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# --- INSTALACIÓN DE DEPENDENCIAS ADICIONALES ---
import os
import sys
import subprocess
os.system("pip install --upgrade gradio")
# --- IMPORTACIONES ---
import os
import io
import tempfile
import traceback
import zipfile
from typing import List, Tuple, Dict, Any, Optional, Union
from abc import ABC, abstractmethod
from unittest.mock import MagicMock
from dataclasses import dataclass
from enum import Enum
import json
from PIL import Image
import gradio as gr
import plotly.graph_objects as go
from plotly.subplots import make_subplots
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.integrate import odeint
from scipy.optimize import curve_fit, differential_evolution
from sklearn.metrics import mean_squared_error, r2_score
from docx import Document
from docx.shared import Inches
from fpdf import FPDF
from fpdf.enums import XPos, YPos
from fastapi import FastAPI
import uvicorn
# --- SISTEMA DE INTERNACIONALIZACIÓN ---
class Language(Enum):
ES = "Español"
EN = "English"
PT = "Português"
FR = "Français"
DE = "Deutsch"
ZH = "中文"
JA = "日本語"
TRANSLATIONS = {
Language.ES: {
"title": "🔬 Analizador de Cinéticas de Bioprocesos",
"subtitle": "Análisis avanzado de modelos matemáticos biotecnológicos",
"welcome": "Bienvenido al Analizador de Cinéticas",
"upload": "Sube tu archivo Excel (.xlsx)",
"select_models": "Modelos a Probar",
"analysis_mode": "Modo de Análisis",
"analyze": "Analizar y Graficar",
"results": "Resultados",
"download": "Descargar",
"biomass": "Biomasa",
"substrate": "Sustrato",
"product": "Producto",
"time": "Tiempo",
"parameters": "Parámetros",
"model_comparison": "Comparación de Modelos",
"dark_mode": "Modo Oscuro",
"light_mode": "Modo Claro",
"language": "Idioma",
"theory": "Teoría y Modelos",
"guide": "Guía de Uso",
"api_docs": "Documentación API"
},
Language.EN: {
"title": "🔬 Bioprocess Kinetics Analyzer",
"subtitle": "Advanced analysis of biotechnological mathematical models",
"welcome": "Welcome to the Kinetics Analyzer",
"upload": "Upload your Excel file (.xlsx)",
"select_models": "Models to Test",
"analysis_mode": "Analysis Mode",
"analyze": "Analyze and Plot",
"results": "Results",
"download": "Download",
"biomass": "Biomass",
"substrate": "Substrate",
"product": "Product",
"time": "Time",
"parameters": "Parameters",
"model_comparison": "Model Comparison",
"dark_mode": "Dark Mode",
"light_mode": "Light Mode",
"language": "Language",
"theory": "Theory and Models",
"guide": "User Guide",
"api_docs": "API Documentation"
},
}
# --- CONSTANTES MEJORADAS ---
C_TIME = 'tiempo'
C_BIOMASS = 'biomass'
C_SUBSTRATE = 'substrate'
C_PRODUCT = 'product'
C_OXYGEN = 'oxygen'
C_CO2 = 'co2'
C_PH = 'ph'
COMPONENTS = [C_BIOMASS, C_SUBSTRATE, C_PRODUCT]
# --- SISTEMA DE TEMAS ---
THEMES = {
"light": gr.themes.Soft(
primary_hue="blue",
secondary_hue="sky",
neutral_hue="gray",
font=[gr.themes.GoogleFont("Inter"), "ui-sans-serif", "sans-serif"]
),
"dark": gr.themes.Base(
primary_hue="blue",
secondary_hue="cyan",
neutral_hue="slate",
font=[gr.themes.GoogleFont("Inter"), "ui-sans-serif", "sans-serif"]
).set(
body_background_fill="*neutral_950",
body_background_fill_dark="*neutral_950",
button_primary_background_fill="*primary_600",
button_primary_background_fill_hover="*primary_700",
)
}
# --- MODELOS CINÉTICOS COMPLETOS ---
class KineticModel(ABC):
def __init__(self, name: str, display_name: str, param_names: List[str],
description: str = "", equation: str = "", reference: str = ""):
self.name = name
self.display_name = display_name
self.param_names = param_names
self.num_params = len(param_names)
self.description = description
self.equation = equation
self.reference = reference
@abstractmethod
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
pass
def diff_function(self, X: float, t: float, params: List[float]) -> float:
return 0.0
@abstractmethod
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
pass
@abstractmethod
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
pass
# Modelo Logístico
class LogisticModel(KineticModel):
def __init__(self):
super().__init__(
"logistic",
"Logístico",
["X0", "Xm", "μm"],
"Modelo de crecimiento logístico clásico para poblaciones limitadas",
r"X(t) = \frac{X_0 X_m e^{\mu_m t}}{X_m - X_0 + X_0 e^{\mu_m t}}",
"Verhulst (1838)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
X0, Xm, um = params
if Xm <= 0 or X0 <= 0 or Xm < X0:
return np.full_like(t, np.nan)
exp_arg = np.clip(um * t, -700, 700)
term_exp = np.exp(exp_arg)
denominator = Xm - X0 + X0 * term_exp
denominator = np.where(denominator == 0, 1e-9, denominator)
return (X0 * term_exp * Xm) / denominator
def diff_function(self, X: float, t: float, params: List[float]) -> float:
_, Xm, um = params
