PyOptik 1.7.3.post0__tar.gz → 1.8.1.post0__tar.gz

{pyoptik-1.7.3.post0 → pyoptik-1.8.1.post0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOptik
-Version: 1.7.3.post0
+Version: 1.8.1.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|
+|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
 ********
@@ -99,10 +100,67 @@ To install PyOptik, simply use `pip` or `conda`:
    pip install PyOptik
    conda install --channels martinpdes pyoptik
 
+Building the Material Library
+*****************************
+
+PyOptik allows you to build and customize a local material library, importing material data from various categories. You can download the following categories of materials from the RefractiveIndex.INFO database:
+
+- `classics`: Commonly used optical materials.
+- `glasses`: Various types of glass materials.
+- `metals`: Different metal materials for optical simulations.
+- `organics`: Organic materials with optical properties.
+- `others`: Other optical materials.
+- `all`: Download all available categories at once.
+
+To build a material library, use the `build_library` function. This will download and save the material data to your local machine.
+
+**Example: Building the Material Library:**
+
+In this example, we will download the `others` category of materials and remove any previously existing data in that category:
+
+.. code:: python
+
+   from PyOptik import MaterialBank
+
+   # Download the 'classics' category and remove previous files
+   MaterialBank.build_library('classics', remove_previous=True)
+
+**Available Categories:**
+
+To download materials from another category, simply pass the category name as an argument to `build_library`. For example:
+
+.. code:: python
+
+   # Download materials from the 'glasses' category
+   MaterialBank.build_library('glasses')
+
+To download all material categories at once:
+
+.. code:: python
+
+   # Download all available material categories
+   MaterialBank.build_library('all')
+
+You can also set the `remove_previous` parameter to `True` to remove old data before downloading new material data.
+
+Viewing Available Materials
+***************************
+
+Once you have built the material library, you can view all the available materials using the `MaterialBank` class. This will print a list of materials stored in your local library.
+
+**Example:**
+
+.. code:: python
+
+   from PyOptik import MaterialBank
+
+   # Print the available materials in a tabulated format
+   MaterialBank.print_materials()
+
 Simple Usage
 ************
 
-After installing PyOptik, you can easily access material properties:
+After installing PyOptik and building the material library, you can easily access material properties:
 
 .. code:: python
 
@@ -113,7 +171,6 @@ After installing PyOptik, you can easily access material properties:
    n = bk7.compute_refractive_index(0.55e-6)
    print(f"Refractive index at 0.55 µm: {n}")
 
-
 Example
 *******
 
@@ -136,8 +193,12 @@ Here is a quick example demonstrating how to use PyOptik to retrieve and plot th
 
 This code produces the following figure: |example_bk7|
 
+Adding and Removing Custom Materials
+************************************
 
-You can also add a custom element to your library providing a URL from `refractiveindex.info <https://refractiveindex.info>`_ website.
+You can add a custom material to your library by providing a URL from `refractiveindex.info <https://refractiveindex.info>`_.
+
+**Adding a Custom Material:**
 
 .. code:: python
 
@@ -150,8 +211,9 @@ You can also add a custom element to your library providing a URL from `refracti
       location=tabulated_data_path
    )
 
-Evidently, you can also remove element from the library using as follows:
+**Removing a Material:**
 
+You can also remove a material from the library as follows:
 
 .. code:: python
 
@@ -185,14 +247,15 @@ 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
+.. |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
@@ -204,14 +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-1.7.3.post0 → pyoptik-1.8.1.post0}/PyOptik/__init__.py

@@ -5,10 +5,9 @@ except ImportError:
     __version__ = "0.0.0"
 
 
-from .utils import build_default_library
-from .material_bank import _MaterialBank
+from .material_bank import MaterialBank
 from .material import TabulatedMaterial
 from .material import SellmeierMaterial
 from .material import base_class
 
