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Merge pull request #37 from lanl/sammy_parfile
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Add top level parameter file module
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@along4
along4 authored Feb 18, 2025
2 parents 81d09d7 + 8626668 commit 47b7258
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287 changes: 287 additions & 0 deletions notebook/sammy.param/example.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Overview\n",
"\n",
"This notebook demonstrates how to use the `sammy.paramter` module to load, construct and manipulate the parameter file (`*.par`) of the SAMMY suite."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import pathlib\n",
"import tempfile\n",
"\n",
"from pleiades.sammy.parfile import SammyParameterFile"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Construct a parameter object manually\n",
"\n",
"Let's build a simple parameter file from scratch."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"entries=[ResonanceEntry(resonance_energy=0.0253, capture_width=0.1, channel1_width=0.2, channel2_width=0.3, channel3_width=0.4, vary_energy=<VaryFlag.NO: 0>, vary_capture_width=<VaryFlag.NO: 0>, vary_channel1=<VaryFlag.NO: 0>, vary_channel2=<VaryFlag.NO: 0>, vary_channel3=<VaryFlag.NO: 0>, igroup=1), ResonanceEntry(resonance_energy=0.0253, capture_width=0.1, channel1_width=0.2, channel2_width=0.3, channel3_width=0.4, vary_energy=<VaryFlag.NO: 0>, vary_capture_width=<VaryFlag.NO: 0>, vary_channel1=<VaryFlag.NO: 0>, vary_channel2=<VaryFlag.NO: 0>, vary_channel3=<VaryFlag.NO: 0>, igroup=2)]\n"
]
}
],
"source": [
"from pleiades.sammy.parameters.helper import VaryFlag\n",
"from pleiades.sammy.parameters.resonance import ResonanceCard, ResonanceEntry\n",
"\n",
"resonance_0 = ResonanceEntry(\n",
" resonance_energy=0.0253,\n",
" capture_width=0.1,\n",
" channel1_width=0.2,\n",
" channel2_width=0.3,\n",
" channel3_width=0.4,\n",
" vary_energy=VaryFlag.NO,\n",
" vary_capture_width=VaryFlag.NO,\n",
" vary_channel1_width=VaryFlag.YES,\n",
" vary_channel2_width=VaryFlag.NO,\n",
" vary_channel3_width=VaryFlag.YES,\n",
" igroup=1,\n",
")\n",
"\n",
"resonance_1 = ResonanceEntry(\n",
" resonance_energy=0.0253,\n",
" capture_width=0.1,\n",
" channel1_width=0.2,\n",
" channel2_width=0.3,\n",
" channel3_width=0.4,\n",
" vary_energy=VaryFlag.NO,\n",
" vary_capture_width=VaryFlag.NO,\n",
" vary_channel1_width=VaryFlag.NO,\n",
" vary_channel2_width=VaryFlag.YES,\n",
" vary_channel3_width=VaryFlag.NO,\n",
" igroup=2,\n",
")\n",
"\n",
"resonance_card = ResonanceCard(entries=[resonance_0, resonance_1])\n",
"\n",
"print(resonance_card)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"parameters=RadiusParameters(effective_radius=1.0, true_radius=2.0, channel_mode=1, vary_effective=<VaryFlag.YES: 1>, vary_true=<VaryFlag.NO: 0>, spin_groups=[1, 2, 3], channels=[1, 2, 3]) particle_pair=None orbital_momentum=None relative_uncertainty=None absolute_uncertainty=None\n"
]
}
],
"source": [
"from pleiades.sammy.parameters.radius import RadiusCard, RadiusParameters\n",
"\n",
"radius_parameters = RadiusParameters(\n",
" effective_radius=1.0,\n",
" true_radius=2.0,\n",
" channel_mode=1,\n",
" vary_effective=VaryFlag.YES,\n",
" vary_true=VaryFlag.NO,\n",
" spin_groups=[1, 2, 3],\n",
" channels=[1, 2, 3],\n",
")\n",
"\n",
"radius_card = RadiusCard(parameters=radius_parameters)\n",
"\n",
"print(radius_card)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"now let's create a parameter object to hold everything"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"fudge=0.2 resonance=ResonanceCard(entries=[ResonanceEntry(resonance_energy=0.0253, capture_width=0.1, channel1_width=0.2, channel2_width=0.3, channel3_width=0.4, vary_energy=<VaryFlag.NO: 0>, vary_capture_width=<VaryFlag.NO: 0>, vary_channel1=<VaryFlag.NO: 0>, vary_channel2=<VaryFlag.NO: 0>, vary_channel3=<VaryFlag.NO: 0>, igroup=1), ResonanceEntry(resonance_energy=0.0253, capture_width=0.1, channel1_width=0.2, channel2_width=0.3, channel3_width=0.4, vary_energy=<VaryFlag.NO: 0>, vary_capture_width=<VaryFlag.NO: 0>, vary_channel1=<VaryFlag.NO: 0>, vary_channel2=<VaryFlag.NO: 0>, vary_channel3=<VaryFlag.NO: 0>, igroup=2)]) external_r=None broadening=None unused_correlated=None normalization=None radius=RadiusCard(parameters=RadiusParameters(effective_radius=1.0, true_radius=2.0, channel_mode=1, vary_effective=<VaryFlag.YES: 1>, vary_true=<VaryFlag.NO: 0>, spin_groups=[1, 2, 3], channels=[1, 2, 3]), particle_pair=None, orbital_momentum=None, relative_uncertainty=None, absolute_uncertainty=None) data_reduction=None orres=None paramagnetic=None user_resolution=None isotope=None\n"
]
}
],
"source": [
"par_file = SammyParameterFile(\n",
" fudge=0.2,\n",
" resonance=resonance_card,\n",
" radius=radius_card,\n",
")\n",
"\n",
"print(par_file)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"we can also view the string format before writing to a file"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" 2.5300E-02 1.0000E-01 2.0000E-01 3.0000E-01 4.0000E-01 0 0 0 0 0 1\n",
