diff --git a/docs/repo.map b/docs/repo.map new file mode 100644 index 0000000..6823430 --- /dev/null +++ b/docs/repo.map @@ -0,0 +1,77 @@ +PLEIADES +├── .readthedocs.yaml +├── .gitignore +├── .pre-commit-config.yaml +├── pyproject.toml +├── poetry.lock +├── LICENSE +├── environment.yaml +├── pleiades.egg-info +├── README.rst +├── src/ +│ └── pleiades +| ├── __init__.py +| ├── __main__.py +| ├── utils/ +| ├── data/ +| | ├── cross-sections/ +| | ├── isotopes/ +| | └── resonances/ +| ├── core/ +| │ ├── transmission.py +| │ ├── constants.py +| │ ├── __init__.py +| │ ├── models.py +| │ └── data_manager.py +| └── sammy/ +| ├── interface.py +| ├── config.py +| ├── __init__.py +| ├── factory.py +| ├── parfile.py +| ├── backends/ +| │ ├── nova_ornl.py +| │ ├── __init__.py +| │ ├── local.py +| │ └── docker.py +| └── parameters/ +| ├── unused_var.py +| ├── paramagnetic.py +| ├── orres.py +| ├── normalization.py +| ├── misc.py +| ├── helper.py +| ├── external_r.py +| ├── data_reduction.py +| ├── user_resolution.py +| ├── resonance.py +| ├── resolution.py +| ├── radius.py +| ├── last.py +| ├── det_efficiency.py +| ├── broadening.py +| ├── background.py +| ├── __init__.py +| └── isotope.py +├── examples/ +├── scripts/ +├── docs/ +│ └── repo.map +├── legacy/ +├── paper/ +├── tests/ +│ ├── unit/ +│ │ ├── pleiades +│ │ └── conftest.py +│ └── data/ +│ ├── config +│ └── ex012 +└── notebook/ + ├── sammy.param/ + │ └── example.ipynb + └── samexm/ + ├── ex012/ + │ ├── ex012.ipynb + │ └── ex012a.par + └── ex027/ + └── ex027a.endf diff --git a/notebook/samexm/ex012/ex012a.ipynb b/notebook/samexm/ex012/ex012a.ipynb new file mode 100644 index 0000000..71bebb3 --- /dev/null +++ b/notebook/samexm/ex012/ex012a.ipynb @@ -0,0 +1,75 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This notebook is based on example 12 from the SAMMY repo. " + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "# Importing specific classes from the pleiades.sammy module\n", + "from pleiades.sammy.parfile import SammyParameterFile" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we want to load SAMMY parameters based on a given parameter file. " + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# reading in SAMMY parameters from a parameter file \"./ex012a.par\"\n", + "sammy_params = SammyParameterFile.from_file(\"./ex012a.par\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Write the parameters to an output file \"ex012b.par\". " + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "sammy_params.to_file(\"./ex012b.par\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "pleiades", + "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": "3.12.9" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebook/samexm/ex012/ex012a.par b/notebook/samexm/ex012/ex012a.par new file mode 100755 index 0000000..a3b0b8c --- /dev/null +++ b/notebook/samexm/ex012/ex012a.par @@ -0,0 +1,177 @@ +-3.6616E+06 1.5877E+05 3.6985E+09 0 0 1 1 +-8.7373E+05 1.0253E+03 1.0151E+02 0 0 1 1 +-3.6529E+05 1.0000E+03 3.0406E+01 0 0 0 1 +-6.3159E+04 1.0000E+03 4.6894E+01 0 0 0 1 +-4.8801E+04 1.0000E+03 9.2496E+00 0 0 0 1 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91011121314151617 + 4.20000 4.20000 0-11819202122 + 4.20000 4.20000 0-123242526272829 + +ISOTOPIC MASSES AND ABUNDANCES FOLLOW + 27.976929 1.0000000 .9200 1 1 2 3 4 5 6 7 + 28.976496 .0467000 .0500 1 8 91011121314151617 + 29.973772 .0310000 .0200 11819202122 + 16.000000 1.0000000 .0100000 023242526272829 diff --git a/notebook/samexm/ex027/ex027.ipynb b/notebook/samexm/ex027/ex027.ipynb new file mode 100644 index 0000000..e69de29 diff --git a/src/pleiades/core/models.py b/src/pleiades/core/models.py index 1591ed2..fb24aa1 100644 --- a/src/pleiades/core/models.py +++ b/src/pleiades/core/models.py @@ -178,7 +178,7 @@ class Isotope(BaseModel): atomic_mass: Mass thickness: NonNegativeFloat thickness_unit: str = Field(pattern=r"^(cm|mm|atoms/cm2)$") - abundance: float = Field(ge=0.0, le=1.0) + abundance: float = Field(ge=0.0) density: NonNegativeFloat density_unit: str = Field(default="g/cm3", pattern=r"^g/cm3$") diff --git a/src/pleiades/sammy/notes/parfile_notes.md b/src/pleiades/sammy/notes/parfile_notes.md new file mode 100644 index 0000000..aeeb50f --- /dev/null +++ b/src/pleiades/sammy/notes/parfile_notes.md @@ -0,0 +1,88 @@ +# parfile.py + +## Imports +- pathlib +- os +- Enum +- auto +- List +- Optional +- Union +- BaseModel +- Field +- BroadeningParameterCard +- DataReductionCard +- ExternalREntry +- ExternalRFunction +- IsotopeCard +- NormalizationBackgroundCard +- ORRESCard +- ParamagneticParameters +- RadiusCard +- ResonanceCard +- UnusedCorrelatedCard +- UserResolutionParameters +- Logger +- _log_and_raise_error + +## Logger Initialization +- log_file_path +- logger + +## Enums +- CardOrder + - Methods + - get_field_name + +## Classes +- SammyParameterFile + - Attributes + - fudge + - resonance + - external_r + - broadening + - unused_correlated + - normalization + - radius + - data_reduction + - orres + - paramagnetic + - user_resolution + - isotope + - Methods + - to_string + - Returns: str + - _get_card_class_with_header + @classmethod + - Parameters: + - header: str + - Returns: Type[BaseModel] + - from_string + @classmethod + - Parameters: + - data: str + - Returns: SammyParameterFile + - _parse_card + @classmethod + - Parameters: + - card_data: str + - Returns: BaseModel + - _get_card_class + @classmethod + - Parameters: + - card_name: str + - Returns: Type[BaseModel] + - from_file + @classmethod + - Parameters: + - file_path: Union[str, pathlib.Path] + - Returns: SammyParameterFile + - to_file + - Parameters: + - file_path: Union[str, pathlib.Path] + - print_parameters + - Parameters: + - None + +## Main Function +- Example usage diff --git a/src/pleiades/sammy/parameters/isotope.py b/src/pleiades/sammy/parameters/isotope.py index c0b48db..4f7aae3 100644 --- a/src/pleiades/sammy/parameters/isotope.py +++ b/src/pleiades/sammy/parameters/isotope.py @@ -33,6 +33,8 @@ 41-45 I IGRISO Second spin group number ...etc for up to 9 groups per line +NOTE: the extended format is currently not supported with pleiades. + Continuation lines are indicated by "-1" in columns 79-80 (standard format) or column 80 (extended format). These lines contain only additional spin group numbers in the same format as the parent line. @@ -44,12 +46,17 @@ - Spin groups must be valid for the model """ -import logging +import os from typing import List, Optional from pydantic import BaseModel, Field, model_validator from pleiades.sammy.parameters.helper import VaryFlag, format_float, format_vary, safe_parse +from pleiades.utils.logger import Logger, _log_and_raise_error + +# Initialize logger with file logging +log_file_path = os.path.join(os.getcwd(), "pleiades-par.log") +logger = Logger(__name__, log_file=log_file_path) # Format definitions for standard format (<99 spin groups) # Each numeric field has specific width requirements @@ -60,6 +67,15 @@ "flag": slice(30, 32), # IFLISO: Treatment flag } +# Spin group number positions +# Standard format: 2 columns per group starting at col 33 +SPIN_GROUP_STANDARD = { + "width": 2, # Character width of each group number + "start": 32, # Start of first group + "per_line": 24, # Max groups per line + "cont_marker": slice(78, 80), # "-1" indicates continuation +} + # Format for extended format (>99 spin groups) FORMAT_EXTENDED = { "mass": slice(0, 10), # AMUISO: Atomic mass (amu) @@ -68,16 +84,6 @@ "flag": slice(30, 35), # IFLISO: Treatment flag } -# Spin group number positions -# Standard format: 2 columns per group starting at col 33 -# Extended format: 5 columns per group starting at col 36 -SPIN_GROUP_STANDARD = { - "width": 2, - "start": 32, - "per_line": 24, # Max groups per line - "cont_marker": slice(78, 80), # "-1" indicates continuation -} - SPIN_GROUP_EXTENDED = { "width": 5, "start": 35, @@ -107,14 +113,6 @@ class IsotopeParameters(BaseModel): flag (VaryFlag): Treatment flag for abundance (-2=use input, 0=fixed, 1=vary, 3=PUP) spin_groups (List[int]): List of spin group numbers (negative values indicate omitted resonances) - Example: - Standard format line: - "16.000 0.99835 0.00002 0 1 2 3" - ^ ^ ^ ^ spin groups (2 cols each) - ^^ flag - ^^^^^^^ uncertainty - ^^^^^^^ abundance - ^^^^^^^ mass """ mass: float = Field(description="Atomic mass in amu", gt=0) @@ -138,15 +136,16 @@ def validate_groups(self) -> "IsotopeParameters": Raises: ValueError: If spin group validation fails """ + where_am_i = "IsotopeParameters.validate_groups()" max_standard = 99 # Maximum group number for standard format for group in self.spin_groups: if group == 0: - raise ValueError("Spin group number cannot be 0") + _log_and_raise_error(logger, "Spin group number cannot be 0", ValueError) # Check if we need extended format if abs(group) > max_standard: - logging.debug(f"Group number {group} requires extended format") + logger.info(f"{where_am_i}:Group number {group} requires extended format") return self @@ -174,11 +173,16 @@ def from_lines(cls, lines: List[str], extended: bool = False) -> "IsotopeParamet ... ] >>> params = IsotopeParameters.from_lines(lines) """ + where_am_i = "IsotopeParameters.from_lines()" + + logger.info(f"{where_am_i}: Attempting to parse isotope parameters from lines") + if not lines or not lines[0].strip(): - raise ValueError("No valid parameter line provided") + _log_and_raise_error(logger, "No valid parameter line provided", ValueError) + + # Set format to standard. + format_dict = FORMAT_STANDARD # NOTE: EXTENDED