galpak 1.31

A tool to extract the intrinsic (i.e. deconvolved) Galaxy Parameters and Kinematics from any 3-Dimensional data.

WHAT IS IT

GalPaK 3D is a tool to extract Galaxy Parameters and Kinematics from 3-Dimensional data, using reverse deconvolution with Bayesian analysis Markov chain Monte Carlo. (random walk)

See the documentation for more details about the API on the web site.

INSTALL

pip install galpak

PYTHON DEPENDENCIES

The galpak module has been developed for Python 2.7 and has been tested with Python 3.5 & 3.7

The following are mandatory python modules that galpak depends upon :

    numpy>=1.14
    scipy
    astropy>=2.0
    matplotlib>=2.0

The following optional python modules improve galpak performances :

    pyfftw : https://pypi.python.org/pypi/pyFFTW
    bottleneck : https://pypi.python.org/pypi/Bottleneck/

The following optional python modules improve galpak functionalities :

    corner : https://pypi.python.org/pypi/corner
    emcee : https://pypi.org/project/emcee/
    mpdaf : http://mpdaf.readthedocs.io/en/latest/

MPDAF PACKAGES

Optional.

GalPaK provides a MUSELineSpreadFunction class that depends on mpdaf.MUSE.LSF. Follow MPDAF install instructions.

GalPaK also accepts MPDAF's Cubes as input.

I FOUND A BUG!

THERE WILL BE BUGS. If you have found a bug in GalPaK3D please report it on the galpak forum/mailing list. Can you reproduce it ? Provide the code and input cube(s). You cannot reproduce it ? just describe what you're doing when it happens.

Also, we encourage everyone to give us feedback and participate in discussions. We can use the galpak3d mailing list as well.

Email the above at [e-mail] and/or add them as test-case in the test suite.

HOW TO TEST

untar and do

python -m pytest 

HOW TO DOCUMENT

Install sphinx :

$ sudo apt-get install python-sphinx

or

$ pip install --user sphinx

Make your changes into the doc/source files.

Once its done, you can either :

$ cd doc
$ make html

or :

$ doit doc

FITS Sanitizer

python fits_sanitizer.py [-h] [--prefix PREFIX] FILE [FILE ...]

Sanitize specified FITS files. By default, this will overwrite the FITS files. To create another file(s), you can specify a prefix using the --prefix option.

What this actually does : - Lowercase 'DEG' unit - that's all ! (it did some other things in the past)

positional arguments: FILE A FITS file to sanitize

optional arguments: -h, --help show this help message and exit --prefix PREFIX A prefix to prepend to the filename(s), to create new files

Tip : you can sanitize a whole folder using the * wildcard : python fits_sanitizer.py /myfits/*.fits

Note that this will be superseded by the HyperspectralCube class sanitize method.

ACRONYMS

Real men never define acronyms. They understand them genetically.

FFT Fast Fourier Transform FITS Flexible Image Transport System FWHM Full Width at Half Maximum HDU Header Data Unit LSF Line Spread Function Wavelength spread due to the dispersion of light in the atmosphere MCMC Markov Chain Monte Carlo MPDAF MUSE Python Data Analysis Framework MUSE Multi Unit Spectroscopic Explorer NFM Narrow Field Mode PA Position Angle PC ParseC PSF Point Spread Function Spatial spread caused by the atmosphere SNR Signal Noise Ratio The relative intensity of the signal from the noise Should be > 1, or the data is useless WFM Wide Field Mode WSC World Coordinates System

BLACKBOARD

It would be smart to use a MCMC module : - pymc3.