Pypeit

Major Changes

- Refactor `PypeIt` input files. Main pypeit file remains the same, except that inclusion of leading and trailing `|` characters in the data table (required in previous versions) will now result in `DeprecationWarning`s. All post-processing scripts (coadding, fluxing, etc) *must* use the new format. See the main documentation pages.

Minor Changes/Improvements

- Apply `find_min_max` when clipping the image for object finding
- Mask bad detector regions for global sky flexure calculation
- Added wavelength diagnostics to the spec2d output

Instrument-specific Changes/Improvements

- Modify `tweak_standard` for Keck-MOSFIRE/J2
- Detector structure correction included in flatfield calibration (Keck-KCWI only)

Hotfix Release

Addresses bug related to downloading from the `reid_arxiv` when using the `reidentify` wavelength calibration method.

Major Changes
-------------

- Reduction of Keck/DEIMOS now defaults to mosaics of red and blue
detector pairs
- Package data is no longer distributed via PyPI. Instead, we use
astropy's downloading/caching system as needed by the user
- Significant refactor of object finding and 2D extraction algorithms
- Added support for:
- VLT FORS2 600z grism
- VLT XShooter UVB arm

Minor Changes/Improvements
--------------------------

- Default `comb_id` ordering matches the sorted file name in
pypeit_setup
- Save output wavelength calibration from `pypeit_identify` to the
cache for direct reuse in data reduction.
- The `pypeit_identify` GUI can now toggle between linear and log
scaling of the arc spectrum flux.
- Dark subtraction now ignores any difference in exposure time, by
default
- Added more flexible quicklook that can handle dithering.
- Bug fixes in local sky subtraction and extraction
- Fixed pypeit_setup issues due to bad LRIS headers.
- Fixed a bug in 2d coadding when objects were not being identified.
- Refactored 2d extraction.
- Minor enhancements to `pypeit_identify` GUI
- Refactoring of `pypeit_show_wvcalib` GUI

Instrument-specific Changes/Improvements
----------------------------------------

- Improve Keck/KCWI automatic frame typing.
- Added wavelength templates for
- Keck/MOSFIRE (OH and arc lines)
- bok_bc 300 grating template
- Improved wavelength solution for Gemini-Nort E2V detector
- Keck/DEIMOS now uses gain/RN values measured periodically by WMKO
- Added enhancements and fixes for Keck lris red Mark4.
- Added code to better parse Gemini/GNIRS dither sequences

Minor release. Changes include:

- Various hotfixes
- Include preliminary support for fluxing with archived SensFunc files
for DEIMOS.

Significant changes

- Code to allow for mosaicing multiple detectors into a single reduction. This is now the default for Gemini GMOS and improves stability of wavelength calibration.
- Introduces pypeit_parse_calib_id script
- Refactored manual extraction
- Update for `LDT/DeVeny` including support for binned data, `use_header` for reading arc lamps used from frames, and `reid_arxiv` templates for three additional gratings.
- Slurps in and uses slitmask design for Keck/LRIS (limited usage)
- Significant improvements in 2D coadding.
- Scripts to explore the noise residuals in PypeIt

Datamodel changes and algorithmic improvements

- Improved performance of L.A. Cosmic implementation
- Now uses stars in alignment boxes for default calculation of slitmask offsets in DEIMOS reductions.
- 2D wavelength calibration image now added to MasterFlat output
- Improved treatment of saturation.
- Dark counts used for calculating the shot noise now includes measured dark images if provided.
- Include sky model in 2nd pass of global sky subtraction (not for IR redux).
- Skymask is now computed also for the maskdef_extract objects.
- Added dedicated fwhm and boxcar_radius for maskdef_extract objects.
- Added pypeit_version to the pypeit file header.
- Set DEIMOS `find_fwhm` default to 0.8" in binned pixels.
- Added row-dependent pattern-noise calculation for KCWI

Bug fixes

- Fixed a bug about how `maskdef_offset` is assigned to each detector
- Fixed 2Dcoadd spec bugs for central wavelength dithers.

Major Changes

- MOSFIRE improvements:
- improved frame typing
- ingestion of slitmask metadata for MOSFIRE with association of extracted spectra to object name and coordinates
- extraction of undetected objects
- incorporates dither pattern from file headers
- Implements new Mark4 detector for Keck/LRISr; selected as the `keck_lris_red_mark4` "spectrograph"

Minor Changes

- Introduces pypeit_parse_calib_id script
- Throw a warning if the chosen spectrograph has a header which does not match expectation
- Pypeit can now read (currently for Keck DEIMOS only) the list of arc lamps from the header and use it for wavelength calibration.
- Allow one to restrict the wavelength range of the arxiv template
- Set DEIMOS FWHM default to 10 pixels
- Fixed a bug in HolyGrail that did not allow for sigdetect and rms_wavelength to be slit dependent lists.