app.py

import random
import numpy as np
import streamlit as st
import plotly.graph_objects as go
from plotly.subplots import make_subplots
import time
from collections import deque  # Add this line
import threading

class Organelle:
    def __init__(self, type):
        self.type = type

class Cell:
    def __init__(self, x, y, cell_type="prokaryote"):
        self.x = x
        self.y = y
        self.energy = 100
        self.cell_type = cell_type
        self.organelles = set()
        self.size = 1
        self.color = "lightblue"
        self.division_threshold = 150
        self.update_properties()

    def update_properties(self):
        if self.cell_type == "early_eukaryote":
            self.organelles.add("nucleus")
            self.color = "green"
            self.size = 2
        elif self.cell_type == "advanced_eukaryote":
            self.organelles.update(["nucleus", "mitochondria"])
            self.color = "red"
            self.size = 3
        elif self.cell_type == "plant_like":
            self.organelles.update(["nucleus", "mitochondria", "chloroplast"])
            self.color = "darkgreen"
            self.size = 4
        elif self.cell_type == "complete":
            self.organelles.update(["nucleus", "mitochondria", "chloroplast", "endoplasmic_reticulum", "golgi_apparatus"])
            self.color = "purple"
            self.size = 5

    def move(self, environment):
        dx, dy = random.uniform(-1, 1), random.uniform(-1, 1)
        self.x = max(0, min(environment.width - 1, self.x + dx))
        self.y = max(0, min(environment.height - 1, self.y + dy))
        self.energy -= 0.5 * self.size

    def feed(self, environment):
        base_energy = environment.grid[int(self.y)][int(self.x)] * 0.1
        if "chloroplast" in self.organelles:
            base_energy += environment.light_level * 2
        self.energy += base_energy
        environment.grid[int(self.y)][int(self.x)] *= 0.9

    def can_divide(self):
        return self.energy > self.division_threshold

    def divide(self):
        if self.can_divide():
            self.energy /= 2
            new_cell = Cell(self.x, self.y, self.cell_type)
            new_cell.organelles = self.organelles.copy()
            return new_cell
        return None

    def can_merge(self, other):
        return (self.cell_type == other.cell_type and
                random.random() < 0.01)  # 1% chance of merging

    def merge(self, other):
        new_cell_type = self.cell_type
        if self.cell_type == "prokaryote":
            new_cell_type = "early_eukaryote"
        elif self.cell_type == "early_eukaryote":
            new_cell_type = "advanced_eukaryote"
        elif self.cell_type == "advanced_eukaryote":
            new_cell_type = "plant_like"
        elif self.cell_type == "plant_like":
            new_cell_type = "complete"

        new_cell = Cell((self.x + other.x) / 2, (self.y + other.y) / 2, new_cell_type)
        new_cell.energy = self.energy + other.energy
        new_cell.organelles = self.organelles.union(other.organelles)
        new_cell.update_properties()
        return new_cell

class Environment:
    def __init__(self, width, height, effects):
        self.width = width
        self.height = height
        self.grid = np.random.rand(height, width) * 10
        self.light_level = 5
        self.cells = []
        self.time = 0
        self.population_history = {
            "prokaryote": [], "early_eukaryote": [],
            "advanced_eukaryote": [], "plant_like": [], "complete": []
        }
        self.effects = effects

    def add_cell(self, cell):
        self.cells.append(cell)

    def update(self):
        self.time += 1
        self.grid += np.random.rand(self.height, self.width) * 0.1
        self.light_level = 5 + np.sin(self.time / 100) * 2

        new_cells = []
        cells_to_remove = []

        for cell in self.cells:
            cell.move(self)
            cell.feed(self)

            if cell.energy <= 0:
                cells_to_remove.append(cell)
            elif cell.can_divide():
                new_cell = cell.divide()
                if new_cell:
                    new_cells.append(new_cell)

        # Handle cell merging
        for i, cell1 in enumerate(self.cells):
            for cell2 in self.cells[i+1:]:
                if cell1.can_merge(cell2):
                    new_cell = cell1.merge(cell2)
                    new_cells.append(new_cell)
                    cells_to_remove.extend([cell1, cell2])

        # Apply effects
        if self.effects['radiation']:
            self.apply_radiation()
        if self.effects['predation']:
            self.apply_predation()
        if self.effects['symbiosis']:
            self.apply_symbiosis()

        # Add new cells and remove dead/merged cells
        self.cells.extend(new_cells)
        self.cells = [cell for cell in self.cells if cell not in cells_to_remove]

        # Record population counts
        for cell_type in self.population_history.keys():
            count = len([cell for cell in self.cells if cell.cell_type == cell_type])
            self.population_history[cell_type].append(count)

    def apply_radiation(self):
        for cell in self.cells:
            if random.random() < 0.01:  # 1% chance of mutation
                cell.energy *= 0.8
                if random.random() < 0.5:
                    cell.organelles.add(random.choice(["nucleus", "mitochondria", "chloroplast", "endoplasmic_reticulum", "golgi_apparatus"]))
                else:
                    if cell.organelles:
                        cell.organelles.remove(random.choice(list(cell.organelles)))
                cell.update_properties()

    def apply_predation(self):
        for i, predator in enumerate(self.cells):
            if predator.cell_type in ["advanced_eukaryote", "plant_like", "complete"]:
                for prey in self.cells[i+1:]:
                    if prey.cell_type in ["prokaryote", "early_eukaryote"] and random.random() < 0.05:
                        predator.energy += prey.energy * 0.5
                        self.cells.remove(prey)

    def apply_symbiosis(self):
        for i, cell1 in enumerate(self.cells):
            for cell2 in self.cells[i+1:]:
                if cell1.cell_type != cell2.cell_type and random.random() < 0.01:
                    shared_energy = (cell1.energy + cell2.energy) * 0.1
                    cell1.energy += shared_energy
                    cell2.energy += shared_energy

    def get_visualization_data(self):
        cell_data = {cell_type: {"x": [], "y": [], "size": []} for cell_type in self.population_history.keys()}
        colors = {"prokaryote": "lightblue", "early_eukaryote": "green", "advanced_eukaryote": "red", "plant_like": "darkgreen", "complete": "purple"}

        for cell in self.cells:
            cell_data[cell.cell_type]["x"].append(cell.x)
            cell_data[cell.cell_type]["y"].append(cell.y)
            cell_data[cell.cell_type]["size"].append(cell.size * 3)

        return cell_data, self.population_history, colors

def setup_figure(env):
    cell_types = list(env.population_history.keys())
    fig = make_subplots(rows=2, cols=2, 
                        subplot_titles=("Cell Distribution", "Total Population", 
                                        "Population by Cell Type", "Organelle Distribution"),
                        vertical_spacing=0.1,
                        horizontal_spacing=0.05)

    cell_data, population_history, colors = env.get_visualization_data()

    # Cell distribution
    for cell_type, data in cell_data.items():
        fig.add_trace(go.Scatter(
            x=data["x"], y=data["y"], mode='markers',
            marker=dict(color=colors[cell_type], size=data["size"]),
            name=cell_type
        ), row=1, col=1)

    # Total population over time
    total_population = [sum(counts) for counts in zip(*population_history.values())]
    fig.add_trace(go.Scatter(y=total_population, mode='lines', name="Total"), row=1, col=2)

    # Population by cell type
    for cell_type, counts in population_history.items():
        fig.add_trace(go.Scatter(y=counts, mode='lines', name=cell_type, line=dict(color=colors[cell_type])), row=2, col=1)

    # Organelle distribution
    organelle_counts = {"nucleus": 0, "mitochondria": 0, "chloroplast": 0, "endoplasmic_reticulum": 0, "golgi_apparatus": 0}
    for cell in env.cells:
        for organelle in cell.organelles:
            organelle_counts[organelle] += 1
    
    fig.add_trace(go.Bar(x=list(organelle_counts.keys()), y=list(organelle_counts.values()), name="Organelles"), row=2, col=2)

    fig.update_xaxes(title_text="X", row=1, col=1)
    fig.update_yaxes(title_text="Y", row=1, col=1)
    fig.update_xaxes(title_text="Time", row=1, col=2)
    fig.update_yaxes(title_text="Population", row=1, col=2)
    fig.update_xaxes(title_text="Time", row=2, col=1)
    fig.update_yaxes(title_text="Population", row=2, col=1)
    fig.update_xaxes(title_text="Organelle", row=2, col=2)
    fig.update_yaxes(title_text="Count", row=2, col=2)

    fig.update_layout(height=800, width=1200, title_text="Advanced Cell Evolution Simulation")

    return fig

def format_number(num):
    if num >= 1_000_000:
        return f"{num/1_000_000:.1f}M"
    elif num >= 1_000:
        return f"{num/1_000:.1f}K"
    else:
        return str(num)

# Streamlit app
st.title("Continuous Cell Evolution Simulation")

# Sidebar for controls and live statistics
st.sidebar.header("Simulation Controls")
initial_cells = st.sidebar.slider("Initial number of cells", 10, 500, 200)
update_interval = st.sidebar.slider("Update interval (seconds)", 0.01, 1.0, 0.05)

st.sidebar.header("Environmental Effects")
radiation = st.sidebar.checkbox("Radiation")
predation = st.sidebar.checkbox("Predation")
symbiosis = st.sidebar.checkbox("Symbiosis")

effects = {
    "radiation": radiation,
    "predation": predation,
    "symbiosis": symbiosis
}

# Live statistics placeholders
st.sidebar.header("Live Statistics")
total_cells_text = st.sidebar.empty()
cell_type_breakdown = st.sidebar.empty()
dominant_type_text = st.sidebar.empty()
avg_energy_text = st.sidebar.empty()
total_merges_text = st.sidebar.empty()

# Event log
st.sidebar.header("Event Log")
event_log = deque(maxlen=10)  # Keep the last 10 events
event_log_text = st.sidebar.empty()

# Create placeholders for the chart
chart_placeholder = st.empty()

# Initialize session state
if 'running' not in st.session_state:
    st.session_state.running = False
if 'total_merges' not in st.session_state:
    st.session_state.total_merges = 0
if 'env' not in st.session_state:
    st.session_state.env = None
if 'fig' not in st.session_state:
    st.session_state.fig = None

def toggle_simulation():
    st.session_state.running = not st.session_state.running
    if st.session_state.running and st.session_state.env is None:
        st.session_state.env = Environment(100, 100, effects)
        for _ in range(initial_cells):
            cell = Cell(random.uniform(0, st.session_state.env.width), random.uniform(0, st.session_state.env.height))
            st.session_state.env.add_cell(cell)
        st.session_state.fig = setup_figure(st.session_state.env)

start_stop_button = st.button("Start/Stop Simulation", on_click=toggle_simulation)

def run_simulation_step():
    if st.session_state.running and st.session_state.env is not None:
        for _ in range(4):  # Update 4 times per frame to increase simulation speed
            initial_cell_count = len(st.session_state.env.cells)
            st.session_state.env.update()
            final_cell_count = len(st.session_state.env.cells)
            
            # Check for merges
            if final_cell_count < initial_cell_count:
                merges = initial_cell_count - final_cell_count
                st.session_state.total_merges += merges
                event_log.appendleft(f"Time {st.session_state.env.time}: {merges} cell merge(s) occurred!")

            # Check for new cell types
            for cell in st.session_state.env.cells:
                if cell.cell_type not in st.session_state.env.population_history:
                    event_log.appendleft(f"Time {st.session_state.env.time}: New cell type '{cell.cell_type}' emerged!")

        update_chart()

def update_chart():
    if st.session_state.running and st.session_state.fig is not None:
        with st.session_state.fig.batch_update():
            cell_data, population_history, colors = st.session_state.env.get_visualization_data()
            
            # Update cell distribution
            for i, (cell_type, data) in enumerate(cell_data.items()):
                st.session_state.fig.data[i].x = data["x"]
                st.session_state.fig.data[i].y = data["y"]
                st.session_state.fig.data[i].marker.size = data["size"]
            
            # Update total population
            total_population = [sum(counts) for counts in zip(*population_history.values())]
            st.session_state.fig.data[len(cell_data)].y = total_population
            
            # Update population by cell type
            for i, (cell_type, counts) in enumerate(population_history.items()):
                st.session_state.fig.data[len(cell_data) + 1 + i].y = counts
            
            # Update organelle distribution
            organelle_counts = {"nucleus": 0, "mitochondria": 0, "chloroplast": 0, "endoplasmic_reticulum": 0, "golgi_apparatus": 0}
            for cell in st.session_state.env.cells:
                for organelle in cell.organelles:
                    organelle_counts[organelle] += 1
            st.session_state.fig.data[-1].y = list(organelle_counts.values())
        
        # Update live statistics
        total_cells = len(st.session_state.env.cells)
        total_cells_text.text(f"Total Cells: {format_number(total_cells)}")
        
        cell_type_counts = {cell_type: len([c for c in st.session_state.env.cells if c.cell_type == cell_type]) for cell_type in st.session_state.env.population_history.keys()}
        cell_type_breakdown.text("Cell Type Breakdown:\n" + "\n".join([f"{cell_type}: {format_number(count)}" for cell_type, count in cell_type_counts.items()]))
        
        dominant_type = max(cell_type_counts, key=cell_type_counts.get)
        dominant_type_text.text(f"Dominant Type: {dominant_type}")
        
        avg_energy = sum(cell.energy for cell in st.session_state.env.cells) / total_cells if total_cells > 0 else 0
        avg_energy_text.text(f"Avg Energy: {avg_energy:.2f}")
        
        total_merges_text.text(f"Total Merges: {st.session_state.total_merges}")
        
        # Update event log
        event_log_text.text("Recent Events:\n" + "\n".join(event_log))
        
        chart_placeholder.plotly_chart(st.session_state.fig, use_container_width=True)

# Main loop placeholder
main_placeholder = st.empty()

# Main loop
while True:
    with main_placeholder.container():
        run_simulation_step()
        time.sleep(update_interval)
    
    # Break the loop if the simulation is stopped
    if not st.session_state.running:
        break