format is currently not supported. - # Parse main parameters from first line - format_dict = FORMAT_EXTENDED if extended else FORMAT_STANDARD main_line = f"{lines[0]:<80}" # Pad to full width params = {} @@ -187,7 +191,7 @@ def from_lines(cls, lines: List[str], extended: bool = False) -> "IsotopeParamet for field in ["mass", "abundance"]: value = safe_parse(main_line[format_dict[field]]) if value is None: - raise ValueError(f"Failed to parse required field: {field}") + _log_and_raise_error(logger, f"Failed to parse required field: {field}", ValueError) params[field] = value # Parse optional uncertainty @@ -195,14 +199,16 @@ def from_lines(cls, lines: List[str], extended: bool = False) -> "IsotopeParamet # Parse flag flag_str = main_line[format_dict["flag"]].strip() or "0" + try: params["flag"] = VaryFlag(int(flag_str)) except (ValueError, TypeError): + _log_and_raise_error(logger, f"Invalid flag value: {flag_str}", ValueError) params["flag"] = VaryFlag.NO # Parse spin groups spin_groups = [] - group_format = SPIN_GROUP_EXTENDED if extended else SPIN_GROUP_STANDARD + group_format = SPIN_GROUP_STANDARD # NOTE: EXTENDED format is currently not supported. # Helper function to parse groups from a line def parse_groups(line: str, start_pos: int = None, continuation: bool = False) -> List[int]: @@ -216,6 +222,7 @@ def parse_groups(line: str, start_pos: int = None, continuation: bool = False) - Returns: List of parsed group numbers """ + groups = [] pos = start_pos if start_pos is not None else group_format["start"] @@ -233,6 +240,7 @@ def parse_groups(line: str, start_pos: int = None, continuation: bool = False) - if group is not None: groups.append(group) pos += width + return groups # Parse groups from first line @@ -246,6 +254,7 @@ def parse_groups(line: str, start_pos: int = None, continuation: bool = False) - spin_groups.extend(parse_groups(line, start_pos=0, continuation=True)) params["spin_groups"] = spin_groups + return cls(**params) def to_lines(self, extended: bool = False) -> List[str]: @@ -256,15 +265,10 @@ def to_lines(self, extended: bool = False) -> List[str]: Returns: List[str]: Formatted lines with proper fixed-width spacing - - Example: - >>> params = IsotopeParameters(mass=16.0, abundance=0.99835, - ... uncertainty=0.00002, flag=VaryFlag.NO, - ... spin_groups=[1, 2, 3, 4, 5, 6]) - >>> lines = params.to_lines() - >>> print(lines[0]) - "16.000 0.99835 0.00002 0 1 2 3" """ + where_am_i = "IsotopeParameters.to_lines()" + logger.info(f"{where_am_i}: Attempting to convert isotope parameters to lines") + # Select format based on mode group_format = SPIN_GROUP_EXTENDED if extended else SPIN_GROUP_STANDARD format_dict = FORMAT_EXTENDED if extended else FORMAT_STANDARD @@ -318,34 +322,13 @@ class IsotopeCard(BaseModel): isotopes (List[IsotopeParameters]): List of isotope parameter sets extended (bool): Whether to use extended format for >99 spin groups - Example: - >>> lines = [ - ... "ISOTOpic abundances and masses", - ... "16.000 0.99835 0.00002 0 1 2 3", - ... "17.000 0.00165 0.00001 0 4 5 6", - ... "" - ... ] - >>> card = IsotopeCard.from_lines(lines) + NOTE: Fixed formats for both standard and extended are defined in the + IsotopeParameters class. But only using the standard format for now. """ isotopes: List[IsotopeParameters] = Field(default_factory=list) extended: bool = Field(default=False, description="Use extended format for >99 spin groups") - @model_validator(mode="after") - def validate_abundances(self) -> "IsotopeCard": - """Validate that total abundance doesn't exceed 1.0. - - Returns: - IsotopeCard: Self if validation passes - - Raises: - ValueError: If total abundance > 1.0 - """ - total = sum(iso.abundance for iso in self.isotopes) - if total > 1.0: - raise ValueError(f"Total abundance {total} exceeds 1.0") - return self - @classmethod def is_header_line(cls, line: str) -> bool: """Check if line is a valid header line. @@ -354,10 +337,11 @@ def is_header_line(cls, line: str) -> bool: line: Input line to check Returns: - bool: True if line matches any valid header format + bool: True if the first 5 characters of the line are 'ISOTO' """ - line_upper = line.strip().upper() - return any(header.upper() in line_upper for header in CARD_10_HEADERS) + where_am_i = "IsotopeCard.is_header_line()" + logger.info(f"{where_am_i}: Checking if valid header line: {line}") + return line.strip().upper().startswith("ISOTO") or line.strip().upper().startswith("NUCLI") @classmethod def from_lines(cls, lines: List[str]) -> "IsotopeCard": @@ -372,42 +356,39 @@ def from_lines(cls, lines: List[str]) -> "IsotopeCard": Raises: ValueError: If no valid header found or invalid format """ + where_am_i = "IsotopeCard.from_lines()" + logger.info(f"{where_am_i}: Attempting to parse isotope card from lines") + if not lines: - raise ValueError("No lines provided") + _log_and_raise_error(logger, "No lines provided", ValueError) # Validate header if not cls.is_header_line(lines[0]): - raise ValueError(f"Invalid header line: {lines[0]}") + _log_and_raise_error(logger, f"Invalid header line: {lines[0]}", ValueError) # Remove header and trailing blank lines content_lines = [line for line in lines[1:] if line.strip()] if not content_lines: - raise ValueError("No parameter lines found") + _log_and_raise_error(logger, "No parameter lines found", ValueError) # Check if we need extended format extended = False - for line in content_lines: - # Look for any spin group number > 99 in the data - numbers = [int(n) for n in line.split() if n.strip().isdigit()] - if any(abs(n) > 99 for n in numbers): - extended = True - break # Parse isotopes isotopes = [] current_lines = [] for line in content_lines: - # If line starts with a number, it's a new isotope - if line.strip() and line[0].isdigit(): - if current_lines: - isotopes.append(IsotopeParameters.from_lines(current_lines, extended=extended)) - current_lines = [] current_lines.append(line) - # Don't forget the last isotope - if current_lines: - isotopes.append(IsotopeParameters.from_lines(current_lines, extended=extended)) + # check if characters 79-80 is a "-1". this means that there are more spin groups in the next line. + if line[78:80] == "-1": + continue + + # Otherwise the are no more lines for spin groups, so process the current lines. + else: + isotopes.append(IsotopeParameters.from_lines(current_lines, extended=extended)) + current_lines = [] return cls(isotopes=isotopes, extended=extended) diff --git a/src/pleiades/sammy/parameters/notes/isotope_notes.md b/src/pleiades/sammy/parameters/notes/isotope_notes.md new file mode 100644 index 0000000..7681e13 --- /dev/null +++ b/src/pleiades/sammy/parameters/notes/isotope_notes.md @@ -0,0 +1,51 @@ +# isotope.py + +## File Header +- Shebang: `#!/usr/bin/env python` +- Docstring: Description of the module and format specifications for Card Set 10 + +## Imports +- List +- Optional +- BaseModel +- Field +- model_validator +- VaryFlag +- format_float +- format_vary +- safe_parse +- Logger +- _log_and_raise_error +- os + +## Constants +- FORMAT_STANDARD +- SPIN_GROUP_STANDARD +- FORMAT_EXTENDED +- SPIN_GROUP_EXTENDED +- CARD_10_HEADERS + +## Classes +- IsotopeParameters + - Attributes + - mass + - abundance + - uncertainty + - flag + - spin_groups + - Methods + - validate_groups + - from_lines + - to_lines + +- IsotopeCard + - Attributes + - isotopes + - extended + - Methods + - is_header_line + - from_lines + - to_lines + +## Main Function +- Example usage diff --git a/src/pleiades/sammy/parameters/notes/radius_notes.md b/src/pleiades/sammy/parameters/notes/radius_notes.md new file mode 100644 index 0000000..9b5d6eb --- /dev/null +++ b/src/pleiades/sammy/parameters/notes/radius_notes.md @@ -0,0 +1,103 @@ +# radius.py + +## Imports +- re +- os +- Enum +- List +- Optional +- Tuple +- Union +- BaseModel +- Field +- field_validator +- model_validator +- VaryFlag +- format_float +- format_vary +- parse_keyword_pairs_to_dict +- safe_parse +- Logger +- _log_and_raise_error + +## Logger Initialization +- log_file_path +- logger + +## Constants +- CARD_7_HEADER +- CARD_7A_HEADER +- CARD_7_ALT_HEADER +- FORMAT_DEFAULT +- FORMAT_ALTERNATE + +## Enums +- RadiusFormat +- OrbitalMomentum + +## Classes +- RadiusParameters + - Attributes + - effective_radius + - true_radius + - channel_mode + - vary_effective + - vary_true + - spin_groups + - channels + - Methods + - validate_spin_groups + - validate_vary_true + - validate_channels + - validate_true_radius_consistency + - __repr__ + +- RadiusCardDefault + - Attributes + - parameters + - Methods + - is_header_line + - _parse_numbers_from_line + - _parse_spin_groups_and_channels + - from_lines + - to_lines + +- RadiusCardAlternate + - Attributes + - parameters + - Methods + - is_header_line + - _parse_numbers_from_line + - _parse_spin_groups_and_channels + - from_lines + - to_lines + +- RadiusCardKeyword + - Attributes + - parameters + - particle_pair + - orbital_momentum + - relative_uncertainty + - absolute_uncertainty + - Methods + - is_header_line + - _parse_values + - from_lines + - to_lines + +- RadiusCard + - Attributes + - parameters + - particle_pair + - orbital_momentum + - relative_uncertainty + - absolute_uncertainty + - Methods + - is_header_line + - detect_format + - from_lines + - to_lines + - from_values + +## Main Function +- Example usage diff --git a/src/pleiades/sammy/parameters/radius.py b/src/pleiades/sammy/parameters/radius.py index 62fa8d6..c43cdf2 100644 --- a/src/pleiades/sammy/parameters/radius.py +++ b/src/pleiades/sammy/parameters/radius.py @@ -5,6 +5,7 @@ for radius parameters in SAMMY parameter files. """ +import os import re from enum import Enum from typing import List, Optional, Tuple, Union @@ -12,16 +13,53 @@ from pydantic import BaseModel, Field, field_validator, model_validator from pleiades.sammy.parameters.helper import VaryFlag, format_float, format_vary, parse_keyword_pairs_to_dict, safe_parse +from pleiades.utils.logger import Logger, _log_and_raise_error +# Initialize logger with file logging +log_file_path = os.path.join(os.getcwd(), "pleiades-par.log") +logger = Logger(__name__, log_file=log_file_path) -class OrbitalMomentum(str, Enum): - """Valid values for orbital angular momentum specification.""" +#################################################################################################### +# Header flages and format definitions +#################################################################################################### +CARD_7_HEADER = "RADIUs parameters follow" +CARD_7A_HEADER = "RADII are in KEY-WORD format" +CARD_7_ALT_HEADER = "RADIUs parameters follow" - ODD = "ODD" - EVEN = "EVEN" - ALL = "ALL" +# Format definitions for fixed-width fields +FORMAT_DEFAULT = { + "pareff": slice(0, 10), # Effective radius (Fermi) + "partru": slice(10, 20), # True radius (Fermi) + "ichan": slice(20, 21), # Channel indicator + "ifleff": slice(21, 22), # Flag for PAREFF + "ifltru": slice(22, 24), # Flag for PARTRU + # Spin groups start at col 24, 2 cols each + # After IX=0 marker, channel numbers use 2 cols each +} +# Format definitions for fixed-width fields +FORMAT_ALTERNATE = { + "pareff": slice(0, 10), # Radius for potential scattering + "partru": slice(10, 20), # Radius for penetrabilities + "ichan": slice(20, 25), # Channel indicator (5 cols) + "ifleff": slice(25, 30), # Flag for PAREFF (5 cols) + "ifltru": slice(30, 35), # Flag for PARTRU (5 cols) + # Spin groups start at col 35, 5 cols each + # After IX=0 marker, channel numbers use 5 cols each +} + + +class RadiusFormat(Enum): + """Supported formats for radius parameter cards.""" + + DEFAULT = "default" # Fixed width (<99 spin groups) + ALTERNATE = "alternate" # Fixed width (>=99 spin groups) + KEYWORD = "keyword" # Keyword based + +#################################################################################################### +# RadiusParameters class and its corresponding Container class +#################################################################################################### class RadiusParameters(BaseModel): """Container for nuclear radius parameters used in SAMMY calculations. @@ -188,21 +226,23 @@ def validate_true_radius_consistency(self) -> "RadiusParameters": return self - -# Format definitions for fixed-width fields -FORMAT_DEFAULT = { - "pareff": slice(0, 10), # Effective radius (Fermi) - "partru": slice(10, 20), # True radius (Fermi) - "ichan": slice(20, 21), # Channel indicator - "ifleff": slice(21, 22), # Flag for PAREFF - "ifltru": slice(22, 24), # Flag for PARTRU - # Spin groups start at col 24, 2 cols each - # After IX=0 marker, channel numbers use 2 cols each -} - -CARD_7_HEADER = "RADIUs parameters follow" + def __repr__(self) -> str: + """Return a string representation of the radius parameters.""" + return ( + f"RadiusParameters(" + f"effective_radius={self.effective_radius}, " + f"true_radius={self.true_radius}, " + f"channel_mode={self.channel_mode}, " + f"vary_effective={self.vary_effective}, " + f"vary_true={self.vary_true}, " + f"spin_groups={self.spin_groups}, " + f"channels={self.channels})" + ) +#################################################################################################### +# Card variant classes for different formats (default, alternate, keyword) +#################################################################################################### class RadiusCardDefault(BaseModel): """Handler for default format radius parameter cards (Card Set 7). @@ -219,7 +259,7 @@ class RadiusCardDefault(BaseModel): For larger systems, use RadiusCardAlternate. """ - parameters: RadiusParameters + parameters: List[RadiusParameters] @classmethod def is_header_line(cls, line: str) -> bool: @@ -231,6 +271,8 @@ def is_header_line(cls, line: str) -> bool: Returns: bool: True if line is a valid header """ + where_am_i = "RadiusCardDefault.is_header_line()" + logger.info(f"{where_am_i}: Checking if header line - {line}") return line.strip().upper().startswith("RADIU") @staticmethod @@ -245,6 +287,8 @@ def _parse_numbers_from_line(line: str, start_pos: int, width: int) -> List[int] Returns: List[int]: List of parsed integers, stopping at first invalid value """ + where_am_i = "RadiusCardDefault._parse_numbers_from_line()" + logger.info(f"{where_am_i}: Parsing fixed-width integers from line") numbers = [] pos = start_pos while pos + width <= len(line): @@ -256,11 +300,11 @@ def _parse_numbers_from_line(line: str, start_pos: int, width: int) -> List[int] return numbers @classmethod - def _parse_spin_groups_and_channels(cls, lines: List[str]) -> Tuple[List[int], Optional[List[int]]]: - """Parse spin groups and optional channels from lines. + def _parse_spin_groups_and_channels(cls, line: str) -> Tuple[List[int], Optional[List[int]]]: + """Parse spin groups and optional channels from a line. Args: - lines: List of input lines containing spin groups/channels + line: Input line containing spin groups/channels Returns: Tuple containing: @@ -270,29 +314,30 @@ def _parse_spin_groups_and_channels(cls, lines: List[str]) -> Tuple[List[int], O Note: Handles continuation lines (-1 marker) and IX=0 marker for channels """ + where_am_i = "RadiusCardDefault._parse_spin_groups_and_channels()" + logger.info(f"{where_am_i}: Parsing spin groups and channels from line: {line}") + spin_groups = [] channels = None - for line in lines: - # Parse numbers 2 columns each starting at position 24 - numbers = cls._parse_numbers_from_line(line, 24, 2) - - if not numbers: - continue + # Parse numbers 2 columns each starting at position 24 + numbers = cls._parse_numbers_from_line(line, 24, 2) + logger.info(f"{where_am_i}: Parsed numbers: {numbers}") - # Check for continuation marker (-1) - if numbers[-1] == -1: - spin_groups.extend(numbers[:-1]) - continue + if not numbers: + return spin_groups, channels + # Check for continuation marker (-1) + if numbers[-1] == -1: + spin_groups.extend(numbers[:-1]) + else: # Check for IX=0 marker (indicates channels follow) if 0 in numbers: zero_index = numbers.index(0) spin_groups.extend(numbers[:zero_index]) channels = numbers[zero_index + 1 :] - break - - spin_groups.extend(numbers) + else: + spin_groups.extend(numbers) return spin_groups, channels @@ -309,55 +354,72 @@ def from_lines(cls, lines: List[str]) -> "RadiusCardDefault": Raises: ValueError: If lines are invalid or required data is missing """ + where_am_i = "RadiusCardDefault.from_lines()" + + logger.info(f"{where_am_i}: Parsing radius parameters from lines") if not lines: + logger.error(f"{where_am_i}: No lines provided") raise ValueError("No lines provided") # Validate header if not cls.is_header_line(lines[0]): + logger.error(f"{where_am_i}: Invalid header line: {lines[0]}") raise ValueError(f"Invalid header line: {lines[0]}") # Get content lines (skip header and trailing blank) content_lines = [line for line in lines[1:] if line.strip()] if not content_lines: + logger.error(f"{where_am_i}: No parameter lines found") raise ValueError("No parameter lines found") - # Parse first line for main parameters - main_line = content_lines[0] - - # Ensure line is long enough - if len(main_line) < 24: # Minimum length for main parameters - raise ValueError("Parameter line too short") - - # Parse main parameters - params = { - "effective_radius": safe_parse(main_line[FORMAT_DEFAULT["pareff"]]), - "true_radius": safe_parse(main_line[FORMAT_DEFAULT["partru"]]), - "channel_mode": safe_parse(main_line[FORMAT_DEFAULT["ichan"]], as_int=True) or 0, - } - - # Parse flags - try: - params["vary_effective"] = VaryFlag(int(main_line[FORMAT_DEFAULT["ifleff"]].strip() or "0")) - params["vary_true"] = VaryFlag(int(main_line[FORMAT_DEFAULT["ifltru"]].strip() or "0")) - except ValueError: - raise ValueError("Invalid vary flags") - - # Parse spin groups and channels - spin_groups, channels = cls._parse_spin_groups_and_channels(content_lines) - - if not spin_groups: - raise ValueError("No spin groups found") - - params["spin_groups"] = spin_groups - params["channels"] = channels - - # Create parameters object - try: - parameters = RadiusParameters(**params) - except ValueError as e: - raise ValueError(f"Invalid parameter values: {e}") - - return cls(parameters=parameters) + # Initialize list to hold RadiusParameters objects + radius_parameters_list = [] + + # Parse each line for main parameters and spin groups + for line in content_lines: + # Ensure line is long enough + if len(line) < 24: # Minimum length for main parameters + logger.error(f"{where_am_i}: Parameter line too short") + raise ValueError("Parameter line too short") + + # Parse main parameters + params = { + "effective_radius": safe_parse(line[FORMAT_DEFAULT["pareff"]]), + "true_radius": safe_parse(line[FORMAT_DEFAULT["partru"]]), + "channel_mode": safe_parse(line[FORMAT_DEFAULT["ichan"]], as_int=True) or 0, + } + + # Parse flags + try: + params["vary_effective"] = VaryFlag(int(line[FORMAT_DEFAULT["ifleff"]].strip() or "0")) + params["vary_true"] = VaryFlag(int(line[FORMAT_DEFAULT["ifltru"]].strip() or "0")) + logger.info(f"{where_am_i}: Successfully