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 freedom

    • bic: 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