pypharm 1.3.6__tar.gz → 1.4.1__tar.gz

{pypharm-1.3.6 → pypharm-1.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypharm
-Version: 1.3.6
+Version: 1.4.1
 Summary: Module for solving pharmacokinetic problems
 Home-page: https://github.com/Krash13/PyPharm
 Author: Krash13
@@ -235,7 +235,7 @@ res = model(90, d=5700, compartment_number=0)
 Если оба параметра не заданы, то модель выраздается 
 в простую BaseCompartmentModel.
 
-**5) Модель MagicCompartmentModel** 
+**5) Модель ReleaseCompartmentModel** 
 
 Данная модель учитывает поправку на высвобождение
 ЛВ в модель вводятся дополнительные параметры:
@@ -272,8 +272,72 @@ plt.show()
 в таком случае, искомое нужно просто задать как None. Тогда вектор неизвестных это
 x = [configuration_matrix (неизвестные), outputs(неизвестные), volumes(неизвестные), release_parameters(неизвестные), v_release]
 
+**6) Использование PBPK модели**
 
-**6) Использование shared_memory** 
+Вы можете использовать PBPK модель как для рассчёта по известным
+данным так и для поиска параметров, исходя из ваших экспериментальных данных.
+
+Чтобы задать исзвестные вам константы, при инициализации объекта следует использовать
+параметры know_k и know_cl, которые содержат словари с известными параметрами, имена органов следует брать
+из класса ORGAN_NAMES.
+
+Ниже приведен пример поиска параметров и построение кривых распределения вещества
+в органах с использованием генетического алгоритма.
+
+```python
+from PyPharm import PBPKmod
+from PyPharm.constants import ORGAN_NAMES, MODEL_CONST
+
+model = PBPKmod()
+print(model.get_unknown_params())
+model.load_optimization_data(
+    time_exp=[12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+    dict_c_exp = {ORGAN_NAMES.LIVER: [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+              ORGAN_NAMES.LUNG: [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+              ORGAN_NAMES.SPLEEN: [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+    },
+    start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V']
+)
+result = model.optimize(
+    method='GA',
+    x_min=17 * [0.0001],
+    x_max=17 * [5],
+    genes=17 * [16],
+	n=300,
+    child_percent=0.3,
+    mutation_chance=0.5,
+    max_mutation=5,
+    t_max=300,
+    printing=True,
+)
+model.update_know_params(result)
+
+result = model(max_time=24 * 60, start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V'], step=0.1)
+model.plot_last_result(
+    organ_names=[ORGAN_NAMES.LUNG, ORGAN_NAMES.LIVER, ORGAN_NAMES.SPLEEN],
+    user_names={
+        ORGAN_NAMES.LUNG: 'Лёгкие',
+        ORGAN_NAMES.LIVER: 'Печень',
+        ORGAN_NAMES.SPLEEN: 'Селезёнка',
+    },
+    theoretic_data={
+        ORGAN_NAMES.LIVER: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+        },
+        ORGAN_NAMES.LUNG: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+        },
+        ORGAN_NAMES.SPLEEN: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+        }
+    }
+)
+```
+
+**7) Использование shared_memory** 
 
 Начиная с версии 1.3.0, вы можете использовать **shared_memory** для получения текущих данных
 оптимизации. Имя нужного вам участка памяти хранится в поле **memory_name**.
@@ -512,7 +576,7 @@ of variables.
 If both parameters are not set, then the model is deleted
 into a simple BaseCompartmentModel.
 
-**5) The MagicCompartmentModel model**
+**5) The ReleaseCompartmentModel model**
 
 This model takes into account the release adjustment
 medicinal substance additional parameters are introduced into the model:
@@ -549,7 +613,72 @@ The release_parameters and v_release parameters can be optimized
 in this case, you just need to set the desired value as None. Then the vector of unknowns is
 x = [configuration_matrix (unknown), outputs(unknown), volumes(unknown), release_parameters(unknown), v_release]
 
-**6) Using shared_memory**
+**6) Using the PBPK model**
+
+You can use the PBPK model both for calculations based on known
+data and for searching for parameters based on your experimental data.
+
+To set constants known to you, when initializing an object, you should use the
+parameters know_k and know_cl, which contain dictionaries with known parameters, the names of organs should be taken
+from the ORGAN_NAMES class.
+
+Below is an example of searching for parameters and constructing distribution curves of a substance
+in organs using a genetic algorithm.
+
+```python
+from PyPharm import PBPKmod
+from PyPharm.constants import ORGAN_NAMES, MODEL_CONST
+
+model = PBPKmod()
+print(model.get_unknown_params())
+model.load_optimization_data(
+    time_exp=[12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+    dict_c_exp = {ORGAN_NAMES.LIVER: [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+              ORGAN_NAMES.LUNG: [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+              ORGAN_NAMES.SPLEEN: [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+    },
+    start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V']
+)
+result = model.optimize(
+    method='GA',
+    x_min=17 * [0.0001],
+    x_max=17 * [5],
+    genes=17 * [16],
+	n=300,
+    child_percent=0.3,
+    mutation_chance=0.5,
+    max_mutation=5,
+    t_max=300,
+    printing=True,
+)
+model.update_know_params(result)
+
+result = model(max_time=24 * 60, start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V'], step=0.1)
+model.plot_last_result(
+    organ_names=[ORGAN_NAMES.LUNG, ORGAN_NAMES.LIVER, ORGAN_NAMES.SPLEEN],
+    user_names={
+        ORGAN_NAMES.LUNG: 'Лёгкие',
+        ORGAN_NAMES.LIVER: 'Печень',
+        ORGAN_NAMES.SPLEEN: 'Селезёнка',
+    },
+    theoretic_data={
+        ORGAN_NAMES.LIVER: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+        },
+        ORGAN_NAMES.LUNG: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+        },
+        ORGAN_NAMES.SPLEEN: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+        }
+    }
+)
+```
+
+**7) Using shared_memory**
 
 Since version 1.3.0, you can use **shared_memory** to get current data
 optimization. The name of the memory location you need is stored in the **memory_name** field.
@@ -563,3 +692,4 @@ print(c)
 
 The data is stored in list format [current_iteration, x0, ... , xn, f], works only for the country_optimization algorithm.
 
