GalPaK v1.34.0

Change log

1.34.0 2024-01-18

• astropy 6.0 compatibility
• bug fix corner plot with pandas

1.33.2 2023-04-17

• python 3.8,3.10 compatibility

1.33.0 2022-10-08

• astropy 5.1 compatibility
• default AdaptiveCauchy for run API

1.32.2 2022-07-25

• proper thickness normalization for thickness_profile
• fix bug zcrop in plot_images

1.32.0 2022-02-01

• added MAOPPY PSF fitter; updates from maoppy version 1.5.0
• added MAOPPY PSF from https://gitlab.lam.fr/lam-grd-public/maoppy

1.31.0 2021-07-26

• bug fix in handling PSF centering. Consequence of 0.5 pixel shifts if even spaxels
• bug fix in handling LSF centering. Consequence of 0.5 pixel shifts if even array

1.30.6 2021-06-16

• bug fix in handling manual variance

1.30.5 2021-05-13

• bug fix in read_model
• save input filenames in run.txt
• multinest outpath option
• added tests

1.30 2020-10-06

• revamped test suite
• better import handling with src/
• few minor bug fixes
• Now available on pypi

1.29 2020-09-10

• bug in read instrument Generic

1.28 2020-05-03

• bug in colormap for true/obs_maps

1.27 2020-04-03

• bug in read_instrument .txt for ALMA
• bug in PA circularization
• better handling pixscale in instruments

1.24 2020-02-24

• change Vmin/Vmax;
• handling circularity pa improvement
• revamped api
• bug fix map indices as floats; impact only for compact galaxies
• NEW option to use flux user-defined map ; as string or ndarray
• NEW option mcmc_sampling to use combo walkers+Cauchy with Emcee doc
• NEW option mcmc_sampling AdaptiveCauchy to adapt Cauchy sampling automatically doc
• NEW option mcmc_method to use multinest doc
• revamped EMCEE (>3.0 only) with mixed Cauchy and StretchMove sampling law

1.20 2019-10-21

• NEW option mcmc_method to use emcee MH or walkers doc
• NEW method_chain option MAP (Maximum A Posteriori)
• NEW added BIC, AIC compute_stats method
• NEW string parser to read/write Model in a CONFIG file doc
• NEW string parser to read/write Instrument in a CONFIG file doc
• more robust handling of nan
• better obs_maps convolution with astropy fft
• added default lsf(lambda) for MUSE
• plot_correlation removed / use plot_corner
• plot_mcmc saved for both sorted and unsorted
• removed chain error maps

1.16.0 2019-07-15

• added Freeman, NFW, Burkert, Spano doc
• revamped model_class
• added boundaries limits to plot_mcmc
• bug fix in convolution when some pixels are nan

1.14.0 2019-07-05

• fix bug in display Mdyn
• fix API logger autorun
• fix bug in display obs_maps (removed moment_maps) using Epinat+2010

1.12.0 2019-04-28

• fix bug in PSF PA

1.11.0 2019-04-05

• New autorun in api to autotune random_scale doc
• New HARMONI class
• added model utilities plot_vprofile & plot_SBprofile
• added cosmology method to model class (Experimental)
• New Extentions class for V22, dvdx

1.10.2 2019-04-02

• save geweke convergence into convergence.dat doc

1.10.1 2019-03-14

• plot geweke diagnostic added
• added error maps
• bug in test reference
• bug when using noLineSpreadFunction

1.10 -- 2019-02-09

• python >3.5 full compatibility
• revamped test suites
• slight improved performances diskmodel / psfextrude

1.9.1 -- 2018-08-01

• bug fix in plot_corner if corner not present
• fix small issue in obs/true maps

1.9.0 -- 2018-04-13

• bug fix in xy_step from cube when RA/Dec not co-aligned with pixels
• enforcing Vmax>0, PA [0, 360]
• improvements on h step
• moved disk calculations to NEW model class DiskModel
• moved line to model class
• added best chi2 in output

1.8.8 -- 2018-03-18

• Generic instrument added default spaxel & cdelt sizes
• fix significant bug in 'mass' rotation_curve for exponential profiles
• added Sersic n=2 flux_profile as 'sersicN2'
• ensured compatibility with numpy >= 1.14
• ensured compatibility with Python3
• improvements in doc on parameter meaning

1.8.7 -- 2018-02-16

• added as_vector and as_table methods to GalaxyParameters class.
• added tutorial info on rereading chains/parameters.
• fixed bug in PA handling around +/-180 using circular statistics
• migrated from asciitable to astropy.io.ascii
• added corner plot
• added tutorial info regarding other statistics [expiremental]
• fixed bug in Vmax min/max boundaries (enforcing they be equal)

1.8.6 -- 2018-01-28

• updates to tutorial regarding variance input
• major overall of variance handling
• fix verbose bug in run api.