-MaterialBank = Material = _MaterialBank()
+Material = MaterialBank  # For retro-compatiibility

pyoptik-1.8.1.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-1.7.3.post0 → pyoptik-1.8.1.post0}/PyOptik/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.7.3.post0'
-__version_tuple__ = version_tuple = (1, 7, 3)
+__version__ = version = '1.8.1.post0'
+__version_tuple__ = version_tuple = (1, 8, 1)

pyoptik-1.8.1.post0/PyOptik/data/classics.yml

@@ -0,0 +1,28 @@
+sellmeier:
+  ZBLAN: https://refractiveindex.info/database/data-nk/glass/misc/ZBLAN/Gan.yml
+  BK7: https://refractiveindex.info/database/data-nk/glass/schott/N-BK7.yml
+  fused_silica: https://refractiveindex.info/database/data-nk/main/SiO2/Malitson.yml
+  BAK1: https://refractiveindex.info/database/data-nk/glass/schott/N-BAK1.yml
+  SF5: https://refractiveindex.info/database/data-nk/glass/schott/N-SF5.yml
+  water: https://refractiveindex.info/database/data-nk/main/H2O/Daimon-19.0C.yml
+  polystyren: https://refractiveindex.info/database/data-nk/organic/(C8H8)n%20-%20polystyrene/Sultanova.yml
+  lithium_niobate: https://refractiveindex.info/database/data-nk/main/LiNbO3/Zelmon-o.yml
+  germanium: https://refractiveindex.info/database/data-nk/main/Ge/Icenogle.yml
+  silicon: https://refractiveindex.info/database/data-nk/main/Si/Salzberg.yml
+  soda_lime_glass: https://refractiveindex.info/database/data-nk/glass/misc/soda-lime/Rubin-clear.yml
+  crown: https://refractiveindex.info/database/data-nk/glass/schott/K7.yml
+  flint: https://refractiveindex.info/database/data-nk/glass/schott/F2.yml
+  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
+
+tabulated:
+  silver: https://refractiveindex.info/database/data-nk/main/Ag/Johnson.yml
+  aluminium: https://refractiveindex.info/database/data-nk/main/Al/Rakic.yml
+  gold: https://refractiveindex.info/database/data-nk/main/Au/Johnson.yml
+  calcium: https://refractiveindex.info/database/data-nk/main/Ca/Mathewson.yml
+  copper: https://refractiveindex.info/database/data-nk/main/Cu/Johnson.yml
+  iron: https://refractiveindex.info/database/data-nk/main/Fe/Johnson.yml
+  sodium: https://refractiveindex.info/database/data-nk/main/Na/Smith.yml
+  nickel: https://refractiveindex.info/database/data-nk/main/Ni/Johnson.yml
+  zinc: https://refractiveindex.info/database/data-nk/main/Zn/Werner.yml

pyoptik-1.8.1.post0/PyOptik/data/glasses.yml

@@ -0,0 +1,20 @@
+sellmeier:
+  ZBLAN: https://refractiveindex.info/database/data-nk/glass/misc/ZBLAN/Gan.yml
+  BK7: https://refractiveindex.info/database/data-nk/glass/schott/N-BK7.yml
+  fused_silica: https://refractiveindex.info/database/data-nk/main/SiO2/Malitson.yml
+  BAK1: https://refractiveindex.info/database/data-nk/glass/schott/N-BAK1.yml
+  BAF10: https://refractiveindex.info/database/data-nk/glass/schott/N-BAF10.yml
+  SF5: https://refractiveindex.info/database/data-nk/glass/schott/N-SF5.yml
+  SF10: https://refractiveindex.info/database/data-nk/glass/schott/N-SF10.yml
+  SF11: https://refractiveindex.info/database/data-nk/glass/schott/N-SF11.yml
+  LASF9: https://refractiveindex.info/database/data-nk/glass/schott/N-LASF9.yml
+  FK51A: https://refractiveindex.info/database/data-nk/glass/schott/N-FK51A.yml
+  water: https://refractiveindex.info/database/data-nk/main/H2O/Daimon-19.0C.yml
+  polystyren: https://refractiveindex.info/database/data-nk/organic/(C8H8)n%20-%20polystyrene/Sultanova.yml
+  lithium_niobate: https://refractiveindex.info/database/data-nk/main/LiNbO3/Zelmon-o.yml
+  germanium: https://refractiveindex.info/database/data-nk/main/Ge/Icenogle.yml
+  silicon: https://refractiveindex.info/database/data-nk/main/Si/Salzberg.yml
+  soda_lime_glass: https://refractiveindex.info/database/data-nk/glass/misc/soda-lime/Rubin-clear.yml
+  crown: https://refractiveindex.info/database/data-nk/glass/schott/K7.yml
+  flint: https://refractiveindex.info/database/data-nk/glass/schott/F2.yml
+

