Create bioprocess_model.py

bioprocess_model.py

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+# bioprocess_model.py
+
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+from scipy.integrate import odeint
+from scipy.optimize import curve_fit
+from sklearn.metrics import mean_squared_error
+import seaborn as sns
+
+class BioprocessModel:
+    def __init__(self):
+        self.params = {}
+        self.r2 = {}
+        self.rmse = {}
+        self.datax = []
+        self.datas = []
+        self.datap = []
+        self.dataxp = []
+        self.datasp = []
+        self.datapp = []
+        self.datax_std = []
+        self.datas_std = []
+        self.datap_std = []
+
+    @staticmethod
+    def logistic(time, xo, xm, um):
+        return (xo * np.exp(um * time)) / (1 - (xo / xm) * (1 - np.exp(um * time)))
+
+    @staticmethod
+    def substrate(time, so, p, q, xo, xm, um):
+        return so - (p * xo * ((np.exp(um * time)) / (1 - (xo / xm) * (1 - np.exp(um * time))) - 1)) - \
+               (q * (xm / um) * np.log(1 - (xo / xm) * (1 - np.exp(um * time))))
+
+    @staticmethod
+    def product(time, po, alpha, beta, xo, xm, um):
+        return po + (alpha * xo * ((np.exp(um * time) / (1 - (xo / xm) * (1 - np.exp(um * time)))) - 1)) + \
+               (beta * (xm / um) * np.log(1 - (xo / xm) * (1 - np.exp(um * time))))
+
+    @staticmethod
+    def logistic_diff(X, t, params):
+        xo, xm, um = params
+        dXdt = um * X * (1 - X / xm)
+        return dXdt
+
+    def substrate_diff(self, S, t, params, biomass_params, X_func):
+        so, p, q = params
+        xo, xm, um = biomass_params
+        X_t = X_func(t)
+        dSdt = -p * (um * X_t * (1 - X_t / xm)) - q * X_t
+        return dSdt
+
+    def product_diff(self, P, t, params, biomass_params, X_func):
+        po, alpha, beta = params
+        xo, xm, um = biomass_params
+        X_t = X_func(t)
+        dPdt = alpha * (um * X_t * (1 - X_t / xm)) + beta * X_t
+        return dPdt
+
+    def process_data(self, df):
+        biomass_cols = [col for col in df.columns if 'Biomasa' in col]
+        substrate_cols = [col for col in df.columns if 'Sustrato' in col]
+        product_cols = [col for col in df.columns if 'Producto' in col]
+
+        time_col = [col for col in df.columns if 'Tiempo' in col][0]
+        time = df[time_col].values
+
+        data_biomass = np.array([df[col].values for col in biomass_cols])
+        self.datax.append(data_biomass)
+        self.dataxp.append(np.mean(data_biomass, axis=0))
+        self.datax_std.append(np.std(data_biomass, axis=0, ddof=1))
+
+        data_substrate = np.array([df[col].values for col in substrate_cols])
+        self.datas.append(data_substrate)
+        self.datasp.append(np.mean(data_substrate, axis=0))
+        self.datas_std.append(np.std(data_substrate, axis=0, ddof=1))
+
+        data_product = np.array([df[col].values for col in product_cols])
+        self.datap.append(data_product)
+        self.datapp.append(np.mean(data_product, axis=0))
+        self.datap_std.append(np.std(data_product, axis=0, ddof=1))
+
+        self.time = time
+
+    def fit_model(self, model_type='logistic'):
+        if model_type == 'logistic':
+            self.fit_biomass = self.fit_biomass_logistic
+            self.fit_substrate = self.fit_substrate_logistic
+            self.fit_product = self.fit_product_logistic
+
+    def fit_biomass_logistic(self, time, biomass, bounds):
+        popt, _ = curve_fit(self.logistic, time, biomass, bounds=bounds, maxfev=10000)
+        self.params['biomass'] = {'xo': popt[0], 'xm': popt[1], 'um': popt[2]}
+        y_pred = self.logistic(time, *popt)
+        self.r2['biomass'] = 1 - (np.sum((biomass - y_pred) ** 2) / np.sum((biomass - np.mean(biomass)) ** 2))
+        self.rmse['biomass'] = np.sqrt(mean_squared_error(biomass, y_pred))
+        return y_pred
+
+    def fit_substrate_logistic(self, time, substrate, biomass_params, bounds):
+        popt, _ = curve_fit(lambda t, so, p, q: self.substrate(t, so, p, q, *biomass_params.values()),
+                            time, substrate, bounds=bounds)
+        self.params['substrate'] = {'so': popt[0], 'p': popt[1], 'q': popt[2]}
+        y_pred = self.substrate(time, *popt, *biomass_params.values())
+        self.r2['substrate'] = 1 - (np.sum((substrate - y_pred) ** 2) / np.sum((substrate - np.mean(substrate)) ** 2))
+        self.rmse['substrate'] = np.sqrt(mean_squared_error(substrate, y_pred))
+        return y_pred
+
+    def fit_product_logistic(self, time, product, biomass_params, bounds):
+        popt, _ = curve_fit(lambda t, po, alpha, beta: self.product(t, po, alpha, beta, *biomass_params.values()),
+                            time, product, bounds=bounds)
+        self.params['product'] = {'po': popt[0], 'alpha': popt[1], 'beta': popt[2]}
+        y_pred = self.product(time, *popt, *biomass_params.values())
+        self.r2['product'] = 1 - (np.sum((product - y_pred) ** 2) / np.sum((product - np.mean(product)) ** 2))
+        self.rmse['product'] = np.sqrt(mean_squared_error(product, y_pred))
+        return y_pred
+
+    def plot_combined_results(self, time, biomass, substrate, product,
+                              y_pred_biomass, y_pred_substrate, y_pred_product,
+                              biomass_std=None, substrate_std=None, product_std=None,
+                              experiment_name='', legend_position='best', params_position='upper right',
+                              show_legend=True, show_params=True,
+                              style='whitegrid', line_color='#0000FF', point_color='#000000',
+                              line_style='-', marker_style='o'):
+        sns.set_style(style)
+
+        fig, ax1 = plt.subplots(figsize=(10, 7))
+        ax1.set_xlabel('Tiempo')
+        ax1.set_ylabel('Biomasa', color=line_color)
+
+        ax1.plot(time, biomass, marker=marker_style, linestyle='', color=point_color, label='Biomasa (Datos)')
+        ax1.plot(time, y_pred_biomass, linestyle=line_style, color=line_color, label='Biomasa (Modelo)')
+        ax1.tick_params(axis='y', labelcolor=line_color)
+
+        ax2 = ax1.twinx()
+        ax2.set_ylabel('Sustrato', color='green')
+        ax2.plot(time, substrate, marker=marker_style, linestyle='', color='green', label='Sustrato (Datos)')
+        ax2.plot(time, y_pred_substrate, linestyle=line_style, color='green', label='Sustrato (Modelo)')
+        ax2.tick_params(axis='y', labelcolor='green')
+
+        ax3 = ax1.twinx()
+        ax3.spines["right"].set_position(("axes", 1.1))
+        ax3.set_ylabel('Producto', color='red')
+        ax3.plot(time, product, marker=marker_style, linestyle='', color='red', label='Producto (Datos)')
+        ax3.plot(time, y_pred_product, linestyle=line_style, color='red', label='Producto (Modelo)')
+        ax3.tick_params(axis='y', labelcolor='red')
+
+        fig.tight_layout()
+        return fig