" 2.5300E-02 1.0000E-01 2.0000E-01 3.0000E-01 4.0000E-01 0 0 0 0 0 2\n",
"\n",
"0.2000 \n",
"RADII are in KEY-WORD format\n",
"Radius= 1.0 2.0\n",
"Flags= 1 0\n",
"Group= 1 Channels= 1 2 3\n",
"Group= 2 Channels= 1 2 3\n",
"Group= 3 Channels= 1 2 3\n",
"\n"
]
}
],
"source": [
"print(par_file.to_string())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"then we can write the parameter object to a file"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" 2.5300E-02 1.0000E-01 2.0000E-01 3.0000E-01 4.0000E-01 0 0 0 0 0 1\n",
" 2.5300E-02 1.0000E-01 2.0000E-01 3.0000E-01 4.0000E-01 0 0 0 0 0 2\n",
"\n",
"0.2000 \n",
"RADII are in KEY-WORD format\n",
"Radius= 1.0 2.0\n",
"Flags= 1 0\n",
"Group= 1 Channels= 1 2 3\n",
"Group= 2 Channels= 1 2 3\n",
"Group= 3 Channels= 1 2 3\n",
"\n"
]
}
],
"source": [
"with tempfile.TemporaryDirectory() as tmpdir:\n",
" par_file_path = pathlib.Path(tmpdir) / \"sammy.par\"\n",
" par_file.to_file(par_file_path)\n",
"\n",
" with open(par_file_path, \"r\") as f:\n",
" print(f.read())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Load from string/file\n",
"\n",
"We can also directly load a parameter file from a string or a file."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"fudge=0.2 resonance=ResonanceCard(entries=[ResonanceEntry(resonance_energy=0.0253, capture_width=0.1, channel1_width=0.2, channel2_width=0.3, channel3_width=0.4, vary_energy=<VaryFlag.NO: 0>, vary_capture_width=<VaryFlag.NO: 0>, vary_channel1=<VaryFlag.NO: 0>, vary_channel2=<VaryFlag.NO: 0>, vary_channel3=<VaryFlag.NO: 0>, igroup=1), ResonanceEntry(resonance_energy=0.0253, capture_width=0.1, channel1_width=0.2, channel2_width=0.3, channel3_width=0.4, vary_energy=<VaryFlag.NO: 0>, vary_capture_width=<VaryFlag.NO: 0>, vary_channel1=<VaryFlag.NO: 0>, vary_channel2=<VaryFlag.NO: 0>, vary_channel3=<VaryFlag.NO: 0>, igroup=2)]) external_r=None broadening=None unused_correlated=None normalization=None radius=RadiusCard(parameters=RadiusParameters(effective_radius=1.0, true_radius=2.0, channel_mode=1, vary_effective=<VaryFlag.YES: 1>, vary_true=<VaryFlag.NO: 0>, spin_groups=[3], channels=[1, 2, 3]), particle_pair=None, orbital_momentum=None, relative_uncertainty=None, absolute_uncertainty=None) data_reduction=None orres=None paramagnetic=None user_resolution=None isotope=None\n",
" 2.5300E-02 1.0000E-01 2.0000E-01 3.0000E-01 4.0000E-01 0 0 0 0 0 1\n",
" 2.5300E-02 1.0000E-01 2.0000E-01 3.0000E-01 4.0000E-01 0 0 0 0 0 2\n",
"\n",
"0.2000 \n",
"RADII are in KEY-WORD format\n",
"Radius= 1.0 2.0\n",
"Flags= 1 0\n",
"Group= 3 Channels= 1 2 3\n",
"\n"
]
}
],
"source": [
"with tempfile.TemporaryDirectory() as tmpdir:\n",
" par_file_path = pathlib.Path(tmpdir) / \"sammy.par\"\n",
" par_file.to_file(par_file_path)\n",
"\n",
" par_file_read = SammyParameterFile.from_file(par_file_path)\n",
" print(par_file_read)\n",
" print(par_file_read.to_string())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "pleiades-j7m2QWN6-py3.13",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.13.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
4 changes: 2 additions & 2 deletions src/pleiades/sammy/parameters/__init__.py
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@@ -1,11 +1,11 @@
from pleiades.sammy.parameters.broadening import BroadeningParameterCard # noqa: F401
from pleiades.sammy.parameters.data_reduction import DataReductionCard # noqa: F401
from pleiades.sammy.parameters.external_r import ExternalREntry # noqa: F401
from pleiades.sammy.parameters.external_r import ExternalREntry, ExternalRFunction # noqa: F401
from pleiades.sammy.parameters.isotope import IsotopeCard # noqa: F401
from pleiades.sammy.parameters.normalization import NormalizationBackgroundCard # noqa: F401
from pleiades.sammy.parameters.orres import ORRESCard # noqa: F401
from pleiades.sammy.parameters.paramagnetic import ParamagneticParameters # noqa: F401
from pleiades.sammy.parameters.radius import RadiusCard # noqa: F401
from pleiades.sammy.parameters.resonance import ResonanceEntry # noqa: F401
from pleiades.sammy.parameters.resonance import ResonanceCard # noqa: F401
from pleiades.sammy.parameters.unused_var import UnusedCorrelatedCard # noqa: F401
from pleiades.sammy.parameters.user_resolution import UserResolutionParameters # noqa: F401
24 changes: 14 additions & 10 deletions src/pleiades/sammy/parameters/broadening.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,38 +200,42 @@ def to_lines(self) -> List[str]:
format_float(self.deltal, width=9),
format_float(self.deltag, width=9),
format_float(self.deltae, width=9),
]
main_seg = " ".join(main_parts)
flag_parts = [
format_vary(self.flag_crfn),
format_vary(self.flag_temp),
format_vary(self.flag_thick),
format_vary(self.flag_deltal),
format_vary(self.flag_deltag),
format_vary(self.flag_deltae),
]
lines.append(" ".join(main_parts))
flag_seg = " ".join(flag_parts)
main_line = f"{main_seg} {flag_seg}"
lines.append(main_line)

