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 informations 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 :
Source, issues and pull requests on a Gitlab instance
Releases on PyPI
Mailing list to get help or discuss issues
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
v2.0 (05/07/2016)
This is the first public release, as an open source project (BSD licensed). MPDAF is also now compatible with Python 3.3+.
New Features
Image.resample <mpdaf.obj.Image.resample>: now applies by default an anti-aliasing filter when asked to lower the resolution of an image. The variance is now computed for the re-sampled image.
Image.regrid <mpdaf.obj.Image.regrid>: new method similar to Image.resample, but more flexible in the positioning of the sky in the re-sampled image, and it accepts signed pixel increments. resample now uses regrid and was conserved for compatibility reasons.
Image.rotate <mpdaf.obj.Image.rotate>: now works correctly on images whose pixels have different angular sizes along the X and Y axes.
Image.align_with_image <mpdaf.obj.Image.align_with_image>: new method to resample the image of the object to give it the same orientation, position, resolution and size as another image.
Image.estimate_coordinate_offset <mpdaf.obj.Image.estimate_coordinate_offset>: new method which uses a full-image auto-correlation to measure the average offsets between the world coordinates of common astronomical features in two images. This was written primarily to determine coordinate offsets between MUSE images and HST reference images.
Image.adjust_coordinates <mpdaf.obj.Image.adjust_coordinates>: new method which determines the world coordinate offsets between an image and a reference image, then applies this shift to the reference pixel index of the image.
Image.mask_region <mpdaf.obj.Image.mask_region> and Cube.mask_region <mpdaf.obj.Cube.mask_region> methods have been revised to support rectangular and square regions that are rotated.
Cube.mask_polygon <mpdaf.obj.Cube.mask_polygon>: new method similar to Image.mask_polygon <mpdaf.obj.Image.mask_polygon>.
Cube.bandpass_image <mpdaf.obj.Cube.bandpass_image>: new method for creating images with a given filter response curve.
WCS.get_axis_increments <mpdaf.obj.WCS.get_axis_increments>: new method which returns the displacements on the sky per pixel increment along the Y and X axes. There is also a new method WCS.set_axis_increments <mpdaf.obj.WCS.set_axis_increments> to update the signed displacements on the sky.
~mpdaf.MUSE.FieldsMap: new class which reads the possible FIELDMAP extension of the MUSE data cube.
~mpdaf.MUSE.FSF: new class which proposes a simple FSF model (Moffat function with a FWHM which varies linearly with the wavelength).
Breaking changes
Remove unused methods:
Remove the peak detection on a spectrum (peak_detection).
Remove interactive plotting methods of Spectrum and Image classes.
Remove filter methods on images (minimum_filter, maximum_filter, median_filter) and spectra (median_filter).
Remove Image.add_poisson_noise.
Remove Image.sum.
Remove methods to create images (mask_image, composite_image, make_image).
Remove PixTable.get_slices.
Remove the SEA script (each step remains available as library).
Remove the drs.calibobj module.
Remove submodules ZAP and GALPAK.
The resize methods of Cube, Image and Spectrum have been renamed crop to better indicate their purpose. The new methods are also faster and use less memory, and return the list of slices that have been used to crop the data.
The rebin_median methods of Cube, Image and Spectrum have been removed because its effect on the variances couldn’t be computed, and because it didn’t seem scientifically useful.
The rebin_factor and rebin_mean methods of Cube, Image and Spectrum have been replace by the rebin method. This method has been simplified to make it more maintainable. The simplification to this function was to effectively truncate the input data to be an integer multiple of the re-binning reduction factor, rather than computing partially sampled output pixels for the edge of the re-binned data.
The method Cube.get_lambda has been renamed ~mpdaf.obj.Cube.select_lambda.
The method Spectrum.get_lambda has been renamed ~mpdaf.obj.Spectrum.subspec.
The weighting options of Cube.sum <mpdaf.obj.Cube.sum> has been reimplemented. The old method with the flux conservation has been moved in the SEA library.
WCS.get_rot has been corrected to always return the angle between north and the Y axis of the image, in the sense of a rotation of north eastwards of Y. The updated versions of Image.get_rot <mpdaf.obj.Image.get_rot> and Image.rotate <mpdaf.obj.Image.rotate> resolve this discrepancy, so any software that has been using these functions may see changes.
The return value of the get_range methods of Cube, Image and DataArray have been changed to a flat array, rather than an array of two coordinate tuples that only denoted image corners for non-rotated images.