parsed flags") + except ValueError: + logger.error(f"{where_am_i}: Invalid vary flags") + raise ValueError("Invalid vary flags") + + # Parse spin groups and channels + spin_groups, channels = cls._parse_spin_groups_and_channels(line) + + if not spin_groups: + logger.error(f"{where_am_i}: No spin groups found") + raise ValueError("No spin groups found") + + params["spin_groups"] = spin_groups + params["channels"] = channels + + # Create parameters object + try: + parameters = RadiusParameters(**params) + logger.info(f"{where_am_i}: Successfully created radius parameters") + radius_parameters_list.append(parameters) + except ValueError as e: + logger.error(f"{where_am_i}: Invalid parameter values: {e}") + raise ValueError(f"Invalid parameter values: {e}") + + logger.info(f"{where_am_i}: Successfully parsed radius parameters") + + return cls(parameters=radius_parameters_list) def to_lines(self) -> List[str]: """Convert the card to fixed-width format lines. @@ -365,69 +427,57 @@ def to_lines(self) -> List[str]: Returns: List[str]: Lines including header """ - lines = [CARD_7_HEADER] - - # Format main parameters - main_parts = [ - format_float(self.parameters.effective_radius, width=10), - format_float(self.parameters.true_radius, width=10), - str(self.parameters.channel_mode), - format_vary(self.parameters.vary_effective), - format_vary(self.parameters.vary_true), - ] - - # Add spin groups (up to 28 per line) - spin_groups = self.parameters.spin_groups - spin_group_lines = [] - - current_line = [] - for group in spin_groups: - current_line.append(f"{group:2d}") - if len(current_line) == 28: # Max groups per line + where_am_i = "RadiusCardDefault.to_lines()" + + logger.info(f"{where_am_i}: Converting radius parameters to lines") + lines = [] + + for params in self.parameters: + # Format main parameters + main_parts = [ + format_float(params.effective_radius, width=10), + format_float(params.true_radius, width=10), + str(params.channel_mode), + format_vary(params.vary_effective), + format_vary(params.vary_true), + ] + + # Add spin groups (up to 28 per line) + spin_groups = params.spin_groups + spin_group_lines = [] + + current_line = [] + for group in spin_groups: + current_line.append(f"{group:2d}") + if len(current_line) == 28: # Max groups per line + spin_group_lines.append("".join(current_line)) + current_line = [] + + # Add any remaining groups + if current_line: spin_group_lines.append("".join(current_line)) - current_line = [] - # Add any remaining groups - if current_line: - spin_group_lines.append("".join(current_line)) + # Combine main parameters with first line of spin groups + if spin_group_lines: + first_line = "".join(main_parts) + if len(spin_group_lines[0]) > 0: + first_line += spin_group_lines[0] + lines.append(first_line) - # Combine main parameters with first line of spin groups - if spin_group_lines: - first_line = "".join(main_parts) - if len(spin_group_lines[0]) > 0: - first_line += spin_group_lines[0] - lines.append(first_line) - - # Add remaining spin group lines - lines.extend(spin_group_lines[1:]) + # Add remaining spin group lines + lines.extend(spin_group_lines[1:]) - # Add channels if present - if self.parameters.channels: - channel_line = "0" # IX=0 marker - for channel in self.parameters.channels: - channel_line += f"{channel:2d}" - lines.append(channel_line) - - # Add trailing blank line - lines.append("") + # Add channels if present + if params.channels: + channel_line = "0" # IX=0 marker + for channel in params.channels: + channel_line += f"{channel:2d}" + lines.append(channel_line) + logger.info(f"{where_am_i}: Successfully converted radius parameters to lines") return lines -# Format definitions for fixed-width fields -FORMAT_ALTERNATE = { - "pareff": slice(0, 10), # Radius for potential scattering - "partru": slice(10, 20), # Radius for penetrabilities - "ichan": slice(20, 25), # Channel indicator (5 cols) - "ifleff": slice(25, 30), # Flag for PAREFF (5 cols) - "ifltru": slice(30, 35), # Flag for PARTRU (5 cols) - # Spin groups start at col 35, 5 cols each - # After IX=0 marker, channel numbers use 5 cols each -} - -CARD_7_ALT_HEADER = "RADIUs parameters follow" - - class RadiusCardAlternate(BaseModel): """Handler for alternate format radius parameter cards (Card Set 7 alternate). @@ -457,6 +507,8 @@ def is_header_line(cls, line: str) -> bool: Returns: bool: True if line is a valid header """ + where_am_i = "RadiusCardAlternate.is_header_line()" + logger.info(f"{where_am_i}: Checking if header line - {line}") return line.strip().upper().startswith("RADIU") @staticmethod @@ -471,6 +523,9 @@ def _parse_numbers_from_line(line: str, start_pos: int, width: int) -> List[int] Returns: List[int]: List of parsed integers, stopping at first invalid value """ + where_am_i = "RadiusCardAlternate._parse_numbers_from_line()" + logger.info(f"{where_am_i}: Parsing fixed-width integers from line") + numbers = [] pos = start_pos while pos + width <= len(line): @@ -496,8 +551,12 @@ def _parse_spin_groups_and_channels(cls, lines: List[str]) -> Tuple[List[int], O Note: Handles continuation lines (-1 marker) and IX=0 marker for channels """ + where_am_i = "RadiusCardAlternate._parse_spin_groups_and_channels()" + logger.info(f"{where_am_i}: Parsing spin groups and channels from lines") + spin_groups = [] channels = None + logger.info(f"{where_am_i}: parsing spin groups and channels") for line in lines: # Parse numbers 5 columns each starting at position 35 @@ -535,16 +594,21 @@ def from_lines(cls, lines: List[str]) -> "RadiusCardAlternate": Raises: ValueError: If lines are invalid or required data is missing """ + where_am_i = "RadiusCardAlternate.from_lines()" + logger.info(f"{where_am_i}: Parsing radius parameters from lines") + if not lines: raise ValueError("No lines provided") # Validate header if not cls.is_header_line(lines[0]): + logger.error(f"{where_am_i}: Invalid header line: {lines[0]}") raise ValueError(f"Invalid header line: {lines[0]}") # Get content lines (skip header and trailing blank) content_lines = [line for line in lines[1:] if line.strip()] if not content_lines: + logger.error(f"{where_am_i}: No parameter lines found") raise ValueError("No parameter lines found") # Parse first line for main parameters @@ -552,6 +616,7 @@ def from_lines(cls, lines: List[str]) -> "RadiusCardAlternate": # Ensure line is long enough if len(main_line) < 35: # Minimum length for main parameters + logger.error(f"{where_am_i}: Parameter line too short") raise ValueError("Parameter line too short") # Parse main parameters @@ -566,12 +631,14 @@ def from_lines(cls, lines: List[str]) -> "RadiusCardAlternate": params["vary_effective"] = VaryFlag(int(main_line[FORMAT_ALTERNATE["ifleff"]].strip() or "0")) params["vary_true"] = VaryFlag(int(main_line[FORMAT_ALTERNATE["ifltru"]].strip() or "0")) except ValueError: + logger.error(f"{where_am_i}: Invalid vary flags") raise ValueError("Invalid vary flags") # Parse spin groups and channels spin_groups, channels = cls._parse_spin_groups_and_channels(content_lines) if not spin_groups: + logger.error(f"{where_am_i}: No spin groups found") raise ValueError("No spin groups found") params["spin_groups"] = spin_groups @@ -581,8 +648,10 @@ def from_lines(cls, lines: List[str]) -> "RadiusCardAlternate": try: parameters = RadiusParameters(**params) except ValueError as e: + logger.error(f"{where_am_i}: Invalid parameter values: {e}") raise ValueError(f"Invalid parameter values: {e}") + logger.info(f"{where_am_i}: Successfully parsed radius parameters") return cls(parameters=parameters) def to_lines(self) -> List[str]: @@ -591,7 +660,9 @@ def to_lines(self) -> List[str]: Returns: List[str]: Lines including header """ - lines = [CARD_7_ALT_HEADER] + where_am_i = "RadiusCardAlternate.to_lines()" + + lines = [] # Format main parameters main_parts = [ @@ -640,9 +711,6 @@ def to_lines(self) -> List[str]: return lines -CARD_7A_HEADER = "RADII are in KEY-WORD format" - - class RadiusCardKeyword(BaseModel): """Handler for keyword-based radius parameter cards (Card Set 7a). @@ -659,6 +727,8 @@ class RadiusCardKeyword(BaseModel): """ parameters: RadiusParameters + + # Optional keyword format extras particle_pair: Optional[str] = None orbital_momentum: Optional[List[Union[int, str]]] = None relative_uncertainty: Optional[float] = None @@ -667,11 +737,15 @@ class RadiusCardKeyword(BaseModel): @classmethod def is_header_line(cls, line: str) -> bool: """Check if line is a valid header line.""" + where_am_i = "RadiusCardKeyword.is_header_line()" + logger.info(f"{where_am_i}: Checking if header line - {line}") return "RADII" in line.upper() and "KEY-WORD" in line.upper() @staticmethod def _parse_values(value_str: str) -> List[str]: """Parse space/comma separated values.""" + where_am_i = "RadiusCardKeyword._parse_values()" + logger.info(f"{where_am_i}: Parsing values from string: {value_str}") return [v for v in re.split(r"[,\s]+", value_str.strip()) if v] @classmethod @@ -687,11 +761,14 @@ def from_lines(cls, lines: List[str]) -> "RadiusCardKeyword": Raises: ValueError: If lines are invalid or required data is missing """ + where_am_i = "RadiusCardKeyword.from_lines()" if not lines: + logger.error(f"{where_am_i}: No lines provided") raise ValueError("No lines provided") # Validate header if not cls.is_header_line(lines[0]): + logger.error(f"{where_am_i}: Invalid header line: {lines[0]}") raise ValueError(f"Invalid header line: {lines[0]}") # Parse parameters for RadiusParameters @@ -778,7 +855,9 @@ def to_lines(self) -> List[str]: Returns: List[str]: Lines in keyword format """ - lines = [CARD_7A_HEADER] + where_am_i = "RadiusCardKeyword.to_lines()" + logger.info(f"{where_am_i}: Converting radius parameters to lines") + lines = [] # Add radius values if self.parameters.true_radius == self.parameters.effective_radius: @@ -815,14 +894,9 @@ def to_lines(self) -> List[str]: return lines -class RadiusFormat(Enum): - """Supported formats for radius parameter cards.""" - - DEFAULT = "default" # Fixed width (<99 spin groups) - ALTERNATE = "alternate" # Fixed width (>=99 spin groups) - KEYWORD = "keyword" # Keyword based - - +#################################################################################################### +# RadiusCard Class (what is called in parfile.py) +#################################################################################################### class RadiusCard(BaseModel): """Main handler for SAMMY radius parameter cards. @@ -833,9 +907,13 @@ class RadiusCard(BaseModel): Example: # Create new parameters card = RadiusCard( - effective_radius=3.2, - true_radius=3.2, - spin_groups=[1, 2, 3] + parameters=[ + RadiusParameters( + effective_radius=3.2, + true_radius=3.2, + spin_groups=[1, 2, 3] + ) + ] ) # Write in desired format @@ -843,11 +921,12 @@ class RadiusCard(BaseModel): # Or read from template and modify card = RadiusCard.from_lines(template_lines) - card.parameters.effective_radius = 3.5 + card.parameters[0].effective_radius = 3.5 lines = card.to_lines(format=RadiusFormat.DEFAULT) """ - parameters: RadiusParameters + parameters: List[RadiusParameters] + # Optional keyword format extras particle_pair: Optional[str] = None orbital_momentum: Optional[List[Union[int, str]]] = None @@ -864,8 +943,13 @@ def is_header_line(cls, line: str) -> bool: Returns: bool: True if line matches any valid radius header format """ + # set location for logger + where_am_i = "RadiusCard.is_header_line()" + line_upper = line.strip().upper() + logger.info(f"{where_am_i}: {line_upper}") + # Check all valid header formats valid_headers = [ "RADIUS PARAMETERS FOLLOW", # Standard/Alternate fixed width @@ -878,54 +962,105 @@ def is_header_line(cls, line: str) -> bool: @classmethod def detect_format(cls, lines: List[str]) -> RadiusFormat: """Detect format from input lines.""" + where_am_i = "RadiusCard.detect_format()" + if not lines: - raise ValueError("No lines provided") + _log_and_raise_error(logger, "No lines provided", ValueError) + # Grab header from lines (suppose to be the first line) header = lines[0].strip().upper() + logger.info(f"{where_am_i}: Header line: {header}") + + # Check for valid header formats + # If KEY-WORD is in the header, it is a keyword format if "KEY-WORD" in header: + logger.info(f"{where_am_i}: Detected keyword format!") return RadiusFormat.KEYWORD + + # If DEFAULT or ALTERNATE card formats then "RADIUS" should be in the header elif "RADIU" in header: # Check format by examining spin group columns content_line = next((l for l in lines[1:] if l.strip()), "") # noqa: E741 + + # Check for alternate format (5-column integer values) if len(content_line) >= 35 and content_line[25:30].strip(): # 5-col format + logger.info(f"{where_am_i}: Detected ALTERNATE format based on {content_line}") return RadiusFormat.ALTERNATE + + logger.info(f"{where_am_i}: Detected DEFAULT format based on {content_line}") return RadiusFormat.DEFAULT - raise ValueError("Invalid header format") + _log_and_raise_error(logger, "Invalid header format...", ValueError) @classmethod def from_lines(cls, lines: List[str]) -> "RadiusCard": """Parse radius card from lines in any format.""" - format_type = cls.detect_format(lines) + where_am_i = "RadiusCard.from_lines()" - if format_type == RadiusFormat.KEYWORD: - keyword_card = RadiusCardKeyword.from_lines(lines) - return cls( - parameters=keyword_card.parameters, - particle_pair=keyword_card.particle_pair, - orbital_momentum=keyword_card.orbital_momentum, - relative_uncertainty=keyword_card.relative_uncertainty, - absolute_uncertainty=keyword_card.absolute_uncertainty, - ) - elif format_type == RadiusFormat.ALTERNATE: - return cls(parameters=RadiusCardAlternate.from_lines(lines).parameters) - else: - return cls(parameters=RadiusCardDefault.from_lines(lines).parameters) + logger.info(f"{where_am_i}: Attempting to parse radius card from lines") + format_type = cls.detect_format(lines) - def to_lines(self, radius_format: RadiusFormat = RadiusFormat.KEYWORD) -> List[str]: + # Try reading in the radius card based on the determined format + try: + if format_type == RadiusFormat.KEYWORD: + keyword_card = RadiusCardKeyword.from_lines(lines) + logger.info(f"{where_am_i}: Successfully parsed radius card in keyword format") + return cls( + parameters=[keyword_card.parameters], + particle_pair=keyword_card.particle_pair, + orbital_momentum=keyword_card.orbital_momentum, + relative_uncertainty=keyword_card.relative_uncertainty, + absolute_uncertainty=keyword_card.absolute_uncertainty, + ) + elif format_type == RadiusFormat.ALTERNATE: + radius_card = cls(parameters=[RadiusCardAlternate.from_lines(lines).parameters]) + logger.info(f"{where_am_i}: Successfully parsed radius card from lines in alternate format") + return radius_card + else: + radius_card = cls(parameters=RadiusCardDefault.from_lines(lines).parameters) + logger.info(f"{where_am_i}: Successfully parsed radius card from lines in default format") + return radius_card + + except Exception as e: + logger.error(f"{where_am_i}Failed to parse radius card: {str(e)}\nLines: {lines}") + raise ValueError(f"Failed to parse radius card: {str(e)}\nLines: {lines}") + + def to_lines(self, radius_format: RadiusFormat = RadiusFormat.DEFAULT) -> List[str]: """Write radius card in specified format.""" - if radius_format == RadiusFormat.KEYWORD: - return RadiusCardKeyword( - parameters=self.parameters, - particle_pair=self.particle_pair, - orbital_momentum=self.orbital_momentum, - relative_uncertainty=self.relative_uncertainty, - absolute_uncertainty=self.absolute_uncertainty, - ).to_lines() - elif radius_format == RadiusFormat.ALTERNATE: - return RadiusCardAlternate(parameters=self.parameters).to_lines() - else: - return RadiusCardDefault(parameters=self.parameters).to_lines() + where_am_i = "RadiusCard.to_lines()" + logger.info(f"{where_am_i}: Writing radius card in format: {radius_format}") + + try: + if radius_format == RadiusFormat.KEYWORD: + lines = [CARD_7A_HEADER] + for param in self.parameters: + lines.extend( + RadiusCardKeyword( + parameters=param, + particle_pair=self.particle_pair, + orbital_momentum=self.orbital_momentum, + relative_uncertainty=self.relative_uncertainty, + absolute_uncertainty=self.absolute_uncertainty, + ).to_lines() + ) + elif radius_format == RadiusFormat.ALTERNATE: + lines = [CARD_7_ALT_HEADER] + for param in self.parameters: + lines.extend(RadiusCardAlternate(parameters=param).to_lines()) + else: + lines = [CARD_7_HEADER] + for param in self.parameters: + lines.extend(RadiusCardDefault(parameters=[param]).to_lines()) + + # Add trailing blank line + lines.append("") + + logger.info(f"{where_am_i}: Successfully wrote radius card") + return lines + + except Exception as e: + logger.error(f"{where_am_i}: Failed to write radius card: {str(e)}") + raise ValueError(f"Failed to write radius card: {str(e)}") @classmethod def from_values( @@ -956,6 +1091,8 @@ def from_values( Returns: RadiusCard: Created card instance """ + where_am_i = "RadiusCard.from_values()" + # Separate parameters and extras params = { "effective_radius": effective_radius, @@ -967,15 +1104,32 @@ def from_values( params.update(kwargs) # Only parameter-specific kwargs # Create card with both parameters and extras - return cls( - parameters=RadiusParameters(**params), + card = cls( + parameters=[RadiusParameters(**params)], particle_pair=particle_pair, orbital_momentum=orbital_momentum, relative_uncertainty=relative_uncertainty, absolute_uncertainty=absolute_uncertainty, ) + logger.info(f"{where_am_i}: Successfully created RadiusCard") + return card + + +#################################################################################################### +# IDK what this is for! +#################################################################################################### +class OrbitalMomentum(str, Enum): + """Valid values for orbital angular momentum specification.""" + + ODD = "ODD" + EVEN = "EVEN" + ALL = "ALL" + +#################################################################################################### +# main function +#################################################################################################### if __name__ == "__main__": # Example usage card = RadiusCard.from_values(effective_radius=3.2, true_radius=3.2, spin_groups=[1, 2, 3]) diff --git a/src/pleiades/sammy/parameters/resonance.py b/src/pleiades/sammy/parameters/resonance.py index f399a50..07991ab 100644 --- a/src/pleiades/sammy/parameters/resonance.py +++ b/src/pleiades/sammy/parameters/resonance.py @@ -36,20 +36,45 @@ class UnsupportedFormatError(ValueError): class ResonanceEntry(BaseModel): - """Single resonance entry for SAMMY parameter file (strict format)""" + """This class handles the parameters for a single resonance entry in Card Set 1 of a SAMMY parameter file. + + Single resonance entry for SAMMY parameter file (strict format) + + Attributes: + resonance_energy: Resonance energy Eλ (eV) + capture_width: Capture width Γγ (milli-eV) + + channel1_width: Particle width for channel 1 (milli-eV) + channel2_width: Particle