Outputs

Here we summarize all the files created by PACMAN when doing a complete run from s00 to s30. This might be partially outdated as it was written during version v0.4.0, but it should give you a good overview of what to expect when running PACMAN and where to find the outputs. The biggest change introduced in v0.5.0 is the new directory structure for the outputs. Just keep this in mind.

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

    uncmulti

    uncmulti2

    npoints

    nfree_param

    dof

    1.158

    246.802

    286.915

    92.68

    0.997

    1719.58

    -824.674

    146.105

    1.571

    1727.16

    -828.464

    1.094

    1.197

    108

    15

    93

    1.204

    229.757

    257.53

    93.126

    1.001

    1729.006

    -829.387

    135.496

    1.457

    1731.096

    -830.432

    1.245

    1.550

    108

    15

    93

    1.250

    220.485

    207.115

    91.986

    0.989

    1699.328

    -814.548

    95.413

    1.026

    1698.917

    -814.343

    0.998

    0.996

    108

    15

    93

    1.296

    212.651

    220.969

    92.818

    0.998

    1727.863

    -828.816

    116.495

    1.253

    1727.217

    -828.493

    1.155

    1.334

    108

    15

    93

    1.342

    213.003

    225.596

    92.113

    0.99

    1731.679

    -830.723

    121.028

    1.301

    1731.572

    -830.67

    1.094

    1.197

    108

    15

    93

    1.389

    219.054

    232.501

    91.178

    0.98

    1728.695

    -829.232

    121.291

    1.304

    1728.057

    -828.913

    1.171

    1.371

    108

    15

    93

    1.435

    220.028

    247.525

    91.959

    0.989

    1739.173

    -834.471

    136.629

    1.469

    1741.127

    -835.447

    1.201

    1.442

    108

    15

    93

    1.481

    222.204

    236.528

    92.363

    0.993

    1721.558

    -825.663

    122.239

    1.314

    1724.92

    -827.344

    0.995

    0.990

    108

    15

    93

    1.527

    221.247

    209.07

    92.192

    0.991

    1699.052

    -814.41

    96.582

    1.039

    1700.062

    -814.915

    1.105

    1.221

    108

    15

    93

    1.573

    221.791

    219.103

    92.653

    0.996

    1708.669

    -819.218

    105.258

    1.132

    1708.287

    -819.028

    1.127

    1.270

    108

    15

    93

    1.619

    226.247

    246.182

    92.282

    0.992

    1722.812

    -826.29

    127.904

    1.375

    1727.441

    -828.605

    1.01

    1.020

    108

    15

    93
    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