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CHANGELOG
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3.6 (28/06/2024)
-------------------
- 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`)
3.5 (01/02/2021)
----------------
- 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)
3.4 (17/01/2020)
----------------
- Update fsf (combine_fsf, fwhm_moffat2gauss, documentation)
- Mask NaN in muselet
- Python 3.6+ is required.
3.3 (09/11/2019)
----------------
- 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.
3.2 (22/05/2019)
----------------
- 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.
3.1 (03/04/2019)
----------------
- 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).
3.0 (10/19/2018)
----------------
MPDAF now requires Python 3.5 or later.
Pixtable
~~~~~~~~
- The self-calibration method is deprecated, as it is available in the DRS
since version 2.4, with the ``autocalib="deepfield"`` parameter.
- Add the `~mpdaf.drs.plot_autocal_factors` function to plot the autocalib
corrections. [:pull:`138`]
Muselet
~~~~~~~
- Fix Muselet issue with AO cubes. [:issue:`513`]
Cube, Image, Spectrum
~~~~~~~~~~~~~~~~~~~~~
- Add `mpdaf.obj.Cube.get_band_image` to create images with the same filters as
the DRS (this includes HST, SDSS, or other filters). [:pull:`146`]
- Add rgb plotting function `~mpdaf.obj.plot_rgb` and a method to Source
objects (`mpdaf.sdetect.Source.show_rgb`). [:pull:`123`]
- Adds parameter to avoid the float32/float64 conversions: by default arrays in
Spectrum/Image/Cube are converted to float32 when saving, to save some disk
space. This can be avoided with ``convert_float32=False``. And when reading
files, a float64 conversion can now be avoided with ``convert_float64=False``.
[!126, !!135]
- Remove duplicate air/vacuum conversion functions, now available as
`mpdaf.obj.airtovac` and `mpdaf.obj.vactoair`. [:pull:`127`]
- Fix subcube when using ``np.ma.nomask`` [:pull:`128`].
- Check that FITS file's naxis is compatible with the class [#505, !129]
- Fix the copy of FITS header to respect the initial order of keywords. [:pull:`137`]
Source, Catalog
~~~~~~~~~~~~~~~
- Support the use of metadata in ``Source`` tables and ``Catalog``. Keywords
IDNAME, RANAME and DECNAME can be used to specify the column names for the ID,
RA and DEC columns that are used in several ``Catalog`` methods. [:pull:`124`]
- Speedup ``get_FSF_from_cube_keywords``. [:pull:`131`]
- Add ``cube.min()``. [:pull:`133`]
- Correct bug in source crackz execution.
- Correct bug in match to return only one catalog when option ``full_output``
is False. [:pull:`139`]
- Fix ``get_emlines`` to use unicode for line type. [:pull:`142`]
Misc
~~~~
- Fix pickling of MPDAF objects when the header does not match the data. [:pull:`141`]
- Fix warnings with recent Numpy versions.
2.5.1 (16/03/2018)
------------------
- Fix ``Spectrum.gauss_fit`` to always return a positive fwhm. [:issue:`501`]
- Fix several issues with the ``CubeList`` C extension:
- Avoid segfault with ``-std=c99``.
- Fix compilation when NAN is not defined.
- Fix the extension when not using OpenMP, which is still the case with Clang.
Support for OpenMP with Clang will be addressed in the future.
- Changes to ``Cube.get_image``:
- It's now possible to use any method from the Cube object that reduces the
data on the wavelength axis to get an image, e.g. mean, sum, max...
- The way to compute the background when asking for a summed image has
changed. Before, it was computed averaging the pixel values of regions
'below' and 'above' the kept wavelengths; now it is calculated as the mean
of the average in each region. This may lead to slightly different results
when working at the edge of the spectrum, when the width of the regions are
different.
2.5 (02/03/2018)
----------------
- Numpy is now installed with ``setup_requires``, which means that it is no
more required to run the setup, and it can be installed directly as
a dependency.
- Allow one to pickle MPDAF objects (``Cube``, ``Image``, ``Spectrum``,
``Source``). This makes it much easier to use these MPDAF objects with
``multiprocessing`` as they can now be passed transparently to the
subprocesses.
- Allow one to specify the wavelength range in ``Cube.subcube_circle_aperture``.
- Speedup ``create_psf_cube``, ``moffat_image`` and ``gauss_image``.
