Stage 00
Set up pcf
In Before Running, we did set up the location of your data directory (=datadir) and run directory (=rundir) in the pcf.
As a quick reminder:
For me, these directories are located at the following places:
datadir = /home/zieba/Desktop/Data/GJ1214_Hubble13021
rundir = /home/zieba/Desktop/Projects/Observations/Hubble/GJ1214_13021
The rundir should contain the following three files:
pacman_script.py
fit_par.txt
obs_par.pcf
Set up which_visits in the pcf
If your datadir contains a lot of visits, but you only want to analyze a subset you can use the
which_visitsparameter in the pcf. If the user downloaded all 15 visits in GO 13021, he or she can choose:which_visits = [5,6]in the pcf. If you only downloaded the two visits as shown in the Download Data instructions, leave the default setting (which should bewhich_visits everything).Run PACMAN
You can give your analysis an “eventlabel” which might make it easier to identify it in the future. Here we just call our analysis: ‘GJ1214_Hubble13021’.
Now navigate to your rundir in your terminal and type:
python pacman_script.py --s00 --eventlabel='GJ1214_Hubble13021'Here, --s00 means we are going to run Stage 00 and --eventlabel will be used in the naming of files and directories.
The --eventlabel argument is just needed when running --s00.
When running s00, the first step creates a new subdirectory in rundir for the analysis which we will call the work directory (=workdir).
It will be saved in the rundir and have a form like:
/home/zieba/Desktop/Projects/Observations/Hubble/GJ1214_13021/run_2022-03-04_15-10-29_GJ1214_Hubble13021The fit_par.txt and obs_par.pcf files which are in the run directory will be copied there.
You should have a data structure similar to the following now:
user
└── Desktop
└── Projects
└── Observations
└── Hubble
└── GJ1214_13021
├── pacman_script.py
├── fit_par.txt
├── obs_par.pcf
└── run_2022-03-04_15-10-29_GJ1214_Hubble13021
├── fit_par.txt
└── obs_par.pcf
Note
All next steps are going to use the pcf and fit_par which is located in the workdir (run_2022-03-04_15-10-29_GJ1214_Hubble13021) and not the pcf and fit_par in the rundir (GJ1214_13021)!!
Note
You can type python pacman_script.py --help to see all possible flags which are available.
Results
After running Stage 00 you should get an output in the terminal similar to this one:
Starting s00 Found 1145 data file(s) ending in ima.fits Reading in files and their headers: 100%|##########| 1145/1145 [00:03<00:00, 303.42it/s] Determining orbit(s) and visit(s): 100%|##########| 1145/1145 [00:00<00:00, 261786.76it/s] The user does not want to analyse every visit (which_visits != everything). The amount of files analyzed therefore reduced from 1145 to 150. Writing table into filelist.txt Saving Metadata Finished s00
You will also end up with a new file called
