diff --git a/docs/examples/transmission_ftir/FIGURES/RESULTS/AC4_OL49_021920_30x30_H2O_a.pdf b/docs/examples/transmission_ftir/FIGURES/RESULTS/AC4_OL49_021920_30x30_H2O_a.pdf new file mode 100644 index 00000000..b5f127ce Binary files /dev/null and b/docs/examples/transmission_ftir/FIGURES/RESULTS/AC4_OL49_021920_30x30_H2O_a.pdf differ diff --git a/docs/examples/transmission_ftir/FIGURES/RESULTS/AC4_OL53_101220_256s_30x30_a.pdf b/docs/examples/transmission_ftir/FIGURES/RESULTS/AC4_OL53_101220_256s_30x30_a.pdf new file mode 100644 index 00000000..45865964 Binary files /dev/null and b/docs/examples/transmission_ftir/FIGURES/RESULTS/AC4_OL53_101220_256s_30x30_a.pdf differ diff --git a/docs/examples/transmission_ftir/FIGURES/RESULTS/STD_D1010_012821_256s_100x100_a.pdf b/docs/examples/transmission_ftir/FIGURES/RESULTS/STD_D1010_012821_256s_100x100_a.pdf new file mode 100644 index 00000000..535f5a80 Binary files /dev/null and b/docs/examples/transmission_ftir/FIGURES/RESULTS/STD_D1010_012821_256s_100x100_a.pdf differ diff --git a/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.log b/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.log new file mode 100644 index 00000000..69de85f1 --- /dev/null +++ b/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.log @@ -0,0 +1,140 @@ + +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + Multi-core Markov-chain Monte Carlo (mc3). + Version 3.1.2. + Copyright (c) 2015-2023 Patricio Cubillos and collaborators. + mc3 is open-source software under the MIT license (see LICENSE). +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + +Least-squares best-fitting parameters: + [ 1.10404705e+00 -1.05049313e+00 9.37626605e-01 -9.34063279e-02 + 3.00000000e-01 1.42799222e+03 2.88533201e+01 1.09429136e-01 + 1.51747427e+03 3.56110411e+01 1.06864326e-01 6.58349188e-01 + 1.12132097e-01 4.47459448e-02 -3.10092179e-04 1.23382528e+00] + +Start MCMC chains (Sat Sep 23 10:59:42 2023) + +[: ] 10.0% completed (Sat Sep 23 10:59:49 2023) +Out-of-bound Trials: +[ 0 0 0 0 4612 0 0 15 0 0 19 0 0 0 + 0 0] +Best Parameters: (chisq=367.7173) +[ 1.10404705e+00 -1.05049313e+00 9.37626605e-01 -9.34063279e-02 + 3.00000000e-01 1.42799222e+03 2.88533201e+01 1.09429136e-01 + 1.51747427e+03 3.56110411e+01 1.06864326e-01 6.58349188e-01 + 1.12132097e-01 4.47459448e-02 -3.10092179e-04 1.23382528e+00] + +[:: ] 20.0% completed (Sat Sep 23 10:59:56 2023) +Out-of-bound Trials: +[ 0 14 1 4 12417 0 14 17 0 1744 20 0 + 0 0 0 0] +Best Parameters: (chisq=367.7173) +[ 1.10404705e+00 -1.05049313e+00 9.37626605e-01 -9.34063279e-02 + 3.00000000e-01 1.42799222e+03 2.88533201e+01 1.09429136e-01 + 1.51747427e+03 3.56110411e+01 1.06864326e-01 6.58349188e-01 + 1.12132097e-01 4.47459448e-02 -3.10092179e-04 1.23382528e+00] + +[::: ] 30.0% completed (Sat Sep 23 11:00:03 2023) +Out-of-bound Trials: +[ 0 67 1 16 22237 0 40 17 0 4532 21 0 + 0 0 0 0] +Best Parameters: (chisq=367.7173) +[ 1.10404705e+00 -1.05049313e+00 9.37626605e-01 -9.34063279e-02 + 3.00000000e-01 1.42799222e+03 2.88533201e+01 1.09429136e-01 + 1.51747427e+03 3.56110411e+01 1.06864326e-01 6.58349188e-01 + 1.12132097e-01 4.47459448e-02 -3.10092179e-04 1.23382528e+00] +Gelman-Rubin statistics for free parameters: +[1.02758701 1.03006589 1.01013986 1.0302875 1.02151683 1.01362119 + 1.0110036 1.0053534 1.00140709 1.01411657 1.01396704 1.00354952 + 1.01455366 1.01528475 1.02960866 1.03066041] + +[:::: ] 40.0% completed (Sat Sep 23 11:00:09 2023) +Out-of-bound Trials: +[ 0 160 1 39 33385 1 89 19 0 7679 22 0 + 0 0 0 0] +Best Parameters: (chisq=367.7173) +[ 1.10404705e+00 -1.05049313e+00 9.37626605e-01 -9.34063279e-02 + 3.00000000e-01 1.42799222e+03 2.88533201e+01 1.09429136e-01 + 1.51747427e+03 3.56110411e+01 1.06864326e-01 6.58349188e-01 + 1.12132097e-01 4.47459448e-02 -3.10092179e-04 1.23382528e+00] +Gelman-Rubin statistics for free parameters: +[1.00527488 1.00566509 1.00341777 1.00622378 1.00378564 1.00362925 + 1.00630397 1.00306528 1.00288694 1.00395637 1.00293476 1.00197907 + 1.00446479 1.00464186 1.00590275 1.00612135] +All parameters converged to within 1% of unity. + +[::::: ] 50.0% completed (Sat Sep 23 11:00:15 2023) +Out-of-bound Trials: +[ 0 216 1 63 45334 3 144 21 0 11271 27 0 + 0 0 0 0] +Best Parameters: (chisq=367.7173) +[ 1.10404705e+00 -1.05049313e+00 9.37626605e-01 -9.34063279e-02 + 3.00000000e-01 1.42799222e+03 2.88533201e+01 1.09429136e-01 + 1.51747427e+03 3.56110411e+01 1.06864326e-01 6.58349188e-01 + 1.12132097e-01 4.47459448e-02 -3.10092179e-04 1.23382528e+00] +Gelman-Rubin statistics for free parameters: +[1.00268548 1.00294819 1.00238469 1.00267984 1.00061936 1.00236462 + 1.00208503 1.00269936 1.00242764 1.00203982 1.00139067 1.00107536 + 1.00141949 1.00245185 1.00298642 1.0030821 ] +All parameters converged to within 1% of unity. + +[:::::: ] 60.0% completed (Sat Sep 23 11:00:21 2023) +Out-of-bound Trials: +[ 0 330 1 94 58057 4 221 22 0 14546 27 0 + 0 0 0 0] +Best Parameters: (chisq=367.7173) +[ 1.10404705e+00 -1.05049313e+00 9.37626605e-01 -9.34063279e-02 + 3.00000000e-01 1.42799222e+03 2.88533201e+01 1.09429136e-01 + 1.51747427e+03 3.56110411e+01 1.06864326e-01 6.58349188e-01 + 1.12132097e-01 4.47459448e-02 -3.10092179e-04 1.23382528e+00] +Gelman-Rubin statistics for free parameters: +[1.00292304 1.00290511 1.00184638 1.00298012 1.00115232 1.00213002 + 1.00133658 1.00126697 1.0007134 1.00162299 1.00170958 1.00058701 + 1.00171359 1.00252559 1.00296456 1.00290198] +All parameters converged to within 1% of unity. + +All parameters satisfy the GR convergence threshold of 1.01, stopping +the MCMC. + +MCMC Summary: +------------- + Number of evaluated samples: 604860 + Number of parallel chains: 9 + Average iterations per chain: 67206 + Burned-in iterations per chain: 20000 + Thinning factor: 5 + MCMC sample size (thinned, burned): 84972 + Acceptance rate: 23.83% + +Parameter name best fit median 1sigma_low 1sigma_hi S/N +--------------- ----------- ----------------------------------- --------- +B_mean 1.1040e+00 1.1313e+00 -3.3272e-02 3.8583e-02 29.8 +B_PC1 -1.0505e+00 -7.6971e-01 -3.5850e-01 4.0680e-01 2.7 +B_PC2 9.3763e-01 9.3474e-01 -2.0511e-02 2.0134e-02 46.4 +B_PC3 -9.3406e-02 -5.8661e-02 -5.5937e-02 6.0893e-02 1.6 +B_PC4 3.0000e-01 2.7975e-01 -2.8528e-02 1.4793e-02 13.0 +G1430_peak 1.4280e+03 1.4280e+03 -1.4333e+00 1.4682e+00 988.3 +G1430_std 2.8853e+01 2.8798e+01 -1.1792e+00 1.2538e+00 23.7 +G1430_amp 1.0943e-01 1.0865e-01 -4.0474e-03 4.0273e-03 27.2 +G1515_peak 1.5175e+03 1.5176e+03 -1.5526e+00 