Changelog

Changelog#

1.0.0 LiMe release (04/29/2024)#

  • First stable release

1.0.1 LiMe minor update (05/04/2024)#

  • Created lime.io.parce_lime_cfg function to convert the .toml sections with lime suffix to the expected format to be its own operation

  • Created lime.plots.spectrum_labels to generate spectrum figure axis labels

  • Delete “log” attribute from lime.Cube class

  • Fix error normalize_fluxes was not cropping the lines frame for an input line list. Need to fix normalize flux error

  • log now returns the dataframe

1.0.2 LiMe minor update (05/09/2024)#

  • SDSS lime.Spectrum.from_file no reads redshift from fits header

1.0.3 LiMe minor update (05/09/2024)#

  • Restored deleted config.toml

1.0.4 LiMe minor update (05/17/2024)#

  • Corrected MANGA flux error measurement

  • New tests for comparison between standard and lime loading of SDSS and MANGA observations

  • Change cm.get_cmap to plt.get_cmap due to matplotlib depreciation

  • Bug fix for multi-index flux extraction function due to pandas depreciation

1.0.5 LiMe minor update (05/25/2024)#

  • Change “continuum_fit” keyword for toml keyword in continuum fitting configuration to “continuum” to match function name

1.0.6 LiMe minor update (06/20/2024)#

  • Fix error in unit conversion of Cubes

  • Clearer messages for bands not matching the spectrum wavelength range

  • Added test for line fitting with line detection using implicit and explicit configuration and bands declaration

  • Plots using the automatic scale now show the scale as in figure text.

  • Added own stringBool from distiutils because it is being discontinued in python 3.12

1.0.7 LiMe minor update (07/19/2024)#

  • define_masks function has been replaces by line.index_bands()

  • The line.index_bands() now warns if line does not have bands at the point of indexing an input spectrum wavelength.

  • Corrections on the measurements documentation page

1.0.8 LiMe minor update (09/15/2024)#

  • The check_fit_cfg function now reviews if the continuum and line_detection functions parameters are present and gives a warning if not.

  • show_masks attribute in Spectrum.plot.spectrum to hide the pixels masks on the output plot.

1.1.0 LiMe medium update (09/30/2024)#

  • By default LiMe will now mask the input spectrum if “nan” and “inf” entries are present in the flux and err_flux arrays but the user does not provide a pixel mask. If the user provides a mask but “nan” or “inf” entries are detected only a warning will be provided.

  • The website now includes the changelog with the LiMe updates.

  • Fixed bug where nan entries would cause an error in the line band detection.

  • New logic operator to store bands which only cover one pixel in band detection.

  • Documentation corrections by E.C. Herenz

1.1.1 LiMe minor update (10/29/2024)#

  • Adding bands from frame function

  • Bug fix for re-normalization in the units_conversion function

  • Bug fix to normalize by 1 if nanmedian flux is <= 0

  • Added security fix for re-normalization in the units_conversion function

  • The review_bands function now checks if all the line_band pixels flux and all the continuum_band pixels flux sum is zero. This is done to avoid all zero line or continuum entries.

1.2.0 LiMe medium update (11/05/2024)#

  • The unit_conversion functions have been updated to avoid bugs on betwen certain units

  • The unit_conversion functions now review the normalization and masking the same way as in the spectrum creation

  • The line detection function has been updated to account for masked data within the input line bands

  • The automatic normalization function now using the mean instead of median as the scale_flux

  • If the scale flux is negative the normalization will remove the lowest pixel value from the mean flux for the automatic normalization.

  • Initial introduction for aspect functions for thea automatic detection of spectral features.

  • New checks to avoid the measurements of bands where all the entries are masked.

1.2.1 LiMe minor update (10/29/2024)#

  • Rename the “line_bands” argument in the lime.Spectrum.plot.spectrum function to “bands” to match library style

  • The lime.Spectrum.plot.spectrum function will now only display “bands” w3 and w4 values are within the rest wavelength range (no need to crop the bands in advance now).

  • Added support for reading MIRI IFU observations with MJy/str and um units

  • Corrected bug on the latex label generation in the lime.line_bands command not reproducing the expected format

  • The unit_conversion function for Cube observations now uses the format from the previous update.

1.3.0 LiMe medium update (12/10/2024)#

  • This update includes ASPECT as an optional dependency and has adapted several functions to include the possibility to use its predictions

  • Added the Spectrum.retrieve attribute to group tasks which return data for the user related to the spectrum

  • Added the Spectrum.retrieve.line_bands to return the line bands which match the observation redshift, wave interval and components detection.

