pypharm 1.2.9__py3-none-any.whl → 1.3.0__py3-none-any.whl

PyPharm/country_optimization.py

@@ -2,6 +2,7 @@ import random
 import numpy as np
 from operator import attrgetter
 from math import ceil, cos, sin
+from multiprocessing import shared_memory
 
 
 class Individual:
@@ -350,7 +351,7 @@ class Country:
 
 class CountriesAlgorithm:
 
-    def __init__(self, f, Xmin, Xmax, M, N, n, p, m, k, l, ep, tmax, printing=False):
+    def __init__(self, f, Xmin, Xmax, M, N, n, p, m, k, l, ep, tmax, printing=False, memory_list=None):
         self.f = f
         self.Xmin = Xmin
         self.Xmax = Xmax
@@ -363,6 +364,7 @@ class CountriesAlgorithm:
         self.tmax = tmax
         self.countries = []
         self.printing = printing
+        self.memory_list = memory_list
         for i in range(M):
             self.countries.append(Country(self.Xmin, self.Xmax, N, self.f))
 
@@ -372,6 +374,8 @@ class CountriesAlgorithm:
         trade = 0
         war = 0
         epedemic = 0
+        if self.memory_list is not None:
+            self.memory_list[0] = False
         while ti <= self.tmax:
             ti += 1
             for country in self.countries:
@@ -457,6 +461,12 @@ class CountriesAlgorithm:
             if self.printing:
                 print(f"{ti}) Лучшее решение: {result.x} - {result.f}, Стран осталось: {len(self.countries)}, Движение/Обмен/Войны/Эпидемии: {motion}/{trade}/{war}/{epedemic}")
                 print(f"Общее количество особей: {sum([len(country.population) for country in self.countries])}")
+
+            if self.memory_list is not None:
+                self.memory_list[0] = ti
+                for i in range(len(result.x)):
+                    self.memory_list[i + 1] = float(result.x[i])
+                self.memory_list[-1] = float(result.f)
         return (result.x, result.f, False, ti)
 
 

PyPharm/models.py

@@ -1,3 +1,5 @@
+from multiprocessing import shared_memory
+
 import numpy as np
 from scipy.integrate import solve_ivp, RK45
 from scipy.integrate._ivp.rk import rk_step, SAFETY, MAX_FACTOR, MIN_FACTOR
@@ -16,7 +18,7 @@ class BaseCompartmentModel:
     _optim = False
     numba_option = False
 
-    def __init__(self, configuration_matrix, outputs, volumes=None, numba_option=False):
+    def __init__(self, configuration_matrix, outputs, volumes=None, numba_option=False, use_shared_memory=False):
         """
         Базовая камерная модель для описания фармакокинетики системы
 
@@ -48,8 +50,18 @@ class BaseCompartmentModel:
             self.volumes_target_count = np.sum(self.volumes == None)
         self.last_result = None
         self.numba_option = numba_option
-
-    def _сompartment_model(self, t, c):
+        self.use_shared_memory = use_shared_memory
+        if self.use_shared_memory:
+            self.memory_size = 2 + self.configuration_matrix_target_count + self.outputs_target_count + self.volumes_target_count
+            self.memory = shared_memory.ShareableList(self.memory_size * [None])
+            self.memory_name = self.memory.shm.name
+
+    def __del__(self):
+        if getattr(self, 'memory', None):
+            self.memory.shm.close()
+            self.memory.shm.unlink()
+
+    def _compartment_model(self, t, c):
         """
         Функция для расчета камерной модели
 
@@ -67,7 +79,7 @@ class BaseCompartmentModel:
 
     @staticmethod
     @njit
-    def _numba_сompartment_model(t, c, configuration_matrix, outputs, volumes):
+    def _numba_compartment_model(t, c, configuration_matrix, outputs, volumes):
         """
         Функция для расчета камерной модели
 
@@ -110,7 +122,7 @@ class BaseCompartmentModel:
             c0 = np.array(c0)
         ts = [0, t_max]
         self.last_result = solve_ivp(
-            fun=self._сompartment_model if not self.numba_option else lambda t, c: self._numba_сompartment_model(t, c, self.configuration_matrix.astype(np.float64), self.outputs.astype(np.float64), self.volumes.astype(np.float64)),
+            fun=self._compartment_model if not self.numba_option else lambda t, c: self._numba_compartment_model(t, c, self.configuration_matrix.astype(np.float64), self.outputs.astype(np.float64), self.volumes.astype(np.float64)),
             t_span=ts,
             y0=c0,
             max_step=max_step,
@@ -206,6 +218,7 @@ class BaseCompartmentModel:
         if method == 'country_optimization':
             CA = CountriesAlgorithm(
                 f=f,
+                memory_list=getattr(self, 'memory', None),
                 **kwargs
             )
             CA.start()
@@ -237,7 +250,7 @@ class BaseCompartmentModel:
         self._optim = False
         return x
 
-    def plot_model(self, compartment_numbers=None, compartment_names={}, left=None, right=None, **kwargs):
+    def plot_model(self, compartment_numbers=None, compartment_names={}, left=None, right=None, y_lims={}, **kwargs):
         """
         Функция для построения графиков модели
 
