File List

Here is a list of all documented files with brief descriptions:

[detail level 123]

► analyses
► 3C279
3c279_mexico.cpp	Driver file for 3c279 analysis with geometric models: Large assymmetric Gaussian background one or more symmetric Gaussians one or more asymmetric Gaussians
3c279_mexico_all_linear.cpp	Driver file for 3c279 analysis with time-variable geometric models: Large assymmetric Gaussian background one or more symmetric Gaussians one or more asymmetric Gaussians
3c279_mexico_hilo.cpp	Driver file for 3c279 analysis of HI+LO with geometric models: Large assymmetric Gaussian background one or more symmetric Gaussians one or more asymmetric Gaussians
► Challenge2
challenge2_VACP_comparison.cpp	Example of fitting a multi-Gaussian image model to visibility amplitude and closure phase data according to the specifications of modeling challenge 2
generate_multigaussian_test_data.cpp	Generates test data comprised of multiple Gaussians, modeling elements of challenge 2 for testing the development of the multi-Gaussian model
test_multigaussian.cpp	Example of fitting a multi-Gaussian image model to test visibility amplitude and closure phase data
► Challenge3
challenge3a_VACP_comparison.cpp	Example of fitting a multi-Gaussian image model to visibility amplitude and closure phase data according to the specifications of modeling challenge 2
challenge3a_VACPCA_comparison.cpp	Example of fitting a multi-Gaussian image model to visibility amplitude and closure phase data according to the specifications of modeling challenge 2
challenge3b_VACP_comparison_mag.cpp	Example of fitting a multi-Asymmetric Gaussian image model to visibility amplitude and closure phase data according to the specifications of modeling challenge 2
► ChallengeJ+
chjp_sX.cpp	Driver file for Challenge J+ analysis with smoothed xsringauss model
► ImageScore
score_matched_filter.cpp	Test model_image_score clas by mcmc runs with gain calibration
► Imaging
imrec.cpp	Generic driver for image reconstruction with Themis
imrecad_complex_deostan.cpp	Generic driver for image reconstruction with Themis with complex visibilities
imrecad_complex_hilo.cpp	Generic driver for image reconstruction with Themis with complex visibilities
imrecad_complex_single.cpp	Generic driver for image reconstruction with Themis with complex visibilities
imrecad_complex_single_deostan.cpp	Generic driver for image reconstruction with Themis with complex visibilities
imrecad_crosshands_deostan.cpp	Generic driver for polarized image reconstruction with Themis with full crosshand visibilities that uses DEO and the Stan NUTS drivers
imrecad_crosshands_hilo.cpp	Generic driver for polarized image reconstruction with Themis with full crosshand visibilities
imrecad_hilo.cpp	Generic driver for image reconstruction with Themis
imrecad_hilo_diffevol.cpp	Generic driver for image reconstruction with Themis
imrecad_hilo_noopt.cpp	Generic driver for image reconstruction with Themis
imrecup.cpp	Generic driver for image reconstruction with Themis that upsamples image
imrecup_hilo.cpp	Generic driver for image reconstruction with Themis that upsamples image
imrecup_scatt_hilo.cpp	Generic driver for image reconstruction with Themis that upsamples image
► J1924
J1924_mexico.cpp	Driver file for J1924 analysis with geometric models: Large assymmetric Gaussian background one or more symmetric Gaussians one or more asymmetric Gaussians
J1924_mexico_all_linear.cpp	Driver file for J1924 analysis with time-variable geometric models: Large assymmetric Gaussian background one or more symmetric Gaussians one or more asymmetric Gaussians
J1924_mexico_hilo.cpp	Driver file for J1924 analysis of HI+LO with geometric models: Large assymmetric Gaussian background one or more symmetric Gaussians one or more asymmetric Gaussians
► M87
m87_ccm_mexico.cpp	Driver file for M87 analysis with the concordance crescent model: Large symmetric Gaussian background smoothed xsringauss one or two asymmetric Gaussians central symmetric Gaussians
m87_ccm_mexico_all.cpp	Driver file for M87 analysis with the concordance crescent model that uses all days and bands: Large symmetric Gaussian background smoothed xsringauss one or two asymmetric Gaussians central symmetric Gaussians
m87_ccm_mexico_double.cpp	Driver file for M87 analysis with the concordance crescent model: Large symmetric Gaussian background smoothed xsringauss one or two asymmetric Gaussians central symmetric Gaussians
