pypharm 1.3.1__tar.gz → 1.3.3__tar.gz

{pypharm-1.3.1 → pypharm-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypharm
-Version: 1.3.1
+Version: 1.3.3
 Summary: Module for solving pharmacokinetic problems
 Home-page: https://github.com/Krash13/PyPharm
 Author: Krash13

{pypharm-1.3.1 → pypharm-1.3.3}/PyPharm/models.py

@@ -2,7 +2,7 @@ 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
+from scipy.integrate import simps
 from scipy.optimize import minimize
 from .country_optimization import CountriesAlgorithm
 from .country_optimization_v2 import CountriesAlgorithm_v2
@@ -129,7 +129,22 @@ class BaseCompartmentModel:
             t_eval=t_eval
         )
         return self.last_result
-    
+
+    def get_kinetic_params(self, t_max, d, compartment_number, max_step=0.01):
+        one_hour_result = self(t_max=1, d=d, compartment_number=compartment_number, max_step=max_step)
+        auc_1h = simps(one_hour_result.y[compartment_number], one_hour_result.t)
+        self(t_max=t_max, d=d, compartment_number=compartment_number, max_step=max_step)
+        auc = simps(self.last_result.y[compartment_number], self.last_result.t)
+        result_dict = {
+            'c_max': self.last_result.y[compartment_number].max(),
+            'V': self.volumes[compartment_number] if self.volumes is not None else None,
+            'AUC': auc,
+            'AUC_1h': auc_1h,
+            'Cl': d / auc
+        }
+        return result_dict
+
+
     def load_data_from_list(self, x):
         if self.configuration_matrix_target:
             self.configuration_matrix[self.configuration_matrix_target] = x[:self.configuration_matrix_target_count]
@@ -323,7 +338,7 @@ class ReleaseCompartmentModel(BaseCompartmentModel):
 
     need_v_release_optimization = False
     release_parameters_target = None
-    release_parameters_target = None
+    accumulation_parameters_target = None
 
     class ReleaseRK45(RK45):
 
@@ -496,6 +511,15 @@ class ReleaseCompartmentModel(BaseCompartmentModel):
             accumulation_type=self.accumulation_type,
             c0=c0
         )
+        self.last_result.model_realized = c0 - self.get_release_function()(self.last_result.t, c0)
+        if self.with_accumulate:
+            model_accumulation = self.get_accumulation_function()(self.last_result.t, c0)
+            if self.accumulation_type == 1:
+                self.last_result.model_realized = model_accumulation - self.get_release_function()(self.last_result.t, c0)
+            elif self.accumulation_type == 2:
+                accumulation_coeffs = model_accumulation / c0
+                self.last_result.model_realized= accumulation_coeffs * self.get_release_function()(self.last_result.t, c0)
+                self.last_result.model_realized = model_accumulation - self.last_result.model_realized
         return self.last_result
 
     def _target_function(self, x, max_step=0.01, metric='R2'):
@@ -523,29 +547,13 @@ class ReleaseCompartmentModel(BaseCompartmentModel):
         if metric == 'R2':
             plus = 0
             if self.teoretic_realized is not None:
-                model_realized = c0 - self.get_release_function()(self.teoretic_x, c0)
-                if self.with_accumulate:
-                    model_accumulation = self.get_accumulation_function()(self.teoretic_x, c0)
-                    if self.accumulation_type == 1:
-                        model_realized = model_accumulation - self.get_release_function()(self.teoretic_x, c0)
-                    elif self.accumulation_type == 2:
-                        accumulation_coeffs = model_accumulation / c0
-                        model_realized = accumulation_coeffs * self.get_release_function()(self.teoretic_x, c0)
-                        model_realized = model_accumulation - model_realized
+                model_realized = self.last_result.model_realized
                 plus = np.sum(((model_realized - self.teoretic_realized) ** 2) / ((self.teoretic_realized - self.teoretic_realized_avg) ** 2))
             return plus + np.sum(np.sum(self.w * ((target_results - self.teoretic_y) ** 2), axis=1) / np.sum((self.teoretic_avg - self.teoretic_y) ** 2, axis=1))
         elif metric == 'norm':
             plus = 0
             if self.teoretic_realized is not None:
-                model_realized = c0 - self.get_release_function()(self.teoretic_x, c0)
-                if self.with_accumulate:
-                    model_accumulation = self.get_accumulation_function()(self.teoretic_x, c0)
-                    if self.accumulation_type == 1:
-                        model_realized = model_accumulation - self.get_release_function()(self.teoretic_x, c0)
-                    elif self.accumulation_type == 2:
-                        accumulation_coeffs = model_accumulation / c0
-                        model_realized = accumulation_coeffs * self.get_release_function()(self.teoretic_x, c0)
-                        model_realized = model_accumulation - model_realized
+                model_realized = self.last_result.model_realized
                 plus = np.linalg.norm(self.teoretic_realized - model_realized)
             return plus + np.linalg.norm(target_results - self.teoretic_y)
         else:
@@ -597,3 +605,17 @@ class ReleaseCompartmentModel(BaseCompartmentModel):
                 s += self.release_parameters_target_count + int(self.need_v_release_optimization)
                 self.accumulation_parameters[self.accumulation_parameters_target] = x[s:s + self.accumulation_parameters_target_count]
         return x
+
+    def plot_model(self, compartment_numbers=None, compartment_names={},
+                   left=None, right=None, y_lims={}, plot_accumulation=False, **kwargs):
+        super().plot_model(compartment_numbers, compartment_names, left, right, y_lims, **kwargs)
+        if plot_accumulation:
+            if hasattr(self, "teoretic_x") and hasattr(self, "teoretic_realized"):
+                plt.plot(self.teoretic_x, self.teoretic_realized, "*r")
+            plt.plot(self.last_result.t, self.last_result.model_realized)
+            plt.title(compartment_names.get('realized', 'realized'))
+            plt.xlim(left=left, right=right)
+            if y_lims.get('realized'):
+                plt.ylim(y_lims.get('realized'))
+            plt.grid()
+            plt.show()

{pypharm-1.3.1 → pypharm-1.3.3}/pypharm.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypharm
-Version: 1.3.1
+Version: 1.3.3
 Summary: Module for solving pharmacokinetic problems
 Home-page: https://github.com/Krash13/PyPharm
 Author: Krash13

{pypharm-1.3.1 → pypharm-1.3.3}/setup.py

@@ -6,7 +6,7 @@ def readme():
 
 setup(
   name='pypharm',
-  version='1.3.1',
+  version='1.3.3',
   author='Krash13',
   author_email='krasheninnikov.r.s@muctr.ru',
   description='Module for solving pharmacokinetic problems',