Releases | Open Source Science

species - species v0.10.0

Several grids of model spectra added
Optimization of FitEvolution
Updated atmospheric retrieval tools
Refactored implementation of uncertainty inflation
Included covariances in chi2 calculation
Added back the extinction of dust with log-normal and power-law distributions
And many more new features, improvements, and some small fixes!

- Python
Published by tomasstolker 10 months ago

species - species v0.9.0

Added support for Python 3.12, dropped support for Python 3.9
Separated atmosphere and disk luminosity in ModelBox parameters
Fixed issue with finding missing grid spectra
Fixed issue with plotting filter profile width
Added pyproject.toml and removed setup.py
Removed most version restrictions from requirements.txt
Added font_size parameter to plot_spectrum
Fixed pathlib error when adding grids with add_custom_model
Updated flux calibration tutorial
Many small improvements and overall code maintenance

- Python
Published by tomasstolker over 1 year ago

species - species v0.8.4

Several small fixes in the retrieval framework (thanks @wbalmer!)
Added flux_units parameter to get_mcmc_photometry
Support for fitting multiple disk_teff and disk_radius parameters in FitModel
Support for fitting the combined photometry of unresolved binary stars with different parallaxes
Multiple improvements for fitting a combination of two spectra in FitModel
Support for flux ratio prior for filters when fitting a binary system
Check for NaNs in the uncertainties when adding a spectrum with add_object
Updated plot_posterior for showing posteriors from binary systems
Returning the individual binary components with get_mcmc_spectra
Added support for coolTLUSTY Y dwarf spectra
Tutorial for comparing data with a model grid of spectra
Support for fitting separate ism_ext parameters for a binary system
Support for PHOENIX Husser et al. (2013) models
Major refactoring of FitModel, improved extinction accuracy, faster interpolation based on Teff prior
Added optional database_file parameter to SpeciesInit
Added fixed_param parameter to add_samples
Added tag parameter and several improvements in get_residuals
Changed the values added with inc_loglike to ln(L)
Included chi2 and n_dof in ResidualBox
Fixed indentation problem in CompareSpectra
Robust implementation for filenames by using the pathlib instead of the os module
Using pooch instead of urllib for downloading files
Fixed bug in get_samples with reading normal priors
Fixed bug with storing the log-likelihood after running run_multinest
Fixed Windows issue with the Linder et al. (2019) isochrones
Check for NaN and inf when calculating the goodness-of-fit statistic in CompareSpectra
Exclude SpeX spectra that can not be flux calibrated when adding with add_spectra
Updated dependency versions
Overall code maintenance, many minor improvements, and updated tutorials

- Python
Published by tomasstolker about 2 years ago

species - species v0.8.3

Another fix in setup.py! Adding a missing JSON file to the package_data.

- Python
Published by tomasstolker over 2 years ago

species - species v0.8.2

Fixing issue with setup.py to include the JSON files in the package on PyPI

- Python
Published by tomasstolker over 2 years ago

species - species v0.8.1

Fixed issue with max_prob parameter in plot_posterior
Included uniform_priors and normal_priors to SamplesBox
Added show_priors parameter to plot_posterior
Fixed issue with wavelength precision in Exo-Rem grid
Added verbose parameter to list_filters method of ReadObject
Implemented the units parameter in plot_spectrum
Added convert_from parameter to convert_units function
Extended the BT-NextGen grid to 5 mm
Allowing to fix the parallax when fitting with FitModel
Including the blackbody radius (calculated from disk_teff) in the posterior with inc_luminosity=True in plot_posterior
Added the add_simple_object method to Database for retrieving data from the SIMPLE Database
Support for providing a spectrum array directly to the spectrum parameter of add_object
Retrieving the f_sed parameter for each cloud species individually by setting global_fsed=False
Added spec_res attribute to ModelBox
Support for Sonora Elf Owl L-, T-, and Y-type grids
Fixed issue with appending mode for opening the HDF5 database
Fixed issue with package_data in setup.py

