PyOptik 1.8.0.post0__tar.gz → 1.8.2.post0__tar.gz

{pyoptik-1.8.0.post0 → pyoptik-1.8.2.post0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOptik
-Version: 1.8.0.post0
+Version: 1.8.2.post0
 Summary: A package for refractive index values.
 Author-email: Martin Poinsinet de Sivry-Houle <martin.poinsinet.de.sivry@gmail.com>
 License: MIT License
@@ -60,26 +60,27 @@ Requires-Dist: pydata-sphinx-theme==0.14.1; extra == "documentation"
 PyOptik
 =======
 
-PyOptik is a powerful Python tool designed to import refractive indexes and extinction coefficients for various materials across different wavelengths. The data provided by PyOptik can be used in numerous applications, including simulating light interactions with particles. All data is sourced from the reputable RefractiveIndex.INFO database.
+PyOptik is a Python tool designed to import refractive indexes and extinction coefficients for various materials across different wavelengths. The data provided by PyOptik can be used in numerous applications, including simulating light interactions with particles. All data is sourced from the reputable RefractiveIndex.INFO database.
 
 |logo|
 
 .. list-table::
-   :widths: 10 25 25 25
+   :widths: 10 25 25
    :header-rows: 1
 
+   * - Meta
+     - |python|
+     - |docs|
    * - Testing
      - |ci/cd|
      - |coverage|
-     -
-   * - Package
+   * - PyPi
      - |PyPi|
      - |PyPi_download|
+   * - Anaconda
      - |anaconda|
-   * - Meta
-     - |python|
-     - |docs|
-     -
+     - |anaconda_download|
+
 
 Features
 ********
@@ -119,10 +120,10 @@ In this example, we will download the `others` category of materials and remove
 
 .. code:: python
 
-   from PyOptik.utils import build_library
+   from PyOptik import MaterialBank
 
-   # Download the 'others' category and remove previous files
-   build_library('others', remove_previous=True)
+   # Download the 'classics' category and remove previous files
+   MaterialBank.build_library('classics', remove_previous=True)
 
 **Available Categories:**
 
@@ -131,14 +132,14 @@ To download materials from another category, simply pass the category name as an
 .. code:: python
 
    # Download materials from the 'glasses' category
-   build_library('glasses')
+   MaterialBank.build_library('glasses')
 
 To download all material categories at once:
 
 .. code:: python
 
    # Download all available material categories
-   build_library('all')
+   MaterialBank.build_library('all')
 
 You can also set the `remove_previous` parameter to `True` to remove old data before downloading new material data.
 
@@ -247,11 +248,14 @@ As of 2024, PyOptik is still under development. If you would like to collaborate
 **Email**: `martin.poinsinet.de.sivry@gmail.com <mailto:martin.poinsinet.de.sivry@gmail.com?subject=PyOptik>`_
 
 .. |python| image:: https://img.shields.io/pypi/pyversions/pyoptik.svg
+   :alt: Python
    :target: https://www.python.org/
 
 .. |logo| image:: https://github.com/MartinPdeS/PyOptik/raw/master/docs/images/logo.png
+   :alt: PyOptik logo
 
 .. |example_bk7| image:: https://github.com/MartinPdeS/PyOptik/raw/master/docs/images/example_bk7.png
+   :alt: PyOptik example: BK7
    :target: https://github.com/MartinPdeS/PyOptik/blob/master/docs/images/example_bk7.png
 
 .. |docs| image:: https://github.com/martinpdes/pyoptik/actions/workflows/deploy_documentation.yml/badge.svg
@@ -263,14 +267,21 @@ As of 2024, PyOptik is still under development. If you would like to collaborate
    :alt: Unittest Status
 
 .. |PyPi| image:: https://badge.fury.io/py/pyoptik.svg
+   :alt: PyPi version
    :target: https://badge.fury.io/py/pyoptik
 
 .. |PyPi_download| image:: https://img.shields.io/pypi/dm/pyoptik.svg
+   :alt: PyPi version
    :target: https://pypistats.org/packages/pyoptik
 
+.. |anaconda_download| image:: https://anaconda.org/martinpdes/pyoptik/badges/downloads.svg
+   :alt: Anaconda downloads
+   :target: https://anaconda.org/martinpdes/pyoptik
+
 .. |coverage| image:: https://raw.githubusercontent.com/MartinPdeS/PyOptik/python-coverage-comment-action-data/badge.svg
    :alt: Unittest coverage
    :target: https://htmlpreview.github.io/?https://github.com/MartinPdeS/PyOptik/blob/python-coverage-comment-action-data/htmlcov/index.html
 