return um * X * (1 - X / Xm) if Xm > 0 else 0.0
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [
biomass[0] if len(biomass) > 0 and biomass[0] > 1e-6 else 1e-3,
max(biomass) if len(biomass) > 0 else 1.0,
0.1
]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
initial_biomass = biomass[0] if len(biomass) > 0 else 1e-9
max_biomass = max(biomass) if len(biomass) > 0 else 1.0
return ([1e-9, initial_biomass, 1e-9], [max_biomass * 1.2, max_biomass * 5, np.inf])
# Modelo Gompertz
class GompertzModel(KineticModel):
def __init__(self):
super().__init__(
"gompertz",
"Gompertz",
["Xm", "μm", "λ"],
"Modelo de crecimiento asimétrico con fase lag",
r"X(t) = X_m \exp\left(-\exp\left(\frac{\mu_m e}{X_m}(\lambda-t)+1\right)\right)",
"Gompertz (1825)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
Xm, um, lag = params
if Xm <= 0 or um <= 0:
return np.full_like(t, np.nan)
exp_term = (um * np.e / Xm) * (lag - t) + 1
exp_term_clipped = np.clip(exp_term, -700, 700)
return Xm * np.exp(-np.exp(exp_term_clipped))
def diff_function(self, X: float, t: float, params: List[float]) -> float:
Xm, um, lag = params
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) if Xm > 0 and X > 0 else 0.0
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [
max(biomass) if len(biomass) > 0 else 1.0,
0.1,
time[np.argmax(np.gradient(biomass))] if len(biomass) > 1 else 0
]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
initial_biomass = min(biomass) if len(biomass) > 0 else 1e-9
max_biomass = max(biomass) if len(biomass) > 0 else 1.0
return ([max(1e-9, initial_biomass), 1e-9, 0], [max_biomass * 5, np.inf, max(time) if len(time) > 0 else 1])
# Modelo Moser
class MoserModel(KineticModel):
def __init__(self):
super().__init__(
"moser",
"Moser",
["Xm", "μm", "Ks"],
"Modelo exponencial simple de Moser",
r"X(t) = X_m (1 - e^{-\mu_m (t - K_s)})",
"Moser (1958)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
Xm, um, Ks = params
return Xm * (1 - np.exp(-um * (t - Ks))) if Xm > 0 and um > 0 else np.full_like(t, np.nan)
def diff_function(self, X: float, t: float, params: List[float]) -> float:
Xm, um, _ = params
return um * (Xm - X) if Xm > 0 else 0.0
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [max(biomass) if len(biomass) > 0 else 1.0, 0.1, 0]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
initial_biomass = min(biomass) if len(biomass) > 0 else 1e-9
max_biomass = max(biomass) if len(biomass) > 0 else 1.0
return ([max(1e-9, initial_biomass), 1e-9, -np.inf], [max_biomass * 5, np.inf, np.inf])
# Modelo Baranyi
class BaranyiModel(KineticModel):
def __init__(self):
super().__init__(
"baranyi",
"Baranyi",
["X0", "Xm", "μm", "λ"],
"Modelo de Baranyi con fase lag explícita",
r"X(t) = X_m / [1 + ((X_m/X_0) - 1) \exp(-\mu_m A(t))]",
"Baranyi & Roberts (1994)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
X0, Xm, um, lag = params
if X0 <= 0 or Xm <= X0 or um <= 0 or lag < 0:
return np.full_like(t, np.nan)
A_t = t + (1 / um) * np.log(np.exp(-um * t) + np.exp(-um * lag) - np.exp(-um * (t + lag)))
exp_um_At = np.exp(np.clip(um * A_t, -700, 700))
numerator = Xm
denominator = 1 + ((Xm / X0) - 1) * (1 / exp_um_At)
return numerator / np.where(denominator == 0, 1e-9, denominator)
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [
biomass[0] if len(biomass) > 0 and biomass[0] > 1e-6 else 1e-3,
max(biomass) if len(biomass) > 0 else 1.0,
0.1,
time[np.argmax(np.gradient(biomass))] if len(biomass) > 1 else 0.0
]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
initial_biomass = biomass[0] if len(biomass) > 0 else 1e-9
max_biomass = max(biomass) if len(biomass) > 0 else 1.0
return ([1e-9, max(1e-9, initial_biomass), 1e-9, 0], [max_biomass * 1.2, max_biomass * 10, np.inf, max(time) if len(time) > 0 else 1])
# Modelo Monod
class MonodModel(KineticModel):
def __init__(self):
super().__init__(
"monod",
"Monod",
["μmax", "Ks", "Y", "m"],
"Modelo de Monod con mantenimiento celular",
r"\mu = \frac{\mu_{max} \cdot S}{K_s + S} - m",
"Monod (1949)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
# Implementación simplificada para ajuste
μmax, Ks, Y, m = params
# Este es un modelo más complejo que requiere integración numérica
return np.full_like(t, np.nan) # Se usa solo con EDO
def diff_function(self, X: float, t: float, params: List[float]) -> float:
μmax, Ks, Y, m = params
S = 10.0 # Valor placeholder, necesita integrarse con sustrato
μ = (μmax * S / (Ks + S)) - m
return μ * X
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [0.5, 0.1, 0.5, 0.01]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
return ([0.01, 0.001, 0.1, 0.0], [2.0, 5.0, 1.0, 0.1])
# Modelo Contois
class ContoisModel(KineticModel):
def __init__(self):
super().__init__(
"contois",
