Stage 00
Set up pcf
In Before Running, we set up the location of the data directory (
datadir) and run directory (rundir) inobs_par.pcf.As a reminder, for this example these directories are: -
datadir = /home/zieba/Desktop/Data/GJ1214_Hubble13021-rundir = /home/zieba/Desktop/Projects/Observations/Hubble/GJ1214_13021The
pacman_run_filesdirectory should contain: -run_pacman.py-fit_par.txt-obs_par.pcfThese template files can be found in the package directory, on GitHub, or downloaded directly here.
As mentioned in the Introduction, this example analyzes two visits taken in the middle of the GO 13021 program: 2013-03-13 and 2013-03-15.
Set up which_visits in the pcf
If your
datadircontains many visits, but you only want to analyze a subset, use thewhich_visitsparameter inobs_par.pcf.So, if you downloaded all 15 visits in GO 13021 (that is 1145 ima files with about 12.5 GB), use:
which_visits [5,6]
If you only downloaded the two visits as shown in the Download Data instructions, leave the default setting:
which_visits everything
In this example, we will assume you downloaded all 15 visits and that you set
which_visitsto [5,6], just to show you how it works.Run PACMAN
Navigate to the
pacman_run_filesdirectory in your terminal:cd /home/zieba/Desktop/Projects/Observations/Hubble/GJ1214_13021/pacman_run_filesOpen
run_pacman.py. It should look similar to this (after the imports):if __name__ == "__main__": meta = s00.run00(pcf_path=pcf_path) # meta = s01.run01(pcf_path=pcf_path) # meta = s02.run02(pcf_path=pcf_path) # meta = s03.run03(pcf_path=pcf_path) # meta = s10.run10(pcf_path=pcf_path) # meta = s20.run20(pcf_path=pcf_path) # meta = s21.run21(pcf_path=pcf_path) # meta = s30.run30(pcf_path=pcf_path)
To run Stage 00, make sure only the
s00line is uncommented. All other stages should remain commented out. In the future you can have multiple stages running at the same time, but for now we will run them one by one.Then run:
python run_pacman.pyWhen Stage 00 is executed, PACMAN creates the
stage00directory and a new timestamped directory insidestage00. The directory name has the form:s00_run_YYYY-MM-DD_HH-MM-SSFor example:
/home/zieba/Desktop/Projects/Observations/Hubble/GJ1214_13021/stage00/s00_run_2022-03-04_15-10-29The
fit_par.txtandobs_par.pcffiles used for this run are copied into this stage run directory. This copy is really just a copy and just for future reference. The files in thepacman_run_filesdirectory are the ones that you should edit to change settings for future runs.You should now have a directory structure similar to this:
user
└── Desktop
└── Projects
└── Observations
└── Hubble
└── GJ1214_13021
├── pacman_run_files
│ ├── run_pacman.py
│ ├── fit_par.txt
│ └── obs_par.pcf
└── stage00
└── s00_run_2022-03-04_15-10-29
├── fit_par.txt
├── obs_par.pcf
├── s00.log
├── WFC3_Meta_Save.dat
└── filelist.txt
Here, s00.log is a log file that contains all terminal output from the Stage 00 run. WFC3_Meta_Save.dat is a file that contains metadata for this stage. filelist.txt is a file that contains information about the files that were analyzed in this stage, such as their names, the visit and orbit they belong to, their time, and more. We will discuss this file in more detail in the Results section below.
Results
After running Stage 00, you should get terminal output similar to this (in this example I had all 15 visits in the data directory, but only wanted to analyze two of them, so the amount of files analyzed was reduced from 1145 to 158):
Starting s00 Output directory: /Users/sebastianzieba/Desktop/Projects/Observations/Hubble/GJ1214_13021_2026/stage00/s00_run_2026-05-26_12-33-34 pcf and fit_par files copied to the Stage 00 run directory: /Users/sebastianzieba/Desktop/Projects/Observations/Hubble/GJ1214_13021_2026/stage00/s00_run_2026-05-26_12-33-34 Found 1145 data file(s) ending in ima.fits Reading in files and their headers: 100%|##########| 1145/1145 [00:01<00:00, 873.37it/s] Determining orbit(s) and visit(s): 100%|##########| 1145/1145 [00:00<00:00, 497202.41it/s] The user does not want to analyse every visit (which_visits != everything). The amount of files analyzed therefore reduced from 1145 to 158. Writing table into filelist.txt Saving Metadata Finished s00
Stage 00 creates a 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 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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 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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 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It has the following columns:
filenamesinstr: The specific filter or grism used in the observation.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 scan1: reverse scan-1: not a spectrum but a direct image
exp: exposure time in seconds.