+

{pypharm-1.3.6 → pypharm-1.4.1}/PyPharm/__init__.py

@@ -1 +1,3 @@
-from .models import BaseCompartmentModel, MagicCompartmentModel, ReleaseCompartmentModel
+from .models import BaseCompartmentModel, MagicCompartmentModel, ReleaseCompartmentModel, PBPKmod
+
+

{pypharm-1.3.6/PyPharm → pypharm-1.4.1/PyPharm/algorithms}/country_optimization.py

@@ -467,4 +467,3 @@ class CountriesAlgorithm:
                     self.memory_list[i + 1] = float(result.x[i])
                 self.memory_list[-1] = float(result.f)
         return (result.x, result.f, False, ti)
-

{pypharm-1.3.6/PyPharm → pypharm-1.4.1/PyPharm/algorithms}/country_optimization_v3.py

@@ -345,30 +345,31 @@ class CountriesAlgorithm:
                         f_min=f_min,
                         f_max=f_max
                     )
-                    # country.extinction(
-                    #     m_min=self.m[0],
-                    #     m_max=self.m[1],
-                    #     f_min=f_min,
-                    #     f_max=f_max
-                    # )
-            self.countries = sorted(self.countries, key=attrgetter('best_function'))
-            f_min = self.countries[0].best_function
-            f_max = self.countries[-1].best_function
-            s = sum(country.roulette_function(f_min, f_max) for country in self.countries if len(country.population) > 1)
-            self.countries.reverse()
-            for country in self.countries:
-                plus = 0
-                if len(country.population) >= 1:
-                    res = country.extinction1(
-                        max(self.N // 2, ceil(country.roulette_function(f_min, f_max) / s * self.N * self.M)) + plus
+                    country.extinction(
+                        m_min=self.m[0],
+                        m_max=self.m[1],
+                        f_min=f_min,
+                        f_max=f_max
                     )
-                    if res:
-                        plus += res
-                    else:
-                        plus = 0
-
-            indexes = np.where(vector_check_population(self.countries) == True)
-            self.countries = [self.countries[i] for i in indexes[0]]
+            self.countries = [country for country in self.countries if len(country.population)]
+            # self.countries = sorted(self.countries, key=attrgetter('best_function'))
+            # f_min = self.countries[0].best_function
+            # f_max = self.countries[-1].best_function
+            # s = sum(country.roulette_function(f_min, f_max) for country in self.countries if len(country.population) > 1)
+            # self.countries.reverse()
+            # for country in self.countries:
+            #     plus = 0
+            #     if len(country.population) >= 1:
+            #         res = country.extinction1(
+            #             max(self.N // 2, ceil(country.roulette_function(f_min, f_max) / s * self.N * self.M)) + plus
+            #         )
+            #         if res:
+            #             plus += res
+            #         else:
+            #             plus = 0
+            #
+            # indexes = np.where(vector_check_population(self.countries) == True)
+            # self.countries = [self.countries[i] for i in indexes[0]]
 
             for individual in e_individuals:
                 random_country = self.countries[random.randint(0, len(self.countries) - 1)]
@@ -392,32 +393,33 @@ class CountriesAlgorithm:
                 for i in range(len(result.real_x)):
                     self.memory_list[i + 1] = float(result.real_x[i])
                 self.memory_list[-1] = float(result.f)
+
         return (result.real_x, result.f, False, ti)
 
 
 
-# def f(x):
-#     return sum([(xi ** 4 - 16 * xi ** 2 + 5 *xi) / 2 for xi in x])
-# #
-# # k = 0
-# # for i in range(100):
-# CA = CountriesAlgorithm(
-#     f=f,
-#     Xmin=[-5.12 for i in range(3)],
-#     Xmax=[5.12 for i in range(3)],
-#     genes=[16 for i in range(3)],
-#     M=20,
-#     N=15,
-#     n=[1, 10],
-#     m=[3, 8],
-#     k=8,
-#     l=3,
-#     ep=[0.2, 0.4],
-#     max_mutation=16,
-#     tmax=300,
-#     printing=True,
-# )
-# r = CA.start()
+def f(x):
+    return sum([(xi ** 4 - 16 * xi ** 2 + 5 *xi) / 2 for xi in x])
+#
+# k = 0
+# for i in range(100):
+CA = CountriesAlgorithm(
+    f=f,
+    Xmin=[-5.12 for i in range(20)],
+    Xmax=[5.12 for i in range(20)],
+    genes=[16 for i in range(20)],
+    M=20,
+    N=15,
+    n=[1, 10],
+    m=[3, 8],
+    k=8,
+    l=3,
+    ep=[0.2, 0.4],
+    max_mutation=16,
+    tmax=300,
+    printing=True,
+)
+r = CA.start()
 
 #     print(i, r[2], r[0], r[1])
 #     if r[2]:

pypharm-1.4.1/PyPharm/constants.py

@@ -0,0 +1,56 @@
+MODEL_CONST = {
+    'human':{
+                  'adipose': {'V':143, 'Q':3.7},
+                  'bone': {'V':124, 'Q': 3.6} ,
+                  'brain': {'V':20.7, 'Q': 10} ,
+                  'gut': {'V':23.6, 'Q': 13} ,
+                  'heart': {'V':3.8, 'Q': 2.14},
+                  'kidney': {'V':4.4, 'Q': 15.7} ,
+                  'liver': {'V':24.1, 'Q': 21} ,
+                  'lung': {'V':16.7, 'Q': 71} ,
+                  'muscle': {'V':429, 'Q': 10.7} ,
+                  'pancreas': {'V':1.2, 'Q': 1.9} ,
+                  'skin': {'V':111, 'Q': 4.3} ,
+                  'spleen': {'V':2.7, 'Q': 1.1},
+                  'stomach': {'V':2.2, 'Q':0.56},
+                  'teaster': {'V':0.51, 'Q':0.04},
+                  'arterial_blood': {'V':25.7} ,
+                  'venous_blood': {'V':51.4}
+               },
+               'rat':{
+                  'adipose': {'V':40, 'Q':1.6},
+                  'bone': {'V':53.2, 'Q': 10.12},
+                  'brain': {'V':6.8, 'Q': 5.32}  ,
+                  'gut': {'V':40, 'Q': 52}  ,
+                  'heart': {'V':3.2, 'Q': 15.68},
+                  'kidney': {'V':9.2, 'Q': 36.92},
+                  'liver': {'V':41.2, 'Q': 80}  ,
+                  'lung': {'V':4, 'Q': 203.2}   ,
+                  'muscle': {'V':487.6, 'Q': 30} ,
+                  'pancreas': {'V':5.2, 'Q': 4}  ,
+                  'skin': {'V':160, 'Q': 20}   ,
+                  'spleen': {'V':2.4, 'Q': 5}  ,
+                  'stomach': {'V':4.4, 'Q':8.2} ,
+                  'teaster': {'V':10, 'Q':1.8}   ,
+                  'arterial_blood': {'V':22.4, 'Q':10.8}  ,
+                  'venous_blood': {'V':45.2}
+               }
+}
+
+class ORGAN_NAMES:
+
+    LUNG = 'lung'
+    HEART = 'heart'
+    BRAIN = 'brain'
+    MUSCLE = 'muscle'
+    ADIPOSE = 'adipose'
+    SKIN = 'skin'
+    BONE = 'bone'
+    KIDNEY = 'kidney'
+    LIVER = 'liver'
+    GUT = 'gut'
+    SPLEEN = 'spleen'
+    STOMACH = 'stomach'
+    PANCREAS = 'pancreas'
+    VENOUS = 'venous_blood'
+    ARTERIAL = 'arterial_blood'

