{
    "info": {
        "author": "Jacopo Chevallard",
        "author_email": "jacopo.chevallard@mailfence.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Astronomy"
        ],
        "description": "# PySpecLines\n\nSome useful scripts to compute integrated line fluxes and equivalent widths from galaxy spectra using 3 different methods:\n\n- numerical (trapezoidal) integration\n- Gaussian fit using a \"standard\" Levenberg-Marquardt algorithm\n- Gaussian fit using an MCMC algorithm\n\n## Installing the package\n\nTo install ``PySpecLines`` you can use ``pip``, which will take care of installing the required dependencies as well\n```\npip install pyspeclines\n```\n\nTo upgrade to the latest available version you can run\n```\npip install pyspeclines --upgrade\n```\n\n## Data format\n\n### FITS binary table\n\n``PySpecLines`` works with FITS tables. Each spectrum should be contained in a separate FITS file, which **must** contain the following columns:\n\n- ``wl``, wavelength array in ``ang``\n- ``flux``, flux array in ``erg s^-1 cm^-2 ang^-1``\n- ``err``, error array in  ``erg s^-1 cm^-2 ang^-1``\n\n### FITS header\n\n``PySpecLines`` also uses the following (**optional**) FITS header keywords:\n\n- ``REDSHIFT``, used to de-redshift a spectrum from the observed-frame to the rest-frame\n- ``RA``, right ascension of the object in ``deg``, in the ``ICRS`` frame, used to correct for Galactic absorption\n- ``DEC``, declination of the object in ``deg``, in the ``ICRS`` frame, used to correct for Galactic absorption\n\nWhen 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).  \n\n### JSON configuration file\n\nA 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.\n\nBelow we report some simple examples:\n\n- single line: \n  ```json\n      {\n      \"HeII4686\" : {\n        \"wl_central\": [4686.0], \n        \"wl_range\":[4680.0, 4681.0], \n        \"continuum_left\":[4672.0, 4679.0],\n        \"continuum_right\":[4692.0, 4700.0]\n      }\n    }\n  ```\n  - ``wl_central`` is used as starting point for the line center in the Gaussian fitting\n  - ``wl_range`` is the range of numerical integration of the line\n  - ``continuum_left`` is the range of numerical integration of the left-continuum\n  - ``continuum_right`` is the range of numerical integration of the right-continuum \n  - when using Gaussian fitting, the range over which the continuum is fitted is ``[continuum_left[0], continuum_right[1]]``\n\n- line doublet: \n  ```json\n    {\n    \"SII6716_SII6731\" : {\n        \"wl_central\": [6716.0, 6731.0], \n        \"wl_range\":[6710.0, 6723.0], \n        \"exclude\":[6710.0, 6721.0, 6726.0, 6740.0],\n        \"continuum_left\":[6695.0, 6705.0],\n        \"continuum_right\":[6740.0, 6750.0]\n      }\n    }\n  ```\n  - wrt to the example above, the ``key`` is composed of two labels separated by an underscore ``_``\n  - ``exclude`` allows to define regions (``[exclude[0], exclude[1]], [exclude[2], exclude[3]]``) excluded from the continuum fitting \n  \n- multiple kinematic components\n  ```json\n    {\n    \"OIII5007N_OIII5007B\" : {\n        \"wl_central\": [5007.0, 5007.0], \n        \"width\": [100.0, 400.0], \n        \"wl_range\":[5000.0, 5014.0], \n        \"exclude\":[4995.0, 5020.0],\n        \"continuum_left\":[4990.0, 5000.0],\n        \"continuum_right\":[5020.0, 5034.0]\n      }\n    }\n  ```\n  - ``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.\n  \n- multiple lines with multiple kinematic components\n  ```json\n    {\n    \"NII6548_HalphaN_HalphaB_NII6584\" : {\n        \"wl_central\": [6548.05, 6563.0, 6563.0, 6584.0], \n        \"width\": [100.0, 100.0, 400.0, 100.0], \n        \"exclude\":[6542.0, 6580.0],\n        \"wl_range\":[6541.0, 6575.0], \n        \"continuum_left\":[6515.0,6542.0],\n        \"continuum_right\":[6595.0,6610.0]\n      }\n    }\n  ```\n  - 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.\n  \n\n\n## Examples\n\nYou can see the different available options running\n```\npyspeclines --help\n```\n\nIf the spectrum is provided in the observed frame, then you must provide a ``REDSHIFT`` keyword in the FITS header containing the object redshift.\n\n- Compute the fluxes and EWs using numerical integration\n  ```\n  pyspeclines --file my_spectrum.fits --json-file  emission_lines_EWs_config.json\n  ```\n\n- Compute the fluxes and EWs using Gaussian fit (Levenberg-Marquardt)\n  ```\n  pyspeclines --file my_spectrum.fits --json-file  emission_lines_EWs_config.json --gaussian-fit\n  ```\n\n- Compute the fluxes and EWs using Gaussian fit (MCMC)\n  ```\n  pyspeclines --file my_spectrum.fits --json-file  emission_lines_EWs_config.json --gaussian-fit --use-PyMC --MCMC-samples 5000\n  ```",
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