Fitting of Spectrum1D

docs/index.rst

@@ -29,6 +29,7 @@ Using specutils
    basic_analysis
    arithmetic
    smoothing
+   fitting
 
 .. toctree::
     :maxdepth: 1

specutils/fitting/__init__.py

@@ -0,0 +1,4 @@
+from __future__ import absolute_import
+
+from .fitmodels import *
+from .continuum import *

specutils/fitting/continuum.py

@@ -0,0 +1,101 @@
+from __future__ import division
+
+from astropy.modeling.polynomial import Chebyshev1D
+from astropy.modeling.fitting import SLSQPLSQFitter
+
+from ..fitting import fit_lines
+from ..manipulation.smoothing import median_smooth
+
+
+__all__ = ['fit_continuum', 'fit_generic_continuum']
+
+
+def fit_generic_continuum(spectrum, median_window=3, model=Chebyshev1D(3),
+                          fitter=SLSQPLSQFitter(),
+                          exclude_regions=None, weights=None):
+    """
+    Basic fitting of the continuum of an input spectrum. The input
+    spectrum is smoothed using a median filter to remove the spikes.
+
+    Parameters
+    ----------
+    spectrum : Spectrum1D
+        The spectrum object overwhich the equivalent width will be calculated.
+
+    model : list of `~astropy.modeling.Model`
+        The list of models that contain the initial guess.
+
+    exclude_regions : list of 2-tuples
+        List of regions to exclude in the fitting. Passed through
+        to the fitmodels routine.
+
+    weights : list  (NOT IMPLEMENTED YET)
+        List of weights to define importance of fitting regions.
+
+    Returns
+    -------
+    continuum_spectrum : Spectrum `~specutils.Spectrum1D`
+        Underlying continuum based on a Chebyshev1D fit (default).
+
+    Notes
+    -----
+       * Could add functionality to set the bounds in
+         ``model`` if they are not set.
+       * The models in the list of ``model`` are added together and passed as a
+         compound model to the `~astropy.modeling.fitting.Fitter` class instance.
+
+    """
+
+    #
+    # Simple median smooth to remove spikes and peaks
+    #
+
+    spectrum_smoothed = median_smooth(spectrum, median_window)
+
+    #
+    # Return the fitted continuum
+    #
+
+    return fit_continuum(spectrum_smoothed, model, fitter, exclude_regions, weights)
+
+
+def fit_continuum(spectrum, model=Chebyshev1D(3), fitter=SLSQPLSQFitter(),
+                  exclude_regions=None, window=None, weights=None):
+    """
+    Entry point for fitting using the `~astropy.modeling.fitting`
+    machinery.
+
+    Parameters
+    ----------
+    spectrum : Spectrum1D
+        The spectrum object overwhich the equivalent width will be calculated.
+
+    model: list of `~astropy.modeling.Model`
+        The list of models that contain the initial guess.
+
+    fitmodels_type: str
+        String representation of fit method to use as defined by the dict fitmodels_types.
+
+    window : tuple of wavelengths  (NOT IMPLEMENTED YET)
+        Start and end wavelengths used for fitting.
+
+    weights : list  (NOT IMPLEMENTED YET)
+        List of weights to define importance of fitting regions.
+
+    Returns
+    -------
+    models : list of `~astropy.modeling.Model`
+        The list of models that contain the fitted model parmeters.
+
+    """
+
+    if window is not None or weights is not None:
+        raise NotImplementedError('window and weights are not yet implemented')
+
+    #
+    # Fit the flux to the model.
+    #
+
+    continuum_spectrum = fit_lines(spectrum, model, fitter, exclude_regions, weights)
+
+    return continuum_spectrum