pypharm-1.4.1/PyPharm/models/__init__.py

@@ -0,0 +1,2 @@
+from .compartment_models import BaseCompartmentModel, MagicCompartmentModel, ReleaseCompartmentModel
+from .pbpk import PBPKmod

pypharm-1.3.6/PyPharm/models.py → pypharm-1.4.1/PyPharm/models/compartment_models.py

@@ -4,9 +4,9 @@ import numpy as np
 from scipy.integrate import solve_ivp, RK45
 from scipy.integrate import simps
 from scipy.optimize import minimize
-from .country_optimization import CountriesAlgorithm
-from .country_optimization_v2 import CountriesAlgorithm_v2
-from .genetic_optimization import GeneticAlgorithm
+from ..algorithms.country_optimization import CountriesAlgorithm
+from ..algorithms.country_optimization_v2 import CountriesAlgorithm_v2
+from ..algorithms.genetic_optimization import GeneticAlgorithm
 from numba import njit
 import matplotlib.pyplot as plt
 

pypharm-1.4.1/PyPharm/models/pbpk.py

@@ -0,0 +1,404 @@
+from multiprocessing import shared_memory
+import datetime
+import numpy as np
+from scipy.integrate import solve_ivp, RK45, odeint
+from scipy.integrate import simps
+from scipy.optimize import minimize
+from PyPharm.algorithms.country_optimization import CountriesAlgorithm
+from PyPharm.algorithms.country_optimization_v2 import CountriesAlgorithm_v2
+from PyPharm.algorithms.genetic_optimization import GeneticAlgorithm
+from PyPharm.constants import MODEL_CONST, ORGAN_NAMES
+from numba import njit, types
+from numba.typed import Dict
+import matplotlib.pyplot as plt
+
+cnst_rat = MODEL_CONST['rat']
+cnst_human = MODEL_CONST['human']
+
+
+class PBPKmod:
+
+    _organs = ['lung', 'heart', 'brain', 'muscle', 'adipose', 'skin', 'bone', 'kidney',
+                  'liver', 'gut', 'spleen', 'stomach', 'pancreas', 'venous_blood', 'arterial_blood']
+    _cl_organs = ['kidney', 'liver']
+    
+    def __init__(self, know_k={}, know_cl={}, numba_option=False):
+        self.know_k = know_k
+        self.know_cl = know_cl
+        self._optim = False
+        self.numba_option = numba_option
+        if numba_option:
+            self.cnst_v_rat = Dict.empty(
+                key_type=types.unicode_type,
+                value_type=types.float64
+            )
+            for k, v in cnst_rat.items():
+                self.cnst_v_rat[k] = v['V']
+            self.cnst_v_human = Dict.empty(
+                key_type=types.unicode_type,
+                value_type=types.float64
+            )
+            for k, v in cnst_human.items():
+                self.cnst_v_human[k] = v['V']
+            self.cnst_q_rat = Dict.empty(
+                key_type=types.unicode_type,
+                value_type=types.float64
+            )
+            for k, v in cnst_rat.items():
+                if v.get('Q'):
+                    self.cnst_q_rat[k] = v['Q']
+            self.cnst_q_human = Dict.empty(
+                key_type=types.unicode_type,
+                value_type=types.float64
+            )
+            for k, v in cnst_human.items():
+                if v.get('Q'):
+                    self.cnst_q_human[k] = v['Q']
+
+    def load_optimization_data(self, time_exp, dict_c_exp, start_c_in_venous, is_human=False):
+        self.time_exp = time_exp
+        self.dict_c_exp = dict_c_exp
+        self.start_c_in_venous = start_c_in_venous
+        self.is_human = is_human
+
+    def fitness(self, k_cl):
+
+        self.k_cl = k_cl
+
+        sol_difurs = self(max(self.time_exp), self.start_c_in_venous, self.is_human)
+        # Список для хранения результатов
+        present_organs_indices = []
+
+        # Проверяем, какие ключи из 'organs' есть в 'dict_n'
+        for organ in self._organs:
+            if organ in self.dict_c_exp:
+                index = self._organs.index(organ)  # Получаем индекс органа в списке organs
+                present_organs_indices.append((organ, index))
+
+        rez_err = 0
+        for organ, index in present_organs_indices:
+            mean_y = sum(sol_difurs[:, index]) / len(sol_difurs[:, index])
+            a = [(sol_difurs[:, index][self.time_exp[i]] - self.dict_c_exp[organ][i]) ** 2 for i in range(len(self.dict_c_exp[organ]))]
+            a = sum(a)
+            b = [(mean_y - self.dict_c_exp[organ][i]) ** 2 for i in
+                 range(len(self.dict_c_exp[organ]))]
+            b = sum(b)
+            rez_err += a / b
+            # rez_err += sum([abs(sol_difurs[:, index][self.time_exp[i]] - self.dict_c_exp[organ][i]) for i in
+            #                 range(len(self.dict_c_exp[organ]))])
+
+        return rez_err
+    
+    def __call__(self, max_time, start_c_in_venous, is_human=False, step=1):
+        self.y0 = [0 for _ in range(15)]  # всего в модели 15 органов
+        self.y0[-2] = start_c_in_venous
+        t = np.linspace(0, max_time, max_time + 1 if self._optim else int(1 / step * max_time) + 1)
+        
+        if not hasattr(self, 'k_cl'):
+            self.k_cl = []
+
+        full_k = []
+        i = 0
+        for name in self._organs:
+            know_k = self.know_k.get(name)
+            if know_k is not None:
+                full_k.append(know_k)
+            else:
+                full_k.append(self.k_cl[i])
+                i += 1
+        full_cl = []
+
+        for name in self._cl_organs:
+            know_k = self.know_cl.get(name)
+            if know_k is not None:
+                full_cl.append(know_k)
+            else:
+                full_cl.append(self.k_cl[i])
+                i += 1
+        if not self.numba_option:
+            sol_difurs = odeint(
+                self.fullPBPKmodel,
+                self.y0,
+                t,
+                args=([*full_k, *full_cl], is_human)
+            )
+        else:
+            k_cl = np.array([*full_k, *full_cl])
+            if is_human:
+                cnst_v = self.cnst_v_human
+                cnst_q = self.cnst_q_human
+            else:
+                cnst_v = self.cnst_v_rat
+                cnst_q = self.cnst_q_rat
+            function = lambda c, t: self.numba_fullPBPK_for_optimization(
+                y=c,
+                t=t,
+                K_CL=k_cl.astype(np.float64),
+                cnst_q=cnst_q,
+                cnst_v=cnst_v
+            )
+            sol_difurs = odeint(
+                function,
+                self.y0,
+                t
+            )
+        if self._optim:
+            return sol_difurs
