v1.4.1

Bug Fixes
Fix bug where Background one sided / two sided was not correctly assigning units to data. [#221]

v1.4.0: parent 080b288fd29ec64810432bf9127c1a34a4f0ed68 (#220)

New Features
^^^^^^^^^^^^

• Added 'interpolated_profile' option for HorneExtract. If The interpolated_profile option
  is used, the image will be sampled in various wavelength bins (set by
  n_bins_interpolated_profile), averaged in those bins, and samples are then
  interpolated between (linear by default, interpolation degree can be set with
  the interp_degree_interpolated_profile parameter) 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]

API Changes
^^^^^^^^^^^

• Fit residuals exposed for wavelength calibration in WavelengthCalibration1D.fit_residuals. [#446]

Bug Fixes
^^^^^^^^^

• 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]

Other changes
^^^^^^^^^^^^^

• 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]

v1.3.0

New Features

• The new FitTrace class (see "API Changes" below) introduces the
  ability to take a polynomial trace of an image [#128]

API Changes

• 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' image attributes are now coerced Spectrum1D
  objects [#144, #154]

• HorneExtract can now handle non-flat traces [#148]

Bug Fixes

• Fixed passing a single Trace object to Background [#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]

---

What's Changed

• BUG: fix passing single Trace object to Background by @kecnry in #146
• Introducing polynomial tracing by @ojustino in #128
• Better handled Spectrum1D images across classes by @ojustino in #144
• Add summary of capabilities/user stories to docs index page by @rosteen in #149
• Fix changelog formatting by @larrybradley in #150
• Introducing spectral extractions for non-flat traces by @bmorris3 in #148
• Update image handling in notebooks by @ojustino in #154
• Use simpler checks for invalid values by @ojustino in #155
• Prepare changelog for release v1.3.0 by @ojustino in #156

New Contributors

• @rosteen made their first contribution in #149
• @larrybradley made their first contribution in #150
• @bmorris3 made their first contribution in #148

Full Changelog: v1.2.0...v1.3.0

v1.2.0

New Features

• Background has new methods for exposing the 1D spectrum of the background or
  background-subtracted regions [#143]

Bug Fixes

• 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]

---

What's Changed

• DOC: No need to automodapi the top-level package by @pllim in #135
• MNT: Remove dead code from APE 17 by @pllim in #136
• MNT: Remove version template by @pllim in #134
• logic to detect background regions extending beyond image limits by @kecnry in #127
• Found cause of background "overlap" error by @ojustino in #125
• Enable nitpicky mode for sphinx and get docs to build cleanly by @tepickering in #140
• basic quickstart examples for spectral extraction by @kecnry in #142
• Background.bkg_spectrum and sub_spectrum by @kecnry in #143
• Rewrite boxcar weights logic by @kecnry in #141
• Prepare changelog for release v1.2.0 by @ojustino in #145

Full Changelog: v1.1.0...v1.2.0

v1.1.0

New Features

• peak_method as an optional argument to KosmosTrace [#115]

API Changes

• HorneExtract no longer requires mask and unit arguments [#105]
• BoxcarExtract and HorneExtract now accept parameters (and require the image and trace) at initialization, and allow overriding any input parameters when calling [#117]

Bug Fixes

• Corrected the default mask created in HorneExtract/OptimalExtract when a user doesn't specify one and gives their image as a numpy array [#118]

What's Changed

• Bump notebook from 6.4.1 to 6.4.10 in /notebook_sandbox/jwst_boxcar by @dependabot in #100
• Made non-required Horne arguments truly optional by @ojustino in #105
• Testing updates and post-release fixes by @tepickering in #107
• Bump notebook from 6.4.10 to 6.4.12 in /notebook_sandbox/jwst_boxcar by @dependabot in #112
• Improved api docs by @kecnry in #111
• Add citation and Zenodo badge by @tepickering in #110
• Bump numpy from 1.21.0 to 1.22.0 in /notebook_sandbox/jwst_boxcar by @dependabot in #113
• HorneExtract: require variance array to be fully positive by @kecnry in #114
• Kosmos trace peak_method options by @kecnry in #115
• Correct license path in README by @ojustino in #119
• Update citation file by @ojustino in #120
• changelog entry for (already merged) KosmosTrace peak_method by @kecnry in #122
• extract: more consistent API compared to other steps by @kecnry in #117
• Correct default mask for array images in HorneExtract by @ojustino in #118
• Added changelog entry for HorneExtract API change by @ojustino in #123
• Preparation for release v1.1.0 by @ojustino in #124

Full Changelog: v1.0.0...v1.1.0

First Official Release

This is the first official release for specreduce.