WCS.get_naxis1 and WCS.get_naxis2 have been removed, because the underlying WCS.naxis1 and WCS.naxis2 values can be queried directly.
WCS.resample and WCS.rotate methods has been removed, because they are no more needed by the equivalent methods in Image.
The method Image.add has been removed because it is easy for a user to do the equivalent by using align_with_image() followed by a simple addition of two images.
PIL dependency has been removed: now MPDAF doesn’t read .PNG, .JPEG or .BMP images.
WCS
When an ~mpdaf.obj.WCS object is initialized via its cdelt1, cdelt2 and rot parameters, the corresponding coordinate transformation matrix is now calculated in the way recommended in equation 189 of FITS paper II (Calabretta, M. R. & Greisen, E. W. 2002 paper II, A&A, 395, 1077-1122).
The ~mpdaf.obj.WCS initializer now accepts a cd argument, which may be used to set the coordinate transformation directly.
~mpdaf.obj.WCS.set_step now changes the pixel scaling correctly for all FITS files. The previous version, which worked for MUSE FITS files, failed on FITS files whose coordinate transform matrix included any shear terms.
A couple of issues have been resolved in ~mpdaf.obj.WCS.get_step. Incorrect values were returned for FITS files with pixels that were rectangular on the sky, rather than square. This didn’t affect typical MUSE FITS files.
Don’t write WCS headers with both CDELT1 and CD1_1.
Data classes (Cube, Image, Spectrum)
Methods which transform the object return now by default an other object. The optional copy argument can be used to request that the input data be transformed in-place.
Fix clone to update the NAXIS keywords in the data header
Change management of the data type (by default Cube object have the type of the DATA extension)
The variance calculation of ~mpdaf.obj.DataArray.sqrt has been corrected.
Fix Cube.median <mpdaf.obj.Cube.median> when used with axis=None.
Cube.get_image <mpdaf.obj.Cube.get_image>: add input parameters in the FITS header.
Allow to overwrite BUNIT for data without unit.
Fix EXPTIME of combined cubes when cubes overlap (using a median of the exposure map give a more realistic estimate).
The mean method of Cube, Image and Spectrum have been rewrote to optionally perform weighted means.
In the sum methods of Cube, Image and Spectrum, the weighted mean of the spectral pixels was being multiplied by the total number of input pixels instead of the number of unmasked pixels. This will have resulted in sums that were too small wherever there were masked spectral pixels.
Propagate mask in Cube.subcube <mpdaf.obj.Cube.subcube>.
Refactor Cube.subcube_circle_aperture <mpdaf.obj.Cube.subcube_circle_aperture> to use Cube.subcube and Cube.mask.
Make Cube.subcube <mpdaf.obj.Cube.subcube> and Image.subimage <mpdaf.obj.Image.subimage> as similar as possible. These methods extract rectangular as well as square areas, and they now work correctly for data with rectangular pixels.
A couple of problems have been fixed in the code that multiplies an image by a spectrum. The original code didn’t handle variances correctly and crashed due to a non-existent variable.
Correct the pixel value shown when moving the mouse over pixels of Image.plot <mpdaf.obj.Image.plot>.
Sources
Correct bug in Catalog.from_sources <mpdaf.sdetect.Catalog.from_sources>
Rewrite Catalog.match <mpdaf.sdetect.Catalog.match> which was not working properly, now it returns a dictionary.
Tell which keyword is missing when creating a source.
Allow to deactivate the masking of invalid values when loading a source. This part (~mpdaf.sdetect.Catalog.masked_invalid) takes ~40% of the total load time for sources with a lot of tables and columns.
Muselet
Optimize matchlines function
Split the main function in several functions
Remove Numpy warning
Use a Numpy array and not a masked array for the weights array
Use masked median of inv_variance
Make Muselet less verbose when running SExtractor
Pixtable
Convert pixtable values to double to avoid precision errors. This avoids discrepancies between _get_pos_sky and _get_pos_sky_numexpr (Numexpr seems to use double precision by default) and probably also with other methods.
Fix initial value for ~mpdaf.drs.PixTable.subtract_slice_median correction. This value was set to 1 which seems wrong for an additive correction. To emphasize the fact that some combination of slices and quadrants are not valid, and allow to filter these values later, this commit changes the init value for the count to -1, and the correction to NaN.
Fix ~mpdaf.drs.PixTable.select_sky in the case of positioned pixel table.
RawFile
Simplify ~mpdaf.drs.RawFile and ~mpdaf.drs.Channel classes
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