 .. |anaconda| image:: https://anaconda.org/martinpdes/pyoptik/badges/version.svg
+   :alt: Anaconda version
    :target: https://anaconda.org/martinpdes/pyoptik

{pyoptik-1.8.0.post0 → pyoptik-1.8.2.post0}/PyOptik/__init__.py

@@ -5,7 +5,6 @@ except ImportError:
     __version__ = "0.0.0"
 
 
-from .utils import build_library
 from .material_bank import MaterialBank
 from .material import TabulatedMaterial
 from .material import SellmeierMaterial

pyoptik-1.8.2.post0/PyOptik/__main__.py

@@ -0,0 +1,7 @@
+from PyOptik import MaterialBank
+import logging
+
+
+if __name__ == '__main__':
+    logging.info('Building material library')
+    MaterialBank.build_library('classics')

{pyoptik-1.8.0.post0 → pyoptik-1.8.2.post0}/PyOptik/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.8.0.post0'
-__version_tuple__ = version_tuple = (1, 8, 0)
+__version__ = version = '1.8.2.post0'
+__version_tuple__ = version_tuple = (1, 8, 2)

{pyoptik-1.8.0.post0 → pyoptik-1.8.2.post0}/PyOptik/data/minimal.yml

@@ -2,6 +2,8 @@ sellmeier:
   argon: https://refractiveindex.info/database/data-nk/main/Ar/Bideau-Mehu.yml
   air: https://refractiveindex.info/database/data-nk/other/mixed%20gases/air/Ciddor.yml
   water: https://refractiveindex.info/database/data-nk/main/H2O/Daimon-19.0C.yml
+  soda_lime_glass: https://refractiveindex.info/database/data-nk/glass/misc/soda-lime/Rubin-clear.yml
+  silicon: https://refractiveindex.info/database/data-nk/main/Si/Salzberg.yml
 
 tabulated:
   zinc: https://refractiveindex.info/database/data-nk/main/Zn/Werner.yml

pyoptik-1.8.2.post0/PyOptik/data/plastics.yml

@@ -0,0 +1,8 @@
+sellmeier:
+  polyetylene: https://refractiveindex.info/database/data-nk/organic/(C2H4)n%20-%20polyethylene/Smith.yml
+  pva: https://refractiveindex.info/database/data-nk/organic/(C2H3Cl)n%20-%20polyvinyl%20chloride/Zhang.yml
+  pvc: https://refractiveindex.info/database/data-nk/organic/(C2H4O)n%20-%20polyvinyl%20alcohol/Schnepf.yml
+  pdms: https://refractiveindex.info/database/data-nk/organic/(C2H6OSi)n%20-%20polydimethylsiloxane/Schneider-RTV615.yml
+  polystyrene: https://refractiveindex.info/database/data-nk/organic/(C8H8)n%20-%20polystyrene/Sultanova.yml
+  polycarbonate: https://refractiveindex.info/database/data-nk/organic/(C16H14O3)n%20-%20polycarbonate/Sultanova.yml
+  cellulose: https://refractiveindex.info/database/data-nk/organic/(C6H10O5)n%20-%20cellulose/Sultanova.yml

{pyoptik-1.8.0.post0 → pyoptik-1.8.2.post0}/PyOptik/material/sellmeier_class.py

@@ -1,17 +1,18 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import yaml
+import numpy
+import itertools
+from MPSPlots.styles import mps
+import matplotlib.pyplot as plt
 from pydantic import Field, ConfigDict
 from pydantic.dataclasses import dataclass
-import matplotlib.pyplot as plt
-import numpy
 from typing import Tuple, Optional, Union
-import yaml
+from PyOptik.units import micrometer, Quantity
 from PyOptik.directories import sellmeier_data_path
-import itertools
 from PyOptik.material.base_class import BaseMaterial
-from MPSPlots.styles import mps
-from PyOptik.units import meter, micrometer, Quantity
+
 
