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Checking for zero-volume cells: Fixes issue #79 #450

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merged 7 commits into from
Dec 10, 2015
Merged

Checking for zero-volume cells: Fixes issue #79 #450

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05d59e6
added check for zero-volume of first cell
Dec 9, 2015
15a626e
found much simpler formulation of zero-volume check
Dec 9, 2015
9acb06c
Revert "found much simpler formulation of zero-volume check"
Dec 9, 2015
acd72ea
-fixed astropy.units.Quantity issue in ascii_reader test (strangely did
Dec 9, 2015
c5fbfff
added another test scenario for the ascii density reader
Dec 9, 2015
cfad0e0
added general check for invalid cell volumes
Dec 9, 2015
7ff44f4
added test specifically triggering the invalid volume exception in the
Dec 9, 2015
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21 changes: 18 additions & 3 deletions tardis/io/model_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def read_density_file(density_filename, density_filetype, time_explosion,
raise ConfigurationError('v_inner_boundary > v_outer_boundary '
'({0:s} > {1:s}). unphysical!'.format(
v_inner_boundary, v_outer_boundary))

if (not np.isclose(v_inner_boundary, 0.0 * u.km / u.s,
atol=1e-8 * u.km / u.s)
and v_inner_boundary > v_inner[0]):
Expand All @@ -52,6 +52,11 @@ def read_density_file(density_filename, density_filetype, time_explosion,
raise ConfigurationError('Inner boundary selected outside of model')

inner_boundary_index = v_inner.searchsorted(v_inner_boundary) - 1
# check for zero volume of designated first cell
if np.isclose(v_inner_boundary, v_inner[inner_boundary_index + 1],
atol=1e-8 * u.km / u.s) and (v_inner_boundary <=
v_inner[inner_boundary_index + 1]):
inner_boundary_index += 1

else:
inner_boundary_index = None
Expand All @@ -66,7 +71,7 @@ def read_density_file(density_filename, density_filetype, time_explosion,
v_outer_boundary = v_outer[-1]
logger.warning("v_outer_boundary requested too large for readin file. Boundary shifted to match file.")


v_inner = v_inner[inner_boundary_index:outer_boundary_index]
v_inner[0] = v_inner_boundary

Expand All @@ -75,6 +80,16 @@ def read_density_file(density_filename, density_filetype, time_explosion,

mean_densities = mean_densities[inner_boundary_index:outer_boundary_index]

invalid_volume_mask = (v_outer - v_inner) <= 0
if invalid_volume_mask.sum() > 0:
message = "\n".join(["cell {0:d}: v_inner {1:s}, v_outer "
"{2:s}".format(i, v_inner_i, v_outer_i) for i,
v_inner_i, v_outer_i in
zip(np.arange(len(v_outer))[invalid_volume_mask],
v_inner[invalid_volume_mask],
v_outer[invalid_volume_mask])])
raise ConfigurationError("Invalid volume of following cell(s):\n"
"{:s}".format(message))

return (v_inner, v_outer, mean_densities,
inner_boundary_index, outer_boundary_index)
Expand Down Expand Up @@ -107,7 +122,7 @@ def read_abundances_file(abundance_filename, abundance_filetype,

