Merge e486830 into 197abbc

docs/guis.rst

@@ -32,7 +32,7 @@ This enables interactive fitting of the unabsorbed continuum for a
 spectrum. A series of 'knot' positions are estimated, and these are
 then joined with a spline to produce a continuum. Spline points can be
 interactively added, deleted or moved to improve the continuum. See
-the notebook for an example.
+the notebook for an example or use the lt_continuumfit script directly.
 
 XSpecGUI
 ========

docs/scripts.rst

@@ -171,13 +171,16 @@ lt_continuumfit
 
 Launch the GUI to continuum fit a spectrum.
 If a redshift is supplied by zsys, then the
-script assumes this is a QSO.::
+script assumes this is a QSO.  Enables spectra
+to be read in via a `specdb <https://specdb.readthedocs.io/en/latest/>`__ file
+which then requires specdb be installed.::
 
    lt_continuumfit input_file output_filename --redshift 0.867
 
 Here is the current usage message::
 
-    usage: lt_continuumfit [-h] [--redshift REDSHIFT] [--wchunk WCHUNK]
+    usage: lt_continuumfit [-h] [--redshift REDSHIFT] [--wchunk WCHUNK] [--native]
+                           [--specdb SPECDB]
                            file outfil
 
     GUI to fit a continuum to a spectrum
@@ -191,3 +194,7 @@ Here is the current usage message::
       -h, --help           show this help message and exit
       --redshift REDSHIFT  Redshift of the Source
       --wchunk WCHUNK      Width of a 'chunk' (Ang)
+      --native             Do not mask input spectrum
+      --specdb SPECDB      Input file is specdb. Input (ra,dec,group) in this
+                           order without spaces
+

linetools/analysis/continuum.py

@@ -226,7 +226,7 @@ def unmask(masked, indices, wa, fl, er, minpix=3):
             masked[ind1] = False
 
 
-def estimate_continuum(s, knots, indices, masked, ax=None, maxiter=1000,
+def estimate_continuum(s, knots, indices, masked, ax=None, maxiter=100,
                        nsig=1.5, debug=False):
     """ Iterate to estimate the continuum.
     """
@@ -255,7 +255,8 @@ def estimate_continuum(s, knots, indices, masked, ax=None, maxiter=1000,
                 print('No further points masked, stopping')
             break
         if count > maxiter:
-            raise RuntimeError('Exceeded maximum iterations')
+            warnings.warn('Exceeded maximum iterations. Continue at your own risk..')
+            break
 
         count +=1
 

linetools/guis/specdbutils.py

@@ -0,0 +1,76 @@
+""" Module for integrating specdb within linetools.  Mainly widgets and scripts"""
+
+try:
+    import specdb
+except ImportError:
+    flg_specdb = False
+else:
+    flg_specdb = True
+    from specdb.specdb import SpecDB
+
+from astropy.coordinates import SkyCoord
+
+
+def load_specb(specdb_file):
+    """
+    Load a specdb_file
+
+    Parameters
+    ----------
+    specdb_file: str
+      Full path to the specdb file
+
+    Returns
+    -------
+    spdb: SpecDB or None
+      Returns None if specdb cannot be imported
+
+    """
+    # Required import?
+    if not flg_specdb:
+        return None
+    #
+    spdb = SpecDB(db_file=specdb_file)
+    return spdb
+
+
+def load_xspec(spdb, ra, dec, group=None, **kwargs):
+    """
+    Load an XSpectrum1D class from a SpecDB object
+
+    Parameters
+    ----------
+    spdb: SpecDB
+    ra: float
+     RA coordinate (ICRS)
+    dec: float
+     DEC coordinate (ICRS)
+    group: str, optional
+     Data group to grab spectrum from
+    **kwargs
+     Passed to XSpectrum1D, e.g. masking
+
+
+    Returns
+    -------
+    spec: XSpectrum1D or None
+      Returns None if specdb cannot be imported
+
+    """
+    # Required import?
+    if not flg_specdb:
+        return None
+
+    # Need a list of group(s)
+    if group is None:
+        group = []
+    else:
+        group = [group]
+
+    # Coord
+    scoord = SkyCoord(ra=ra, dec=dec, unit='deg')
+
+    spec, _ = spdb.spectra_from_coord(scoord, groups=group, **kwargs)
+
+    # Return
+    return spec

linetools/scripts/lt_continuumfit.py

@@ -19,20 +19,35 @@ def main(*args, **kwargs):
     parser.add_argument("--redshift", type=float, help="Redshift of the Source")
     parser.add_argument("--wchunk", type=float, help="Width of a 'chunk' (Ang)")
     parser.add_argument("--native", default=True, action='store_true', help="Do not mask input spectrum")
+    parser.add_argument("--specdb", type=str, help="Input file is specdb.  Input (ra,dec,group) in this order without spaces")
     #parser.add_argument("-exten", type=int, help="FITS extension")
 
     pargs = parser.parse_args()
 
 
-    from linetools.guis.xspecgui import XSpecGui
+    from linetools.guis import specdbutils
     from linetools.spectra import io as lsio
 
     # Read spectrum
     if pargs.native:
         masking = 'none'
     else:
         masking = 'edges'
-    xspec = lsio.readspec(pargs.file, masking=masking)
+
+    # Load from simple file
+    if pargs.specdb is None:
+        xspec = lsio.readspec(pargs.file, masking=masking)
+    else:
+        # Load specdb
+        spdb = specdbutils.load_specb(pargs.file)
+        if spdb is None:
+            print("You have not yet installed specdb!!")
+            print("Exiting..")
+            return
+        # Parse
+        ra,dec,group = pargs.specdb.split(',')
+        # Load
+        xspec = specdbutils.load_xspec(spdb, float(ra), float(dec), group=group, masking=masking)
 
     kwrds = {}
     if pargs.wchunk is not None:

linetools/spectra/tests/test_xspec_attrib.py

@@ -19,8 +19,7 @@ def data_path(filename):
     return os.path.join(data_dir, filename)
 
 
-@pytest.fixture
-def dummy_spec(wave=None, npix=2000, s2n=10., seed=None):
+def dummy_spec(wave=None, s2n=10., npix=2000, seed=None):
     """
     Parameters
     ----------

linetools/spectra/xspectrum1d.py

@@ -10,7 +10,6 @@
 
 from astropy import units as u
 from astropy.units import Quantity, UnitBase
-from astropy import constants as const
 from astropy.io import fits
 #from astropy.nddata import StdDevUncertainty
 from astropy.table import QTable, Column, Table