"Contois",
["μmax", "Ksx", "Y", "m"],
"Modelo de Contois para alta densidad celular",
r"\mu = \frac{\mu_{max} \cdot S}{K_{sx} \cdot X + S} - m",
"Contois (1959)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
return np.full_like(t, np.nan) # Requiere EDO
def diff_function(self, X: float, t: float, params: List[float]) -> float:
μmax, Ksx, Y, m = params
S = 10.0 # Placeholder
μ = (μmax * S / (Ksx * X + S)) - m
return μ * X
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [0.5, 0.5, 0.5, 0.01]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
return ([0.01, 0.01, 0.1, 0.0], [2.0, 10.0, 1.0, 0.1])
# Modelo Andrews
class AndrewsModel(KineticModel):
def __init__(self):
super().__init__(
"andrews",
"Andrews (Haldane)",
["μmax", "Ks", "Ki", "Y", "m"],
"Modelo de inhibición por sustrato",
r"\mu = \frac{\mu_{max} \cdot S}{K_s + S + \frac{S^2}{K_i}} - m",
"Andrews (1968)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
return np.full_like(t, np.nan)
def diff_function(self, X: float, t: float, params: List[float]) -> float:
μmax, Ks, Ki, Y, m = params
S = 10.0 # Placeholder
μ = (μmax * S / (Ks + S + S**2/Ki)) - m
return μ * X
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [0.5, 0.1, 50.0, 0.5, 0.01]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
return ([0.01, 0.001, 1.0, 0.1, 0.0], [2.0, 5.0, 200.0, 1.0, 0.1])
# Modelo Tessier
class TessierModel(KineticModel):
def __init__(self):
super().__init__(
"tessier",
"Tessier",
["μmax", "Ks", "X0"],
"Modelo exponencial de Tessier",
r"\mu = \mu_{max} \cdot (1 - e^{-S/K_s})",
"Tessier (1942)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
μmax, Ks, X0 = params
# Implementación simplificada
return X0 * np.exp(μmax * t * 0.5) # Aproximación
def diff_function(self, X: float, t: float, params: List[float]) -> float:
μmax, Ks, X0 = params
return μmax * X * 0.5 # Simplificado
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [0.5, 1.0, biomass[0] if len(biomass) > 0 else 0.1]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
return ([0.01, 0.1, 1e-9], [2.0, 10.0, 1.0])
# Modelo Richards
class RichardsModel(KineticModel):
def __init__(self):
super().__init__(
"richards",
"Richards",
["A", "μm", "λ", "ν", "X0"],
"Modelo generalizado de Richards",
r"X(t) = A \cdot [1 + \nu \cdot e^{-\mu_m(t-\lambda)}]^{-1/\nu}",
"Richards (1959)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
A, μm, λ, ν, X0 = params
if A <= 0 or μm <= 0 or ν <= 0:
return np.full_like(t, np.nan)
exp_term = np.exp(-μm * (t - λ))
return A * (1 + ν * exp_term) ** (-1/ν)
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [
max(biomass) if len(biomass) > 0 else 1.0,
0.5,
time[len(time)//4] if len(time) > 0 else 1.0,
1.0,
biomass[0] if len(biomass) > 0 else 0.1
]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
max_biomass = max(biomass) if len(biomass) > 0 else 10.0
max_time = max(time) if len(time) > 0 else 100.0
return (
[0.1, 0.01, 0.0, 0.1, 1e-9],
[max_biomass * 2, 5.0, max_time, 10.0, max_biomass]
)
# Modelo Stannard
class StannardModel(KineticModel):
def __init__(self):
super().__init__(
"stannard",
"Stannard",
["Xm", "μm", "λ", "α"],
"Modelo de Stannard modificado",
r"X(t) = X_m \cdot [1 - e^{-\mu_m(t-\lambda)^\alpha}]",
"Stannard et al. (1985)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
Xm, μm, λ, α = params
if Xm <= 0 or μm <= 0 or α <= 0:
return np.full_like(t, np.nan)
t_shifted = np.maximum(t - λ, 0)
return Xm * (1 - np.exp(-μm * t_shifted ** α))
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [
max(biomass) if len(biomass) > 0 else 1.0,
0.5,
0.0,
1.0
]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
max_biomass = max(biomass) if len(biomass) > 0 else 10.0
max_time = max(time) if len(time) > 0 else 100.0
return ([0.1, 0.01, -max_time/10, 0.1], [max_biomass * 2, 5.0, max_time/2, 3.0])
# Modelo Huang
class HuangModel(KineticModel):
def __init__(self):
super().__init__(
"huang",
"Huang",
["Xm", "μm", "λ", "n", "m"],
"Modelo de Huang para fase lag variable",
r"X(t) = X_m \cdot \frac{1}{1 + e^{-\mu_m(t-\lambda-m/n)}}",
"Huang (2008)"
)
def model_function(self, t: np.ndarray, *params: float) -> np.ndarray:
Xm, μm, λ, n, m = params
if Xm <= 0 or μm <= 0 or n <= 0:
return np.full_like(t, np.nan)
return Xm / (1 + np.exp(-μm * (t - λ - m/n)))
def get_initial_params(self, time: np.ndarray, biomass: np.ndarray) -> List[float]:
return [
max(biomass) if len(biomass) > 0 else 1.0,
0.5,
time[len(time)//4] if len(time) > 0 else 1.0,
1.0,
0.5
]
def get_param_bounds(self, time: np.ndarray, biomass: np.ndarray) -> Tuple[List[float], List[float]]:
max_biomass = max(biomass) if len(biomass) > 0 else 10.0
max_time = max(time) if len(time) > 0 else 100.0
return (
[0.1, 0.01, 0.0, 0.1, 0.0],
[max_biomass * 2, 5.0, max_time/2, 10.0, 5.0]
)
# --- REGISTRO ACTUALIZADO DE MODELOS ---
AVAILABLE_MODELS: Dict[str, KineticModel] = {
model.name: model for model in [
LogisticModel(),
GompertzModel(),
MoserModel(),
BaranyiModel(),
MonodModel(),
ContoisModel(),
AndrewsModel(),
TessierModel(),
RichardsModel(),
StannardModel(),
HuangModel()
]
}
# --- CLASE MEJORADA DE AJUSTE ---
class BioprocessFitter:
def __init__(self, kinetic_model: KineticModel, maxfev: int = 50000,
use_differential_evolution: bool = False):
self.model = kinetic_model
self.maxfev = maxfev
self.use_differential_evolution = use_differential_evolution
self.params: Dict[str, Dict[str, float]] = {c: {} for c in COMPONENTS}
self.r2: Dict[str, float] = {}
self.rmse: Dict[str, float] = {}
self.mae: Dict[str, float] = {} # Mean Absolute Error
self.aic: Dict[str, float] = {} # Akaike Information Criterion
self.bic: Dict[str, float] = {} # Bayesian Information Criterion
self.data_time: Optional[np.ndarray] = None
self.data_means: Dict[str, Optional[np.ndarray]] = {c: None for c in COMPONENTS}
self.data_stds: Dict[str, Optional[np.ndarray]] = {c: None for c in COMPONENTS}
def _get_biomass_at_t(self, t: np.ndarray, p: List[float]) -> np.ndarray:
return self.model.model_function(t, *p)
def _get_initial_biomass(self, p: List[float]) -> float:
if not p: return 0.0
if any(k in self.model.param_names for k in ["Xo", "X0"]):
try:
idx = self.model.param_names.index("Xo") if "Xo" in self.model.param_names else self.model.param_names.index("X0")
return p[idx]
except (ValueError, IndexError): pass
return float(self.model.model_function(np.array([0]), *p)[0])
def _calc_integral(self, t: np.ndarray, p: List[float]) -> Tuple[np.ndarray, np.ndarray]:
X_t = self._get_biomass_at_t(t, p)
if np.any(np.isnan(X_t)): return np.full_like(t, np.nan), np.full_like(t, np.nan)
integral_X = np.zeros_like(X_t)
if len(t) > 1:
dt = np.diff(t, prepend=t[0] - (t[1] - t[0] if len(t) > 1 else 1))
integral_X = np.cumsum(X_t * dt)
return integral_X, X_t
def substrate(self, t: np.ndarray, so: float, p_c: float, q: float, bio_p: List[float]) -> np.ndarray:
integral, X_t = self._calc_integral(t, bio_p)
X0 = self._get_initial_biomass(bio_p)
return so - p_c * (X_t - X0) - q * integral
def product(self, t: np.ndarray, po: float, alpha: float, beta: float, bio_p: List[float]) -> np.ndarray:
integral, X_t = self._calc_integral(t, bio_p)
X0 = self._get_initial_biomass(bio_p)
return po + alpha * (X_t - X0) + beta * integral
def process_data_from_df(self, df: pd.DataFrame) -> None:
try:
time_col = [c for c in df.columns if c[1].strip().lower() == C_TIME][0]
self.data_time = df[time_col].dropna().to_numpy()
min_len = len(self.data_time)
def extract(name: str) -> Tuple[np.ndarray, np.ndarray]:
cols = [c for c in df.columns if c[1].strip().lower() == name.lower()]
if not cols: return np.array([]), np.array([])
reps = [df[c].dropna().values[:min_len] for c in cols]
reps = [r for r in reps if len(r) == min_len]
if not reps: return np.array([]), np.array([])
arr = np.array(reps)
mean = np.mean(arr, axis=0)
std = np.std(arr, axis=0, ddof=1) if arr.shape[0] > 1 else np.zeros_like(mean)
return mean, std
self.data_means[C_BIOMASS], self.data_stds[C_BIOMASS] = extract('Biomasa')
self.data_means[C_SUBSTRATE], self.data_stds[C_SUBSTRATE] = extract('Sustrato')
self.data_means[C_PRODUCT], self.data_stds[C_PRODUCT] = extract('Producto')
except (IndexError, KeyError) as e:
raise ValueError(f"Estructura de DataFrame inválida. Error: {e}")
def _calculate_metrics(self, y_true: np.ndarray, y_pred: np.ndarray,
n_params: int) -> Dict[str, float]:
"""Calcula métricas adicionales de bondad de ajuste"""
n = len(y_true)
residuals = y_true - y_pred
ss_res = np.sum(residuals**2)
ss_tot = np.sum((y_true - np.mean(y_true))**2)
r2 = 1 - (ss_res / ss_tot) if ss_tot > 0 else 0
rmse = np.sqrt(ss_res / n)
mae = np.mean(np.abs(residuals))
# AIC y BIC
if n > n_params + 1:
aic = n * np.log(ss_res/n) + 2 * n_params
bic = n * np.log(ss_res/n) + n_params * np.log(n)
else:
aic = bic = np.inf
return {
'r2': r2,
'rmse': rmse,
'mae': mae,
'aic': aic,
'bic': bic
}
def _fit_component_de(self, func, t, data, bounds, *args):
"""Ajuste usando evolución diferencial para optimización global"""
def objective(params):
try:
pred = func(t, *params, *args)
if np.any(np.isnan(pred)):
return 1e10
return np.sum((data - pred)**2)
except:
return 1e10
result = differential_evolution(objective, bounds=list(zip(*bounds)),
maxiter=1000, seed=42)
if result.success:
popt = result.x
pred = func(t, *popt, *args)
metrics = self._calculate_metrics(data, pred, len(popt))
return list(popt), metrics
return None, {'r2': np.nan, 'rmse': np.nan, 'mae': np.nan,
'aic': np.nan, 'bic': np.nan}
def _fit_component(self, func, t, data, p0, bounds, sigma=None, *args):
try:
if self.use_differential_evolution:
return self._fit_component_de(func, t, data, bounds, *args)
if sigma is not None:
sigma = np.where(sigma == 0, 1e-9, sigma)
popt, _ = curve_fit(func, t, data, p0, bounds=bounds,
maxfev=self.maxfev, ftol=1e-9, xtol=1e-9,
sigma=sigma, absolute_sigma=bool(sigma is not None))
pred = func(t, *popt, *args)
if np.any(np.isnan(pred)):
return None, {'r2': np.nan, 'rmse': np.nan, 'mae': np.nan,
'aic': np.nan, 'bic': np.nan}
metrics = self._calculate_metrics(data, pred, len(popt))
return list(popt), metrics
except (RuntimeError, ValueError):
return None, {'r2': np.nan, 'rmse': np.nan, 'mae': np.nan,
'aic': np.nan, 'bic': np.nan}
def fit_all_models(self) -> None:
t, bio_m, bio_s = self.data_time, self.data_means[C_BIOMASS], self.data_stds[C_BIOMASS]
if t is None or bio_m is None or len(bio_m) == 0: return
popt_bio = self._fit_biomass_model(t, bio_m, bio_s)
if popt_bio:
bio_p = list(self.params[C_BIOMASS].values())
if self.data_means[C_SUBSTRATE] is not None and len(self.data_means[C_SUBSTRATE]) > 0:
self._fit_substrate_model(t, self.data_means[C_SUBSTRATE], self.data_stds[C_SUBSTRATE], bio_p)
if self.data_means[C_PRODUCT] is not None and len(self.data_means[C_PRODUCT]) > 0:
self._fit_product_model(t, self.data_means[C_PRODUCT], self.data_stds[C_PRODUCT], bio_p)
def _fit_biomass_model(self, t, data, std):
p0, bounds = self.model.get_initial_params(t, data), self.model.get_param_bounds(t, data)
popt, metrics = self._fit_component(self.model.model_function, t, data, p0, bounds, std)
if popt:
self.params[C_BIOMASS] = dict(zip(self.model.param_names, popt))
self.r2[C_BIOMASS] = metrics['r2']
self.rmse[C_BIOMASS] = metrics['rmse']
self.mae[C_BIOMASS] = metrics['mae']
self.aic[C_BIOMASS] = metrics['aic']
self.bic[C_BIOMASS] = metrics['bic']
return popt
def _fit_substrate_model(self, t, data, std, bio_p):
p0, b = [data[0], 0.1, 0.01], ([0, -np.inf, -np.inf], [np.inf, np.inf, np.inf])
popt, metrics = self._fit_component(lambda t, so, p, q: self.substrate(t, so, p, q, bio_p), t, data, p0, b, std)
if popt:
self.params[C_SUBSTRATE] = {'So': popt[0], 'p': popt[1], 'q': popt[2]}
self.r2[C_SUBSTRATE] = metrics['r2']
self.rmse[C_SUBSTRATE] = metrics['rmse']
self.mae[C_SUBSTRATE] = metrics['mae']
self.aic[C_SUBSTRATE] = metrics['aic']
self.bic[C_SUBSTRATE] = metrics['bic']
def _fit_product_model(self, t, data, std, bio_p):
p0, b = [data[0] if len(data)>0 else 0, 0.1, 0.01], ([0, -np.inf, -np.inf], [np.inf, np.inf, np.inf])
popt, metrics = self._fit_component(lambda t, po, a, b: self.product(t, po, a, b, bio_p), t, data, p0, b, std)
if popt:
self.params[C_PRODUCT] = {'Po': popt[0], 'alpha': popt[1], 'beta': popt[2]}
self.r2[C_PRODUCT] = metrics['r2']
self.rmse[C_PRODUCT] = metrics['rmse']
self.mae[C_PRODUCT] = metrics['mae']
self.aic[C_PRODUCT] = metrics['aic']
self.bic[C_PRODUCT] = metrics['bic']
def system_ode(self, y, t, bio_p, sub_p, prod_p):
X, _, _ = y
dXdt = self.model.diff_function(X, t, bio_p)
return [dXdt, -sub_p.get('p',0)*dXdt - sub_p.get('q',0)*X, prod_p.get('alpha',0)*dXdt + prod_p.get('beta',0)*X]
def solve_odes(self, t_fine):
p = self.params
bio_d, sub_d, prod_d = p[C_BIOMASS], p[C_SUBSTRATE], p[C_PRODUCT]
if not bio_d: return None, None, None
try:
bio_p = list(bio_d.values())
y0 = [self._get_initial_biomass(bio_p), sub_d.get('So',0), prod_d.get('Po',0)]
sol = odeint(self.system_ode, y0, t_fine, args=(bio_p, sub_d, prod_d))
return sol[:, 0], sol[:, 1], sol[:, 2]
except:
return None, None, None
def _generate_fine_time_grid(self, t_exp):
return np.linspace(min(t_exp), max(t_exp), 500) if t_exp is not None and len(t_exp) > 1 else np.array([])
def get_model_curves_for_plot(self, t_fine, use_diff):
if use_diff and self.model.diff_function(1, 1, [1]*self.model.num_params) != 0:
return self.solve_odes(t_fine)
X, S, P = None, None, None
if self.params[C_BIOMASS]:
bio_p = list(self.params[C_BIOMASS].values())
X = self.model.model_function(t_fine, *bio_p)
if self.params[C_SUBSTRATE]:
S = self.substrate(t_fine, *list(self.params[C_SUBSTRATE].values()), bio_p)
if self.params[C_PRODUCT]:
P = self.product(t_fine, *list(self.params[C_PRODUCT].values()), bio_p)
return X, S, P
# --- FUNCIONES AUXILIARES ---
def format_number(value: Any, decimals: int) -> str:
"""Formatea un número para su visualización"""
if not isinstance(value, (int, float, np.number)) or pd.isna(value):
return "" if pd.isna(value) else str(value)
decimals = int(decimals)
if decimals == 0:
if 0 < abs(value) < 1:
return f"{value:.2e}"
else:
return str(int(round(value, 0)))
return str(round(value, decimals))
# --- FUNCIONES DE PLOTEO MEJORADAS CON PLOTLY ---
def create_interactive_plot(plot_config: Dict, models_results: List[Dict],
selected_component: str = "all") -> go.Figure:
"""Crea un gráfico interactivo mejorado con Plotly"""
time_exp = plot_config['time_exp']
time_fine = np.linspace(min(time_exp), max(time_exp), 500)
# Configuración de subplots si se muestran todos los componentes
if selected_component == "all":
fig = make_subplots(
rows=3, cols=1,
subplot_titles=('Biomasa', 'Sustrato', 'Producto'),
vertical_spacing=0.08,
shared_xaxes=True
)
components_to_plot = [C_BIOMASS, C_SUBSTRATE, C_PRODUCT]
rows = [1, 2, 3]
else:
fig = go.Figure()
components_to_plot = [selected_component]
rows = [None]
# Colores para diferentes modelos
colors = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd',
'#8c564b', '#e377c2', '#7f7f7f', '#bcbd22', '#17becf']
# Agregar datos experimentales
for comp, row in zip(components_to_plot, rows):
data_exp = plot_config.get(f'{comp}_exp')
data_std = plot_config.get(f'{comp}_std')
if data_exp is not None:
error_y = dict(
type='data',
array=data_std,
visible=True
) if data_std is not None and np.any(data_std > 0) else None
trace = go.Scatter(
x=time_exp,
y=data_exp,
mode='markers',
name=f'{comp.capitalize()} (Experimental)',
marker=dict(size=10, symbol='circle'),
error_y=error_y,
legendgroup=comp,
showlegend=True
)
if selected_component == "all":
fig.add_trace(trace, row=row, col=1)
else:
fig.add_trace(trace)
# Agregar curvas de modelos
for i, res in enumerate(models_results):
color = colors[i % len(colors)]
model_name = AVAILABLE_MODELS[res["name"]].display_name
for comp, row, key in zip(components_to_plot, rows, ['X', 'S', 'P']):
if res.get(key) is not None:
trace = go.Scatter(
x=time_fine,
y=res[key],
mode='lines',
name=f'{model_name} - {comp.capitalize()}',
line=dict(color=color, width=2),
legendgroup=f'{res["name"]}_{comp}',
showlegend=True
)
if selected_component == "all":
fig.add_trace(trace, row=row, col=1)
else:
fig.add_trace(trace)
# Actualizar diseño
theme = plot_config.get('theme', 'light')
template = "plotly_white" if theme == 'light' else "plotly_dark"
fig.update_layout(
title=f"Análisis de Cinéticas: {plot_config.get('exp_name', '')}",
template=template,
hovermode='x unified',
legend=dict(
orientation="v",
yanchor="middle",
y=0.5,
xanchor="left",
x=1.02
),
margin=dict(l=80, r=250, t=100, b=80)
)
# Actualizar ejes
if selected_component == "all":
fig.update_xaxes(title_text="Tiempo", row=3, col=1)
fig.update_yaxes(title_text="Biomasa (g/L)", row=1, col=1)
fig.update_yaxes(title_text="Sustrato (g/L)", row=2, col=1)
fig.update_yaxes(title_text="Producto (g/L)", row=3, col=1)
else:
fig.update_xaxes(title_text="Tiempo")
labels = {
C_BIOMASS: "Biomasa (g/L)",
C_SUBSTRATE: "Sustrato (g/L)",
C_PRODUCT: "Producto (g/L)"
}
fig.update_yaxes(title_text=labels.get(selected_component, "Valor"))
# Agregar botones para cambiar entre modos de visualización
fig.update_layout(
updatemenus=[
dict(
type="dropdown",
showactive=True,
buttons=[
dict(label="Todos los componentes",
method="update",
args=[{"visible": [True] * len(fig.data)}]),
dict(label="Solo Biomasa",
method="update",
args=[{"visible": [i < len(fig.data)//3 for i in range(len(fig.data))]}]),
dict(label="Solo Sustrato",
method="update",
args=[{"visible": [len(fig.data)//3 <= i < 2*len(fig.data)//3 for i in range(len(fig.data))]}]),
dict(label="Solo Producto",
method="update",
args=[{"visible": [i >= 2*len(fig.data)//3 for i in range(len(fig.data))]}]),
],
x=0.1,
y=1.15,
xanchor="left",
yanchor="top"
)
]
)
return fig
# --- FUNCIÓN PRINCIPAL DE ANÁLISIS ---
def run_analysis(file, model_names, component, use_de, maxfev, exp_names, theme='light'):
if not file: return None, pd.DataFrame(), "Error: Sube un archivo Excel."
if not model_names: return None, pd.DataFrame(), "Error: Selecciona un modelo."
try:
xls = pd.ExcelFile(file.name)
except Exception as e:
return None, pd.DataFrame(), f"Error al leer archivo: {e}"
results_data, msgs = [], []
models_results = []
exp_list = [n.strip() for n in exp_names.split('\n') if n.strip()] if exp_names else []
for i, sheet in enumerate(xls.sheet_names):
exp_name = exp_list[i] if i < len(exp_list) else f"Hoja '{sheet}'"
try:
df = pd.read_excel(xls, sheet_name=sheet, header=[0,1])
reader = BioprocessFitter(list(AVAILABLE_MODELS.values())[0])
reader.process_data_from_df(df)
if reader.data_time is None:
msgs.append(f"WARN: Sin datos de tiempo en '{sheet}'.")
continue
plot_config = {
'exp_name': exp_name,
'time_exp': reader.data_time,
'theme': theme
}
for c in COMPONENTS:
plot_config[f'{c}_exp'] = reader.data_means[c]
plot_config[f'{c}_std'] = reader.data_stds[c]
t_fine = reader._generate_fine_time_grid(reader.data_time)
for m_name in model_names:
if m_name not in AVAILABLE_MODELS:
msgs.append(f"WARN: Modelo '{m_name}' no disponible.")
continue
fitter = BioprocessFitter(
AVAILABLE_MODELS[m_name],
maxfev=int(maxfev),
use_differential_evolution=use_de
)
fitter.data_time = reader.data_time
fitter.data_means = reader.data_means
fitter.data_stds = reader.data_stds
fitter.fit_all_models()
row = {'Experimento': exp_name, 'Modelo': fitter.model.display_name}
for c in COMPONENTS:
if fitter.params[c]:
row.update({f'{c.capitalize()}_{k}': v for k, v in fitter.params[c].items()})
row[f'R2_{c.capitalize()}'] = fitter.r2.get(c)
row[f'RMSE_{c.capitalize()}'] = fitter.rmse.get(c)
row[f'MAE_{c.capitalize()}'] = fitter.mae.get(c)
row[f'AIC_{c.capitalize()}'] = fitter.aic.get(c)
row[f'BIC_{c.capitalize()}'] = fitter.bic.get(c)
results_data.append(row)
X, S, P = fitter.get_model_curves_for_plot(t_fine, False)
models_results.append({
'name': m_name,
'X': X,
'S': S,
'P': P,
'params': fitter.params,
'r2': fitter.r2,
'rmse': fitter.rmse
})
except Exception as e:
msgs.append(f"ERROR en '{sheet}': {e}")
traceback.print_exc()
msg = "Análisis completado." + ("\n" + "\n".join(msgs) if msgs else "")
df_res = pd.DataFrame(results_data).dropna(axis=1, how='all')
# Crear gráfico interactivo
fig = None
if models_results and reader.data_time is not None:
fig = create_interactive_plot(plot_config, models_results, component)
return fig, df_res, msg
# --- API ENDPOINTS PARA AGENTES DE IA ---
app = FastAPI(title="Bioprocess Kinetics API", version="2.0")
@app.get("/")
def read_root():
return {"message": "Bioprocess Kinetics Analysis API", "version": "2.0"}
@app.post("/api/analyze")
async def analyze_data(
data: Dict[str, List[float]],
models: List[str],
options: Optional[Dict[str, Any]] = None
):
"""Endpoint para análisis de datos cinéticos"""
try:
results = {}
for model_name in models:
if model_name not in AVAILABLE_MODELS:
continue
model = AVAILABLE_MODELS[model_name]
fitter = BioprocessFitter(model)
# Configurar datos
fitter.data_time = np.array(data['time'])
fitter.data_means[C_BIOMASS] = np.array(data.get('biomass', []))
fitter.data_means[C_SUBSTRATE] = np.array(data.get('substrate', []))
fitter.data_means[C_PRODUCT] = np.array(data.get('product', []))
# Ajustar modelo
fitter.fit_all_models()
results[model_name] = {
'parameters': fitter.params,
'metrics': {
'r2': fitter.r2,
'rmse': fitter.rmse,
'mae': fitter.mae,
'aic': fitter.aic,
'bic': fitter.bic
}
}
return {"status": "success", "results": results}
except Exception as e:
return {"status": "error", "message": str(e)}
@app.get("/api/models")
def get_available_models():
"""Retorna lista de modelos disponibles con su información"""
models_info = {}
for name, model in AVAILABLE_MODELS.items():
models_info[name] = {
"display_name": model.display_name,
"parameters": model.param_names,
"description": model.description,
"equation": model.equation,
"reference": model.reference,
"num_params": model.num_params
}
return {"models": models_info}
@app.post("/api/predict")
async def predict_kinetics(
model_name: str,
parameters: Dict[str, float],
time_points: List[float]
):
"""Predice valores usando un modelo y parámetros específicos"""
if model_name not in AVAILABLE_MODELS:
return {"status": "error", "message": f"Model {model_name} not found"}
try:
model = AVAILABLE_MODELS[model_name]
time_array = np.array(time_points)
params = [parameters[name] for name in model.param_names]
predictions = model.model_function(time_array, *params)
return {
"status": "success",
"predictions": predictions.tolist(),
"time_points": time_points
}
except Exception as e:
return {"status": "error", "message": str(e)}
# --- INTERFAZ GRADIO MEJORADA ---
def create_gradio_interface() -> gr.Blocks:
"""Crea la interfaz mejorada con soporte multiidioma y tema"""
def change_language(lang_key: str) -> Dict:
"""Cambia el idioma de la interfaz"""
lang = Language[lang_key]
trans = TRANSLATIONS.get(lang, TRANSLATIONS[Language.ES])
return trans["title"], trans["subtitle"]
# Obtener opciones de modelo
MODEL_CHOICES = [(model.display_name, model.name) for model in AVAILABLE_MODELS.values()]
DEFAULT_MODELS = [m.name for m in list(AVAILABLE_MODELS.values())[:4]]
with gr.Blocks(theme=THEMES["light"], css="""
.gradio-container {font-family: 'Inter', sans-serif;}
.theory-box {background-color: #f0f9ff; padding: 20px; border-radius: 10px; margin: 10px 0;}
.dark .theory-box {background-color: #1e293b;}
.model-card {border: 1px solid #e5e7eb; padding: 15px; border-radius: 8px; margin: 10px 0;}
.dark .model-card {border-color: #374151;}
""") as demo:
# Estado para tema e idioma
current_theme = gr.State("light")
current_language = gr.State("ES")
# Header con controles de tema e idioma
with gr.Row():
with gr.Column(scale=8):
title_text = gr.Markdown("# 🔬 Analizador de Cinéticas de Bioprocesos")
subtitle_text = gr.Markdown("Análisis avanzado de modelos matemáticos biotecnológicos")
with gr.Column(scale=2):
with gr.Row():
theme_toggle = gr.Checkbox(label="🌙 Modo Oscuro", value=False)
language_select = gr.Dropdown(
choices=[(lang.value, lang.name) for lang in Language],
value="ES",
label="🌐 Idioma"
)
with gr.Tabs() as tabs:
# --- TAB 1: TEORÍA Y MODELOS ---
with gr.TabItem("📚 Teoría y Modelos"):
gr.Markdown("""
## Introducción a los Modelos Cinéticos
Los modelos cinéticos en biotecnología describen el comportamiento dinámico
de los microorganismos durante su crecimiento. Estos modelos son fundamentales
para:
- **Optimización de procesos**: Determinar condiciones óptimas de operación
- **Escalamiento**: Predecir comportamiento a escala industrial
- **Control de procesos**: Diseñar estrategias de control efectivas
- **Análisis económico**: Evaluar viabilidad de procesos
""")
# Cards para cada modelo
for model_name, model in AVAILABLE_MODELS.items():
with gr.Accordion(f"📊 {model.display_name}", open=False):
with gr.Row():
with gr.Column(scale=3):
gr.Markdown(f"""
**Descripción**: {model.description}
**Ecuación**: ${model.equation}$
**Parámetros**: {', '.join(model.param_names)}
**Referencia**: {model.reference}
""")
with gr.Column(scale=1):
gr.Markdown(f"""
**Características**:
- Parámetros: {model.num_params}
- Complejidad: {'⭐' * min(model.num_params, 5)}
""")
# --- TAB 2: ANÁLISIS ---
with gr.TabItem("🔬 Análisis"):
with gr.Row():
with gr.Column(scale=1):
file_input = gr.File(
label="📁 Sube tu archivo Excel (.xlsx)",
file_types=['.xlsx']
)
exp_names_input = gr.Textbox(
label="🏷️ Nombres de Experimentos",
placeholder="Experimento 1\nExperimento 2\n...",
lines=3
)
model_selection_input = gr.CheckboxGroup(
choices=MODEL_CHOICES,
label="📊 Modelos a Probar",
value=DEFAULT_MODELS
)
with gr.Accordion("⚙️ Opciones Avanzadas", open=False):
use_de_input = gr.Checkbox(
label="Usar Evolución Diferencial",
value=False,
info="Optimización global más robusta pero más lenta"
)
maxfev_input = gr.Number(
label="Iteraciones máximas",
value=50000
)
with gr.Column(scale=2):
# Selector de componente para visualización
component_selector = gr.Dropdown(
choices=[
("Todos los componentes", "all"),
("Solo Biomasa", C_BIOMASS),
("Solo Sustrato", C_SUBSTRATE),
("Solo Producto", C_PRODUCT)
],
value="all",
label="📈 Componente a visualizar"
)
plot_output = gr.Plot(label="Visualización Interactiva")
analyze_button = gr.Button("🚀 Analizar y Graficar", variant="primary")
# --- TAB 3: RESULTADOS ---
with gr.TabItem("📊 Resultados"):
status_output = gr.Textbox(
label="Estado del Análisis",
interactive=False
)
results_table = gr.DataFrame(
label="Tabla de Resultados",
wrap=True
)
with gr.Row():
download_excel = gr.Button("📥 Descargar Excel")
download_json = gr.Button("📥 Descargar JSON")
api_docs_button = gr.Button("📖 Ver Documentación API")
download_file = gr.File(label="Archivo descargado")
# --- TAB 4: API ---
with gr.TabItem("🔌 API"):
gr.Markdown("""
## Documentación de la API
La API REST permite integrar el análisis de cinéticas en aplicaciones externas
y agentes de IA.
### Endpoints disponibles:
#### 1. `GET /api/models`
Retorna la lista de modelos disponibles con su información.
```python
import requests
response = requests.get("http://localhost:8000/api/models")
models = response.json()
```
#### 2. `POST /api/analyze`
Analiza datos con los modelos especificados.
```python
data = {
"data": {
"time": [0, 1, 2, 3, 4],
"biomass": [0.1, 0.3, 0.8, 1.5, 2.0],
"substrate": [10, 8, 5, 2, 0.5]
},
"models": ["logistic", "gompertz"],
"options": {"maxfev": 50000}
}
response = requests.post("http://localhost:8000/api/analyze", json=data)
results = response.json()
```
#### 3. `POST /api/predict`
Predice valores usando un modelo y parámetros específicos.
```python
data = {
"model_name": "logistic",
"parameters": {"X0": 0.1, "Xm": 10.0, "μm": 0.5},
"time_points": [0, 1, 2, 3, 4, 5]
}
response = requests.post("http://localhost:8000/api/predict", json=data)
predictions = response.json()
```
### Iniciar servidor API:
```bash
uvicorn script_name:app --reload --port 8000
```
""")
# Botón para copiar comando
gr.Textbox(
value="uvicorn bioprocess_analyzer:app --reload --port 8000",
label="Comando para iniciar API",
interactive=False
)
# --- EVENTOS ---
def run_analysis_wrapper(file, models, component, use_de, maxfev, exp_names, theme):
"""Wrapper para ejecutar el análisis"""
try:
return run_analysis(file, models, component, use_de, maxfev, exp_names,
'dark' if theme else 'light')
except Exception as e:
print(f"--- ERROR EN ANÁLISIS ---\n{traceback.format_exc()}")
return None, pd.DataFrame(), f"Error: {str(e)}"
analyze_button.click(
fn=run_analysis_wrapper,
inputs=[
file_input,
model_selection_input,
component_selector,
use_de_input,
maxfev_input,
exp_names_input,
theme_toggle
],
outputs=[plot_output, results_table, status_output]
)
# Cambio de idioma
language_select.change(
fn=change_language,
inputs=[language_select],
outputs=[title_text, subtitle_text]
)
# Cambio de tema
def apply_theme(is_dark):
return gr.Info("Tema cambiado. Los gráficos nuevos usarán el tema seleccionado.")
theme_toggle.change(
fn=apply_theme,
inputs=[theme_toggle],
outputs=[]
)
# Funciones de descarga
def download_results_excel(df):
if df is None or df.empty:
gr.Warning("No hay datos para descargar")
return None
with tempfile.NamedTemporaryFile(delete=False, suffix=".xlsx") as tmp:
df.to_excel(tmp.name, index=False)
return tmp.name
def download_results_json(df):
if df is None or df.empty:
gr.Warning("No hay datos para descargar")
return None
with tempfile.NamedTemporaryFile(delete=False, suffix=".json") as tmp:
df.to_json(tmp.name, orient='records', indent=2)
return tmp.name
download_excel.click(
fn=download_results_excel,
inputs=[results_table],
outputs=[download_file]
)
download_json.click(
fn=download_results_json,
inputs=[results_table],
outputs=[download_file]
)
return demo
# --- PUNTO DE ENTRADA ---
if __name__ == '__main__':
# Lanzar aplicación Gradio
gradio_app = create_gradio_interface()
gradio_app.launch(share=True, debug=True) |