Getting Started
Installation
Installation from PyPI
Installation from Github
Testing
species
Running
species
Initiating
species
Adding a photometric library
Adding companion data
Reading color-magnitude data
Plotting a color-magnitude diagram
User Documentation
Overview
Introduction
Supported data
Analysis tools
Output boxes
Configuration
Tutorials
Flux and magnitude conversion
Getting started
Magnitude to flux
Flux to magnitude
Zero point flux
Synthetic photometry
Getting started
Jupiter spectrum
Synthetic flux and magnitude
Spectral library
Getting started
Adding a spectral library to the database
Reading a spectral library
Opening a SpectrumBox
Synthetic photometry
Plotting spectrum and synthetic fluxes
Color-magnitude diagram: broadband filters
Initiating
species
Adding data to the database
Database content
Synthetic photometry from isochrones
Photometry of directly imaged objects
Reading color-magnitude data
Plotting a color-magnitude diagram
Color-magnitude diagram: narrowband filters
Getting started
Adding data and models
Synthetic colors and magnitudes
Selecting directly imaged planets
Plotting a color-magnitude diagram
Atmospheric models
Getting started
Adding model spectra to the database
Interpolating the model grid
Extracting a spectrum at a grid point
Calculating synthetic photometry
Comparison of data and model
Initiating
species
Adding model spectra
Adding companion data
Reading model spectra
Reading companion data
Synthetic photometry for all filters
Creating flux residuals
Opening Box objects
Plotting spectra, fluxes and filters
Photometric calibration: fitting a stellar spectrum
Getting started
Adding an object and calibration spectrum
Fitting the stellar spectrum
Plotting the results
Photometric calibration
Fitting photometric data with model spectra
Getting started
Adding data to the database
Fitting data with MCMC
Plotting the MCMC samples
Extracting boxes with results
Plotting the SED and MCMC results
API documentation
species package
Subpackages
species.analysis package
Submodules
species.analysis.fit_model module
species.analysis.fit_planck module
species.analysis.fit_spectrum module
species.analysis.photometry module
Module contents
species.core package
Submodules
species.core.box module
species.core.constants module
species.core.setup module
Module contents
species.data package
Submodules
species.data.ames_cond module
species.data.ames_dusty module
species.data.btnextgen module
species.data.btsettl module
species.data.companions module
species.data.database module
species.data.drift_phoenix module
species.data.exo_rem module
species.data.filters module
species.data.irtf module
species.data.isochrones module
species.data.leggett module
species.data.petitcode module
species.data.spex module
species.data.vega module
species.data.vlm_plx module
Module contents
species.plot package
Submodules
species.plot.plot_color module
species.plot.plot_mcmc module
species.plot.plot_spectrum module
Module contents
species.read package
Submodules
species.read.read_calibration module
species.read.read_color module
species.read.read_filter module
species.read.read_isochrone module
species.read.read_model module
species.read.read_object module
species.read.read_planck module
species.read.read_spectrum module
Module contents
species.util package
Submodules
species.util.data_util module
species.util.phot_util module
species.util.plot_util module
species.util.query_util module
species.util.read_util module
species.util.test_util module
Module contents
Module contents
About species
Contributing
About
Questions & feedback
Attribution
species
Docs
»
Index
Edit on GitHub
Index
A
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B
|
C
|
D
|
F
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G
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I
|
L
|
M
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N
|
O
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P
|
Q
|
R
|
S
|
U
|
W
|
Z
A
absolute_to_apparent() (in module species.util.phot_util)
add_ames_cond() (in module species.data.ames_cond)
add_ames_dusty() (in module species.data.ames_dusty)
add_baraffe() (in module species.data.isochrones)
add_btnextgen() (in module species.data.btnextgen)
add_btsettl() (in module species.data.btsettl)
add_calibration() (species.data.database.Database method)
add_companion() (species.data.database.Database method)
add_drift_phoenix() (in module species.data.drift_phoenix)
add_exo_rem() (in module species.data.exo_rem)
