restructure scienta-PEAK-ibw update

[lukaspie]

Summary by Sourcery

Update the Scienta parser to support newer .ibw files and improve data handling. Flatten nested dictionaries within the metadata for easier access. Standardize energy scales and units. Add support for exporting axes data for plotting. Update example data and identifiers.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request restructures the Scienta PEAK IBW update by refactoring parser logic, updating data mapping and unit handling, and introducing JSON schema validation for PEAK metadata. Major changes include reorganizing parser classes into abstract and version-specific implementations, refactoring how raw spectrum data is processed and flattened, and streamlining unit mappings across the project.

Updated class diagram for Scienta Parser refactoring

classDiagram
    %% Base mapping class
    class XPSMapper {
      <<abstract>>
    }

    %% MapperScienta inherits from XPSMapper and uses parser logic
    class MapperScienta {
      - _xps_dict : dict
      + construct_data()
      + _select_parser()
      + _update_xps_dict_with_spectrum(spectrum: Dict)
    }
    XPSMapper <|-- MapperScienta

    %% Abstract parser class
    class ScientaIgorParser {
      <<abstract>>
      + parse_file(file: Union[str, Path])
      + _parse_unit(bunit: bytes) : List[Tuple[str, Optional[str]]]
      + axis_for_dim(wave_header: Dict, dim: int) : np.ndarray
      + axis_units_for_dim(wave_header: Dict, dim: int) : str
      # _parse_note(bnote: bytes) : Dict
      # _parse_region_metadata(region_id: int, notes: Dict) : Dict
    }

    %% Parser implementation for old data export
    class ScientaIgorParserOld {
      + _parse_note(bnote: bytes) : Dict
      + _parse_region_metadata(region_id: int, notes: Dict) : Dict
    }
    ScientaIgorParser <|-- ScientaIgorParserOld

    %% Parser implementation for PEAK software export
    class ScientaIgorParserPEAK {
      + _parse_note(bnote: bytes) : Dict
      + _parse_region_metadata(region_id: int, notes: Dict) : Dict
    }
    ScientaIgorParser <|-- ScientaIgorParserPEAK

    %% Utility function as a helper (not a class but represented for clarity)
    class flatten_dict {
      <<utility>>
      + flatten_dict(d: Dict, parent_key: str, sep: str) : Dict
    }

    %% Relationships
    MapperScienta ..> ScientaIgorParser : uses
    MapperScienta ..> flatten_dict : calls

Loading

File-Level Changes

Change	Details	Files
Refactoring and improvements in the scienta_reader module	Introduced a new utility function to flatten nested dictionaries for easier key management. Added logging configuration via a dedicated logger. Reworked the _select_parser method to use a try-except block that distinguishes between the PEAK and legacy IBW formats. Updated the construct_data and _update_xps_dict_with_spectrum methods to remove hard-coded mapping templates, instead iterating over spectrum data dynamically. Modified handling of energy axis and intensity arrays: replaced direct use of 'energy' with generalized 'axes' and improved data array assignment.	src/pynxtools_xps/scienta/scienta_reader.py
Enhancements to parser abstractions and implementations	Changed the base ScientaIgorParser class to an abstract class (using ABC), requiring implementation of parsing methods. Introduced two distinct parser implementations: one for PEAK exports (ScientaIgorParserPEAK) and one legacy version (ScientaIgorParserOld). Rewrote the _parse_note methods so that the PEAK parser validates against a JSON schema, while the legacy parser handles JSON decoding flexibly. Updated the _parse_unit method to return a list of label-unit tuples using regex, supporting multiple unit formats.	src/pynxtools_xps/scienta/scienta_reader.py src/pynxtools_xps/scienta/scienta_data_model.py
Addition of JSON schema for Scienta PEAK metadata	Defined a comprehensive JSON schema (scienta_igor_peak_schema) for validating PEAK export metadata. Removed obsolete dataclass definitions unnecessary for the new PEAK format.	src/pynxtools_xps/scienta/scienta_data_model.py
Streamlining unit mappings	Simplified the UNIT mapping keys in the scienta_mappings module by removing grouped prefixes. Ensured consistency across unit assignments in the data conversion and mapping functions.	src/pynxtools_xps/scienta/scienta_mappings.py
Enhancements in data extraction in the reader module	Extended the get_signals function to include 'axes' alongside energy channels. Modified the get_data function to handle extraction of axes data correctly from xarray coordinates. Added fallback handling for cases where a KeyError might occur when retrieving axis information.	src/pynxtools_xps/reader.py
Minor configuration and example updates	Updated instrument and sample identifiers in the example YAML file for clarity and consistency. Adjusted the instrument identifier in the Scienta configuration JSON file.	examples/scienta/ibw/eln_data_scienta_ibw.yaml src/pynxtools_xps/config/config_scienta.json

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