Improve Handling of J Values in CMFGEN Data #409

[manas-dhyani]

📝 Description

Type: 🚀 feature

This PR addresses issue #409 by implementing a cleaner handling of J values in CMFGEN data. Previously, J values were dropped in cross_sections_squeeze, causing loss of information. Since storing J values in ion_levels is not feasible due to shape mismatch, this PR introduces a separate DataFrame for J values.

Changes made:

-Extracted J values from energy levels.

-Computed J values using the formula: .

-Stored J values in a new DataFrame indexed by atomic_number, ion_charge, and ID.

-Added self.j_values attribute to CMFGENReader to store J values.

-Ensured J values are properly structured and retrievable.

This update ensures that J values are preserved and can be used in future calculations, improving the overall data handling in Carsus.

Closes #409.

📌 Resources

CMFGEN Atomic Data

Carsus Documentation

🚦 Testing

How did you test these changes?

• Testing pipeline
• Other method (describe)
• My changes can't be tested (explain why)

☑️ Checklist

• I requested two reviewers for this pull request
• I updated the documentation according to my changes
• I built the documentation by applying the build_docs label

Note: If you are not allowed to perform any of these actions, ping (@) a contributor.

from carsus.io.cmfgen import CMFGENReader, CMFGENEnergyLevelsParser, CMFGENOscillatorStrengthsParser

levels_path = "al2_osc_split.dat"  
lines_path = "al2_osc_split.dat"    

al2_lvl_parser = CMFGENEnergyLevelsParser(levels_path)
al2_osc_parser = CMFGENOscillatorStrengthsParser(lines_path)

al2_lvl_data = {
    (13, 2): {
        "levels": al2_lvl_parser.base,  # Energy levels
        "lines": al2_osc_parser.base    # Spectral lines (oscillator strengths)
    }
}

reader = CMFGENReader(al2_lvl_data)

# Generate levels, lines, and J values
reader._get_levels_lines(al2_lvl_data, hyd_n_phixs_stop2start_energy_ratio=1.0, hyd_n_phixs_num_points=100)

# Access stored data
print(reader.j_values) 

Output

[github-actions]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (19196cd).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

48	F405	[ ] undefined-local-with-import-star-usage
5	E741	[ ] ambiguous-variable-name
1	F401	[*] unused-import
1	F403	[ ] undefined-local-with-import-star
1	F541	[*] f-string-missing-placeholders

Complete output(might be large):

carsus/io/cmfgen/base.py:9:19: F401 [*] `scipy.interpolate` imported but unused
carsus/io/cmfgen/base.py:15:1: F403 `from .util import *` used; unable to detect undefined names
carsus/io/cmfgen/base.py:34:18: F405 `parse_header` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:35:23: F405 `find_row` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:55:26: F405 `find_row` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:106:18: F405 `parse_header` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:107:23: F405 `find_row` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:158:35: F405 `to_float` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:159:35: F405 `to_float` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:179:18: F405 `parse_header` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:180:23: F405 `find_row` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:191:18: F405 `find_row` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:197:26: F405 `find_row` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:202:44: F405 `to_float` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:218:39: F405 `to_float` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:282:67: F405 `to_float` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:289:41: F405 `to_float` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:300:18: F405 `parse_header` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:301:14: F405 `open_cmfgen_file` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:354:18: F405 `parse_header` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:364:23: F405 `find_row` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:373:20: E741 Ambiguous variable name: `l`
carsus/io/cmfgen/base.py:401:12: E741 Ambiguous variable name: `l`
carsus/io/cmfgen/base.py:448:12: E741 Ambiguous variable name: `l`
carsus/io/cmfgen/base.py:566:25: F405 `CMFGEN_ATOM_DICT` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:610:25: E741 Ambiguous variable name: `l`
carsus/io/cmfgen/base.py:681:21: F405 `HC_IN_EV_ANGSTROM` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:681:62: F405 `RYD_TO_EV` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:684:42: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:685:35: F405 `get_null_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:688:21: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:689:21: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:690:21: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:701:21: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:702:21: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:714:39: F405 `get_null_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:717:39: F405 `get_seaton_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:721:44: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:731:43: F405 `get_hydrogenic_n_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:741:21: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:742:21: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:754:35: F405 `get_hydrogenic_nl_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:761:44: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:770:35: F405 `get_opproject_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:774:44: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:783:35: F405 `get_hummer_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:787:44: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:796:35: F405 `get_vy95_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:800:44: F405 `CrossSectionType` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:810:39: F405 `get_leibowitz_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:816:29: F541 [*] f-string without any placeholders
carsus/io/cmfgen/base.py:818:39: F405 `get_null_phixs_table` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:917:42: F405 `HC_IN_EV_ANGSTROM` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:920:46: F405 `RYD_TO_EV` may be undefined, or defined from star imports
carsus/io/cmfgen/base.py:925:29: E741 Ambiguous variable name: `l`
carsus/io/cmfgen/base.py:928:35: F405 `RYD_TO_EV` may be undefined, or defined from star imports
Found 56 errors.
[*] 2 fixable with the `--fix` option.