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linetools · Aug 4, 2016 · 04045cd · 04045cd
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diff --git a/docs/abscomp.rst b/docs/abscomp.rst
@@ -47,16 +47,14 @@ The default sets the properties listed above::
 More commonly, one will instantiate with one
 `~linetools.spectralline.AbsLine` object::
 
-    lya = AbsLine(1215.670*u.AA)
-    lya.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lya.attrib['z'] = 2.92939
+    lya = AbsLine(1215.670*u.AA, z=2.92939)
+    lya.limits.set([-300.,300.]*u.km/u.s)  # vlim
     abscomp1 = AbsComponent.from_abslines([lya])
 
 or multiple::
 
-    lyb = AbsLine(1025.7222*u.AA)
-    lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lyb.attrib['z'] = lya.attrib['z']
+    lyb = AbsLine(1025.7222*u.AA, z=lya.attrib['z'])
+    lyb.limits.set([-300.,300.]*u.km/u.s)  # vlim
     abscomp = AbsComponent.from_abslines([lya,lyb])
 
 One may also instantiate from a *dict*, usually read

diff --git a/docs/abssys.rst b/docs/abssys.rst
@@ -46,12 +46,10 @@ More commonly, one will instantiate with one or more AbsComponent objects::
 
     # HI Lya, Lyb
     radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
-    lya = AbsLine(1215.670*u.AA)
-    lya.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lya.attrib['z'] = 2.92939
-    lyb = AbsLine(1025.7222*u.AA)
-    lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lyb.attrib['z'] = lya.attrib['z']
+    lya = AbsLine(1215.670*u.AA, z=2.92939)
+    lya.limits.set([-300.,300.]*u.km/u.s)  # vlim
+    lyb = AbsLine(1025.7222*u.AA, z=lya.attrib['z'])
+    lyb.limits.set([-300.,300.]*u.km/u.s)  # vlim
     abscomp = AbsComponent.from_abslines([lya,lyb])
     abscomp.coord = radec
     # Finish

