Parse Curated CubIXSS Line List#

Athiray curated a line list for both MOXSI and SASS. This notebook cleans up this line list a bit and builds it into a machine readable format. It also adds a few additional lines.

[1]:

import fiasco
import astropy.io.ascii
import copy
import numpy as np
import astropy.units as u
import matplotlib.pyplot as plt

Additional Lines#

[2]:

si14 = fiasco.Ion('Si XIV', np.logspace(6,8,10000)*u.K)
goft_si14 = si14.contribution_function(1e9*u.cm**(-3))
# I selected this particular transition from the more complete line list
transition = 6.1803998947143555  * u.AA
i_transition = np.argmin(np.fabs(si14.transitions.wavelength[~si14.transitions.is_twophoton] - transition))
goft_si14_select = goft_si14[..., i_transition].squeeze()

WARNING: No proton data available for Si 14. Not including proton excitation and de-excitation in level populations calculation. [fiasco.ions]

[3]:

plt.plot(si14.temperature, goft_si14_select)
plt.xscale('log')
plt.yscale('log')
plt.ylim(1e-28,1e-24)

[3]:

(1e-28, 1e-24)

../_images/reports_pruned_line_list_4_1.png

Parse Table#

[4]:

def parse_grid_table(text):
    import docutils.statemachine
    import docutils.parsers.rst.tableparser
    # Clean up the input: get rid of empty lines and strip all leading and
    # trailing whitespace.
    lines = filter(bool, (line.strip() for line in text.splitlines()))
    parser = docutils.parsers.rst.tableparser.GridTableParser()
    return parser.parse(docutils.statemachine.StringList(list(lines)))

[5]:

athiray_line_table = """
+------+---------------+-------+----------+--------+---------+-------+
| **I  | **Wavelength  | **Di  | **Inst** | **Peak | **Peak  | **Sen |
| on** | (A)**         | agnos |          | Emis   | Emi     | sitiv |
|      |               | tic** |          | sivity | ssivity | ity** |
|      |               |       |          | Temp   | Temp    |       |
|      |               |       |          | (Maxw  | (k=2)** |       |
|      |               |       |          | ell)** |         |       |
+======+===============+=======+==========+========+=========+=======+
| Fe   | 1.86          | T     | SASS     | 7.5    | 7.5     | FL    |
| XXV  |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Ca   | 3.21          | T     | SASS     | 7.4    | 7.5     | FL    |
| XIX  |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Si   | 6.74          | T     | SAS      | 7.     | 7.1     | FL    |
| XIII |               |       | S/MOXSI? |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Mg   | 8.419         | T     | SAS      | 7.     | 7.2     | FL    |
| XII  |               |       | S/MOXSI? |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Mg   | 9.169, 9.314  | T     | MOXSI    | 6.8    | 7.0     | FL/AR |
| XI   |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Fe   | 11.2          | T, κ  | MOXSI    | 6.8    | 6.9     | FL/AR |
| XVII | 5,15.015,15.2 |       |          |        |         |       |
|      | 5,16.78,17.05 |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Fe   | 12.83         | T     | MOXSI    | 7      | 7.2     | FL    |
| XX   |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Ne   | 13.447,13.669 | T, κ  | MOXSI    | 6.6    | 6.7     | FL/AR |
| IX   |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Fe   | 13.53         | T     | MOXSI    | 7.     | 7.2     | FL    |
| XIX  |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Fe   | 14.204,       | T, κ  | MOXSI    | 6.9    | 7.      | FL/AR |
| X    | 17.621        |       |          |        |         |       |
| VIII |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| O    | 18.967,       | T, κ, | MOXSI    | 6.5    | 6.6     | FL/AR |
| VIII | 16.006        | n     |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| O    | 21.60, 21.81, | T, κ, | MOXSI    | 6.3    | 6.4     | FL/AR |
| VII  | 22.10, 18.67  | n     |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| N    | 24.77         | T     | MOXSI    | 6.3    | 6.5     | FL/AR |
| VII  |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| C VI | 33.73         | T     | MOXSI    | 6.1    | 6.3     | AR    |
+------+---------------+-------+----------+--------+---------+-------+
| C V  | 40.27         | T     | MOXSI    | 6.     | 6.1     | AR    |
+------+---------------+-------+----------+--------+---------+-------+
| Si   | 44.16         | T     | MOXSI    | 6.3    | 6.5     | FL/AR |
| XII  |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Si   | 49.18         | T     | MOXSI    | 6.2    | 6.3     | AR    |
| XI   |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Fe   | 11.171        | T     | SASS?/   | 7.3    | 7.5     | FL    |
| XXIV |               |       | MOXSI    |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Fe   | 11.737        | T     | SASS?/   | 7.2    | 7.5     | FL    |
| X    |               |       | MOXSI    |        |         |       |
| XIII |               |       |          |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+
| Ne X | 12.137        | T     | SASS?/   | 6.8    | 6.9     | FL/AR |
|      |               |       | MOXSI    |        |         |       |
+------+---------------+-------+----------+--------+---------+-------+