# Add uncertainties line if any uncertainties are present
if any(getattr(self, f"d_{param}") is not None for param in ["crfn", "temp", "thick", "deltal", "deltag", "deltae"]):
unc_parts = [
format_float(getattr(self, f"d_{param}", 0.0), width=10)
for param in ["crfn", "temp", "thick", "deltal", "deltag", "deltae"]
format_float(getattr(self, f"d_{param}", 0.0), width=9) for param in ["crfn", "temp", "thick", "deltal", "deltag", "deltae"]
]
lines.append("".join(unc_parts))
lines.append(" ".join(unc_parts))

# Add Gaussian parameters if present
if self.deltc1 is not None and self.deltc2 is not None:
gaussian_parts = [
format_float(self.deltc1, width=10),
format_float(self.deltc2, width=10),
" " * 50, # Padding
format_float(self.deltc1, width=9),
format_float(self.deltc2, width=9),
" " * 40, # Padding
format_vary(self.flag_deltc1),
format_vary(self.flag_deltc2),
]
lines.append("".join(gaussian_parts))
lines.append(" ".join(gaussian_parts))

# Add Gaussian uncertainties if present
if self.d_deltc1 is not None or self.d_deltc2 is not None:
gaussian_unc_parts = [format_float(self.d_deltc1 or 0.0, width=10), format_float(self.d_deltc2 or 0.0, width=10)]
lines.append("".join(gaussian_unc_parts))
gaussian_unc_parts = [format_float(self.d_deltc1 or 0.0, width=9), format_float(self.d_deltc2 or 0.0, width=9)]
lines.append(" ".join(gaussian_unc_parts))

return lines

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