 config_dict = ConfigDict(
     arbitrary_types_allowed=True

pyoptik-1.8.2.post0/PyOptik/material_bank.py

@@ -0,0 +1,388 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import numpy
+import os
+import re
+import yaml
+import logging
+from pathlib import Path
+from typing import List, Union, Optional, Tuple
+from PyOptik.directories import data_path
+from PyOptik.material.sellmeier_class import SellmeierMaterial
+from PyOptik.material.tabulated_class import TabulatedMaterial
+from PyOptik.utils import download_yml_file
+from tabulate import tabulate
+from dataclasses import dataclass
+
+
+@dataclass(frozen=True, slots=True)
+class _MaterialBank():
+    """
+    A class representing a centralized material bank for common optical materials available in the PyOptik library.
+
+    The `_MaterialBank` class provides access to a predefined list of materials used in optical simulations,
+    categorized into Sellmeier and Tabulated materials. It allows users to dynamically retrieve materials
+    based on their names without the need to instantiate the class. The material bank can be expanded
+    or modified by adding or removing materials from the bank, and it provides utilities to fetch material data
+    dynamically when accessed as class attributes.
+
+    Attributes
+    ----------
+    all : list
+        A combined list of all materials, including both Sellmeier and Tabulated materials.
+
+    Usage
+    -----
+    Materials can be accessed directly as class attributes:
+
+    >>> material = _MaterialBank
+    >>> bk7_material = material.BK7  # Dynamically retrieves the BK7 material.
+
+    To add a new material to the Sellmeier bank:
+
+    >>> material.add_sellmeier_to_bank("new_material.yml", "http://example.com/material.yml")
+
+    To remove a material from the bank:
+
+    >>> MaterialBank.remove_item("obsolete_material.yml")
+
+    Raises
+    ------
+    FileNotFoundError
+        If a material is not found in either the Sellmeier or Tabulated material lists.
+    """
+
+    def __getattr__(self, material_name: str) -> Union[SellmeierMaterial, TabulatedMaterial]:
+        """
+        Retrieve a material by name dynamically at the class level.
+
+        Parameters
+        ----------
+        material_name : str
+            The name of the material to retrieve.
+
+        Returns
+        -------
+        Union[SellmeierMaterial, TabulatedMaterial]
+            An instance of the material if found.
+
+        Raises
+        ------
+        FileNotFoundError
+            If the material is not found in either the Sellmeier or Tabulated lists.
+        """
+        if material_name in self.sellmeier:
+            return SellmeierMaterial(filename=material_name)
+
+        if material_name in self.tabulated:
+            return TabulatedMaterial(filename=material_name)
+
+        raise AttributeError(f"'{self.__class__.__name__}' object has no attribute '{material_name}'")
+
+    @property
+    def sellmeier(self) -> List[str]:
+        return [
+            os.path.splitext(f)[0] for f in os.listdir(data_path / 'sellmeier') if os.path.isfile(os.path.join(data_path / 'sellmeier', f)) and f.endswith('.yml')
+        ]
+
+    @property
+    def tabulated(self) -> List[str]:
+        return [
+            os.path.splitext(f)[0] for f in os.listdir(data_path / 'tabulated') if os.path.isfile(os.path.join(data_path / 'tabulated', f)) and f.endswith('.yml')
+        ]
+
+    @property
+    def all(self) -> List[str]:
+        return self.sellmeier + self.tabulated
+
+    def print_materials(cls) -> None:
+        """
+        Prints out all the available Sellmeier and Tabulated materials in a tabulated format.
+        """
+        sellmeier_materials = cls.sellmeier
+        tabulated_materials = cls.tabulated
+
+        # Create data for the table
+        table_data = []
+        max_len = max(len(sellmeier_materials), len(tabulated_materials))
+        for i in range(max_len):
+            sellmeier = sellmeier_materials[i] if i < len(sellmeier_materials) else ""
+            tabulated = tabulated_materials[i] if i < len(tabulated_materials) else ""
+            table_data.append([sellmeier, tabulated])
+
+        # Define headers
+        headers = ["Sellmeier Materials", "Tabulated Materials"]
+
+        # Print the table using tabulate
+        print(tabulate(table_data, headers=headers, tablefmt="grid"))
+
+    @classmethod
+    def add_sellmeier_to_bank(cls, filename: str, url: str) -> None:
+        """
+        Add a Sellmeier material to the material bank.
+
+        Downloads a YAML file containing the Sellmeier material data from a specified URL and stores it
+        in the Sellmeier materials directory.
+
+        Parameters
+        ----------
+        filename : str
+            The name of the file to be saved in the Sellmeier material bank.
+        url : str
+            The URL from where the material file is downloaded.
+
+        Returns
+        -------
+        None
+        """
+        return download_yml_file(filename=filename, url=url, location=data_path / 'sellmeier')
+
+    @classmethod
+    def add_tabulated_to_bank(cls, filename: str, url: str) -> None:
+        """
