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Fix issue with custom_composition reader #843

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Jul 23, 2018
Merged

Fix issue with custom_composition reader #843

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07a8b9e
Update read_csv call in read_csv_isotope_abundances
unoebauer Jul 20, 2018
8db1982
Update docstring
unoebauer Jul 20, 2018
348b3b9
Update documentation
unoebauer Jul 20, 2018
678c525
Add testing data files
unoebauer Jul 20, 2018
3c8b6fd
Update cmfgen_density reader
unoebauer Jul 20, 2018
27c376c
Fix remaining shape mismatches in model_reader.py
unoebauer Jul 20, 2018
99a9051
Extend tests
unoebauer Jul 20, 2018
506fe33
Fix reference values in tests
unoebauer Jul 20, 2018
fbe5ae7
Fix cmfgen composition reader
unoebauer Jul 20, 2018
91be33c
Fix cmfgen reader tests
unoebauer Jul 20, 2018
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6 changes: 6 additions & 0 deletions docs/examples/abundancecust.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,11 @@ work on a mesh with ten cells should be formatted like this:

.. literalinclude:: tardis_model_abund.csv

.. note::

The file should always contain the cell index as a running index in the
first column.

.. danger::

The header line for the isotopic abundance structure can under no
Expand All @@ -75,6 +80,7 @@ In this file:

- Header row contains element and isotopes symbol
- the remaining entries in each row give the set of elemental and isotopic abundances.
- the first column contains a running index

The abundances are specified as mass fractions (i.e. the sum of columns
in each row should be 1.0). The mass fractions specified will be adopted directly in
Expand Down
22 changes: 11 additions & 11 deletions docs/examples/tardis_model_abund.csv
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
C O Mg Si Ni56 Ni58
0 0 0 0.6 0.4 0
0 0 0 0.1 0.5 0.4
0 0 0 0.3 0 0.7
0 0.2 0.8 0 0 0
0 0.3 0.7 0 0 0
0 0.2 0.8 0 0 0
0 0.2 0.8 0 0 0
0 0.2 0.8 0 0 0
0.5 0.5 0 0 0 0
0.5 0.5 0 0 0 0
Index C O Mg Si Ni56 Ni58
0 0 0 0 0.6 0.4 0
1 0 0 0 0.1 0.5 0.4
2 0 0 0 0.3 0 0.7
3 0 0.2 0.8 0 0 0
4 0 0.3 0.7 0 0 0
5 0 0.2 0.8 0 0 0
6 0 0.2 0.8 0 0 0
7 0 0.2 0.8 0 0 0
8 0.5 0.5 0 0 0 0
9 0.5 0.5 0 0 0 0
55 changes: 33 additions & 22 deletions tardis/io/model_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -251,10 +251,14 @@ def read_cmfgen_density(fname):
Reading a density file of the following structure (example; lines starting with a hash will be ignored):
The first density describes the mean density in the center of the model and is not used.
The file consists of a header row and next row contains unit of the respective attributes
velocity densities electron_densities temperature
km/s g/cm^3 /cm^3 K
871.66905 4.2537191e-09 2.5953807e+14 7.6395577
877.44269 4.2537191e-09 2.5953807e+14 7.6395577
Note that the first column has to contain a running index

Example:

index velocity densities electron_densities temperature
- km/s g/cm^3 /cm^3 K
0 871.66905 4.2537191e-09 2.5953807e+14 7.6395577
1 877.44269 4.2537191e-09 2.5953807e+14 7.6395577

Rest columns contain abundances of elements and isotopes

Expand Down Expand Up @@ -290,11 +294,11 @@ def read_cmfgen_density(fname):
elif row_index == 2:
quantities = line.split()

velocity = u.Quantity(df['velocity'].values, quantities[0]).to('cm/s')
temperature = u.Quantity(df['temperature'].values, quantities[1])[1:]
mean_density = u.Quantity(df['densities'].values, quantities[2])[1:]
velocity = u.Quantity(df['velocity'].values, quantities[1]).to('cm/s')
temperature = u.Quantity(df['temperature'].values, quantities[2])[1:]
mean_density = u.Quantity(df['densities'].values, quantities[3])[1:]
electron_densities = u.Quantity(
df['electron_densities'].values, quantities[3])[1:]
df['electron_densities'].values, quantities[4])[1:]

return time_of_model, velocity, mean_density, electron_densities, temperature

Expand Down Expand Up @@ -345,7 +349,8 @@ def read_cmfgen_composition(fname, delimiter='\s+'):
DeprecationWarning)

return read_csv_isotope_abundances(fname, delimiter=delimiter,
skip_columns=4, skip_rows=[0, 2])
skip_columns=4, skip_rows=[0, 2, 3])


def read_csv_composition(fname, delimiter='\s+'):
"""Read composition from a simple CSV file
Expand All @@ -372,21 +377,26 @@ def read_csv_isotope_abundances(fname, delimiter='\s+', skip_columns=0,
"""
A generic parser for a TARDIS composition stored as a CSV file

The parser can read in both elemental and isotopic abundances. It also
allows for additional information to be stored in the first skip_columns
columns. These will be ignored if skip_columns > 0. Specific header lines
can be skipped by the skip_rows keyword argument
The parser can read in both elemental and isotopic abundances. The first
column is always expected to contain a running index, labelling the grid
cells. The parser also allows for additional information to be stored in
the first skip_columns columns. These will be ignored if skip_columns > 0.
Note that the first column, containing the cell index is not taken into
account here.

Specific header lines can be skipped by the skip_rows keyword argument

It is expected that the first row of the date block (after skipping the
rows specified in skip_rows) specifies the different elements and isotopes.
Each row after contains the composition in the corresponding grid shell.
The first composition row describes the composition of the photosphere and
is essentially ignored (for the default value of skip_rows).

Example
C O Ni56
1 1 1
0.4 0.3 0.2
Example:

Index C O Ni56
0 1 1 1
1 0.4 0.3 0.2

Parameters
----------
Expand All @@ -401,29 +411,30 @@ def read_csv_isotope_abundances(fname, delimiter='\s+', skip_columns=0,
abundances: ~pandas.DataFrame
isotope_abundance: ~pandas.MultiIndex
"""

df = pd.read_csv(fname, comment='#',
delimiter=delimiter, skiprows=skip_rows)
sep=delimiter, skiprows=skip_rows, index_col=0)
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let's rename it into skiprows to be in line with pandas

df = df.transpose()

abundance = pd.DataFrame(columns=np.arange(df.shape[1] - 1),
abundance = pd.DataFrame(columns=np.arange(df.shape[1]),
index=pd.Index([],
name='atomic_number'),
dtype=np.float64)

isotope_index = pd.MultiIndex(
[[]] * 2, [[]] * 2, names=['atomic_number', 'mass_number'])
isotope_abundance = pd.DataFrame(columns=np.arange(df.shape[1] - 1),
isotope_abundance = pd.DataFrame(columns=np.arange(df.shape[1]),
index=isotope_index,
dtype=np.float64)

for element_symbol_string in df.index[skip_columns:]:
if element_symbol_string in nucname.name_zz:
z = nucname.name_zz[element_symbol_string]
abundance.loc[z, :] = df.loc[element_symbol_string].tolist()[1:]
abundance.loc[z, :] = df.loc[element_symbol_string].tolist()
else:
z = nucname.znum(element_symbol_string)
mass_no = nucname.anum(element_symbol_string)
isotope_abundance.loc[(
z, mass_no), :] = df.loc[element_symbol_string].tolist()[1:]
z, mass_no), :] = df.loc[element_symbol_string].tolist()