@@ -252,10 +265,12 @@ class BaseCompartmentModel:
         self(**kwargs)
         for i in compartment_numbers:
             if hasattr(self, "teoretic_x") and hasattr(self, "teoretic_y") and i in self.know_compartments:
-                plt.plot(self.teoretic_x, self.teoretic_y[i], "*r")
+                plt.plot(self.teoretic_x, self.teoretic_y[self.know_compartments.index(i)], "*r")
             plt.plot(self.last_result.t, self.last_result.y[i])
             plt.title(compartment_names.get(i, i))
             plt.xlim(left=left, right=right)
+            if y_lims.get(i):
+                plt.ylim(y_lims.get(i))
             plt.grid()
             plt.show()
 
@@ -264,11 +279,19 @@ class MagicCompartmentModel(BaseCompartmentModel):
 
     need_magic_optimization = False
 
-    def __init__(self, configuration_matrix, outputs, volumes=None, magic_coefficient=1, exclude_compartments=[], numba_option=False):
-        super().__init__(configuration_matrix, outputs, volumes, numba_option)
+    def __init__(self, configuration_matrix, outputs, volumes=None, magic_coefficient=1, exclude_compartments=[], numba_option=False, use_shared_memory=False):
+        super().__init__(configuration_matrix, outputs, volumes, numba_option, use_shared_memory)
         self.magic_coefficient = magic_coefficient
         self.exclude_compartments = np.array(exclude_compartments)
         self.need_magic_optimization = self.magic_coefficient is None
+        if getattr(self, "memory", None):
+            self.memory.shm.close()
+            self.memory.shm.unlink()
+            self.memory_size += int(self.need_magic_optimization)
+            self.memory = shared_memory.ShareableList(
+                sequence=self.memory_size * [None]
+            )
+            self.memory_name = self.memory.shm.name
 
     def __call__(self, t_max, c0=None, d=None, compartment_number=None, max_step=0.01, t_eval=None):
         if not self._optim and not self.magic_coefficient:
@@ -348,6 +371,15 @@ class ReleaseCompartmentModel(BaseCompartmentModel):
         self.release_compartment = release_compartment
         self.release_function = release_function
 
+        if getattr(self, "memory", None):
+            self.memory.shm.close()
+            self.memory.shm.unlink()
+            self.memory_size += self.release_parameters_target_count + int(self.need_v_release_optimization)
+            self.memory = shared_memory.ShareableList(
+                sequence=self.memory_size * [None]
+            )
+            self.memory_name = self.memory.shm.name
+
     def load_data_from_list(self, x):
         super().load_data_from_list(x)
         s = self.configuration_matrix_target_count + self.outputs_target_count + self.volumes_target_count

{pypharm-1.2.9.dist-info → pypharm-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypharm
-Version: 1.2.9
+Version: 1.3.0
 Summary: Module for solving pharmacokinetic problems
 Home-page: https://github.com/Krash13/PyPharm
 Author: Krash13
@@ -207,6 +207,22 @@ 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 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**.
+
+```python
+from multiprocessing import shared_memory
+
+c = shared_memory.ShareableList(name='<your model.memory_name>')
+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')
+```
+
+Данные хранятся в формате списка [текущая_итерация, x0, ... , xn, f], работает только для алгоритма country_optimization.
+
 **ENG documentation**
 ----------
 
@@ -397,3 +413,17 @@ 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**
+
+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.
+```python
+from multiprocessing import shared_memory
+
+c = shared_memory.ShareableList(name='<your model.memory_name>')
+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.
+

pypharm-1.3.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+PyPharm/__init__.py,sha256=hxhMRlWpLMARQV-ZNYkmvhQ9gCYI18an75vlySWjA6s,90
+PyPharm/country_optimization.py,sha256=WsjfAWAWbxRnUUfBiMi1VatCSVbru7F1_G6kQBRVyA0,20452
+PyPharm/country_optimization_v2.py,sha256=3d2mt15DXdr1V3soIJS51xuCv6uzH8pirah1RnI5--8,13156
+PyPharm/models.py,sha256=Lhd_2EUtGQUrratvlqZ115zLeF9fFLDPI1gi-mzjv_o,25663
+pypharm-1.3.0.dist-info/METADATA,sha256=cUh197fi8fP5x7Do-6Is-RpC2X-z6j8ZLo-ZkJOSTrU,14464
+pypharm-1.3.0.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
+pypharm-1.3.0.dist-info/top_level.txt,sha256=yybfSkKw8q1G3aEcnlfVL7_L9ufGFSAYZnpc7q6oYJk,8
+pypharm-1.3.0.dist-info/RECORD,,

pypharm-1.2.9.dist-info/RECORD

@@ -1,8 +0,0 @@
-PyPharm/__init__.py,sha256=hxhMRlWpLMARQV-ZNYkmvhQ9gCYI18an75vlySWjA6s,90
-PyPharm/country_optimization.py,sha256=nbg5kuJcOhMMfPR0_1O8KUzyqHApUcnqgs_I2I0Z1Gs,20008
-PyPharm/country_optimization_v2.py,sha256=3d2mt15DXdr1V3soIJS51xuCv6uzH8pirah1RnI5--8,13156
-PyPharm/models.py,sha256=6SRscPbPrIyKDlQk8WdtQW35GWWwk8rfm0V_QEVSs7c,24115
-pypharm-1.2.9.dist-info/METADATA,sha256=uOrCVB8X3Z8lw9DTGpn51D8lBLAyjbgQ0lz6umRiqZY,12910
-pypharm-1.2.9.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-pypharm-1.2.9.dist-info/top_level.txt,sha256=yybfSkKw8q1G3aEcnlfVL7_L9ufGFSAYZnpc7q6oYJk,8
-pypharm-1.2.9.dist-info/RECORD,,