diff --git a/docs/examples/AbsComponent_ColumnDensities.ipynb b/docs/examples/AbsComponent_ColumnDensities.ipynb
diff --git a/docs/examples/AbsComponent_examples.ipynb b/docs/examples/AbsComponent_examples.ipynb
diff --git a/docs/examples/AbsLine_examples.ipynb b/docs/examples/AbsLine_examples.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Examples for AbsLine class (v1.3)"
+    "# Examples for AbsLine class (v1.4)"
    ]
   },
   {
@@ -42,10 +42,18 @@
     "collapsed": false
    },
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Loading abundances from Asplund2009\n",
+      "Abundances are relative by number on a logarithmic scale with H=12\n"
+     ]
+    },
     {
      "data": {
       "text/plain": [
-       "<AbsLine: CIV 1548, wrest=1548.1950 Angstrom>"
+       "<AbsLine: CIV 1548, z=0.0000 wrest=1548.1950 Angstrom>"
       ]
      },
      "execution_count": 2,
@@ -84,6 +92,7 @@
        " 'Jk': 0.0,\n",
        " 'Ref': 'Verner1994',\n",
        " 'Z': 6,\n",
+       " 'abundance': 8.4299999999999997,\n",
        " 'col0': masked,\n",
        " 'col7': masked,\n",
        " 'el': 0,\n",
@@ -93,13 +102,17 @@
        " 'gk': 4,\n",
        " 'group': 1,\n",
        " 'ion': 4,\n",
+       " 'ion_correction': 0.0,\n",
+       " 'ion_name': u'CIV',\n",
        " 'is_EUV': False,\n",
        " 'is_HI': False,\n",
        " 'is_Strong': True,\n",
+       " 'log(w*f)': 2.4685792560428057,\n",
        " 'mol': '',\n",
        " 'name': 'CIV 1548',\n",
        " 'nj': 0,\n",
        " 'nk': 0,\n",
+       " 'rel_strength': 10.898579256042805,\n",
        " 'wrest': <Quantity 1548.195 Angstrom>}"
       ]
      },
@@ -134,9 +147,7 @@
        "  u'flag_kin': 0,\n",
        "  u'flg_eye': 0,\n",
        "  u'flg_limit': 0,\n",
-       "  u'name': 'CIV 1548',\n",
-       "  u'vlim': {'unit': u'km / s', 'value': [0.0, 0.0]},\n",
-       "  u'wvlim': {'unit': u'Angstrom', 'value': [0.0, 0.0]}},\n",
+       "  u'name': 'CIV 1548'},\n",
        " 'attrib': {u'DEC': 0.0,\n",
        "  u'EW': {'unit': u'Angstrom', 'value': 0.0},\n",
        "  u'N': {'unit': u'1 / cm2', 'value': 0.0},\n",
@@ -162,20 +173,25 @@
        "  'Jk': 0.0,\n",
        "  'Ref': 'Verner1994',\n",
        "  'Z': 6,\n",
+       "  'abundance': 8.43,\n",
        "  'el': 0,\n",
        "  'f': 0.1899999976158142,\n",
        "  'gamma': {'unit': u'1 / s', 'value': 0.0},\n",
        "  'gj': 2,\n",
        "  'gk': 4,\n",
        "  'group': 1,\n",
        "  'ion': 4,\n",
+       "  'ion_correction': 0.0,\n",
+       "  'ion_name': u'CIV',\n",
        "  'is_EUV': False,\n",
        "  'is_HI': False,\n",
        "  'is_Strong': True,\n",
+       "  'log(w*f)': 2.4685792560428057,\n",
        "  'mol': '',\n",
        "  'name': 'CIV 1548',\n",
        "  'nj': 0,\n",
        "  'nk': 0,\n",
+       "  'rel_strength': 10.898579256042805,\n",
        "  'wrest': {'unit': u'Angstrom', 'value': 1548.195}},\n",
        " 'ltype': u'Abs',\n",
        " 'name': 'CIV 1548',\n",
@@ -210,7 +226,7 @@
     {
      "data": {
       "text/plain": [
-       "<AbsLine: CIV 1548, wrest=1548.1950 Angstrom>"
+       "<AbsLine: CIV 1548, z=0.0000 wrest=1548.1950 Angstrom>"
       ]
      },
      "execution_count": 5,
@@ -260,7 +276,7 @@
     }
    ],
    "source": [
-    "wrest_values = ltlu.parse_abslines(abslines, 'wrest')\n",
+    "wrest_values = ltlu.parse_speclines(abslines, 'wrest')\n",
     "wrest_values"
    ]
   },
@@ -282,22 +298,22 @@
      "data": {
       "text/html": [
        "&lt;Table length=2&gt;\n",
-       "<table id=\"table4594379280\">\n",
-       "<thead><tr><th>wrest</th><th>name</th><th>Z</th><th>ion</th><th>Ej</th><th>z</th><th>EW</th><th>sig_EW</th><th>flag_N</th><th>logN</th></tr></thead>\n",
-       "<thead><tr><th>Angstrom</th><th></th><th></th><th></th><th>1 / cm</th><th></th><th>Angstrom</th><th>Angstrom</th><th></th><th></th></tr></thead>\n",
-       "<thead><tr><th>float64</th><th>str8</th><th>int64</th><th>int64</th><th>float64</th><th>float64</th><th>float64</th><th>float64</th><th>int64</th><th>float64</th></tr></thead>\n",
-       "<tr><td>1215.67</td><td>HI 1215</td><td>1</td><td>1</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0</td><td>0.0</td></tr>\n",
-       "<tr><td>1548.195</td><td>CIV 1548</td><td>6</td><td>4</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0</td><td>0.0</td></tr>\n",
+       "<table id=\"table4599800336\">\n",
+       "<thead><tr><th>wrest</th><th>name</th><th>Z</th><th>ion</th><th>Ej</th><th>z</th><th>EW</th><th>sig_EW</th><th>flag_N</th><th>logN</th><th>sig_logN</th></tr></thead>\n",
+       "<thead><tr><th>Angstrom</th><th></th><th></th><th></th><th>1 / cm</th><th></th><th>Angstrom</th><th>Angstrom</th><th></th><th></th><th></th></tr></thead>\n",
+       "<thead><tr><th>float64</th><th>str8</th><th>int64</th><th>int64</th><th>float64</th><th>float64</th><th>float64</th><th>float64</th><th>int64</th><th>float64</th><th>float64</th></tr></thead>\n",
+       "<tr><td>1215.67</td><td>HI 1215</td><td>1</td><td>1</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0</td><td>0.0</td><td>0.0</td></tr>\n",