m87_ccm_mexico_smallR.cpp	Driver file for M87 analysis with the concordance crescent model: Large symmetric Gaussian background smoothed xsringauss one or two asymmetric Gaussians central symmetric Gaussians
m87_sXa2g.cpp	Driver file for M87 analysis with smoothed xsringauss model plus components based on eponymous Challenge J+ file
m87_sXa2g_double.cpp	Driver file for M87 analysis with smoothed xsringauss model plus components based on eponymous Challenge J+ file. Analyzes files two at a time (i.e., four at a time)
m87_sXa2g_double_sgt.cpp	Driver file for M87 analysis with smoothed xsringauss model plus components based on eponymous Challenge J+ file. Analyzes files two at a time (i.e., four at a time)
m87_sXa2g_sgt.cpp	Driver file for M87 analysis with smoothed xsringauss model plus components based on eponymous Challenge J+ file
m87_sXaag_sgt_mexico.cpp	Driver file for M87 analysis with smoothed xsringauss model plus components based on eponymous Challenge J+ file
m87_sXag.cpp	Driver file for M87 analysis with smoothed xsringauss model plus components based on eponymous Challenge J+ file
m87_sXag_ai.cpp	Driver file for M87 analysis with smoothed xsringauss model plus components based on eponymous Challenge J+ file
► M87_variable
m87_ccm_mexico_lo_linear.cpp	Driver file for M87 analysis with the concordance crescent model that uses all days and bands: Large symmetric Gaussian background smoothed xsringauss one or two asymmetric Gaussians central symmetric Gaussians
► Score
score_many_vacp_gain_iter.cpp	Test model_image_score clas by mcmc runs with gain calibration
► SgrA
sgra_eccm_linear.cpp	Driver file for M87 analysis with the concordance crescent model that uses all days and bands: Large symmetric Gaussian background smoothed xsringauss one or two asymmetric Gaussians central symmetric Gaussians
sgrA_general_riaf_fitting_diff.cpp	Driver file for SgrA analysis with Broderick et al. 2016 RIAF model which is static
sgrA_general_sspotriaf_fitting_diff.cpp	Driver file for SgrA analysis with Broderick et al. 2016 RIAF model + shearing hotspot
► analysis
diagnostics.py	Python script to run diagnostics on MCMC chains
plot_vrt2_images.py	Python script to plot image files generated by VRT2
plots.py	Python script to generate triangle, trace, log-likelihoood and chi2 plots
vrt2_images.py	Visualize polarization maps computed and output by vrt2
► data
data_closure_amplitude.cpp	Implements datum and data objects containing closure amplitudes
data_closure_amplitude.h	Header file for datum and data objects containing closure amplitudes
data_closure_phase.cpp	Implements datum and data objects containing closure phases
data_closure_phase.h	Header file for datum and data objects containing closure phases
data_crosshand_visibilities.cpp	Implements datum and data objects containing crosshand visibilities (RR, LL, RL, LR)
data_crosshand_visibilities.h	Header file for datum and data objects containing full RR, LL, RL and LR visibilities
data_flux.cpp	Implements datum and data objects containing fluxes
data_flux.h	Header file for datum and data objects containing fluxes
data_polarization_fraction.cpp	Implements a fractional polarization data class
data_polarization_fraction.h	Header file for a fractional polarization data class
data_visibility.cpp	Implements datum and data objects containing visibilities
data_visibility.h	Header file for datum and data objects containing visibilities
data_visibility_amplitude.cpp	Implements datum and data objects containing visibility amplitudes
data_visibility_amplitude.h	Header file for datum and data objects containing visibility amplitudes
► examples
astroray_image.cpp	Test model for astroray image
astroray_image_sampler.cpp	Example demonstrating how to drive the external raditaive transfer code ASTRORAY
eggbox_mcmc_sampling.cpp	Example of how to use the Affine invariant parallel tempered MCMC sampling routine
generate_crescent_image.cpp	To be added
generate_movie_orbiting_spot.cpp	Example illustrating the creation of a orbiting spot movie model
generate_movie_shearing_spot.cpp	Example illustrating the creation of a shearing spot movie model
generate_riaf_image.cpp	Example illustrating the creationg of a RIAF model
grtrans_image.cpp	Test model for grtrans image
ipole_image_sampler.cpp	Example demonstrating how to drive the external radiative transfer code IPOLE