- Add option to plot images with world coordinates axes, using
``astropy.visualization.wcsaxes``. This can be used with
``Image.plot(..., use_wcs=True)``
Sources
~~~~~~~
- Better completions for Source attributes, and for keys in IPython.
- Allow one to load a "fieldmap" from a dedicated file (in ``Source.add_FSF``).
- New method to get FSF keywords from a Source (``Source.get_FSF``).
Catalog
~~~~~~~
- Remove the index that was added by default on the 'ID' column, as it was
causing errors with some operations due to bugs in the Astropy
implementations. Indexes can still be added manually if needed.
- Allow one to pass additional Ellipse arguments to ``Catalog.plot_symb``.
- Allow one to export coordinates from their columns to
a ``astropy.coordinates.SkyCoord`` object (``Catalog.to_skycoord``) and to
ds9 region file (``Catalog.to_ds9_regions``).
- New methods ``Catalog.nearest``, to get the nearest sources with respect to
a given coordinate, and ``Catalog.match3Dline``, to match elements of the
current catalog with another using spatial (RA, DEC) and a list of spectral
lines location.
- ``Catalog.plot_id`` is deprecated, in favor of ``Catalog.plot_symb`` with
``label=True``.
- Allow one to use a mask in ``Catalog.select``.
- Add workaround for reading FITS table written with ``Catalog``, with Astropy
3.0 (because of a bug introduced with their new serialization feature, which
does not work with subclasses).
2.4 (24/11/2017)
----------------
- Compatibility with Scipy 1.0 (removal of ``scipy.stat.threshold``).
- Add compressed FITS files (``.fits.fz``) to the supported extensions.
Image
~~~~~
- Add a ``var`` option to plot the variance extension with ``.plot()``.
Cube
~~~~
- Fix bug in ``cube.spatial_erosion``.
Sources
~~~~~~~
- Keep the original order of the header keywords in ``.info()``.
- Allow one to set the size of a source without needing the white image.
- New option to add the white image directly within ``add_cube``.
Catalog
~~~~~~~
- Fix unit conversion in ``Catalog.edgedist``.
- Avoid forcing the ra/dec column names to uppercase.
2.3 (13/09/2017)
----------------
- New function to create a PSF cube in `~mpdaf.MUSE.create_psf_cube`.
- Update the ``mpdaf.drs.rawobj`` module.
- New ``extract_cube_fieldsMap`` script.
WCS
~~~
- Avoid useless unit conversions in ``pix2sky`` and ``sky2pix``.
- Add back the ``WCS.rotate`` method.
Spectrum
~~~~~~~~
- Fix ``Spectrum.plot`` when unit is not angstrom.
- Add wavelength filtering, thanks to Markus Rexroth (EPFL):
`~mpdaf.obj.Spectrum.wavelet_filter`.
Image
~~~~~
- Fix ``align_with_image`` which was modifying the input data.
- Several bugfixes for Gaussian and Moffat fits.
- Margin of 1/100th of pixel added in `~mpdaf.obj.Image.inside`.
- Allow one to set the center outside the parent image in `~mpdaf.obj.Image.subimage`.
Cube
~~~~
- Add `~mpdaf.obj.Cube.max`, `~mpdaf.obj.Cube.spatial_erosion`.
CubeList
~~~~~~~~
- Avoid warnings with HIERARCH keywords
- Mask NaNs in the output cube, useful when creating the white-image after.
Sources
~~~~~~~
- Fix removal of extension with the optimized source writing. [:pull:`87`]
- Add an overwrite parameter to `~mpdaf.sdetect.Source.write`. [:issue:`485`]
- Fix text truncated in source history.
- New optimal extraction algorithm for "CCD spectroscopy", Horne, K. 1986.
- Allow one to set the order for the spline interpolation in
`~mpdaf.sdetect.Source.add_image`.
Catalog
~~~~~~~
- Correct bug (naxis inversion) in catalog.select and catalog.edgedist
Pixtable
~~~~~~~~
- Bugfix for `~mpdaf.drs.PixTable.selfcalibrate`: make sure that we have enough
pixels with a flux in each slice.
v2.2 (24/01/2017)
-----------------
- Compatibility with Astropy 1.3
- Fix direct replacement of .data in a Cube/Image/Spectrum object. [:pull:`82`]
WCS
~~~
- Fix bugs with the handling of ``CROTa``. [:pull:`77`]
Image
~~~~~
- Fix bug in `~mpdaf.obj.Image.rebin` when the ``factor`` parameter is a tuple.
