Merge 69bbd6c into 556fd9a

linetools/isgm/tests/test_init_abscomp.py

@@ -7,11 +7,12 @@
 import pytest
 from astropy import units as u
 import numpy as np
+import pytest
 
 from linetools.isgm.abscomponent import AbsComponent
 from linetools.spectralline import AbsLine
 
-#import pdb
+import pdb
 #pdb.set_trace()
 # Set of Input lines
 
@@ -21,6 +22,15 @@ def test_init():
     # Test
     assert abscomp.Zion[0] == 14
     np.testing.assert_allclose(abscomp.zcomp,1.0)
+    print(abscomp)
+
+def test_init_failures():
+    with pytest.raises(IOError):
+        AbsComponent.from_abslines('blah')
+    with pytest.raises(IOError):
+        AbsComponent.from_abslines(['blah'])
+    with pytest.raises(IOError):
+        AbsComponent.from_component('blah')
 
 def test_init_single_absline():
     # Single AbsLine
@@ -31,6 +41,7 @@ def test_init_single_absline():
     # Test
     assert abscomp.Zion[0] == 1
     np.testing.assert_allclose(abscomp.zcomp,2.92939)
+    print(abscomp)
 
 def test_init_multi_absline():
     # AbsLine(s)

linetools/isgm/tests/test_use_abscomp.py

@@ -26,7 +26,7 @@
 #pdb.set_trace()
 # Set of Input lines
 
-def mk_comp(ctype,vlim=[-300.,300]*u.km/u.s,add_spec=False):
+def mk_comp(ctype,vlim=[-300.,300]*u.km/u.s,add_spec=False, use_rand=True):
     # Read a spectrum Spec
     if add_spec:
         xspec = lsio.readspec(lt_path+'/spectra/tests/files/UM184_nF.fits')
@@ -41,7 +41,11 @@ def mk_comp(ctype,vlim=[-300.,300]*u.km/u.s,add_spec=False):
     for trans in all_trans:
         iline = AbsLine(trans)
         iline.attrib['z'] = 2.92939
-        iline.attrib['logN'] = 13.3 + np.random.rand()
+        if use_rand:
+            rnd = np.random.rand()
+        else:
+            rnd = 0.
+        iline.attrib['logN'] = 13.3 + rnd
         iline.attrib['sig_logN'] = 0.15
         iline.attrib['flag_N'] = 1
         iline.analy['spec'] = xspec
@@ -65,6 +69,30 @@ def test_synthesize_colm():
     abscomp.synthesize_colm(redo_aodm=True)
     # Test
     np.testing.assert_allclose(abscomp.logN,13.594447075294818)
+    # Reset flags (for testing)
+    abscomp2,_ = mk_comp('SiII', vlim=[-250,80.]*u.km/u.s, add_spec=True, use_rand=False)
+    for iline in abscomp2._abslines:
+        if iline.data['name'] == 'SiII 1260':
+            iline.attrib['flag_N'] = 2
+        elif iline.data['name'] == 'SiII 1808':
+            iline.attrib['flag_N'] = 3
+        else:
+            iline.attrib['flag_N'] = 1
+    abscomp2.synthesize_colm()
+    # Test
+    np.testing.assert_allclose(abscomp2.logN, 13.3)
+    # Another
+    abscomp3,_ = mk_comp('SiII', vlim=[-250,80.]*u.km/u.s, add_spec=True, use_rand=False)
+    for iline in abscomp3._abslines:
+        if iline.data['name'] == 'SiII 1260':
+            iline.attrib['flag_N'] = 3
+        elif iline.data['name'] == 'SiII 1808':
+            iline.attrib['flag_N'] = 2
+        else:
+            iline.attrib['flag_N'] = 1
+    abscomp3.synthesize_colm()
+    # Test
+    np.testing.assert_allclose(abscomp3.logN, 13.3)
 
 def test_build_components_from_lines():
     # Lines
@@ -94,6 +122,7 @@ def test_synthesize_components():
     synth_SiII = ltiu.synthesize_components([SiIIcomp1,SiIIcomp2])
     np.testing.assert_allclose(synth_SiII.logN,13.862456155250918)
     np.testing.assert_allclose(synth_SiII.sig_logN,0.010146948602759272)
+
 """
 def test_stack_plot():
     # AbsLine(s)

linetools/isgm/utils.py

@@ -11,15 +11,11 @@
 
 import pdb
 import numpy as np
-from collections import OrderedDict
 
 from astropy import constants as const
 from astropy import units as u
-from astropy.coordinates import SkyCoord
 from astropy.table import QTable
-from astropy.io import ascii
 