- Python
Published by tomasstolker over 2 years ago

species - species v0.8.0

Improved package structure by including additional subpackages and modules
The implicit import of classes and functions is removed from the initialization of the package, instead these should be explicitly imported by the user
Started with implementing improved output printing, added print_section function in core_util
Support for BT-NextGen subsolar metallicity grid (tag='bt-nextgen-subsolar')
Changed default transmission threshold from 0.05 to 0.01 in SyntheticPhotometry
GJ 758 B included in companion_data.json (thanks @mperrin!)
Tutorial included for plotting companion properties
Fitting a flux scaling and offset in FitModel
Updated add_model_grid such that only spectra files are unpacked within the selected teff_range
Added unpack_tar parameter to add_model
Update links in tutorials and documentation pages
Added verbose parameter to available_models and list_companions
Fixed issue with float type returned by likelihood function
Fixed issue with np.inf in the likelihood that can not be handled by UltraNest
Added setup_retrieval method to AtmosphericRetrieval
Added gradient P-T parameterization from Zhang et al. 2023 (thanks @wbalmer!)
Support for nested sampling with Dynesty in AtmosphericRetrieval with run_dynesty method (thanks @wbalmer!)
Refactoring of the prior function in FitModel so it is shared by the sampling routines
Added normal_prior parameter to FitModel and deprecated the prior parameter in run_multinest and run_ultranest
Added resume and kwargs_multinest parameters to run_multinest
Added resume and kwargs_ultranest parameters to run_ultranest
Spectra are no longer removed when rerunning add_object with different spectrum labels
Changed scipy.interpolate.interp1d to numpy.interp which produces the same output but interp1d is considered a legacy function
Added calc_phot parameter to contrast_to_mass
Retrieving log_p_base with physical clouds instead of using the condensation profile
Added param_fmt parameter to plot_spectrum
Fixed issue with appending to database during multiprocessing
Added verbose parameter to get_median_sample, get_probably_sample, and get_compare_sample
Store priors from FitModel in the database results
Removed interp_method from configuration so linear interpolation is used
Added rad_vel and vsini as optional retrieval parameters in AtmosphericRetrieval
Added support for nested sampling with Dynesty in FitModel with run_dynesty method
Renamed the spec_res parameter in add_model to wavel_sampling
Deprecated the smooth parameter in ReadModel and ReadPlanck since the spec_res parameter is sufficient
Renamed the get_spec_res method in ReadModel to get_sampling
Moved the convert_model_name function to the model_util module
Added option to use wavel_range parameter without setting wavel_sampling in order to not resample but store a restricted wavelength range
Increased dependency versions in requirements.txt
Updated documentation and tutorials
Many small enhancements and several minor bug fixes

- Python
Published by tomasstolker over 2 years ago

species - species v0.7.4

Added the contrast_to_mass method to ReadIsochrone for converting contrast values for a given filter into masses
Support for clear and cloudy model spectra of the petitCODE grid that is used for the isochrones from Linder et al. (2019)
Possibility to include only photometric fluxes when comparing a grid of model spectra with CompareSpectra

- Python
Published by tomasstolker over 2 years ago

species - species v0.7.3

Removed deprecated update_spectra function
Some minor maintenance of util and plot functions
Updated notebook tutorials

- Python
Published by tomasstolker almost 3 years ago

species - species v0.7.2

Updated the type annotations so they are compatible with Python 3.11
Tested the notebook tutorials and fixed several small issues due to code changes

- Python
Published by tomasstolker almost 3 years ago

species - species v0.7.1

SPHINX model spectra: add_model('sphinx')
BEX isochrones from Linder et al. (2019): add_isochrones('linder2019')
Keck NIRC Y-band filter: add_filter('Keck/NIRC.Y')