filelist.txt. It should look like this:================== ===== ====== ====== ======== ================== ================== ================== ==== ========== filenames instr ivisit iorbit iexp_orb t_mjd t_visit t_orbit scan exp ================== ===== ====== ====== ======== ================== ================== ================== ==== ========== ibxy07p9q_ima.fits F130N 0 0 -1 56364.52973075 0.0 0.0 -1 0.833445 ibxy07paq_ima.fits G141 0 0 0 56364.531017044996 1.85226479312405 1.85226479312405 0 103.128586 ibxy07pbq_ima.fits G141 0 0 1 56364.532660565004 4.218933605588973 4.218933605588973 1 103.128586 ibxy07pcq_ima.fits G141 0 0 2 56364.534304085 6.585602397099137 6.585602397099137 0 103.128586 ibxy07pdq_ima.fits G141 0 0 3 56364.5359476 8.952264001127332 8.952264001127332 1 103.128586 ibxy07pfq_ima.fits G141 0 0 4 56364.537591119995 11.318932792637497 11.318932792637497 0 103.128586 ibxy07pgq_ima.fits G141 0 0 5 56364.539234640004 13.68560160510242 13.68560160510242 1 103.128586 ibxy07phq_ima.fits G141 0 0 6 56364.540878155 16.052263198653236 16.052263198653236 0 103.128586 ibxy07pjq_ima.fits G141 0 0 7 56364.542521675 18.41893200064078 18.41893200064078 1 103.128586 ibxy07pkq_ima.fits G141 0 0 8 56364.544165195 20.785600802628323 20.785600802628323 0 103.128586 ibxy07plq_ima.fits G141 0 0 9 56364.54580871 23.15226239617914 23.15226239617914 1 103.128586 ibxy07pnq_ima.fits G141 0 0 10 56364.54745223 25.518931198166683 25.518931198166683 0 103.128586 ibxy07poq_ima.fits G141 0 0 11 56364.54909575 27.885600000154227 27.885600000154227 1 103.128586 ibxy07ppq_ima.fits G141 0 0 12 56364.550739269995 30.25226879166439 30.25226879166439 0 103.128586 ibxy07prq_ima.fits G141 0 0 13 56364.55238279 32.618937604129314 32.618937604129314 1 103.128586 ibxy07psq_ima.fits G141 0 0 14 56364.554026305 34.98559919768013 34.98559919768013 0 103.128586 ibxy07ptq_ima.fits G141 0 0 15 56364.555669825 37.352267999667674 37.352267999667674 1 103.128586 ibxy07pvq_ima.fits G141 0 0 16 56364.557313345 39.71893680165522 39.71893680165522 0 103.128586 ibxy07pwq_ima.fits G141 0 0 17 56364.55895686 42.085598395206034 42.085598395206034 1 103.128586 ibxy07pxq_ima.fits F130N 0 1 -1 56364.59243889499 90.29972878983244 0.0 -1 0.833445 ibxy07pyq_ima.fits G141 0 1 0 56364.59372538 92.15226719970815 1.8525384098757058 0 103.128586 ibxy07q0q_ima.fits G141 0 1 1 56364.595368894996 94.51892879325897 4.219200003426522 1 103.128586 ibxy07q1q_ima.fits G141 0 1 2 56364.597012415004 96.88559760572389 6.585868815891445 0 103.128586 ibxy07q2q_ima.fits G141 0 1 3 56364.598655935 99.25226639723405 8.95253760740161 1 103.128586 ibxy07q4q_ima.fits G141 0 1 4 56364.600299455 101.6189351992216 11.319206409389153 0 103.128586 ibxy07q5q_ima.fits G141 0 1 5 56364.601942975 103.98560400120914 13.685875211376697 1 103.128586 ibxy07q6q_ima.fits G141 0 1 6 56364.603586490004 106.35226560523733 16.052536815404892 0 103.128586 ibxy07q8q_ima.fits G141 0 1 7 56364.60523001 108.7189343967475 18.419205606915057 1 103.128586 ibxy07q9q_ima.fits G141 0 1 8 56364.60687353 111.08560319873504 20.7858744089026 0 103.128586 ibxy07qaq_ima.fits G141 0 1 9 56364.608517045 113.45226480276324 23.152536012930796 1 103.128586 ibxy07qcq_ima.fits G141 0 1 10 56364.610160565004 115.81893360475078 25.51920481491834 0 103.128586 ibxy07qdq_ima.fits G141 0 1 11 56364.611804085 118.18560239626095 27.885873606428504 1 103.128586 ibxy07qeq_ima.fits G141 0 1 12 56364.6134476 120.55226400028914 30.2525352104567 