radphen-iadpython 0.7.0__py3-none-any.whl

radphen_iadpython-0.7.0.dist-info/METADATA

@@ -0,0 +1,264 @@
+Metadata-Version: 2.4
+Name: radphen-iadpython
+Version: 0.7.0
+Summary: Forward and inverse radiative transport using adding-doubling
+Author-email: Scott Prahl <scott.prahl@oit.edu>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/PanxoPanza/iadpython
+Project-URL: Documentation, https://iadpython.readthedocs.io
+Project-URL: Source, https://github.com/PanxoPanza/iadpython
+Project-URL: Tracker, https://github.com/PanxoPanza/iadpython/issues
+Project-URL: Changelog, https://github.com/PanxoPanza/iadpython/blob/main/docs/CHANGELOG.rst
+Keywords: absorption,scattering,reflection,transmission,optical properties,radiative transport,scattering coefficient,scattering anisotropy
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+Requires-Dist: scipy>=1.10
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=1.5
+Requires-Dist: matplotlib
+Provides-Extra: docs
+Requires-Dist: Sphinx==8.1.3; extra == "docs"
+Requires-Dist: nbsphinx==0.9.7; extra == "docs"
+Requires-Dist: sphinx_automodapi; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: imageio; extra == "dev"
+Requires-Dist: requests; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: yamllint; extra == "dev"
+Requires-Dist: rstcheck; extra == "dev"
+Requires-Dist: pylint; extra == "dev"
+Requires-Dist: pyroma; extra == "dev"
+Requires-Dist: black[jupyter]; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: check-manifest; extra == "dev"
+Requires-Dist: libarchive-c; extra == "dev"
+Requires-Dist: pyyaml; extra == "dev"
+Requires-Dist: setuptools; extra == "dev"
+Requires-Dist: jupyterlab; extra == "dev"
+Requires-Dist: nbconvert; extra == "dev"
+Requires-Dist: nbformat; extra == "dev"
+Provides-Extra: lite
+Requires-Dist: jupyterlite-core==0.6.4; extra == "lite"
+Requires-Dist: jupyterlite-pyodide-kernel==0.6.1; extra == "lite"
+Dynamic: license-file
+
+radphen-iadpython
+=================
+
+This is the MIT-licensed RadPhen fork of Scott Prahl's iadpython, maintained
+at https://github.com/PanxoPanza/iadpython for empylib. Distribution version
+0.7.0 retains the original ``iadpython`` import namespace and ``iadp``
+command. The distribution name alone is ``radphen-iadpython``.
+
+Install with ``python -m pip install radphen-iadpython``. For example::
+
+    import iadpython as iad
+    sample = iad.Sample(a=0.9, b=1.0, g=0.5)
+    print(sample.rt())
+
+The fork preserves HG, TABULATED and MOMENTS phase functions, complex sample
+and exterior boundary indices, and diffuse-cone transport from the audited
+source. See PROVENANCE.md for the exact source and release procedure.
+Both distributions provide ``iadpython`` and ``iadp``; install this fork in a
+fresh environment without the upstream ``iadpython`` distribution. They cannot
+coexist safely in one environment because their package paths overlap.
+
+Original upstream README (historical attribution)
+=================================================
+
+.. |pypi| image:: https://img.shields.io/pypi/v/iadpython?color=68CA66
+   :target: https://pypi.org/project/iadpython/
+   :alt: pypi
+
+.. |github| image:: https://img.shields.io/github/v/tag/scottprahl/iadpython?label=github&color=68CA66
+   :target: https://github.com/scottprahl/iadpython
+   :alt: github
+
+.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/iadpython?label=conda&color=68CA66
+   :target: https://github.com/conda-forge/iadpython-feedstock
+   :alt: conda
+
+.. |doi| image:: https://zenodo.org/badge/102148844.svg
+   :target: https://zenodo.org/badge/latestdoi/102148844
+   :alt: doi
+
+.. |license| image:: https://img.shields.io/github/license/scottprahl/iadpython?color=68CA66
+   :target: https://github.com/scottprahl/iadpython/blob/main/LICENSE.txt
+   :alt: License
+
+.. |test| image:: https://github.com/scottprahl/iadpython/actions/workflows/test.yaml/badge.svg
+   :target: https://github.com/scottprahl/iadpython/actions/workflows/test.yaml
+   :alt: Testing
+
+.. |docs| image:: https://readthedocs.org/projects/iadpython/badge
+   :target: https://iadpython.readthedocs.io
+   :alt: Docs
+
+.. |downloads| image:: https://img.shields.io/pypi/dm/iadpython?color=68CA66
+   :target: https://pypi.org/project/iadpython/
+   :alt: Downloads
+
+iadpython
+=========
+
+by Scott Prahl
+
+|pypi| |github| |conda| |doi|
+
+|license| |test| |docs| |downloads|
+
+`iadpython` will be a pure Python module to do forward and inverse multiple light
+scattering (radiative transport) in layered materials.  Calculations are done using 
+van de Hulst's adding-doubling technique.
+
+The original adding-doubling algorithm was developed by van de Hulst to model light
+propagation through layered media.  I extended it to handle Fresnel 
+reflection at boundaries as well as interactions with integrating spheres. 
+
+Finally, the code was further extended to handle lost light using
+Monte Carlo techniques for inverse calculations.
+
+Version v0.4.0 started the migration to a pure-python implementation.  This 
+version includes the ability to do forward calculations of light transport through
+layered 1D structures.  
+
+The long-term goal is rewrite the integrating sphere, inverse algorithm, and
+lost light calculations in pure python so that one can do 
+inverse calculations (i.e., reflection and transmission measurements to 
+intrinsic absorption and scattering properties). 
+
+Both inverse and forward calculations are currently possible using the `iadc` framework.
+This is a python interface to the inverse 
+adding-doubling package written in C by Scott Prahl 
+<https://github.com/scottprahl/iad>.  This works now
+but is a nuisance to install and maintain because of its dependence on compiling
+and installing a C library.
+
+See <https://iadpython.readthedocs.io> for full documentation of `iadpython`.
+
+Differences from upstream iadpython (this fork)
+-----------------------------------------------
+
+This fork adds first-class multilayer support and **changes how arrays are
+interpreted** relative to upstream.  If you are migrating code, read this
+section.
+
+**Layer API.**  A multilayer sample is built from explicit ``Layer`` objects;
+each layer may have its own refractive index (large index mismatches between
+layers are handled exactly, including total internal reflection), its own
+Henyey-Greenstein anisotropy *or* tabulated phase function, and its own
+wavelength dependence::
+
+    import numpy as np
+    import iadpython as iad
+
+    l0 = iad.Layer(a=0.95, b=0.84, g=0.20, n=1.35, d=0.10)
+    l1 = iad.Layer(a=0.81, b=0.31, g=0.85, n=2.00, d=0.05)
+    l2 = iad.Layer(a=0.90, b=1.00, n=1.45, pf_type='TABULATED', pf_data=df)
+
+    s = iad.Sample(layers=[l0, l1, l2], n_above=1.5, quad_pts=16)
+    ur1, ut1, uru, utu = s.rt()
+
+**Axis rule.**  The two axes of a simulation are now structurally distinct
+and cannot be confused:
+
+* *layer axis* = position in the ``layers`` list;
+* *wavelength axis* = arrays **inside** each attribute (``a``/``b``/``g``/``n``
+  of a ``Layer`` may each be a scalar or a wavelength array; a ``TABULATED``
+  phase function holds one ``pf_data`` column per wavelength).  Scalar-valued
+  layers are automatically held constant across the sweep.
+
+**Breaking change.**  Upstream allowed ``sample.a = np.array([...])`` followed
+by ``rt_matrices()`` to mean *layers* while the same array passed to ``rt()``
+meant *wavelengths*.  That ambiguity is removed: flat arrays on ``a``/``b``/``g``
+now **always mean wavelengths**, and array-valued ``n`` on a flat sample is an
+error.  Code using the old flat-arrays-as-layers form fails with::
+
+    RuntimeError: array-valued a/b/g now mean wavelengths, not layers; build a
+    multilayer sample with iadpython.Sample(layers=[iadpython.Layer(...), ...])
+
+Classic single-layer usage (scalars, or wavelength arrays with ``rt()``) is
+unchanged, as are all inverse-calculation entry points.
+
+Usage
+-----
+
+The following will do a forward calculation::
+
+    import iadpython as iad
+
+    mu_s = 10  # scattering coefficient [1/mm]
+    mu_a = 0.1 # absorption coefficient [1/mm]
+    g = 0.9    # scattering anisotropy
+    d = 1      # thickness mm
+
+    a = mu_s/(mu_a+mu_s)
+    b = (mu_a+mu_s) * d
+
+    # air / glass / sample / glass / air
+    s = iadpython.Sample(a=a, b=b, g=g, n=1.4, n_above=1.5, n_below=1.5)
+    ur1, ut1, uru, utu = s.rt()
+
+    print('Collimated light incident perpendicular to sample')
+    print('  total reflection = %.5f' % ur1)
+    print('  total transmission = %.5f' % ut1)
+ 
+    print('Diffuse light incident on sample')
+    print('  total reflection = %.5f' % uru)
+    print('  total transmission = %.5f' % utu)
+
+`Sample` also accepts tabulated phase-function data via the ``pf_data``
+keyword. When ``pf_type`` is ``'TABULATED'``, ``pf_data`` may hold one column per
+wavelength and must have the same length as other wavelength-dependent inputs.
+
+
+Installation
+------------
+
+Use ``pip``::
+
+    pip install iadpython
+
+or ``conda``::
+
+    conda install -c conda-forge iadpython
+
+or use immediately by clicking the Google Colaboratory button below
+
+.. image:: https://colab.research.google.com/assets/colab-badge.svg
+  :target: https://colab.research.google.com/github/scottprahl/iadpython/blob/main
+  :alt: Colab
+
+Inverse Calculations
+---------------------
+
+As of version 0.5.3, the forward and inverse calculations work fine as long as you do not need to
+include integrating sphere effects or lost-light calculations.
+
+If you want to do these, then you're probably best served by downloading and compiling
+the C-code (on unix or macos) or the `.exe` file for Windows.  <https://omlc.org/software/iad/>
+
+
+Dependencies
+------------
+
+Required Python modules: numpy, matplotlib, ctypes, scipy
+
+
+License
+-------
+
+`iadpython` is licensed under the terms of the MIT license.

radphen_iadpython-0.7.0.dist-info/RECORD

@@ -0,0 +1,28 @@
+iadpython/__init__.py,sha256=0RjPAM8p5fJQ64zzwS6tW9pI-TL9RCb1yBzBFc1KDhk,1778
+iadpython/ad.py,sha256=VsflOqzks8B3DaDUammY9zDfHHYSiEzBzttwAtpBf-Q,58155
+iadpython/agrid.py,sha256=GxsoD9imS79ZXV_Xm5k3H4k5S-aq54bDnVHcwCdOM4M,10747
+iadpython/cache.py,sha256=T137_YxLEDh5GOMXEbHyf8DKzZNSboIxKMHDl6VqeaE,3744
+iadpython/combine.py,sha256=l5VU72L0JNrVxR8LEOTJOWPo0uEm25MRFMUtoonrFkY,23809
+iadpython/constants.py,sha256=x8PS_FiHLiwPLa_PURf_XJ-tcBksd7mfwpiZMQmsXps,81
+iadpython/double.py,sha256=vSa1e33Dmxrwh51tO3MWVhu2VodGSXMfcAonZswtgio,12999
+iadpython/fresnel.py,sha256=YfClK_V3FXn9XxY6xUVIFA9qNjTy9byz3a0y8Xsl5zk,21837
+iadpython/grid.py,sha256=Oc2w58Cqn_9J8ecZBjL5LSjDbXdV5nwES_K_b42qyAc,3813
+iadpython/iad.py,sha256=bw8ZkEC30QM9rMq_RrLBKJRSVidxgexFu11MVhr_-CY,20656
+iadpython/iadc.py,sha256=th7pziN8sdD_V5ZHnyc-mVQbvU0KOSyIfMMGUXuw4MA,33016
+iadpython/iadcommand.py,sha256=x-UGfNPpPE3l79-FZfbh3h53yC98txbNiY0wMhaQTSY,21625
+iadpython/layer.py,sha256=DT0o5gNrNFKYtR6bGm9IT_kCDjDhxjYY_WanLphk1qg,10157
+iadpython/nist.py,sha256=MiAfL5TtmOsf2OsEh2x96nUmGEHqk1UIhWn9yHBI658,3046
+iadpython/port.py,sha256=vwORubI9GYyzRVW50qJ40XG76TKJNfXI8BeCXq19WS4,9741
+iadpython/quadrature.py,sha256=GVBHp0-AvIU5cv837341ylM9scHSzfDuo1DE1MTIOB8,4876
+iadpython/redistribution.py,sha256=ItdIblYkw4cA5HDkEwtfceLXDzV865L6tfkqzJD6vqk,11534
+iadpython/rxt.py,sha256=bry1HMRLhFJzcO6Anfae0DLccplH7pYAQbqRBpD-PF8,6383
+iadpython/sphere.py,sha256=HpPHQjo2ovqCC5QSXRk31PpwQEMF9W4KrpC9waT2K_0,22340
+iadpython/start.py,sha256=qfXDb1OD3DE-w3GYjWA2D1-OoEJJ3O4pVNpBz7a40mE,13035
+iadpython/txt.py,sha256=wkPPYkJzOBs81cB2hn4vfHezhEaUHO1-BFxNYeVErqY,4501
+iadpython/data/M38597.csv,sha256=zpqsc12dg7S4dLmNRfHr2mgs3A5lL4BO_gCrL84MJdk,2119696
+radphen_iadpython-0.7.0.dist-info/licenses/LICENSE.txt,sha256=g9-BWWRLvMDMQ1Zflxliku7Sleom1_SbXHQHOLGgqqk,1055
+radphen_iadpython-0.7.0.dist-info/METADATA,sha256=HIWciUTXAYAIJpdzG0t6S4VkvHuOqyfIZtGjl5JP4Pk,10267
+radphen_iadpython-0.7.0.dist-info/WHEEL,sha256=mOdXR9C3wMVov7cSY8PY-XCzo3SmmWCHvGQr5csJoao,91
+radphen_iadpython-0.7.0.dist-info/entry_points.txt,sha256=JKvuEI8iM3nx0J4zyw1Gs5lxmIx8ZF8hefRyjCtn-ns,51
+radphen_iadpython-0.7.0.dist-info/top_level.txt,sha256=OYHVgl4RKNT4etTl1K8AEnchCeR5O8zru08wrKBwQPg,10
+radphen_iadpython-0.7.0.dist-info/RECORD,,

radphen_iadpython-0.7.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (84.2.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

radphen_iadpython-0.7.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+iadp = iadpython.iadcommand:main

radphen_iadpython-0.7.0.dist-info/licenses/LICENSE.txt

@@ -0,0 +1,18 @@
+Copyright 2017-2021 Scott Prahl
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

radphen_iadpython-0.7.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+iadpython