1.5446e+00 987.8 +G1515_std 3.5611e+01 3.5889e+01 -2.0729e+00 2.1202e+00 18.1 +G1515_amp 1.0686e-01 1.0685e-01 -3.5914e-03 3.4978e-03 30.2 +H1635_mean 6.5835e-01 6.5862e-01 -3.0742e-03 3.0234e-03 215.4 +H1635_PC1 1.1213e-01 1.1006e-01 -1.5937e-02 1.6761e-02 6.9 +H1635_PC2 4.4746e-02 4.3519e-02 -2.0578e-02 1.9659e-02 2.2 +m -3.1009e-04 -2.6229e-04 -6.0538e-05 6.9422e-05 4.6 +b 1.2338e+00 1.2196e+00 -2.1480e-02 1.9352e-02 58.8 + + Best-parameter's chi-squared: 366.4053 + Best-parameter's -2*log(posterior): 367.7173 + Bayesian Information Criterion: 468.6492 + Reduced chi-squared: 0.6317 + Standard deviation of residuals: 0.00784075 + +For a detailed summary with all parameter posterior statistics see +/Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a_statistics.txt + +Output sampler files: + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a_statistics.txt + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.npz + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.log diff --git a/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.log b/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.log new file mode 100644 index 00000000..8169a8f3 --- /dev/null +++ b/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.log @@ -0,0 +1,139 @@ + +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + Multi-core Markov-chain Monte Carlo (mc3). + Version 3.1.2. + Copyright (c) 2015-2023 Patricio Cubillos and collaborators. + mc3 is open-source software under the MIT license (see LICENSE). +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + +Least-squares best-fitting parameters: + [ 5.11735236e-01 -2.96327877e+00 2.75707715e-01 -5.06637046e-01 + 2.26248986e-01 1.42725865e+03 3.43512091e+01 5.02432187e-02 + 1.51923346e+03 3.24143045e+01 5.30599427e-02 2.99675069e-01 + -5.25464614e-02 4.67980624e-02 -4.44873222e-04 7.21255305e-01] + +Start MCMC chains (Sat Sep 23 11:00:45 2023) + +[: ] 10.0% completed (Sat Sep 23 11:00:52 2023) +Out-of-bound Trials: +[ 0 18551 0 26 0 2 0 352 4 0 82 1 + 0 0 0 0] +Best Parameters: (chisq=49.7843) +[ 5.11735236e-01 -2.96327877e+00 2.75707715e-01 -5.06637046e-01 + 2.26248986e-01 1.42725865e+03 3.43512091e+01 5.02432187e-02 + 1.51923346e+03 3.24143045e+01 5.30599427e-02 2.99675069e-01 + -5.25464614e-02 4.67980624e-02 -4.44873222e-04 7.21255305e-01] + +[:: ] 20.0% completed (Sat Sep 23 11:00:59 2023) +Out-of-bound Trials: +[ 1 23222 0 240 150 101 1322 372 14 1027 86 1 + 0 0 0 0] +Best Parameters: (chisq=49.7843) +[ 5.11735236e-01 -2.96327877e+00 2.75707715e-01 -5.06637046e-01 + 2.26248986e-01 1.42725865e+03 3.43512091e+01 5.02432187e-02 + 1.51923346e+03 3.24143045e+01 5.30599427e-02 2.99675069e-01 + -5.25464614e-02 4.67980624e-02 -4.44873222e-04 7.21255305e-01] + +[::: ] 30.0% completed (Sat Sep 23 11:01:07 2023) +Out-of-bound Trials: +[ 3 31661 0 916 755 234 3874 383 42 2559 90 2 + 0 0 0 0] +Best Parameters: (chisq=49.7843) +[ 5.11735236e-01 -2.96327877e+00 2.75707715e-01 -5.06637046e-01 + 2.26248986e-01 1.42725865e+03 3.43512091e+01 5.02432187e-02 + 1.51923346e+03 3.24143045e+01 5.30599427e-02 2.99675069e-01 + -5.25464614e-02 4.67980624e-02 -4.44873222e-04 7.21255305e-01] +Gelman-Rubin statistics for free parameters: +[1.0331394 1.03454814 1.00977936 1.02099123 1.02667308 1.019098 + 1.026297 1.00112975 1.00917225 1.01897136 1.00705804 1.00581763 + 1.00958724 1.01509338 1.03437309 1.03342544] + +[:::: ] 40.0% completed (Sat Sep 23 11:01:14 2023) +Out-of-bound Trials: +[ 10 41599 0 1677 1443 435 7029 397 80 4221 99 2 + 0 0 0 0] +Best Parameters: (chisq=49.7843) +[ 5.11735236e-01 -2.96327877e+00 2.75707715e-01 -5.06637046e-01 + 2.26248986e-01 1.42725865e+03 3.43512091e+01 5.02432187e-02 + 1.51923346e+03 3.24143045e+01 5.30599427e-02 2.99675069e-01 + -5.25464614e-02 4.67980624e-02 -4.44873222e-04 7.21255305e-01] +Gelman-Rubin statistics for free parameters: +[1.01115427 1.01212427 1.00163074 1.01074558 1.00498583 1.0035084 + 1.01366423 1.00096845 1.002415 1.00462555 1.00209489 1.00082206 + 1.00078257 1.00207599 1.01186969 1.01226642] + +[::::: ] 50.0% completed (Sat Sep 23 11:01:21 2023) +Out-of-bound Trials: +[ 11 52210 0 2587 2253 669 10543 415 114 6160 105 2 + 0 0 0 0] +Best Parameters: (chisq=49.7843) +[ 5.11735236e-01 -2.96327877e+00 2.75707715e-01 -5.06637046e-01 + 2.26248986e-01 1.42725865e+03 3.43512091e+01 5.02432187e-02 + 1.51923346e+03 3.24143045e+01 5.30599427e-02 2.99675069e-01 + -5.25464614e-02 4.67980624e-02 -4.44873222e-04 7.21255305e-01] +Gelman-Rubin statistics for free parameters: +[1.00274988 1.00297377 1.00189966 1.00290737 1.00196551 1.0014147 + 1.0043706 1.00178592 1.00120418 1.00275346 1.00105156 1.00155051 + 1.00069121 1.00211739 1.00292017 1.00299406] +All parameters converged to within 1% of unity. + +[:::::: ] 60.0% completed (Sat Sep 23 11:01:28 2023) +Out-of-bound Trials: +[ 15 63110 0 3484 3254 874 14418 431 174 8392 113 2 + 0 0 0 0] +Best Parameters: (chisq=49.7843) +[ 5.11735236e-01 -2.96327877e+00 2.75707715e-01 -5.06637046e-01 + 2.26248986e-01 1.42725865e+03 3.43512091e+01 5.02432187e-02 + 1.51923346e+03 3.24143045e+01 5.30599427e-02 2.99675069e-01 + -5.25464614e-02 4.67980624e-02 -4.44873222e-04 7.21255305e-01] +Gelman-Rubin statistics for free parameters: +[1.00136932 1.00146962 1.00158353 1.00134223 1.00130049 1.00112265 + 1.00297882 1.00130396 1.00030204 1.00295048 1.00121805 1.00153511 + 1.00116868 1.00163784 1.0014347 1.00144199] +All parameters converged to within 1% of unity. + +All parameters satisfy the GR convergence threshold of 1.01, stopping +the MCMC. + +MCMC Summary: +------------- + Number of evaluated samples: 604670 + Number of parallel chains: 9 + Average iterations per chain: 67185 + Burned-in iterations per chain: 20000 + Thinning factor: 5 + MCMC sample size (thinned, burned): 84934 + Acceptance rate: 23.91% + +Parameter name best fit median 1sigma_low 1sigma_hi S/N +--------------- ----------- ----------------------------------- --------- +B_mean 5.1174e-01 5.5602e-01 -3.3889e-02 5.3078e-02 11.7 +B_PC1 -2.9633e+00 -2.5085e+00 -3.4928e-01 5.5367e-01 6.6 +B_PC2 2.7571e-01 2.6984e-01 -2.1082e-02 2.0490e-02 13.4 +B_PC3 -5.0664e-01 -4.4857e-01 -4.8410e-02 7.2774e-02 8.2 +B_PC4 2.2625e-01 1.8934e-01 -4.6524e-02 3.8298e-02 5.3 +G1430_peak 1.4273e+03 1.4271e+03 -3.0366e+00 3.1965e+00 458.0 +G1430_std 3.4351e+01 3.4442e+01 -3.0058e+00 2.9100e+00 12.3 +G1430_amp 5.0243e-02 4.9892e-02 -4.3164e-03 4.5145e-03 11.5 +G1515_peak 1.5192e+03 1.5195e+03 -2.7836e+00 2.6822e+00 550.3 +G1515_std 