- Python
Published by tomasstolker almost 3 years ago

species - species v0.7.0

Added support for Python 3.11 and dropped support for Python 3.8
Added a check in ReadColorMagnitude for selecting an incorrect filter name that is not part of a photometric library
Retrieving free abundances that vary with altitude using AtmosphericRetrieval
Included FitEvolution for estimating ages and masses from luminosities
Changed use of interp2d to RegularGridInterpolator
Optimization in CompareSpectra so it runs faster
Added plot_abundances function to plot_retrieval module
Added the res_mode and lbl_opacity_sampling parameters to AtmosphericRetrieval
Changed lbl_species parameter of AtmosphericRetrieval to ccf_species
Added lbl_opacity_sampling parameter to ReadRadtrans
Generalized the implementation of the mean_molecular_weight function
Changed photometric uncertainty inflation in FitModel to relative to the uncertainties instead of relative to the flux
Changed weights parameter in FitModel to apply_weights and improved its functionality
Added convert_units_plot function to plot_util
Capital sensitive unit conversion with convert_units function
Added inc_abund parameter to plot_posterior
Added units parameter to add_object
Added extra_param parameter to plot_grid_statistic
Added plot_model_spectra to plot_comparison module
Maintenance of plot_comparison functions
Updated dependency versions, documentation, and docstrings
A lot of small improvements and maintenance!

- Python
Published by tomasstolker almost 3 years ago

species - species v0.6.0

The calibration spectrum of Vega has been updated to the latest version from STScI CALSPEC
Added vega_mag parameter to the configuration file
Refactored the data.vega module
Added optional zero_point parameter to SyntheticPhotometry
The zp_flux parameter of magnitude_to_flux is set to deprecated
Improved CompareSpectra functionalities
Added add_custom_model to Database for adding manual grid
Support for fitting vsin(i) and RV parameters with FitModel
Refactored the ReadIsochrone class
Added get_photometry and get_spectrum methods to ReadIsochrone
Support for non-self-consistent coupling with atmospheric models in ReadIsochrone
Added extra_param parameter to several methods of ReadIsochrone
Using pooch for downloading grids of model spectra
Support for using ATMO isochrones and grids of model spectra
Added ext_filter parameter to FitModel and convert_to_av function to dust_util
Remove NaN fluxes when calculating synthetic photometry from spectrum
Check for NaNs when sampling the uncertainty on a synthetic flux
Improved use of field_range parameter in plot_color_color and plot_color_magnitude
Additional attributes in SynphotBox
All plot functions return the Figure object such that manual adjustments are possible
Added radius attribute to IsochroneBox and CoolingBox
Added return_box parameter to get_flux and get_magnitude in ReadModel
Multiple smaller improvements and bug fixes
Updated documentation, tutorials, and docstrings
Overall maintenance and code style improvements

- Python
Published by tomasstolker about 3 years ago

species - species v0.5.5

Added the add_accretion method to Database for adding the accretion coefficients (see Aoyama et al. 2021), including the extrapolation from Marleau & Aoyama (2022).
Feature in EmissionLine for converting hydrogen line luminosities in accretion luminosities (see updated tutorial)
Support for the clear and cloudy model spectra from Saumon & Marley (2008), to be added with the tags 'saumon2008-clear' and 'saumon2008-cloudy'
Support for the grid of model spectra from Petrus et al. (2023), to be added with the tag 'petrus2023'
Safe extraction of TAR files (thanks to @TrellixVulnTeam)
Added envelope parameter to plot_pt_profile and plot_spectrum
Added create_color_magnitude and create_color_color methods to ReadModel
Support in plot_color_magnitude and plot_color_color for output from ReadModel
Refactored working with companion data and added the companion_data.json file to the repository (see updated tutorial)
Started implementing pooch for downloading files
Added spectra of GQ Lup B to companion_spectra
Added inc_model_name parameter to plot_spectrum
Added get_condensation_curve function to retrieval_util
Updated documentation, docstrings, and tutorials
Minor maintenance and improvements to code style

- Python
Published by tomasstolker over 3 years ago

species - species v0.5.4

Support for Saumon & Marley (2008), Baraffe et al. (2015), and NextGen isochrones
Added get_cooling_curve, get_filters, get_mass, and get_radius methods to ReadIsochrone
Ignore parameters in ReadModel that are not mandatory
Bug fix with reading the Sonora Bobcat evolutionary models
Support for Mg2SiO4 cloud species in AtmosphericRetrieval
Added grid_hspace parameter to plot_spectrum
Added get_magnitude method to ReadRadtrans
Support for rad_vel and vsini parameters in ReadRadtrans
Added inc_log_mass parameter to plot_posterior
Notebook tutorial for ReadIsochrone
Minor maintenance and improvements to code and documentation