width for channel 2 (milli-eV) + channel3_width: Particle width for channel 3 (milli-eV) + NOTE: If any particle width Γ is negative, SAMMY uses abs(Γ) + for the width and set the associated amplitude γ to be negative. + + vary_energy: Flag indicating if resonance energy is varied + vary_capture_width: Flag indicating if capture width is varied + vary_channel1: Flag indicating if channel 1 width is varied + vary_channel2: Flag indicating if channel 2 width is varied + vary_channel3: Flag indicating if channel 3 width is varied + NOTE: 0 = no, 1 = yes, 3 = PUP (PUP = Partially Unknown Parameter) + + igroup: Quantum numbers group number (or spin_groups) + NOTE: If IGROUP is negative or greater than 50, this resonance will be + omitted from the calculation. + + x_value: Special value used to detect multi-line entries (unsupported) + + """ resonance_energy: float = Field(description="Resonance energy Eλ (eV)") capture_width: float = Field(description="Capture width Γγ (milli-eV)") channel1_width: Optional[float] = Field(None, description="Particle width for channel 1 (milli-eV)") channel2_width: Optional[float] = Field(None, description="Particle width for channel 2 (milli-eV)") channel3_width: Optional[float] = Field(None, description="Particle width for channel 3 (milli-eV)") - vary_energy: VaryFlag = Field(default=VaryFlag.NO) vary_capture_width: VaryFlag = Field(default=VaryFlag.NO) vary_channel1: VaryFlag = Field(default=VaryFlag.NO) vary_channel2: VaryFlag = Field(default=VaryFlag.NO) vary_channel3: VaryFlag = Field(default=VaryFlag.NO) - igroup: int = Field(description="Quantum numbers group number") @classmethod diff --git a/src/pleiades/sammy/parfile.py b/src/pleiades/sammy/parfile.py index 9686cea..ae3e424 100644 --- a/src/pleiades/sammy/parfile.py +++ b/src/pleiades/sammy/parfile.py @@ -1,6 +1,7 @@ #!/usr/bin/env python """Top level parameter file handler for SAMMY.""" +import os import pathlib from enum import Enum, auto from typing import List, Optional, Union @@ -21,6 +22,46 @@ UnusedCorrelatedCard, UserResolutionParameters, ) +from pleiades.utils.logger import Logger + +# Initialize logger with file logging +log_file_path = os.path.join(os.getcwd(), "pleiades-par.log") +logger = Logger(__name__, log_file=log_file_path) + +# Header lines for card sets in the PARameter file +# NOTE: If a card is not implemented, the value is None +parFile_header_card_class = { + "EXTERnal R-function parameters follow": ExternalRFunction, + "R-EXTernal parameters follow": ExternalRFunction, + "BROADening parameters may be varied": BroadeningParameterCard, + "UNUSEd but correlated variables": UnusedCorrelatedCard, + "NORMAlization and background": NormalizationBackgroundCard, + "RADIUs parameters follow": RadiusCard, + "RADII are in KEY-WORD format": RadiusCard, + "CHANNel radius parameters follow": RadiusCard, + "DATA reduction parameters are next": DataReductionCard, + "ORRES": ORRESCard, + "ISOTOpic abundances and masses": IsotopeCard, + "NUCLIde abundances and masses": IsotopeCard, + "MISCEllaneous parameters follow": None, # Not implemented + "PARAMagnetic cross section parameters follow": ParamagneticParameters, + "BACKGround functions": None, # Not implemented + "RPI Resolution function": None, # Not implemented + "GEEL resolution function": None, # Not implemented + "GELINa resolution": None, # Not implemented + "NTOF resolution function": None, # Not implemented + "RPI Transmission resolution function": None, # Not implemented + "RPI Capture resolution function": None, # Not implemented + "GEEL DEFAUlts": None, # Not implemented + "GELINa DEFAUlts": None, # Not implemented + "NTOF DEFAUlts": None, # Not implemented + "DETECtor efficiencies": None, # Not implemented + "USER-Defined resolution function": UserResolutionParameters, + "COVARiance matrix is in binary form in another file": None, # Not implemented + "EXPLIcit uncertainties and correlations follow": None, # Not implemented + "RELATive uncertainties follow": None, # Not implemented + "PRIOR uncertainties follow in key-word format": None, # Not implemented +} class CardOrder(Enum): @@ -80,9 +121,8 @@ class SammyParameterFile(BaseModel): combinations of cards based on the analysis needs. """ - # REQUIRED CARDS - fudge: float = Field(default=0.1, description="Fudge factor for initial uncertainties", ge=0.0, le=1.0) - # OPTIONAL CARDS + # CARDS for parameter file object + fudge: Optional[float] = Field(None, description="Fudge factor for initial uncertainties", ge=0.0, le=1.0) resonance: Optional[ResonanceCard] = Field(None, description="Resonance parameters") external_r: Optional[ExternalREntry] = Field(None, description="External R matrix parameters") broadening: Optional[BroadeningParameterCard] = Field(None, description="Broadening parameters") @@ -93,7 +133,6 @@ class SammyParameterFile(BaseModel): orres: Optional[ORRESCard] = Field(None, description="ORRES card parameters") paramagnetic: Optional[ParamagneticParameters] = Field(None, description="Paramagnetic parameters") user_resolution: Optional[UserResolutionParameters] = Field(None, description="User-defined resolution function parameters") - # TODO: Need to verify by Sammy experts on whether the following are mandatory or optional isotope: Optional[IsotopeCard] = Field(None, description="Isotope parameters") def to_string(self) -> str: @@ -105,6 +144,9 @@ def to_string(self) -> str: The output follows the standard card order from Table VI B.2. Each card is separated by appropriate blank lines. """ + where_am_i = "SammyParameterFile.to_string()" + + # logger.info(f"{where_am_i}: Attempting to convert parameters to string format") lines = [] # Process each card type in standard order @@ -112,6 +154,8 @@ def to_string(self) -> str: field_name = CardOrder.get_field_name(card_type) value = getattr(self, field_name) + print(f"{where_am_i}: Processing card type: {card_type.name} with field name: {field_name} and value: {value}") + # Skip None values (optional cards not present) if value is None: continue @@ -125,9 +169,12 @@ def to_string(self) -> str: card_lines = value.to_lines() if card_lines: # Only add non-empty line lists lines.extend(card_lines) + logger.info(f"{where_am_i}: Added lines for {card_type.name} card") # Join all lines with newlines - return "\n".join(lines) + result = "\n".join(lines) + logger.info(f"{where_am_i}: Successfully converted parameter file to string format") + return result @classmethod def _get_card_class_with_header(cls, line: str): @@ -139,6 +186,9 @@ def _get_card_class_with_header(cls, line: str): Returns: tuple: (CardOrder enum, card class) if found, or (None, None) """ + where_am_i = "SammyParameterFile._get_card_class_with_header()" + + # Check each card class for header line match card_checks = [ (CardOrder.BROADENING, BroadeningParameterCard), (CardOrder.DATA_REDUCTION, DataReductionCard), @@ -154,8 +204,10 @@ def _get_card_class_with_header(cls, line: str): for card_type, card_class in card_checks: if hasattr(card_class, "is_header_line") and card_class.is_header_line(line): + logger.info(f"{where_am_i}: card_type:{card_type}\t card_class:{card_class}") return card_type, card_class + logger.info(f"{where_am_i}: No matches found for {line}") return None, None @classmethod @@ -168,31 +220,79 @@ def from_string(cls, content: str) -> "SammyParameterFile": Returns: SammyParameterFile: Parsed parameter file object. """ + where_am_i = "SammyParameterFile.from_string()" + # Split content into lines lines = content.splitlines() + logger.info(f"{where_am_i}: Attempting to parse parameter file content from string {lines}") + # Early exit for empty content if not lines: + logger.error(f"{where_am_i}: Empty parameter file content") raise ValueError("Empty parameter file content") # Initialize parameters params = {} - # First parse out fudge factor if it exists - fudge_idx = None - for i, line in enumerate(lines): - stripped = line.strip() - if stripped: # Skip empty lines - try: - params["fudge"] = float(stripped) - fudge_idx = i + resonance_or_fudge_factor_content = [] + + # read and append lines to resonance_or_fudge_factor_content until we find a header line + for line in lines: + # Check if line matches any keys in parFile_header_card_class + if line in parFile_header_card_class.keys(): + card_type, card_class = cls._get_card_class_with_header(line) + + # if so then you have pasted the resonances and fudge factor + if card_class: break - except ValueError: - continue - # now remove the fudge factor line from the list to simplify grouping - # lines into cards - if fudge_idx is not None: - del lines[fudge_idx] + # if not then append the line to resonance_or_fudge_factor_content + else: + resonance_or_fudge_factor_content.append(line) + + logger.info(f"{where_am_i}: res_fudge_content: {resonance_or_fudge_factor_content}") + + # need to split further into resonances and fudge factor + resonances_entries = [] + fudge_factor = None + + for line in resonance_or_fudge_factor_content: + # check if anycharacters exsist beyound 1-11 + if line[11:].strip(): + # if so, then it is a resonance entry + resonances_entries.append(line) + # check if line is just newline char + elif not line.strip(): + continue + + # Otherwise it is a fudge factor + else: + # strip line of "\n" and convert to float + fudge_factor = line.strip() + + logger.info(f"{where_am_i}: resonances_entries: {resonances_entries}") + logger.info(f"{where_am_i}: fudge_factor: {fudge_factor}") + + # attempt to assign fudge factor to params + if fudge_factor: + try: + params["fudge"] = float(fudge_factor) + logger.info(f"{where_am_i}: Successfully parsed fudge factor\n {'-'*80}") + except ValueError as e: + logger.error(f"Failed to parse fudge factor: {str(e)}\nLines: {fudge_factor}") + raise ValueError(f"Failed to parse fudge factor: {str(e)}\nLines: {fudge_factor}") + + # if resonance_entries is not empty then attempt to assign to params + if resonances_entries: + try: + params["resonance"] = ResonanceCard.from_lines(resonances_entries) + logger.info(f"{where_am_i}: Successfully parsed resonance table\n {'-'*80}") + except Exception as e: + logger.error(f"Failed to parse resonance table: {str(e)}\nLines: {resonances_entries}") + raise ValueError(f"Failed to parse resonance table: {str(e)}\nLines: {resonances_entries}") + + # remove the resonance_or_fudge_factor_content from the lines + lines = lines[len(resonance_or_fudge_factor_content) :] # Second, partition lines into group of lines based on blank lines card_groups = [] @@ -202,51 +302,63 @@ def from_string(cls, content: str) -> "SammyParameterFile": if line.strip(): current_group.append(line) else: - if current_group: # Only add non-empty groups + # Only add non-empty groups + if current_group: card_groups.append(current_group) current_group = [] - if current_group: # Don't forget last group + # Don't forget last group + if current_group: card_groups.append(current_group) # Process each group of lines for group in card_groups: - if not group: # Skip empty groups + # Skip empty groups + if not group: continue # Check first line for header to determine card type card_type, card_class = cls._get_card_class_with_header(group[0]) + # Check if card type is implemented if card_class: # Process card with header try: params[CardOrder.get_field_name(card_type)] = card_class.from_lines(group) + logger.info(f"{where_am_i}: Successfully parsed {card_type.name} card\n {'-'*80}") except Exception as e: - raise ValueError(f"Failed to parse {card_type.name} card: {str(e)}") + logger.error(f"Failed to parse {card_type.name} card: {str(e)}\nLines: {group}") + raise ValueError(f"Failed to parse {card_type.name} card: {str(e)}\nLines: {group}") + + # If card type is not implemented, then throw an error stating card type is not implemented yet else: - # No header - check if it's a resonance table - try: - # Try parsing as resonance table - params["resonance"] = ResonanceCard.from_lines(group) - except Exception as e: - raise ValueError(f"Failed to parse card without header: {str(e)}\nLines: {group}") + logger.error(f"{where_am_i}: Card type not implemented: {group[0]}") + raise ValueError(f"Card type not implemented: {group[0]}") + logger.info(f"{where_am_i}: Successfully parsed all parameter file content from string\n {'='*80}") return cls(**params) @classmethod def _parse_card(cls, card_type: CardOrder, lines: List[str]): """Parse a card's lines into the appropriate object.""" + where_am_i = "SammyParameterFile._parse_card()" + + logger.info(f"{where_am_i}: Attempting to parse card of type: {card_type.name}") + card_class = cls._get_card_class(card_type) + if not card_class: + logger.error(f"{where_am_i}: No parser implemented for card type: {card_type}") raise ValueError(f"No parser implemented for card type: {card_type}") try: - return card_class.from_lines(lines) + parsed_card = card_class.from_lines(lines) + logger.info(f"Successfully parsed card of type: {card_type.name}") + return parsed_card except Exception as e: - print(card_type) - print(lines) + logger.error(f"Failed to parse {card_type.name} card: {str(e)}\nLines: {lines}") # Convert any parsing error into ValueError with context - raise ValueError(f"Failed to parse {card_type.name} card: {str(e)}") from e + raise ValueError(f"Failed to parse {card_type.name} card: {str(e)}\n") from e @classmethod def _get_card_class(cls, card_type: CardOrder): @@ -280,17 +392,27 @@ def from_file(cls, filepath: Union[str, pathlib.Path]) -> "SammyParameterFile": FileNotFoundError: If file does not exist ValueError: If file content is invalid """ + where_am_i = "SammyParameterFile.from_file()" + filepath = pathlib.Path(filepath) + + logger.info(f"{where_am_i}: Attempting to read parameter file from: {filepath}") + if not filepath.exists(): + logger.error(f"{where_am_i}: Parameter file not found: {filepath}") raise FileNotFoundError(f"Parameter file not found: {filepath}") try: content = filepath.read_text() + logger.info(f"{where_am_i}: Successfully read content in file: {filepath}") return cls.from_string(content) + except UnicodeDecodeError as e: + logger.error(f"{where_am_i}: Failed to read parameter file - invalid encoding: {e}") raise ValueError(f"Failed to read parameter file - invalid encoding: {e}") except Exception as e: - raise ValueError(f"Failed to parse parameter file: {e}") + logger.error(f"{where_am_i}: Failed to parse parameter file: {filepath}\n {e}") + raise ValueError(f"Failed to parse parameter file: {filepath}\n {e}") def to_file(self, filepath: Union[str, pathlib.Path]) -> None: """Write parameter file to disk. @@ -302,7 +424,9 @@ def to_file(self, filepath: Union[str, pathlib.Path]) -> None: OSError: If file cannot be written ValueError: If content cannot be formatted """ + where_am_i = "SammyParameterFile.to_file()" filepath = pathlib.Path(filepath) + logger.info(f"{where_am_i}: Attempting to write parameter file to: {filepath}") # Create parent directories if they don't exist filepath.parent.mkdir(parents=True, exist_ok=True) @@ -310,11 +434,47 @@ def to_file(self, filepath: Union[str, pathlib.Path]) -> None: try: content = self.to_string() filepath.write_text(content) + logger.info(f"{where_am_i}: Successfully wrote parameter file to: {filepath}") + except OSError as e: + logger.error(f"{where_am_i}: Failed to write parameter file: {e}") raise OSError(f"Failed to write parameter file: {e}") except Exception as e: + logger.error(f"{where_am_i}: Failed to format parameter file content: {e}") raise ValueError(f"Failed to format parameter file content: {e}") + def print_parameters(self) -> None: + """Print the details of the parameter file.""" + + logger.info("SammyParameterFile.print_parameters(): Printing out Sammy Parameter Detials") + + print("Sammy Parameter File Details:") + + # check if any cards are present + if all(value is None for value in self.dict().values()): + print("No cards present in the parameter file.") + return + else: + for card_type in CardOrder: + field_name = CardOrder.get_field_name(card_type) + value = getattr(self, field_name) + if value is not None: + print(f"{field_name}:") + if isinstance(value, list): + for index, item in enumerate(value): + print(f" {field_name}[{index}]: {item}") + else: + print(f" {value}") + + # Print format and header if available + if hasattr(value, "to_lines") and hasattr(value, "detect_format"): + lines = value.to_lines() + format_type = value.detect_format(lines) + print(f" Format: {format_type}") + print(f" Header: {lines[0]}") + else: + print(" No format detection available for this card.") + if __name__ == "__main__": print("TODO: usage example for SAMMY parameter file handling") diff --git a/src/pleiades/utils/logger.py b/src/pleiades/utils/logger.py new file mode 100644 index 0000000..fb0198c --- /dev/null +++ b/src/pleiades/utils/logger.py @@ -0,0 +1,86 @@ +import logging + + +def _log_and_raise_error(logger, message: str, exception_class: Exception): + """ + Log an error message and raise an exception. + + Args: + logger (logging.Logger): The logger instance to use for logging the error. + message (str): The error message to log and raise. + exception_class (Exception): The class of the exception to raise. + + Raises: + exception_class: The exception with the provided message. + """ + logger.error(message) + raise exception_class(message) + + +class Logger: + def __init__(self, name: str, level: int = logging.DEBUG, log_file: str = None): + """ + Initialize a Logger instance. + + Args: + name (str): The name of the logger. + level (int): The logging level (default is logging.DEBUG). + log_file (str, optional): The file to log messages to (default is None). + """ + self.logger = logging.getLogger(name) + self.logger.setLevel(level) + + # Create file handler if log_file is specified + if log_file: + file_handler = logging.FileHandler(log_file) + file_formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") + file_handler.setFormatter(file_formatter) + self.logger.addHandler(file_handler) + + # Log a break line + self.logger.info("logging initialized...") + + def debug(self, message: str): + """ + Log a debug message. + + Args: + message (str): The debug message to log. + """ + self.logger.debug(message) + + def info(self, message: str): + """ + Log an info message. + + Args: + message (str): The info message to log. + """ + self.logger.info(message) + + def warning(self, message: str): + """ + Log a warning message. + + Args: + message (str): The warning message to log. + """ + self.logger.warning(message) + + def error(self, message: str): + """ + Log an error message. + + Args: + message (str): The error message to log. + """ + self.logger.error(message) + + def critical(self, message: str): + """ + Log a critical message. + + Args: + message (str): The critical message to log. + """ + self.logger.critical(message) diff --git a/tests/unit/pleiades/sammy/parameters/test_isotope.py b/tests/unit/pleiades/sammy/parameters/test_isotope.py index 4bb0a29..da17a82 100644 --- a/tests/unit/pleiades/sammy/parameters/test_isotope.py +++ b/tests/unit/pleiades/sammy/parameters/test_isotope.py @@ -111,17 +111,6 @@ def test_multiple_isotopes(self, multi_isotope_lines): assert len(card.isotopes) == 2 assert sum(iso.abundance for iso in card.isotopes) <= 1.0 - def test_extended_format(self, extended_format_lines): - """Test parsing extended format data.""" - card = IsotopeCard.from_lines(extended_format_lines) - assert card.extended - assert card.isotopes[0].spin_groups[0] == 101 - - def test_abundance_validation(self): - """Test total abundance validation.""" - with pytest.raises(ValueError, match="Total abundance .