3.2414e+01 3.3084e+01 -2.7336e+00 3.0069e+00 11.8 +G1515_amp 5.3060e-02 5.3340e-02 -3.7498e-03 3.7488e-03 14.2 +H1635_mean 2.9968e-01 3.0016e-01 -3.0700e-03 3.0477e-03 96.7 +H1635_PC1 -5.2546e-02 -5.5400e-02 -1.6189e-02 1.6408e-02 3.2 +H1635_PC2 4.6798e-02 4.6252e-02 -1.8050e-02 1.7189e-02 2.6 +m -4.4487e-04 -3.6764e-04 -5.9283e-05 9.4660e-05 5.8 +b 7.2126e-01 6.9815e-01 -2.8336e-02 1.7699e-02 31.2 + + Best-parameter's chi-squared: 48.7939 + Best-parameter's -2*log(posterior): 49.7843 + Bayesian Information Criterion: 151.0377 + Reduced chi-squared: 0.0841 + Standard deviation of residuals: 0.00286127 + +For a detailed summary with all parameter posterior statistics see +/Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL53_101220_256s_30x30_a_statistics.txt + +Output sampler files: + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL53_101220_256s_30x30_a_statistics.txt + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.npz + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.log diff --git a/docs/examples/transmission_ftir/LOGFILES/RESULTS/STD_D1010_012821_256s_100x100_a.log b/docs/examples/transmission_ftir/LOGFILES/RESULTS/STD_D1010_012821_256s_100x100_a.log new file mode 100644 index 00000000..a3e920e3 --- /dev/null +++ b/docs/examples/transmission_ftir/LOGFILES/RESULTS/STD_D1010_012821_256s_100x100_a.log @@ -0,0 +1,140 @@ + +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + Multi-core Markov-chain Monte Carlo (mc3). + Version 3.1.2. + Copyright (c) 2015-2023 Patricio Cubillos and collaborators. + mc3 is open-source software under the MIT license (see LICENSE). +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + +Least-squares best-fitting parameters: + [ 4.00000000e+00 7.61701619e-01 -4.43002861e-01 -3.78998982e-01 + 1.78618384e-01 1.43145229e+03 3.10666651e+01 6.75782626e-02 + 1.52297536e+03 3.53705344e+01 7.55599753e-02 1.73486516e-01 + 7.66582441e-02 -2.79768767e-02 -2.32146688e-04 2.46235255e+00] + +Start MCMC chains (Sat Sep 23 11:01:54 2023) + +[: ] 10.0% completed (Sat Sep 23 11:02:01 2023) +Out-of-bound Trials: +[20054 0 0 44 20 1 6 101 6 0 72 17 + 0 0 0 0] +Best Parameters: (chisq=1772.7011) +[ 4.00000000e+00 7.61701619e-01 -4.43002861e-01 -3.78998982e-01 + 1.78618384e-01 1.43145229e+03 3.10666651e+01 6.75782626e-02 + 1.52297536e+03 3.53705344e+01 7.55599753e-02 1.73486516e-01 + 7.66582441e-02 -2.79768767e-02 -2.32146688e-04 2.46235255e+00] + +[:: ] 20.0% completed (Sat Sep 23 11:02:08 2023) +Out-of-bound Trials: +[35608 0 0 87 67 2 50 120 23 29 81 22 + 0 0 0 0] +Best Parameters: (chisq=1772.7011) +[ 4.00000000e+00 7.61701619e-01 -4.43002861e-01 -3.78998982e-01 + 1.78618384e-01 1.43145229e+03 3.10666651e+01 6.75782626e-02 + 1.52297536e+03 3.53705344e+01 7.55599753e-02 1.73486516e-01 + 7.66582441e-02 -2.79768767e-02 -2.32146688e-04 2.46235255e+00] + +[::: ] 30.0% completed (Sat Sep 23 11:02:15 2023) +Out-of-bound Trials: +[49957 0 0 113 171 16 361 127 71 2089 84 24 + 0 0 0 0] +Best Parameters: (chisq=1772.7011) +[ 4.00000000e+00 7.61701619e-01 -4.43002861e-01 -3.78998982e-01 + 1.78618384e-01 1.43145229e+03 3.10666651e+01 6.75782626e-02 + 1.52297536e+03 3.53705344e+01 7.55599753e-02 1.73486516e-01 + 7.66582441e-02 -2.79768767e-02 -2.32146688e-04 2.46235255e+00] +Gelman-Rubin statistics for free parameters: +[1.00837284 1.00468118 1.00566582 1.01259324 1.02649752 1.01680349 + 1.0162433 1.02308003 1.01211999 1.0274273 1.01395626 1.00249493 + 1.0016592 1.00944999 1.00428025 1.00423129] + +[:::: ] 40.0% completed (Sat Sep 23 11:02:21 2023) +Out-of-bound Trials: +[65068 1 0 151 279 40 744 132 132 5942 85 25 + 0 0 0 0] +Best Parameters: (chisq=1772.7011) +[ 4.00000000e+00 7.61701619e-01 -4.43002861e-01 -3.78998982e-01 + 1.78618384e-01 1.43145229e+03 3.10666651e+01 6.75782626e-02 + 1.52297536e+03 3.53705344e+01 7.55599753e-02 1.73486516e-01 + 7.66582441e-02 -2.79768767e-02 -2.32146688e-04 2.46235255e+00] +Gelman-Rubin statistics for free parameters: +[1.00235187 1.00272771 1.00046184 1.00407381 1.00926483 1.0030351 + 1.00783818 1.00650083 1.00416929 1.00411072 1.00185228 1.00081555 + 1.00069837 1.00196534 1.00160955 1.00206071] +All parameters converged to within 1% of unity. + +[::::: ] 50.0% completed (Sat Sep 23 11:02:30 2023) +Out-of-bound Trials: +[80325 3 0 204 401 74 1157 145 205 10161 87 26 + 0 0 0 0] +Best Parameters: (chisq=1772.7011) +[ 4.00000000e+00 7.61701619e-01 -4.43002861e-01 -3.78998982e-01 + 1.78618384e-01 1.43145229e+03 3.10666651e+01 6.75782626e-02 + 1.52297536e+03 3.53705344e+01 7.55599753e-02 1.73486516e-01 + 7.66582441e-02 -2.79768767e-02 -2.32146688e-04 2.46235255e+00] +Gelman-Rubin statistics for free parameters: +[1.00241734 1.00095907 1.00064742 1.0019688 1.00751344 1.00155616 + 1.00590603 1.00595566 1.00408932 1.00251899 1.00173514 1.00066281 + 1.00099891 1.00147261 1.00059378 1.00064195] +All parameters converged to within 1% of unity. + +[:::::: ] 60.0% completed (Sat Sep 23 11:02:39 2023) +Out-of-bound Trials: +[95365 3 1 253 554 101 1718 155 294 14391 92 28 + 0 0 0 0] +Best Parameters: (chisq=1772.7011) +[ 4.00000000e+00 7.61701619e-01 -4.43002861e-01 -3.78998982e-01 + 1.78618384e-01 1.43145229e+03 3.10666651e+01 6.75782626e-02 + 1.52297536e+03 3.53705344e+01 7.55599753e-02 1.73486516e-01 + 7.66582441e-02 -2.79768767e-02 -2.32146688e-04 2.46235255e+00] +Gelman-Rubin statistics for free parameters: +[1.00336399 1.00156652 1.00019826 1.00097954 1.00383614 1.00154828 + 1.00150362 1.00233212 1.00133135 1.00128961 1.00098111 1.00043188 + 1.00075433 1.00102829 1.00144164 1.00081972] +All parameters converged to within 1% of unity. + +All parameters satisfy the GR convergence threshold of 1.01, stopping +the MCMC. + +MCMC Summary: +------------- + Number of evaluated samples: 604310 + Number of parallel chains: 9 + Average iterations per chain: 67145 + Burned-in iterations per chain: 20000 + Thinning factor: 5 + MCMC sample size (thinned, burned): 84862 + Acceptance rate: 20.66% + +Parameter name best fit median 1sigma_low 1sigma_hi S/N +--------------- ----------- ----------------------------------- --------- +B_mean 4.0000e+00 3.9956e+00 -7.2386e-03 3.2846e-03 649.6 +B_PC1 7.6170e-01 7.0442e-01 -1.0035e-01 9.0532e-02 7.7 +B_PC2 -4.4300e-01 -4.4216e-01 -1.9455e-02 1.9055e-02 23.0 +B_PC3 -3.7900e-01 -3.8707e-01 -2.6904e-02 2.7093e-02 14.2 +B_PC4 1.7862e-01 1.8403e-01 -2.2563e-02 2.4223e-02 7.5 +G1430_peak 1.4315e+03 1.4316e+03 -2.1456e+00 2.3127e+00 634.9 +G1430_std 3.1067e+01 3.1350e+01 -2.2564e+00 2.4540e+00 