multi-gaussian_mc_fe_wg_challenge2.cpp	Example of fitting a multi-Gaussian image model to visibility amplitude and closure phase data according to the specifications of modeling challenge 2
raptor_image_sampler.cpp	Example demonstrating how to drive the external radiative transfer code RAPTOR
reading_data.cpp	Example of how to read and access common EHT data types
riaf_model_fitting.cpp	Example illustrating the use of the RIAF model
scattered_gaussian_fitting.cpp	Example of fitting a Gaussian image model to visibility amplitude data
► likelihood
likelihood.cpp	Implementation file for the Likelihood class
likelihood.h	Header file for the Likelihood class
likelihood_base.cpp	Implementation file for the Base Likelihood class
likelihood_base.h	Header file for the Base Likelihood class
likelihood_cauchy.h	Header file for the Egg box likelihood class. Ref: https://mathworld.wolfram.com/LorentzianFunction.html
likelihood_closure_amplitude.cpp	Implementation file for the Closure Amplitude Likelihood class
likelihood_closure_amplitude.h	Header file for the clsoure Amplitude Likelihood class
likelihood_closure_phase.cpp	Implementation file for the Closure Phase Likelihood class
likelihood_closure_phase.h	Header file for the Closure Phase Likelihood class
likelihood_crosshand_visibilities.cpp	Implementation file for the crosshand visibilities likelihood class
likelihood_crosshand_visibilities.h	Header file for the crosshand visibilities likelihood class
likelihood_eggbox.h	Header file for the Egg box likelihood class
likelihood_flux.cpp	Implementation file for the flux likelihood class
likelihood_flux.h	Header file for the flux likelihood class
likelihood_gaussian.h	Header file for the Gaussian likelihood class
likelihood_griewank.h	Header file for the Egg box likelihood class. Ref: https://mathworld.wolfram.com/GriewankFunction.html
likelihood_lorentzian.h	Header file for the Egg box likelihood class. Ref: https://mathworld.wolfram.com/LorentzianFunction.html
likelihood_marginalized_closure_phase.cpp	Implementation file for the Marginalized Closure Phase Likelihood class
likelihood_marginalized_closure_phase.h	Header file for the Marginalized Closure Phase Likelihood class
likelihood_marginalized_visibility_amplitude.cpp	Implementation file for the Marginalized Visibility Amplitude Likelihood class
likelihood_marginalized_visibility_amplitude.h	Header file for the Marginalized Visibility Amplitude Likelihood class
likelihood_matched_filter.cpp	Implementation file for the matched filter likelihood class
likelihood_matched_filter.h	Header file for the matched filter likelihood class
likelihood_optimal_complex_gain_constrained_crosshand_visibilities.cpp	Implementation file for the likelihood_optimal_complex_gain_constrained_crosshand_visibilities likelihood class
likelihood_optimal_complex_gain_constrained_crosshand_visibilities.h	Header file for the likelihood_optimal_complex_gain_constrained_crosshand_visibilities likelihood class
likelihood_optimal_complex_gain_visibility.cpp	Implementation file for the likelihood_optimal_complex_gain_visibility likelihood class
likelihood_optimal_complex_gain_visibility.h	Header file for the likelihood_optimal_complex_gain_visibility likelihood class
likelihood_optimal_gain_correction_visibility_amplitude.cpp	Implementation file for the likelihood_optimal_gain_gorrection_visibility_amplitude likelihood class
likelihood_optimal_gain_correction_visibility_amplitude.h	Header file for the likelihood_optimal_gain_correction_visibility_amplitude likelihood class
likelihood_polarization_fraction.cpp	Implementation file for the fractional polarization Likelihood class
likelihood_polarization_fraction.h	Header file for the Fractional Polarization Likelihood class
likelihood_power_tempered.h	Modifies the likelihood according to a power tempering scheme
likelihood_rosenbrock.h	Header file for the Rosenbrock likelihood class
likelihood_visibility.cpp	Implementation file for the Visibility Likelihood class
likelihood_visibility.h	Header file for the Visibility Likelihood class
likelihood_visibility_amplitude.cpp	Implementation file for the Visibility Amplitude Likelihood class
likelihood_visibility_amplitude.h	Header file for the Visibility Amplitude Likelihood class
prior.h	Header file for prior class
prior_base.h	Header file for prior_base class
prior_gaussian.h	Header file for prior_gaussian class
prior_linear.h	Header file for prior_base class
prior_logarithmic.h	Header file for the prior_logarithmic class