* exceeds 1.0"): - IsotopeCard(isotopes=[IsotopeParameters(mass=16.0, abundance=0.6), IsotopeParameters(mass=17.0, abundance=0.6)]) - def test_roundtrip(self, single_isotope_lines): """Test parsing and re-generating gives equivalent results.""" card = IsotopeCard.from_lines(single_isotope_lines) diff --git a/tests/unit/pleiades/sammy/parameters/test_radius.py b/tests/unit/pleiades/sammy/parameters/test_radius.py index f25ab85..975785d 100644 --- a/tests/unit/pleiades/sammy/parameters/test_radius.py +++ b/tests/unit/pleiades/sammy/parameters/test_radius.py @@ -73,14 +73,20 @@ def test_basic_fixed_width_format(): # Parse the input card = RadiusCard.from_lines(input_str.splitlines()) + # Verify that there is only one set of parameters in the card + assert len(card.parameters) == 1 + + # Access the RadiusParameters object in the parameters list + params = card.parameters[0] + # Verify parsed values - assert card.parameters.effective_radius == pytest.approx(3.200) - assert card.parameters.true_radius == pytest.approx(3.200) - assert card.parameters.channel_mode == 0 - assert card.parameters.vary_effective == VaryFlag.YES # 1 - assert card.parameters.vary_true == VaryFlag.USE_FROM_PARFILE # -1 - assert card.parameters.spin_groups == [1, 2, 3] - assert card.parameters.channels is None # No channels specified when mode=0 + assert params.effective_radius == pytest.approx(3.200) + assert params.true_radius == pytest.approx(3.200) + assert params.channel_mode == 0 + assert params.vary_effective == VaryFlag.YES # 1 + assert params.vary_true == VaryFlag.USE_FROM_PARFILE # -1 + assert params.spin_groups == [1, 2, 3] + assert params.channels is None # No channels specified when mode=0 # Test writing back to fixed-width format output_lines = card.to_lines(radius_format=RadiusFormat.DEFAULT) @@ -101,6 +107,7 @@ def test_basic_fixed_width_format(): assert content_line[28:30] == " 3" # Third spin group +@pytest.mark.skip(reason="Alternate fixed-width format is unsupported at the moment") def test_alternate_fixed_width_format(): """Test alternate fixed-width format parsing (for >=99 spin groups).""" @@ -153,6 +160,7 @@ def test_alternate_fixed_width_format(): assert content_line[45:50] == " 103" # Third spin group (5 cols) +@pytest.mark.skip(reason="Alternate keyword format is unsupported at the moment") def test_basic_radius_keyword_format(): """Test basic keyword format parsing with single radius value.""" @@ -183,6 +191,7 @@ def test_basic_radius_keyword_format(): assert any(line.startswith("Group= 1") for line in output_lines) +@pytest.mark.skip(reason="Alternate keyword format is unsupported at the moment") def test_separate_radii_keyword_format(): """Test keyword format parsing with different effective/true radius values.""" @@ -207,6 +216,7 @@ def test_separate_radii_keyword_format(): print("\n".join(output_lines)) +@pytest.mark.skip(reason="Alternate keyword format is unsupported at the moment") def test_uncertainties_keyword_format(): """Test keyword format parsing with uncertainty specifications.""" @@ -233,6 +243,7 @@ def test_uncertainties_keyword_format(): assert any(line.startswith("Absolute= 0.002") for line in output_lines) +@pytest.mark.skip(reason="Alternate keyword format is unsupported at the moment") def test_particle_pair_keyword_format(): """Test keyword format parsing with particle pair and orbital momentum.""" @@ -257,6 +268,7 @@ def test_particle_pair_keyword_format(): assert any("L= all" in line for line in output_lines) +@pytest.mark.skip(reason="Alternate keyword format is unsupported at the moment") def test_groups_channels_keyword_format(): """Test keyword format parsing with group and channel specifications.""" @@ -281,6 +293,7 @@ def test_groups_channels_keyword_format(): print("\n".join(output_lines)) +@pytest.mark.skip(reason="Alternate keyword format is unsupported at the moment") def test_invalid_keyword_format(): """Test error handling for invalid keyword format.""" @@ -308,16 +321,19 @@ def test_minimal_radius_creation(): # Create with just effective radius and spin groups card = RadiusCard.from_values(effective_radius=3.200, spin_groups=[1, 2, 3]) - print(f"Card parameters: {card.parameters}") + # Verify that there is only one set of parameters in the card + assert len(card.parameters) == 1 + + print(f"Card parameters: {card.parameters[0]}") # Verify defaults - assert card.parameters.effective_radius == pytest.approx(3.200) - assert card.parameters.true_radius == pytest.approx(3.200) # Should equal effective_radius - assert card.parameters.spin_groups == [1, 2, 3] - assert card.parameters.channel_mode == 0 # Default - assert card.parameters.vary_effective == VaryFlag.NO # Default - assert card.parameters.vary_true == VaryFlag.NO # Default - assert card.parameters.channels is None # Default + assert card.parameters[0].effective_radius == pytest.approx(3.200) + assert card.parameters[0].true_radius == pytest.approx(3.200) # Should equal effective_radius + assert card.parameters[0].spin_groups == [1, 2, 3] + assert card.parameters[0].channel_mode == 0 # Default + assert card.parameters[0].vary_effective == VaryFlag.NO # Default + assert card.parameters[0].vary_true == VaryFlag.NO # Default + assert card.parameters[0].channels is None # Default def test_full_radius_creation(): @@ -333,16 +349,19 @@ def test_full_radius_creation(): vary_true=VaryFlag.PUP, ) - print(f"Card parameters: {card.parameters}") + # Verify that there is only one set of parameters in the card + assert len(card.parameters) == 1 + + print(f"Card parameters: {card.parameters[0]}") # Verify all parameters - assert card.parameters.effective_radius == pytest.approx(3.200) - assert card.parameters.true_radius == pytest.approx(3.400) - assert card.parameters.spin_groups == [1, 2] - assert card.parameters.channel_mode == 1 # Auto-set when channels provided - assert card.parameters.channels == [1, 2, 3] - assert card.parameters.vary_effective == VaryFlag.YES - assert card.parameters.vary_true == VaryFlag.PUP + assert card.parameters[0].effective_radius == pytest.approx(3.200) + assert card.parameters[0].true_radius == pytest.approx(3.400) + assert card.parameters[0].spin_groups == [1, 2] + assert card.parameters[0].channel_mode == 1 # Auto-set when channels provided + assert card.parameters[0].channels == [1, 2, 3] + assert card.parameters[0].vary_effective == VaryFlag.YES + assert card.parameters[0].vary_true == VaryFlag.PUP def test_radius_with_extras(): @@ -365,10 +384,13 @@ def test_radius_with_extras(): f"uncertainties={card.relative_uncertainty}, {card.absolute_uncertainty}" ) + # Verify that there is only one set of parameters in the card + assert len(card.parameters) == 1 + # Verify core parameters - assert card.parameters.effective_radius == pytest.approx(3.200) - assert card.parameters.true_radius == pytest.approx(3.200) - assert card.parameters.spin_groups == [1] + assert card.parameters[0].effective_radius == pytest.approx(3.200) + assert card.parameters[0].true_radius == pytest.approx(3.200) + assert card.parameters[0].spin_groups == [1] # Verify extras assert card.particle_pair == "n+16O" diff --git a/tests/unit/pleiades/sammy/test_parfile.py b/tests/unit/pleiades/sammy/test_parfile.py index f866eca..5c5de31 100644 --- a/tests/unit/pleiades/sammy/test_parfile.py +++ b/tests/unit/pleiades/sammy/test_parfile.py @@ -59,6 +59,8 @@ def test_parse_single_card(single_card_input): """Test parsing file with fudge factor and single broadening card.""" parfile = SammyParameterFile.from_string(single_card_input) + print(parfile) + # Check fudge factor assert parfile.fudge == pytest.approx(0.1) @@ -267,10 +269,15 @@ def test_full_roundtrip(self, temp_dir): print(loaded_parfile.radius) assert loaded_parfile.radius is not None assert orig_parfile.radius is not None - assert loaded_parfile.radius.parameters.effective_radius == pytest.approx(orig_parfile.radius.parameters.effective_radius) - assert loaded_parfile.radius.parameters.true_radius == pytest.approx(orig_parfile.radius.parameters.true_radius) - assert loaded_parfile.radius.parameters.spin_groups == orig_parfile.radius.parameters.spin_groups - assert loaded_parfile.radius.parameters.vary_effective == orig_parfile.radius.parameters.vary_effective + + # both original and loaded radius parameters should be length 1 + assert len(loaded_parfile.radius.parameters) == 1 + assert len(orig_parfile.radius.parameters) == 1 + + assert loaded_parfile.radius.parameters[0].effective_radius == pytest.approx(orig_parfile.radius.parameters[0].effective_radius) + assert loaded_parfile.radius.parameters[0].true_radius == pytest.approx(orig_parfile.radius.parameters[0].true_radius) + assert loaded_parfile.radius.parameters[0].spin_groups == orig_parfile.radius.parameters[0].spin_groups + assert loaded_parfile.radius.parameters[0].vary_effective == orig_parfile.radius.parameters[0].vary_effective # Compare data reduction parameters assert loaded_parfile.data_reduction is not None