index, abundances = file_parsers[abundance_filetype](abundance_filename)
if outer_boundary_index is not None:
outer_boundary_index_m1 = outer_boundary_index - 1
outer_boundary_index_m1 = outer_boundary_index - 1
else:
outer_boundary_index_m1 = None
index = index[inner_boundary_index:outer_boundary_index]
Expand Down
72 changes: 72 additions & 0 deletions tardis/io/tests/data/invalid_artis_model.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
70
0.00114661
1 1.259375e+03 -5.449497e-05 9.969498e-01 9.787696e-01 6.973734e-06 5.052319e-06 6.168110e-07
2 1.574219e+03 3.013383e-04 9.969307e-01 9.788986e-01 6.845718e-06 5.013408e-06 6.140697e-07
3 1.889063e+03 -1.982630e-02 9.968976e-01 9.789760e-01 6.720018e-06 4.915389e-06 6.130545e-07
4 2.203907e+03 -4.429480e-02 9.968509e-01 9.790147e-01 6.608687e-06 4.839975e-06 6.060005e-07
5 2.518750e+03 -5.767948e-02 9.967775e-01 9.789697e-01 6.505750e-06 4.727071e-06 6.067441e-07
6 2.833594e+03 -7.370731e-02 9.966485e-01 9.787804e-01 6.395329e-06 4.580685e-06 6.268937e-07
7 3.148438e+03 -1.013941e-01 9.964382e-01 9.783643e-01 6.259683e-06 4.443940e-06 6.797306e-07
8 3.463282e+03 -1.223770e-01 9.961101e-01 9.776204e-01 6.090588e-06 4.411024e-06 7.830217e-07
9 3.778126e+03 -1.441526e-01 9.956658e-01 9.765878e-01 5.894967e-06 4.667291e-06 9.375288e-07
10 4.092969e+03 -1.710595e-01 9.951726e-01 9.754603e-01 5.696173e-06 5.264160e-06 1.113761e-06
11 4.407813e+03 -1.921165e-01 9.946904e-01 9.743882e-01 5.505227e-06 6.087066e-06 1.275082e-06
12 4.722657e+03 -2.190449e-01 9.942578e-01 9.734612e-01 5.318957e-06 6.965121e-06 1.406783e-06
13 5.037501e+03 -2.503739e-01 9.938884e-01 9.727036e-01 5.138882e-06 7.761285e-06 1.503072e-06
14 5.352345e+03 -2.796168e-01 9.936060e-01 9.721567e-01 4.966839e-06 8.340429e-06 1.549395e-06
15 5.667188e+03 -3.105920e-01 9.934865e-01 9.719984e-01 4.797945e-06 8.454966e-06 1.503797e-06
16 5.667188e+03 -3.413327e-01 9.937069e-01 9.726593e-01 4.642989e-06 7.660500e-06 1.276586e-06
17 6.296876e+03 -3.751951e-01 9.946118e-01 9.750052e-01 4.504424e-06 5.799124e-06 7.959853e-07
18 6.611720e+03 -4.087162e-01 9.968127e-01 9.809170e-01 4.377842e-06 1.154036e-05 2.120706e-07
19 6.926563e+03 -4.452069e-01 9.993206e-01 9.838294e-01 4.787479e-06 7.603537e-03 1.054282e-04
20 7.241407e+03 -4.782779e-01 9.934882e-01 9.623342e-01 7.808212e-06 2.142014e-02 4.893291e-04
21 7.556251e+03 -5.144547e-01 9.801450e-01 9.390609e-01 7.891220e-06 2.628785e-02 7.470313e-04
22 7.871095e+03 -5.506459e-01 9.570934e-01 9.065100e-01 7.418816e-06 2.935965e-02 9.643208e-04
23 8.185939e+03 -5.838073e-01 9.166762e-01 8.554363e-01 6.813265e-06 3.148066e-02 1.174981e-03
24 8.500782e+03 -6.187967e-01 8.444416e-01 7.711242e-01 6.021313e-06 3.228287e-02 1.373482e-03
25 8.815626e+03 -6.478082e-01 7.205625e-01 6.360884e-01 4.926903e-06 3.042671e-02 1.489358e-03
26 9.130470e+03 -6.772585e-01 5.522046e-01 4.633726e-01 3.580056e-06 2.523080e-02 1.421018e-03
27 9.445314e+03 -7.025316e-01 3.798727e-01 2.967333e-01 2.290327e-06 1.821502e-02 1.174456e-03
28 9.360158e+03 -7.393099e-01 2.434208e-01 1.729650e-01 1.321915e-06 1.181660e-02 8.653664e-04
29 1.007500e+04 -7.769093e-01 1.593954e-01 1.020666e-01 7.627219e-07 7.574566e-03 6.170831e-04
30 1.038985e+04 -8.221853e-01 1.137370e-01 6.635599e-02 4.797101e-07 5.202758e-03 4.581936e-04
31 1.070469e+04 -8.745196e-01 8.964338e-02 4.874161e-02 3.390994e-07 3.947096e-03 3.661284e-04
32 1.101953e+04 -9.296468e-01 7.628418e-02 3.940266e-02 2.635893e-07 3.241346e-03 3.114475e-04
33 1.133438e+04 -9.903432e-01 6.722356e-02 3.232460e-02 2.087902e-07 2.646639e-03 2.642194e-04
34 1.164922e+04 -1.044582e+00 5.923151e-02 2.301299e-02 1.443657e-07 1.793031e-03 1.973346e-04
35 1.196406e+04 -1.107672e+00 5.226578e-02 1.259155e-02 7.754713e-08 8.991098e-04 1.268152e-04
36 1.227891e+04 -1.166106e+00 4.718720e-02 5.081296e-03 3.147591e-08 3.251325e-04 7.181194e-05
37 1.259375e+04 -1.224244e+00 3.832284e-02 1.308496e-03 1.028649e-08 6.508490e-05 2.581188e-05
38 1.290860e+04 -1.278808e+00 2.325070e-02 1.854372e-04 8.404720e-09 5.333218e-06 3.988807e-06
39 1.322344e+04 -1.319016e+00 9.104333e-03 1.132432e-05 2.479127e-09 3.431589e-07 4.391149e-07
40 1.353828e+04 -1.339697e+00 9.852053e-04 1.299599e-07 7.783476e-11 1.265313e-08 2.057230e-08
41 1.385313e+04 -1.350281e+00 3.185364e-05 9.492013e-10 1.632555e-12 1.190779e-10 2.088784e-10
42 1.416797e+04 -1.366863e+00 1.474822e-05 2.220123e-10 5.309134e-13 4.447397e-11 7.551816e-11
43 1.448281e+04 -1.408773e+00 8.973184e-06 8.011853e-11 2.082280e-13 3.914228e-11 5.869264e-11
44 1.479766e+04 -1.484229e+00 6.154459e-06 2.021216e-11 5.137364e-14 2.829258e-11 6.464542e-11
45 1.511250e+04 -1.576636e+00 5.280028e-06 6.933790e-12 1.465119e-14 1.530388e-11 6.442062e-11
46 1.542735e+04 -1.673018e+00 5.236783e-06 3.220037e-12 6.011255e-15 8.828028e-12 6.008495e-11
47 1.574219e+04 -1.779685e+00 5.475689e-06 1.656054e-12 3.293192e-15 5.715768e-12 5.706669e-11
48 1.605703e+04 -1.876238e+00 5.822625e-06 8.090158e-13 1.990751e-15 3.956454e-12 5.687796e-11
49 1.637188e+04 -1.990179e+00 6.233115e-06 4.442047e-13 1.473151e-15 3.072241e-12 5.915856e-11
50 1.668672e+04 -2.082134e+00 6.693559e-06 2.602742e-13 1.196462e-15 2.628631e-12 6.268807e-11
51 1.700156e+04 -2.189603e+00 7.080294e-06 1.937764e-13 1.302169e-15 2.424756e-12 6.402162e-11
52 1.731641e+04 -2.251445e+00 7.367846e-06 1.874260e-13 2.002987e-15 2.292432e-12 6.198017e-11
53 1.763125e+04 -2.336874e+00 7.487331e-06 2.089537e-13 3.862363e-15 2.145276e-12 5.615828e-11
54 1.794610e+04 -2.413082e+00 7.481771e-06 2.284368e-13 7.610089e-15 1.892516e-12 4.869019e-11
55 1.826094e+04 -2.525231e+00 7.307651e-06 2.426003e-13 1.494172e-14 1.604724e-12 4.093251e-11
