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Changelog

v.1.2.3

Two bug fixes; new functions; minor, backward-compatible API changes; additional tests

  • fit.py
    • Adds call to 'utilities.check_uv' in fit runner
  • test.py
    • Adds tests for utilities objects and for radial_fitters.FrankFitter.log_evidence_laplace
  • utilities.py
    • Adds function check_uv
    • Adds option in get_fit_stat_uncer to return log uncertainty for LogNormal model
    • Adds option in make_mock_data to reproject
    • Fixes bug in normalize_uv
    • Fixes two bugs in sweep_profile
  • setup.cfg
    • Excludes scipy versions with known bug for scipy.optimize.nnls
    • Updates supported Python versions
  • Docs:
    • Minor updates to tutorials using utilities.make_mock_data

v.1.2.2

One bug fix, some code refactoring, a couple new functionalities, integrates scale-height fits into command-line UI

  • default_parameters.json, parameter_descriptions.json:
    • Adds parameters: 'convergence_failure', 'I_scale', 'save_figures', 'scale_height'
  • filter.py
    • Breaks 'spectral_smoothing_matrix' out of 'CriticalFilter'; some restructuring of 'covariance_MAP' and 'log_prior'
  • fit.py
    • Adds 'get_scale_height' function
  • hankel.py
    • Adds 'interpolation_coefficients' and 'interpolate' functions
  • io.py
    • Fixed a bug that was saving incorrect uncertainty for LogNormal brightness profile
  • make_figs.py
    • Adds non-negative fit to figures
  • radial_fitters.py
    • Adds 'convergence_failure' arg to FrankFitter
    • Adds 'log_evidence_laplace' function to FrankFitter
  • statistical_models.py
    • Adds 'DHT_coefficients' and 'interpolate' functions to 'VisibilityMapping'
  • test.py
    • Adds tests for non-negative solver ('test_solve_non_negative') and solution object IO ('test_save_load_sol')
  • utilities.py
    • Adds 'get_fit_stat_uncer' function

v.1.2.1

Fixed a bug that caused non-python files to not be installed through pip

v.1.2.0

Introduction of log-normal fits, large amount of code refactoring to support both 'Gaussian' and 'LogNormal' methods

  • default_parameters.json, parameter_descriptions.json:
    • Adds parameters: 'rescale_flux', 'method'
  • debris_fitters.py
    • Adds support for fitting optically thin but geometrically thick disks with a known Gaussian scale height.
  • filter.py:
    • New module that now hosts the routine for optimizing for power spectrum priors, 'CriticalFilter'
  • fit.py:
    • Adds ability to run either a standard or log-normal fit
  • geometry.py:
    • Adds routine to rescale the total flux according to the source geometry, 'rescale_total_flux'
    • Adds 'rescale_factor' property to 'SourceGeometry'
    • Adds the option to keep all three Fourier components (u,v,w) when deprojecting
  • minimizer.py:
    • New module that hosts routines for solving non-linear minimization problems: 'BaseLineSearch', 'LineSearch', 'MinimizeNewton'
  • radial_fitters.py:
    • Code refactoring:
      • Removes '_HankelRegressor' class
      • Adds 'FrankGaussianFit' and 'FrankLogNormalFit' classes
      • Adds 'FrankRadialFit' class
      • Moves some core functionalities to 'frank.filter' and 'frank.statistical_models'
    • Adds 'MAP', 'I', 'info' properties, and 'assume_optically_thick' parameter, to 'FrankRadialFit'
  • statistical_models.py:
    • New module that now hosts 'GaussianModel' class (containing much of the functionality of the now deprecated '_HankelRegressor'), and adds analogous 'LogNormalMAPModel' class
    • Adds a VisibilityMapping that abstracts the mapping between the brightness profile and visibilities. Handles optically thick (default), optically thin, and debris disk models.
  • tests.py:
    • Adds test for a log-normal fit
  • Docs:
    • Updates API
  • Miscellaneous:
    • Minor bug and typo fixes

v.1.1.0

A number of bug fixes, some increased flexibility in fits from terminal and figure generation, several new optional fit parameters

  • default_parameters.json, parameter_descriptions.json:
    • Adds additional parameters: 'asinh_a', 'fit_inc_pa', 'gamma', 'norm_residuals', 'norm_wle', 'plot_in_logx', 'stretch', 'use_median_weight'
  • fit.py:
    • Fixes bug in which 'norm_wle' parameter was not checked
  • geometry.py:
    • Fixes bug in 'deproject' that was redefining global variable 'u'
    • Fixes unit conversion bug in 'FitGeometryGaussian' when inc and/or PA are user-provided, fixes 'guess' bug in '__init__'
    • Adds option to only fit for dRA and dDec
  • io.py:
    • Adds more careful checks of UVtable format
  • make_figs.py:
    • Fixes a few plot generation bugs in figures
    • Adds some more flexibility to figure generation, including arcsinh colorscale for 2D image
  • tests.py:
    • Adds a few tests
  • utilities.py:
    • Fixes bug in 'convolve_profile'
    • Fixes bug in 'estimate_weights', adds optional 'q' argument
    • Updates 'sweep_profile' to optionally return reprojected 2D image, adds optional 'dr' argument
    • Updates 'UVDataBinner' to optionally only intake real component of visibilities
    • Adds a couple logging messages
  • Docs:
    • Updates jupyter notebooks and figures to be consistent with current code version
    • Updates paper links to point to ADS
    • Adds changelog ('HISTORY.rst')
    • Adds video tutorial
    • Adds more verbose descriptions in some parts of docs
  • Miscellaneous:
    • Fixes 'MaskedArray' warnings in 'utilities.py', 'plot.py'
    • Fixes a few other minor bugs

v.1.0.0

Initial production/stable release as used in Jennings et al. 2020

  • default_parameters.json, parameter_descriptions.json:
    • Adds 'initial_guess' parameter for geometry fitting routines
  • geometry.py:
    • Adds nonparametric geometry fitting routine
    • Adds routine to clip inclination and PA to expected range
  • tests.py:
    • Adds several tests
  • Docs:
    • Adds hyperlinks, badges to README
    • Adds code coverage
  • Miscellaneous:
    • Fixes a few other minor bugs

v.0.1.0

Initial release of frank codebase for submission to MNRAS

  • In progress: geometry fitting routines, README, docs