Emsystem #416

tiffanyhsyu · 2017-10-04T20:13:42Z

No description provided.

profxj

Need docs and more tests.

profxj · 2017-10-05T12:22:00Z

linetools/analysis/emline.py

+    Returns
+    -------
+    """
+    if method == 'PG16':


Can you add a http link to the paper here?

This has been added

profxj · 2017-10-05T12:22:54Z

linetools/isgm/emsystem.py

+
+        Parameters
+        ----------
+        alis_file


profxj · 2017-10-05T12:24:07Z

linetools/isgm/emsystem.py

+    def __init__(self, radec, zem, vlim=None, em_type=None, name=None):
+
+        self.zem = zem
+        if vlim is None:


We need to use the zLimits Class here.

I can help set that up. Remind me.

This is now in Issue #419

profxj · 2017-10-05T12:25:20Z

linetools/isgm/emsystem.py

+        #
+        return test
+
+    def chk_emline(self, component):


We don't use components with EmLine (at least not now).

Remove components and/or this method.

Same goes for anywhere else you see components.

profxj · 2017-10-05T12:25:34Z

linetools/isgm/emsystem.py

+        self._ionN = ltiu.iontable_from_components(self._components, **kwargs)
+
+    def fill_trans(self, **kwargs):
+        """ Fills the ionN Table from the list of components


list of emlines

profxj · 2017-10-05T12:26:20Z

linetools/isgm/emsystem.py

+        else:
+            return [self._emlines[ii] for ii in mt]
+
+    def get_component(self, inp):


remove this method

profxj · 2017-10-05T12:26:32Z

linetools/isgm/emsystem.py

+        return None
+
+    def measure_restew(self, spec=None, **kwargs):
+        """ Measure rest-frame EWs for lines in the AbsSystem


profxj · 2017-10-05T12:26:55Z

linetools/isgm/emsystem.py

+            vlim = self.vlim
+        ltap.stack_plot(self.list_of_abslines(), vlim=vlim, **kwargs)
+
+    def to_dict(self):


Does this work?

Just checked that this works! There is also a test for it now.

profxj · 2017-10-05T12:27:48Z

linetools/isgm/tests/test_init_emsys.py

+    data_dir = os.path.join(os.path.dirname(__file__), 'files')
+    return os.path.join(data_dir, filename)
+
+


Add some other, simpler tests for instantiating the object.

I've added a test for creating an EmSystem object

profxj · 2017-10-05T12:28:21Z

linetools/tests/test_io.py

+
+def test_emline_from_alis():
+    lio.emlines_from_alis_output(data_path('spec1d_J0018p2345_KASTb_coadd.mod.out'))
+


Add some checks that this actually worked.

removed some methods not used for EmSystems

…s/linetools into emsystem

profxj · 2017-10-13T11:51:57Z

Hey @tiffanyhsyu -- One test is still failing:


def test_emline_from_alis():
    J0018_emlines = lio.emlines_from_alis_output(data_path('spec1d_J0018p2345_KASTb_coadd.mod.out'))

    assert len(J0018_emlines) == 8
    np.testing.assert_allclose(J0018_emlines[0].z, 0.01540425)
    np.testing.assert_allclose(J0018_emlines[1].wrest.value, 4341.684) #Hgamma

That is because the file is not in the repo. And you may need to edit one
other thing too. But add that file in first. Thanks

profxj · 2017-10-13T11:52:18Z

The test, by the way, is

tests/test_io.py

…o emsystem

tiffanyhsyu · 2017-10-13T18:30:39Z

@profxj I've added a 'files' folder under 'test' and uploaded the ALIS .mod.out file there -- is that ok, as far as the organization of the files?

coveralls · 2017-10-23T21:57:47Z

Coverage decreased (-0.02%) to 71.735% when pulling ee25b81 on emsystem into 9ff0b74 on master.

…s/linetools into emsystem

coveralls · 2017-10-23T22:58:47Z

Coverage decreased (-0.05%) to 71.735% when pulling d1a1fca on emsystem into dd5c4a8 on master.

profxj · 2017-10-24T12:18:16Z

merging!

profxj and others added 11 commits December 8, 2016 16:49

emsystem begins

464385a

small edit

41e0568

small edit

613ecca

Merge branches 'emsystem' and 'master' of https://github.com/linetool…

d5597e5

…s/linetools into emsystem

flux errors

06f11bb

metallicity method

469b9d2

flag

51fc912

Merge branches 'emsystem' and 'master' of https://github.com/linetool…

c60ba51

…s/linetools into emsystem

match ALIS wavelength to closest in linelist

31c8831

write

6c593ad

add HeI 7283 line

f67d8f7

profxj requested changes Oct 5, 2017

View reviewed changes

tiffanyhsyu and others added 10 commits October 5, 2017 16:35

add link to paper for metallicity estimate method

1ff10a6

address some of JXP's comments

2f8f76f

removed some methods not used for EmSystems

Merge branches 'emsystem' and 'master' of https://github.com/linetool…

fe247ca

…s/linetools into emsystem

small edits

505f5ef

add test on creating emline from ALIS output file

2188dad

brought back chk_emline

cb9398f

test for initializing an EmSystem

4464d76

add test for writing EmSystem to a dict

eed137f

test fixes

788d588

travis fix

e312dc3

tiffanyhsyu added 2 commits October 13, 2017 11:24

add sample ALIS output file for tests

f38a94d

Merge branch 'emsystem' of https://github.com/linetools/linetools int…

a772649

…o emsystem

profxj added 3 commits October 16, 2017 14:24

test files

246688f

remove setup_package.py

c296b4d

fussing more..

76892f6

profxj added 2 commits October 16, 2017 15:44

still struggling

61db5fa

desparation

ee25b81

Merge branches 'emsystem' and 'master' of https://github.com/linetool…

d1a1fca

…s/linetools into emsystem

profxj approved these changes Oct 24, 2017

View reviewed changes

Merge branch 'master' into emsystem

bb74d0d

profxj merged commit 5ebd872 into master Oct 24, 2017

profxj deleted the emsystem branch October 24, 2017 12:18

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Emsystem #416

Emsystem #416

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profxj commented Oct 13, 2017

profxj commented Oct 13, 2017

tiffanyhsyu commented Oct 13, 2017 •

edited

coveralls commented Oct 23, 2017

coveralls commented Oct 23, 2017

profxj commented Oct 24, 2017

		data_dir = os.path.join(os.path.dirname(__file__), 'files')
		return os.path.join(data_dir, filename)


		def test_emline_from_alis():
		lio.emlines_from_alis_output(data_path('spec1d_J0018p2345_KASTb_coadd.mod.out'))

Emsystem #416

Emsystem #416

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tiffanyhsyu commented Oct 4, 2017

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profxj commented Oct 13, 2017

profxj commented Oct 13, 2017

tiffanyhsyu commented Oct 13, 2017 • edited

coveralls commented Oct 23, 2017

coveralls commented Oct 23, 2017

profxj commented Oct 24, 2017

tiffanyhsyu commented Oct 13, 2017 •

edited