+
+        self.last_result = {
+            't': t
+        }
+        for organ in self._organs:
+            index = self._organs.index(organ)
+            self.last_result[organ] = np.array([sol_difurs[i][index] for i in range(t.size)])
+        return self.last_result
+
+    def plot_last_result(self, organ_names=[], left=None, right=None, user_names={}, theoretic_data={}, y_lims={}):
+        if hasattr(self, 'last_result'):
+            for name in organ_names:
+                if theoretic_data.get(name):
+                    plt.plot(theoretic_data[name]['x'], theoretic_data[name]['y'], '*r')
+                plt.plot(
+                    self.last_result['t'],
+                    self.last_result.get(name),
+                )
+                plt.title(user_names.get(name, name))
+                plt.xlim(left=left, right=right)
+                if y_lims.get(name):
+                    plt.ylim(y_lims.get(name))
+                plt.grid()
+                plt.show()
+
+    def optimize(self, method=None, user_method=None, method_is_func=True,
+                 optimization_func_name='__call__', **kwargs):
+        """
+        Функция оптимизации модели
+
+        Args:
+            method: Метод оптимизации, любой доступный minimize + 'country_optimization' и 'country_optimization_v2'
+            max_step: Максимальный шаг при решении СДУ
+            **kwargs: Дополнительные именованные аргументы
+
+        Returns:
+            None
+        """
+        self._optim = True
+        f = lambda x: self.fitness(x)
+        if user_method is not None:
+            if method_is_func:
+                x = user_method(f, **kwargs)
+            else:
+                optimization_obj = user_method(f, **kwargs)
+                x = getattr(optimization_obj, optimization_func_name)()
+        else:
+            if method == 'country_optimization':
+                CA = CountriesAlgorithm(
+                    f=f,
+                    memory_list=getattr(self, 'memory', None),
+                    **kwargs
+                )
+                CA.start()
+                x = CA.countries[0].population[0].x
+            elif method == 'country_optimization_v2':
+                CA = CountriesAlgorithm_v2(
+                    f=f,
+                    **kwargs
+                )
+                CA.start()
+                x = CA.countries[0].population[0].x
+            elif method == 'GA':
+                CA = GeneticAlgorithm(
+                    f=f,
+                    **kwargs
+                )
+                x = CA.start()
+            else:
+                res = minimize(
+                    fun=f,
+                    method=method,
+                    **kwargs
+                )
+                x = res.x
+        self._optim = False
+        return x
+
+    def update_know_params(self, k_cl):
+        i = 0
+        for name in self._organs:
+            know_k = self.know_k.get(name)
+            if know_k is None:
+                self.know_k[name] = k_cl[i]
+                i += 1
+        for name in self._cl_organs:
+            know_cl = self.know_cl.get(name)
+            if know_cl is None:
+                self.know_cl[name] = k_cl[i]
+                i += 1
+
+    def get_unknown_params(self):
+        result = []
+        for name in self._organs:
+            know_k = self.know_k.get(name)
+            if know_k is None:
+                result.append(f"k_{name}")
+        for name in self._cl_organs:
+            know_cl = self.know_cl.get(name)
+            if know_cl is None:
+                result.append(f"cl_{name}")
+        return result
+
+    def fullPBPKmodel(self, y, t, K_CL, is_human=False):  # V, Q, K, CL):
+        # 15 органов
+        if is_human:
+            cnst = cnst_human
+        else:
+            cnst = cnst_rat
+        C_lung, C_heart, C_brain, C_muscle, C_fat, C_skin, C_bone, \
+            C_kidney, C_liver, C_gut, C_spleen, C_stomach, C_pancreas, C_V, C_A = y
+
+        K_lung, K_heart, K_brain, K_muscle, K_fat, K_skin, K_bone, \
+            K_kidney, K_liver, K_gut, K_spleen, K_stomach, K_pancreas, K_liver_cl, K_kidney_cl = K_CL[:15]
+        CL_kidney, CL_liver = K_CL[15:]
+
+        dC_lung_dt = cnst['lung']['Q'] * (C_V - C_lung / K_lung) / cnst['lung']['V']
+        dC_heart_dt = cnst['heart']['Q'] * (C_A - C_heart / K_heart) / cnst['heart']['V']
+        dC_brain_dt = cnst['brain']['Q'] * (C_A - C_brain / K_brain) / cnst['brain']['V']
+        dC_muscle_dt = cnst['muscle']['Q'] * (C_A - C_muscle / K_muscle) / cnst['muscle']['V']
+        dC_fat_dt = cnst['adipose']['Q'] * (C_A - C_fat / K_fat) / cnst['adipose']['V']
+        dC_skin_dt = cnst['skin']['Q'] * (C_A - C_skin / K_skin) / cnst['skin']['V']
+        dC_bone_dt = cnst['bone']['Q'] * (C_A - C_bone / K_bone) / cnst['bone']['V']
+        # Kidney        V(Kidney)*dC(Kidney)/dt = Q(Kidney)*C(A)-Q(Kidney)*CV(Kidney)-CL(Kidney,int)*CV(Kidney,int)?
+        dC_kidney_dt = (cnst['kidney']['Q'] * (C_A - C_kidney / K_kidney) - CL_kidney * C_kidney / K_kidney_cl) / \
+                       cnst['kidney']['V']  # ???
+
+        # Liver         V(Liver)*dC(Liver)/dt = (Q(Liver)-Q(Spleen)-Q(Gut)-Q(Pancreas)-Q(Stomach))*C(A) + Q(Spleen)*CV(Spleen) +
+        #                                     + Q(Gut)*CV(Gut) + Q(Pancreas)*CV(Pancreas) + Q(Stomach)*CV(Stomach) -
+        #                                     - Q(Liver)*CV(Liver) - CL(Liver,int)*CV(Liver,int)? # тут скорее всего нужно вычитать потоки из друг друга дополнительно по крови что бы сохранить массовый баланс
+        Q_liver_in_from_art = cnst['liver']['Q'] - cnst['gut']['Q'] - cnst['spleen']['Q'] - \
+                              cnst['pancreas']['Q'] - cnst['stomach']['Q']
+        dC_liver_dt = (
+                              Q_liver_in_from_art * C_A + cnst['gut']['Q'] * C_gut / K_gut
+                              + cnst['spleen']['Q'] * C_spleen / K_spleen
+                              + cnst['stomach']['Q'] * C_stomach / K_stomach
+                              + cnst['pancreas']['Q'] * C_pancreas / K_pancreas
+                              - cnst['liver']['Q'] * C_liver / K_liver
+                              - CL_liver * C_liver / K_liver_cl  # ???
+                      ) / cnst['liver']['V']
+
+        dC_gut_dt = cnst['gut']['Q'] * (C_A - C_gut / K_gut) / cnst['gut']['V']