pyoptik-1.8.1.post0/PyOptik/data/metals.yml

@@ -0,0 +1,20 @@
+tabulated:
+  silver: https://refractiveindex.info/database/data-nk/main/Ag/Johnson.yml
+  aluminium: https://refractiveindex.info/database/data-nk/main/Al/Rakic.yml
+  gold: https://refractiveindex.info/database/data-nk/main/Au/Johnson.yml
+  calcium: https://refractiveindex.info/database/data-nk/main/Ca/Mathewson.yml
+  copper: https://refractiveindex.info/database/data-nk/main/Cu/Johnson.yml
+  iron: https://refractiveindex.info/database/data-nk/main/Fe/Johnson.yml
+  sodium: https://refractiveindex.info/database/data-nk/main/Na/Smith.yml
+  nickel: https://refractiveindex.info/database/data-nk/main/Ni/Johnson.yml
+  zinc: https://refractiveindex.info/database/data-nk/main/Zn/Werner.yml
+  chromium: https://refractiveindex.info/database/data-nk/main/Cr/Johnson.yml
+  titanium: https://refractiveindex.info/database/data-nk/main/Ti/Johnson.yml
+  tungsten: https://refractiveindex.info/database/data-nk/main/W/Werner.yml
+  lead: https://refractiveindex.info/database/data-nk/main/Pb/Werner.yml
+  bismuth: https://refractiveindex.info/database/data-nk/main/Bi/Werner.yml
+  magnesium: https://refractiveindex.info/database/data-nk/main/Mg/Hagemann.yml
+  paladium: https://refractiveindex.info/database/data-nk/main/Pd/Johnson.yml
+  rhodium: https://refractiveindex.info/database/data-nk/main/Rh/Arndt.yml
+  vanadium: https://refractiveindex.info/database/data-nk/main/V/Johnson.yml
+  tantalum: https://refractiveindex.info/database/data-nk/main/Ta/Werner.yml

pyoptik-1.8.1.post0/PyOptik/data/minimal.yml

@@ -0,0 +1,9 @@
+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-1.8.1.post0/PyOptik/data/organics.yml

@@ -0,0 +1,11 @@
+sellmeier:
+  ethanol: https://refractiveindex.info/database/data-nk/organic/C2H6O%20-%20ethanol/Rheims.yml
+  methanol: https://refractiveindex.info/database/data-nk/organic/CH4O%20-%20methanol/El-Kashef.yml
+  propanol: https://refractiveindex.info/database/data-nk/organic/C3H8O%20-%20propanol/Kozma.yml
+  ethylene: https://refractiveindex.info/database/data-nk/organic/C2H4%20-%20ethylene/Loria.yml
+  acetylene: https://refractiveindex.info/database/data-nk/organic/C2H2%20-%20acetylene/Loria.yml
+  methane: https://refractiveindex.info/database/data-nk/organic/CH4%20-%20methane/Loria.yml
+  ethane: https://refractiveindex.info/database/data-nk/organic/C2H6%20-%20ethane/Loria.yml
+  acetone: https://refractiveindex.info/database/data-nk/organic/C3H6O%20-%20acetone/Rheims.yml
+  glycerol: https://refractiveindex.info/database/data-nk/organic/C3H8O3%20-%20glycerol/Rheims.yml
+

pyoptik-1.8.1.post0/PyOptik/data/others.yml

@@ -0,0 +1,4 @@
+sellmeier:
+  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
+  argon: https://refractiveindex.info/database/data-nk/main/Ar/Bideau-Mehu.yml

pyoptik-1.8.1.post0/PyOptik/data/sellmeier/air.yml

@@ -0,0 +1,15 @@
+# this file is part of refractiveindex.info database
+# refractiveindex.info database is in the public domain
+# copyright and related rights waived via CC0 1.0
+
+REFERENCES: "P. E. Ciddor. Refractive index of air: new equations for the visible and near infrared, <a href=\"https://doi.org/10.1364/AO.35.001566\"><i>Appl. Optics</i> <b>35</b>, 1566-1573 (1996)</a><br>[<a href=\"https://github.com/polyanskiy/refractiveindex.info-scripts/blob/master/scripts/Ciddor%201996%20-%20air.py\">Calculation script (Python)</a> - can be used to calculate the refractive index of air for specific values of humidity, temperature, pressure, and CO<sub>2</sub> concentration]"
+COMMENTS: "Standard air: dry air at 15 °C, 101.325 kPa and with 450 ppm CO<sub>2</sub> content."
+DATA:
+  - type: formula 6
+    wavelength_range: 0.23 1.690
+    coefficients: 0 0.05792105 238.0185 0.00167917 57.362
+SPECS:
+    n_is_absolute: true
+    wavelength_is_vacuum: true
+    temperature: 15 °C
+    pressure: 101325 Pa