13.2 +G1430_amp 6.7578e-02 6.7431e-02 -3.9488e-03 4.0386e-03 16.8 +G1515_peak 1.5230e+03 1.5233e+03 -2.2911e+00 2.4630e+00 641.3 +G1515_std 3.5371e+01 3.5564e+01 -2.4867e+00 2.4977e+00 15.1 +G1515_amp 7.5560e-02 7.5170e-02 -3.4146e-03 3.3721e-03 22.3 +H1635_mean 1.7349e-01 1.7336e-01 -3.1376e-03 2.9724e-03 56.4 +H1635_PC1 7.6658e-02 7.8227e-02 -1.6552e-02 1.6291e-02 4.7 +H1635_PC2 -2.7977e-02 -3.0304e-02 -2.1832e-02 2.0880e-02 1.3 +m -2.3215e-04 -2.4152e-04 -1.4502e-05 1.2273e-05 16.2 +b 2.4624e+00 2.4653e+00 -6.2171e-03 6.5585e-03 381.2 + + Best-parameter's chi-squared: 1771.5019 + Best-parameter's -2*log(posterior): 1772.7011 + Bayesian Information Criterion: 1873.7457 + Reduced chi-squared: 3.0543 + Standard deviation of residuals: 0.0172404 + +For a detailed summary with all parameter posterior statistics see +/Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/STD_D1010_012821_256s_100x100_a_statistics.txt + +Output sampler files: + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/STD_D1010_012821_256s_100x100_a_statistics.txt + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/STD_D1010_012821_256s_100x100_a.npz + /Users/sarahcshi/Documents/GitHub/PyIRoGlass/docs/examples/transmission_ftir/LOGFILES/RESULTS/STD_D1010_012821_256s_100x100_a.log diff --git a/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a_statistics.txt b/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a_statistics.txt new file mode 100644 index 00000000..12aafe58 --- /dev/null +++ b/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a_statistics.txt @@ -0,0 +1,159 @@ +Summary of posterior statistics: + +Parameter estimates: + Median Mean Max-posterior Mode Parameter + 1.1312615e+00 1.1341086e+00 1.1040470e+00 1.1273989e+00 B_mean +-7.6971015e-01 -7.4229375e-01 -1.0504931e+00 -7.9339637e-01 B_PC1 + 9.3474305e-01 9.3463438e-01 9.3762661e-01 9.3843078e-01 B_PC2 +-5.8661484e-02 -5.6394904e-02 -9.3406328e-02 -6.0238088e-02 B_PC3 + 2.7975307e-01 2.7350553e-01 3.0000000e-01 2.9335249e-01 B_PC4 + 1.4279746e+03 1.4279965e+03 1.4279922e+03 1.4280344e+03 G1430_peak + 2.8797820e+01 2.8838643e+01 2.8853320e+01 2.8698270e+01 G1430_std + 1.0864800e-01 1.0863858e-01 1.0942914e-01 1.0889142e-01 G1430_amp + 1.5175858e+03 1.5175772e+03 1.5174743e+03 1.5175989e+03 G1515_peak + 3.5888771e+01 3.5883545e+01 3.5611041e+01 3.5835909e+01 G1515_std + 1.0684642e-01 1.0682782e-01 1.0686433e-01 1.0725752e-01 G1515_amp + 6.5862106e-01 6.5861276e-01 6.5834919e-01 6.5847198e-01 H1635_mean + 1.1006254e-01 1.1030862e-01 1.1213210e-01 1.0627922e-01 H1635_PC1 + 4.3519402e-02 4.3264924e-02 4.4745945e-02 4.5065905e-02 H1635_PC2 +-2.6228605e-04 -2.5770726e-04 -3.1009218e-04 -2.6859585e-04 m + 1.2195531e+00 1.2183500e+00 1.2338253e+00 1.2230514e+00 b + + Std_deviation Parameter + 3.7062114e-02 B_mean + 3.9393738e-01 B_PC1 + 2.0213306e-02 B_PC2 + 5.9287830e-02 B_PC3 + 2.3043209e-02 B_PC4 + 1.4448643e+00 G1430_peak + 1.2162066e+00 G1430_std + 4.0247397e-03 G1430_amp + 1.5362417e+00 G1515_peak + 1.9726351e+00 G1515_std + 3.5385520e-03 G1515_amp + 3.0559226e-03 H1635_mean + 1.6367578e-02 H1635_PC1 + 2.0154466e-02 H1635_PC2 + 6.6737217e-05 m + 2.0987716e-02 b + +Central quintile credible intervals: + 2sigma_low 1sigma_low 1sigma_up 2sigma_up Parameter + 1.0682970e+00 1.0979892e+00 1.1698444e+00 1.2183340e+00 B_mean +-1.4562034e+00 -1.1282135e+00 -3.6290853e-01 1.4286657e-01 B_PC1 + 8.9421776e-01 9.1423226e-01 9.5487731e-01 9.7490949e-01 B_PC2 +-1.6919698e-01 -1.1459828e-01 2.2312578e-03 6.7265786e-02 B_PC3 + 2.1350933e-01 2.5122494e-01 2.9454632e-01 2.9923783e-01 B_PC4 + 1.4251965e+03 1.4265413e+03 1.4294427e+03 1.4309371e+03 G1430_peak + 2.6494186e+01 2.7618615e+01 3.0051606e+01 3.1366919e+01 G1430_std + 1.0058249e-01 1.0460057e-01 1.1267529e-01 1.1665124e-01 G1430_amp + 1.5144502e+03 1.5160332e+03 1.5191304e+03 1.5205853e+03 G1515_peak + 3.2023446e+01 3.3815877e+01 3.8008992e+01 3.9546496e+01 G1515_std + 9.9826625e-02 1.0325503e-01 1.1034422e-01 1.1399433e-01 G1515_amp + 6.5250302e-01 6.5554685e-01 6.6164450e-01 6.6474021e-01 H1635_mean + 7.7802827e-02 9.4125797e-02 1.2682353e-01 1.4374875e-01 H1635_PC1 + 2.4753596e-03 2.2941155e-02 6.3178064e-02 8.3032975e-02 H1635_PC2 +-3.7689551e-04 -3.2282385e-04 -1.9286429e-04 -1.0679358e-04 m + 1.1719883e+00 1.1980732e+00 1.2389048e+00 1.2567209e+00 b + +Highest-posterior-density credible intervals: + 2sigma_low 1sigma_low 1sigma_up 2sigma_up Parameter + 1.0623850e+00 1.0933198e+00 1.1650279e+00 1.2115823e+00 B_mean +-1.5176815e+00 -1.1752148e+00 -4.1157791e-01 7.8723797e-02 B_PC1 + 8.9376194e-01 9.1407971e-01 9.5496733e-01 9.7503302e-01 B_PC2 +-1.7347206e-01 -1.1812380e-01 -7.6646409e-04 6.5524572e-02 B_PC3 + 2.2594584e-01 2.6659859e-01 2.9999977e-01 2.9999977e-01 B_PC4 + 1.4251484e+03 1.4264879e+03 1.4294002e+03 1.4309353e+03 G1430_peak + 2.6424534e+01 2.7540732e+01 2.9991642e+01 3.1326355e+01 G1430_std + 1.0046798e-01 1.0452770e-01 1.1268637e-01 1.1667746e-01 G1430_amp + 1.5144646e+03 1.5160255e+03 1.5191391e+03 1.5206379e+03 G1515_peak + 3.2316667e+01 3.3827565e+01 3.8011305e+01 3.9726378e+01 G1515_std + 9.9669429e-02 1.0323411e-01 1.1037304e-01 1.1392817e-01 G1515_amp + 6.5247344e-01 6.5549602e-01 6.6164996e-01 6.6479686e-01 H1635_mean + 7.7435360e-02 9.3898128e-02 1.2673296e-01 1.4383066e-01 H1635_PC1 + 1.9769071e-03 2.3204998e-02 6.3762734e-02 8.3149907e-02 H1635_PC2 +-3.8835015e-04 -3.3073764e-04 -2.0101891e-04 -1.1912944e-04 m + 1.1749491e+00 1.1998642e+00 1.2408877e+00 1.2596715e+00 b + + +LaTeX format +Median and 1sigma central-quantile statistics +$\overline{B}$ & $1.131^{+0.039}_{-0.033}$ +$\overline{B}_{PC1}$ & $-0.77^{+0.41}_{-0.36}$ +$\overline{B}_{PC2}$ & $0.935^{+0.020}_{-0.021}$ +$\overline{B}_{PC3}$ & $-0.059^{+0.061}_{-0.056}$ +$\overline{B}_{PC4}$ & $0.280^{+0.015}_{-0.029}$ +$\mu_{1430}$ & $1428.0^{+1.5}_{-1.4}$ +$\sigma_{1430}$ & $28.8^{+1.3}_{-1.2}$ +$a_{1430}$ & $0.1086^{+0.0040}_{-0.0040}$ +$\mu_{1515}$ & $1517.6^{+1.5}_{-1.6}$ +$\sigma_{1515}$ & $35.9^{+2.1}_{-2.1}$ +$a_{1515}$ & $0.1068^{+0.0035}_{-0.0036}$ +$\overline{H_{1635}}$ & $0.6586^{+0.0030}_{-0.0031}$ +$\overline{H_{1635}}_{PC1}$ & $0.110^{+0.017}_{-0.016}$ +$\overline{H_{1635}}_{PC2}$ & $0.044^{+0.020}_{-0.021}$ +$m$ & $-0.000262^{+0.000069}_{-0.000061}$ +$b$ & $1.220^{+0.019}_{-0.021}$ + +Median and 2sigma central-quantile statistics +$\overline{B}$ & $1.131^{+0.087}_{-0.063}$ +$\overline{B}_{PC1}$ & $-0.77^{+0.91}_{-0.69}$ +$\overline{B}_{PC2}$ & $0.935^{+0.040}_{-0.041}$ +$\overline{B}_{PC3}$ & $-0.06^{+0.13}_{-0.11}$ +$\overline{B}_{PC4}$ & $0.280^{+0.019}_{-0.066}$ +$\mu_{1430}$ & $1428.0^{+3.0}_{-2.8}$ +$\sigma_{1430}$ & $28.8^{+2.6}_{-2.3}$ +$a_{1430}$ & $0.1086^{+0.0080}_{-0.0081}$ +$\mu_{1515}$ & $1517.6^{+3.0}_{-3.1}$ +$\sigma_{1515}$ & $35.9^{+3.7}_{-3.9}$ +$a_{1515}$ & $0.1068^{+0.0071}_{-0.0070}$ +$\overline{H_{1635}}$ & $0.6586^{+0.0061}_{-0.0061}$ +$\overline{H_{1635}}_{PC1}$ & $0.110^{+0.034}_{-0.032}$ +$\overline{H_{1635}}_{PC2}$ & $0.044^{+0.040}_{-0.041}$ +$m$ & $-0.00026^{+0.00016}_{-0.00011}$ +$b$ & $1.220^{+0.037}_{-0.048}$ + +Marginal max_posterior (mode) and 1sigma-HPD statistics +$\overline{B}$ & $1.127^{+0.038}_{-0.034}$ +$\overline{B}_{PC1}$ & $-0.79^{+0.38}_{-0.38}$ +$\overline{B}_{PC2}$ & $0.938^{+0.017}_{-0.024}$ +$\overline{B}_{PC3}$ & $-0.060^{+0.059}_{-0.058}$ +$\overline{B}_{PC4}$ & $0.2934^{+0.0066}_{-0.0268}$ +$\mu_{1430}$ & $1428.0^{+1.4}_{-1.5}$ +$\sigma_{1430}$ & $28.7^{+1.3}_{-1.2}$ +$a_{1430}$ & $0.1089^{+0.0038}_{-0.0044}$ +$\mu_{1515}$ & $1517.6^{+1.5}_{-1.6}$ +$\sigma_{1515}$ & $35.8^{+2.2}_{-2.0}$ +$a_{1515}$ & $0.1073^{+0.0031}_{-0.0040}$ +$\overline{H_{1635}}$ & $0.6585^{+0.0032}_{-0.0030}$ +$\overline{H_{1635}}_{PC1}$ & $0.106^{+0.020}_{-0.012}$ +$\overline{H_{1635}}_{PC2}$ & $0.045^{+0.019}_{-0.022}$ +$m$ & $-0.000269^{+0.000068}_{-0.000062}$ +$b$ & $1.223^{+0.018}_{-0.023}$ + +Marginal max_posterior (mode) and 2sigma-HPD statistics +$\overline{B}$ & $1.127^{+0.084}_{-0.065}$ +$\overline{B}_{PC1}$ & $-0.79^{+0.87}_{-0.72}$ +$\overline{B}_{PC2}$ & $0.938^{+0.037}_{-0.045}$ +$\overline{B}_{PC3}$ & $-0.06^{+0.13}_{-0.11}$ +$\overline{B}_{PC4}$ & $0.2934^{+0.0066}_{-0.0674}$ +$\mu_{1430}$ & $1428.0^{+2.9}_{-2.9}$ +$\sigma_{1430}$ & $28.7^{+2.6}_{-2.3}$ +$a_{1430}$ & $0.1089^{+0.0078}_{-0.0084}$ +$\mu_{1515}$ & $1517.6^{+3.0}_{-3.1}$ +$\sigma_{1515}$ & $35.8^{+3.9}_{-3.5}$ +$a_{1515}$ & $0.1073^{+0.0067}_{-0.0076}$ +$\overline{H_{1635}}$ & $0.6585^{+0.0063}_{-0.0060}$ +$\overline{H_{1635}}_{PC1}$ & $0.106^{+0.038}_{-0.029}$ +$\overline{H_{1635}}_{PC2}$ & $0.045^{+0.038}_{-0.043}$ +$m$ & $-0.00027^{+0.00015}_{-0.00012}$ +$b$ & $1.223^{+0.037}_{-0.048}$ + + +Best-parameter's chi-squared: 366.4053 +Best-parameter's -2*log(posterior): 367.7173 +Bayesian Information Criterion: 468.6492 +Reduced chi-squared: 0.6317 +Standard deviation of residuals: 0.00784075 + + diff --git a/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL53_101220_256s_30x30_a_statistics.txt b/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL53_101220_256s_30x30_a_statistics.txt new file mode 100644 index 00000000..f0cbe780 --- /dev/null +++ b/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL53_101220_256s_30x30_a_statistics.txt @@ -0,0 +1,159 @@ +Summary of posterior statistics: + +Parameter estimates: + Median Mean Max-posterior Mode Parameter + 5.5602450e-01 5.6471872e-01 5.1173524e-01 5.2747018e-01 B_mean +-2.5084621e+00 -2.4133297e+00 -2.9632788e+00 -2.8322020e+00 B_PC1 + 2.6983778e-01 2.6969458e-01 2.7570772e-01 2.6836194e-01 B_PC2 +-4.4857216e-01 -4.3774214e-01 -5.0663705e-01 -4.7596326e-01 B_PC3 + 1.8934215e-01 1.8556955e-01 2.2624899e-01 1.9639099e-01 B_PC4 + 1.4270649e+03 1.4271332e+03 1.4272587e+03 1.4268812e+03 G1430_peak + 3.4441710e+01 3.4370266e+01 3.4351209e+01 3.4548718e+01 G1430_std + 4.9891647e-02 4.9954742e-02 5.0243219e-02 4.9668236e-02 G1430_amp + 1.5194851e+03 1.5194489e+03 1.5192335e+03 1.5196551e+03 G1515_peak + 3.3083638e+01 3.3179866e+01 3.2414305e+01 3.2820706e+01 G1515_std + 5.3339853e-02 5.3352648e-02 5.3059943e-02 5.3249529e-02 G1515_amp + 3.0016009e-01 3.0016284e-01 2.9967507e-01 3.0046086e-01 H1635_mean +-5.5400086e-02 -5.5388354e-02 -5.2546461e-02 -5.5487067e-02 H1635_PC1 + 4.6251965e-02 4.5840618e-02 4.6798062e-02 4.7941618e-02 H1635_PC2 +-3.6763536e-04 -3.5151763e-04 -4.4487322e-04 -4.2198790e-04 m + 6.9815119e-01 6.9325587e-01 7.2125530e-01 7.1358296e-01 b + + Std_deviation Parameter + 4.3885476e-02 B_mean + 4.4954720e-01 B_PC1 + 2.0597816e-02 B_PC2 + 6.1669411e-02 B_PC3 + 4.2384325e-02 B_PC4 + 3.1164426e+00 G1430_peak + 2.8015157e+00 G1430_std + 4.3838876e-03 G1430_amp + 2.7609119e+00 G1515_peak + 2.7549499e+00 G1515_std + 3.7458640e-03 G1515_amp + 3.0991015e-03 H1635_mean + 1.6509230e-02 H1635_PC1 + 1.7747109e-02 H1635_PC2 + 7.6608647e-05 m + 2.3113135e-02 b + +Central quintile credible intervals: + 2sigma_low 1sigma_low 1sigma_up 2sigma_up Parameter + 5.0568437e-01 5.2213512e-01 6.0910253e-01 6.7223321e-01 B_mean +-2.9786694e+00 -2.8577471e+00 -1.9547888e+00 -1.3050302e+00 B_PC1 + 2.2837900e-01 2.4875596e-01 2.9032821e-01 3.1034384e-01 B_PC2 +-5.3123066e-01 -4.9698231e-01 -3.7579805e-01 -2.8932234e-01 B_PC3 + 9.1725405e-02 1.4281776e-01 2.2764033e-01 2.6018528e-01 B_PC4 + 1.4210485e+03 1.4240282e+03 1.4302614e+03 1.4335014e+03 G1430_peak + 2.8676812e+01 3.1435918e+01 3.7351685e+01 3.9447588e+01 G1430_std + 4.1271249e-02 4.5575273e-02 5.4406161e-02 5.8757607e-02 G1430_amp + 1.5138591e+03 1.5167015e+03 1.5221673e+03 1.5249395e+03 G1515_peak + 2.7949262e+01 3.0350013e+01 3.6090527e+01 3.8793278e+01 G1515_std + 4.5975399e-02 4.9590045e-02 5.7088649e-02 6.0852679e-02 G1515_amp + 2.9398444e-01 2.9709010e-01 3.0320783e-01 3.0642965e-01 H1635_mean +-8.9268486e-02 -7.1589001e-02 -3.8991884e-02 -2.2683900e-02 H1635_PC1 + 9.0914492e-03 2.8202338e-02 6.3441410e-02 7.9954083e-02 H1635_PC2 +-4.4970189e-04 -4.2691796e-04 -2.7297577e-04 -1.6391185e-04 m + 6.3647573e-01 6.6981469e-01 7.1584991e-01 7.2321789e-01 b + +Highest-posterior-density credible intervals: + 2sigma_low 1sigma_low 1sigma_up 2sigma_up Parameter + 4.9627345e-01 5.0923959e-01 5.8732892e-01 6.5752158e-01 B_mean +-2.9999341e+00 -2.9888137e+00 -2.2409697e+00 -1.4903456e+00 B_PC1 + 2.2768841e-01 2.4929117e-01 2.9104214e-01 3.1038227e-01 B_PC2 +-5.4286475e-01 -5.1346409e-01 -3.9901155e-01 -3.0555948e-01 B_PC3 + 9.5890137e-02 1.5063613e-01 2.3445343e-01 2.6502328e-01 B_PC4 + 1.4208829e+03 1.4239103e+03 1.4301911e+03 1.4334123e+03 G1430_peak + 2.9288760e+01 3.1585361e+01 3.7485616e+01 3.9771634e+01 G1430_std + 4.1180545e-02 4.5407748e-02 5.4283765e-02 5.8799438e-02 G1430_amp + 1.5138283e+03 1.5167326e+03 1.5222417e+03 1.5250008e+03 G1515_peak + 2.7986476e+01 3.0096531e+01 3.5838819e+01 3.8793945e+01 G1515_std + 4.5821572e-02 4.9540418e-02 5.7104667e-02 6.0852719e-02 G1515_amp + 2.9388859e-01 2.9705272e-01 3.0323145e-01 3.0641133e-01 H1635_mean +-8.8788122e-02 -7.1780287e-02 -3.8860360e-02 -2.1661961e-02 H1635_PC1 + 9.6150990e-03 