Metadata-Version: 1.1
Name: pyspeclines
Version: 0.2.1
Summary: Package to compute integrated line fluxes and equivalent widths from galaxy spectra
Home-page: https://github.com/jacopo-chevallard/PySpecLines
Author: Jacopo Chevallard
Author-email: jacopo.chevallard@mailfence.com
License: MIT
Description: 
        # PySpecLines
        
        Some 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 package
        
        To 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 absorption
        
        When 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 file
        
        A 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.
          
        
        
        ## Examples
        
        You 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
          ```
        
Keywords: astronomy galaxies statistics visualization
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Astronomy
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