+       "<tr><td>1548.195</td><td>CIV 1548</td><td>6</td><td>4</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0</td><td>0.0</td><td>0.0</td></tr>\n",
        "</table>"
       ],
       "text/plain": [
        "<Table length=2>\n",
-       " wrest     name     Z    ion     Ej      z       EW     sig_EW  flag_N   logN \n",
-       "Angstrom                       1 / cm         Angstrom Angstrom               \n",
-       "float64    str8   int64 int64 float64 float64 float64  float64  int64  float64\n",
-       "-------- -------- ----- ----- ------- ------- -------- -------- ------ -------\n",
-       " 1215.67  HI 1215     1     1     0.0     0.0      0.0      0.0      0     0.0\n",
-       "1548.195 CIV 1548     6     4     0.0     0.0      0.0      0.0      0     0.0"
+       " wrest     name     Z    ion     Ej   ...  sig_EW  flag_N   logN  sig_logN\n",
+       "Angstrom                       1 / cm ... Angstrom                        \n",
+       "float64    str8   int64 int64 float64 ... float64  int64  float64 float64 \n",
+       "-------- -------- ----- ----- ------- ... -------- ------ ------- --------\n",
+       " 1215.67  HI 1215     1     1     0.0 ...      0.0      0     0.0      0.0\n",
+       "1548.195 CIV 1548     6     4     0.0 ...      0.0      0     0.0      0.0"
       ]
      },
      "execution_count": 8,
@@ -338,7 +354,7 @@
    "outputs": [],
    "source": [
     "# Set analysis range\n",
-    "abslin.analy['wvlim'] = [6080.78, 6087.82]*u.AA"
+    "abslin.limits.set([6080.78, 6087.82]*u.AA)  # wvlim"
    ]
   },
   {
@@ -377,11 +393,10 @@
    },
    "outputs": [],
    "source": [
-    "abslin.analy['wvlim'] = [0.,0.]*u.AA # Zero out for test\n",
     "#\n",
     "abslin.analy['spec'] = lsio.readspec('../../linetools/spectra/tests/files/UM184_nF.fits')\n",
-    "abslin.analy['vlim'] = (-150., 150.)*u.km/u.s\n",
-    "abslin.attrib['z'] = 2.92929"
+    "abslin.setz(2.92929)\n",
+    "abslin.limits.set((-150., 150.)*u.km/u.s)  # vlim"
    ]
   },
   {
@@ -416,7 +431,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "metadata": {
     "collapsed": false
    },
@@ -425,25 +440,25 @@
      "data": {
       "text/html": [
        "&lt;Table length=2&gt;\n",
-       "<table id=\"table4595718160\">\n",
-       "<thead><tr><th>wrest</th><th>name</th><th>Z</th><th>ion</th><th>Ej</th><th>z</th><th>EW</th><th>sig_EW</th><th>flag_N</th><th>logN</th></tr></thead>\n",
-       "<thead><tr><th>Angstrom</th><th></th><th></th><th></th><th>1 / cm</th><th></th><th>Angstrom</th><th>Angstrom</th><th></th><th></th></tr></thead>\n",
-       "<thead><tr><th>float64</th><th>str8</th><th>int64</th><th>int64</th><th>float64</th><th>float64</th><th>float64</th><th>float64</th><th>int64</th><th>float64</th></tr></thead>\n",
-       "<tr><td>1215.67</td><td>HI 1215</td><td>1</td><td>1</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0</td><td>0.0</td></tr>\n",
-       "<tr><td>1548.195</td><td>CIV 1548</td><td>6</td><td>4</td><td>0.0</td><td>2.92929</td><td>0.993502101206</td><td>0.0527114204241</td><td>1</td><td>13.9050897399</td></tr>\n",
+       "<table id=\"table4599866256\">\n",
+       "<thead><tr><th>wrest</th><th>name</th><th>Z</th><th>ion</th><th>Ej</th><th>z</th><th>EW</th><th>sig_EW</th><th>flag_N</th><th>logN</th><th>sig_logN</th></tr></thead>\n",
+       "<thead><tr><th>Angstrom</th><th></th><th></th><th></th><th>1 / cm</th><th></th><th>Angstrom</th><th>Angstrom</th><th></th><th></th><th></th></tr></thead>\n",
+       "<thead><tr><th>float64</th><th>str8</th><th>int64</th><th>int64</th><th>float64</th><th>float64</th><th>float64</th><th>float64</th><th>int64</th><th>float64</th><th>float64</th></tr></thead>\n",
+       "<tr><td>1215.67</td><td>HI 1215</td><td>1</td><td>1</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0</td><td>0.0</td><td>0.0</td></tr>\n",
+       "<tr><td>1548.195</td><td>CIV 1548</td><td>6</td><td>4</td><td>0.0</td><td>2.92929</td><td>0.993502101206</td><td>0.0527114204241</td><td>1</td><td>13.9050897399</td><td>0.0207026007539</td></tr>\n",
        "</table>"
       ],
       "text/plain": [
        "<Table length=2>\n",
-       " wrest     name     Z    ion  ...      sig_EW     flag_N      logN    \n",
-       "Angstrom                      ...     Angstrom                        \n",
-       "float64    str8   int64 int64 ...     float64     int64     float64   \n",
-       "-------- -------- ----- ----- ... --------------- ------ -------------\n",
-       " 1215.67  HI 1215     1     1 ...             0.0      0           0.0\n",
-       "1548.195 CIV 1548     6     4 ... 0.0527114204241      1 13.9050897399"
+       " wrest     name     Z    ion  ... flag_N      logN         sig_logN   \n",
+       "Angstrom                      ...                                     \n",
+       "float64    str8   int64 int64 ... int64     float64        float64    \n",
+       "-------- -------- ----- ----- ... ------ ------------- ---------------\n",
+       " 1215.67  HI 1215     1     1 ...      0           0.0             0.0\n",
+       "1548.195 CIV 1548     6     4 ...      1 13.9050897399 0.0207026007539"
       ]
      },
-     "execution_count": 15,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }