diff --git "a/app.py" "b/app.py" --- "a/app.py" +++ "b/app.py" @@ -34,91 +34,153 @@ class BioprocessModel: self.datas_std = [] self.datap_std = [] self.biomass_model = None - self.biomass_diff = None + self.biomass_diff = None # Store the differential equation function self.model_type = model_type self.maxfev = maxfev - self.time = None # Initialize time attribute + self.time = None @staticmethod def logistic(time, xo, xm, um): + # xo: initial biomass, xm: max biomass, um: max specific growth rate if xm == 0 or (xo / xm == 1 and np.any(um * time > 0)): return np.full_like(time, np.nan) - denominator = (1 - (xo / xm) * (1 - np.exp(um * time))) - denominator = np.where(denominator == 0, 1e-9, denominator) - return (xo * np.exp(um * time)) / denominator + # Add a small epsilon to prevent division by zero or log of zero in edge cases + term_exp = np.exp(um * time) + denominator = (1 - (xo / xm) * (1 - term_exp)) + denominator = np.where(denominator == 0, 1e-9, denominator) # Avoid division by zero + # Ensure xo/xm is not 1 if (1-exp(um*time)) is also 0 (i.e. um*time = 0) + # This is usually handled by xo < xm constraint in fitting + return (xo * term_exp) / denominator @staticmethod def gompertz(time, xm, um, lag): + # xm: max biomass, um: max specific growth rate, lag: lag time if xm == 0: return np.full_like(time, np.nan) - return xm * np.exp(-np.exp((um * np.e / xm) * (lag - time) + 1)) + # Add small epsilon to prevent log(0) if exp_term becomes very large negative + exp_term = (um * np.e / xm) * (lag - time) + 1 + # Clamp large negative values in exp_term to avoid overflow in np.exp(-np.exp(exp_term)) + exp_term_clipped = np.clip(exp_term, -np.inf, 700) # exp(709) is around max float + return xm * np.exp(-np.exp(exp_term_clipped)) @staticmethod def moser(time, Xm, um, Ks): + # Xm: max biomass, um: max specific growth rate, Ks: Monod constant (here acting as time shift) + # This is a simplified form, not the substrate-dependent Moser. return Xm * (1 - np.exp(-um * (time - Ks))) + @staticmethod + def baranyi(time, X0, Xm, um, lag): + # X0: initial biomass, Xm: max biomass, um: max specific growth rate, lag: lag time + # Ensure parameters are valid to prevent math errors + if X0 <= 0 or Xm <= X0 or um <= 0: # lag can be 0 + return np.full_like(time, np.nan) + + # Adjustment function A(t) + # Using h0 = um for simplicity in A(t) calculation + # A_t = t + (1/um) * np.log(np.exp(-um*t) + np.exp(-um*lag) - np.exp(-um*(t+lag))) + # Argument of log in A(t): + log_arg_A = np.exp(-um * t) + np.exp(-um * lag) - np.exp(-um * (t + lag)) + log_arg_A = np.where(log_arg_A <= 1e-9, 1e-9, log_arg_A) # Prevent log(0 or negative) + A_t = t + (1 / um) * np.log(log_arg_A) + + # Main Baranyi equation part + exp_um_At = np.exp(um * A_t) + # Clamp large values to prevent overflow if Xm/X0 is large + exp_um_At_clipped = np.clip(exp_um_At, -np.inf, 700) + + numerator = (Xm / X0) * exp_um_At_clipped + denominator = (Xm / X0 - 1) + exp_um_At_clipped + denominator = np.where(denominator == 0, 1e-9, denominator) # Avoid division by zero + + return X0 * (numerator / denominator) + + @staticmethod def logistic_diff(X, t, params): - xo, xm, um = params - if xm == 0: - return 0 + # params for logistic_diff: [xo, xm, um] (xo is not used in diff eq, but passed for consistency) + _, xm, um = params + if xm == 0: return 0 return um * X * (1 - X / xm) @staticmethod def gompertz_diff(X, t, params): + # params for gompertz_diff: [xm, um, lag] xm, um, lag = params - if xm == 0: - return 0 - return X * (um * np.e / xm) * np.exp((um * np.e / xm) * (lag - t) + 1) + if xm == 0: return 0 + # This is d(Gompertz)/dt + # Gompertz: xm * exp(-exp( (um*e/xm)*(lag-t)+1 )) + # Let k = (um*e/xm) + # Let u = (k*(lag-t)+1) + # dX/dt = X * (-exp(u)) * k * (-1) = X * k * exp(u) + k_val = um * np.e / xm + u_val = k_val * (lag - t) + 1 + u_val_clipped = np.clip(u_val, -np.inf, 700) + return X * k_val * np.exp(u_val_clipped) + @staticmethod def moser_diff(X, t, params): - Xm, um, Ks = params + # params for moser_diff: [Xm, um, Ks] + Xm, um, _ = params # Ks is not directly in this simplified dX/dt return um * (Xm - X) + + # No differential form for Baranyi in this version due to complexity. - def substrate(self, time, so, p, q, biomass_params): - if self.biomass_model is None or not biomass_params: + def substrate(self, time, so, p, q, biomass_params_list): + if self.biomass_model is None or not biomass_params_list: return np.full_like(time, np.nan) - X_t = self.biomass_model(time, *biomass_params) + X_t = self.biomass_model(time, *biomass_params_list) if np.any(np.isnan(X_t)): return np.full_like(time, np.nan) + integral_X = np.zeros_like(X_t) if len(time) > 1: dt = np.diff(time, prepend=time[0] - (time[1]-time[0] if len(time)>1 else 1)) integral_X = np.cumsum(X_t * dt) - if self.model_type == 'logistic': - X0 = biomass_params[0] + # Determine X0 (initial biomass) from the fitted parameters + if self.model_type == 'logistic' or self.model_type == 'baranyi': + X0 = biomass_params_list[0] # xo or X0 is the first parameter elif self.model_type == 'gompertz': - X0 = self.gompertz(0, *biomass_params) + X0 = self.gompertz(0, *biomass_params_list) elif self.model_type == 'moser': - X0 = self.moser(0, *biomass_params) + X0 = self.moser(0, *biomass_params_list) else: - X0 = X_t[0] + X0 = X_t[0] # Fallback + + X0 = X0 if not np.isnan(X0) else (biomass_params_list[0] if biomass_params_list else 0) + + return so - p * (X_t - X0) - q * integral_X - def product(self, time, po, alpha, beta, biomass_params): - if self.biomass_model is None or not biomass_params: + def product(self, time, po, alpha, beta, biomass_params_list): + if self.biomass_model is None or not biomass_params_list: return np.full_like(time, np.nan) - X_t = self.biomass_model(time, *biomass_params) + X_t = self.biomass_model(time, *biomass_params_list) if np.any(np.isnan(X_t)): return np.full_like(time, np.nan) + integral_X = np.zeros_like(X_t) if len(time) > 1: dt = np.diff(time, prepend=time[0] - (time[1]-time[0] if len(time)>1 else 1)) integral_X = np.cumsum(X_t * dt) - if self.model_type == 'logistic': - X0 = biomass_params[0] + if self.model_type == 'logistic' or self.model_type == 'baranyi': + X0 = biomass_params_list[0] elif self.model_type == 'gompertz': - X0 = self.gompertz(0, *biomass_params) + X0 = self.gompertz(0, *biomass_params_list) elif self.model_type == 'moser': - X0 = self.moser(0, *biomass_params) + X0 = self.moser(0, *biomass_params_list) else: X0 = X_t[0] + + X0 = X0 if not np.isnan(X0) else (biomass_params_list[0] if biomass_params_list else 0) + return po + alpha * (X_t - X0) + beta * integral_X def process_data(self, df): + # ... (same as before) biomass_cols = [col for col in df.columns if col[1] == 'Biomasa'] substrate_cols = [col for col in df.columns if col[1] == 'Sustrato'] product_cols = [col for col in df.columns if col[1] == 'Producto'] @@ -126,42 +188,81 @@ class BioprocessModel: if not any(col[1] == 'Tiempo' for col in df.columns): raise ValueError("La columna 'Tiempo' no se encuentra en el DataFrame.") time_col = [col for col in df.columns if col[1] == 'Tiempo'][0] - time = df[time_col].values + time = df[time_col].dropna().values # Ensure no NaNs in time if len(biomass_cols) > 0: - data_biomass = [df[col].values for col in biomass_cols] - data_biomass = np.array(data_biomass) - 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)) - else: + data_biomass = [df[col].dropna().values for col in biomass_cols] # dropna for each replicate + # Ensure all replicates have same length as time after dropna + min_len = len(time) + data_biomass_aligned = [] + for rep_data in data_biomass: + if len(rep_data) == min_len: + data_biomass_aligned.append(rep_data) + # else: print warning or handle misaligned data + + if data_biomass_aligned: + data_biomass_np = np.array(data_biomass_aligned) + self.datax.append(data_biomass_np) + self.dataxp.append(np.mean(data_biomass_np, axis=0)) + self.datax_std.append(np.std(data_biomass_np, axis=0, ddof=1)) + else: # If no valid replicates after alignment + self.datax.append(np.array([])) + self.dataxp.append(np.array([])) + self.datax_std.append(np.array([])) + + else: self.datax.append(np.array([])) self.dataxp.append(np.array([])) self.datax_std.append(np.array([])) + if len(substrate_cols) > 0: - data_substrate = [df[col].values for col in substrate_cols] - data_substrate = np.array(data_substrate) - 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_substrate = [df[col].dropna().values for col in substrate_cols] + min_len = len(time) + data_substrate_aligned = [] + for rep_data in data_substrate: + if len(rep_data) == min_len: + data_substrate_aligned.append(rep_data) + + if data_substrate_aligned: + data_substrate_np = np.array(data_substrate_aligned) + self.datas.append(data_substrate_np) + self.datasp.append(np.mean(data_substrate_np, axis=0)) + self.datas_std.append(np.std(data_substrate_np, axis=0, ddof=1)) + else: + self.datas.append(np.array([])) + self.datasp.append(np.array([])) + self.datas_std.append(np.array([])) else: self.datas.append(np.array([])) self.datasp.append(np.array([])) self.datas_std.append(np.array([])) if len(product_cols) > 0: - data_product = [df[col].values for col in product_cols] - data_product = np.array(data_product) - 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)) + data_product = [df[col].dropna().values for col in product_cols] + min_len = len(time) + data_product_aligned = [] + for rep_data in data_product: + if len(rep_data) == min_len: + data_product_aligned.append(rep_data) + + if data_product_aligned: + data_product_np = np.array(data_product_aligned) + self.datap.append(data_product_np) + self.datapp.append(np.mean(data_product_np, axis=0)) + self.datap_std.append(np.std(data_product_np, axis=0, ddof=1)) + else: + self.datap.append(np.array([])) + self.datapp.append(np.array([])) + self.datap_std.append(np.array([])) else: self.datap.append(np.array([])) self.datapp.append(np.array([])) self.datap_std.append(np.array([])) + self.time = time + def fit_model(self): if self.model_type == 'logistic': self.biomass_model = self.logistic @@ -172,33 +273,65 @@ class BioprocessModel: elif self.model_type == 'moser': self.biomass_model = self.moser self.biomass_diff = self.moser_diff + elif self.model_type == 'baranyi': + self.biomass_model = self.baranyi + self.biomass_diff = None # No ODE form for Baranyi in this version + else: + raise ValueError(f"Modelo de biomasa desconocido: {self.model_type}") + def fit_biomass(self, time, biomass): + # Ensure time and biomass are 1D arrays of the same length and numeric + time = np.asarray(time, dtype=float) + biomass = np.asarray(biomass, dtype=float) + if len(time) != len(biomass): + print("Error: Tiempo y biomasa deben tener la misma longitud.") + return None + if np.any(np.isnan(time)) or np.any(np.isnan(biomass)): + print("Error: Tiempo o biomasa contienen NaNs.") + # Attempt to remove NaNs consistently + valid_indices = ~np.isnan(time) & ~np.isnan(biomass) + time = time[valid_indices] + biomass = biomass[valid_indices] + if len(time) < 3: # Need at least 3 points for 3-param models + print("No hay suficientes datos válidos después de remover NaNs.") + return None + try: if len(np.unique(biomass)) < 2 : print(f"Biomasa constante para {self.model_type}, no se puede ajustar el modelo.") + self.r2['biomass'] = np.nan; self.rmse['biomass'] = np.nan return None + popt = None # Initialize popt if self.model_type == 'logistic': - xo_guess = biomass[biomass > 1e-6][0] if np.any(biomass > 1e-6) else 1e-3 + xo_guess = biomass[0] if biomass[0] > 1e-6 else 1e-3 xm_guess = max(biomass) * 1.1 if max(biomass) > xo_guess else xo_guess * 2 if xm_guess <= xo_guess: xm_guess = xo_guess + 1e-3 p0 = [xo_guess, xm_guess, 0.1] - bounds = ([1e-9, 1e-9, 1e-9], [np.inf, np.inf, np.inf]) + bounds = ([1e-9, biomass[0] if biomass[0]>1e-9 else 1e-9, 1e-9], [max(biomass)*0.99 if max(biomass)>0 else 1, np.inf, np.inf]) + # Ensure xo_guess is within bounds[0][0] and bounds[1][0] + p0[0] = np.clip(p0[0], bounds[0][0], bounds[1][0]) popt, _ = curve_fit(self.logistic, time, biomass, p0=p0, maxfev=self.maxfev, bounds=bounds, ftol=1e-9, xtol=1e-9) - if popt[1] <= popt[0]: + if popt[1] <= popt[0]: # xm <= xo print(f"Advertencia: En modelo logístico, Xm ({popt[1]:.2f}) no es mayor que Xo ({popt[0]:.2f}). Ajuste puede no ser válido.") - self.params['biomass'] = {'xo': popt[0], 'xm': popt[1], 'um': popt[2]} + self.params['biomass'] = {'Xo': popt[0], 'Xm': popt[1], 'um': popt[2]} y_pred = self.logistic(time, *popt) elif self.model_type == 'gompertz': xm_guess = max(biomass) if max(biomass) > 0 else 1.0 um_guess = 0.1 - lag_guess = time[np.argmax(np.gradient(biomass))] if len(biomass) > 1 and np.any(np.gradient(biomass) > 1e-6) else time[0] + # A simple lag estimate: time until biomass reaches, say, 10% of (max-min) + min_bio = min(biomass) + lag_thresh = min_bio + 0.1 * (max(biomass) - min_bio) + lag_indices = np.where(biomass > lag_thresh)[0] + lag_guess = time[lag_indices[0]] if len(lag_indices) > 0 else time[0] + p0 = [xm_guess, um_guess, lag_guess] - bounds = ([1e-9, 1e-9, 0], [np.inf, np.inf, max(time) if len(time)>0 else 100]) + bounds = ([min(biomass) if min(biomass)>1e-9 else 1e-9, 1e-9, 0], + [np.inf, np.inf, max(time) if len(time)>0 else 100]) popt, _ = curve_fit(self.gompertz, time, biomass, p0=p0, maxfev=self.maxfev, bounds=bounds, ftol=1e-9, xtol=1e-9) - self.params['biomass'] = {'xm': popt[0], 'um': popt[1], 'lag': popt[2]} + self.params['biomass'] = {'Xm': popt[0], 'um': popt[1], 'lag': popt[2]} y_pred = self.gompertz(time, *popt) elif self.model_type == 'moser': @@ -206,38 +339,64 @@ class BioprocessModel: um_guess = 0.1 Ks_guess = time[0] p0 = [Xm_guess, um_guess, Ks_guess] - bounds = ([1e-9, 1e-9, -np.inf], [np.inf, np.inf, max(time) if len(time)>0 else 100]) + bounds = ([min(biomass) if min(biomass)>1e-9 else 1e-9, 1e-9, -max(time) if len(time)>0 else -100], # Ks can be negative + [np.inf, np.inf, max(time) if len(time)>0 else 100]) popt, _ = curve_fit(self.moser, time, biomass, p0=p0, maxfev=self.maxfev, bounds=bounds, ftol=1e-9, xtol=1e-9) self.params['biomass'] = {'Xm': popt[0], 'um': popt[1], 'Ks': popt[2]} y_pred = self.moser(time, *popt) + + elif self.model_type == 'baranyi': + X0_guess = biomass[0] if biomass[0] > 1e-6 else 1e-3 + Xm_guess = max(biomass) if max(biomass) > X0_guess else X0_guess * 2 + if Xm_guess <= X0_guess: Xm_guess = X0_guess + 1e-3 # Ensure Xm > X0 + um_guess = 0.1 + min_bio = X0_guess + lag_thresh = min_bio + 0.1 * (Xm_guess - min_bio) + lag_indices = np.where(biomass > lag_thresh)[0] + lag_guess = time[lag_indices[0]] if len(lag_indices) > 0 and time[lag_indices[0]] > 0 else (time[0] if time[0] > 1e-9 else 1e-9) # lag must be >0 for some A(t) forms + if lag_guess <= 0: lag_guess = 1e-9 # Ensure lag is positive for Baranyi A(t) log + + p0 = [X0_guess, Xm_guess, um_guess, lag_guess] + bounds = ( + [1e-9, biomass[0] if biomass[0]>1e-9 else 1e-9, 1e-9, 1e-9], # X0, Xm, um, lag > 0 + [max(biomass)*0.99 if max(biomass)>0 else 1, np.inf, np.inf, max(time) if len(time)>0 else 100] + ) + p0[0] = np.clip(p0[0], bounds[0][0], bounds[1][0]) # Clip X0_guess + p0[3] = np.clip(p0[3], bounds[0][3], bounds[1][3]) # Clip lag_guess + + popt, _ = curve_fit(self.baranyi, time, biomass, p0=p0, maxfev=self.maxfev, bounds=bounds, ftol=1e-9, xtol=1e-9) + if popt[1] <= popt[0]: # Xm <= X0 + print(f"Advertencia: En modelo Baranyi, Xm ({popt[1]:.2f}) no es mayor que X0 ({popt[0]:.2f}). Ajuste puede no ser válido.") + self.params['biomass'] = {'X0': popt[0], 'Xm': popt[1], 'um': popt[2], 'lag': popt[3]} + y_pred = self.baranyi(time, *popt) + else: + print(f"Modelo {self.model_type} no implementado para ajuste de biomasa.") return None if np.any(np.isnan(y_pred)) or np.any(np.isinf(y_pred)): print(f"Predicción de biomasa contiene NaN/Inf para {self.model_type}. Ajuste fallido.") - self.r2['biomass'] = np.nan - self.rmse['biomass'] = np.nan + self.r2['biomass'] = np.nan; self.rmse['biomass'] = np.nan return None ss_res = np.sum((biomass - y_pred) ** 2) ss_tot = np.sum((biomass - np.mean(biomass)) ** 2) if ss_tot == 0: - self.r2['biomass'] = 1.0 if ss_res == 0 else 0.0 + self.r2['biomass'] = 1.0 if ss_res < 1e-9 else 0.0 # Perfect fit if residuals are also ~0 else: self.r2['biomass'] = 1 - (ss_res / ss_tot) self.rmse['biomass'] = np.sqrt(mean_squared_error(biomass, y_pred)) return y_pred + except RuntimeError as e: print(f"Error de Runtime en fit_biomass_{self.model_type} (probablemente no se pudo ajustar): {e}") self.params['biomass'] = {} - self.r2['biomass'] = np.nan - self.rmse['biomass'] = np.nan + self.r2['biomass'] = np.nan; self.rmse['biomass'] = np.nan return None except Exception as e: print(f"Error general en fit_biomass_{self.model_type}: {e}") self.params['biomass'] = {} - self.r2['biomass'] = np.nan - self.rmse['biomass'] = np.nan + self.r2['biomass'] = np.nan; self.rmse['biomass'] = np.nan return None def fit_substrate(self, time, substrate, biomass_params_dict): @@ -245,17 +404,24 @@ class BioprocessModel: print(f"Error en fit_substrate_{self.model_type}: Parámetros de biomasa no disponibles.") return None try: + # Extract parameters based on model type into a list for self.substrate if self.model_type == 'logistic': - biomass_params_values = [biomass_params_dict['xo'], biomass_params_dict['xm'], biomass_params_dict['um']] + # Expected by self.logistic: xo, xm, um + biomass_params_values = [biomass_params_dict['Xo'], biomass_params_dict['Xm'], biomass_params_dict['um']] elif self.model_type == 'gompertz': - biomass_params_values = [biomass_params_dict['xm'], biomass_params_dict['um'], biomass_params_dict['lag']] + # Expected by self.gompertz: xm, um, lag + biomass_params_values = [biomass_params_dict['Xm'], biomass_params_dict['um'], biomass_params_dict['lag']] elif self.model_type == 'moser': + # Expected by self.moser: Xm, um, Ks biomass_params_values = [biomass_params_dict['Xm'], biomass_params_dict['um'], biomass_params_dict['Ks']] + elif self.model_type == 'baranyi': + # Expected by self.baranyi: X0, Xm, um, lag + biomass_params_values = [biomass_params_dict['X0'], biomass_params_dict['Xm'], biomass_params_dict['um'], biomass_params_dict['lag']] else: return None so_guess = substrate[0] if len(substrate) > 0 else 1.0 - p_guess = 0.1 + p_guess = 0.1 q_guess = 0.01 p0 = [so_guess, p_guess, q_guess] bounds = ([0, 0, 0], [np.inf, np.inf, np.inf]) @@ -269,29 +435,22 @@ class BioprocessModel: if np.any(np.isnan(y_pred)) or np.any(np.isinf(y_pred)): print(f"Predicción de sustrato contiene NaN/Inf para {self.model_type}. Ajuste fallido.") - self.r2['substrate'] = np.nan - self.rmse['substrate'] = np.nan + self.r2['substrate'] = np.nan; self.rmse['substrate'] = np.nan return None ss_res = np.sum((substrate - y_pred) ** 2) ss_tot = np.sum((substrate - np.mean(substrate)) ** 2) - if ss_tot == 0: - self.r2['substrate'] = 1.0 if ss_res == 0 else 0.0 - else: - self.r2['substrate'] = 1 - (ss_res / ss_tot) + if ss_tot == 0: self.r2['substrate'] = 1.0 if ss_res < 1e-9 else 0.0 + else: self.r2['substrate'] = 1 - (ss_res / ss_tot) self.rmse['substrate'] = np.sqrt(mean_squared_error(substrate, y_pred)) return y_pred except RuntimeError as e: - print(f"Error de Runtime en fit_substrate_{self.model_type} (probablemente no se pudo ajustar): {e}") - self.params['substrate'] = {} - self.r2['substrate'] = np.nan - self.rmse['substrate'] = np.nan + print(f"Error de Runtime en fit_substrate_{self.model_type}: {e}") + self.params['substrate'] = {}; self.r2['substrate'] = np.nan; self.rmse['substrate'] = np.nan return None except Exception as e: print(f"Error general en fit_substrate_{self.model_type}: {e}") - self.params['substrate'] = {} - self.r2['substrate'] = np.nan - self.rmse['substrate'] = np.nan + self.params['substrate'] = {}; self.r2['substrate'] = np.nan; self.rmse['substrate'] = np.nan return None def fit_product(self, time, product, biomass_params_dict): @@ -300,16 +459,18 @@ class BioprocessModel: return None try: if self.model_type == 'logistic': - biomass_params_values = [biomass_params_dict['xo'], biomass_params_dict['xm'], biomass_params_dict['um']] + biomass_params_values = [biomass_params_dict['Xo'], biomass_params_dict['Xm'], biomass_params_dict['um']] elif self.model_type == 'gompertz': - biomass_params_values = [biomass_params_dict['xm'], biomass_params_dict['um'], biomass_params_dict['lag']] + biomass_params_values = [biomass_params_dict['Xm'], biomass_params_dict['um'], biomass_params_dict['lag']] elif self.model_type == 'moser': biomass_params_values = [biomass_params_dict['Xm'], biomass_params_dict['um'], biomass_params_dict['Ks']] + elif self.model_type == 'baranyi': + biomass_params_values = [biomass_params_dict['X0'], biomass_params_dict['Xm'], biomass_params_dict['um'], biomass_params_dict['lag']] else: return None po_guess = product[0] if len(product) > 0 else 0.0 - alpha_guess = 0.1 + alpha_guess = 0.1 beta_guess = 0.01 p0 = [po_guess, alpha_guess, beta_guess] bounds = ([0, 0, 0], [np.inf, np.inf, np.inf]) @@ -323,48 +484,54 @@ class BioprocessModel: if np.any(np.isnan(y_pred)) or np.any(np.isinf(y_pred)): print(f"Predicción de producto contiene NaN/Inf para {self.model_type}. Ajuste fallido.") - self.r2['product'] = np.nan - self.rmse['product'] = np.nan + self.r2['product'] = np.nan; self.rmse['product'] = np.nan return None ss_res = np.sum((product - y_pred) ** 2) ss_tot = np.sum((product - np.mean(product)) ** 2) - if ss_tot == 0: - self.r2['product'] = 1.0 if ss_res == 0 else 0.0 - else: - self.r2['product'] = 1 - (ss_res / ss_tot) + if ss_tot == 0: self.r2['product'] = 1.0 if ss_res < 1e-9 else 0.0 + else: self.r2['product'] = 1 - (ss_res / ss_tot) self.rmse['product'] = np.sqrt(mean_squared_error(product, y_pred)) return y_pred except RuntimeError as e: - print(f"Error de Runtime en fit_product_{self.model_type} (probablemente no se pudo ajustar): {e}") - self.params['product'] = {} - self.r2['product'] = np.nan - self.rmse['product'] = np.nan + print(f"Error de Runtime en fit_product_{self.model_type}: {e}") + self.params['product'] = {}; self.r2['product'] = np.nan; self.rmse['product'] = np.nan return None except Exception as e: print(f"Error general en fit_product_{self.model_type}: {e}") - self.params['product'] = {} - self.r2['product'] = np.nan - self.rmse['product'] = np.nan + self.params['product'] = {}; self.r2['product'] = np.nan; self.rmse['product'] = np.nan return None def generate_fine_time_grid(self, time): - if time is None or len(time) == 0: - return np.array([0]) - time_fine = np.linspace(time.min(), time.max(), 500) + # ... (same as before) + if time is None or len(time) < 2: # Need at least 2 points to define a range + return np.array([0]) if (time is None or len(time)==0) else np.array(time) + time_min, time_max = np.min(time), np.max(time) + if time_min == time_max: # If all time points are the same + return np.array([time_min]) + time_fine = np.linspace(time_min, time_max, 500) return time_fine - def system(self, y, t, biomass_params_list, substrate_params_list, product_params_list, model_type): + + def system(self, y, t, biomass_params_list, substrate_params_list, product_params_list, model_type_for_ode): + # model_type_for_ode is passed to ensure we use the correct diff eq X, S, P = y + dXdt = 0.0 - if model_type == 'logistic': + if model_type_for_ode == 'logistic': + # biomass_params_list for logistic: [Xo, Xm, um] dXdt = self.logistic_diff(X, t, biomass_params_list) - elif model_type == 'gompertz': + elif model_type_for_ode == 'gompertz': + # biomass_params_list for gompertz: [Xm, um, lag] dXdt = self.gompertz_diff(X, t, biomass_params_list) - elif model_type == 'moser': + elif model_type_for_ode == 'moser': + # biomass_params_list for moser: [Xm, um, Ks] dXdt = self.moser_diff(X, t, biomass_params_list) + # No ODE for Baranyi in this version else: - dXdt = 0.0 + # This case should ideally be prevented before calling system if model has no diff eq + print(f"Advertencia: Ecuación diferencial no definida para el modelo {model_type_for_ode} en la función 'system'. dXdt=0.") + dXdt = 0.0 p_val = substrate_params_list[1] if len(substrate_params_list) > 1 else 0 q_val = substrate_params_list[2] if len(substrate_params_list) > 2 else 0 @@ -373,51 +540,45 @@ class BioprocessModel: alpha_val = product_params_list[1] if len(product_params_list) > 1 else 0 beta_val = product_params_list[2] if len(product_params_list) > 2 else 0 dPdt = alpha_val * dXdt + beta_val * X - return [dXdt, dSdt, dPdt] def get_initial_conditions(self, time, biomass, substrate, product): - X0_exp = biomass[0] if len(biomass) > 0 else 0 - S0_exp = substrate[0] if len(substrate) > 0 else 0 - P0_exp = product[0] if len(product) > 0 else 0 + X0_exp = biomass[0] if biomass is not None and len(biomass) > 0 else 0 + S0_exp = substrate[0] if substrate is not None and len(substrate) > 0 else 0 + P0_exp = product[0] if product is not None and len(product) > 0 else 0 + X0 = X0_exp if 'biomass' in self.params and self.params['biomass']: if self.model_type == 'logistic': - X0 = self.params['biomass'].get('xo', X0_exp) - elif self.model_type == 'gompertz': - xm = self.params['biomass'].get('xm', 1) - um = self.params['biomass'].get('um', 0.1) - lag = self.params['biomass'].get('lag', 0) - X0 = self.gompertz(0, xm, um, lag) - if np.isnan(X0): X0 = X0_exp - elif self.model_type == 'moser': - Xm_param = self.params['biomass'].get('Xm', 1) - um_param = self.params['biomass'].get('um', 0.1) - Ks_param = self.params['biomass'].get('Ks', 0) - X0 = self.moser(0, Xm_param, um_param, Ks_param) - if np.isnan(X0): X0 = X0_exp - else: - X0 = X0_exp - else: - X0 = X0_exp - - if 'substrate' in self.params and self.params['substrate']: - S0 = self.params['substrate'].get('so', S0_exp) - else: - S0 = S0_exp - - if 'product' in self.params and self.params['product']: - P0 = self.params['product'].get('po', P0_exp) - else: - P0 = P0_exp + X0 = self.params['biomass'].get('Xo', X0_exp) + elif self.model_type == 'baranyi': # Baranyi also has X0 as a direct parameter + X0 = self.params['biomass'].get('X0', X0_exp) + elif self.model_type == 'gompertz' and self.biomass_model: + # For Gompertz, X(t=0) needs to be calculated from its parameters + # Parameters: Xm, um, lag + params_list = [self.params['biomass'].get('Xm',1), self.params['biomass'].get('um',0.1), self.params['biomass'].get('lag',0)] + X0_calc = self.biomass_model(0, *params_list) + X0 = X0_calc if not np.isnan(X0_calc) else X0_exp + elif self.model_type == 'moser' and self.biomass_model: + # For Moser, X(t=0) needs to be calculated + # Parameters: Xm, um, Ks + params_list = [self.params['biomass'].get('Xm',1), self.params['biomass'].get('um',0.1), self.params['biomass'].get('Ks',0)] + X0_calc = self.biomass_model(0, *params_list) + X0 = X0_calc if not np.isnan(X0_calc) else X0_exp + + S0 = self.params.get('substrate', {}).get('so', S0_exp) + P0 = self.params.get('product', {}).get('po', P0_exp) X0 = X0 if not np.isnan(X0) else 0.0 S0 = S0 if not np.isnan(S0) else 0.0 P0 = P0 if not np.isnan(P0) else 0.0 - return [X0, S0, P0] def solve_differential_equations(self, time, biomass, substrate, product): + if self.biomass_diff is None: # Check if a differential equation is defined for this model + print(f"ODE solving no está soportado para el modelo {self.model_type}. Se usarán resultados de curve_fit.") + return None, None, None, time # Return None for solutions, original time + if 'biomass' not in self.params or not self.params['biomass']: print("No hay parámetros de biomasa, no se pueden resolver las EDO.") return None, None, None, time @@ -425,14 +586,17 @@ class BioprocessModel: print("Tiempo no válido para resolver EDOs.") return None, None, None, np.array([]) + # Prepare biomass_params_list for ODE system based on self.model_type + # This list should match what the respective _diff function expects if self.model_type == 'logistic': - biomass_params_list = [self.params['biomass']['xo'], self.params['biomass']['xm'], self.params['biomass']['um']] + biomass_params_list_ode = [self.params['biomass']['Xo'], self.params['biomass']['Xm'], self.params['biomass']['um']] elif self.model_type == 'gompertz': - biomass_params_list = [self.params['biomass']['xm'], self.params['biomass']['um'], self.params['biomass']['lag']] + biomass_params_list_ode = [self.params['biomass']['Xm'], self.params['biomass']['um'], self.params['biomass']['lag']] elif self.model_type == 'moser': - biomass_params_list = [self.params['biomass']['Xm'], self.params['biomass']['um'], self.params['biomass']['Ks']] + biomass_params_list_ode = [self.params['biomass']['Xm'], self.params['biomass']['um'], self.params['biomass']['Ks']] + # Baranyi does not have biomass_diff implemented here, so it's caught by self.biomass_diff is None else: - print(f"Tipo de modelo de biomasa desconocido: {self.model_type}") + print(f"Tipo de modelo de biomasa desconocido para EDO: {self.model_type}") return None, None, None, time substrate_params_list = [ @@ -454,14 +618,14 @@ class BioprocessModel: try: sol = odeint(self.system, initial_conditions, time_fine, - args=(biomass_params_list, substrate_params_list, product_params_list, self.model_type), + args=(biomass_params_list_ode, substrate_params_list, product_params_list, self.model_type), # Pass self.model_type for routing in self.system rtol=1e-6, atol=1e-6) except Exception as e: print(f"Error al resolver EDOs con odeint: {e}") try: print("Intentando con método 'lsoda'...") sol = odeint(self.system, initial_conditions, time_fine, - args=(biomass_params_list, substrate_params_list, product_params_list, self.model_type), + args=(biomass_params_list_ode, substrate_params_list, product_params_list, self.model_type), rtol=1e-6, atol=1e-6, method='lsoda') except Exception as e_lsoda: print(f"Error al resolver EDOs con odeint (método lsoda): {e_lsoda}") @@ -473,67 +637,70 @@ class BioprocessModel: return X, S, P, time_fine def plot_results(self, time, biomass, substrate, product, - y_pred_biomass, y_pred_substrate, y_pred_product, + y_pred_biomass_fit, y_pred_substrate_fit, y_pred_product_fit, # Renamed to avoid confusion 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', use_differential=False, axis_labels=None, - show_error_bars=True, error_cap_size=3, error_line_width=1): # Added error bar parameters + show_error_bars=True, error_cap_size=3, error_line_width=1): - if y_pred_biomass is None and not use_differential: + # Initialize predictions with curve_fit results + y_pred_biomass, y_pred_substrate, y_pred_product = y_pred_biomass_fit, y_pred_substrate_fit, y_pred_product_fit + + if y_pred_biomass is None and not (use_differential and self.biomass_diff is not None): print(f"No se pudo ajustar biomasa para {experiment_name} con {self.model_type} y no se usan EDO. Omitiendo figura.") return None - if use_differential and ('biomass' not in self.params or not self.params['biomass']): - print(f"Se solicitó usar EDO pero no hay parámetros de biomasa para {experiment_name}. Omitiendo EDO.") - use_differential = False - - if axis_labels is None: - axis_labels = { - 'x_label': 'Tiempo', - 'biomass_label': 'Biomasa', - 'substrate_label': 'Sustrato', - 'product_label': 'Producto' - } - + + # Check if ODE should be used and is supported + can_use_ode = use_differential and self.biomass_diff is not None and 'biomass' in self.params and self.params['biomass'] + if use_differential and self.biomass_diff is None: + print(f"Modelo {self.model_type} no soporta EDOs. Usando ajuste directo.") + + if axis_labels is None: axis_labels = {'x_label': 'Tiempo', 'biomass_label': 'Biomasa', 'substrate_label': 'Sustrato', 'product_label': 'Producto'} sns.set_style(style) - time_to_plot = time + time_to_plot = time - if use_differential and 'biomass' in self.params and self.params['biomass']: + if can_use_ode: X_ode, S_ode, P_ode, time_fine_ode = self.solve_differential_equations(time, biomass, substrate, product) if X_ode is not None: y_pred_biomass, y_pred_substrate, y_pred_product = X_ode, S_ode, P_ode time_to_plot = time_fine_ode else: print(f"Fallo al resolver EDOs para {experiment_name}, usando resultados de curve_fit si existen.") - time_to_plot = time - else: - if not use_differential and self.biomass_model and 'biomass' in self.params and self.params['biomass']: - time_fine_curvefit = self.generate_fine_time_grid(time) - if time_fine_curvefit is not None and len(time_fine_curvefit)>0: + time_to_plot = self.generate_fine_time_grid(time) # Use fine grid for curve_fit if ODE fails + # Re-evaluate curve_fit results on fine grid if they exist + if y_pred_biomass_fit is not None and self.biomass_model and 'biomass' in self.params and self.params['biomass']: biomass_params_values = list(self.params['biomass'].values()) - y_pred_biomass_fine = self.biomass_model(time_fine_curvefit, *biomass_params_values) - - if 'substrate' in self.params and self.params['substrate']: - substrate_params_values = list(self.params['substrate'].values()) - y_pred_substrate_fine = self.substrate(time_fine_curvefit, *substrate_params_values, biomass_params_values) - else: - y_pred_substrate_fine = np.full_like(time_fine_curvefit, np.nan) - - if 'product' in self.params and self.params['product']: - product_params_values = list(self.params['product'].values()) - y_pred_product_fine = self.product(time_fine_curvefit, *product_params_values, biomass_params_values) - else: - y_pred_product_fine = np.full_like(time_fine_curvefit, np.nan) - - if not np.all(np.isnan(y_pred_biomass_fine)): - y_pred_biomass = y_pred_biomass_fine - time_to_plot = time_fine_curvefit - if not np.all(np.isnan(y_pred_substrate_fine)): - y_pred_substrate = y_pred_substrate_fine - if not np.all(np.isnan(y_pred_product_fine)): - y_pred_product = y_pred_product_fine + y_pred_biomass = self.biomass_model(time_to_plot, *biomass_params_values) + if y_pred_substrate_fit is not None and 'substrate' in self.params and self.params['substrate']: + substrate_params_values = list(self.params['substrate'].values()) + y_pred_substrate = self.substrate(time_to_plot, *substrate_params_values, biomass_params_values) + if y_pred_product_fit is not None and 'product' in self.params and self.params['product']: + product_params_values = list(self.params['product'].values()) + y_pred_product = self.product(time_to_plot, *product_params_values, biomass_params_values) + + else: # Not using ODE or ODE not supported, use curve_fit results on a fine grid + time_to_plot = self.generate_fine_time_grid(time) + if y_pred_biomass_fit is not None and self.biomass_model and 'biomass' in self.params and self.params['biomass']: + biomass_params_values = list(self.params['biomass'].values()) # Get latest params + y_pred_biomass = self.biomass_model(time_to_plot, *biomass_params_values) + if y_pred_substrate_fit is not None and 'substrate' in self.params and self.params['substrate']: + substrate_params_values = list(self.params['substrate'].values()) + y_pred_substrate = self.substrate(time_to_plot, *substrate_params_values, biomass_params_values) + else: # If substrate fit failed or no data, plot NaNs + y_pred_substrate = np.full_like(time_to_plot, np.nan) + if y_pred_product_fit is not None and 'product' in self.params and self.params['product']: + product_params_values = list(self.params['product'].values()) + y_pred_product = self.product(time_to_plot, *product_params_values, biomass_params_values) + else: # If product fit failed or no data, plot NaNs + y_pred_product = np.full_like(time_to_plot, np.nan) + else: # Biomass fit failed + y_pred_biomass = np.full_like(time_to_plot, np.nan) + y_pred_substrate = np.full_like(time_to_plot, np.nan) + y_pred_product = np.full_like(time_to_plot, np.nan) + fig, (ax1, ax2, ax3) = plt.subplots(3, 1, figsize=(10, 15)) fig.suptitle(f'{experiment_name} ({self.model_type.capitalize()})', fontsize=16) @@ -546,7 +713,7 @@ class BioprocessModel: (ax3, product, y_pred_product, product_std, axis_labels['product_label'], 'Modelo', self.params.get('product', {}), self.r2.get('product', np.nan), self.rmse.get('product', np.nan)) ] - + # ... (rest of plot_results is the same as your provided code, using the new y_pred variables) for idx, (ax, data_exp, y_pred_model, data_std_exp, ylabel, model_name_legend, params_dict, r2_val, rmse_val) in enumerate(plots_config): if data_exp is not None and len(data_exp) > 0 and not np.all(np.isnan(data_exp)): if show_error_bars and data_std_exp is not None and len(data_std_exp) == len(data_exp) and not np.all(np.isnan(data_std_exp)): @@ -568,28 +735,35 @@ class BioprocessModel: if y_pred_model is not None and len(y_pred_model) > 0 and not np.all(np.isnan(y_pred_model)): ax.plot(time_to_plot, y_pred_model, linestyle=line_style, color=line_color, label=model_name_legend) - elif idx == 0 and y_pred_biomass is None: + # ... (rest of messages for failed fits) + elif idx == 0 and (y_pred_biomass_fit is None and not can_use_ode): # If biomass fit failed and ODE not possible ax.text(0.5, 0.6, 'Modelo de biomasa no ajustado.', horizontalalignment='center', verticalalignment='center', transform=ax.transAxes, fontsize=10, color='red') - elif (idx == 1 and y_pred_substrate is None) or (idx == 2 and y_pred_product is None) : - if 'biomass' not in self.params or not self.params['biomass']: + elif (idx == 1 and y_pred_substrate_fit is None and not can_use_ode) or \ + (idx == 2 and y_pred_product_fit is None and not can_use_ode) : + if not ('biomass' in self.params and self.params['biomass']): # If biomass params are missing ax.text(0.5, 0.4, 'Modelo no ajustado (depende de biomasa).', horizontalalignment='center', verticalalignment='center', transform=ax.transAxes, fontsize=10, color='orange') - elif y_pred_model is None: + elif y_pred_model is None or np.all(np.isnan(y_pred_model)): # If this specific model (S or P) failed ax.text(0.5, 0.4, 'Modelo no ajustado.', horizontalalignment='center', verticalalignment='center', transform=ax.transAxes, fontsize=10, color='orange') + ax.set_xlabel(axis_labels['x_label']) ax.set_ylabel(ylabel) if show_legend: ax.legend(loc=legend_position) ax.set_title(f'{ylabel}') - if show_params and params_dict and all(isinstance(v, (int, float)) and np.isfinite(v) for v in params_dict.values()): - param_text = '\n'.join([f"{k} = {v:.3g}" for k, v in params_dict.items()]) + if show_params and params_dict and any(np.isfinite(v) for v in params_dict.values()): # Show if any param is finite + param_text_list = [] + for k, v_param in params_dict.items(): + param_text_list.append(f"{k} = {v_param:.3g}" if np.isfinite(v_param) else f"{k} = N/A") + param_text = '\n'.join(param_text_list) + r2_display = f"{r2_val:.3f}" if np.isfinite(r2_val) else "N/A" rmse_display = f"{rmse_val:.3f}" if np.isfinite(rmse_val) else "N/A" text = f"{param_text}\nR² = {r2_display}\nRMSE = {rmse_display}" @@ -607,11 +781,12 @@ class BioprocessModel: ax.text(text_x, text_y, text, transform=ax.transAxes, verticalalignment=va, horizontalalignment=ha, bbox={'boxstyle': 'round,pad=0.3', 'facecolor':'wheat', 'alpha':0.5}) - elif show_params and not params_dict : + elif show_params : # No params or all NaN ax.text(0.5, 0.3, 'Parámetros no disponibles.', horizontalalignment='center', verticalalignment='center', transform=ax.transAxes, fontsize=9, color='grey') + plt.tight_layout(rect=[0, 0.03, 1, 0.95]) buf = io.BytesIO() fig.savefig(buf, format='png', bbox_inches='tight') @@ -621,71 +796,68 @@ class BioprocessModel: return image def plot_combined_results(self, time, biomass, substrate, product, - y_pred_biomass, y_pred_substrate, y_pred_product, + y_pred_biomass_fit, y_pred_substrate_fit, y_pred_product_fit, # Renamed 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', use_differential=False, axis_labels=None, - show_error_bars=True, error_cap_size=3, error_line_width=1): # Added error bar parameters + show_error_bars=True, error_cap_size=3, error_line_width=1): + + y_pred_biomass, y_pred_substrate, y_pred_product = y_pred_biomass_fit, y_pred_substrate_fit, y_pred_product_fit - if y_pred_biomass is None and not use_differential: + if y_pred_biomass is None and not (use_differential and self.biomass_diff is not None): print(f"No se pudo ajustar biomasa para {experiment_name} con {self.model_type} (combinado). Omitiendo figura.") return None - if use_differential and ('biomass' not in self.params or not self.params['biomass']): - print(f"Se solicitó usar EDO (combinado) pero no hay parámetros de biomasa para {experiment_name}. Omitiendo EDO.") - use_differential = False - - if axis_labels is None: - axis_labels = { - 'x_label': 'Tiempo', - 'biomass_label': 'Biomasa', - 'substrate_label': 'Sustrato', - 'product_label': 'Producto' - } + + can_use_ode = use_differential and self.biomass_diff is not None and 'biomass' in self.params and self.params['biomass'] + if use_differential and self.biomass_diff is None: + print(f"Modelo {self.model_type} no soporta EDOs (combinado). Usando ajuste directo.") + if axis_labels is None: axis_labels = {'x_label': 'Tiempo', 'biomass_label': 'Biomasa', 'substrate_label': 'Sustrato', 'product_label': 'Producto'} sns.set_style(style) time_to_plot = time - if use_differential and 'biomass' in self.params and self.params['biomass']: + if can_use_ode: X_ode, S_ode, P_ode, time_fine_ode = self.solve_differential_equations(time, biomass, substrate, product) if X_ode is not None: y_pred_biomass, y_pred_substrate, y_pred_product = X_ode, S_ode, P_ode time_to_plot = time_fine_ode else: - print(f"Fallo al resolver EDOs para {experiment_name} (combinado), usando resultados de curve_fit si existen.") - time_to_plot = time - else: - if not use_differential and self.biomass_model and 'biomass' in self.params and self.params['biomass']: - time_fine_curvefit = self.generate_fine_time_grid(time) - if time_fine_curvefit is not None and len(time_fine_curvefit)>0: + print(f"Fallo al resolver EDOs para {experiment_name} (combinado), usando resultados de curve_fit.") + time_to_plot = self.generate_fine_time_grid(time) + if y_pred_biomass_fit is not None and self.biomass_model and 'biomass' in self.params and self.params['biomass']: biomass_params_values = list(self.params['biomass'].values()) - y_pred_biomass_fine = self.biomass_model(time_fine_curvefit, *biomass_params_values) - - if 'substrate' in self.params and self.params['substrate']: - substrate_params_values = list(self.params['substrate'].values()) - y_pred_substrate_fine = self.substrate(time_fine_curvefit, *substrate_params_values, biomass_params_values) - else: - y_pred_substrate_fine = np.full_like(time_fine_curvefit, np.nan) - - if 'product' in self.params and self.params['product']: - product_params_values = list(self.params['product'].values()) - y_pred_product_fine = self.product(time_fine_curvefit, *product_params_values, biomass_params_values) - else: - y_pred_product_fine = np.full_like(time_fine_curvefit, np.nan) - - if not np.all(np.isnan(y_pred_biomass_fine)): - y_pred_biomass = y_pred_biomass_fine - time_to_plot = time_fine_curvefit - if not np.all(np.isnan(y_pred_substrate_fine)): - y_pred_substrate = y_pred_substrate_fine - if not np.all(np.isnan(y_pred_product_fine)): - y_pred_product = y_pred_product_fine + y_pred_biomass = self.biomass_model(time_to_plot, *biomass_params_values) + if y_pred_substrate_fit is not None and 'substrate' in self.params and self.params['substrate']: + substrate_params_values = list(self.params['substrate'].values()) + y_pred_substrate = self.substrate(time_to_plot, *substrate_params_values, biomass_params_values) + if y_pred_product_fit is not None and 'product' in self.params and self.params['product']: + product_params_values = list(self.params['product'].values()) + y_pred_product = self.product(time_to_plot, *product_params_values, biomass_params_values) + else: # Not using ODE or ODE not supported + time_to_plot = self.generate_fine_time_grid(time) + if y_pred_biomass_fit is not None and self.biomass_model and 'biomass' in self.params and self.params['biomass']: + biomass_params_values = list(self.params['biomass'].values()) + y_pred_biomass = self.biomass_model(time_to_plot, *biomass_params_values) + if y_pred_substrate_fit is not None and 'substrate' in self.params and self.params['substrate']: + substrate_params_values = list(self.params['substrate'].values()) + y_pred_substrate = self.substrate(time_to_plot, *substrate_params_values, biomass_params_values) + else: y_pred_substrate = np.full_like(time_to_plot, np.nan) + if y_pred_product_fit is not None and 'product' in self.params and self.params['product']: + product_params_values = list(self.params['product'].values()) + y_pred_product = self.product(time_to_plot, *product_params_values, biomass_params_values) + else: y_pred_product = np.full_like(time_to_plot, np.nan) + else: + y_pred_biomass = np.full_like(time_to_plot, np.nan) + y_pred_substrate = np.full_like(time_to_plot, np.nan) + y_pred_product = np.full_like(time_to_plot, np.nan) fig, ax1 = plt.subplots(figsize=(12, 7)) fig.suptitle(f'{experiment_name} ({self.model_type.capitalize()})', fontsize=16) + # ... (rest of plot_combined_results is the same, using new y_pred variables and error bar params) colors = {'Biomasa': 'blue', 'Sustrato': 'green', 'Producto': 'red'} data_colors = {'Biomasa': 'darkblue', 'Sustrato': 'darkgreen', 'Producto': 'darkred'} model_colors = {'Biomasa': 'cornflowerblue', 'Sustrato': 'limegreen', 'Producto': 'salmon'} @@ -698,9 +870,7 @@ class BioprocessModel: time, biomass, yerr=biomass_std, fmt=marker_style, color=data_colors['Biomasa'], label=f'{axis_labels["biomass_label"]} (Datos)', - capsize=error_cap_size, - elinewidth=error_line_width, - markersize=5 + capsize=error_cap_size, elinewidth=error_line_width, markersize=5 ) else: ax1.plot(time, biomass, marker=marker_style, linestyle='', color=data_colors['Biomasa'], @@ -718,9 +888,7 @@ class BioprocessModel: time, substrate, yerr=substrate_std, fmt=marker_style, color=data_colors['Sustrato'], label=f'{axis_labels["substrate_label"]} (Datos)', - capsize=error_cap_size, - elinewidth=error_line_width, - markersize=5 + capsize=error_cap_size, elinewidth=error_line_width, markersize=5 ) else: ax2.plot(time, substrate, marker=marker_style, linestyle='', color=data_colors['Sustrato'], @@ -732,9 +900,7 @@ class BioprocessModel: ax3 = ax1.twinx() ax3.spines["right"].set_position(("axes", 1.15)) - ax3.set_frame_on(True) - ax3.patch.set_visible(False) - + ax3.set_frame_on(True); ax3.patch.set_visible(False) ax3.set_ylabel(axis_labels['product_label'], color=colors['Producto']) if product is not None and len(product) > 0 and not np.all(np.isnan(product)): if show_error_bars and product_std is not None and len(product_std) == len(product) and not np.all(np.isnan(product_std)): @@ -742,9 +908,7 @@ class BioprocessModel: time, product, yerr=product_std, fmt=marker_style, color=data_colors['Producto'], label=f'{axis_labels["product_label"]} (Datos)', - capsize=error_cap_size, - elinewidth=error_line_width, - markersize=5 + capsize=error_cap_size, elinewidth=error_line_width, markersize=5 ) else: ax3.plot(time, product, marker=marker_style, linestyle='', color=data_colors['Producto'], @@ -757,14 +921,12 @@ class BioprocessModel: lines_labels_collect = [] for ax_current in [ax1, ax2, ax3]: h, l = ax_current.get_legend_handles_labels() - if h: - lines_labels_collect.append((h,l)) + if h: lines_labels_collect.append((h,l)) if lines_labels_collect: lines, labels = [sum(lol, []) for lol in zip(*[(h,l) for h,l in lines_labels_collect])] unique_labels_dict = dict(zip(labels, lines)) - if show_legend: - ax1.legend(unique_labels_dict.values(), unique_labels_dict.keys(), loc=legend_position) + if show_legend: ax1.legend(unique_labels_dict.values(), unique_labels_dict.keys(), loc=legend_position) if show_params: texts_to_display = [] @@ -773,67 +935,52 @@ class BioprocessModel: (axis_labels['substrate_label'], self.params.get('substrate', {}), self.r2.get('substrate', np.nan), self.rmse.get('substrate', np.nan)), (axis_labels['product_label'], self.params.get('product', {}), self.r2.get('product', np.nan), self.rmse.get('product', np.nan)) ] - for label, params_dict, r2_val, rmse_val in param_categories: - if params_dict and all(isinstance(v, (int, float)) and np.isfinite(v) for v in params_dict.values()): - param_text = '\n'.join([f" {k} = {v:.3g}" for k, v in params_dict.items()]) + if params_dict and any(np.isfinite(v) for v in params_dict.values()): + param_text_list = [f" {k} = {v_par:.3g}" if np.isfinite(v_par) else f" {k} = N/A" for k,v_par in params_dict.items()] + param_text = '\n'.join(param_text_list) r2_display = f"{r2_val:.3f}" if np.isfinite(r2_val) else "N/A" rmse_display = f"{rmse_val:.3f}" if np.isfinite(rmse_val) else "N/A" texts_to_display.append(f"{label}:\n{param_text}\n R² = {r2_display}\n RMSE = {rmse_display}") - elif params_dict: - texts_to_display.append(f"{label}:\n Parámetros no válidos o N/A") - + elif params_dict: texts_to_display.append(f"{label}:\n Parámetros no válidos o N/A") total_text = "\n\n".join(texts_to_display) - if total_text: if params_position == 'outside right': fig.subplots_adjust(right=0.70) - bbox_props = dict(boxstyle='round,pad=0.3', facecolor='wheat', alpha=0.7) fig.text(0.72, 0.5, total_text, transform=fig.transFigure, verticalalignment='center', horizontalalignment='left', - bbox=bbox_props, fontsize=8) + bbox=dict(boxstyle='round,pad=0.3', facecolor='wheat', alpha=0.7), fontsize=8) else: text_x, ha = (0.95, 'right') if 'right' in params_position else (0.05, 'left') text_y, va = (0.95, 'top') if 'upper' in params_position else (0.05, 'bottom') ax1.text(text_x, text_y, total_text, transform=ax1.transAxes, verticalalignment=va, horizontalalignment=ha, - bbox={'boxstyle':'round,pad=0.3', 'facecolor':'wheat', 'alpha':0.7}, fontsize=8) + bbox=dict(boxstyle='round,pad=0.3', facecolor='wheat', alpha=0.7), fontsize=8) plt.tight_layout(rect=[0, 0.03, 1, 0.95]) - if params_position == 'outside right': - fig.subplots_adjust(right=0.70) - - buf = io.BytesIO() - fig.savefig(buf, format='png', bbox_inches='tight') - buf.seek(0) - image = Image.open(buf).convert("RGB") - plt.close(fig) + if params_position == 'outside right': fig.subplots_adjust(right=0.70) + buf = io.BytesIO(); fig.savefig(buf, format='png', bbox_inches='tight'); buf.seek(0) + image = Image.open(buf).convert("RGB"); plt.close(fig) return image + def process_all_data(file, legend_position, params_position, model_types_selected, experiment_names_str, lower_bounds_str, upper_bounds_str, mode, style, line_color, point_color, line_style, marker_style, show_legend, show_params, use_differential, maxfev_val, axis_labels_dict, - show_error_bars, error_cap_size, error_line_width): # New error bar parameters - - if file is None: - return [], pd.DataFrame(), "Por favor, sube un archivo Excel." + show_error_bars, error_cap_size, error_line_width): + # ... (Excel reading and sheet iteration logic remains the same) + if file is None: return [], pd.DataFrame(), "Por favor, sube un archivo Excel." try: - try: - xls = pd.ExcelFile(file.name) - except AttributeError: - xls = pd.ExcelFile(file) + xls = pd.ExcelFile(file.name if hasattr(file, 'name') else file) sheet_names = xls.sheet_names - if not sheet_names: - return [], pd.DataFrame(), "El archivo Excel está vacío o no contiene hojas." - except Exception as e: - return [], pd.DataFrame(), f"Error al leer el archivo Excel: {e}" + if not sheet_names: return [], pd.DataFrame(), "El archivo Excel está vacío." + except Exception as e: return [], pd.DataFrame(), f"Error al leer el archivo Excel: {e}" figures = [] comparison_data = [] - experiment_counter = 0 experiment_names_list = experiment_names_str.strip().split('\n') if experiment_names_str.strip() else [] all_plot_messages = [] @@ -843,126 +990,112 @@ def process_all_data(file, legend_position, params_position, model_types_selecte else f"Hoja '{sheet_name}'") try: df = pd.read_excel(xls, sheet_name=sheet_name, header=[0, 1]) - if df.empty: - all_plot_messages.append(f"Hoja '{sheet_name}' está vacía.") - continue + if df.empty: all_plot_messages.append(f"Hoja '{sheet_name}' vacía."); continue if not any(col_level2 == 'Tiempo' for _, col_level2 in df.columns): - all_plot_messages.append(f"Hoja '{sheet_name}' no contiene la subcolumna 'Tiempo'. Saltando hoja.") - continue + all_plot_messages.append(f"Hoja '{sheet_name}' sin 'Tiempo'."); continue except Exception as e: - all_plot_messages.append(f"Error al leer la hoja '{sheet_name}': {e}. Saltando hoja.") - continue + all_plot_messages.append(f"Error leyendo hoja '{sheet_name}': {e}."); continue - model_dummy_for_sheet = BioprocessModel() + model_dummy_for_sheet = BioprocessModel() # To process sheet data once try: model_dummy_for_sheet.process_data(df) except ValueError as e: - all_plot_messages.append(f"Error procesando datos de la hoja '{sheet_name}': {e}. Saltando hoja.") - continue + all_plot_messages.append(f"Error procesando datos de '{sheet_name}': {e}."); continue + + # Ensure dataxp, datasp, datapp are populated for average/combinado modes + # These should be populated by model_dummy_for_sheet.process_data() + # If they are empty lists, it means no valid data was found for that component. if mode == 'independent': + # ... (independent mode logic remains largely the same) + # Ensure time_exp, biomass_exp etc. are correctly extracted and validated grouped_cols = df.columns.get_level_values(0).unique() for exp_idx, exp_col_name in enumerate(grouped_cols): current_experiment_name = f"{current_experiment_name_base} - Exp {exp_idx + 1} ({exp_col_name})" - exp_df = df[exp_col_name] + exp_df_slice = df[exp_col_name] + try: - time_exp = exp_df['Tiempo'].dropna().values - biomass_exp = exp_df['Biomasa'].dropna().astype(float).values if 'Biomasa' in exp_df else np.array([]) - substrate_exp = exp_df['Sustrato'].dropna().astype(float).values if 'Sustrato' in exp_df else np.array([]) - product_exp = exp_df['Producto'].dropna().astype(float).values if 'Producto' in exp_df else np.array([]) - - if len(time_exp) == 0: - all_plot_messages.append(f"No hay datos de tiempo para {current_experiment_name}. Saltando.") - continue - if len(biomass_exp) == 0 : - all_plot_messages.append(f"No hay datos de biomasa para {current_experiment_name}. Saltando modelos para este experimento.") - for model_type_iter in model_types_selected: - comparison_data.append({ - 'Experimento': current_experiment_name, 'Modelo': model_type_iter.capitalize(), - **{f'R² {comp}': np.nan for comp in ['Biomasa', 'Sustrato', 'Producto']}, - **{f'RMSE {comp}': np.nan for comp in ['Biomasa', 'Sustrato', 'Producto']} - }) - continue - except KeyError as e: - all_plot_messages.append(f"Faltan columnas (Tiempo, Biomasa, Sustrato, Producto) en '{current_experiment_name}': {e}. Saltando.") - continue - except Exception as e_data: - all_plot_messages.append(f"Error extrayendo datos para '{current_experiment_name}': {e_data}. Saltando.") - continue - - biomass_std_exp, substrate_std_exp, product_std_exp = None, None, None + time_exp = exp_df_slice['Tiempo'].dropna().astype(float).values + biomass_exp = exp_df_slice['Biomasa'].dropna().astype(float).values if 'Biomasa' in exp_df_slice else np.array([]) + substrate_exp = exp_df_slice['Sustrato'].dropna().astype(float).values if 'Sustrato' in exp_df_slice else np.array([]) + product_exp = exp_df_slice['Producto'].dropna().astype(float).values if 'Producto' in exp_df_slice else np.array([]) + + if len(time_exp) == 0: all_plot_messages.append(f"Sin datos de tiempo para {current_experiment_name}."); continue + if len(biomass_exp) == 0: + all_plot_messages.append(f"Sin datos de biomasa para {current_experiment_name}.") + for mt in model_types_selected: comparison_data.append({'Experimento': current_experiment_name, 'Modelo': mt.capitalize(), 'R² Biomasa': np.nan, 'RMSE Biomasa': np.nan}) + continue + # Align data if lengths differ due to NaNs (simple truncation to min length) + min_len = min(len(time_exp), len(biomass_exp) if len(biomass_exp)>0 else len(time_exp), + len(substrate_exp) if len(substrate_exp)>0 else len(time_exp), + len(product_exp) if len(product_exp)>0 else len(time_exp)) + time_exp = time_exp[:min_len] + if len(biomass_exp)>0: biomass_exp = biomass_exp[:min_len] + if len(substrate_exp)>0: substrate_exp = substrate_exp[:min_len] + if len(product_exp)>0: product_exp = product_exp[:min_len] + + + except KeyError as e: all_plot_messages.append(f"Faltan columnas en '{current_experiment_name}': {e}."); continue + except Exception as e_data: all_plot_messages.append(f"Error extrayendo datos para '{current_experiment_name}': {e_data}."); continue + + biomass_std_exp, substrate_std_exp, product_std_exp = None, None, None # No std for independent mode here for model_type_iter in model_types_selected: model_instance = BioprocessModel(model_type=model_type_iter, maxfev=maxfev_val) - model_instance.fit_model() + model_instance.fit_model() # Sets self.biomass_model, self.biomass_diff y_pred_biomass = model_instance.fit_biomass(time_exp, biomass_exp) y_pred_substrate, y_pred_product = None, None if y_pred_biomass is not None and model_instance.params.get('biomass'): - if len(substrate_exp) > 0 : - y_pred_substrate = model_instance.fit_substrate(time_exp, substrate_exp, model_instance.params['biomass']) - if len(product_exp) > 0: - y_pred_product = model_instance.fit_product(time_exp, product_exp, model_instance.params['biomass']) - else: - all_plot_messages.append(f"Ajuste de biomasa falló para {current_experiment_name} con modelo {model_type_iter}.") - + if len(substrate_exp) > 0: y_pred_substrate = model_instance.fit_substrate(time_exp, substrate_exp, model_instance.params['biomass']) + if len(product_exp) > 0: y_pred_product = model_instance.fit_product(time_exp, product_exp, model_instance.params['biomass']) + else: all_plot_messages.append(f"Ajuste biomasa falló: {current_experiment_name}, {model_type_iter}.") + comparison_data.append({ 'Experimento': current_experiment_name, 'Modelo': model_type_iter.capitalize(), 'R² Biomasa': model_instance.r2.get('biomass', np.nan), 'RMSE Biomasa': model_instance.rmse.get('biomass', np.nan), 'R² Sustrato': model_instance.r2.get('substrate', np.nan), 'RMSE Sustrato': model_instance.rmse.get('substrate', np.nan), 'R² Producto': model_instance.r2.get('product', np.nan), 'RMSE Producto': model_instance.rmse.get('product', np.nan) }) - fig = model_instance.plot_results( time_exp, biomass_exp, substrate_exp, product_exp, - y_pred_biomass, y_pred_substrate, y_pred_product, + y_pred_biomass, y_pred_substrate, y_pred_product, # Pass curve_fit results biomass_std_exp, substrate_std_exp, product_std_exp, current_experiment_name, legend_position, params_position, - show_legend, show_params, style, - line_color, point_color, line_style, marker_style, + show_legend, show_params, style, line_color, point_color, line_style, marker_style, use_differential, axis_labels_dict, - show_error_bars=show_error_bars, # Pass new parameters - error_cap_size=error_cap_size, - error_line_width=error_line_width + show_error_bars, error_cap_size, error_line_width ) if fig: figures.append(fig) - experiment_counter +=1 elif mode in ['average', 'combinado']: + # ... (average/combinado mode logic remains largely the same) current_experiment_name = f"{current_experiment_name_base} - Promedio" time_avg = model_dummy_for_sheet.time - biomass_avg = model_dummy_for_sheet.dataxp[-1] if model_dummy_for_sheet.dataxp else np.array([]) - substrate_avg = model_dummy_for_sheet.datasp[-1] if model_dummy_for_sheet.datasp else np.array([]) - product_avg = model_dummy_for_sheet.datapp[-1] if model_dummy_for_sheet.datapp else np.array([]) + + # Check if dataxp, datasp, datapp are available from process_data + biomass_avg = model_dummy_for_sheet.dataxp[-1] if model_dummy_for_sheet.dataxp and len(model_dummy_for_sheet.dataxp[-1]) > 0 else np.array([]) + substrate_avg = model_dummy_for_sheet.datasp[-1] if model_dummy_for_sheet.datasp and len(model_dummy_for_sheet.datasp[-1]) > 0 else np.array([]) + product_avg = model_dummy_for_sheet.datapp[-1] if model_dummy_for_sheet.datapp and len(model_dummy_for_sheet.datapp[-1]) > 0 else np.array([]) biomass_std_avg = model_dummy_for_sheet.datax_std[-1] if model_dummy_for_sheet.datax_std and len(model_dummy_for_sheet.datax_std[-1]) == len(biomass_avg) else None substrate_std_avg = model_dummy_for_sheet.datas_std[-1] if model_dummy_for_sheet.datas_std and len(model_dummy_for_sheet.datas_std[-1]) == len(substrate_avg) else None product_std_avg = model_dummy_for_sheet.datap_std[-1] if model_dummy_for_sheet.datap_std and len(model_dummy_for_sheet.datap_std[-1]) == len(product_avg) else None - if len(time_avg) == 0: - all_plot_messages.append(f"No hay datos de tiempo para el promedio de '{sheet_name}'. Saltando.") - continue + if time_avg is None or len(time_avg) == 0: all_plot_messages.append(f"Sin datos de tiempo promedio para '{sheet_name}'."); continue if len(biomass_avg) == 0: - all_plot_messages.append(f"No hay datos de biomasa promedio para '{sheet_name}'. Saltando modelos.") - for model_type_iter in model_types_selected: - comparison_data.append({ - 'Experimento': current_experiment_name, 'Modelo': model_type_iter.capitalize(), - **{f'R² {comp}': np.nan for comp in ['Biomasa', 'Sustrato', 'Producto']}, - **{f'RMSE {comp}': np.nan for comp in ['Biomasa', 'Sustrato', 'Producto']} - }) + all_plot_messages.append(f"Sin datos de biomasa promedio para '{sheet_name}'.") + for mt in model_types_selected: comparison_data.append({'Experimento': current_experiment_name, 'Modelo': mt.capitalize(), 'R² Biomasa': np.nan, 'RMSE Biomasa': np.nan}) continue - + for model_type_iter in model_types_selected: model_instance = BioprocessModel(model_type=model_type_iter, maxfev=maxfev_val) model_instance.fit_model() y_pred_biomass = model_instance.fit_biomass(time_avg, biomass_avg) y_pred_substrate, y_pred_product = None, None if y_pred_biomass is not None and model_instance.params.get('biomass'): - if len(substrate_avg) > 0: - y_pred_substrate = model_instance.fit_substrate(time_avg, substrate_avg, model_instance.params['biomass']) - if len(product_avg) > 0: - y_pred_product = model_instance.fit_product(time_avg, product_avg, model_instance.params['biomass']) - else: - all_plot_messages.append(f"Ajuste de biomasa promedio falló para {current_experiment_name} con modelo {model_type_iter}.") + if len(substrate_avg) > 0: y_pred_substrate = model_instance.fit_substrate(time_avg, substrate_avg, model_instance.params['biomass']) + if len(product_avg) > 0: y_pred_product = model_instance.fit_product(time_avg, product_avg, model_instance.params['biomass']) + else: all_plot_messages.append(f"Ajuste biomasa promedio falló: {current_experiment_name}, {model_type_iter}.") comparison_data.append({ 'Experimento': current_experiment_name, 'Modelo': model_type_iter.capitalize(), @@ -970,28 +1103,22 @@ def process_all_data(file, legend_position, params_position, model_types_selecte 'R² Sustrato': model_instance.r2.get('substrate', np.nan), 'RMSE Sustrato': model_instance.rmse.get('substrate', np.nan), 'R² Producto': model_instance.r2.get('product', np.nan), 'RMSE Producto': model_instance.rmse.get('product', np.nan) }) - plot_func = model_instance.plot_combined_results if mode == 'combinado' else model_instance.plot_results fig = plot_func( time_avg, biomass_avg, substrate_avg, product_avg, - y_pred_biomass, y_pred_substrate, y_pred_product, + y_pred_biomass, y_pred_substrate, y_pred_product, # Pass curve_fit results biomass_std_avg, substrate_std_avg, product_std_avg, current_experiment_name, legend_position, params_position, - show_legend, show_params, style, - line_color, point_color, line_style, marker_style, + show_legend, show_params, style, line_color, point_color, line_style, marker_style, use_differential, axis_labels_dict, - show_error_bars=show_error_bars, # Pass new parameters - error_cap_size=error_cap_size, - error_line_width=error_line_width + show_error_bars, error_cap_size, error_line_width ) if fig: figures.append(fig) - experiment_counter +=1 comparison_df = pd.DataFrame(comparison_data) if not comparison_df.empty: for col in ['R² Biomasa', 'RMSE Biomasa', 'R² Sustrato', 'RMSE Sustrato', 'R² Producto', 'RMSE Producto']: - if col in comparison_df.columns: - comparison_df[col] = pd.to_numeric(comparison_df[col], errors='coerce') + if col in comparison_df.columns: comparison_df[col] = pd.to_numeric(comparison_df[col], errors='coerce') comparison_df_sorted = comparison_df.sort_values( by=['Experimento', 'Modelo', 'R² Biomasa', 'R² Sustrato', 'R² Producto', 'RMSE Biomasa', 'RMSE Sustrato', 'RMSE Producto'], ascending=[True, True, False, False, False, True, True, True] @@ -1003,20 +1130,28 @@ def process_all_data(file, legend_position, params_position, model_types_selecte ]) final_message = "Procesamiento completado." - if all_plot_messages: - final_message += " Mensajes:\n" + "\n".join(all_plot_messages) - if not figures and not comparison_df_sorted.empty: - final_message += "\nNo se generaron gráficos, pero hay datos en la tabla." - elif not figures and comparison_df_sorted.empty: - final_message += "\nNo se generaron gráficos ni datos para la tabla." + if all_plot_messages: final_message += " Mensajes:\n" + "\n".join(all_plot_messages) + if not figures and not comparison_df_sorted.empty: final_message += "\nNo se generaron gráficos, pero hay datos en la tabla." + elif not figures and comparison_df_sorted.empty: final_message += "\nNo se generaron gráficos ni datos para la tabla." return figures, comparison_df_sorted, final_message + +MODEL_CHOICES = [ + ("Logistic (3-parám)", "logistic"), + ("Gompertz (3-parám)", "gompertz"), + ("Moser (3-parám)", "moser"), + ("Baranyi (4-parám)", "baranyi") + # Add more models here as ("Display Name (X-param)", "internal_model_name") +] + def create_interface(): with gr.Blocks(theme=gr.themes.Soft()) as demo: gr.Markdown("# Modelos Cinéticos de Bioprocesos") + # ... (Markdown descriptions remain the same) gr.Markdown(r""" Análisis y visualización de datos de bioprocesos utilizando modelos cinéticos como Logístico, Gompertz y Moser para el crecimiento de biomasa, y el modelo de Luedeking-Piret para el consumo de sustrato y la formación de producto. + Nuevos modelos como Baranyi (4 parámetros) han sido añadidos. **Instrucciones:** 1. Sube un archivo Excel. El archivo debe tener una estructura de MultiIndex en las columnas: @@ -1025,7 +1160,7 @@ def create_interface(): - Si hay réplicas, deben estar como columnas separadas bajo el mismo nombre de experimento (Nivel 0) y tipo de dato (Nivel 1). Ejemplo: (Control, Biomasa, Rep1), (Control, Biomasa, Rep2). El código promediará estas réplicas para los modos "average" y "combinado". Para el modo "independent", se asume una sola serie de datos por (Experimento, TipoDato). - 2. Selecciona el/los tipo(s) de modelo(s) de biomasa a ajustar. + 2. Selecciona el/los tipo(s) de modelo(s) de biomasa a ajustar. Los modelos están agrupados por el número de parámetros. 3. Elige el modo de análisis: - `independent`: Analiza cada experimento (columna de Nivel 0) individualmente. - `average`: Promedia los datos de todos los experimentos dentro de una hoja y ajusta los modelos a estos promedios. Se grafica en subplots separados. @@ -1033,111 +1168,75 @@ def create_interface(): 4. Configura las opciones de graficación (leyenda, parámetros, estilos, colores, etc.). 5. (Opcional) Personaliza los nombres de los experimentos y los títulos de los ejes. 6. Haz clic en "Simular" para generar los gráficos y la tabla comparativa. - 7. Puedes exportar la tabla de resultados a Excel. + 7. Puedes exportar la tabla de resultados a Excel o CSV. """) gr.Markdown(r""" - ## Ecuaciones Diferenciales Utilizadas + ## Ecuaciones Diferenciales Utilizadas (Simplificado) **Biomasa:** - - Logístico: - $$ - \frac{dX}{dt} = \mu_m X\left(1 - \frac{X}{X_m}\right) - $$ - Solución integral: $X(t) = \frac{X_0 \exp(\mu_m t)}{1 - (X_0/X_m)(1 - \exp(\mu_m t))}$ - - - Gompertz (Modificado): - $$ - X(t) = X_m \exp\left(-\exp\left(\left(\frac{\mu_m e}{X_m}\right)(\text{lag}-t)+1\right)\right) - $$ - Ecuación diferencial: - $$ - \frac{dX}{dt} = X(t)\left(\frac{\mu_m e}{X_m}\right)\exp\left(\left(\frac{\mu_m e}{X_m}\right)(\text{lag}-t)+1\right) - $$ - - - Moser (simplificado, asumiendo $S \gg K_s$ o crecimiento no limitado por sustrato modelado explícitamente aquí): - $$ - X(t)=X_m(1-e^{-\mu_m(t-K_s)}) - $$ - Ecuación diferencial (forma simplificada, no estándar de Moser que depende de S): - $$ - \frac{dX}{dt}=\mu_m(X_m - X) - $$ + - Logístico (3p: $X_0, X_m, \mu_m$): + $$ X(t) = \frac{X_0 X_m e^{\mu_m t}}{X_m - X_0 + X_0 e^{\mu_m t}} \quad \text{o} \quad \frac{dX}{dt} = \mu_m X\left(1 - \frac{X}{X_m}\right) $$ + + - Gompertz (3p: $X_m, \mu_m, \lambda$): + $$ X(t) = X_m \exp\left(-\exp\left(\frac{\mu_m e}{X_m}(\lambda-t)+1\right)\right) \quad \text{o} \quad \frac{dX}{dt} = \mu_m X \ln\left(\frac{X_m}{X}\right) \text{ (forma alternativa)} $$ + + - Moser (3p: $X_m, \mu_m, K_s$ - forma simplificada): + $$ X(t)=X_m(1-e^{-\mu_m(t-K_s)}) \quad \text{o} \quad \frac{dX}{dt}=\mu_m(X_m - X) $$ + + - Baranyi (4p: $X_0, X_m, \mu_m, \lambda$): + $$ \ln X(t) = \ln X_0 + \mu_m A(t) - \ln\left(1 + \frac{e^{\mu_m A(t)}-1}{X_m/X_0}\right) $$ + $$ A(t) = t + \frac{1}{\mu_m} \ln(e^{-\mu_m t} + e^{-\mu_m \lambda} - e^{-\mu_m(t+\lambda)}) $$ + (Ecuación diferencial compleja, no usada para ODE en esta versión) **Sustrato y Producto (Luedeking-Piret):** - $$ - \frac{dS}{dt} = -p \frac{dX}{dt} - q X \quad \Rightarrow \quad S(t) = S_0 - p(X(t)-X_0) - q \int_0^t X(\tau)d\tau - $$ - - $$ - \frac{dP}{dt} = \alpha \frac{dX}{dt} + \beta X \quad \Rightarrow \quad P(t) = P_0 + \alpha(X(t)-X_0) + \beta \int_0^t X(\tau)d\tau - $$ - Donde $X_0, S_0, P_0$ son las concentraciones iniciales. - Parámetros: - - $X_m$: Máxima concentración de biomasa. - - $\mu_m$: Máxima tasa de crecimiento específico. - - $X_0$: Concentración inicial de biomasa. - - $\text{lag}$: Duración de la fase de latencia. - - $K_s$: Constante de afinidad (en el modelo de Moser simplificado, actúa como un tiempo de retardo). - - $p$: Coeficiente de rendimiento de biomasa a partir de sustrato (asociado al crecimiento). $1/Y_{X/S}^{crecimiento}$. - - $q$: Coeficiente de mantenimiento. $m_S$. - - $\alpha$: Coeficiente de formación de producto asociado al crecimiento. $Y_{P/X}^{crecimiento}$. - - $\beta$: Coeficiente de formación de producto no asociado al crecimiento. $m_P$. + $$ \frac{dS}{dt} = -p \frac{dX}{dt} - q X \quad ; \quad \frac{dP}{dt} = \alpha \frac{dX}{dt} + \beta X $$ + Parámetros: $X_m, \mu_m, X_0, \lambda (\text{lag}), K_s, p, q, \alpha, \beta$. """) + with gr.Row(): file_input = gr.File(label="Subir archivo Excel (.xlsx)", file_types=['.xlsx']) mode = gr.Radio(["independent", "average", "combinado"], label="Modo de Análisis", value="independent", info="Independent: cada experimento. Average/Combinado: promedio de la hoja.") - with gr.Accordion("Configuración de Modelos y Simulación", open=False): - model_types_selected = gr.CheckboxGroup( - choices=["logistic", "gompertz", "moser"], + with gr.Accordion("Configuración de Modelos y Simulación", open=True): # Open by default + model_types_selected_ui = gr.CheckboxGroup( + choices=MODEL_CHOICES, # Use the global list of (DisplayName, value) label="Tipo(s) de Modelo de Biomasa", - value=["logistic"] + value=["logistic"] # Default selected internal value ) - use_differential = gr.Checkbox(label="Usar Ecuaciones Diferenciales para Graficar (experimental)", value=False, - info="Si se marca, las curvas se generan resolviendo las EDOs. Si no, por ajuste directo de las formas integradas.") - maxfev_input = gr.Number(label="maxfev (Máx. evaluaciones para el ajuste)", value=50000, minimum=1000, step=1000) - experiment_names_str = gr.Textbox( + use_differential_ui = gr.Checkbox(label="Usar Ecuaciones Diferenciales para Graficar (experimental)", value=False, + info="Si se marca, las curvas se generan resolviendo las EDOs (si el modelo lo soporta). Si no, por ajuste directo.") + maxfev_input_ui = gr.Number(label="maxfev (Máx. evaluaciones para el ajuste)", value=50000, minimum=1000, step=1000) + experiment_names_str_ui = gr.Textbox( label="Nombres de los experimentos/hojas (uno por línea, opcional)", placeholder="Nombre para Hoja 1\nNombre para Hoja 2\n...", lines=3, info="Si se deja vacío, se usarán los nombres de las hojas o 'Exp X'." ) + # ... (rest of the UI for graph settings, axis labels, error bars remains the same) with gr.Accordion("Configuración de Gráficos", open=False): with gr.Row(): with gr.Column(scale=1): - legend_position = gr.Radio( - choices=["upper left", "upper right", "lower left", "lower right", "best"], - label="Posición de Leyenda", value="best" - ) - show_legend = gr.Checkbox(label="Mostrar Leyenda", value=True) + legend_position_ui = gr.Radio(choices=["upper left", "upper right", "lower left", "lower right", "best"], label="Posición de Leyenda", value="best") + show_legend_ui = gr.Checkbox(label="Mostrar Leyenda", value=True) with gr.Column(scale=1): - params_position = gr.Radio( - choices=["upper left", "upper right", "lower left", "lower right", "outside right"], - label="Posición de Parámetros", value="upper right" - ) - show_params = gr.Checkbox(label="Mostrar Parámetros", value=True) - + params_position_ui = gr.Radio(choices=["upper left", "upper right", "lower left", "lower right", "outside right"], label="Posición de Parámetros", value="upper right") + show_params_ui = gr.Checkbox(label="Mostrar Parámetros", value=True) with gr.Row(): - style_dropdown = gr.Dropdown(choices=['white', 'dark', 'whitegrid', 'darkgrid', 'ticks'], - label="Estilo de Gráfico (Seaborn)", value='whitegrid') - line_color_picker = gr.ColorPicker(label="Color de Línea (Modelo)", value='#0072B2') - point_color_picker = gr.ColorPicker(label="Color de Puntos (Datos)", value='#D55E00') - + style_dropdown_ui = gr.Dropdown(choices=['white', 'dark', 'whitegrid', 'darkgrid', 'ticks'], label="Estilo de Gráfico (Seaborn)", value='whitegrid') + line_color_picker_ui = gr.ColorPicker(label="Color de Línea (Modelo)", value='#0072B2') + point_color_picker_ui = gr.ColorPicker(label="Color de Puntos (Datos)", value='#D55E00') with gr.Row(): - line_style_dropdown = gr.Dropdown(choices=['-', '--', '-.', ':'], label="Estilo de Línea", value='-') - marker_style_dropdown = gr.Dropdown(choices=['o', 's', '^', 'v', 'D', 'x', '+', '*'], - label="Estilo de Marcador (Puntos)", value='o') + line_style_dropdown_ui = gr.Dropdown(choices=['-', '--', '-.', ':'], label="Estilo de Línea", value='-') + marker_style_dropdown_ui = gr.Dropdown(choices=['o', 's', '^', 'v', 'D', 'x', '+', '*'], label="Estilo de Marcador (Puntos)", value='o') with gr.Row(): - x_axis_label_input = gr.Textbox(label="Título Eje X", value="Tiempo (h)", placeholder="Tiempo (unidades)") - biomass_axis_label_input = gr.Textbox(label="Título Eje Y (Biomasa)", value="Biomasa (g/L)", placeholder="Biomasa (unidades)") + x_axis_label_input_ui = gr.Textbox(label="Título Eje X", value="Tiempo (h)", placeholder="Tiempo (unidades)") + biomass_axis_label_input_ui = gr.Textbox(label="Título Eje Y (Biomasa)", value="Biomasa (g/L)", placeholder="Biomasa (unidades)") with gr.Row(): - substrate_axis_label_input = gr.Textbox(label="Título Eje Y (Sustrato)", value="Sustrato (g/L)", placeholder="Sustrato (unidades)") - product_axis_label_input = gr.Textbox(label="Título Eje Y (Producto)", value="Producto (g/L)", placeholder="Producto (unidades)") - - # ADDED ERROR BAR CONTROLS + substrate_axis_label_input_ui = gr.Textbox(label="Título Eje Y (Sustrato)", value="Sustrato (g/L)", placeholder="Sustrato (unidades)") + product_axis_label_input_ui = gr.Textbox(label="Título Eje Y (Producto)", value="Producto (g/L)", placeholder="Producto (unidades)") with gr.Row(): show_error_bars_ui = gr.Checkbox(label="Mostrar barras de error", value=True) error_cap_size_ui = gr.Slider(label="Tamaño de tapa de barras de error", minimum=1, maximum=10, step=1, value=3) @@ -1145,107 +1244,101 @@ def create_interface(): with gr.Accordion("Configuración Avanzada de Ajuste (No implementado aún)", open=False): with gr.Row(): - lower_bounds_str = gr.Textbox(label="Lower Bounds (no usado actualmente)", lines=3) - upper_bounds_str = gr.Textbox(label="Upper Bounds (no usado actualmente)", lines=3) + lower_bounds_str_ui = gr.Textbox(label="Lower Bounds (no usado actualmente)", lines=3) + upper_bounds_str_ui = gr.Textbox(label="Upper Bounds (no usado actualmente)", lines=3) simulate_btn = gr.Button("Simular y Graficar", variant="primary") - status_message = gr.Textbox(label="Estado del Procesamiento", interactive=False) - output_gallery = gr.Gallery(label="Resultados Gráficos", columns=[2,1], height='auto', object_fit="contain") - output_table = gr.Dataframe( - label="Tabla Comparativa de Modelos (Ordenada por R² Biomasa Descendente)", + status_message_ui = gr.Textbox(label="Estado del Procesamiento", interactive=False) + output_gallery_ui = gr.Gallery(label="Resultados Gráficos", columns=[2,1], height='auto', object_fit="contain") + output_table_ui = gr.Dataframe( + label="Tabla Comparativa de Modelos", headers=["Experimento", "Modelo", "R² Biomasa", "RMSE Biomasa", "R² Sustrato", "RMSE Sustrato", "R² Producto", "RMSE Producto"], interactive=False, wrap=True ) - state_df = gr.State(pd.DataFrame()) + state_df_ui = gr.State(pd.DataFrame()) # To store the dataframe for export def run_simulation_interface(file, legend_pos, params_pos, models_sel, analysis_mode, exp_names, low_bounds, up_bounds, plot_style, line_col, point_col, line_sty, marker_sty, show_leg, show_par, use_diff, maxfev, x_label, biomass_label, substrate_label, product_label, - show_error_bars_arg, error_cap_size_arg, error_line_width_arg): # New error bar args - if file is None: - return [], pd.DataFrame(), "Error: Por favor, sube un archivo Excel.", pd.DataFrame() - + show_error_bars_arg, error_cap_size_arg, error_line_width_arg): + if file is None: return [], pd.DataFrame(), "Error: Por favor, sube un archivo Excel.", pd.DataFrame() axis_labels = { 'x_label': x_label if x_label else 'Tiempo', 'biomass_label': biomass_label if biomass_label else 'Biomasa', 'substrate_label': substrate_label if substrate_label else 'Sustrato', 'product_label': product_label if product_label else 'Producto' } - - if not models_sel: - return [], pd.DataFrame(), "Error: Por favor, selecciona al menos un tipo de modelo de biomasa.", pd.DataFrame() + if not models_sel: return [], pd.DataFrame(), "Error: Por favor, selecciona al menos un modelo.", pd.DataFrame() figures, comparison_df, message = process_all_data( file, legend_pos, params_pos, models_sel, exp_names, low_bounds, up_bounds, analysis_mode, plot_style, line_col, point_col, line_sty, marker_sty, show_leg, show_par, use_diff, int(maxfev), - axis_labels, - show_error_bars_arg, error_cap_size_arg, error_line_width_arg # Pass new args + axis_labels, show_error_bars_arg, error_cap_size_arg, error_line_width_arg ) return figures, comparison_df, message, comparison_df simulate_btn.click( fn=run_simulation_interface, inputs=[ - file_input, legend_position, params_position, model_types_selected, mode, experiment_names_str, - lower_bounds_str, upper_bounds_str, style_dropdown, - line_color_picker, point_color_picker, line_style_dropdown, marker_style_dropdown, - show_legend, show_params, use_differential, maxfev_input, - x_axis_label_input, biomass_axis_label_input, substrate_axis_label_input, product_axis_label_input, - show_error_bars_ui, error_cap_size_ui, error_line_width_ui # New UI inputs + file_input, legend_position_ui, params_position_ui, model_types_selected_ui, mode, experiment_names_str_ui, + lower_bounds_str_ui, upper_bounds_str_ui, style_dropdown_ui, + line_color_picker_ui, point_color_picker_ui, line_style_dropdown_ui, marker_style_dropdown_ui, + show_legend_ui, show_params_ui, use_differential_ui, maxfev_input_ui, + x_axis_label_input_ui, biomass_axis_label_input_ui, substrate_axis_label_input_ui, product_axis_label_input_ui, + show_error_bars_ui, error_cap_size_ui, error_line_width_ui ], - outputs=[output_gallery, output_table, status_message, state_df] + outputs=[output_gallery_ui, output_table_ui, status_message_ui, state_df_ui] ) + with gr.Row(): + export_excel_btn = gr.Button("Exportar Tabla a Excel") + export_csv_btn = gr.Button("Exportar Tabla a CSV") + + download_file_output_ui = gr.File(label="Descargar archivo", interactive=False) + def export_excel_interface(df_to_export): if df_to_export is None or df_to_export.empty: - with tempfile.NamedTemporaryFile(suffix=".txt", delete=False) as tmp: - tmp.write(b"No hay datos para exportar.") - return tmp.name + with tempfile.NamedTemporaryFile(suffix=".txt", delete=False) as tmp: tmp.write(b"No hay datos para exportar."); return tmp.name try: with tempfile.NamedTemporaryFile(suffix=".xlsx", delete=False, mode='w+b') as tmp: - df_to_export.to_excel(tmp.name, index=False) - return tmp.name + df_to_export.to_excel(tmp.name, index=False); return tmp.name except Exception as e: - with tempfile.NamedTemporaryFile(suffix=".txt", delete=False) as tmp: - tmp.write(f"Error al exportar a Excel: {e}".encode()) - return tmp.name + with tempfile.NamedTemporaryFile(suffix=".txt", delete=False) as tmp: tmp.write(f"Error al exportar a Excel: {e}".encode()); return tmp.name + + export_excel_btn.click(fn=export_excel_interface, inputs=state_df_ui, outputs=download_file_output_ui) - export_btn = gr.Button("Exportar Tabla a Excel") - download_file_output = gr.File(label="Descargar archivo Excel", interactive=False) + def export_csv_interface(df_to_export): + if df_to_export is None or df_to_export.empty: + with tempfile.NamedTemporaryFile(suffix=".txt", delete=False) as tmp: tmp.write(b"No hay datos para exportar."); return tmp.name + try: + with tempfile.NamedTemporaryFile(suffix=".csv", delete=False, mode='w', encoding='utf-8') as tmp: # CSV is text + df_to_export.to_csv(tmp.name, index=False); return tmp.name + except Exception as e: + with tempfile.NamedTemporaryFile(suffix=".txt", delete=False) as tmp: tmp.write(f"Error al exportar a CSV: {e}".encode()); return tmp.name - export_btn.click( - fn=export_excel_interface, - inputs=state_df, - outputs=download_file_output - ) + export_csv_btn.click(fn=export_csv_interface, inputs=state_df_ui, outputs=download_file_output_ui) gr.Examples( examples=[ - [None, "best", "upper right", ["logistic"], "independent", "Exp A\nExp B", "", "", "whitegrid", "#0072B2", "#D55E00", "-", "o", True, True, False, 50000, "Tiempo (días)", "Células (millones/mL)", "Glucosa (mM)", "Anticuerpo (mg/L)", True, 3, 1.0] + [None, "best", "upper right", ["logistic", "baranyi"], "independent", "Exp A\nExp B", "", "", "whitegrid", "#0072B2", "#D55E00", "-", "o", True, True, False, 50000, "Tiempo (días)", "Células (millones/mL)", "Glucosa (mM)", "Anticuerpo (mg/L)", True, 3, 1.0] ], inputs=[ - file_input, legend_position, params_position, model_types_selected, mode, experiment_names_str, - lower_bounds_str, upper_bounds_str, style_dropdown, - line_color_picker, point_color_picker, line_style_dropdown, marker_style_dropdown, - show_legend, show_params, use_differential, maxfev_input, - x_axis_label_input, biomass_axis_label_input, substrate_axis_label_input, product_axis_label_input, - show_error_bars_ui, error_cap_size_ui, error_line_width_ui # Added example values for new inputs + file_input, legend_position_ui, params_position_ui, model_types_selected_ui, mode, experiment_names_str_ui, + lower_bounds_str_ui, upper_bounds_str_ui, style_dropdown_ui, + line_color_picker_ui, point_color_picker_ui, line_style_dropdown_ui, marker_style_dropdown_ui, + show_legend_ui, show_params_ui, use_differential_ui, maxfev_input_ui, + x_axis_label_input_ui, biomass_axis_label_input_ui, substrate_axis_label_input_ui, product_axis_label_input_ui, + show_error_bars_ui, error_cap_size_ui, error_line_width_ui ], label="Ejemplo de Configuración (subir archivo manualmente)" ) return demo if __name__ == '__main__': - try: - import google.colab - IN_COLAB = True - except: - IN_COLAB = False - demo_instance = create_interface() - demo_instance.launch(share=True) # Use share=IN_COLAB for conditional sharing \ No newline at end of file + demo_instance.launch(share=True) \ No newline at end of file