{pyoptik-1.7.3.post0 → pyoptik-1.8.1.post0}/PyOptik/directories.py

@@ -30,6 +30,8 @@ examples_path = root_path.joinpath('examples')
 sellmeier_data_path = root_path.joinpath('data/sellmeier')
 tabulated_data_path = root_path.joinpath('data/tabulated')
 
+data_path = root_path.joinpath('data')
+
 
 if __name__ == '__main__':
     for path_name in __all__:

{pyoptik-1.7.3.post0 → pyoptik-1.8.1.post0}/PyOptik/material/base_class.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+from typing import Callable
 from PyOptik.units import Quantity, meter
 import numpy
 import warnings
@@ -28,13 +29,13 @@ class BaseMaterial:
         """
         return self.__str__()
 
-    def _check_wavelength(self, wavelength_range: Quantity) -> None:
+    def _check_wavelength(self, wavelength: Quantity) -> None:
         """
         Checks if a wavelength is within the material's allowable range and raises a warning if it is not.
 
         Parameters
         ----------
-        lambda_um : float
+        wavelength : Quantity
             The wavelength to check, in micrometers.
 
         Raises
@@ -45,29 +46,31 @@ class BaseMaterial:
         if self.wavelength_bound is not None:
             min_value, max_value = self.wavelength_bound
 
-            if numpy.any((wavelength_range < min_value) | (wavelength_range > max_value)):
+            if numpy.any((wavelength < min_value) | (wavelength > max_value)):
                 warnings.warn(
-                    f"Wavelength range goes from {wavelength_range.min().to_compact()} to {wavelength_range.max().to_compact()} "
+                    f"Wavelength range goes from {wavelength.min().to_compact()} to {wavelength.max().to_compact()} "
                     f"which is outside the allowable range of {min_value.to_compact()} to {max_value.to_compact()} µm. "
                     f"[Material: {self.filename}]"
                 )
 
-    def ensure_units(func):
+    def ensure_units(func) -> Callable:
         """
         Decorator to ensure that the wavelength parameter has the correct units.
 
         Parameters
         ----------
-        func : callable
+        func : Callable
             The function to wrap.
 
         Returns
         -------
-        callable
+        Callable
             The wrapped function that ensures wavelength is a Quantity in meters.
         """
         def wrapper(self, wavelength: Quantity = None, *args, **kwargs):
             if wavelength is None:
+                if self.wavelength_bound is None:
+                    raise ValueError('Wavelenght must be provided for computation.')
                 wavelength = numpy.linspace(self.wavelength_bound[0].magnitude, self.wavelength_bound[1].magnitude, 100) * self.wavelength_bound.units
 
             if not isinstance(wavelength, Quantity):

{pyoptik-1.7.3.post0 → pyoptik-1.8.1.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
@@ -36,6 +37,7 @@ class SellmeierMaterial(BaseMaterial):
         The formula type to use for refractive index calculation.
     """
     filename: str
+
     coefficients: Optional[numpy.ndarray] = Field(default=None)
     wavelength_bound: Optional[Tuple[float, float]] = Field(default=None)
     reference: Optional[str] = Field(default=None)
@@ -73,12 +75,13 @@ class SellmeierMaterial(BaseMaterial):
         # Extract wavelength range
         if 'wavelength_range' in parsed_yaml['DATA'][0]:
             data_str = parsed_yaml['DATA'][0]['wavelength_range'].split()
+
             self.wavelength_bound = numpy.array([float(val) for val in data_str]) * micrometer
 
         else:
             self.wavelength_bound = None
 
-        # Extract reference
+        # # Extract reference
         self.reference = parsed_yaml.get('REFERENCES', None)
 
     @BaseMaterial.ensure_units
@@ -185,4 +188,4 @@ class SellmeierMaterial(BaseMaterial):
             f"wavelength_range: {self.wavelength_bound},\n"
             f"formula_type: {self.formula_type},\n"
             f"reference: '{self.reference}')"
-        )
+        )

{pyoptik-1.7.3.post0 → pyoptik-1.8.1.post0}/PyOptik/material/tabulated_class.py

@@ -5,7 +5,6 @@ import numpy
 from pydantic.dataclasses import dataclass, Field
 from typing import Optional, Union
 import yaml
-import warnings
 from PyOptik.directories import tabulated_data_path
 from PyOptik.material.base_class import BaseMaterial
 from MPSPlots.styles import mps