[:issue:`483`]
Spectrum
~~~~~~~~
- Add HST filters to the list of filters available in
`~mpdaf.obj.Spectrum.abmag_filter_name`. [:issue:`484`]
Cube
~~~~
- Fix issue with `~mpdaf.obj.Cube.subcube_circle_aperture` which was masking
the original cube.
- Add ``is_sum`` option in `~mpdaf.obj.Cube.aperture`.
CubeList
~~~~~~~~
- Fix offset computation in `~mpdaf.obj.CubeMosaic`, using CRPIX from the
output cube.
- More options in the ``pycombine`` methods: MAD, scales, offsets.
Sources
~~~~~~~
- Correct behaviour when adding an image not overlapping with Source. [:issue:`482`]
Catalog
~~~~~~~
- Fix issue in `~mpdaf.sdetect.Catalog.match`
Pixtable
~~~~~~~~
- A new method `~mpdaf.drs.PixTable.selfcalibrate` was added to correct the
background levels of the slices. This method replaces the
``subtract_slice_median`` and ``divide_slice_median`` methods (which have
been removed). The new method works differently, gives better results, and no
more requires to pre-compute a mean sky spectrum with
`~mpdaf.drs.PixTable.sky_ref`. [:pull:`78`]
v2.1 (16/11/2016)
-----------------
New Features
~~~~~~~~~~~~
* Allow one to pass optional arguments when opening a FITS file, using the
``fits_kwargs`` parameter.
* Allow one to write ``CHECKSUM``/``DATASUM`` when saving a FITS file (use
``checksum=True``). [:pull:`53`]
* ``Image`` and ``Spectrum`` objects keep now by default the type of the FITS
data (like ``Cube``). [:pull:`50`]
* Add ``dtype`` property to Data classes (Spectrum/Image/Cube).
* Add ``WCS`` naxis1/naxis2 properties which uses naxis from the underlying wcs
object.
* Determine the reference frame from the primary header if possible and don't
force it if not found in the primary header. HST and MUSE files usually have
the EQUINOX/RADESYS/RADECSYS keywords only in the primary header, which cause
MPDAF to use ICRS instead of FK5. [:pull:`47`] Add reference frame in ``WCS.info``.
* Enhance ``fftconvolve`` and add this method for ``Cube``. [:pull:`52`]
* New method `MUSE.get_FSF_from_cube_keywords
<mpdaf.MUSE.get_FSF_from_cube_keywords>` which creates a cube of FSFs
corresponding to the keywords presents in the MUSE data cube primary header.
* Add small utility function to create field maps.
* Make ``zscale`` available from ``mpdaf.tools``.
* Move tests and data inside the MPDAF package so that they are installed with
MPDAF.
* Replace nosetest with py.test to run test.
Breaking changes
~~~~~~~~~~~~~~~~
* ``Spectrum`` methods that return a value of flux or magnitude, return
now a tuple (value, error). This breaking change concerns: ``flux2mag``,
``mean``, ``sum``, ``integrate``, ``abmag_band``, ``abmag_filter_name``,
``abmag_filter``.
* Forbid the use of several (not implemented) methods in ``CubeMosaic``.
* Remove ``WCS.set_naxis`` methods.
WCS
~~~
* Remove ``WCS.set_naxis`` methods.
* Add ``WCS`` naxis1/naxis2 properties which uses naxis from the underlying wcs
object.
* Determine the reference frame from the primary header if possible and don't
force it if not found in the primary header. HST and MUSE files usually have
the EQUINOX/RADESYS/RADECSYS keywords only in the primary header, which cause
mpdaf to use ICRS instead of FK5. Add reference frame in ``WCS.info``.
* Simplify ``deg2sexa`` and ``sexa2deg``.
Data classes (Cube, Image, Spectrum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Enhance reading from an HDUList without having to specify a filename.
* ``Image`` and ``Spectrum`` objects keep now by default the type of the FITS
data (like ``Cube``).
* Add ``dtype`` property to Data classes (Spectrum/Image/Cube).
* Make ``DataArray[item]`` preserve WCS and/or wavelength info for all legal
item selections. Prior to this patch, if ``c`` was a cube, ``c[10]`` returned
an MPDAF Image that didn't have any WCS information, and ``c[10:20]`` returned
a Cube without either WCS or wavelength information.
* Refactor Spectrum/Image/Cube's methods ``.convolve`` and ``.fftconvolve``,
with variance propagation.
