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Elements table generator #25

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5 changes: 5 additions & 0 deletions deploy_scattering_table.sh
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#!/bin/bash

TARGET_DIR=${TARGET_DIR:-/var/www/html/resources/n-lengths}

python -m util.scattering_table_html $TARGET_DIR
179 changes: 179 additions & 0 deletions util/scattering_table_html.py
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from pathlib import Path

import numpy as np
from periodictable.core import default_table, PeriodicTable
from periodictable.nsf import Neutron

# TODO: add a citation column to the html scattering table
def scattering_table_html(path: Path|str|None=None, table: PeriodicTable|None=None) -> str:
"""
Generate an html table, returning it as a string. If path is given, write the
html to that path.

Note: requires the uncertainties package, which is not otherwise required by periodictable.
"""
from uncertainties import ufloat as U # type: ignore[import-untyped]

head = """\
<head>
<meta charset="UTF-8">
<title>Neutron Cross Sections</title>
<style>
table {
border-collapse: separate;
border-spacing: 0;
}
tbody tr {
/* This offset ensures the target row isn't hidden behind the sticky header */
scroll-margin-top: 60px;
}
tbody tr:target td,
tbody tr:has(td:target) td {
background-color: yellow;
transition: background-color 2s ease-out;
}
tr, td {
scroll-margin-top: 2em;
}
th, td {
border: 1px solid black;
padding: 5px;
border-top: none;
border-right: none;
}
tr:first-child td, tr:first-child th {
border-top: 1px solid black;
}
td:last-child, th:last-child {
border-right: 1px solid black;
}
th {
position: sticky;
top: 0;
background: #e8edf3;
z-index: 1;
}
.centered {
text-align: center;
}

</style>
</head>"""
table = default_table(table)

def format_num(re, re_unc, im=None, im_unc=None):
# Note: using NaN for uncertainty for derived values that should be
# left blank in the table (currently 191,193Ir cross sections)
re_str = "" if re is None or np.isnan(re_unc) else f"{U(re, re_unc):fS}" if re_unc else str(re) if re else "0"
if im is not None:
im_value = f"{U(abs(im), im_unc):fS}" if im_unc else str(abs(im))
im_str = f"<br>{'+' if im >= 0 else '–'} {im_value}j"
else:
im_str = ""
return f"{re_str}{im_str}"

rows = []
rows.append(f"""
<tr>
<th></th>
<th>Z</th>
<th>A</th>
<th>I(π)</th>
<th>abundance %</th>
<th>b<sub>c</sub> {Neutron.b_c_units}</th>
<th>b<sub>+</sub> {Neutron.bp_units}</th>
<th>b<sub>–</sub> {Neutron.bm_units}</th>
<th>σ<sub>c</sub> {Neutron.coherent_units}</th>
<th>σ<sub>i</sub> {Neutron.incoherent_units}</th>
<th>σ<sub>s</sub> {Neutron.total_units}</th>
<th>σ<sub>a</sub> {Neutron.absorption_units}</th>
</tr>""")

# Generate table rows
for el in [table.n, *table]:
element_number = el.number
isotopes = [iso for iso in el if iso.neutron.absorption is not None or iso.abundance]
singleton = len(isotopes) == 1
symbol = el.symbol
row_id = symbol if symbol != "n" else "" # Special case for bare neutron
# print(f"{el=} {A=} {singleton=} {el.neutron.has_sld()=} {[*el]}")
if element_number <= 96 and not singleton:
# Multiple isotopes: put element summary above
n = el.neutron
rows.append(f"""
<tr class="element-row" id="{row_id}">
<td id="{row_id.lower()}">{symbol}</td>
<td>{element_number}</td>
<td></td>
<td></td>
<td></td>
<td>{format_num(n.b_c, n.b_c_unc, n.b_c_i, n.b_c_i_unc)}</td>
<td>{format_num(n.bp, n.bp_unc, n.bp_i, n.bp_i_unc)}</td>
<td>{format_num(n.bm, n.bm_unc, n.bm_i, n.bm_i_unc)}</td>
<td>{format_num(n.coherent, n.coherent_unc)}</td>
<td>{format_num(n.incoherent, n.incoherent_unc)}</td>
<td>{format_num(n.total, n.total_unc)}</td>
<td>{format_num(n.absorption, n.absorption_unc)}</td>
</tr>""")

for iso in isotopes:
isotope_number = iso.isotope
spin = getattr(iso, "nuclear_spin", "")
n = iso.neutron
abundance = (
f"{U(iso.abundance, iso._abundance_unc):fS}" if iso._abundance_unc
else "100" if iso.abundance == 100.0
else "" if iso.abundance == 0.0
else f"{iso.abundance}"
)
rows.append(f"""
<tr{f' class="element-row" id="{row_id}"' if singleton else ''}>
<td{f' id="{row_id.lower()}"' if singleton else ''}>{symbol if singleton else ''}</td>
<td>{element_number if singleton else ''}</td>
<td>{isotope_number}</td>
<td class="centered">{spin}</td>
<td>{abundance}</td>
<td>{format_num(n.b_c, n.b_c_unc, n.b_c_i, n.b_c_i_unc)}</td>
<td>{format_num(n.bp, n.bp_unc, n.bp_i, n.bp_i_unc)}</td>
<td>{format_num(n.bm, n.bm_unc, n.bm_i, n.bm_i_unc)}</td>
<td>{format_num(n.coherent, n.coherent_unc)}</td>
<td>{format_num(n.incoherent, n.incoherent_unc)}</td>
<td>{format_num(n.total, n.total_unc)}</td>
<td>{format_num(n.absorption, n.absorption_unc)}</td>
</tr>""")

# Note: don't need \n between rows since we add it to each.
formatted_table = ''.join(rows)
html = f"""
<!DOCTYPE html>
<html>
{head}
<body>
<p>Scattering lengths and cross sections for various isotopes evaluated at 2200 m s<sup>–1</sup>
</p>
<table>
{formatted_table}
</table>
<p>This table has been compiled from various sources for the user's convenience and does not represent a critical evaluation by the NIST Center for Neutron Research.
See <a href="https://github.com/python-periodictable/periodictable/blob/master/periodictable/nsf.py">python-periodictable</a> on github for a list of citations.</p>
<p>Natural abundance is from IUPAC Commission on Isotopic Abundances and Atomic Weights (<a href="ciaaw.org">CIAAW</a>)</p>
</body>
</html>
"""

if path:
# Save the HTML to a file
with open(path, 'w', encoding='utf-8') as f:
f.write(html)

print(f"HTML table saved to {str(path)}")

return html

if __name__ == "__main__":
import sys
# Example usage: generate the HTML table and save it to a file
output_dir = sys.argv[1] if len(sys.argv) > 1 else "."
output_filename = sys.argv[2] if len(sys.argv) > 2 else "scattering_table.html"
output_path = Path(output_dir) / output_filename
scattering_table_html(path=output_path)