"""

[6]:

# This is parsed from an RST version of the table that was curated by Athiray
parsed_rst = parse_grid_table(athiray_line_table)
column_names = [''.join(col[-1]) for col in parsed_rst[1][0]]
column_names = [n[2:-2] for n in column_names]
rows = []
for _row in parsed_rst[2]:
    row = [''.join(col[-1]) for col in _row]
    rows.append(row)
line_table = astropy.table.QTable(rows=rows, names=column_names)
# Split out rows with multiple transitions into a new table
new_rows = []
rows_to_remove = []
for row in line_table:
    if len(wavelengths:=row['Wavelength(A)'].split(',')) > 1:
        for wave in wavelengths:
            new_row = copy.deepcopy(row)
            new_row['Wavelength(A)'] = wave
            new_rows.append(new_row)
        rows_to_remove.append(row.index)
new_rows = astropy.table.vstack(new_rows)
line_table.remove_rows(rows_to_remove)
line_table = astropy.table.vstack([line_table, new_rows])
line_table.rename_columns(
    ['Ion','Wavelength(A)', 'PeakEmissivityTemp(Maxwell)', 'PeakEmissivityTemp(k=2)'],
    ['ion name','wavelength', 'T_max (Maxwellian)', 'T_max (kappa=2)']
)
line_table = astropy.table.QTable(line_table,dtype=[str,float,str,str,float,float,str])
# Fix inconsistent spacing in ion names
def fix_ion_name_string(name):
    components = name.split(' ')
    if len(components) == 2:
        return name
    if name[1] == name[1].lower():
        i_sep = 2
    else:
        i_sep = 1
    return f'{name[:i_sep]} {name[i_sep:]}'
line_table['ion name'] = list(map(fix_ion_name_string, line_table['ion name']))
line_table['wavelength'].unit = 'Angstrom'
line_table['T_max (Maxwellian)'] = 10**line_table['T_max (Maxwellian)'] * u.K
line_table['T_max (kappa=2)'] = 10**line_table['T_max (kappa=2)'] * u.K
# Split up Diagnostic column
def does_row_contain(x, col):
    return list(map(lambda _x: x in _x, col))
line_table['temperature diagnostic'] = does_row_contain('T', line_table['Diagnostic'])
line_table['density diagnostic'] = does_row_contain('n', line_table['Diagnostic'])
line_table['kappa diagnostic'] = does_row_contain('κ', line_table['Diagnostic'])
# Split up Instrument column
line_table['sass'] = does_row_contain('SASS', line_table['Inst'])
line_table['moxsi'] = does_row_contain('MOXSI', line_table['Inst'])
# Split up Sensitivity column
line_table['flare line'] = does_row_contain('FL', line_table['Sensitivity'])
line_table['active region line'] = does_row_contain('AR', line_table['Sensitivity'])
# Remove all composite columns
line_table.remove_columns(['Diagnostic', 'Inst', 'Sensitivity'])
# Add additional columns here
line_table.add_row({
    'ion name': 'Si XIV',
    'wavelength': si14.transitions.wavelength[~si14.transitions.is_twophoton][i_transition],
    'T_max (Maxwellian)': si14.temperature[goft_si14_select.argmax()],
    'T_max (kappa=2)': np.nan * u.K,
    'temperature diagnostic': True,
    'density diagnostic': False,
    'kappa diagnostic': False,
    'sass': True,
    'moxsi': True,
    'flare line': True,
    'active region line': True,
})
# This should be done last
line_table.sort('wavelength')
# Add metadata
line_table.meta['comment'] = "This line list was originally curated by P.S. Athiray on 10/23, starting with the original line list from the CubIXSS. Determinations of Kappa sensitivity are based on Dudík et al. (2019); kappa temperatures are computed using the KAPPA database."

