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MUSE Python Data Analysis Framework is a python framework in view of the analysis of MUSE data in the context of the GTO.

Project description

MPDAF, the MUSE Python Data Analysis Framework, is an open-source (BSD licensed) Python package, developed and maintained by CRAL and partially funded by the ERC advanced grant 339659-MUSICOS (see Authors and Credits for more details).

It has been developed and used in the MUSE Consortium for several years, and is now available freely for the community.

It provides tools to work with MUSE-specific data (raw data, pixel tables, etc.), and with more general data like spectra, images and data cubes. Although its main use is to work with MUSE data, it is also possible to use it other data, for example HST images. MPDAF also provides MUSELET, a SExtractor-based tool to detect emission lines in a datacube, and a format to gather all the information on a source in one FITS file.

Bug reports, comments, and help with development are very welcome.

MPDAF is compatible with Python 2.7 and 3.3+.

Links :

Reporting Issues

If you have found a bug in MPDAF please report it.

The preferred way is to create a new issue on the MPDAF gitlab issue page . This requires creating a account on git-cral if you don’t have one. To create an account, please send email to mpdaf-support@osulistes.univ-lyon1.fr

2.5.1 (16/03/2018)

  • Fix Spectrum.gauss_fit to always return a positive fwhm. [#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 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 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 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 to pass additional Ellipse arguments to Catalog.plot_symb.
  • Allow 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 an other 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 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 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 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. [!87]
  • Add an overwrite parameter to ~mpdaf.sdetect.Source.write. [#485]
  • Fix text truncated in source history.
  • New optimal extraction algorithm for “CCD spectroscopy”, Horne, K. 1986.
  • Allow 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. [!82]

WCS

  • Fix bugs with the handling of CROTa. [!77]

Image

  • Fix bug in ~mpdaf.obj.Image.rebin when the factor parameter is a tuple. [#483]

Spectrum

  • Add HST filters to the list of filters available in ~mpdaf.obj.Spectrum.abmag_filter_name. [#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. [#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. [!78]

v2.1 (16/11/2016)

New Features

  • Allow to pass optional arguments when opening a FITS file, using the fits_kwargs parameter.
  • Allow to write CHECKSUM/DATASUM when saving a FITS file (use checksum=True). [!53]
  • Image and Spectrum objects keep now by default the type of the FITS data (like Cube). [!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. [!47] Add reference frame in WCS.info.
  • Enhance fftconvolve and add this method for Cube. [!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. [!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 [!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 [!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 to work on PixTable object without the .filename attribute.
  • Fix PixTable.divide_slice_median.
  • Add repr info for PixTable objects.
  • Add unit tests.

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