Merge pull request #351 from linetools/chk_z

EW using do_analysis

docs/absline.rst

@@ -109,5 +109,6 @@ generate_voigt
 measure_aodm
 ------------
 
+
 Output
 ======

docs/abssys.rst

@@ -85,18 +85,47 @@ AbsLines
 --------
 
 There are a few methods related to the AbsLine objects within
-an AbsSystem.  One can generate a list of all the AbsLine objects
+an AbsSystem.
+
+List
+++++
+
+One can generate a list of all the AbsLine objects
 with::
 
    lines = abssys.list_of_abslines()
 
+
+get absline
++++++++++++
+
 One can retrieve one or more AbsLine objects matching the name
 or rest-wavelength of a transition, e.g. ::
 
    lyb = abssys.get_absline('HI 1025')
    # or
    lyb = abssys.get_absline(1025.72*u.AA)  # Nearest 0.01 A is required
 
+measure_restew
+++++++++++++++
+
+Measure the rest-frame equivalent widths for all AbsLine objects
+in the system.
+In addition to the inputs described in :ref:`measure-ew`,
+each line to be measured must have line.analy['do_anlaysis']=1.
+Here is an example::
+
+   abssys.measure_restew(spec=xspec_object)
+
+
+fill transitions
+++++++++++++++++
+
+Generate an astropy.Table of information on the absorption lines
+in the system.  This is stored in the ._trans attribute::
+
+   abssys.fill_trans()
+   print(abssys._trans)
 
 Components
 ----------
@@ -122,6 +151,8 @@ These are derived from the components ::
    abssys.fill_ionN()
    print(abssys._ionN)
 
+
+
 Output
 ======
 

docs/specline.rst

@@ -50,7 +50,7 @@ within its own object.  It is also accessible as a property, e.g.::
 
    z = sline.z
 
-.. _specanalysis
+.. _spec-analysis:
 
 Analysis
 ========
@@ -91,6 +91,8 @@ and whether they are from the same ion::
    print specline.ismatch(another_line)
 
 
+.. _measure-ew:
+
 measure_ew
 ----------
 
@@ -99,19 +101,21 @@ Following absorption-line convention, absorption will
 have a positive value and emission will have a negative value.
 
 To perform the calculation, the line must be associated to
-a spectrum (see `Analysis_`) and either wvlim or vlim must
-be specified.  When executed, the EW and sig_EW attibutes
-are filled::
+a spectrum (see `Analysis`_ above) and the LineLimits of the line
+must have previously been specified.
+
+When executed, the EW and sig_EW attibutes are filled::
 
    specline.measure_ew()
+   print(specline.attrib['EW'])
 
 
 measure_kin
 -----------
 
 Measure kinematic characteristics of an AbsLine.
 To perform the calculation, the line must be associated to
-a spectrum (see `Analysis_`) and vlim must
+a spectrum (see `Analysis`_) and vlim must
 be specified.  When executed, the 'kin' attribute is filled
 with a dict of measurements.  Default set of measurements
 are the v90, fedg, and fmm statistics of Prochaska & Wolfe 1997::
@@ -123,7 +127,7 @@ measure_restew
 --------------
 
 Measure the rest-frame Equivalent width of a SpectralLine.
-See `measure_ew`_ for details.
+See :ref:`measure-ew` for other details.
 
 to_dict
 -------

linetools/analysis/plots.py

@@ -13,7 +13,7 @@
 import matplotlib.gridspec as gridspec
 import matplotlib as mpl
 
-def stack_plot(abslines, vlim=[-300,300.]*u.km/u.s, nrow=6, show=True,
+def stack_plot(abslines, vlim=[-300,300.]*u.km/u.s, nrow=6, show=True, spec=None,
                ymnx=(-0.1,1.1), figsz=(18,11), return_fig=False, tight_layout=False):
     """Show a stack plot of the input lines
     Assumes the data are normalized.
@@ -49,6 +49,10 @@ def stack_plot(abslines, vlim=[-300,300.]*u.km/u.s, nrow=6, show=True,
     for iline in abslines:
         if isinstance(iline.analy['spec'], XSpectrum1D):
             gdiline.append(iline)
+        else:
+            if spec is not None:
+                iline.analy['spec'] = spec
+                gdiline.append(iline)
     nplt = len(gdiline)
     if nplt == 0:
         print("Load spectra into the absline.analy['spec']")