- Python
Published by tomasstolker almost 4 years ago

species - species v0.5.3

Support for BT-Dusty model spectra (add_model('bt-dusty'))
Support for BT-Settl isochrones (add_isochrones('bt-settl'))
The integrate_spectrum method is added to ReadModel for integrating the bolometric luminosity
The param_inc and object_type parameters are added to the plot_posterior function
Several enhancements for handling calibration spectra
Some code maintenance and improvements in the documentation and tutorials

- Python
Published by tomasstolker almost 4 years ago

species - species v0.5.2

Several enhancements with the isochrone functionalities
Support for Sonora Bobcat isochrones (add_isochrones('sonora'))
Use of the parallax parameter in addition to distance (e.g. in add_object, add_companion, SyntheticPhotometry)
The analysis routines (e.g. FitModel, EmissionLine, AtmosphericRetrieval) use by default the parallax as free parameter with a Gaussian prior
Removed the run_mcmc (i.e. using emcee) method in FitModel, because it was no longer maintained and it is recommended to use the nested sampling routines
Support for Koester white dwarf spectra (for calibration purpose)
Options for retrieving parametrized cloud opacities with AtmosphericRetrieval
Included the interp_method parameter in the configuration file for setting the method for the grid interpolation
Improvements with the labels in various plots and the font style
Many minor enhancements, maintenance, and updated tutorials and documentation

- Python
Published by tomasstolker about 4 years ago

species - species v0.5.1

Fixed issue with the prior of distance when using FitModel.run_ultranest
Enhancement with the integrated autocorrelation time that is calculated in Database.add_samples
The plot_filename parameters in EmissionLine can be set to None to show instead of save a plot
The default zorder is only added to the plot_kwargs dictionaries in plot_spectrum if not already included
Updated notebook tutorials
Style improvements and minor maintenance
Updated setup.py

- Python
Published by tomasstolker about 4 years ago

species - species v0.5.0

Framework for free retrievals with petitRADTRANS in the AtmosphericRetrieval class
Notebook tutorials for free retrievals and reading companion data
Changed the co parameter to c_o_ratio
Added list_filters method to ReadObject
Support for fitting blended stars/companions with FitModel
Photometric error inflation per instrument
Added synthetic_photometry method to ModelBox
Possibility to show a plot instead of writing to a file
Refactoring of add_model
Support for Sonora model spectra
Added available_models to Database for details about the atmospheric models
Added reduced chi2 calculation to get_residuals
Added get_evidence method to Database
Added support for Python 3.10 and removed support for Python 3.7
Updated documentation, docstrings, and dependency versions
Many small new features, enhancements, and bug fixes!

- Python
Published by tomasstolker over 4 years ago

species - species v0.4.0

T/Y spectra from Morley et al. (2012)
Libraries with empirical low-gravity spectra
Companions spectra in data.companions
Improvements in comparison tools for spectra
Some additional parameters and minor functionalities
Code maintenance and a few minor bug fixes
Dropped support for Python 3.6 and added support for Python 3.9
Changed CI from Travis to Github Actions

- Python
Published by tomasstolker almost 5 years ago

species - species v0.3.6

Functionalities for the analysis of emission lines (see EmissionLine and the notebook tutorial).
Update in data.filters to comply with the change on the SVO website regarding the detector type.
The wavel_resample parameter was added to Database.get_mcmc_spectra and ReadPlanck.get_spectrum.
The phot_type parameter was added to Database.get_mcmc_photometry.
The smooth_spectrum and resample_spectrum methods were added to ModelBox.
The read_util.gaussian_spectrum function was added.
Stellar and companion properties were added to data.companions.
Functionalities for comparing a spectrum with a grid of model spectra (see CompareSpectra.compare_model, Database.get_compare_sample, and plot_grid_statistic).
Some refactoring in ReadModel for improved readability.
A number of smaller improvements to the code and documentation.

