quarter_entry['SAP_QUALITY'][finite_idxs])
kobj_sap_fluxes.append(quarter_entry['SAP_FLUX'][finite_idxs])
kobj_sap_errors.append(quarter_entry['SAP_FLUX_ERR'][finite_idxs])
kobj_quarters.append(oq)
kobj_times = np.array(kobj_times, dtype=object)
kobj_pdc_fluxes = np.array(kobj_pdc_fluxes, dtype=object)
kobj_pdc_errors = np.array(kobj_pdc_errors, dtype=object)
kobj_flags = np.array(kobj_flags, dtype=object)
kobj_sap_fluxes = np.array(kobj_sap_fluxes, dtype=object)
kobj_sap_errors = np.array(kobj_sap_errors, dtype=object)
kobj_quarters = np.array(kobj_quarters, dtype=object)
print('kobj_quarters = ', kobj_quarters)
print('len(kobj_quarters) = ', len(kobj_quarters))
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
if lc_format == 'pdc':
return kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters
elif lc_format == 'sap':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters
elif lc_format == 'both':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters
def kplr_coord_download(ra, dec, coord_format='degrees', quarters='all', search_radius=5, lc_format='pdc', clobber='n', short_cadence=False):
print('calling mp_lcfind.py/kplr_coord_download().')
### find the object in Simbad using it's coordinates, and call kplr_target_download
print('ra,dec = ', ra, dec)
object_name, object_number = Simbad_query(ra=ra, dec=dec, coord_format=coord_format, telescope=self.telescope)
if lc_format == 'pdc':
kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = kplr_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'sap':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters = kplr_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'both':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = kplr_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence, clobber=clobber)
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
if lc_format == 'pdc':
return kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'sap':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'both':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
def tess_coord_download(ra, dec, coord_format='degrees', quarters='all', search_radius=5, lc_format='pdc', short_cadence=False):
print('calling mp_lcfind.py/tess_coord_download().')
### find the object in Simbad using it's coordinates, and call kplr_target_download
print('ra,dec = ', ra, dec)
try:
object_name, object_number = Simbad_query(ra=ra, dec=dec, coord_format=coord_format, telescope=self.telescope)
except:
print('SIMBAD QUERY FAILED.')
#### try to find TIC number another way
try:
ticnumber = self.ticnum
object_name, object_number = ticnumber, ticnumber[4:]
except:
try:
ticnumber = np.array(self.exofop_data['TIC ID'][self.exofop_rowidx])[0]
object_name, object_number = ticnumber, ticnumber[4:]
except:
print('EXHAUSTED ALL TRIES TO FIND TIC.')
if lc_format == 'pdc':
kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = tess_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'sap':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters = tess_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'both':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = tess_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
if lc_format == 'pdc':
return kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'sap':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'both':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
def tess_target_download(targID, sectors='all', short_cadence=True, lc_format='pdc', delete_fits='n', is_neighbor='n'):
print('calling mp_lcfind.py/tess_target_download().')
### this function interfaces with MASS to download light curves based on the TIC #.
print('targID: ', targID)
print('type(targID): ', type(targID))
if type(targID) != str:
targID = targID[0]
if os.path.exists(moonpydir+'/TESS_lcs'):
pass
else:
os.system('mkdir '+moonpydir+'/TESS_lcs')
### first try a simple curl script!
all_times = []
all_fluxes = []
all_errors = []
all_flags = []
sectors = []
lcfiles = []
try:
if targID.lower().startswith('tic'):
ticnum = str(targID)[3:]
if ticnum.startswith(' '):
ticnum = str(ticnum)[1:]
elif ticnum.startswith('-'):
ticnum = str(ticnum)[1:]
else:
#if targID.lower().startswith('toi'):
#### find it in exofop!
ticnum = self.exofop_data['TIC ID'][self.exofop_rowidx] #### I'm not sure where the self comes from, but it works! (for known TOIs)
#ticnum = exofop_data['TIC ID'][exofop_rowidx]
#ticnum = str(targID) ### you've already handled the TOI already!
if ticnum.startswith(' '):
ticnum = ticnum[1:]
#### now we have the ticnum, we can establish the download directory.
download_directory = central_data_dir+'/TESS_lightcurves/TIC'+str(ticnum)
if os.path.exists(download_directory):
pass
else:
os.system('mkdir '+download_directory)
### prepare for the query
query_num = ticnum
while len(query_num) < 16:
query_num = '0'+query_num
assert len(query_num) == 16
sector_prefixes, sector_suffixes = {}, {}
### these can be found at archive.stsci.edu/tess/bulk_downloads/bulk_downloads_ffi-tp-lc-dv.html,
### in the tesscurl_sector_NN_lc.sh files.
nsectors = 99
nactual_sectors = 0
last_existing_sector = 1
nempty_in_a_row = 0
sector_numbers = []
empty_curlscript_sectors = []
sector_filename = 'tess_sectors.txt'
if os.path.exists(moonpydir+'/'+sector_filename):
#### see if it is more than one day old:
current_time = time.time()
sectorfile_createtime = os.path.getctime(moonpydir+'/'+sector_filename)
if current_time - sectorfile_createtime > 86400: #### more than one day
### we're going to make a new one
create_new_sectorfile = True
else:
create_new_sectorfile = False
else:
#### just create it
create_new_sectorfile = True
os.system('touch '+moonpydir+'/'+sector_filename)
if create_new_sectorfile == True:
sectorfile = open(moonpydir+'/'+sector_filename, mode='w')
for sector in np.arange(1,nsectors,1):
### get the curl script... then extract the prefixes and suffixes from the first line.
print('looking for sector: ', sector)
try:
if os.path.exists(curlscript_dir+'/sector'+str(sector)+"_curlscript.txt"):
print('curlscript exists.')
pass
else:
print('attempting to download curlscript for the first time.')
sector_curl_URL = 'http://archive.stsci.edu/missions/tess/download_scripts/sector/tesscurl_sector_'+str(sector)+'_lc.sh'
print('sector_curl_URL')
os.system('wget --tries=1 -N "'+sector_curl_URL+'" -O '+curlscript_dir+'/sector'+str(sector)+"_curlscript.txt")
curltxt = open(curlscript_dir+'/sector'+str(sector)+'_curlscript.txt', mode='r')
first_line = curltxt.readline()
second_line = curltxt.readline()
sector_prefix = second_line[16:40]
sector_suffix = second_line[56:71]
### now read the first line of that
sector_prefixes[sector], sector_suffixes[sector] = sector_prefix, sector_suffix
print('sector_prefix = ', sector_prefix)
print('len(sector_prefix) = ', len(sector_prefix))
if len(sector_prefix) > 0:
#print("sector_prefix, sector_suffix = ", sector_prefix, sector_suffix)
nactual_sectors += 1
#last_existing_sector = copy.copy(sector)
nsectors = sector
### reset nempty_in_a_row
nempty_in_a_row = 0
sectorfile.write('sector '+str(sector)+'\n')
else:
print('sector '+str(sector)+' curlscript file was empty...')
print("REMOVING!")
empty_curlscript_sectors.append(sector)
nempty_in_a_row += 1
#### remove it!
os.system('rm -rf '+curlscript_dir+'/sector'+str(sector)+'_curlscript.txt')
#break
#continue
if nempty_in_a_row == 5:
break
else:
continue
except:
traceback.print_exc()
break_loop = input('Do you want to break loop? y/n: ')
if break_loop == 'y':
break
sectorfile.close()
elif create_new_sectorfile == False:
##### means you already queried the database once today, no need to do it again!
sector_numbers = []