  • The lime.line_bands and Spectrum.retrieve.line_bands now use the argument “redshift” to adjust the output bands which are within a “wave_intvl” for that redshift (for the Spectrum.retrieve.line_bands this is always the case)

  • The lime.line_bands has been moved to the workflow.py file

  • The “.line_bands” have now use the new unit conversion function and includes more functionality via new update_labels=True, update_latex=True.

  • The inst_FWHM at the creation of observations has been replaced by res_power (resolving power) and now can be a float or an array (same length as the observation wavelength). This provides a more robust computation of the sigma_instr

  • The sigma_instr and sigma_thermal corrections are not computed within the sigma_corrections function

  • During the lime.Sample.get_spectrum the user can now specify kwargs arguments to update the creation kwargs for that object.

  • Several bugs were corrected on the lime.redshift_calculation to avoid very large errors when weak lines were present.

  • Bug correction on the previous update lime.Spectrum.plot.spectrum to plot bands within the observation wavelength range.

  • The lime.Sample.check.redshift function now has a new “initial_z” argument for the initial guess of the redshift measurement.

  • The lime.Sample.check.redshift “title_label” argument has been renamed -> “title” for consistency

  • The air_to_vacuum_function now only applies the theoretical relation, its inputs and outputs are wavelength arrays.

  • The new lime.Line.update_label function can be used to update the line label by reviewing the line properties.

2.0.1 LiMe Mayor update (10/20/2025)#

  • Change installer convention from “setup.py + requirements.txt” to pyproject.toml

  • Updated dependencies to current version of packages and for python 3.12

  • Renamed cfg.toml to lime.toml

  • Arrange library .py files into folder structure reproducing the .fit, .infer, .retrieve, .plot functions. The functions related to file types are are located in archives folder.

  • Added new mechanic to compute the lines continuum from the line band edges or the continua bands.

  • Added new mechanic to compute the pixel uncertainty from the provided uncertainty flux or the adjacent continua bands.

  • Fix error where the error from the line profile center and sigma parameters was uncertainty was 0 if the line kinematics were imported from a previously measured line.

  • Added support for bokeh plots.

  • The theme configuration parameters are stored now in the src/plotting/theme_lime.toml.

  • The .fit.report function now formats the output report to include the component label name and has the argument return_text=False to give the option to return the report message as a variable instead of printing on the terminal.

  • Fix a bug where the kinematics export function was not applying the correct rest frame wavelength length on the radial velocity calculation.

  • New “.infer” to host high level functions to predict spectroscopic features

  • The “Spectrum.line_detection()” has been moved to “Spectrum.infer.peaks_troughs()”. The old function now raises and error moving to the new function.

  • Now the observations wave, flux, err_flux and wave_rest arrays are always masked arrays

  • The lines database name has been changed from parent_bands.txt to “lines_database_v2.0.0.txt”. The wavelength are based on van Hoof, P.A.M., 2018, Galaxies, 6, 63 and Roueff+ (2019).

  • The central wavelenght bands are now calculated assuming a bands_vsigma=70 and n_sigma=4

  • The function lime.Spectrum.retrieve.spectrum() returns the spectrum axes as a recarray or saves it into a text file if the user provides a file address.

  • lime.Spectrum.from_file(“fname”, instrument=‘text’) can now read the file from a text file following the format from the lime.Spectrum.retrieve.spectrum() function.

  • Bug the .plot.spectrum(include_fittings) does not show the combined profile

  • Rename term “_conf” to “_cfg” across function names and arguments for uniformity

  • Fitting functions now have the update_default=True argument. In the default behaviour the default configuration updates the default one. If set to update_default=False only the obj_cfg is used if available else the default one.

  • Creating a spectrum object where all the entries are masked now produces a critical warning instead of raising an error.

  • By default line_bands.

  • Added bands_from_log function

  • Change “output_address” argument name to “fname” across functions

  • Now the cont_source argument in the .fit functions gives the option to fit the line continuum using the central and adjacent bands in addition to the fit continuum.

2.0.4 LiMe minor update (12/05/2025)#

  • Added function to rebinned spectrum given a wavelength range, a number of pixels, or a pixel width (no documenation entry yet): lime.Spectrum.retrieve.rebinned

  • The lime.save_cfg function first two arguments have changed order (first file location and the file name)

  • The default colors for the continuum fitting plots and peak dectection plots have changed

  • Added suport for KCWI cubes

  • Further development for the functions involving redshift a line fitting using aspect

  • The spatial masking functions should not require the ‘PARAM’, ‘PARAMIDX’, ‘PARAMVAL’ and ‘NUMSPAXE’ in the .fits headers to plot the mask overlays