Other changes
- Fix bug where Background one sided / two sided was not correctly assigning units to data. [#221]
- Added 'interpolated_profile' option for HorneExtract. If The
interpolated_profileoption is used, the image will be sampled in various wavelength bins (set byn_bins_interpolated_profile), averaged in those bins, and samples are then interpolated between (linear by default, interpolation degree can be set with theinterp_degree_interpolated_profileparameter) to generate a continuously varying spatial profile that can be evaluated at any wavelength. [#173] - Added a function to measure a cross-dispersion profile. A profile can be obtained at a single pixel/wavelength, or an average profile can be obtained from a range/set of wavelengths. [#214]
- Fit residuals exposed for wavelength calibration in
WavelengthCalibration1D.fit_residuals. [#446]
- Output 1D spectra from Background no longer include NaNs. Output 1D spectra from BoxcarExtract no longer include NaNs when none are present in the extraction window. NaNs in the window will still propagate to BoxcarExtract's extracted 1D spectrum. [#159]
- Backgrounds using median statistic properly ignore zero-weighted pixels. [#159]
- HorneExtract now accepts 'None' as a vaild option for
bkgrd_prof. [#171] - Fix in FitTrace to set fully-masked column bin peaks to NaN. Previously, for peak_method='max' these were set to 0.0, and for peak_method='centroid' they were set to the number of rows in the image, biasing the final fit to all bin peaks. Previously for Gaussian, the entire fit failed. [#205, #206]
- Fixed input of traces in Background. Added a condition to 'FlatTrace' that trace position must be a positive number. [#211]
- The following packages are now optional dependencies because they are not
required for core functionality:
matplotlib,photutils,synphot. To install them anyway, use the[all]specifier when you install specreduce; e.g.:pip install specreduce[all][#202]
- The new FitTrace class (see "API Changes" below) introduces the ability to take a polynomial trace of an image [#128]
- Renamed KosmosTrace as FitTrace, a conglomerate class for traces that are fit to images instead of predetermined [#128]
- The default number of bins for FitTrace is now its associated image's number of dispersion pixels instead of 20. Its default peak_method is now 'max' [#128]
- All operations now accept Spectrum1D and Quantity-type images. All accepted image types are now processed internally as Spectrum1D objects [#144, #154]
- All operations'
imageattributes are now coerced Spectrum1D objects [#144, #154] - HorneExtract can now handle non-flat traces [#148]
- Fixed passing a single
Traceobject toBackground[#146] - Moved away from creating image masks with numpy's
mask_invalid()function after change to upstream API. This will make specreduce be compatible with numpy 1.24 or later. [#155]
Backgroundhas new methods for exposing the 1D spectrum of the background or background-subtracted regions [#143]
- Improved errors/warnings when background region extends beyond bounds of image [#127]
- Fixed boxcar weighting bug that often resulted in peak pixels having weight above 1 and erroneously triggered overlapping background errors [#125]
- Fixed boxcar weighting to handle zero width and edge of image cases [#141]
peak_methodas an optional argument toKosmosTrace[#115]
HorneExtractno longer requiresmaskandunitarguments [#105]BoxcarExtractandHorneExtractnow accept parameters (and require the image and trace) at initialization, and allow overriding any input parameters when calling [#117]
- Corrected the default mask created in
HorneExtract/OptimalExtractwhen a user doesn't specify one and gives their image as a numpy array [#118]
- Added
Traceclasses - Added basic synthetic data routines
- Added
BoxcarExtract - Added
HorneExtract, a.k.a.OptimalExtract - Added basic
Backgroundsubtraction
- Update
codecov-actiontov2 - Change default branch from
mastertomain - Test fixes; bump CI to python 3.8 and 3.9 and deprecate support for 3.7