.. _Outputs: 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 This might be partially outdated as it was written during version v0.4.0, but it should give you a good overview of what to expect when running PACMAN and where to find the outputs.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: .. include:: media/s30/spectroscopic/fit_results.txt 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