2.8687537e-02 6.4198601e-02 8.1227564e-02 H1635_PC2 +-4.6502071e-04 -4.4985205e-04 -3.1696145e-04 -1.9396346e-04 m + 6.4492407e-01 6.8237438e-01 7.2289600e-01 7.2794882e-01 b + + +LaTeX format +Median and 1sigma central-quantile statistics +$\overline{B}$ & $0.556^{+0.053}_{-0.034}$ +$\overline{B}_{PC1}$ & $-2.51^{+0.55}_{-0.35}$ +$\overline{B}_{PC2}$ & $0.270^{+0.020}_{-0.021}$ +$\overline{B}_{PC3}$ & $-0.449^{+0.073}_{-0.048}$ +$\overline{B}_{PC4}$ & $0.189^{+0.038}_{-0.047}$ +$\mu_{1430}$ & $1427.1^{+3.2}_{-3.0}$ +$\sigma_{1430}$ & $34.4^{+2.9}_{-3.0}$ +$a_{1430}$ & $0.0499^{+0.0045}_{-0.0043}$ +$\mu_{1515}$ & $1519.5^{+2.7}_{-2.8}$ +$\sigma_{1515}$ & $33.1^{+3.0}_{-2.7}$ +$a_{1515}$ & $0.0533^{+0.0037}_{-0.0037}$ +$\overline{H_{1635}}$ & $0.3002^{+0.0030}_{-0.0031}$ +$\overline{H_{1635}}_{PC1}$ & $-0.055^{+0.016}_{-0.016}$ +$\overline{H_{1635}}_{PC2}$ & $0.046^{+0.017}_{-0.018}$ +$m$ & $-0.000368^{+0.000095}_{-0.000059}$ +$b$ & $0.698^{+0.018}_{-0.028}$ + +Median and 2sigma central-quantile statistics +$\overline{B}$ & $0.556^{+0.116}_{-0.050}$ +$\overline{B}_{PC1}$ & $-2.51^{+1.20}_{-0.47}$ +$\overline{B}_{PC2}$ & $0.270^{+0.041}_{-0.041}$ +$\overline{B}_{PC3}$ & $-0.449^{+0.159}_{-0.083}$ +$\overline{B}_{PC4}$ & $0.189^{+0.071}_{-0.098}$ +$\mu_{1430}$ & $1427.1^{+6.4}_{-6.0}$ +$\sigma_{1430}$ & $34.4^{+5.0}_{-5.8}$ +$a_{1430}$ & $0.0499^{+0.0089}_{-0.0086}$ +$\mu_{1515}$ & $1519.5^{+5.5}_{-5.6}$ +$\sigma_{1515}$ & $33.1^{+5.7}_{-5.1}$ +$a_{1515}$ & $0.0533^{+0.0075}_{-0.0074}$ +$\overline{H_{1635}}$ & $0.3002^{+0.0063}_{-0.0062}$ +$\overline{H_{1635}}_{PC1}$ & $-0.055^{+0.033}_{-0.034}$ +$\overline{H_{1635}}_{PC2}$ & $0.046^{+0.034}_{-0.037}$ +$m$ & $-0.000368^{+0.000204}_{-0.000082}$ +$b$ & $0.698^{+0.025}_{-0.062}$ + +Marginal max_posterior (mode) and 1sigma-HPD statistics +$\overline{B}$ & $0.527^{+0.060}_{-0.018}$ +$\overline{B}_{PC1}$ & $-2.83^{+0.59}_{-0.16}$ +$\overline{B}_{PC2}$ & $0.268^{+0.023}_{-0.019}$ +$\overline{B}_{PC3}$ & $-0.476^{+0.077}_{-0.038}$ +$\overline{B}_{PC4}$ & $0.196^{+0.038}_{-0.046}$ +$\mu_{1430}$ & $1426.9^{+3.3}_{-3.0}$ +$\sigma_{1430}$ & $34.5^{+2.9}_{-3.0}$ +$a_{1430}$ & $0.0497^{+0.0046}_{-0.0043}$ +$\mu_{1515}$ & $1519.7^{+2.6}_{-2.9}$ +$\sigma_{1515}$ & $32.8^{+3.0}_{-2.7}$ +$a_{1515}$ & $0.0532^{+0.0039}_{-0.0037}$ +$\overline{H_{1635}}$ & $0.3005^{+0.0028}_{-0.0034}$ +$\overline{H_{1635}}_{PC1}$ & $-0.055^{+0.017}_{-0.016}$ +$\overline{H_{1635}}_{PC2}$ & $0.048^{+0.016}_{-0.019}$ +$m$ & $-0.000422^{+0.000105}_{-0.000028}$ +$b$ & $0.7136^{+0.0093}_{-0.0312}$ + +Marginal max_posterior (mode) and 2sigma-HPD statistics +$\overline{B}$ & $0.527^{+0.130}_{-0.031}$ +$\overline{B}_{PC1}$ & $-2.83^{+1.34}_{-0.17}$ +$\overline{B}_{PC2}$ & $0.268^{+0.042}_{-0.041}$ +$\overline{B}_{PC3}$ & $-0.476^{+0.170}_{-0.067}$ +$\overline{B}_{PC4}$ & $0.196^{+0.069}_{-0.101}$ +$\mu_{1430}$ & $1426.9^{+6.5}_{-6.0}$ +$\sigma_{1430}$ & $34.5^{+5.2}_{-5.3}$ +$a_{1430}$ & $0.0497^{+0.0091}_{-0.0085}$ +$\mu_{1515}$ & $1519.7^{+5.3}_{-5.8}$ +$\sigma_{1515}$ & $32.8^{+6.0}_{-4.8}$ +$a_{1515}$ & $0.0532^{+0.0076}_{-0.0074}$ +$\overline{H_{1635}}$ & $0.3005^{+0.0060}_{-0.0066}$ +$\overline{H_{1635}}_{PC1}$ & $-0.055^{+0.034}_{-0.033}$ +$\overline{H_{1635}}_{PC2}$ & $0.048^{+0.033}_{-0.038}$ +$m$ & $-0.000422^{+0.000228}_{-0.000043}$ +$b$ & $0.714^{+0.014}_{-0.069}$ + + +Best-parameter's chi-squared: 48.7939 +Best-parameter's -2*log(posterior): 49.7843 +Bayesian Information Criterion: 151.0377 +Reduced chi-squared: 0.0841 +Standard deviation of residuals: 0.00286127 + + diff --git a/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/STD_D1010_012821_256s_100x100_a_statistics.txt b/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/STD_D1010_012821_256s_100x100_a_statistics.txt new file mode 100644 index 00000000..8c984da2 --- /dev/null +++ b/docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/STD_D1010_012821_256s_100x100_a_statistics.txt @@ -0,0 +1,159 @@ +Summary of posterior statistics: + +Parameter estimates: + Median Mean Max-posterior Mode Parameter + 3.9955900e+00 3.9936966e+00 4.0000000e+00 3.9986871e+00 B_mean + 7.0441516e-01 6.9850777e-01 7.6170162e-01 7.2670650e-01 B_PC1 +-4.4216388e-01 -4.4219269e-01 -4.4300286e-01 -4.4184093e-01 B_PC2 +-3.8707278e-01 -3.8716134e-01 -3.7899898e-01 -3.8580196e-01 B_PC3 + 1.8402756e-01 1.8482220e-01 1.7861838e-01 1.8012862e-01 B_PC4 + 1.4316403e+03 1.4317299e+03 1.4314523e+03 1.4312930e+03 G1430_peak + 3.1350063e+01 3.1455471e+01 3.1066665e+01 3.1291077e+01 G1430_std + 6.7430953e-02 6.7467032e-02 6.7578263e-02 6.7764825e-02 G1430_amp + 1.5233338e+03 1.5234019e+03 1.5229754e+03 1.5233281e+03 G1515_peak + 3.5564467e+01 3.5506842e+01 3.5370534e+01 3.5293826e+01 G1515_std + 7.5169554e-02 7.5149276e-02 7.5559975e-02 7.5330341e-02 G1515_amp + 1.7335787e-01 1.7330514e-01 1.7348652e-01 1.7362734e-01 H1635_mean + 7.8227120e-02 7.8152501e-02 7.6658244e-02 7.8651349e-02 H1635_PC1 +-3.0303654e-02 -3.0670612e-02 -2.7976877e-02 -2.8906200e-02 H1635_PC2 +-2.4151817e-04 -2.4283945e-04 -2.3214669e-04 -2.4042691e-04 m + 2.4652724e+00 2.4654612e+00 2.4623525e+00 2.4651365e+00 b + + Std_deviation Parameter + 6.1580427e-03 B_mean + 9.9338640e-02 B_PC1 + 1.9280657e-02 B_PC2 + 2.6715285e-02 B_PC3 + 2.3694361e-02 B_PC4 + 2.2546940e+00 G1430_peak + 2.3585344e+00 G1430_std + 4.0308389e-03 G1430_amp + 2.3747279e+00 G1515_peak + 2.3440763e+00 G1515_std + 3.3909234e-03 G1515_amp + 3.0751160e-03 H1635_mean + 1.6356863e-02 H1635_PC1 + 2.1268324e-02 H1635_PC2 + 1.4356289e-05 m + 6.4593711e-03 b + +Central quintile credible intervals: + 2sigma_low 1sigma_low 1sigma_up 2sigma_up Parameter + 3.9765230e+00 3.9883513e+00 3.9988746e+00 3.9998564e+00 B_mean + 4.7787431e-01 6.0406458e-01 7.9494743e-01 8.7955326e-01 B_PC1 +-4.8082193e-01 -4.6161870e-01 -4.2310932e-01 -4.0380088e-01 B_PC2 +-4.4039100e-01 -4.1397651e-01 -3.5997979e-01 -3.3443589e-01 B_PC3 + 1.3860900e-01 1.6146464e-01 2.0825088e-01 2.3424051e-01 B_PC4 + 1.4274551e+03 1.4294947e+03 1.4339530e+03 1.4365516e+03 G1430_peak + 2.7050533e+01 2.9093659e+01 3.3804050e+01 3.6492397e+01 G1430_std + 5.9577396e-02 6.3482171e-02 7.1469529e-02 7.5703882e-02 G1430_amp + 1.5188362e+03 1.5210427e+03 1.5257967e+03 1.5283011e+03 G1515_peak + 3.0627818e+01 3.3077804e+01 3.8062182e+01 3.9625645e+01 G1515_std + 6.8383064e-02 7.1754932e-02 7.8541681e-02 8.1966952e-02 G1515_amp + 1.6712917e-01 1.7022024e-01 1.7633026e-01 1.7941762e-01 H1635_mean + 4.5637437e-02 6.1675035e-02 9.4517819e-02 1.1043077e-01 