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Add top level parameter file module #37

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merged 8 commits into from
Feb 18, 2025
Merged

Add top level parameter file module #37

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2da5efa
add to_string method for top level
KedoKudo Feb 10, 2025
3d218d5
add from string and aux func to top param class
KedoKudo Feb 12, 2025
cb7f20a
fix unit basic unit tests
KedoKudo Feb 12, 2025
31a2fdb
fix broadening card str format issue
KedoKudo Feb 12, 2025
df3fcfb
fixing logic errors in parsing cards
KedoKudo Feb 13, 2025
a4ce75b
radius card has serious issue, need special attention, disable for now
KedoKudo Feb 13, 2025
a266b93
Fix radius card bug
KedoKudo Feb 17, 2025
8626668
remove debug print and add usage example notebook
KedoKudo Feb 17, 2025
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287 changes: 287 additions & 0 deletions notebook/sammy.param/example.ipynb
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@@ -0,0 +1,287 @@
{
"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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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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