Outputs
Here we summarize all the files created by PACMAN when doing a complete run from s00 to s30.
Stage 00
directories
- workdir (e.g.: run_2022-12-16_10-46-31_dec2022)
the main directory of your analysis
- workdir/figs
all figures will be saved into here
workdir/figs/s00_obs_dates
plots
workdir/figs/s00_obs_dates/obs_dates.png
workdir/figs/s00_obs_dates/obs_dates_all.png
other files
- workdir/WFC3_dec2022_Meta_Save.dat
the meta file: this file will collect a lot of useful information when finishing a stage and then accessed by the next stage.
- workdir/filelist.txt
a list containing all *ima.fits files in the datadir and some information from their headers.
- workdir/fit_par.txt
this fit_par.txt will be used for the fitting in s30
- workdir/obs_par.pcf
this is the main obs_par.pcf file for all future stages
Stage 01
directories
ancil
ancil/horizons
other files
ancil/horizons/horizons_results_v0.txt
Stage 02
directories
workdir/figs/s02_barycorr
plots
workdir/figs/s02_barycorr/bjdcorr_horizons_results_v0.png
Stage 03
directories
workdir/ancil/refspec
workdir/ancil/stellar_models
workdir/figs/s03_refspec
workdir/figs/s03_smooth
plots
workdir/figs/s03_refspec/refspec.png
workdir/figs/s03_smooth/smooth.png
other files
workdir/ancil/stellar_models/k93models/kp03_3500.fits
Stage 10
directories
workdir/figs/s10_images
plots
workdir/figs/di_0.png
workdir/figs/quick_di0.png
other files
workdir/xrefyref.txt
Stage 21
directories
workdir/extracted_lc/2022-12-16_11-22-12
workdir/figs/s20_badmask
workdir/figs/s20_bkg_evo
workdir/figs/s20_bkg_hist
workdir/figs/s20_drift
workdir/figs/s20_optextr
workdir/figs/s20_refspec_fit
workdir/figs/s20_sp1d
workdir/figs/s20_sp1d_diff
workdir/figs/s20_sp2d
workdir/figs/s20_trace
workdir/figs/s20_utr
workdir/figs/s20_utr_aper_evo
plots
workdir/figs/s20_badmask/badmask_0
workdir/figs/s20_bkg_evo/bkg_evo.png
workdir/figs/s20_bkg_hist/bkg_hist0-0.png
workdir/figs/s20_drift/drift.png
workdir/figs/s20_optextr/optextr0-0.png
workdir/figs/s20_refspec_fit/refspec_fit_0.png
workdir/figs/s20_sp1d/sp1d_0.png
workdir/figs/s20_sp1d_diff/sp1d_diff_0.png
workdir/figs/s20_sp2d/sp2d_0.png
workdir/figs/s20_trace/trace_0.png
workdir/figs/s20_utr/utr0-0.png
workdir/figs/s20_utr_aper_evo/utr_aper_evo.png
other files
workdir/extracted_lc/2022-12-16_11-22-12/diagnostics.txt
workdir/extracted_lc/2022-12-16_11-22-12/lc_spec.txt
workdir/extracted_lc/2022-12-16_11-22-12/lc_white.txt
- workdir/extracted_lc/2022-12-16_11-22-12/obs_par.pcf
this pcf is just a copy of the pcf which was used when s20 was run. The purpose of this copy is just so that the user can trace back which settings were uses when running this stage.
Stage 20
directories
workdir/extracted_sp
workdir/extracted_sp/bins11_2022-12-16_11-52-46
plots
workdir/extracted_sp/bins11_2022-12-16_11-52-46/spec_bins11.png
other files
workdir/extracted_sp/bins11_2022-12-16_11-52-46/speclc1.158.txt
workdir/extracted_sp/bins11_2022-12-16_11-52-46/wvl_table.dat
Stage 30 (white)
directories
workdir/fit_white
workdir/fit_white/fit_2022-12-16_12-02-03_dec2022
workdir/fit_white/fit_2022-12-16_12-02-03_dec2022/fit_lc
workdir/fit_white/fit_2022-12-16_12-02-03_dec2022/lsq_res
workdir/fit_white/fit_2022-12-16_12-02-03_dec2022/mcmc_res
workdir/fit_white/fit_2022-12-16_12-02-03_dec2022/raw_lc
plots
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/fit_lc/lsq_lc_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/fit_lc/mcmc_lc_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/fit_lc/newfit_lc_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/lsq_res/corr_plot_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/lsq_res/lsq_params_vs_wvl.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/corr_plot_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/mcmc_chains_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/mcmc_chains_noburn_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/mcmc_pairs_bin0_wvl1.400.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/mcmc_params_vs_wvl.png
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/raw_lc/raw_lc_bin0_wvl1.400.png
other files
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/fit_lc/fit_lc_data_model_bin0_wvl1.400.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/fit_lc/fit_lc_data_nosys_bin0_wvl1.400.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/lsq_res/corr_data_bin0_wvl1.400.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/lsq_res/lsq_res_bin0_wvl1.400.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/corr_data_bin0_wvl1.400.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/mcmc_out_bin0_wvl1.400.p
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/mcmc_res/mcmc_res_bin0_wvl1.400.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/raw_lc/raw_lc_data_bin0_wvl1.400.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/fit_par.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/fit_results.txt
workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/obs_par.pcf
- workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/white_systematics.txt
file for divide white with the best systematics model after the least squares fit
- workdir/fit_white/fit_2022-12-16_14-51-31_dec2022/white_systematics_mcmc.txt
file for divide white with the best systematics model after the mcmc
Stage 30 (spec)
directories
workdir/fit_spec
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/fit_lc
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/lsq_res
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/raw_lc
plots
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/fit_lc/lsq_lc_bin0_wvl1.158.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/fit_lc/newfit_lc_bin0_wvl1.158.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/lsq_res/corr_plot_bin0_wvl1.158.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/lsq_res/lsq_params_vs_wvl.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/lsq_res/lsq_rprs.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/corr_plot_bin0_wvl1.158.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_chains_bin0_wvl1.158.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_chains_noburn_bin0_wvl1.158.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_pairs_bin0_wvl1.158.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_params_vs_wvl.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_rprs.png
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/raw_lc/raw_lc_bin0_wvl1.158.png
other files
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/fit_par.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/fit_results.txt
Here an example of a fit_resutlts.txt file:
wave
rms_pred
rms
chi2
chi2red
bic
ln_like
chi2_notrescaled
chi2red_notrescaled
bic_notrescaled
ln_like_notrescaled
npoints
nfree_param
dof
1.158
247.257
284.441
93.05
0.979
1711.148
-825.14
143.033
1.506
1714.698
-826.915
108
13
95
1.204
229.721
250.839
89.47
0.942
1714.542
-826.837
128.622
1.354
1714.493
-826.813
108
13
95
1.250
220.843
212.878
93.465
0.984
1695.436
-817.284
100.451
1.057
1694.637
-816.885
108
13
95
1.296
212.792
221.103
87.954
0.926
1719.518
-829.325
116.482
1.226
1717.707
-828.42
108
13
95
1.342
213.148
222.264
89.804
0.945
1719.704
-829.418
117.307
1.235
1718.353
-828.743
108
13
95
1.389
219.237
229.906
90.108
0.949
1716.892
-828.012
118.46
1.247
1715.699
-827.415
108
13
95
1.435
220.256
249.262
93.53
0.985
1730.668
-834.9
138.251
1.455
1733.184
-836.158
108
13
95
1.481
222.435
236.198
93.63
0.986
1714.989
-827.06
121.62
1.28
1714.731
-826.932
108
13
95
1.527
221.682
215.73
93.335
0.982
1697.484
-818.308
102.429
1.078
1696.537
-817.835
108
13
95
1.573
222.021
215.512
89.944
0.947
1696.632
-817.882
101.657
1.07
1695.124
-817.128
108
13
95
1.619
226.484
243.15
90.961
0.957
1714.84
-826.986
124.507
1.311
1714.482
-826.807
108
13
95
- It includes the following columns:
wave: mid wavelength of the bin
rms_pred: expected photon noise
rms: rms of residuals
chi2: chi squared:
= np.sum((self.resid/data.err)**2)
chi2red:
= chi2/dof
, with dof being the degrees of freedombic: baysian information criterium:
= -2. * ln_like + nfree_param * np.log(npoints)
ln_like: log likelihood
= (-0.5 * (np.sum((residuals/errors)**2 + np.log(2.0 * np.pi) + 2 * np.log(errors)))
npoints: number of data points
nfree_param: number of free parameters
dof: degree of freedom
The next parameters will just appear if the errorbars were rescaled in the analysis. So if either “meta.uncert_rescale = True” or “uncmulti” was used as a model. The “notrescaled” refers to the fact that for the calculation of these chi2, chi2red, bic and ln_like values, the original errorbars were NOT rescaled.
chi2_notrescaled
chi2red_notrescaled
bic_notrescaled
ln_like_notrescaled
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/obs_par.pcf
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/fit_lc/fit_lc_data_model_bin0_wvl1.158.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/fit_lc/fit_lc_data_nosys_bin0_wvl1.158.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/lsq_res/corr_data_bin0_wvl1.158.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/lsq_res/lsq_res_bin0_wvl1.158.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/lsq_res/lsq_rprs.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/corr_data_bin0_wvl1.158.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_out_bin0_wvl1.158.p
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_res_bin0_wvl1.158.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/mcmc_res/mcmc_rprs.txt
workdir/fit_spec/fit_2022-12-16_16-50-21_dec2022/raw_lc/raw_lc_data_bin1_wvl1.204.txt