H1635_PC1 +-7.3955926e-02 -5.2135765e-02 -9.4233162e-03 1.0695736e-02 H1635_PC2 +-2.7640651e-04 -2.5602047e-04 -2.2924566e-04 -2.1835242e-04 m + 2.4530669e+00 2.4590553e+00 2.4718309e+00 2.4791450e+00 b + +Highest-posterior-density credible intervals: + 2sigma_low 1sigma_low 1sigma_up 2sigma_up Parameter + 3.9804723e+00 3.9923415e+00 3.9999995e+00 3.9999995e+00 B_mean + 4.9314510e-01 6.1269165e-01 8.0507249e-01 8.9357997e-01 B_PC1 +-4.8124827e-01 -4.6169312e-01 -4.2292937e-01 -4.0347323e-01 B_PC2 +-4.4077939e-01 -4.1362010e-01 -3.5930153e-01 -3.3367956e-01 B_PC3 + 1.3729112e-01 1.6022017e-01 2.0738261e-01 2.3346955e-01 B_PC4 + 1.4272166e+03 1.4293372e+03 1.4338281e+03 1.4363473e+03 G1430_peak + 2.6854666e+01 2.8842680e+01 3.3545904e+01 3.6360514e+01 G1430_std + 5.9417130e-02 6.3260431e-02 7.1283182e-02 7.5653116e-02 G1430_amp + 1.5187315e+03 1.5208565e+03 1.5256232e+03 1.5282648e+03 G1515_peak + 3.1239379e+01 3.3295983e+01 3.8231832e+01 3.9919086e+01 G1515_std + 6.8349474e-02 7.1687345e-02 7.8511027e-02 8.2043068e-02 G1515_amp + 1.6705300e-01 1.7016248e-01 1.7634914e-01 1.7945863e-01 H1635_mean + 4.5198216e-02 6.1830813e-02 9.4814099e-02 1.1083589e-01 H1635_PC1 +-7.3728547e-02 -5.1397318e-02 -8.4403485e-03 1.1705724e-02 H1635_PC2 +-2.7327339e-04 -2.5355678e-04 -2.2699170e-04 -2.1573752e-04 m + 2.4525812e+00 2.4587578e+00 2.4715888e+00 2.4787397e+00 b + + +LaTeX format +Median and 1sigma central-quantile statistics +$\overline{B}$ & $3.9956^{+0.0033}_{-0.0072}$ +$\overline{B}_{PC1}$ & $0.704^{+0.091}_{-0.100}$ +$\overline{B}_{PC2}$ & $-0.442^{+0.019}_{-0.019}$ +$\overline{B}_{PC3}$ & $-0.387^{+0.027}_{-0.027}$ +$\overline{B}_{PC4}$ & $0.184^{+0.024}_{-0.023}$ +$\mu_{1430}$ & $1431.6^{+2.3}_{-2.1}$ +$\sigma_{1430}$ & $31.4^{+2.5}_{-2.3}$ +$a_{1430}$ & $0.0674^{+0.0040}_{-0.0039}$ +$\mu_{1515}$ & $1523.3^{+2.5}_{-2.3}$ +$\sigma_{1515}$ & $35.6^{+2.5}_{-2.5}$ +$a_{1515}$ & $0.0752^{+0.0034}_{-0.0034}$ +$\overline{H_{1635}}$ & $0.1734^{+0.0030}_{-0.0031}$ +$\overline{H_{1635}}_{PC1}$ & $0.078^{+0.016}_{-0.017}$ +$\overline{H_{1635}}_{PC2}$ & $-0.030^{+0.021}_{-0.022}$ +$m$ & $-0.000242^{+0.000012}_{-0.000015}$ +$b$ & $2.4653^{+0.0066}_{-0.0062}$ + +Median and 2sigma central-quantile statistics +$\overline{B}$ & $3.9956^{+0.0043}_{-0.0191}$ +$\overline{B}_{PC1}$ & $0.70^{+0.18}_{-0.23}$ +$\overline{B}_{PC2}$ & $-0.442^{+0.038}_{-0.039}$ +$\overline{B}_{PC3}$ & $-0.387^{+0.053}_{-0.053}$ +$\overline{B}_{PC4}$ & $0.184^{+0.050}_{-0.045}$ +$\mu_{1430}$ & $1431.6^{+4.9}_{-4.2}$ +$\sigma_{1430}$ & $31.4^{+5.1}_{-4.3}$ +$a_{1430}$ & $0.0674^{+0.0083}_{-0.0079}$ +$\mu_{1515}$ & $1523.3^{+5.0}_{-4.5}$ +$\sigma_{1515}$ & $35.6^{+4.1}_{-4.9}$ +$a_{1515}$ & $0.0752^{+0.0068}_{-0.0068}$ +$\overline{H_{1635}}$ & $0.1734^{+0.0061}_{-0.0062}$ +$\overline{H_{1635}}_{PC1}$ & $0.078^{+0.032}_{-0.033}$ +$\overline{H_{1635}}_{PC2}$ & $-0.030^{+0.041}_{-0.044}$ +$m$ & $-0.000242^{+0.000023}_{-0.000035}$ +$b$ & $2.465^{+0.014}_{-0.012}$ + +Marginal max_posterior (mode) and 1sigma-HPD statistics +$\overline{B}$ & $3.9987^{+0.0013}_{-0.0063}$ +$\overline{B}_{PC1}$ & $0.727^{+0.078}_{-0.114}$ +$\overline{B}_{PC2}$ & $-0.442^{+0.019}_{-0.020}$ +$\overline{B}_{PC3}$ & $-0.386^{+0.027}_{-0.028}$ +$\overline{B}_{PC4}$ & $0.180^{+0.027}_{-0.020}$ +$\mu_{1430}$ & $1431.3^{+2.5}_{-2.0}$ +$\sigma_{1430}$ & $31.3^{+2.3}_{-2.4}$ +$a_{1430}$ & $0.0678^{+0.0035}_{-0.0045}$ +$\mu_{1515}$ & $1523.3^{+2.3}_{-2.5}$ +$\sigma_{1515}$ & $35.3^{+2.9}_{-2.0}$ +$a_{1515}$ & $0.0753^{+0.0032}_{-0.0036}$ +$\overline{H_{1635}}$ & $0.1736^{+0.0027}_{-0.0035}$ +$\overline{H_{1635}}_{PC1}$ & $0.079^{+0.016}_{-0.017}$ +$\overline{H_{1635}}_{PC2}$ & $-0.029^{+0.020}_{-0.022}$ +$m$ & $-0.000240^{+0.000013}_{-0.000013}$ +$b$ & $2.4651^{+0.0065}_{-0.0064}$ + +Marginal max_posterior (mode) and 2sigma-HPD statistics +$\overline{B}$ & $3.9987^{+0.0013}_{-0.0182}$ +$\overline{B}_{PC1}$ & $0.73^{+0.17}_{-0.23}$ +$\overline{B}_{PC2}$ & $-0.442^{+0.038}_{-0.039}$ +$\overline{B}_{PC3}$ & $-0.386^{+0.052}_{-0.055}$ +$\overline{B}_{PC4}$ & $0.180^{+0.053}_{-0.043}$ +$\mu_{1430}$ & $1431.3^{+5.1}_{-4.1}$ +$\sigma_{1430}$ & $31.3^{+5.1}_{-4.4}$ +$a_{1430}$ & $0.0678^{+0.0079}_{-0.0083}$ +$\mu_{1515}$ & $1523.3^{+4.9}_{-4.6}$ +$\sigma_{1515}$ & $35.3^{+4.6}_{-4.1}$ +$a_{1515}$ & $0.0753^{+0.0067}_{-0.0070}$ +$\overline{H_{1635}}$ & $0.1736^{+0.0058}_{-0.0066}$ +$\overline{H_{1635}}_{PC1}$ & $0.079^{+0.032}_{-0.033}$ +$\overline{H_{1635}}_{PC2}$ & $-0.029^{+0.041}_{-0.045}$ +$m$ & $-0.000240^{+0.000025}_{-0.000033}$ +$b$ & $2.465^{+0.014}_{-0.013}$ + + +Best-parameter's chi-squared: 1771.5019 +Best-parameter's -2*log(posterior): 1772.7011 +Bayesian Information Criterion: 1873.7457 +Reduced chi-squared: 3.0543 +Standard deviation of residuals: 0.0172404 + + diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/AC4_OL49_021920_30x30_H2O_a_histogram.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/AC4_OL49_021920_30x30_H2O_a_histogram.pdf new file mode 100644 index 00000000..80e16f40 Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/AC4_OL49_021920_30x30_H2O_a_histogram.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/AC4_OL53_101220_256s_30x30_a_histogram.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/AC4_OL53_101220_256s_30x30_a_histogram.pdf new file mode 100644 index 00000000..870c39ee Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/AC4_OL53_101220_256s_30x30_a_histogram.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/STD_D1010_012821_256s_100x100_a_histogram.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/STD_D1010_012821_256s_100x100_a_histogram.pdf new file mode 100644 index 00000000..85049f4e Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/STD_D1010_012821_256s_100x100_a_histogram.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/AC4_OL49_021920_30x30_H2O_a_modelfit.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/AC4_OL49_021920_30x30_H2O_a_modelfit.pdf new file mode 100644 index 00000000..aab7b55e Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/AC4_OL49_021920_30x30_H2O_a_modelfit.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/AC4_OL53_101220_256s_30x30_a_modelfit.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/AC4_OL53_101220_256s_30x30_a_modelfit.pdf new file mode 100644 index 00000000..54e420f5 Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/AC4_OL53_101220_256s_30x30_a_modelfit.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/STD_D1010_012821_256s_100x100_a_modelfit.