Package: pyspeclines
# PySpecLinesSome useful scripts to compute integrated line fluxes and equivalent widths from galaxy spectra using 3 different methods:- numerical (trapezoidal) integration- Gaussian fit using a "standard" Levenberg-Marquardt algorithm- Gaussian fit using an MCMC algorithm## Installing the packageTo install ``PySpecLines`` you can use ``pip``, which will take care of installing the required dependencies as well```pip install pyspeclines```To upgrade to the latest available version you can run```pip install pyspeclines --upgrade```## Data format### FITS binary table``PySpecLines`` works with FITS tables. Each spectrum should be contained in a separate FITS file, which **must** contain the following columns:- ``wl``, wavelength array in ``ang``- ``flux``, flux array in ``erg s^-1 cm^-2 ang^-1``- ``err``, error array in  ``erg s^-1 cm^-2 ang^-1``### FITS header``PySpecLines`` also uses the following (**optional**) FITS header keywords:- ``REDSHIFT``, used to de-redshift a spectrum from the observed-frame to the rest-frame- ``RA``, right ascension of the object in ``deg``, in the ``ICRS`` frame, used to correct for Galactic absorption- ``DEC``, declination of the object in ``deg``, in the ``ICRS`` frame, used to correct for Galactic absorptionWhen both keywords ``RA`` and ``DEC`` are present, ``PySpecLines`` can de-redden the spectrum (passing the option ``-deredden``) using the Galactic dust map of Schlegel, Finkbeiner & Davis (1998) recalibrated by Schlafly & Finkbeiner (2011), and the ``R_V=3.1`` extinction curve of Fitzpatrick (1999).### JSON configuration fileA JSON file allows you to select and configure the emission lines to be measured. Some example JSON files are provided in the [PySpecLines/files](https://github.com/jacopo-chevallard/PySpecLines/tree/master/PySpecLines/files) folder. The JSON file contains a dictionary of ``key : values`` where ``key`` labels the line (or group of lines) and ``values`` contains multiple entries.Below we report some simple examples:- single line:```json{"HeII4686" : {"wl_central": [4686.0],"wl_range":[4680.0, 4681.0],"continuum_left":[4672.0, 4679.0],"continuum_right":[4692.0, 4700.0]}}```- ``wl_central`` is used as starting point for the line center in the Gaussian fitting- ``wl_range`` is the range of numerical integration of the line- ``continuum_left`` is the range of numerical integration of the left-continuum- ``continuum_right`` is the range of numerical integration of the right-continuum- when using Gaussian fitting, the range over which the continuum is fitted is ``[continuum_left[0], continuum_right[1]]``- line doublet:```json{"SII6716_SII6731" : {"wl_central": [6716.0, 6731.0],"wl_range":[6710.0, 6723.0],"exclude":[6710.0, 6721.0, 6726.0, 6740.0],"continuum_left":[6695.0, 6705.0],"continuum_right":[6740.0, 6750.0]}}```- wrt to the example above, the ``key`` is composed of two labels separated by an underscore ``_``- ``exclude`` allows to define regions (``[exclude[0], exclude[1]], [exclude[2], exclude[3]]``) excluded from the continuum fitting- multiple kinematic components```json{"OIII5007N_OIII5007B" : {"wl_central": [5007.0, 5007.0],"width": [100.0, 400.0],"wl_range":[5000.0, 5014.0],"exclude":[4995.0, 5020.0],"continuum_left":[4990.0, 5000.0],"continuum_right":[5020.0, 5034.0]}}```- ``width`` allows to define multiple kinematic components, in this case a "narrow" (labelled ``OIII5007N``) and a "broad" (labelled ``OIII5007B``) component, whose starting widths **must** be set to different values.- multiple lines with multiple kinematic components```json{"NII6548_HalphaN_HalphaB_NII6584" : {"wl_central": [6548.05, 6563.0, 6563.0, 6584.0],"width": [100.0, 100.0, 400.0, 100.0],"exclude":[6542.0, 6580.0],"wl_range":[6541.0, 6575.0],"continuum_left":[6515.0,6542.0],"continuum_right":[6595.0,6610.0]}}```- in this case we want to use the same width for different lines (``NII6548``, ``HalphaN`` and ``NII6584``) and a different width for ``HalphaB``. We thus use the same ``width`` value for ``NII6548``, ``HalphaN`` and ``NII6584``, as this will "tie" together their widths during the Gaussian fitting, while the ``width`` of ``HalphaB`` will be kept separate.## ExamplesYou can see the different available options running```pyspeclines --help```If the spectrum is provided in the observed frame, then you must provide a ``REDSHIFT`` keyword in the FITS header containing the object redshift.- Compute the fluxes and EWs using numerical integration```pyspeclines --file my_spectrum.fits --json-file  emission_lines_EWs_config.json```- Compute the fluxes and EWs using Gaussian fit (Levenberg-Marquardt)```pyspeclines --file my_spectrum.fits --json-file  emission_lines_EWs_config.json --gaussian-fit```- Compute the fluxes and EWs using Gaussian fit (MCMC)```pyspeclines --file my_spectrum.fits --json-file  emission_lines_EWs_config.json --gaussian-fit --use-PyMC --MCMC-samples 5000```