CasaXPS data analysis results parsing

[lukaspie]

This implements parsing the data analysis as performed in CasaXPS to fill the NXfit group in the NeXus file. The resulting file (tests/data/vms_analysis/vms_analysis_ref.nxs) looks like this:

Summary by Sourcery

Implement parsing of CasaXPS data analysis results to populate the NXfit group in NeXus files. Store peak fitting parameters, including regions, components, backgrounds, and atomic concentrations, in the NXxps structure.

New Features:

• Parse CasaXPS analysis results, including peak fitting parameters and atomic concentrations, and store them in the NXfit group within NeXus files, adhering to the NXxps application definition.

Tests:

• Added a reference NeXus file containing CasaXPS analysis results.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request implements parsing of data analysis results from CasaXPS, which are stored in the VAMAS comments, and maps them to the NXfit group in the NeXus file. It also includes a new reader for TXT files exported from CasaXPS.

Sequence diagram for CasaXPS data analysis parsing

sequenceDiagram
    participant VamasMapper
    participant CasaProcess
    participant Region
    participant Component

    VamasMapper->>CasaProcess: process_comments(comment_list)
    CasaProcess->>Region: calculate_background(x, y)
    Region-->>CasaProcess: background data
    CasaProcess->>Component: calculate_lineshape(x)
    Component-->>CasaProcess: peak data
    CasaProcess->>VamasMapper: flattened_metadata()
    VamasMapper->>NXfit: map data to NXfit group

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Class diagram for peak fitting and background models

classDiagram
    class Peak {
        +float position
        +float width
        +float area
        +__init__(position, width, area)
    }

    class Gaussian {
        +calc_lineshape(x)
        +formula()
    }

    class Lorentzian {
        +calc_lineshape(x)
        +formula()
    }

    class GaussianLorentzianSum {
        +float fraction_gauss
        +calc_lineshape(x)
        +formula()
    }

    class GaussianLorentzianProduct {
        +float fraction_gauss
        +calc_lineshape(x)
        +formula()
    }

    class DoniachSunjic {
        +float beta
        +calc_lineshape(x)
        +formula()
    }

    Peak <|-- Gaussian
    Peak <|-- Lorentzian
    Peak <|-- GaussianLorentzianSum
    Peak <|-- GaussianLorentzianProduct
    Peak <|-- DoniachSunjic