+        Add a Tabulated material to the material bank.
+
+        Downloads a YAML file containing the Tabulated material data from a specified URL and stores it
+        in the Tabulated materials directory.
+
+        Parameters
+        ----------
+        filename : str
+            The name of the file to be saved in the Tabulated material bank.
+        url : str
+            The URL from where the material file is downloaded.
+
+        Returns
+        -------
+        None
+        """
+        return download_yml_file(filename=filename, url=url, location=data_path / 'tabulated')
+
+    @classmethod
+    def remove_item(cls, filename: str, location: str = 'any') -> None:
+        """
+        Remove a file associated with a given element name from the specified location.
+
+        Parameters
+        ----------
+        filename : str
+            The name of the file to remove, without the '.yml' suffix.
+        location : str
+            The location to search for the file, either 'sellmeier', 'tabulated', or 'any' (default is 'any').
+
+        Raises
+        ------
+        FileNotFoundError
+            If the specified file does not exist.
+        ValueError
+            If an invalid location is provided.
+        """
+        location = location.lower()
+
+        if location not in ['any', 'sellmeier', 'tabulated']:
+            raise ValueError("Invalid location. Please choose 'sellmeier', 'tabulated', or 'any'.")
+
+        if location in ['any', 'sellmeier']:
+            sellmeier_file = data_path / 'sellmeier' / f"{filename}.yml"
+            if sellmeier_file.exists():
+                sellmeier_file.unlink()
+
+        if location in ['any', 'tabulated']:
+            tabulated_file = data_path / 'tabulated' / f"{filename}.yml"
+            if tabulated_file.exists():
+                tabulated_file.unlink()
+
+    def clean_data_files(self, regex: str, location: str = 'any') -> None:
+        """
+        Remove all files matching the given regex from the specified location.
+
+        Parameters
+        ----------
+        regex : str
+            The regex pattern to match the filenames (without the '.yml' suffix).
+        location : str
+            The location to search for files, either 'sellmeier', 'tabulated', or 'any' (default is 'any').
+
+        Raises
+        ------
+        ValueError
+            If an invalid location is provided.
+        """
+        # Compile the regex pattern
+        pattern = re.compile(regex)
+
+        # Normalize the location parameter
+        location = location.lower()
+
+        if location not in ['any', 'sellmeier', 'tabulated']:
+            raise ValueError("Invalid location. Please choose 'sellmeier', 'tabulated', or 'any'.")
+
+        # Function to remove matching files in a given directory
+        def remove_matching_files(directory: Path):
+            if not directory.exists():
+                return
+            for file in directory.glob("*.yml"):
+                if pattern.match(file.stem):
+                    logging.info(f"Removing file: {file}")
+                    file.unlink()
+
+        # Remove files from the sellmeier location if specified
+        if location in ['any', 'sellmeier']:
+            remove_matching_files(data_path / 'sellmeier')
+
+        # Remove files from the tabulated location if specified
+        if location in ['any', 'tabulated']:
+            remove_matching_files(data_path / 'tabulated')
+
+
+    def build_library(self, library: Union[str, List[str]] = 'classics', remove_previous: bool = False) -> None:
+        """
+        Downloads and saves materials data from the specified URLs.
+
+        Parameters
+        ----------
+        library : str | list[str]
+            The name or list of names of the libraries to download.
+        remove_previous : bool
+            If True, removes existing files before downloading new ones.
+        """
+        AVAILABLE_LIBRARIES = {'classics', 'glasses', 'metals', 'organics', 'others', 'minimal'}
+
+        libraries_to_download = AVAILABLE_LIBRARIES if library == 'all' else set(numpy.atleast_1d(library))
+
+        # Ensure the requested library exists
+        assert libraries_to_download.issubset(AVAILABLE_LIBRARIES), f"Library value should be in {AVAILABLE_LIBRARIES}"
+
+        # Remove previous files if the flag is set
+        if remove_previous:
+            logging.info(f"Removing previous files from the library.")
+            self.clean_data_files(regex=".*", location="sellmeier")  # Remove all sellmeier files
+            self.clean_data_files(regex=".*", location="tabulated")  # Remove all tabulated files
+
+        for lib in libraries_to_download:
+            file_path = data_path / lib
+            with open(file_path.with_suffix('.yml'), 'r') as file:
+                data_dict = yaml.safe_load(file)
+
+            # Download new files for sellmeier
+            if data_dict.get('sellmeier', False):
+                for element_name, url in data_dict['sellmeier'].items():
+                    download_yml_file(url=url, filename=element_name, location=data_path / 'sellmeier')
+
+            # Download new files for tabulated
+            if data_dict.get('tabulated', False):
