Mpdaf

-------------------

- Compatibility with NumPy 2.0

- Replace the strict check on BUNIT keyword to a warning in case of not FITS standard

- `mpdaf.sdetect.linelist.extract_spectra` raises an error in case of no valid pixels

- Compatibility with SciPy 1.11.0

- Add of superclass `mpdaf.obj.Spectrum1D_MPDAF` to use specutils method with spectrum of mpdaf

- Improve of the check of the possible data correlation before variance calculation

- Add the pow operator to the data arithmetic

- `mpdaf.obj.Image.write_mask_file` saves the image mask as a FITS file with a primary header containing WCS information

- Rename `mpdaf.obj.Image.fwhm` by `mpdaf.obj.Image.fwhm_gauss`

- Add `mpdaf.obj.Spectrum.to_abmag` function

- Correct bug in `mpdaf.obj.Spectrum.poly_fit` for multiple iterations

- Add parameter extent to `mpdaf.sdetect.Catalog.plot_symb`

- Add option to return fit and residula in `mpdaf.MUSE.MoffatModel2.from_starfit`

- Fix a bug in `mpdaf.obj.Cube.subcube_circle_aperture`

- Fix a bug in sextractor initialization

- Add flag to save segmentation table in source (`mpdaf.sdetect.sea`)

----------------

- Update FSF module (new Moffat model, correct fsf centering in get_2darray)

- Correct bug in `mpdaf.obj.Spectrum.mean()`

- Solve rounding problem in cubemosaic

- Add wcs.get_center() and wcs.coord()

- Allow reading not-projected pixtable (when astrometry was not applied)

- Fix documentation link

- Correct a bug in `mpdaf.obj.image.peak()`

- Change NeV1238 and NeV1248 to NV1238, NV1248 in `mpdaf.sdetect.linelist`

- Add a parameter in `mpdaf.sdetect.linelist.get_emlines` to exclude a wavelength range (useful for AO spectra with masked Na region)

----------------

- Update fsf (combine_fsf, fwhm_moffat2gauss, documentation)

- Mask NaN in muselet

- Python 3.6+ is required.

----------------

- In `mpdaf.obj.cube.get_image` add an option to compute background from
a median filter. Propagate this addition to `mpdaf.sdetect.source.add_narrow_band_image`

- In `mpdaf.sdetect.get_emlines`, encode the DNAME column in bytes to make it
easier to export tables with this into FITS.

- Remove lo and up columns (not used) and add a vdisp column (to identify AGN type lines) in `mpdaf.sdetect.linelist`.

- Add OIII1660, replace CII 2326 line by a quadruplet in `mpdaf.sdetect.linelist`.

- Fix conversion to pixel coordinates in `mpdaf.sdetect.Catalog.select`.

- Avoid crashes with `mpdaf.sdetect.Source.add_table` when some extension are
missing in the Source. By default, ``select_in`` and ``col_dist`` are not
used.

- Use lowercase extension names when writing a `~mpdaf.drs.PixTable`, otherwise
the DRS is not able to read it. This fixes a regression introduced in
a previous version.

- Add `mpdaf.drs.PixTable.get_row` to access pixtable rows.

----------------

- New `mpdaf.sdetect.Source.add_cat` method.
[:pull:`172`]

- Fix `mpdaf.sdetect.Source.info` to correctly print header comments.

- Allow one to use a correction for zero offset in `mpdaf.obj.CubeList.combine`.
[:pull:`163`]

- Fix precision issue with `mpdaf.obj.WCS.isEqual` and add precision keywords.
[:pull:`164`]

- Fix issue with `mpdaf.sdetect.Catalog.meta` copy to make it compatible with
Astropy 3.2.

- Several bugfixes for `mpdaf.MUSE.FSFModel`.

- Add some utilities : `mpdaf.tools.isiter`, `mpdaf.tools.progressbar`,
`mpdaf.tools.isnotebook`.

- New `mpdaf.sdetect.Segmap` class to manage segmentation maps, and
`mpdaf.sdetect.create_masks_from_segmap` function to create masks from
a segmentation map. [:pull:`166`]

- The `WaveCoord.coord` now accepts a ``medium`` parameter to force getting the
air or the vacuum wavelength coordinates. [:pull:`167`]

- Add more emission lines and fix a bug in `mpdaf.sdetect.get_emlines` when
``restframe=True``. [:pull:`168`]

- Fix a bug in Muselet, when some id are missing in the segmentation map.
[:issue:`521`]

Removal of deprecated code:

- ``Spectrum.line_gauss_fit`` has been removed, it has been deprecated since
v2.3.

- ``Source.add_masks`` has been removed, it has been deprecated since v1.2.

- The self-calibration code has been removed (``PixTable.selfcalibrate`` and
``PixTable.sky_ref``). The self-calibration method is available in the DRS
since version 2.4, with the ``autocalib="deepfield"`` parameter. This should
be preferred as it is more efficient (no need to save the Pixtable to read it
in MPDAF), includes a few bug fixes, and allows one to use the DRS
sky-subtraction after the autocalib. New DRS versions may also include more
features.

----------------

- Compatibility with Astropy 3.1 for wcs shape.

- Add function to merge ``AUTOCAL_FACTORS`` files
(`mpdaf.drs.merge_autocal_factors`).

- Fix bug in `mpdaf.sdetect.Source.add_FSF` when source is close to the edge.

- Fix `mpdaf.obj.Image.subimage` to keep the same dtype as the input data.
[:pull:`153`]

- Increase the number of files that can be combined with `mpdaf.obj.CubeList`.

- Support method parameter in `mpdaf.sdetect.Source.add_narrow_band_images`.
[:pull:`155`]

- Fix writing sources with non-float extensions. [:pull:`154`]

- Fix pickle issue, making sure that ``data_header`` always match the object
state. [:pull:`157`]

- Add a `mpdaf.obj.Spectrum.to_spectrum1d` method to interact with specutils.
[:pull:`158`]

- Ensure that a Unit object is created from the unit parameter, and fix variance
units for multiply and divide. [:pull:`150`]

- Add function to create a mask of sources (`mpdaf.obj.mask_sources`), using
photutils.

- Compute a better estimate of EXPTIME for combined cubes, using the mode
instead of the median.

- Add function to get z for given line position (`mpdaf.sdetect.z_if_linepos`).
[:pull:`159`]

- Speed up `mpdaf.sdetect.crackz` by only testing redshifts of line pairs.

- Fix bug in `mpdaf.obj.Image.subimage` where mask is False.

- Fix issue with the display of NaNs or masked values in `mpdaf.obj.Image.plot`,
removing the clipping when normalizing pixel values.

- Add a new class to manage FSF models (`mpdaf.MUSE.FSFModel`). The old tools
are deprecated (``mpdaf.MUSE.get_FSF_from_cube_keywords``,
``mpdaf.MUSE.FSF``). [:pull:`151`]

Muselet
~~~~~~~

Numerous changes to muselet. [:pull:`160`]

- Improved treatment of extended sources: expand image sizes, as needed, returns
sextractor segmentation mask.

- Each narrow band now uses a corresponding weight map, not a global one.

- More robust cleaning of false detections outside FoV.

- Changes to merging algorithms. Results in slightly more objects (i.e. more
fragmentation, not necessarily more detections).

- Fixed "too many files open error" (hopefully).

- Merged "cont" and "sing" catalogs into one "object" catalog.

- Performance also improved via multiprocessing (but disabled by default).