-from linetools.spectralline import AbsLine
 from linetools.analysis import absline as ltaa
 from linetools.isgm.abscomponent import AbsComponent
 

linetools/spectra/io.py

@@ -198,6 +198,10 @@ def readspec(specfil, inflg=None, efil=None, verbose=False, flux_tags=None,
             else:
                 wave = hdulist['WAVELENGTH'].data * u.AA
                 fx = hdulist['FLUX'].data
+                # Sort
+                srt = np.argsort(wave)
+                wave = wave[srt]
+                fx = fx[srt]
                 xspec1d = XSpectrum1D.from_array(wave, u.Quantity(fx))
 
             # Error array
@@ -252,7 +256,12 @@ def readspec(specfil, inflg=None, efil=None, verbose=False, flux_tags=None,
             uwave = u.Quantity(wave, unit=u.AA)
         else:
             uwave = u.Quantity(wave)
+        # Sort
+        srt = np.argsort(uwave)
+        uwave = uwave[srt]
+        fx = fx[srt]
         if sig is not None:
+            sig = sig[srt]
             xspec1d = XSpectrum1D.from_array(uwave, u.Quantity(fx),
                                              uncertainty=StdDevUncertainty(sig))
         else:

linetools/spectra/xspectrum1d.py

@@ -92,7 +92,7 @@ def from_spec1d(cls, spec1d):
         return slf
 
     @classmethod
-    def from_tuple(cls,ituple):
+    def from_tuple(cls, ituple):
         """Make an XSpectrum1D from a tuple of arrays.
 
         Parameters
@@ -109,16 +109,25 @@ def from_tuple(cls,ituple):
             if wv_unit is None:
                 wv_unit = u.AA
         uwave = u.Quantity(ituple[0], unit=wv_unit)
+
+        # Sort
+        ltuple = list(ituple)
+        srt = np.argsort(uwave)
+        uwave = uwave[srt]
+        for ii in range(1, len(ituple)):
+            ltuple[ii] = ituple[ii][srt]
+
+
         # Generate
-        if len(ituple) == 2:  # wave, flux
-            spec = cls.from_array(uwave, u.Quantity(ituple[1]))
-        elif len(ituple) == 3:
-            spec = cls.from_array(uwave, u.Quantity(ituple[1]),
-                uncertainty=StdDevUncertainty(ituple[2]))
+        if len(ltuple) == 2:  # wave, flux
+            spec = cls.from_array(uwave, u.Quantity(ltuple[1]))
+        elif len(ltuple) == 3:
+            spec = cls.from_array(uwave, u.Quantity(ltuple[1]),
+                uncertainty=StdDevUncertainty(ltuple[2]))
         else:
-            spec = cls.from_array(uwave, u.Quantity(ituple[1]),
-                uncertainty=StdDevUncertainty(ituple[2]))
-            spec.co = ituple[3]
+            spec = cls.from_array(uwave, u.Quantity(ltuple[1]),
+                uncertainty=StdDevUncertainty(ltuple[2]))
+            spec.co = ltuple[3]
 
         spec.filename = 'none'
         # Return

linetools/tests/test_utils.py

@@ -1,9 +1,30 @@
 from __future__ import print_function, absolute_import, division, unicode_literals
 
-from ..utils import between
+from ..utils import between, v_from_z, savejson, loadjson, z_from_v
 import numpy as np
+from astropy import units as u
 
 def test_between():
     x = [1,2,3,4,5]
     c0 = between(x, 2.5, 3.5)
     assert np.all(c0 == np.array([False, False, True, False, False]))
+
+def test_zfromv():
+    z = z_from_v(2., 1000.)
+    #
+    np.testing.assert_allclose(z, 2.0100236684175417)
+
+def test_vfromz():
+    v = v_from_z(2., 2.1)
+    #
+    assert v.unit == u.km/u.s
+    np.testing.assert_allclose(v.value, -9826.62006340679)
+
+def test_save_load_json():
+    tmp_dict = dict(a=1, b=2, c='adsf')
+    # Write
+    savejson('tmp.json', tmp_dict, overwrite=True)
+    # Load
+    new_dict = loadjson('tmp.json')
+    assert new_dict['a'] == 1
+