0 103.128586 ibxy07qgq_ima.fits G141 0 1 13 56364.615091119995 122.9189327917993 32.619204001966864 1 103.128586 ibxy07qhq_ima.fits G141 0 1 14 56364.61673464 125.28560160426423 34.98587281443179 0 103.128586 ibxy07qiq_ima.fits G141 0 1 15 56364.618378155 127.65226319781505 37.3525344079826 1 103.128586 ibxy07qkq_ima.fits G141 0 1 16 56364.620021675 130.0189319998026 39.719203209970146 0 103.128586 ibxy07qlq_ima.fits G141 0 1 17 56364.621665195 132.38560080179013 42.08587201195769 1 103.128586 ibxy07qmq_ima.fits G141 0 1 18 56364.62330871 134.75226239534095 44.452533605508506 0 103.128586 ibxy07qoq_ima.fits F130N 0 2 -1 56364.658908525 186.01599600166082 0.0 -1 0.833445 ibxy07qpq_ima.fits G141 0 2 0 56364.66019501 187.86853440105915 1.8525383993983269 0 103.128586 ibxy07qqq_ima.fits G141 0 2 1 56364.66183871 190.2354624029249 4.2194664012640715 1 103.128586 ibxy07qrq_ima.fits G141 0 2 2 56364.663482045 192.6018647965975 6.585868794936687 0 103.128586 ibxy07qtq_ima.fits G141 0 2 3 56364.665125750005 194.96880000689998 8.952804005239159 1 103.128586 ibxy07quq_ima.fits G141 0 2 4 56364.666769085 197.3352024005726 11.319206398911774 0 103.128586 ibxy07qvq_ima.fits G141 0 2 5 56364.66841279 199.7021376003977 13.686141598736867 1 103.128586 ibxy07qxq_ima.fits G141 0 2 6 56364.67005612 202.06853279611096 16.052536794450134 0 103.128586 ibxy07qyq_ima.fits G141 0 2 7 56364.671699825005 204.43546800641343 18.419472004752606 1 103.128586 ibxy07qzq_ima.fits G141 0 2 8 56364.67334316 206.80187040008605 20.78587439842522 0 103.128586 ibxy07r1q_ima.fits G141 0 2 9 56364.67498686 209.1687984019518 23.152802400290966 1 103.128586 ibxy07r2q_ima.fits G141 0 2 10 56364.676630195 211.5352007956244 25.51920479396358 0 103.128586 ibxy07r3q_ima.fits G141 0 2 11 56364.678273900005 213.90213600592688 27.886140004266053 1 103.128586 ibxy07r5q_ima.fits G141 0 2 12 56364.679917229994 216.26853119116277 30.25253518950194 0 103.128586 ibxy07r6q_ima.fits G141 0 2 13 56364.681560935 218.63546640146524 32.61947039980441 1 103.128586 ibxy07r7q_ima.fits G141 0 2 14 56364.68320427 221.00186879513785 34.98587279347703 0 103.128586 ibxy07r9q_ima.fits G141 0 2 15 56364.68484797 223.3687967970036 37.35280079534277 1 103.128586 ibxy07raq_ima.fits G141 0 2 16 56364.686491304994 225.7351991906762 39.71920318901539 0 103.128586 ibxy07rbq_ima.fits G141 0 2 17 56364.68813501 228.10213440097868 42.08613839931786 1 103.128586 ibxy07rdq_ima.fits G141 0 2 18 56364.689778340005 230.46852960716933 44.452533605508506 0 103.128586 ibxy07req_ima.fits F130N 0 3 -1 56364.72539019 281.74959359457716 0.0 -1 0.833445 ibxy07rfq_ima.fits G141 0 3 0 56364.72667649 283.60186559613794 1.8522720015607774 0 103.128586 ibxy07rgq_ima.fits G141 0 3 1 56364.728320195005 285.9688008064404 4.2192072118632495 1 103.128586 ibxy07riq_ima.fits G141 0 3 2 56364.72996353 288.335203200113 6.585609605535865 0 103.128586 ibxy07rjq_ima.fits G141 0 3 3 56364.73160723 290.7021312019788 8.95253760740161 1 103.128586 ibxy07rkq_ima.fits G141 0 3 4 56364.733250565 293.0685335956514 11.318940001074225 0 103.128586 ibxy07rlq_ima.fits G141 0 3 5 56364.734894270005 295.43546880595386 13.685875211376697 1 103.128586 ibxy07rmq_ima.fits G141 0 3 6 56364.736537599994 297.80186399118975 16.052270396612585 0 103.128586 ibxy07rnq_ima.fits G141 0 3 7 56364.738181305 300.1687992014922 18.419205606915057 1 103.128586 ibxy07roq_ima.fits G141 0 3 8 56364.73982464 302.53520159516484 20.785608000587672 0 103.128586 ibxy07rpq_ima.fits G141 0 3 9 56364.74146834 304.9021295970306 23.152536002453417 1 103.128586 ibxy07rqq_ima.fits G141 0 3 10 56364.743111674994 307.2685319907032 25.518938396126032 0 103.128586 ibxy07rrq_ima.fits G141 0 3 11 56364.74475538 309.63546720100567 27.885873606428504 1 103.128586 ibxy07rsq_ima.fits G141 0 3 12 56364.746398710005 312.0018624071963 30.25226881261915 0 103.128586 ibxy07rtq_ima.fits G141 0 3 13 56364.748042415 314.368797596544 32.619204001966864 1 103.128586 ibxy07ruq_ima.fits G141 0 3 14 56364.749685749994 316.73519999021664 34.98560639563948 0 103.128586 ibxy07rvq_ima.fits G141 0 3 15 56364.751329455 319.1021352005191 37.35254160594195 1 103.128586 ibxy07rwq_ima.fits G141 0 3 16 56364.75297279 321.46853759419173 39.71894399961457 0 103.128586 ibxy07rxq_ima.fits G141 0 3 17 56364.75461649 323.8354655960575 42.08587200148031 1 103.128586 ibxy07ryq_ima.fits G141 0 3 18 56364.75625982499 326.2018679897301 44.452274395152926 0 103.128586 ibxy06d0q_ima.fits F130N 1 0 -1 56366.125031495 0.0 0.0 -1 0.833445 ibxy06d1q_ima.fits G141 1 0 0 56366.126317785 1.8522575951647013 1.8522575951647013 0 103.128586 ibxy06d2q_ima.fits G141 1 0 1 56366.127961305 4.218926397152245 4.218926397152245 1 103.128586 ibxy06d3q_ima.fits G141 1 0 2 56366.129604825 6.585595199139789 6.585595199139789 0 103.128586 ibxy06d4q_ima.fits G141 1 0 3 56366.131248339996 8.952256792690605 8.952256792690605 1 103.128586 ibxy06d6q_ima.fits G141 1 0 4 56366.132891860005 11.318925605155528 11.318925605155528 0 103.128586 ibxy06d7q_ima.fits G141 1 0 5 56366.13453538 13.685594396665692 13.685594396665692 1 103.128586 ibxy06d8q_ima.fits G141 1 0 6 56366.136178895 16.052256000693887 16.052256000693887 0 103.128586 ibxy06daq_ima.fits G141 1 0 7 56366.137822414996 18.418924792204052 18.418924792204052 1 103.128586 ibxy06dbq_ima.fits G141 1 0 8 56366.139465935004 20.785593604668975 20.785593604668975 0 103.128586 ibxy06dcq_ima.fits G141 1 0 9 56366.141109455 23.15226239617914 23.15226239617914 1 103.128586 ibxy06deq_ima.fits G141 1 0 10 56366.142752975 25.518931198166683 25.518931198166683 0 103.128586 ibxy06dfq_ima.fits G141 1 0 11 56366.144396489995 27.8855927917175 27.8855927917175 1 103.128586 ibxy06dgq_ima.fits G141 1 0 12 56366.146040010004 30.252261604182422 30.252261604182422 0 103.128586 ibxy06diq_ima.fits G141 1 0 13 56366.14768353 32.61893039569259 32.61893039569259 1 103.128586 ibxy06djq_ima.fits G141 1 0 14 56366.149327045 34.98559199972078 34.98559199972078 0 103.128586 ibxy06dnq_ima.fits G141 1 0 15 56366.150970564995 37.35226079123095 37.35226079123095 1 103.128586 ibxy06dpq_ima.fits G141 1 0 16 56366.152614085004 39.71892960369587 39.71892960369587 0 103.128586 ibxy06dqq_ima.fits G141 1 0 17 56366.1542576 42.085591197246686 42.085591197246686 1 103.128586 ibxy06dvq_ima.fits F130N 1 1 -1 56366.187809265 90.39998879889026 0.0 -1 0.833445 ibxy06dwq_ima.fits G141 1 1 0 56366.189095565 92.25226080045104 1.8522720015607774 0 103.128586 ibxy06dyq_ima.fits G141 1 1 1 56366.190739084996 94.6189295919612 4.218940793070942 1 103.128586 ibxy06dzq_ima.fits G141 1 1 2 56366.192382605004 96.98559840442613 6.585609605535865 0 103.128586 ibxy06e0q_ima.fits G141 1 1 3 56366.19402612 99.35225999797694 8.952271199086681 1 103.128586 ibxy06e2q_ima.fits G141 1 1 4 56366.19566964 101.71892879996449 11.318940001074225 0 103.128586 ibxy06e3q_ima.fits G141 1 1 5 56366.197313159995 104.08559759147465 13.68560879258439 1 103.128586 ibxy06e4q_ima.fits G141 1 1 6 56366.198956675 106.45225919550285 16.052270396612585 0 103.128586 ibxy06e6q_ima.fits G141 1 1 7 56366.20060019501 108.81892800796777 18.418939209077507 1 103.128586 ibxy06e7q_ima.fits G141 1 1 8 56366.202243715 111.18559679947793 20.785608000587672 0 103.128586 ibxy06e8q_ima.fits G141 1 1 9 56366.20388723 113.55225840350613 23.152269604615867 1 103.128586 ibxy06eaq_ima.fits G141 1 1 10 56366.20553075 115.9189271950163 25.518938396126032 0 103.128586 ibxy06ebq_ima.fits G141 1 1 11 56366.20717427001 118.28559600748122 27.885607208590955 1 103.128586 ibxy06ecq_ima.fits G141 1 1 12 56366.208817785 120.65225760103203 30.25226880214177 0 103.128586 ibxy06eeq_ima.fits G141 1 1 13 56366.210461305 123.01892640301958 32.618937604129314 1 103.128586 ibxy06efq_ima.fits G141 1 1 14 56366.212104825 125.38559519452974 34.98560639563948 0 103.128586 ibxy06egq_ima.fits G141 1 1 15 56366.21374834 127.75225679855794 37.352267999667674 1 103.128586 ibxy06eiq_ima.fits G141 1 1 16 56366.215391859994 130.1189255900681 39.71893679117784 0 103.128586 ibxy06ejq_ima.fits G141 1 1 17 56366.21703538 132.48559440253302 42.08560560364276 1 103.128586 ibxy06ekq_ima.fits G141 1 1 18 56366.218678895 134.85225599608384 44.45226719719358 0 103.128586 ibxy06enq_ima.fits F130N 1 2 -1 56366.254279265006 186.11678880639374 0.0 -1 0.833445 ibxy06eoq_ima.fits G141 1 2 0 56366.255565750005 187.96932720579207 1.8525383993983269 0 103.128586 ibxy06epq_ima.fits G141 1 2 1 56366.257209085 190.33572959946468 4.218940793070942 1 103.128586 ibxy06eqq_ima.fits G141 1 2 2 56366.25885279 192.70266479928978 6.585875992896035 0 103.128586 ibxy06esq_ima.fits G141 1 2 3 56366.26049612 195.06905999500304 8.952271188609302 1 103.128586 ibxy06etq_ima.fits G141 1 2 4 56366.262139825005 197.43599520530552 11.319206398911774 0 103.128586 ibxy06euq_ima.fits G141 1 2 5 56366.26378316 199.80239759897813 13.68560879258439 1 103.128586 ibxy06ewq_ima.fits G141 1 2 6 56366.26542686 202.16932560084388 16.052536794450134 0 103.128586 ibxy06exq_ima.fits G141 1 2 7 56366.267070195 204.5357279945165 18.41893918812275 1 103.128586 ibxy06eyq_ima.fits G141 1 2 8 56366.268713900005 206.90266320481896 20.78587439842522 0 103.128586 ibxy06f0q_ima.fits G141 1 2 9 56366.270357229994 209.26905839005485 23.15226958366111 1 103.128586 ibxy06f1q_ima.fits G141 1 2 10 56366.272000935 211.63599360035732 25.51920479396358 0 103.128586 ibxy06f2q_ima.fits G141 1 2 11 56366.27364427 214.00239599402994 27.885607187636197 1 103.128586 ibxy06f4q_ima.fits G141 1 2 12 