56 1.857578e+04 -2.598198e+00 6.904268e-06 2.392776e-13 2.741366e-14 1.286481e-12 3.355300e-11
57 1.889063e+04 -2.582957e+00 6.180129e-06 2.125336e-13 4.712860e-14 9.528658e-13 2.601973e-11
58 1.920547e+04 -2.732132e+00 5.130247e-06 1.782245e-13 7.413013e-14 6.634504e-13 1.942738e-11
59 1.952032e+04 -2.787764e+00 4.160961e-06 1.395227e-13 9.871988e-14 4.585879e-13 1.521031e-11
60 1.983516e+04 -2.847531e+00 3.126174e-06 9.689468e-14 1.121511e-13 2.803738e-13 1.103460e-11
61 2.015000e+04 -2.861318e+00 2.165275e-06 6.563661e-14 1.260716e-13 1.659489e-13 7.817914e-12
62 2.046485e+04 -2.984034e+00 1.489794e-06 4.275136e-14 1.315134e-13 9.863714e-14 5.815667e-12
63 2.077969e+04 -2.888253e+00 8.864073e-07 2.107301e-14 1.053168e-13 4.595312e-14 3.655108e-12
64 2.109453e+04 -3.077504e+00 5.232797e-07 8.675422e-15 6.905988e-14 1.760052e-14 2.341958e-12
65 2.140938e+04 -3.169650e+00 3.201423e-07 3.365656e-15 3.595022e-14 6.162002e-15 1.394190e-12
66 2.172422e+04 -3.103242e+00 1.856889e-07 1.293778e-15 1.860925e-14 2.033915e-15 8.039162e-13
67 2.203907e+04 -3.195011e+00 1.027709e-07 3.343978e-16 5.949844e-15 5.858914e-16 4.132950e-13
68 2.235391e+04 -3.304330e+00 5.443506e-08 7.937542e-17 1.640208e-15 1.396395e-16 1.943107e-13
69 2.266875e+04 -3.441502e+00 2.939781e-08 1.475479e-17 3.430180e-16 4.586563e-17 9.063403e-14
70 2.298360e+04 -3.453566e+00 1.464506e-08 2.619737e-18 6.785903e-17 1.021336e-17 3.857130e-14
11 changes: 9 additions & 2 deletions tardis/io/tests/test_ascii_readers.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,8 @@ def test_simple_ascii_abundance_reader():
(0.0 * u.km/u.s, np.inf * u.km/u.s, np.nan, np.nan, None, None),
(500 * u.km/u.s, 6000 * u.km/u.s, np.nan, 6000 * u.km/u.s, None, 16),
(1300 * u.km/u.s, 6000 * u.km/u.s, 1300 * u.km/u.s, 6000 * u.km/u.s, 0, 16),
(1600 * u.km/u.s, 6000 * u.km/u.s, 1600 * u.km/u.s, 6000 * u.km/u.s, 1, 16)
(1600 * u.km/u.s, 6000 * u.km/u.s, 1600 * u.km/u.s, 6000 * u.km/u.s, 1, 16),
(1889.063 * u.km/u.s, np.inf * u.km/u.s, 1889.063 * u.km/u.s, np.nan, 2, None)
])
def test_ascii_reader_density_boundaries(v_inner_boundary, v_outer_boundary, actual_v_inner, actual_v_outer,
inner_index, outer_index):
Expand All @@ -55,6 +56,12 @@ def test_ascii_reader_density_boundaries(v_inner_boundary, v_outer_boundary, act
actual_v_inner.to(v_inner[0].unit).value)

if not np.isnan(actual_v_outer):
npt.assert_allclose(v_outer[-1],
npt.assert_allclose(v_outer[-1].value,
actual_v_outer.to(v_outer[-1].unit).value)

def test_ascii_reader_invalid_volumes():

with pytest.raises(io.model_reader.ConfigurationError):
v_inner, v_outer, mean_densities, inner_boundary_index, outer_boundary_index = \
io.read_density_file(data_path('invalid_artis_model.dat'), 'artis', 19 *
u.day, 0.0 * u.km/u.s, np.inf * u.km/u.s)