- Python
Published by tomasstolker about 5 years ago

species - species v0.3.5

Support for nested sampling with UltraNest. The run_ultranest method is added in FitModel.
Added the spec_res parameter in ReadCalibration.resample_spectrum to smooth a spectrum before resampling.
Tools for empirical analysis. CompareSpectra.spectral_type can be used for determining the spectral type.
The plot_statistic and plot_empirical_spectra functions can be used for plotting the results from CompareSpectra.
Support for the SDSS spectra from Kesseli et al. (2017).
Support for running FitModel with MPI. Requires the manual installation of mpi4py.
Improved notebook tutorial for fitting data with model spectra.
Some minor maintenance. Several warnings and errors added.

- Python
Published by tomasstolker over 5 years ago

species - species v0.3.4

Moved the remote storage location of the model grids.
Reading corr_len and corr_amp parameters from bounds and use default values otherwise.
Added effective_width method to ReadFilter.
Updated README and Makefile.

- Python
Published by tomasstolker over 5 years ago

species - species v0.3.3

Compatibility with Python 3.8. The CI tests with Python 3.6, 3.7 and 3.8.
Updated README, documentation and some minor maintenance.

- Python
Published by tomasstolker over 5 years ago

species - species v0.3.2

Support for fitting power-law spectra with FitModel.
Support for fitting a blackbody disk component in FitModel.
Support for ATMO, BT-Cond, and (now publically available) petitCODE hot grid spectra.
Added the inc_mass parameter in plot_posterior.
Improved title_fmt parameter in plot_posterior.
Added the flux_density parameter in add_object.
Support for ALMA fluxes.
Renamed plot_photometry to plot_mag_posterior.
Support of get_mcmc_photometry for calibration spectra.
Improved sampling of the log-normal grain size distribution. The grid of cross sections has been recalculated.
New error inflation approach. A scaling relative to the model fluxes is fitted instead of a constant value.
A large number of smaller, new features and improvements.
Some maintenance and updated dependencies.
Updated tutorials, documentation and docstrings.
Additional type hints and type checks.

- Python
Published by tomasstolker over 5 years ago

species - species v0.3.1

The spectra of AMES-Cond, AMES-Dusty, DRIFT-PHOENIX, BT-Settl, and BT-NextGen have been resampled to a spectral resolution of R=2000 and moved to a new download location (https://people.phys.ethz.ch/~ipa/tstolker/). The data size of these grids are typically several hundred MBs so downloading and processing is much faster now.
Support for photon-counting detectors when calculating synthetic photometry. The detector type is stored as attribute with the filter profile.
Extinction parameters have been added to FitModel: ISM extinction, a power-law size distribution of silicate grains, or a log-normal size distribution of silicate grains (see documentation for details).
Functions in plot_mcmc for plotting the sampled extinction and size distributions: plot_extinction and plot_size_distributions.
Refactoring of dust_util.
Bug fix when fixing missing grid points with add_model.
Support for the BT-Settl CIFIST spectra ('bt-settl-cifist').
Additional unit tests and updated documentation.
Several minor improvements, bug fixes, new features, and maintenance.

- Python
Published by tomasstolker almost 6 years ago

species - species v0.3.0

Nested sampling support by FitModel with run_multinest.
Fitting blackbody spectra has been merged in FitModel and FitPlanck has been deprecated
Support of FitModel for fitting calibration parameters, including a Gaussian process for correlated noise.
Support for duplicate filter names.
The inc_phot and inc_spec parameters allow for subsets of data.
Added optical constants and a reddening parameter in plot_color_magnitude and plot_color_color.
Added the inc_luminosity parameter in `plot_posterior.
Improved and faster use of parallaxes.
Type checks added to some of the classes and methods.
Compatibility of add_object with the GRAVITY FITS format.
Several new features for fine-tuning of plots, including the plot_kwargs parameter in plot_spectrum.
Many small improvements and a few bug fixes.

- Python
Published by tomasstolker about 6 years ago