return abundance.index, abundance, isotope_abundance
24 changes: 12 additions & 12 deletions tardis/io/tests/data/cmfgen_model.csv
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
t0: 0.976 day
velocity temperature densities electron_densities C O Mg Si Ni56 Ni58
km/s K g/cm^3 /cm^3 1 1 1 1 1 1
871.66905 76395.577 4.2537191E-09 2.60E+14 0 0 0 0.6 0.4 0
877.44269 76395.577 4.2537191E-09 2.60E+14 0 0 0 0.1 0.5 0.4
894.99407 76395.631 4.2537191E-09 2.60E+14 0 0 0 0.3 0 0.7
931.1571 76396.057 4.2537191E-09 2.60E+14 0 0.2 0.8 0 0 0
990.30752 76399.042 4.2537271E-09 2.60E+14 0 0.3 0.7 0 0 0
1050.8676 76411.983 4.2539537E-09 2.60E+14 0 0.2 0.8 0 0 0
1115.1545 76459.592 4.2563604E-09 2.60E+14 0 0.2 0.8 0 0 0
1183.3741 76633.367 4.2683079E-09 2.61E+14 0 0.2 0.8 0 0 0
1255.767 77312.12 4.290997E-09 2.64E+14 0.5 0.5 0 0 0 0
1332.5886 79602.375 4.3396835E-09 2.72E+14 0.5 0.5 0 0 0 0
Index velocity temperature densities electron_densities C O Mg Si Ni56 Ni58
- km/s K g/cm^3 /cm^3 1 1 1 1 1 1
0 871.66905 76395.577 4.2537191E-09 2.60E+14 0 0 0 0.6 0.4 0
1 877.44269 76395.577 4.2537191E-09 2.60E+14 0 0 0 0.1 0.5 0.4
2 894.99407 76395.631 4.2537191E-09 2.60E+14 0 0 0 0.3 0 0.7
3 931.1571 76396.057 4.2537191E-09 2.60E+14 0 0.2 0.8 0 0 0
4 990.30752 76399.042 4.2537271E-09 2.60E+14 0 0.3 0.7 0 0 0
5 1050.8676 76411.983 4.2539537E-09 2.60E+14 0 0.2 0.8 0 0 0
6 1115.1545 76459.592 4.2563604E-09 2.60E+14 0 0.2 0.8 0 0 0
7 1183.3741 76633.367 4.2683079E-09 2.61E+14 0 0.2 0.8 0 0 0
8 1255.767 77312.12 4.290997E-09 2.64E+14 0.5 0.5 0 0 0 0
9 1332.5886 79602.375 4.3396835E-09 2.72E+14 0.5 0.5 0 0 0 0
24 changes: 12 additions & 12 deletions tardis/io/tests/data/csv_composition.csv
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
C O Mg Si Ni56 Ni58
1 1 1 1 1 1
0 0 0 0.6 0.4 0
0 0 0 0.1 0.5 0.4
0 0 0 0.3 0 0.7
0 0.2 0.8 0 0 0
0 0.3 0.7 0 0 0
0 0.2 0.8 0 0 0
0 0.2 0.8 0 0 0
0 0.2 0.8 0 0 0
0.5 0.5 0 0 0 0
0.5 0.5 0 0 0 0
Index C O Mg Si Ni56 Ni58
0 1 1 1 1 1 1
1 0 0 0 0.6 0.4 0
2 0 0 0 0.1 0.5 0.4
3 0 0 0 0.3 0 0.7
4 0 0.2 0.8 0 0 0
5 0 0.3 0.7 0 0 0
6 0 0.2 0.8 0 0 0
7 0 0.2 0.8 0 0 0
8 0 0.2 0.8 0 0 0
9 0.5 0.5 0 0 0 0
10 0.5 0.5 0 0 0 0
11 changes: 7 additions & 4 deletions tardis/io/tests/test_model_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,11 @@ def test_read_simple_isotope_abundances(csv_composition_fname):
csv_composition_fname)
assert np.isclose(abundances.loc[6, 8], 0.5, atol=1.e-12)
assert np.isclose(abundances.loc[12, 5], 0.8, atol=1.e-12)
assert np.isclose(abundances.loc[14, 1], 0.3, atol=1.e-12)
assert np.isclose(isotope_abundance.loc[(28, 56), 0], 0.5, atol=1.e-12)
assert np.isclose(isotope_abundance.loc[(28, 58), 1], 0.7, atol=1.e-12)
assert np.isclose(abundances.loc[14, 1], 0.1, atol=1.e-12)
assert np.isclose(isotope_abundance.loc[(28, 56), 0], 0.4, atol=1.e-12)
assert np.isclose(isotope_abundance.loc[(28, 58), 2], 0.7, atol=1.e-12)
assert abundances.shape == (4, 10)
assert isotope_abundance.shape == (2, 10)


def test_read_cmfgen_isotope_abundances(cmfgen_fname):
Expand All @@ -69,7 +71,8 @@ def test_read_cmfgen_isotope_abundances(cmfgen_fname):
assert np.isclose(abundances.loc[14, 1], 0.3, atol=1.e-12)
assert np.isclose(isotope_abundance.loc[(28, 56), 0], 0.5, atol=1.e-12)
assert np.isclose(isotope_abundance.loc[(28, 58), 1], 0.7, atol=1.e-12)

assert abundances.shape == (4, 9)
assert isotope_abundance.shape == (2, 9)


def test_read_uniform_abundances(isotope_uniform_abundance):
Expand Down