add_filter() (species.data.database.Database method)
add_irtf() (in module species.data.irtf)
add_isochrones() (species.data.database.Database method)
add_leggett() (in module species.data.leggett)
add_luminosity() (in module species.util.read_util)
add_marleau() (in module species.data.isochrones)
add_missing() (in module species.util.data_util)
add_model() (species.data.database.Database method)
add_object() (species.data.database.Database method)
add_petitcode_cool_clear() (in module species.data.petitcode)
add_petitcode_cool_cloudy() (in module species.data.petitcode)
add_petitcode_hot_clear() (in module species.data.petitcode)
add_petitcode_hot_cloudy() (in module species.data.petitcode)
add_photometry() (species.data.database.Database method)
add_samples() (species.data.database.Database method)
add_spectrum() (species.data.database.Database method)
add_spex() (in module species.data.spex)
add_vega() (in module species.data.vega)
add_vlm_plx() (in module species.data.vlm_plx)
apparent_to_absolute() (in module species.util.phot_util)
B
Box (class in species.core.box)
C
ColorColorBox (class in species.core.box)
ColorMagBox (class in species.core.box)
correlation_to_covariance() (in module species.util.data_util)
create_box() (in module species.core.box)
create_config() (in module species.util.test_util)
D
Database (class in species.data.database)
delete_data() (species.data.database.Database method)
download_filter() (in module species.data.filters)
F
field_bounds_ticks() (in module species.util.plot_util)
filter_fwhm() (species.read.read_filter.ReadFilter method)
FitModel (class in species.analysis.fit_model)
FitPlanck (class in species.analysis.fit_planck)
FitSpectrum (class in species.analysis.fit_spectrum)
flux_to_magnitude() (species.analysis.photometry.SyntheticPhotometry method)
G
get_absmag() (species.read.read_object.ReadObject method)
get_bounds() (species.read.read_model.ReadModel method)
get_color_color() (species.read.read_color.ReadColorColor method)
(species.read.read_isochrone.ReadIsochrone method)
(species.read.read_planck.ReadPlanck method)
get_color_magnitude() (species.read.read_color.ReadColorMagnitude method)
(species.read.read_isochrone.ReadIsochrone method)
(species.read.read_planck.ReadPlanck method)
get_data() (in module species.data.companions)
(species.read.read_model.ReadModel method)
get_distance() (in module species.util.query_util)
(species.read.read_object.ReadObject method)
get_filter() (species.read.read_filter.ReadFilter method)
get_flux() (species.read.read_calibration.ReadCalibration method)
(species.read.read_model.ReadModel method)
(species.read.read_planck.ReadPlanck method)
(species.read.read_spectrum.ReadSpectrum method)
get_isochrone() (species.read.read_isochrone.ReadIsochrone method)
get_magnitude() (species.read.read_calibration.ReadCalibration method)
(species.read.read_model.ReadModel method)
(species.read.read_planck.ReadPlanck method)
(species.read.read_spectrum.ReadSpectrum method)
get_mass() (in module species.util.read_util)
get_mcmc_photometry() (species.data.database.Database method)
get_mcmc_spectra() (species.data.database.Database method)
get_median_sample() (species.data.database.Database method)
get_model() (species.read.read_model.ReadModel method)
get_object() (species.data.database.Database method)
get_parallax() (in module species.util.query_util)
get_parameters() (species.read.read_model.ReadModel method)
get_photometry() (species.read.read_object.ReadObject method)
get_points() (species.read.read_model.ReadModel method)
get_probable_sample() (species.data.database.Database method)
get_residuals() (in module species.util.phot_util)
get_samples() (species.data.database.Database method)
get_simbad() (in module species.util.query_util)
get_spectrum() (species.read.read_calibration.ReadCalibration method)
(species.read.read_object.ReadObject method)
(species.read.read_planck.ReadPlanck method)
(species.read.read_spectrum.ReadSpectrum method)
get_wavelengths() (species.read.read_model.ReadModel method)
I
interpolate_filter() (species.read.read_filter.ReadFilter method)
interpolate_grid() (species.read.read_model.ReadModel method)
interpolate_model() (species.read.read_model.ReadModel method)
IsochroneBox (class in species.core.box)
L
list_companions() (species.data.database.Database static method)
list_content() (species.data.database.Database method)
lnlike() (in module species.analysis.fit_model)
(in module species.analysis.fit_planck)
lnprior() (in module species.analysis.fit_model)