+        dC_spleen_dt = cnst['spleen']['Q'] * (C_A - C_spleen / K_spleen) / cnst['spleen']['V']
+        dC_stomach_dt = cnst['stomach']['Q'] * (C_A - C_stomach / K_stomach) / cnst['stomach']['V']
+        dC_pancreas_dt = cnst['pancreas']['Q'] * (C_A - C_pancreas / K_pancreas) / cnst['pancreas']['V']
+
+        dC_venouse_dt = (
+                                cnst['heart']['Q'] * C_heart / K_heart
+                                + cnst['brain']['Q'] * C_brain / K_brain
+                                + cnst['muscle']['Q'] * C_muscle / K_muscle
+                                + cnst['skin']['Q'] * C_skin / K_skin
+                                + cnst['adipose']['Q'] * C_fat / K_fat
+                                + cnst['bone']['Q'] * C_bone / K_bone
+                                + cnst['kidney']['Q'] * C_kidney / K_kidney
+                                + cnst['liver']['Q'] * C_liver / K_liver
+                                - cnst['lung']['Q'] * C_V
+                        ) / cnst['venous_blood']['V']
+
+        dC_arterial_dt = cnst['lung']['Q'] * (C_lung / K_lung - C_A) / cnst['arterial_blood']['V']
+
+        y_new = [dC_lung_dt, dC_heart_dt, dC_brain_dt, dC_muscle_dt, dC_fat_dt, dC_skin_dt, dC_bone_dt, \
+                 dC_kidney_dt, dC_liver_dt, dC_gut_dt, dC_spleen_dt, dC_stomach_dt, dC_pancreas_dt, dC_venouse_dt,
+                 dC_arterial_dt]
+        return y_new
+
+    @staticmethod
+    @njit
+    def numba_fullPBPK_for_optimization(y, t, K_CL, cnst_q, cnst_v):
+        C_lung, C_heart, C_brain, C_muscle, C_fat, C_skin, C_bone, \
+            C_kidney, C_liver, C_gut, C_spleen, C_stomach, C_pancreas, C_V, C_A = y
+
+        K_lung, K_heart, K_brain, K_muscle, K_fat, K_skin, K_bone, \
+            K_kidney, K_liver, K_gut, K_spleen, K_stomach, K_pancreas, K_liver_cl, K_kidney_cl = K_CL[:15]
+        CL_kidney, CL_liver = K_CL[15:]
+
+        dC_lung_dt = cnst_q['lung'] * (C_V - C_lung / K_lung) / cnst_v['lung']
+        dC_heart_dt = cnst_q['heart'] * (C_A - C_heart / K_heart) / cnst_v['heart']
+        dC_brain_dt = cnst_q['brain'] * (C_A - C_brain / K_brain) / cnst_v['brain']
+        dC_muscle_dt = cnst_q['muscle'] * (C_A - C_muscle / K_muscle) / cnst_v['muscle']
+        dC_fat_dt = cnst_q['adipose'] * (C_A - C_fat / K_fat) / cnst_v['adipose']
+        dC_skin_dt = cnst_q['skin'] * (C_A - C_skin / K_skin) / cnst_v['skin']
+        dC_bone_dt = cnst_q['bone'] * (C_A - C_bone / K_bone) / cnst_v['bone']
+        # Kidney        V(Kidney)*dC(Kidney)/dt = Q(Kidney)*C(A)-Q(Kidney)*CV(Kidney)-CL(Kidney,int)*CV(Kidney,int)?
+        dC_kidney_dt = (cnst_q['kidney'] * (C_A - C_kidney / K_kidney) - CL_kidney * C_kidney / K_kidney_cl) / \
+                       cnst_v['kidney']  # ???
+
+        # Liver         V(Liver)*dC(Liver)/dt = (Q(Liver)-Q(Spleen)-Q(Gut)-Q(Pancreas)-Q(Stomach))*C(A) + Q(Spleen)*CV(Spleen) +
+        #                                     + Q(Gut)*CV(Gut) + Q(Pancreas)*CV(Pancreas) + Q(Stomach)*CV(Stomach) -
+        #                                     - Q(Liver)*CV(Liver) - CL(Liver,int)*CV(Liver,int)? # тут скорее всего нужно вычитать потоки из друг друга дополнительно по крови что бы сохранить массовый баланс
+        Q_liver_in_from_art = cnst_q['liver'] - cnst_q['gut'] - cnst_q['spleen'] - \
+                              cnst_q['pancreas'] - cnst_q['stomach']
+        dC_liver_dt = (
+                              Q_liver_in_from_art * C_A + cnst_q['gut'] * C_gut / K_gut
+                              + cnst_q['spleen'] * C_spleen / K_spleen
+                              + cnst_q['stomach'] * C_stomach / K_stomach
+                              + cnst_q['pancreas'] * C_pancreas / K_pancreas
+                              - cnst_q['liver'] * C_liver / K_liver
+                              - CL_liver * C_liver / K_liver_cl  # ???
+                      ) / cnst_v['liver']
+
+        dC_gut_dt = cnst_q['gut'] * (C_A - C_gut / K_gut) / cnst_v['gut']
+        dC_spleen_dt = cnst_q['spleen'] * (C_A - C_spleen / K_spleen) / cnst_v['spleen']
+        dC_stomach_dt = cnst_q['stomach'] * (C_A - C_stomach / K_stomach) / cnst_v['stomach']
+        dC_pancreas_dt = cnst_q['pancreas'] * (C_A - C_pancreas / K_pancreas) / cnst_v['pancreas']
+
+        dC_venouse_dt = (
+                                cnst_q['heart'] * C_heart / K_heart
+                                + cnst_q['brain'] * C_brain / K_brain
+                                + cnst_q['muscle'] * C_muscle / K_muscle
+                                + cnst_q['skin'] * C_skin / K_skin
+                                + cnst_q['adipose'] * C_fat / K_fat
+                                + cnst_q['bone'] * C_bone / K_bone
+                                + cnst_q['kidney'] * C_kidney / K_kidney
+                                + cnst_q['liver'] * C_liver / K_liver
+                                - cnst_q['lung'] * C_V
+                        ) / cnst_v['venous_blood']
+
+        dC_arterial_dt = cnst_q['lung'] * (C_lung / K_lung - C_A) / cnst_v['arterial_blood']
+
+        y_new = np.array([dC_lung_dt, dC_heart_dt, dC_brain_dt, dC_muscle_dt, dC_fat_dt, dC_skin_dt, dC_bone_dt, \
+                 dC_kidney_dt, dC_liver_dt, dC_gut_dt, dC_spleen_dt, dC_stomach_dt, dC_pancreas_dt, dC_venouse_dt,
+                 dC_arterial_dt]).astype(np.float64)
+        return y_new
+
+
+model = PBPKmod(numba_option=True)
+print(model.get_unknown_params())
+model.load_optimization_data(
+    time_exp=[12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+    dict_c_exp = {ORGAN_NAMES.LIVER: [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+              ORGAN_NAMES.LUNG: [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+              ORGAN_NAMES.SPLEEN: [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+    },
+    start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V']
+)
+
+result = model.optimize(
+    method='country_optimization',
+    Xmin=17 * [0.0001],
+    Xmax=17 * [5],
+    M=20,
+    N=25,
+    n=[1, 10],
+    p=[0.00001, 2],
+    m=[1, 8],
+    k=8,
+    l=3,
+    ep=[0.2, 0.4],
+    tmax=3,
+    printing=True,
+)
+model.update_know_params(result)
+
+result = model(max_time=24 * 60, start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V'], step=0.1)
+
+model_furs = PBPKmod(numba_option=True)
+
+print()