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/STD_D1010_012821_256s_100x100_a_modelfit.pdf new file mode 100644 index 00000000..16e9964a Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/STD_D1010_012821_256s_100x100_a_modelfit.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/AC4_OL49_021920_30x30_H2O_a_pairwise.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/AC4_OL49_021920_30x30_H2O_a_pairwise.pdf new file mode 100644 index 00000000..ee279789 Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/AC4_OL49_021920_30x30_H2O_a_pairwise.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/AC4_OL53_101220_256s_30x30_a_pairwise.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/AC4_OL53_101220_256s_30x30_a_pairwise.pdf new file mode 100644 index 00000000..34792308 Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/AC4_OL53_101220_256s_30x30_a_pairwise.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/STD_D1010_012821_256s_100x100_a_pairwise.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/STD_D1010_012821_256s_100x100_a_pairwise.pdf new file mode 100644 index 00000000..8030a16f Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/STD_D1010_012821_256s_100x100_a_pairwise.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/AC4_OL49_021920_30x30_H2O_a_trace.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/AC4_OL49_021920_30x30_H2O_a_trace.pdf new file mode 100644 index 00000000..8f118a42 Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/AC4_OL49_021920_30x30_H2O_a_trace.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/AC4_OL53_101220_256s_30x30_a_trace.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/AC4_OL53_101220_256s_30x30_a_trace.pdf new file mode 100644 index 00000000..cfa70083 Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/AC4_OL53_101220_256s_30x30_a_trace.pdf differ diff --git a/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/STD_D1010_012821_256s_100x100_a_trace.pdf b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/STD_D1010_012821_256s_100x100_a_trace.pdf new file mode 100644 index 00000000..99eff367 Binary files /dev/null and b/docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/STD_D1010_012821_256s_100x100_a_trace.pdf differ diff --git a/docs/examples/transmission_ftir/PyIRoGlass_Transmission.ipynb b/docs/examples/transmission_ftir/PyIRoGlass_Transmission.ipynb index c790e31e..3f22208d 100644 --- a/docs/examples/transmission_ftir/PyIRoGlass_Transmission.ipynb +++ b/docs/examples/transmission_ftir/PyIRoGlass_Transmission.ipynb @@ -418,7 +418,7 @@ "source": [ "# Concentrations\n", "\n", - "We now want to convert all those peak heights (with uncertainties) to concentrations (with uncertainties), by applying the Beer-Lambert Law. We do so by using the Concentration_Output function, which takes in these parameters and samples over N samples for a secondary MCMC: \n", + "We now want to convert all those peak heights (with uncertainties) to concentrations (with uncertainties), by applying the Beer-Lambert Law. We do so by using the calculate_concentrations function, which takes in these parameters and samples over N samples for a secondary MCMC: \n", "\n", "- DF_OUTPUT: Output from Run_All_Spectra\n", "- N: Number of samples for this MCMC\n", @@ -440,10 +440,9 @@ "P_ROOM = 1 # Bar\n", "\n", "N = 500000 # MCMC samples\n", - "DENSITY_EPSILON, MEGA_SPREADSHEET = pig.calculate_concentrations(DF_OUTPUT, N, CHEMISTRY, THICKNESS, T_ROOM, P_ROOM)\n", + "concentrations_df = pig.calculate_concentrations(DF_OUTPUT, N, CHEMISTRY, THICKNESS, T_ROOM, P_ROOM)\n", "\n", - "DENSITY_EPSILON.to_csv('DensityEpsilon.csv')\n", - "MEGA_SPREADSHEET.to_csv('H2OCO2.csv')" + "concentrations_df.to_csv('H2OCO2.csv')" ] }, { @@ -461,14 +460,14 @@ }, "outputs": [], "source": [ - "MEGA_SPREADSHEET" + "concentrations_df" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "There are a few things to note. Each column with the suffix _MEAN represents the mean value, _BP represents the best-parameter from MCMC, and _STD represents the standard deviation. We recommend the use of the 'H2OT_MEAN', 'H2OT_STD', 'CO2_MEAN', and 'CO2_STD' columns. The columns with the suffix _S2N show the signal-to-noise ratio of the NIR peaks, and the columns with the prefix ERR_ just process this information, returning a '-' if the peaks are meaningful and a '*' if the signal is too low. \n", + "There are a few things to note. Each column with the suffix _MEAN represents the mean value, _BP represents the best-parameter from MCMC, and _STD represents the standard deviation. We recommend the use of the 'H2OT_MEAN', 'H2OT_STD', 'CO2_MEAN', and 'CO2_STD' columns. The columns with the suffix _STN show the signal-to-noise ratio of the NIR peaks, and the columns with the prefix ERR_ just process this information, returning a '-' if the peaks are meaningful and a '*' if the signal is too low. \n", "\n", "Concentrations of $\\mathrm{H_2O}$ depend on whether your sample is saturated or not. If your sample is unsaturated (marked by H2OT_3550_SAT == '-'), the column 'H2OT_MEAN'=='H2OT_3550_M'. If your sample is saturated (marked by H2OT_3550_SAT == '*'), the column of 'H2OT_MEAN'=='H2Om_1635_BP'+'OH_4500_M'. The $\\mathrm{H_2O_{t, 3550}}$ peak cannot be used, given potential nonlinearity in the Beer-Lambert Law. See the discussion of this handling of speciation in the paper. \n" ] @@ -477,22 +476,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Here is also all the other relevant information for calculating these concentrations. All the density and molar absorptivity information is stored in this dataframe. \n", - "\n", "The column 'Density' contains the densities used for the final concentration. The values between 'Density' and 'Density_Sat' will be different if the sample is saturated, showing the difference in densities when using variable concentrations of $\\mathrm{H_2O_m}$. \n", "\n", - "'Tau' and 'Na/Na+Ca' calculate the compositional parameters required for determining molar absorptivity. All calculated molar absorptivities and their uncertainties (sigma_ prefix) from the inversion are provided in the dataframe. \n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "DENSITY_EPSILON" + "'Tau' and 'Eta' calculate the compositional parameters required for determining molar absorptivity. All calculated molar absorptivities and their uncertainties (sigma_ prefix) from the inversion are provided in the dataframe. \n" ] }, {