(in module species.analysis.fit_planck)
lnprob() (in module species.analysis.fit_model)
(in module species.analysis.fit_planck)
(in module species.analysis.fit_spectrum)
M
magnitude_to_flux() (species.analysis.photometry.SyntheticPhotometry method)
mean_wavelength() (species.read.read_filter.ReadFilter method)
model_name() (in module species.util.plot_util)
ModelBox (class in species.core.box)
multi_photometry() (in module species.util.phot_util)
N
NoStdStreams (class in species.util.query_util)
O
ObjectBox (class in species.core.box)
open_box() (species.core.box.Box method)
open_database() (species.read.read_model.ReadModel method)
P
PhotometryBox (class in species.core.box)
planck() (species.read.read_planck.ReadPlanck static method)
plot_color_color() (in module species.plot.plot_color)
plot_color_magnitude() (in module species.plot.plot_color)
plot_photometry() (in module species.plot.plot_mcmc)
plot_posterior() (in module species.plot.plot_mcmc)
plot_spectrum() (in module species.plot.plot_spectrum)
plot_walkers() (in module species.plot.plot_mcmc)
Q
quantity_unit() (in module species.util.plot_util)
R
ReadCalibration (class in species.read.read_calibration)
ReadColorColor (class in species.read.read_color)
ReadColorMagnitude (class in species.read.read_color)
ReadFilter (class in species.read.read_filter)
ReadIsochrone (class in species.read.read_isochrone)
ReadModel (class in species.read.read_model)
ReadObject (class in species.read.read_object)
ReadPlanck (class in species.read.read_planck)
ReadSpectrum (class in species.read.read_spectrum)
resample_spectrum() (species.read.read_calibration.ReadCalibration method)
ResidualsBox (class in species.core.box)
run_mcmc() (species.analysis.fit_model.FitModel method)
(species.analysis.fit_planck.FitPlanck method)
(species.analysis.fit_spectrum.FitSpectrum method)
run_multinest() (species.analysis.fit_model.FitModel method)
S
SamplesBox (class in species.core.box)
smooth_spectrum() (in module species.util.read_util)
sort_data() (in module species.util.data_util)
species (module)
species.analysis (module)
species.analysis.fit_model (module)
species.analysis.fit_planck (module)
species.analysis.fit_spectrum (module)
species.analysis.photometry (module)
species.core (module)
species.core.box (module)
species.core.constants (module)
species.core.setup (module)
species.data (module)
species.data.ames_cond (module)
species.data.ames_dusty (module)
species.data.btnextgen (module)
species.data.btsettl (module)
species.data.companions (module)
species.data.database (module)
species.data.drift_phoenix (module)
species.data.exo_rem (module)
species.data.filters (module)
species.data.irtf (module)
species.data.isochrones (module)
species.data.leggett (module)
species.data.petitcode (module)
species.data.spex (module)
species.data.vega (module)
species.data.vlm_plx (module)
species.plot (module)
species.plot.plot_color (module)
species.plot.plot_mcmc (module)
species.plot.plot_spectrum (module)
species.read (module)
species.read.read_calibration (module)
species.read.read_color (module)
species.read.read_filter (module)
species.read.read_isochrone (module)
species.read.read_model (module)
species.read.read_object (module)
species.read.read_planck (module)
species.read.read_spectrum (module)
species.util (module)
species.util.data_util (module)
species.util.phot_util (module)
species.util.plot_util (module)
species.util.query_util (module)
species.util.read_util (module)
species.util.test_util (module)
SpeciesInit (class in species.core.setup)
spectrum_to_flux() (species.analysis.photometry.SyntheticPhotometry method)
spectrum_to_magnitude() (species.analysis.photometry.SyntheticPhotometry method)
SpectrumBox (class in species.core.box)
sptype_stellar() (in module species.util.plot_util)
sptype_substellar() (in module species.util.plot_util)
SynphotBox (class in species.core.box)
SyntheticPhotometry (class in species.analysis.photometry)
U
update_filter() (in module species.util.data_util)
update_labels() (in module species.util.plot_util)
update_parameters() (species.read.read_planck.ReadPlanck static method)
update_spectra() (in module species.util.read_util)
update_sptype() (in module species.util.data_util)
W
wavelength_points() (species.read.read_model.ReadModel method)
wavelength_range() (species.read.read_filter.ReadFilter method)
write_data() (in module species.util.data_util)
Z
zero_point() (species.analysis.photometry.SyntheticPhotometry method)
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