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File-Level Changes

Change	Details	Files
Implements parsing of CasaXPS data analysis results from VAMAS comments.	Adds a new class CasaProcess to parse CasaXPS data analysis results. Adds classes for different CasaXPS data analysis parameters, such as CasaEnergyCalibration, CasaIntensityCalibration, CasaRegion, and CasaComponent. Updates the VamasMapper class to parse the CasaXPS data analysis results and map them to the NXfit group. Updates the XPSReader class to handle the new CasaXPS data analysis results. Adds documentation for the new CasaXPS data analysis results parsing. Adds a new test case for the CasaXPS data analysis results parsing. Adds a new example for the CasaXPS data analysis results parsing. Adds a new script to regenerate the reference files for the CasaXPS data analysis results parsing. Adds a new script to regenerate the examples for the CasaXPS data analysis results parsing. Adds a new script to regenerate the examples for the CasaXPS data analysis results parsing without documentation. Adds a new script to generate the reference JSON files for the CasaXPS data analysis results parsing. Adds a new example ELN file for the CasaXPS data analysis results parsing. Adds a new test ELN file for the CasaXPS data analysis results parsing. Adds a new module for the models used in the CasaXPS data analysis results parsing. Adds a new README file for the CasaXPS data analysis results parsing example. Adds a new example VAMAS file for the CasaXPS data analysis results parsing. Adds a new example CSV file for the CasaXPS data analysis results parsing. Adds a new test VAMAS file for the CasaXPS data analysis results parsing. Adds a new test TXT file for the CasaXPS data analysis results parsing. Adds a new test CSV file for the CasaXPS data analysis results parsing. Adds new classes for the different lineshapes used in the CasaXPS data analysis results parsing. Adds new classes for the different backgrounds used in the CasaXPS data analysis results parsing.	src/pynxtools_xps/vms/vamas.py src/pynxtools_xps/vms/casa_data_model.py src/pynxtools_xps/vms/vamas_comment_handler.py src/pynxtools_xps/reader.py docs/explanation/data_processing.md docs/reference/vms.md tests/test_reader.py scripts/regenerate_ref_nxs_files.sh scripts/regenerate_examples.sh scripts/regenerate_examples_undocumented.sh scripts/generate_ref_comments_jsons.py examples/vms/data_analysis/eln.yaml tests/data/vms_analysis/eln.yaml src/pynxtools_xps/models/__init__.py examples/vms/data_analysis/README.md examples/vms/data_analysis/FeO_analyzed.vms examples/vms/data_analysis/FeO_analyzed_results.csv tests/data/vms_analysis/FeO_analyzed.vms tests/data/vms_analysis/FeO_analyzed_lineshapes_cols.txt tests/data/vms_analysis/FeO_analyzed_results.csv src/pynxtools_xps/models/lineshapes.py src/pynxtools_xps/models/backgrounds.py
Adds a new reader for TXT files exported from CasaXPS.	Adds a new class TxtMapperVamasExport to parse TXT files exported from CasaXPS. Adds a new class TextParserRows to parse TXT files exported from CasaXPS using the 'Rows of Tables' option. Adds a new class TextParserColumns to parse TXT files exported from CasaXPS using the 'Columns of Tables' option. Updates the XPSReader class to handle the new TXT files exported from CasaXPS. Adds a new README file for the TXT export example. Adds a new example TXT file for the TXT export example. Adds a new script to regenerate the examples for the TXT export example. Adds a new script to regenerate the examples for the TXT export example without documentation.	src/pynxtools_xps/vms/vamas_export.py src/pynxtools_xps/reader.py examples/vms/txt_export/README.md examples/vms/vms_txt_export.txt scripts/regenerate_examples.sh scripts/regenerate_examples_undocumented.sh
Adds a new reader for CSV files exported from CasaXPS.	Adds a new class CsvMapperVamasResult to parse CSV files exported from CasaXPS. Adds a new class CsvResultParser to parse CSV files exported from CasaXPS. Updates the XPSReader class to handle the new CSV files exported from CasaXPS.	src/pynxtools_xps/vms/vamas_export.py src/pynxtools_xps/reader.py
Adds a new function to check for multiple file extensions.	Adds a new function _check_multiple_extensions to check for multiple file extensions.	src/pynxtools_xps/reader.py
Adds a new parameter to the XPSReader to overwrite keys.	Adds a new parameter overwrite_keys to the XPSReader class.	src/pynxtools_xps/reader.py
Adds a new function to convert from kinetic to binding energy.	Adds a new function convert_to_binding_energy_scale to the VamasBlock class.	src/pynxtools_xps/vms/vamas_data_model.py
Adds a new function to split a string after the leading letters.	Adds a new function split_after_letters to split a string after the leading letters.	src/pynxtools_xps/vms/casa_data_model.py
Adds a new function to handle repetitions in a list of strings.	Adds a new function handle_repetitions to handle repetitions in a list of strings.	src/pynxtools_xps/vms/vamas_export.py
Adds a new function to select items from a list according to a specified pattern.	Adds a new function select_from_list to select items from a list according to a specified pattern.	src/pynxtools_xps/vms/vamas_export.py
Adds a new function to map a list of header strings to their corresponding keys.	Adds a new function get_dict_keys to map a list of header strings to their corresponding keys.	src/pynxtools_xps/vms/vamas_export.py
Removes the root path from the XPSMapper class.	Removes the _root_path attribute from the XPSMapper class.	src/pynxtools_xps/reader_utils.py
Adds a new function to align name parts.	Adds a new function align_name_part to align name parts.	src/pynxtools_xps/reader_utils.py
Updates the config file for the VAMAS reader.	Updates the config file for the VAMAS reader.	src/pynxtools_xps/config/config_vms.json
Removes the config file for the TXT VAMAS export reader.	Removes the config file for the TXT VAMAS export reader.	src/pynxtools_xps/config/config_txt_vamas_export.json
Removes the TXT VAMAS export reader.	Removes the TXT VAMAS export reader.	src/pynxtools_xps/vms/txt_vamas_export.py

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[sourcery-ai]

Hey @lukaspie - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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