linetools/isgm/abssystem.py

@@ -260,6 +260,7 @@ def add_component(self, abscomp, tol=0.2*u.arcsec,
         else:
             testcoord = True
         # Now redshift/velocity
+        testz = True
         if chk_z:
             # Will avoid Quantity for speed
             comp_vlim_mks = abscomp.vlim.to('km/s').value
@@ -348,7 +349,7 @@ def get_absline(self, inp):
             warnings.warn("No absline with input={}".format(inp))
             return None
         elif len(mt) == 1:
-            return abslines[mt]
+            return abslines[mt[0]]
         else:
             return [abslines[ii] for ii in mt]
 
@@ -421,6 +422,8 @@ def list_of_abslines(self):
 
     def measure_restew(self, spec=None, **kwargs):
         """ Measure rest-frame EWs for lines in the AbsSystem
+        Analysis is only performed on lines with analy['do_analysis'] != 0
+
         Parameters
         ----------
         spec : XSpectrum1D, optional
@@ -437,8 +440,12 @@ def measure_restew(self, spec=None, **kwargs):
             # Fill in spec?
             if spec is not None:
                 iline.analy['spec'] = spec
-            # Measure
-            iline.measure_restew(**kwargs)
+            # Check for analysis
+            if iline.analy['do_analysis'] == 0:
+                warnings.warn("Skipping {:s} because do_analysis=0".format(iline.name))
+            else:
+                # Measure
+                iline.measure_restew(**kwargs)
 
     def measure_aodm(self, spec=None, **kwargs):
         """ Measure ADOM columns for the list of lines

linetools/isgm/tests/test_use_abssys.py

@@ -31,21 +31,18 @@ def data_path(filename):
 def init_system():
     radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
     # HI Lya, Lyb
-    lya = AbsLine(1215.670*u.AA)
+    lya = AbsLine(1215.670*u.AA, z=2.92939)
     lya.limits.set([-300.,300.]*u.km/u.s)
-    lya.attrib['z'] = 2.92939
     lya.attrib['coord'] = radec
-    lyb = AbsLine(1025.7222*u.AA)
+    lyb = AbsLine(1025.7222*u.AA, z=lya.z)
     lyb.limits.set([-300.,300.]*u.km/u.s)
-    lyb.attrib['z'] = lya.attrib['z']
     lyb.attrib['coord'] = radec
     abscomp = AbsComponent.from_abslines([lya,lyb])
     # SiII
     SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
     abslines = []
     for trans in SiIItrans:
-        iline = AbsLine(trans)
-        iline.attrib['z'] = 2.92939
+        iline = AbsLine(trans, z=2.92939)
         iline.attrib['coord'] = radec
         iline.limits.set([-250.,80.]*u.km/u.s)
         abslines.append(iline)
@@ -64,8 +61,6 @@ def test_list_of_abslines():
     abslines = gensys.list_of_abslines()
     # Test
     assert len(abslines) == 6
-    # Measure EWs
-    gensys.measure_restew(spec=spec)
     # Measure AODM
     gensys.measure_aodm(spec=spec)
     # trans table
@@ -77,6 +72,19 @@ def test_list_of_abslines():
     lyb = gensys.get_absline(1025.72*u.AA)
     np.testing.assert_allclose(lyb.wrest.value, 1025.7222)
 
+def test_measure_ew():
+    spec = io.readspec(data_path('UM184_nF.fits'))
+    gensys = init_system()
+    # Measure EWs
+    gensys.measure_restew(spec=spec)
+    for aline in gensys.list_of_abslines():
+        assert aline.attrib['flag_EW'] == 1
+    # Skip do_analysis = 0
+    gensys2 = init_system()
+    lyb = gensys2.get_absline('HI 1025')
+    lyb.analy['do_analysis'] = 0
+    gensys2.measure_restew(spec=spec)
+    assert lyb.attrib['flag_EW'] == 0
 
 def test_ionn():
     gensys = init_system()