-------------------
- Fixed a bug about how `maskdef_offset` is assigned to each detector
- Changed default behavior for how PypeIt computes `maskdef_offset` for
DEIMOS. It now uses by default the stars in the alignment boxes.
- Introduces pypeit_parse_calib_id script
- Refactor manual extraction
- Fixed 2Dcoadd spec bugs for central wavelength dithers.
- GMOS doc updates
- Add 2D wavelength calibration image to MasterFlat output; include
wavelength calibration in pypeit_chk_flat ginga display.
- Introduce mosaicing
- `det` arguments can now be tuples with a list of detectors to
combine into a mosaic. Mosaics can now be defined in the pypeit
file using `detnum`; e.g., `detnum=(1,2)` creates a mosaic of
detectors 1 and 2.
- The tuples must be one among an allowed set defined by each
spectrograph class; see `gemini_gmos.py`.
- `DETECTOR` extensions in output files can now be either a
`DetectorContainer` object or a `Mosaic` object. Both are now
written using `astropy.table.Table` instances. `Mosaic` objects
just have more columns.
- The `otype` of `DataContainer` data-model components can now be a
tuple of `DataContainer` subclasses indicating that the component
has an optional type.
- Added the `one_row_table` class attribute to `DataContainer`,
which will try to force all the elements of a datamodel into a
binary table extension with a single row.
- Started propagation of name changes from, e.g., `DET01` to
`MSC01`, where the latter indicates the reduction uses the first
mosaic option for the spectrograph. Keys for master calibration
frames are now, e.g., `A_1_DET01` instead of `A_1_01`.
- Currently only implemented for `gemini_gmos`.
- During processing, bias and dark images are left as separate
detector images, whereas all other images are mosaiced for further
processing. This means that `RawImage` is now *always* 3D, where
`PypeItImage` can be either 2D or 3D.
- Added a `det_img` to `PypeItImage` datamodel to keep track of the
parent detector for each pixel in a mosaic.
- Added a `amp_img` to `PypeItImage` datamodel to keep track of the
parent amplifier for each pixel in a mosaic; this is the result of
mosaicing the `datasec_img` objects for each detector.
- Improve performance of L.A.Cosmic algorithm:
- Switch to using ndimage.binary_dilation for growing masked regions
- Switch to astropy convolution for Laplace convolution
- Added faster block replication algorithm
- Fix iteration logic
- Intermediate update to BPM. Preference given to pulling this from the
relevant `PypeItImage` calibration image instead of always building it
from scratch. That latter complicated things for mosaics.
- First steps toward more robust treatment of saturation.
- Dark counts used for calculating the shot noise now includes measured
dark images if provided
- `PypeIt` file parameters can now parse sets of tuples; e.g.,
`detnum=(1,2),(3,4)` should get parsed as `par['detnum'] = [(1,2),
(3,4)]`.
- `PypeIt.select_detectors` has been moved to `Spectrograph`.
- 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)
- Hotfix for `gemini_gmos` mosaic tracing parameters
- 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
- Improvements in `pypeit_coadd_2dspec`:
- `maskdef_id` assigned to each slit
- Assigning object's name, ra and dec to detected objects is now
available
- Force extract of undetected objects is now available
- `maskdef_offset` can be use as offsets in the coadd
- Coadding only a specific sets of slits is now possible with the
parset `--only_slits`
- If the user inputs a list of offsets, the weights can still be
computed if a bright object is found, otherwise uniform weigths
will be used
- Fixed manual extraction bug
- Various improvements in the flow of the code
- spec1d*.txt is now produced also for coadd2d
- Scripts to explore the noise residuals in PypeIt
- Added Coadd2D HOWTO docs
- Fixes a bug in echelle object finding
- Attempt to make the threshold computation for object finding more robust.
- Fixed a bug in extraction for echelle spectrographs for IR reductions.
- Tuned up preivious refactor of object finding and extraction classes.
- Fixed a bug that was introduced in skymask definition.
- Fixed a bug where negative objects were not being found for IR reductions of standard stars.
- Add template wavelength solution for soar_goodman_red 400_SYZY