{pypharm-1.3.6 → pypharm-1.4.1}/README.md

@@ -219,7 +219,7 @@ res = model(90, d=5700, compartment_number=0)
 Если оба параметра не заданы, то модель выраздается 
 в простую BaseCompartmentModel.
 
-**5) Модель MagicCompartmentModel** 
+**5) Модель ReleaseCompartmentModel** 
 
 Данная модель учитывает поправку на высвобождение
 ЛВ в модель вводятся дополнительные параметры:
@@ -256,8 +256,72 @@ plt.show()
 в таком случае, искомое нужно просто задать как None. Тогда вектор неизвестных это
 x = [configuration_matrix (неизвестные), outputs(неизвестные), volumes(неизвестные), release_parameters(неизвестные), v_release]
 
+**6) Использование PBPK модели**
 
-**6) Использование shared_memory** 
+Вы можете использовать PBPK модель как для рассчёта по известным
+данным так и для поиска параметров, исходя из ваших экспериментальных данных.
+
+Чтобы задать исзвестные вам константы, при инициализации объекта следует использовать
+параметры know_k и know_cl, которые содержат словари с известными параметрами, имена органов следует брать
+из класса ORGAN_NAMES.
+
+Ниже приведен пример поиска параметров и построение кривых распределения вещества
+в органах с использованием генетического алгоритма.
+
+```python
+from PyPharm import PBPKmod
+from PyPharm.constants import ORGAN_NAMES, MODEL_CONST
+
+model = PBPKmod()
+print(model.get_unknown_params())
+model.load_optimization_data(
+    time_exp=[12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+    dict_c_exp = {ORGAN_NAMES.LIVER: [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+              ORGAN_NAMES.LUNG: [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+              ORGAN_NAMES.SPLEEN: [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+    },
+    start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V']
+)
+result = model.optimize(
+    method='GA',
+    x_min=17 * [0.0001],
+    x_max=17 * [5],
+    genes=17 * [16],
+	n=300,
+    child_percent=0.3,
+    mutation_chance=0.5,
+    max_mutation=5,
+    t_max=300,
+    printing=True,
+)
+model.update_know_params(result)
+
+result = model(max_time=24 * 60, start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V'], step=0.1)
+model.plot_last_result(
+    organ_names=[ORGAN_NAMES.LUNG, ORGAN_NAMES.LIVER, ORGAN_NAMES.SPLEEN],
+    user_names={
+        ORGAN_NAMES.LUNG: 'Лёгкие',
+        ORGAN_NAMES.LIVER: 'Печень',
+        ORGAN_NAMES.SPLEEN: 'Селезёнка',
+    },
+    theoretic_data={
+        ORGAN_NAMES.LIVER: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+        },
+        ORGAN_NAMES.LUNG: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+        },
+        ORGAN_NAMES.SPLEEN: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+        }
+    }
+)
+```
+
+**7) Использование shared_memory** 
 
 Начиная с версии 1.3.0, вы можете использовать **shared_memory** для получения текущих данных
 оптимизации. Имя нужного вам участка памяти хранится в поле **memory_name**.
@@ -496,7 +560,7 @@ of variables.
 If both parameters are not set, then the model is deleted
 into a simple BaseCompartmentModel.
 
-**5) The MagicCompartmentModel model**
+**5) The ReleaseCompartmentModel model**
 
 This model takes into account the release adjustment
 medicinal substance additional parameters are introduced into the model:
@@ -533,7 +597,72 @@ The release_parameters and v_release parameters can be optimized
 in this case, you just need to set the desired value as None. Then the vector of unknowns is
 x = [configuration_matrix (unknown), outputs(unknown), volumes(unknown), release_parameters(unknown), v_release]
 
-**6) Using shared_memory**
+**6) Using the PBPK model**
+
+You can use the PBPK model both for calculations based on known
+data and for searching for parameters based on your experimental data.
+
+To set constants known to you, when initializing an object, you should use the
+parameters know_k and know_cl, which contain dictionaries with known parameters, the names of organs should be taken
+from the ORGAN_NAMES class.
+
+Below is an example of searching for parameters and constructing distribution curves of a substance
+in organs using a genetic algorithm.
+
+```python
+from PyPharm import PBPKmod
+from PyPharm.constants import ORGAN_NAMES, MODEL_CONST
+
+model = PBPKmod()
+print(model.get_unknown_params())
+model.load_optimization_data(
+    time_exp=[12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+    dict_c_exp = {ORGAN_NAMES.LIVER: [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+              ORGAN_NAMES.LUNG: [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+              ORGAN_NAMES.SPLEEN: [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+    },
+    start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V']
+)
+result = model.optimize(
+    method='GA',
+    x_min=17 * [0.0001],
+    x_max=17 * [5],
+    genes=17 * [16],
+	n=300,
+    child_percent=0.3,
+    mutation_chance=0.5,
+    max_mutation=5,
+    t_max=300,
+    printing=True,
+)
+model.update_know_params(result)
+
+result = model(max_time=24 * 60, start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V'], step=0.1)
+model.plot_last_result(
+    organ_names=[ORGAN_NAMES.LUNG, ORGAN_NAMES.LIVER, ORGAN_NAMES.SPLEEN],
+    user_names={
+        ORGAN_NAMES.LUNG: 'Лёгкие',
+        ORGAN_NAMES.LIVER: 'Печень',
+        ORGAN_NAMES.SPLEEN: 'Селезёнка',
+    },
+    theoretic_data={
+        ORGAN_NAMES.LIVER: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+        },
+        ORGAN_NAMES.LUNG: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+        },
+        ORGAN_NAMES.SPLEEN: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+        }
+    }
+)
+```
+
+**7) Using shared_memory**
 