+                for element_name, url in data_dict['tabulated'].items():
+                    download_yml_file(url=url, filename=element_name, location=data_path / 'tabulated')
+
+    def create_sellmeier_file(
+        self,
+        filename: str,
+        formula_type: int,
+        coefficients: List[float],
+        wavelength_range: Optional[Tuple[float, float]] = None,
+        reference: Optional[str] = None,
+        comments: Optional[str] = None,
+        specs: Optional[dict] = None) -> None:
+        """
+        Creates a YAML file with custom Sellmeier coefficients in the correct format.
+
+        Parameters
+        ----------
+        filename : str
+            The name of the file to create (without the extension).
+        formula_type : int
+            The type of Sellmeier formula.
+        coefficients :  list[float]
+            A list of coefficients for the Sellmeier equation.
+        wavelength_range : Tuple[float, float]
+            The range of wavelengths, in micrometers.
+        reference : str
+            A reference for the material data.
+        comments : Optional[str]
+            Additional comments about the material.
+        specs : Optional[dict]
+            Additional specifications, such as temperature and whether the wavelength is in a vacuum.
+        """
+        reference = 'None' if reference is None else reference
+
+        # Create the data dictionary for YAML
+        data = {}
+        data['REFERENCES'] = reference
+        data['DATA'] = dict(
+            type=f'formula {formula_type}',
+            coefficients=" ".join(map(str, coefficients))
+        )
+
+        if wavelength_range is not None:
+            min_bound, max_bound = wavelength_range
+            data['DATA'].update({'wavelength_range': f"{min_bound} {max_bound}"})
+
+        data['DATA'] = [data['DATA']]
+        # Add comments if provided
+        if comments:
+            data['COMMENTS'] = comments
+
+        # Add specs if provided
+        if specs:
+            data['SPECS'] = specs
+
+        # Define the file path
+        file_path = data_path / 'sellmeier' / f"{filename}.yml"
+
+        # Write the data to a YAML file
+        with open(file_path, 'w') as file:
+            yaml.dump(data, file, default_flow_style=False)
+
+        logging.info(f"Sellmeier data saved to {file_path}")
+
+    def create_tabulated_file(
+        self,
+        filename: str,
+        data: List[Tuple[float, float, float]],
+        reference: Optional[str] = None,
+        comments: Optional[str] = None) -> None:
+        """
+        Creates a YAML file with tabulated nk data in the correct format.
+
+        Parameters
+        ----------
+        filename : str)
+            The name of the file to create (without the extension).
+        data : List[Tuple[float, float, float]])
+            The tabulated nk data.
+        reference : Optional[str])
+            A reference for the material data.
+        comments : Optional[str])
+            Additional comments about the material.
+        """
+        reference = 'None' if reference is None else reference
+
+        # Convert the data list to a formatted string
+        data_str = "\n".join(" ".join(map(str, row)) for row in data)
+
+        # Create the data dictionary for YAML
+        yaml_data = {
+            'REFERENCES': reference,
+            'DATA': [
+                {
+                    'type': 'tabulated nk',
+                    'data': data_str,
+                }
+            ]
+        }
+
+        # Add comments if provided
+        if comments:
+            yaml_data['COMMENTS'] = comments
+
+        # Define the file path
+        file_path = data_path / 'tabulated' / f"{filename}.yml"
+
+        # Write the data to a YAML file
+        with open(file_path, 'w') as file:
+            yaml.dump(yaml_data, file, default_flow_style=False)
+
+        logging.info(f"Tabulated nk data saved to {file_path}")
+
+MaterialBank = _MaterialBank()

pyoptik-1.8.2.post0/PyOptik/utils.py

@@ -0,0 +1,38 @@
+import requests
+
+
+def download_yml_file(url: str, filename: str, location: str) -> None:
+    """
+    Downloads a .yml file from a specified URL and saves it locally.
+
+    Parameters
+    ----------
+    url : str
+        The URL of the .yml file to download.
+    save_path : str
+        The local path where the .yml file should be saved.
+
+    Raises
+    ------
+        HTTPError: If the download fails due to an HTTP error.
+    """
+    file_path = location / f"{filename}.yml"
+    try:
+        # Send a GET request to the URL
+        response = requests.get(url)
+        response.raise_for_status()  # Raise an error for bad status codes
+
+        # Save the content of the response as a file
+        file_path.parent.mkdir(parents=True, exist_ok=True)  # Create directories if they don't exist
+
+        with open(file_path, 'wb') as file:
+            file.write(response.content)
+
+        print(f"File downloaded and saved to {file_path}")
+
+    except requests.exceptions.HTTPError as http_err:
+        print(f"HTTP error occurred: {http_err}")
+    except Exception as err:
+        print(f"An error occurred: {err}")
+
+