1.8.5 -- 2017-09-12 (formally 1.9.1)

• fixed handling of variance

1.8.4 -- 2017-07-13 (formally 1.9.0)

• fixed a few ident and \t issues
• fixed api
• updated tutorial example
• update papers.md

1.8.3 -- 2017-04-10

• allow either alpha or FWHM for MOFFAT; both in arcsec

1.8.2 -- 2017-03-21

• Fixed minor bugs when both CD3_3 and CDELT3 present
• Added FWHM to MOFFAT PSF; moved MOFFAT alpha to arcsec

1.8.1 -- 2017-02-15

• Fixed several minor bugs in plot_true_maps and plot_obs_maps (added slit)

1.8.0 -- 2017-02-13

• Fixed a major bug for compact galaxies (a RunTime error div 0) which lead to occasional Chi2=0, and reduced length of chains
• Improved MUSELineSpreadFunction LSF handling (FWHM computed from moments)

1.7.1 -- 2017-02-09

• Fixed a bug with writeto with MaskedArrays in Hyperspectral
• Allow the possibility to set Cube.var=None to force the variance out

1.7.0 -- 2016-07-14

• Fixed a bug in observed moment & dispersion maps for line singlets ; convolved_cube unaffected

1.6.8 -- 2016-05-23

• Fixed a bug in saving chain
• Fixed a bug in syntax boolean check for psf from an image (and re-normalized)
• Fixed a bug in observed moment & dispersion maps for line doublets; convolved_cube unaffected

1.6.7 -- 2016-03-30

• Fixed a bug for 'observed moment maps' for saved observed maps.fits

1.6.6 -- 2016-03-17

• Fixed a bug for 'observed moment maps' for doublets like OII

1.6.5 -- 2016-03-02

• Added support to save 'observed moment maps'

1.6.4 -- 2016-01-16

• minor bug fix in api; swap orders in get_steps

1.6.3 -- 201508-25

• Added support for Poisson statistics

1.6.2 -- 2015-08-19

• Adding ISOthermal rotation curve

1.6.1 -- 2015-07-08

• minor bug fixes

1.6.0 -- 2015-05-28

• change max_boundaries for the 1/2 light radius to 3/8th of cube_size in pixels [was set to 4"]
• bug fix at the central pixel of the model [showed up when half-light radius is very small < 2pixels]
• remove hidden call with atpy to asciitable
• updated tutorial with file used in paper.
• fix issues with setup.py
• fix small issues with custom PSF images

1.5.0 -- 2015-05-15

• Add a setup.py using distutils.
• Implement doit tasks (for developer only):
  • doit website, or just doit, to rebuild the whole website.
  • doit tarball, to rebuild the distributed tarball.
  • doit publish to upload the website to the remote server.
  • doit all to do it all: doc, tarball, website, publication
• Fix the test suite, which is now ran with the simple nosetests command.

1.4.7 -- 2015-05-11

• Added upper/lower confidence intervals on galaxy parameters from custom percentiles [default = 95%]. (specified with percentile parameter to run_mcmc)
• Make plot_mcmc show -log[chi2] with plot_mcmc(plot_likelihood=True).
• Add hz_profile [profile perpendicular to disk] gaussian [default] exponential or sech2.
• Add a read_files method.

1.4.6 -- 2015-02-19

• Revert to anti-clockwise for PSF_PA.
• Fix minor bug in min/max boundaries.

1.4.5 -- 2014-12-24

• Add support for hyperbolic rotation curve tanh().

1.4.4 -- 2014-12-20

• Change the default chain fraction to 60%.

1.4.3 -- 2014-12-15

• Add a generic Instrument with no defaults.
• Fix a bug introduced in 1.4.1 for initial_parameters.

1.4.2 -- 2014-12-12

• Add KMOS Instrument support.
• Revamp the documentation.

1.4.1 -- 2014-12-10

• Improve support of CUNIT.
• Fix a bug introduced with 1.3.0.

1.3.0 -- 2014-12-09

• Add ALMA Instrument support.

1.2.0 -- 2014-11-01

• Add film_images() video generator.

1.1.3 -- 2014-10-22

• Add ImagePointSpreadFunction.
• Add VectorLineSpreadFunction.
• Removed interpolation on velocity plots.

1.1.2 -- 2014-10-17

• Fix issue with true_maps image origin.
• Update the documentation.

1.1.1 -- 2014-10-13

• Add GalaxyParameters.PA accessor alias.
• Fix matplotlib's "math domain error" issue that happened in various plots.

1.1.0 -- 2014-10-10

• Easen the process of adding a new GalaxyParameter.

1.0.4 -- 2014-10-01

• Add support for CD3_3 header card.
• Add 3dkernel as output.
• Minor edits.

1.0.2 -- 2014-09-09

• Add support for OII/OIII/SII doublets (and others).

1.0.1 -- 2014-07-07

• Bugfixes.
• More bugfixes.
• Website http://galpak.irap.omp.eu/

1.0.0 -- 2014-05-05

• Initial release of galpak.