 Since version 1.3.0, you can use **shared_memory** to get current data
 optimization. The name of the memory location you need is stored in the **memory_name** field.
@@ -545,4 +674,4 @@ print(c)
 # ShareableList([4, 3.5192100752465563, 1.4158559227257506, 1.7264077213115414, 0.008336751860551, 0.2549196311342251, 0.5160375718404234, 6.915499993374695, 2.944744649331201, 0.5, 1.907294741996761], name='wnsm_0c50aa90')
 ```
 
-The data is stored in list format [current_iteration, x0, ... , xn, f], works only for the country_optimization algorithm.
+The data is stored in list format [current_iteration, x0, ... , xn, f], works only for the country_optimization algorithm.

{pypharm-1.3.6 → pypharm-1.4.1}/pypharm.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypharm
-Version: 1.3.6
+Version: 1.4.1
 Summary: Module for solving pharmacokinetic problems
 Home-page: https://github.com/Krash13/PyPharm
 Author: Krash13
@@ -235,7 +235,7 @@ res = model(90, d=5700, compartment_number=0)
 Если оба параметра не заданы, то модель выраздается 
 в простую BaseCompartmentModel.
 
-**5) Модель MagicCompartmentModel** 
+**5) Модель ReleaseCompartmentModel** 
 
 Данная модель учитывает поправку на высвобождение
 ЛВ в модель вводятся дополнительные параметры:
@@ -272,8 +272,72 @@ plt.show()
 в таком случае, искомое нужно просто задать как None. Тогда вектор неизвестных это
 x = [configuration_matrix (неизвестные), outputs(неизвестные), volumes(неизвестные), release_parameters(неизвестные), v_release]
 
+**6) Использование PBPK модели**
 
-**6) Использование shared_memory** 
+Вы можете использовать PBPK модель как для рассчёта по известным
+данным так и для поиска параметров, исходя из ваших экспериментальных данных.
+
+Чтобы задать исзвестные вам константы, при инициализации объекта следует использовать
+параметры know_k и know_cl, которые содержат словари с известными параметрами, имена органов следует брать
+из класса ORGAN_NAMES.
+
+Ниже приведен пример поиска параметров и построение кривых распределения вещества
+в органах с использованием генетического алгоритма.
+
+```python
+from PyPharm import PBPKmod
+from PyPharm.constants import ORGAN_NAMES, MODEL_CONST
+
+model = PBPKmod()
+print(model.get_unknown_params())
+model.load_optimization_data(
+    time_exp=[12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+    dict_c_exp = {ORGAN_NAMES.LIVER: [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+              ORGAN_NAMES.LUNG: [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+              ORGAN_NAMES.SPLEEN: [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+    },
+    start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V']
+)
+result = model.optimize(
+    method='GA',
+    x_min=17 * [0.0001],
+    x_max=17 * [5],
+    genes=17 * [16],
+	n=300,
+    child_percent=0.3,
+    mutation_chance=0.5,
+    max_mutation=5,
+    t_max=300,
+    printing=True,
+)
+model.update_know_params(result)
+
+result = model(max_time=24 * 60, start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V'], step=0.1)
+model.plot_last_result(
+    organ_names=[ORGAN_NAMES.LUNG, ORGAN_NAMES.LIVER, ORGAN_NAMES.SPLEEN],
+    user_names={
+        ORGAN_NAMES.LUNG: 'Лёгкие',
+        ORGAN_NAMES.LIVER: 'Печень',
+        ORGAN_NAMES.SPLEEN: 'Селезёнка',
+    },
+    theoretic_data={
+        ORGAN_NAMES.LIVER: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+        },
+        ORGAN_NAMES.LUNG: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+        },
+        ORGAN_NAMES.SPLEEN: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+        }
+    }
+)
+```
+
+**7) Использование shared_memory** 
 
 Начиная с версии 1.3.0, вы можете использовать **shared_memory** для получения текущих данных
 оптимизации. Имя нужного вам участка памяти хранится в поле **memory_name**.
@@ -512,7 +576,7 @@ of variables.
 If both parameters are not set, then the model is deleted
 into a simple BaseCompartmentModel.
 
-**5) The MagicCompartmentModel model**
+**5) The ReleaseCompartmentModel model**
 
 This model takes into account the release adjustment
 medicinal substance additional parameters are introduced into the model:
@@ -549,7 +613,72 @@ The release_parameters and v_release parameters can be optimized
 in this case, you just need to set the desired value as None. Then the vector of unknowns is
 x = [configuration_matrix (unknown), outputs(unknown), volumes(unknown), release_parameters(unknown), v_release]
 
-**6) Using shared_memory**
+**6) Using the PBPK model**
+
+You can use the PBPK model both for calculations based on known
+data and for searching for parameters based on your experimental data.
+
+To set constants known to you, when initializing an object, you should use the
+parameters know_k and know_cl, which contain dictionaries with known parameters, the names of organs should be taken
+from the ORGAN_NAMES class.
+
+Below is an example of searching for parameters and constructing distribution curves of a substance
+in organs using a genetic algorithm.
+
+```python
+from PyPharm import PBPKmod
+from PyPharm.constants import ORGAN_NAMES, MODEL_CONST
+
+model = PBPKmod()
+print(model.get_unknown_params())
+model.load_optimization_data(
+    time_exp=[12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+    dict_c_exp = {ORGAN_NAMES.LIVER: [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+              ORGAN_NAMES.LUNG: [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+              ORGAN_NAMES.SPLEEN: [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+    },
+    start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V']
+)
+result = model.optimize(
+    method='GA',
+    x_min=17 * [0.0001],
+    x_max=17 * [5],
+    genes=17 * [16],
+	n=300,
+    child_percent=0.3,
+    mutation_chance=0.5,
+    max_mutation=5,
+    t_max=300,
+    printing=True,
+)
+model.update_know_params(result)
+
+result = model(max_time=24 * 60, start_c_in_venous=150 * 1e-3 / MODEL_CONST['rat']['venous_blood']['V'], step=0.1)
+model.plot_last_result(
+    organ_names=[ORGAN_NAMES.LUNG, ORGAN_NAMES.LIVER, ORGAN_NAMES.SPLEEN],
+    user_names={
+        ORGAN_NAMES.LUNG: 'Лёгкие',
+        ORGAN_NAMES.LIVER: 'Печень',
+        ORGAN_NAMES.SPLEEN: 'Селезёнка',
+    },
+    theoretic_data={
+        ORGAN_NAMES.LIVER: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [103.2 * 1e-6, 134.54 * 1e-6, 87.89 * 1e-6, 81.87 * 1e-6, 45.83 * 1e-6, 28.48 * 1e-6],
+        },
+        ORGAN_NAMES.LUNG: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [26.96 * 1e-6, 22.67 * 1e-6, 15.51 * 1e-6, 12.07 * 1e-6, 4.53 * 1e-6, 0 * 1e-6],
+        },
+        ORGAN_NAMES.SPLEEN: {
+            'x': [12, 60, 3 * 60, 5* 60, 15 * 60, 24 * 60],
+            'y': [11.84 * 1e-6, 12.22 * 1e-6, 8.52 * 1e-6, 7.01 * 1e-6, 3.65 * 1e-6, 2.16 * 1e-6]
+        }
+    }
+)
+```
+
+**7) Using shared_memory**
 
 Since version 1.3.0, you can use **shared_memory** to get current data
 optimization. The name of the memory location you need is stored in the **memory_name** field.
@@ -563,3 +692,4 @@ print(c)
 
 The data is stored in list format [current_iteration, x0, ... , xn, f], works only for the country_optimization algorithm.
 
+

pypharm-1.4.1/pypharm.egg-info/SOURCES.txt

@@ -0,0 +1,19 @@
+README.md
+setup.cfg
+setup.py
+PyPharm/__init__.py
+PyPharm/constants.py
+PyPharm/algorithms/__init__.py
+PyPharm/algorithms/country_optimization.py
+PyPharm/algorithms/country_optimization_v2.py
+PyPharm/algorithms/country_optimization_v3.py
+PyPharm/algorithms/genetic_optimization.py
+PyPharm/algorithms/gold_digger_optimization.py
+PyPharm/models/__init__.py
+PyPharm/models/compartment_models.py
+PyPharm/models/pbpk.py
+pypharm.egg-info/PKG-INFO
+pypharm.egg-info/SOURCES.txt
+pypharm.egg-info/dependency_links.txt
+pypharm.egg-info/requires.txt
+pypharm.egg-info/top_level.txt

{pypharm-1.3.6 → pypharm-1.4.1}/setup.py

@@ -6,7 +6,7 @@ def readme():
 
 setup(
   name='pypharm',
-  version='1.3.6',
+  version='1.4.1',
   author='Krash13',
   author_email='krasheninnikov.r.s@muctr.ru',
   description='Module for solving pharmacokinetic problems',

pypharm-1.3.6/pypharm.egg-info/SOURCES.txt

@@ -1,15 +0,0 @@
-README.md
-setup.cfg
-setup.py
-PyPharm/__init__.py
-PyPharm/country_optimization.py
-PyPharm/country_optimization_v2.py
-PyPharm/country_optimization_v3.py
-PyPharm/genetic_optimization.py
-PyPharm/gold_digger_optimization.py
-PyPharm/models.py
-pypharm.egg-info/PKG-INFO
-pypharm.egg-info/SOURCES.txt
-pypharm.egg-info/dependency_links.txt
-pypharm.egg-info/requires.txt
-pypharm.egg-info/top_level.txt