transform_base.h	Header file for transform_base class
transform_fixed.h	Header file for transform_fixed class
transform_logarithmic.h	Header file for transform_logarithmic class
transform_logit.h	Header file for transform_logit class
transform_none.h	Header file for transform_none class
► model
model_circular_binary.cpp	Implements binary model based on two Gaussians
model_circular_binary.h	Header file for binary model class
model_closure_amplitude.cpp	Implements visibility ampitude model class
model_closure_amplitude.h	Header file for visibility ampitude model class
model_closure_phase.cpp	Implements closure phase model class
model_closure_phase.h	Header file for closure phase model class
model_crosshand_visibilities.cpp	Implements crosshand visibility model class
model_crosshand_visibilities.h	Header file for crosshand visibilities model class
model_ensemble_averaged_parameterized_scattered_image.cpp	Header file for ensemble averaged, parameterized scattering interface
model_ensemble_averaged_parameterized_scattered_image.h	Header file for ensemble averaged parameterized scattering interface
model_ensemble_averaged_scattered_image.cpp	Header file for ensemble averaged scattering interface
model_ensemble_averaged_scattered_image.h	Header file for ensemble averaged scattering interface
model_flux.cpp	Implements flux model class
model_flux.h	Header file for flux model class
model_galactic_center_diffractive_scattering_screen.cpp	Implementation file for galactic center diffractive scattering interface
model_galactic_center_diffractive_scattering_screen.h	Header file for diffractive scattering interface
model_image.cpp	Implements image model class
model_image.h	Header file for image model class
model_image_adaptive_splined_raster.cpp	Implements the model_image_splined_raster image class
model_image_adaptive_splined_raster.h	Header file for the model_image_adaptive_splined_raster image class
model_image_astroray.cpp	Implements driver to ASTRORAY executable
model_image_astroray.h	Header file for astroray driver
model_image_asymmetric_gaussian.cpp	Implements asymmetric Gaussian image class
model_image_asymmetric_gaussian.h	Header file for the asymmetric Gaussian image class
model_image_crescent.cpp	Implements Geometric Crescent Model Image class
model_image_crescent.h	Header file for the Geometric Crescent Model Image class
model_image_gaussian.cpp	Implements the asymmetric Gaussian image class
model_image_gaussian.h	Header file for the Gaussian image class
model_image_general_riaf.cpp	Implements the RIAF image model class
model_image_general_riaf.h	Header file for the extended RIAF image model class with mass scaling
model_image_general_riaf_shearing_spot.cpp	Implements Shearing spot image class
model_image_general_riaf_shearing_spot.h	Header file for the shearing spot model class
model_image_grtrans.cpp	Implements driver to GRTRANS executable
model_image_grtrans.h	Header file for grtrans driver
model_image_ipole.cpp	Implements driver to IPOLE executable
model_image_ipole.h	Header file for ipole driver
model_image_multi_asymmetric_gaussian.cpp	Implements the multi-Asymmetric Gaussian image class originally motivated by model fitting challenge 3 within the MCFE WG
model_image_multi_asymmetric_gaussian.h	Header file for the Multi-Asymmetric Gaussian image class originally motivated by the model fitting challenge 3 in the MCFE WG
model_image_multigaussian.cpp	Implements the multi-Gaussian image class originally motivated by model fitting challenge 2 within the MCFE WG
model_image_multigaussian.h	Header file for the Multi-Gaussian image class originally motivated by the model fitting challenge 2 in the MCFE WG
model_image_orbiting_spot.cpp	Implements Shearing spot image class
model_image_orbiting_spot.h	Header file for the shearing spot model class
model_image_polynomial_variable.cpp	Implements the model_image_polynomial_variable class, which generates a variable model by permitting model parameters to vary with time. All parameters are constrained to vary as polynomial functions of time, though the order of each may differ. A reference time may be set
model_image_polynomial_variable.h	Header file for the model_image_polynomial_variable class, which generates a variable model by permitting model parameters to vary with time. All parameters are constrained to vary as polynomial functions of time, though the order of each may differ. A reference time may be set
model_image_raptor.cpp	Implements driver to RAPTOR executable