56366.27528797 216.36932399589568 30.25253518950194 0 103.128586 ibxy06f5q_ima.fits G141 1 2 13 56366.276931304994 218.7357263895683 32.61893758317456 1 103.128586 ibxy06f6q_ima.fits G141 1 2 14 56366.27857501 221.10266159987077 34.98587279347703 0 103.128586 ibxy06f8q_ima.fits G141 1 2 15 56366.280218340005 223.46905680606142 37.352267999667674 1 103.128586 ibxy06f9q_ima.fits G141 1 2 16 56366.281862045 225.83599199540913 39.71920318901539 0 103.128586 ibxy06faq_ima.fits G141 1 2 17 56366.28350538 228.20239439955913 42.08560559316538 1 103.128586 ibxy06fcq_ima.fits G141 1 2 18 56366.285149085 230.56932959938422 44.452540792990476 0 103.128586 ibxy06fdq_ima.fits F130N 1 3 -1 56366.32076075 281.8501271994319 0.0 -1 0.833445 ibxy06feq_ima.fits G141 1 3 0 56366.32204723 283.70265840087086 1.8525312014389783 0 103.128586 ibxy06ffq_ima.fits G141 1 3 1 56366.323690565 286.0690607945435 4.218933595111594 1 103.128586 ibxy06fhq_ima.fits G141 1 3 2 56366.325334270005 288.43599600484595 6.585868805414066 0 103.128586 ibxy06fiq_ima.fits G141 1 3 3 56366.326977599994 290.80239119008183 8.952263990649953 1 103.128586 ibxy06fjq_ima.fits G141 1 3 4 56366.328621305 293.1693264003843 11.319199200952426 0 103.128586 ibxy06fkq_ima.fits G141 1 3 5 56366.33026464 295.5357287940569 13.685601594625041 1 103.128586 ibxy06flq_ima.fits G141 1 3 6 56366.33190834 297.90265679592267 16.052529596490785 0 103.128586 ibxy06fmq_ima.fits G141 1 3 7 56366.333551674994 300.2690591895953 18.4189319901634 1 103.128586 ibxy06fnq_ima.fits G141 1 3 8 56366.33519538 302.63599439989775 20.785867200465873 0 103.128586 ibxy06foq_ima.fits G141 1 3 9 56366.336838710005 305.0023896060884 23.15226240665652 1 103.128586 ibxy06fpq_ima.fits G141 1 3 10 56366.338482415 307.3693247954361 25.519197596004233 0 103.128586 ibxy06fqq_ima.fits G141 1 3 11 56366.34012574999 309.73572718910873 27.885599989676848 1 103.128586 ibxy06frq_ima.fits G141 1 3 12 56366.341769455 312.1026623994112 30.25253519997932 0 103.128586 ibxy06fsq_ima.fits G141 1 3 13 56366.34341279 314.4690647930838 32.618937593651935 1 103.128586 ibxy06ftq_ima.fits G141 1 3 14 56366.34505649 316.83599279494956 34.98586559551768 0 103.128586 ibxy06fuq_ima.fits G141 1 3 15 56366.346699825 319.20239519909956 37.352267999667674 1 103.128586 ibxy06fvq_ima.fits G141 1 3 16 56366.34834353 321.56933039892465 39.71920319949277 0 103.128586 ibxy06fwq_ima.fits G141 1 3 17 56366.349986860005 323.9357256051153 42.08559840568341 1 103.128586 ibxy06fxq_ima.fits G141 1 3 18 56366.351630565 326.302660794463 44.45253359503113 0 103.128586 ================== ===== ====== ====== ======== ================== ================== ================== ==== ==========
It has the following columns:
filenames
instr: The specific filter or grism used in the obervation
ivisit: Current visit of the observation
iorbit: Current orbit of the observation
t_mjd: Time in Modified Julian Date (MJD)
t_visit: Time since the first exposure in the visit in minutes
t_orbit: Time since the first exposure in the orbit in minutes
scan: Scan direction:
0: forward scan
1: reverse scan
-1: not a spectrum but a direct image
exp: exposure time in seconds