New Features

• Added Trace classes
• Added basic synthetic data routines
• Added BoxcarExtraction
• Added HorneExtraction, a.k.a. OptimalExtraction
• Added basic Background subtraction

Bug Fixes

• Update codecov-action to v2
• Change default branch from master to main
• Test fixes; bump CI to python 3.8 and 3.9 and deprecate support for 3.7

What's Changed

• Update template files by @tepickering in #1
• copied README format from specutils, but forgot to make it .rst by @tepickering in #2
• WIP: Add some example sketches of spectroscopic DR sequences by @jehturner in #3
• Add initial batch line lists by @tepickering in #4
• Added more NIST lists (.Astro Hack Day) by @lprichard in #33
• Adding table parsing utils for NIST master table (dotAstronomy hack day) by @mfixstsci in #32
• Adding script to clean and combine line lists plus table (dotAstronomy hack day) by @mfixstsci in #31
• Set read the docs by @simontorres in #35
• Update travis config by @tepickering in #36
• First test by @crawfordsm in #38
• Add standard star data to specreduce via "onedstds" directory by @kakirastern in #43
• Implement APE 17 by @tepickering in #47
• More spectrophotometric standard star data by @tepickering in #49
• Remove Travis CI and stick with Github Actions by @tepickering in #50
• Complete move of reference data to specreduce_data package by @tepickering in #58
• Make classes for atmospheric extinction data by @tepickering in #59
• Add functions to load spectrophotometric standard star data by @tepickering in #62
• Operation class by @crawfordsm in #53
• Fix SpecreduceOperation class by @tepickering in #63
• Add draft of flux calibration functionality to specreduce by @kakirastern in #45
• MNT: Replace master with main by @pllim in #66
• make matplotlib a default requirement by @tepickering in #67
• Add jradavenport notebooks by @eteq in #69
• MNT: Remove unused astropy config code by @pllim in #68
• Fix workflow CI and bump up python versions being tested by @tepickering in #72
• MNT: Update codecov-action version to v2 by @pllim in #70
• Synthetic 2D data by @tepickering in #74
• Bug fixes in boxcar extraction code by @ibusko in #73
• Initial tracing implementation by @tepickering in #75
• Remove .ipynb file that was actually a tar file containing ipynb files by @tepickering in #77
• Remove Cython Pin: Building on Windows by @duytnguyendtn in #78
• Introduce JWST Boxcar Development Notebook from Ivo Busko by @duytnguyendtn in #79
• Bump notebook from 6.1.5 to 6.4.1 in /notebook_sandbox/jwst_boxcar by @dependabot in #80
• Bump numpy from 1.19.2 to 1.21.0 in /notebook_sandbox/jwst_boxcar by @dependabot in #81
• Boxcar extraction using Trace class by @ibusko in #82
• Add GitHub Actions workflow to automatically publish to PyPI by @tepickering in #90
• Added kosmos trace algorithm by @ojustino in #85
• MNT: Fix publish workflow by @pllim in #92
• Introducing Horne extraction by @ojustino in #84
• Basic (boxcar) background subtraction by @kecnry in #86
• Included KosmosTrace in optimal_extract_VLT.ipynb by @ojustino in #97

New Contributors

• @jehturner made their first contribution in #3
• @lprichard made their first contribution in #33
• @mfixstsci made their first contribution in #32
• @simontorres made their first contribution in #35
• @crawfordsm made their first contribution in #38
• @kakirastern made their first contribution in #43
• @pllim made their first contribution in #66
• @eteq made their first contribution in #69
• @ibusko made their first contribution in #73
• @duytnguyendtn made their first contribution in #78
• @kecnry made their first contribution in #86

Full Changelog: https://github.com/astropy/specreduce/commits/v1.0.0