model_image_raster.cpp	Implements the model_image_raster image class
model_image_raster.h	Header file for the model_image_raster image class
model_image_refractive_scattering.cpp	Implementation file for refractive scattering interface
model_image_refractive_scattering.h	Header file for refractive scattering interface
model_image_riaf.cpp	Implements the RIAF image model class
model_image_riaf.h	Header file for the extended RIAF image model class
model_image_ring.cpp	Implements a Ring Model Image class
model_image_ring.h	Header file for the Geometric Ring Model Image class
model_image_score.cpp	Implements SED-fitted RIAF model class
model_image_score.h	Header file for score model class
model_image_sed_fitted_riaf.cpp	Test model_image_score clas by mcmc runs with gain calibration
model_image_sed_fitted_riaf.h	Header file for SED-fitted RIAF model class
model_image_sed_fitted_riaf_intensity.cpp	Implements SED-fitted RIAF model class
model_image_sed_fitted_riaf_intensity.h	Header file for SED-fitted RIAF model class
model_image_sed_fitted_riaf_johannsen.cpp	Implements SED-fitted RIAF model class with Johannsen metric
model_image_sed_fitted_riaf_johannsen.h	Header file for SED-fitted RIAF model class with Johannsen metric
model_image_shearing_spot.cpp	Implements Shearing spot image class
model_image_shearing_spot.h	Header file for the shearing spot model class
model_image_shearing_spot_johannsen.cpp	Implements Shearing spot image class
model_image_shearing_spot_johannsen.h	Header file for the shearing spot model class
model_image_slashed_ring.cpp	Implements Slashed Ring Model Image class
model_image_slashed_ring.h	Header file for the Geometric Slashed Ring Model Image class
model_image_smooth.cpp	Header file for ensemble averaged, parameterized scattering interface
model_image_smooth.h	Header file for model_image_smooth
model_image_splined_raster.cpp	Implements the model_image_splined_raster image class
model_image_splined_raster.h	Header file for the model_image_splined_raster image class
model_image_sum.cpp	Implements the model_image_sum class, which sums different model images, generating a convenient way to create multi-component image models from single image components
model_image_sum.h	Header file for the model_image_sum class, which sums different model images, generating a convenient way to create multi-component image models from single image components
model_image_symmetric_gaussian.cpp	Implements symmetric Gaussian image class
model_image_symmetric_gaussian.h	Header file for the symmetric Gaussian image class
model_image_upsample.cpp	Implements the model_image_upsample image class
model_image_upsample.h	Header file for the model_image_upsample image class
model_image_vrt2_pmap.cpp	Implements the asymmetric model_image_vrt2_pmap image class
model_image_vrt2_pmap.h	Header file for the model_image_vrt2_pmap image class
model_image_xsring.cpp	Implements Slashed Ring Model Image class
model_image_xsring.h	Header file for the Geometric Slashed Ring Model Image class
model_image_xsringauss.cpp	Implements the geometric nine-parameter eccentric slashed ring (xsringauss) model image class
model_image_xsringauss.h	Header file for the geometric nine-parameter eccentric slashed ring (xsringauss) model image class
model_movie.h	Header file for the model movie class
model_movie_general_riaf_shearing_spot.cpp	Implements extended shearing spot movie class
model_movie_general_riaf_shearing_spot.h	Header file for creating a movie object for shearing spot based on model_image_shearing_spot
model_movie_orbiting_spot.cpp	Implements orbiting spot movie class
model_movie_orbiting_spot.h	Header file for creating a movie object for orbiting spot based on model_image_orbiting_spot and Broderick & Loeb 2006
model_movie_refractive_scattering.h	Header file for refractively scattering a model_movie using model_image_refractive_scattering
model_movie_shearing_spot.cpp	Implements extended shearing spot movie class
model_movie_shearing_spot.h	Header file for creating a movie object for shearing spot based on model_image_shearing_spot
model_movie_shearing_spot_johannsen.cpp	Implements extended shearing spot movie class
model_movie_shearing_spot_johannsen.h	Header file for creating a movie object for shearing spot based on model_image_shearing_spot_johannsen
model_polarization_fraction.cpp	Implements fractional polarization model class
model_polarized_image.cpp	Implements polarized image model class
model_polarized_image.h	Header file for polarized image model class
model_polarized_image_adaptive_splined_raster.cpp	Implements the model_polarized_image_splined_raster image class
model_polarized_image_adaptive_splined_raster.h	Header file for the model_polarized_image_adaptive_splined_raster image class
model_polarized_image_constant_polarization.cpp	Header file for a polarized image model class with a constant polarization applied to a model image
model_polarized_image_constant_polarization.h	Header file for a polarized image model class with a constant polarization applied to a model image
model_polarized_image_sum.cpp	Implements the model_polarized_image_sum class, which sums different model images, generating a convenient way to create multi-component image models from single image components
model_polarized_image_sum.h	Header file for the model_polarized_image_sum class, which sums different model polarized images, generating a convenient way to create multi-component image models from single image components
model_riaf.cpp	Implements extended RIAF image+flux model class
model_riaf.h	Header file for extended RIAF image+flux model class
model_riaf_wrapper.cpp	Implements extended RIAF image+flux model wrapper class
model_riaf_wrapper.h	Header file for extended RIAF image+flux model wrapper class
model_ring.cpp	Implements a ring model class
model_ring.h	Header file for the ring model class
model_symmetric_gaussian.h	Header file for symmetric Gaussian image class
model_visibility.cpp	Implements visibility model class
model_visibility.h	Header file for visibility model class
model_visibility_amplitude.cpp	Implements visibility ampitude model class
model_visibility_amplitude.h	Header file for visibility ampitude model class
model_visibility_galactic_center_diffractive_scattering_screen.cpp	Implementation file for galactic center diffractive scattering interface
model_visibility_galactic_center_diffractive_scattering_screen.h	Header file for diffractive scattering interface
model_vrt2_library.cpp	Implements the asymmetric model_vrt2_library image class
model_vrt2_library.h	Header file for the model_image_vrt2_library image class
► optimizing
optimizer_kickout_powell.cpp	Implementation file for the optimizer_kickout_powell class
optimizer_kickout_powell.h	Header file for optimizer_kickout_powell class
optimizer_powell.cpp	Implementation file for the optimizer_powell class
optimizer_powell.h	Header file for optimizer_powell class
optimizer_simplex.cpp	Implementation file for the optimizer_simplex class
optimizer_simplex.h	Header file for optimizer_simplex class
► sampling
sampler_affine_invariant_tempered_MCMC.cpp	Implementation file for the sampler_affine_invariant_tempered_MCMC class
sampler_affine_invariant_tempered_MCMC.h	Header file for sampler_affine_invariant_tempered_MCMC class
sampler_automated_factor_slice_sampler_MCMC.cpp	Implementation file for the sampler_automated_factor_slice_sampler_MCMC
sampler_automated_factor_slice_sampler_MCMC.h	Header file for a generic single factor slice sampler used in Themis. This uses slice sampling to explore the distribution. The sampler will perform well as long as there are not strong non-linear correlation between the parameters. One benefit is that the sampler is rejection free, albeit it only moves in one direction per sample. For more information see https://www.ncbi.nlm.nih.gov/pubmed/24955002 and Neal's introduction to slice sampling https://projecteuclid.org/euclid.aos/1056562461
sampler_deo_tempering_MCMC.h	Header file for sampler_deo_tempering_MCMC class
sampler_differential_evolution_deo_tempered_MCMC.cpp	Implementation file for the sampler_differential_evolution_deo_tempered_MCMC class
sampler_differential_evolution_deo_tempered_MCMC.h	Header file for sampler_differential_evolution_deo_tempered_MCMC class
sampler_differential_evolution_tempered_MCMC.cpp	Implementation file for the sampler_differential_evolution_tempered_MCMC class
sampler_differential_evolution_tempered_MCMC.h	Header file for sampler_differential_evolution_tempered_MCMC class
sampler_grid_search.cpp	Implementation file for the sampler_grid_search class
sampler_grid_search.h	Header file for Grid Search class
sampler_MCMC_base.cpp	Implementation file for the abstract mcmc base class
sampler_MCMC_base.h	Header file for base markov chain monte carlo sampler
sampler_stan_adapt_dense_e_nuts_MCMC.cpp	Implementation file for the sampler_stan_adapt_dense_e_nuts_MCMC