[7]:

line_table

[7]:

QTable length=32

ion name	wavelength	T_max (Maxwellian)	T_max (kappa=2)	temperature diagnostic	density diagnostic	kappa diagnostic	sass	moxsi	flare line	active region line
	Angstrom	K	K
str8	float64	float64	float64	bool	bool	bool	bool	bool	bool	bool
Fe XXV	1.86	31622776.60168379	31622776.60168379	True	False	False	True	False	True	False
Ca XIX	3.21	25118864.315095823	31622776.60168379	True	False	False	True	False	True	False
Si XIV	6.1804	16185305.906356486	nan	True	False	False	True	True	True	True
Si XIII	6.74	10000000.0	12589254.117941663	True	False	False	True	True	True	False
Mg XII	8.419	10000000.0	15848931.924611142	True	False	False	True	True	True	False
Mg XI	9.169	6309573.44480193	10000000.0	True	False	False	False	True	True	True
Mg XI	9.314	6309573.44480193	10000000.0	True	False	False	False	True	True	True
Fe XXIV	11.171	19952623.149688788	31622776.60168379	True	False	False	True	True	True	False
Fe XVII	11.25	6309573.44480193	7943282.347242822	True	False	True	False	True	True	True
Fe XXIII	11.737	15848931.924611142	31622776.60168379	True	False	False	True	True	True	False
Ne X	12.137	6309573.44480193	7943282.347242822	True	False	False	True	True	True	True
Fe XX	12.83	10000000.0	15848931.924611142	True	False	False	False	True	True	False
Ne IX	13.447	3981071.7055349695	5011872.336272725	True	False	True	False	True	True	True
Fe XIX	13.53	10000000.0	15848931.924611142	True	False	False	False	True	True	False
Ne IX	13.669	3981071.7055349695	5011872.336272725	True	False	True	False	True	True	True
Fe XVIII	14.204	7943282.347242822	10000000.0	True	False	True	False	True	True	True
Fe XVII	15.015	6309573.44480193	7943282.347242822	True	False	True	False	True	True	True
Fe XVII	15.25	6309573.44480193	7943282.347242822	True	False	True	False	True	True	True
O VIII	16.006	3162277.6601683795	3981071.7055349695	True	True	True	False	True	True	True
Fe XVII	16.78	6309573.44480193	7943282.347242822	True	False	True	False	True	True	True
Fe XVII	17.05	6309573.44480193	7943282.347242822	True	False	True	False	True	True	True
Fe XVIII	17.621	7943282.347242822	10000000.0	True	False	True	False	True	True	True
O VII	18.67	1995262.3149688789	2511886.4315095823	True	True	True	False	True	True	True
O VIII	18.967	3162277.6601683795	3981071.7055349695	True	True	True	False	True	True	True
O VII	21.6	1995262.3149688789	2511886.4315095823	True	True	True	False	True	True	True
O VII	21.81	1995262.3149688789	2511886.4315095823	True	True	True	False	True	True	True
O VII	22.1	1995262.3149688789	2511886.4315095823	True	True	True	False	True	True	True
N VII	24.77	1995262.3149688789	3162277.6601683795	True	False	False	False	True	True	True
C VI	33.73	1258925.411794166	1995262.3149688789	True	False	False	False	True	False	True
C V	40.27	1000000.0	1258925.411794166	True	False	False	False	True	False	True
Si XII	44.16	1995262.3149688789	3162277.6601683795	True	False	False	False	True	True	True
Si XI	49.18	1584893.1924611141	1995262.3149688789	True	False	False	False	True	False	True

[8]:

line_table.write('../data/line_lists/curated_line_list.asdf')

WARNING: UnitsWarning: The unit 'Angstrom' has been deprecated in the VOUnit standard. Suggested: 0.1nm. [astropy.units.format.utils]
WARNING: UnitsWarning: The unit 'Angstrom' has been deprecated in the VOUnit standard. Suggested: 0.1nm. [astropy.units.format.utils]

TODO: augment this list with some of the lower-energy lines > 40 Angstroms, particularly those from Fe XIV, XV, XVI

[ ]: