skinoptics 0.0.1__py3-none-any.whl

skinoptics/utils.py

@@ -0,0 +1,420 @@
+'''
+| SkinOptics
+| Copyright (C) 2024-2025 Victor Lima
+
+    | This program is free software: you can redistribute it and/or modify
+    | it under the terms of the GNU General Public License as published by
+    | the Free Software Foundation, either version 3 of the License, or
+    | (at your option) any later version.
+
+    | This program is distributed in the hope that it will be useful,
+    | but WITHOUT ANY WARRANTY; without even the implied warranty of
+    | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    | GNU General Public License for more details.
+
+    | You should have received a copy of the GNU General Public License
+    | along with this program.  If not, see <https://www.gnu.org/licenses/>.
+    
+| Victor Lima
+| victorporto\@ifsc.usp.br
+| victor.lima\@ufscar.br
+| victorportog.github.io
+
+| Release date:
+| October 2024
+| Last modification:
+| October 2024
+
+| References:
+
+| [WSS13] Wyman, Sloan & Shirley 2013.
+| Simple Analytic Approximations to the CIE XYZ Color Matching Functions
+| https://jcgt.org/published/0002/02/01/
+'''
+
+import numpy as np
+
+def dict_from_arrays(array_keys, array_values):
+    r'''
+    Construct a dictionary from two arrays.
+    
+    :param array_keys: array with the dictionary keys
+    :type array_keys: np.ndarray
+    
+    :param array_values: array with the dictionary values
+    :type array_values: np.ndarray
+    
+    :return: - **dict** (*dictionary*) – dictionary constructed with the two arrays
+    '''
+    
+    return {array_keys[i]: array_values[i] for i in range(len(array_keys))}
+    
+def circle(r, xc, yc, theta_i = 0., theta_f = 360., n_points = 1000):
+    r'''
+    The points that compose a circle.
+    
+    :math:`\left \{ \begin{matrix}
+    x = r \cos \theta + x_c\\
+    y = r \sin \theta + y_c
+    \end{matrix} \right.`
+        
+    :param r: radius
+    :type r: float
+    
+    :param xc: center x-coordinate
+    :type xc: float
+    
+    :param yc: center y-coordinate
+    :type yc: float
+    
+    :param theta_i: initial angle [degrees] (default to 0.)
+    :type theta_i: float
+    
+    :param theta_f: final angle [degrees] (default to 360.)
+    :type theta_f: float
+          
+    :param n_points: number of points (default to 1000)
+    :type n_points: int
+    
+    :return: - **x** (*np.ndarray*) – x-coordinantes of a circle
+    
+       - **y** (*np.ndarray*) – y-coordinantes of a circle
+    '''
+    
+    theta = np.linspace(theta_i*np.pi/180., theta_f*np.pi/180., n_points)
+    x = r*np.cos(theta) + xc
+    y = r*np.sin(theta) + yc
+    
+    return x, y
+    
+def linear(x, a, b):
+    r'''
+    The linear function.
+    
+    :math:`f(x) = ax + b`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: slope
+    :type a: float
+
+    :param b: y-intercept
+    :type b: float
+
+    :return: - **f** (*float or np.ndarray*) – evaluated linear function 
+    '''
+    
+    return a*x + b
+    
+def quadratic(x, a, b, c):
+    r'''
+    The quadratic function.
+    
+    :math:`f(x) = ax^2 + bx + c`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+
+    :return: - **f** (*float or np.ndarray*) – evaluated quadratic function
+    '''
+    
+    return a*np.power(x, 2, dtype = 'float64') + b*x + c
+
+def cubic(x, a, b, c, d):
+    r'''
+    The cubic function.
+    
+    :math:`f(x) = ax^3 + bx^2 + cx + d`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+
+    :param d: function constant
+    :type d: float
+
+    :return: - **f** (*float or np.ndarray*) – evaluated cubic function
+    '''
+    
+    return a*np.power(x, 3, dtype = 'float64') + b*np.power(x, 2, dtype = 'float64') + c*x + d
+
+def exp_decay(x, a, b, c):
+    r'''
+    The exponential decay function.
+    
+    :math:`f(x) = a \mbox{ exp}(-|b|x) + c`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+
+    :return: - **f** (*float or np.ndarray*) – evaluated exponential decay function
+    '''
+    
+    return a*np.exp(-np.abs(b)*x) + c
+
+def biexp_decay(x, a, b, c, d, e):
+    r'''
+    The biexponential decay function.
+    
+    :math:`f(x) = a\mbox{ exp}(-|b|x) + c \mbox{ exp}(-|d|x) + e`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+
+    :param d: function constant
+    :type d: float
+
+    :param e: function constant
+    :type e: float
+    
+    :return: - **f** (*float or np.ndarray*) – evaluated biexponential decay function
+    '''
+        
+    return a*np.exp(-np.abs(b)*x) + c*np.exp(-np.abs(d)*x)  + e
+
+def exp_decay_inc_form(x, a, b, c):
+    r'''
+    The increasing form of the exponential decay function.
+    
+    :math:`f(x) = a \mbox{ [}1 - \mbox{exp}(-|b|x)] + c`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+    
+    :return: - **f** (*float or np.ndarray*) – evaluated exponential decay (increasing form) function
+    '''
+    
+    return a*(1 - np.exp(-np.abs(b)*x)) + c
+
+def natural_log(x, a, b, c):
+    r'''
+    The natural logarithm function.
+    
+    :math:`f(x) = a \mbox{ ln}(x + b) + c`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+    
+    :return: - **f** (*float or np.ndarray*) – evaluated natural logarithm function
+    '''
+        
+    return a*np.log(x + b) + c
+
+def gaussian(x, a, b, c):
+    r'''
+    The Gaussian function.
+    
+    :math:`f(x) = a \mbox{ exp}\left[-\frac{1}{2}\frac{(x - b)^2}{c^2}\right]`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+    
+    :return: - **f** (*float or np.ndarray*) – evaluated Gaussian function
+    '''
+    
+    return a*np.exp(-1./2.*(x - b)**2/c**2)
+
+def heaviside(x):
+    r'''
+    The Heaviside step function.
+    
+    :math:`H(x) =  
+    \left \{ \begin{matrix}
+    0, & \mbox{if } g < 0 \\
+    \frac{1}{2}, & \mbox{if } g = 0 \\
+    1, & \mbox{if } g > 0 \\
+    \end{matrix} \right.`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+    
+    :return: - **H** (*float or np.ndarray*) – evaluated Heaviside step function
+    '''
+    
+    if isinstance(x, np.ndarray) == True:
+        H = np.zeros(len(x))
+        for i in range(len(x)):
+            if x[i] < 0.:
+                H[i] = 0.
+            elif x[i] == 0.:
+                H[i] = 1./2.
+            else:
+                H[i] = 1.        
+    elif isinstance(x, (int, float)) == True:
+        if x < 0.:
+            H = 0.
+        elif x == 0.:
+            H = 1./2.
+        else:
+            H = 1.
+    else:
+        msg = 'x must be int, float or np.ndarray.'
+        raise Exception(msg)
+    
+    return H
+    
+def mod_gaussian_Wyman(x, a, b, c, d):
+    r'''
+    | The modified Gaussian function needed to calculate some analytical functions 
+    | from Wyman, Sloan & Shirley 2013 [WSS13] (see function :meth:`skinoptics.colors.cmfs`).
+    
+    :math:`f(x) = a \mbox{ exp}\left\{-d \mbox{ } \left[\mbox{ ln}\left(\frac{x - b}{c}\right)\right]^2\right\}`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+
+    :param d: function constant
+    :type d: float
+
+    :return: - **f** (*float or np.ndarray*) – evaluated function
+    '''
+        
+    return a*np.exp(-d*(np.log((x - b)/c))**2)
+
+def selector_function_Wyman(x, y, z): 
+    r'''
+    | The selector function needed to calculate some analytical functions 
+    | from Wyman, Sloan & Shirley 2013 [WSS13] (see function :meth:`skinoptics.colors.cmfs`).
+    
+    :math:`S(x,y,z) = y \mbox{ } (1 - H(x)) + z \mbox{ } H(x)`
+    
+    in which :math:`H(x)` is the Heaviside step function :meth:`skinoptics.utils.heaviside`.
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param y: function variable
+    :type y: float or np.ndarray
+
+    :param z: function variable
+    :type z: float or np.ndarray
+    
+    :return: - **S** (*float or np.ndarray*) – evaluated selector function
+    '''
+    
+    return y*(1 - heaviside(x)) + z*heaviside(x)
+
+def piecewise_gaussian_Wyman(x, a, b, c, d):
+    r'''
+    | The piecewise Gaussian function needed to calculate some analytical functions 
+    | from Wyman, Sloan & Shirley 2013 [WSS13] (see function :meth:`skinoptics.colors.cmfs`).
+    
+    :math:`f(x) = a \mbox{ exp}\left\{-\frac{1}{2}[(x - b)\mbox{ }S(x - b \mbox{, }c \mbox{, }d)]^2\right\}`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+
+    :param d: function constant
+    :type d: float
+    
+    :return: - **f** (*float or np.ndarray*) – evaluated function
+    '''
+    
+    return a*np.exp(-1./2.*((x - b)*selector_function_Wyman(x - b, c, d))**2)
+
+def hyperbolic_cossine(x, a, b, c, d):
+    r'''
+    The hyperbolic cossine function (with four parameters).
+    
+    :math:`f(x) = a \mbox{ cosh}\left[\frac{(x - b)}{c}\right] + d`
+    
+    :param x: function variable
+    :type x: float or np.ndarray
+
+    :param a: function constant
+    :type a: float
+
+    :param b: function constant
+    :type b: float
+
+    :param c: function constant
+    :type c: float
+
+    :param d: function constant
+    :type d: float
+    
+    :return: - **f** (*float or np.ndarray*) – evaluated hyperbolic cossine function
+    '''
+    
+    return a*np.cosh((x - b)/c) + d

skinoptics-0.0.1.dist-info/METADATA

@@ -0,0 +1,31 @@
+Metadata-Version: 2.4
+Name: skinoptics
+Version: 0.0.1
+Summary: SkinOptics: a python package with tools for building human skin computational models for Monte Carlo simulations of light transport
+Author-email: Victor Lima <victorporto@ifsc.usp.br>
+Project-URL: Homepage, https://github.com/victorportog/skinoptics
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: Microsoft :: Windows :: Windows 10
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy<2.0.0,>=1.26.4
+Requires-Dist: scipy<2.0.0,>=1.13.0
+Requires-Dist: pandas<3.0.0,>=2.2.2
+Dynamic: license-file
+
+SkinOptics
+==========
+
+**SkinOptics** is an open source Python package with tools for building human skin computational
+models for Monte Carlo simulations of light transport, as well as tools for analyzing simulation
+outputs. It can also be used for teaching and exploring about Optical Properties and Colorimetry.
+
+**SkinOptics** is under continuous development.
+
+New features may be available in the future.
+
+Please remember that **SkinOptics** is available without any warranty.
+
+You can access **SkinOptics** documentation at https://skinoptics.readthedocs.io/.

skinoptics-0.0.1.dist-info/RECORD

@@ -0,0 +1,44 @@
+skinoptics/__init__.py,sha256=ogqCEMFmoRaJINGAH1rYvCC9phRePtRtaY3HlS_7tQY,1575
+skinoptics/absorption_coefficient.py,sha256=f5mKTqgEiXKk0MDhPyL6t3w3jPDriJqI3R65U8mZNy8,36292
+skinoptics/anisotropy_factor.py,sha256=_Yxma1DJYy5nezwrgi0hay-6NXpbU2RYTKa4zFrjF9E,38594
+skinoptics/colors.py,sha256=mUAQOyLiwM-PnLjDLNSz7Lt57iRBawXutsDxDwNMY4g,56759
+skinoptics/dataframes.py,sha256=EMN1Cr0gJu0TM5fZJTP5qk8Dfu5VqvhnxUq5mcS2zQQ,6485
+skinoptics/refractive_index.py,sha256=1zuSNIjy3KkbPH30YNbkPosASENTBtkxym8IML0Uy0A,14994
+skinoptics/scattering_coefficient.py,sha256=3rsbwkqD2OeHfmu9z8bEGCBJ1RTjKzPV9fSu78gtrco,15244
+skinoptics/utils.py,sha256=qjBM3B9mTIPsYZNvt4u32rd96mnn4bovOoZfA6Y7aNA,10899
+skinoptics/datasets/colors/Lab_Alaluf2002.txt,sha256=PEmAPud84qe7U7V0kQliYvPwng3NuT-9qKLqabQWMYo,610
+skinoptics/datasets/colors/Lab_Xiao2017.txt,sha256=fx7y84PN5OFSDH6Z4rUNML6U8QOnHDr7MTWoxvNFBRs,903
+skinoptics/datasets/colors/cmfs.txt,sha256=q4Veg2SoCipCBRj2DL5pSzEH5RW4YORUmXxyVytB7KE,44381
+skinoptics/datasets/colors/rspds_A_D50_D65.txt,sha256=eV5hU07TI1wJZpLy0F54VYd--_Bh-WJ7XCWhca27YyA,15978
+skinoptics/datasets/colors/rspds_D55_D75.txt,sha256=UGljPp6-OiJewAEuSRptJ6Iof1IkioFndfBe6g_l8Xw,1974
+skinoptics/datasets/optical_properties/DE_Salomatina.txt,sha256=pNGNevgAaj_h8PaWP1zqOEO0WEQG-a4k1rbDt5AdmXU,24624
+skinoptics/datasets/optical_properties/DE_Shimojo.txt,sha256=g847CsdYbbOqqnoyPJs1XYVaiyEnPZWZHnEK-zzRfPo,281
+skinoptics/datasets/optical_properties/EP_Salomatina.txt,sha256=87UjyYbKBP0k__g_N1j3NuBvZybnEJZ7bKDYSsfxJkM,22791
+skinoptics/datasets/optical_properties/EP_Shimojo.txt,sha256=f78tGdUHiabV1tm6w904hVKAD4r9FuvcmICWX5vfvB0,281
+skinoptics/datasets/optical_properties/HY_Salomatina.txt,sha256=QE3I1dO3rZlPxHwh_OI72Z83PGaFI2dTDGXNi0g5QVc,22761
+skinoptics/datasets/optical_properties/HY_Shimojo.txt,sha256=5kzuMpS-TDdUNuRAGYu35u-UuycyjA-8mRd_GGa0yOw,281
+skinoptics/datasets/optical_properties/SCC_Salomatina.txt,sha256=p9Qa11PFBlEbgcI6uz7SiP4DZdTOK6P_f9yRGpgquF4,22938
+skinoptics/datasets/optical_properties/beta_oxy_Friebel.txt,sha256=94e4JCgKKxVOZtYGYBk-wupTOQOE_9tLuBsXw3HbS-k,1123
+skinoptics/datasets/optical_properties/ext_and_molarext_eum_Sarna.txt,sha256=u9BCCx8Ic-r5JFXbD4wpFqliMR-642hfR1V1jxwcyVg,701
+skinoptics/datasets/optical_properties/ext_and_molarext_oxy_and_deo_Prahl.txt,sha256=QecQ42RddkF0vTYCQeR_8eCB0t5tYWNG3XeR5fFKM3Q,6898
+skinoptics/datasets/optical_properties/ext_and_molarext_phe_Sarna.txt,sha256=VpRwJxAtI_CaHnrRb-c5_hUGR5IZFXytFzDPjSII1F0,1077
+skinoptics/datasets/optical_properties/iBCC_Salomatina.txt,sha256=pYSiuHf2YjIbWv-hGmq6skCI3D_WuTla2Zm08m79gGw,22843
+skinoptics/datasets/optical_properties/molarext_bil_Li.txt,sha256=Gi3k8BNQROnhZ6AxzOeSAuszimsSjCFHeDzsdl1_HAM,21294
+skinoptics/datasets/optical_properties/mua_fat_vanVeen.txt,sha256=U3pKXHEV6uv5A9-rg7dqKZPRK_XnkOwn4Ei83pptlUw,6810
+skinoptics/datasets/optical_properties/mua_wat_Hale.txt,sha256=NYQtCwD97mtWzI3yKEDARzo72TVh98aPdcE08RSOFfg,3590
+skinoptics/datasets/optical_properties/mua_wat_Segelstein.txt,sha256=ByJkeSTIahsyBjPRhMqC2GEBM9WJaAr-cGF4gINMLSQ,17805
+skinoptics/datasets/optical_properties/nBCC_Salomatina.txt,sha256=8y6eicmlXPrltQ2bHKvhgspNE-V2ZnX3NBFUX-EfSEY,25090
+skinoptics/datasets/optical_properties/n_AT_Matiatou.txt,sha256=L0pb8lvfl4kf8DExY-VwapGHvSPc0d9TaWlHyHb7n1w,109
+skinoptics/datasets/optical_properties/n_HY_Matiatou.txt,sha256=Ta9L4TeH-KuQ6XnZUoNvi9I8tmiy0U5fYpAzlo0ieB8,109
+skinoptics/datasets/optical_properties/n_and_k_DE_Ding.txt,sha256=oUetHghLih0Xt-yFY6JwFRWaS8mctUkHeYl6hEwdTBQ,350
+skinoptics/datasets/optical_properties/n_and_k_EP_Ding.txt,sha256=fNJRTLxfGn0PwuNs0t8b-7Ap6i8MYeMMq2RN5vJrnx4,351
+skinoptics/datasets/optical_properties/n_and_k_wat_Hale.txt,sha256=9Npq4eb94K5Nan7QnJazUnCl-6SBE33cTxddfjtWwb4,3045
+skinoptics/datasets/optical_properties/n_and_k_wat_Segelstein.txt,sha256=EZIS5158tj2MIAdDQLZH6L3BqopaMO0i2erJTdCywXs,36593
+skinoptics/datasets/optical_properties/oxy_and_deo_Bosschaart.txt,sha256=eF96Ao44TDUYRo6-8p0L7I9Q8h6wLNpEUyrcbo7FySA,24972
+skinoptics/datasets/spectra/Xiao2016/skindatabaseSpectra/readmeSpectra.docx,sha256=ren4htGe154BIlBridkvBvbc8AYY1RRmp4CVICYwDvc,15147
+skinoptics/datasets/spectra/Xiao2016/skindatabaseSpectra/skin spectra data.xlsx,sha256=z7shS1rZzqpaRGi_Ji0nYcSzIxEmADQOtaJ_Uwcotcc,1434709
+skinoptics-0.0.1.dist-info/licenses/LICENSE.txt,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
+skinoptics-0.0.1.dist-info/METADATA,sha256=od6-ADZjGDmPp9t-rjTzukaqn7_KjhNQQ9jhDYrWiCQ,1322
+skinoptics-0.0.1.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+skinoptics-0.0.1.dist-info/top_level.txt,sha256=4NYJW3uliYlvbd-Zywg2MxJOGe4wYA7Oz_I5EZF4YEQ,11
+skinoptics-0.0.1.dist-info/RECORD,,

skinoptics-0.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (77.0.3)
+Root-Is-Purelib: true
+Tag: py3-none-any
+