sampler_stan_adapt_dense_e_nuts_MCMC.h	Header file stan sampler used in Themis
sampler_stan_adapt_diag_e_nuts_MCMC.cpp	Implementation file for the sampler_stan_adapt_diag_e_nuts_MCMC
sampler_stan_adapt_diag_e_nuts_MCMC.h	Header file stan sampler used in Themis
► tests
asymmetric_gaussian_image_comparison.cpp	Fit an asymmetric Gaussian model to visibility amplitude data
base_DE_mcmc_sampling.cpp	Test problem for the differential evolution parallel tempered MCMC sampling
base_grid_search.cpp	Test problem for the grid search sampling
base_mcmc_sampling.cpp	Test problem for the Affine invariant parallel tempered MCMC sampling
closure_amplitude_test.cpp	Fits a symmetric Gaussian model to simulated closure amplitudes
datatypes.cpp	Main file illustrating read-in of the various EHT observation data
gaussian_blob.cpp	Check FFTs by comparing analytical to numerical visibilities in Gaussian model
gaussian_image_comparison.cpp	Fits a Gaussian model to visibility amplitude data
gaussian_image_comparison_numerical.cpp	Fits Gaussian model to visibility amplitude data
parameterized_scattering_model_test.cpp
symmetric_gaussian_comparison.cpp	Fits a symmetric Gaussian model to visibility amplitude data
visibility_test.cpp	Tests the visibility construction for simple models
► util
constants.h	Provides a list of constants (in cgs) to be used throughout Themis
image_family_error.cpp	Source file for a utility class that generates an approximation of the systemtic error as measured by the variance among images
image_family_error.h	Header file for a utility class that generates an approximation of the systemtic error as measured by the variance among images
interpolator1D.cpp	Implements a multipurpose linear interpolation function
interpolator1D.h	Header file for a multipurpose linear interpolation function
interpolator2D.cpp	Implements a general purpose 2D interpolator class that implements a variety of interpolation schemes
interpolator2D.h	Header file for a general purpose 2D interpolator class that implements a variety of interpolation schemes
quadrature.cpp	Implements a Gaussian Quadrature integration scheme with Legendre or Hermite polynomial weights
quadrature.h	Header file for a general purpose Gaussian Quadrature class that implements a variety of integration schemes
random_number_generator.cpp	Implements various random number generators using the algorithms in "Numerical Recipes in C" by Flannery, Teukolsky, Press, and Vettering
random_number_generator.h	Header file for various random number generators using the algorithms in "Numerical Recipes in C" by Flannery, Teukolsky, Press, and Vettering
stop_watch.cpp	Header file for a general purpose timer based on the C time function
stop_watch.h	Header file for a general purpose timer based on the C time function
utils.cpp	Implements a variety of utility functions within Themis
utils.h	Header file for a variety of utility functions within Themis
► validation
asymmetric_gaussian_image_comparison.cpp	Fits an asymmetric Gaussian model to visibility amplitude data for validation purposes
complex_visibilities_tests.cpp	Test rig for developing and testing the likelihood_small_gain_correction_visibility_amplitude class
crescent_image_comparison.cpp	Fits a crescent model to visibility amplitude data for validation purposes
crescent_image_comparison_themistan.cpp	Fits a crescent model to visibility amplitude data using the deo tempering sampler with the stan exploration kernel. This is a validation and test for it
crosshand_visibilities_tests.cpp	Test rig for developing and testing the likelihood_small_gain_correction_visibility_amplitude class
eggbox_mcmc_sampling.cpp	Samples an extremely muti-modal and spiky likelihood surface in five dimentions
griewank_mcmc_sampling.cpp	Samples a N-dimensional Griewank function
lorentz_mcmc_sampling.cpp	Samples a 1D Lorentzian function
riaf_lklhd_va.cpp	To be added
riaf_va_cp.cpp	Validation test for the RIAF model with visibility amplitude and closure pahase data ..
riaf_visibility_amplitude.cpp	Test main file for the RIAF model with visibility amplitude data
rosenbrock_mcmc_sampling.cpp	Samples a 2D Rosenbrock function
small_gain_tests.cpp	Test rig for developing and testing the likelihood_small_gain_correction_visibility_amplitude class
symmetric_gaussian_comparison.cpp	Fits a symmetric Gaussian model to visibility amplitude data for validation purposes