In the previous implementation of Image and Spectrum.fftconvolve(), the shape
of the 'other' array had to match the size of the Image or Spectrum. In the
new version, the 'other' array can be any size up to the size of the MPDAF
object that is being convolved.
The optional ``interp`` argument of ``Image.fftconvolve()`` has been removed.
Filling masked data and variances with zeros for the duration of the
convolution should be sufficient in most cases.
Spectrum
~~~~~~~~
* Set default limits on the x axis for ``Spectrum`` plots.
* Simplify ``Spectrum.correlate``, ``Spectrum.fftconvolve_gauss``,
``Spectrum.median_filter`` and ``Spectrum._interp``.
* Return flux/magnitude error if relevant.
* Rewrote ``Spectrum.resample``: When pixel sizes are being increased
a decimation filtering stage is now used before regridding, whereas the
original behavior was to perform piecewise integrations for each output pixel.
When pixel sizes are being reduced, simple linear interpolation is followed by
decimation filtering.
Image
~~~~~
* Fix ``Image.fwhm`` which was returning twice the FWHM.
* Fix bug which caused resample to change the sign of the X-axis increment.
* Simplify creation of subimages in ``Image.segment``.
* Reduced memory usage in ``Image.truncate``, ``Image.regrid``,
``Image.align_with_image.`` This speeds up ``align_with_image`` significantly.
* Fix exceptions in ``Image.plot`` when ``.wcs`` is None.
* Fix bug that sometimes caused ``Image.plot`` to fail to show the cursor
coordinates of an image.
* Use zscale from Astropy if available (1.2 and later).
* Add method ``.to_ds9()`` to visualize data in ds9 and interact with it (using
pyds9).
Cube
~~~~
* Fix bug in ``Cube.rebin``. [:pull:`471`]
* Improved the method ``bandpass_image``:
- If their isn't a complete overlap between the bandpasses of the filter-curve
and the cube, truncate the filter at the edges of the cube instead of
raising an exception.
- When integrating the filter curve over each wavelength channel of the cube,
use linear interpolation by default, rather than cubic.
Sources
~~~~~~~
* Increase the file reading speed by loading values of dictionaries (spectra,
images, cubes and tables) just if necessary.
* ``CUBE*`` keywords became mandatory:
- ``CUBE``: Name of the MUSE data cube.
- ``CUBE_V``: Cube version.
* Some keywords are renamed:
- ``ORIGIN`` -> ``FROM`` (Name of the software used to detect the source)
- ``ORIGIN_V`` -> ``FROM_V`` (Version of the software used to detect the
source)
- ``SRC_VERS`` -> ``SRC_V`` (Source version)
- ``SOURCE_V`` -> ``FORMAT`` (Version of the mpdaf.sdetect.Source class used
to create the source)
- ``CONFI`` -> ``CONFID`` (Expert confidence index)
* Change format of COMMENT and HISTORY
- ``COM***`` -> ``COMMENT``
- ``HIST***`` -> ``HISTORY``
[Date Author] User comment/History
* Updated ``Source.info``: comments and histories printed more properly.
* ``extract_spectra``: Add the possibility to extract MOFFAT PSF weighted
spectra in addition to the Gaussian PSF.
* Add primary indexes (with unicity constraint) to `mag['BAND']` and
``z['Z_DESC']`` for simpler indexing.
* Correct behaviour when trying to add image not overlapping with Source [:pull:`482`].
Catalogs
~~~~~~~~
* Optimize catalog initialization by not loading all tables.
* Update the initialization in order to be correct for Numpy arrays and masked
arrays.
* Make Catalog compatible with Python 3.
* Add comments and histories in catalog generated from a list of Source objects.
* Update Catalog documentation [:pull:`467`]
* Correct issue #466:
- Raise ValueError if astropy.Table try to convert a string to float/int. The
message gives the name of the column.
- Add warning if a keyword has not the same type in all sources but the
conversion is possible.
- ``CUBE_V`` is now a mandatory keyword with the string format.
muselet
~~~~~~~
* Changed default SExtractor parameters (QUIET and no segmentation).
* Little optimization (don't use mask array for the continuum computation, write
NB images with ``astropy.io.fits``, remove ``RuntimeWarning`` warnings).
* muselet now compatible with Python 3.
Pixtable
~~~~~~~~
* Use a more efficient implementation for ``PixTable.sky_ref``.
* Allow one to work on ``PixTable`` object without the ``.filename`` attribute.
* Fix ``PixTable.divide_slice_median``.
* Add repr info for PixTable objects.
* Add unit tests.