utils/app_utils_old.py

import os, numpy as np, pyvista as pv, trimesh, matplotlib.pyplot as plt
from scipy.spatial import cKDTree
from functools import wraps
import time
from scipy.ndimage import gaussian_filter
from vtk.util import numpy_support as nps
from scipy.spatial.distance import cosine


def _to_vertex_colors(values):
    v = np.asarray(values, dtype=float)
    vmin, vmax = float(np.nanmin(v)), float(np.nanmax(v) + 1e-12)
    norm = (v - vmin) / (vmax - vmin)
    return (plt.get_cmap("viridis")(norm)[:, :3] * 255).astype(np.uint8)

def _pv_to_trimesh(poly: pv.PolyData, colors=None):
    V = np.asarray(poly.points)
    F = poly.faces.reshape(-1, 4)[:, 1:4] if poly.faces.size else None
    m = trimesh.Trimesh(vertices=V, faces=F, process=False)
    if colors is not None and len(colors) == len(V):
        if colors.dtype != np.uint8:
            colors = (np.clip(colors, 0, 1) * 255).astype(np.uint8)
        m.visual.vertex_colors = colors
    return m

def vtp_to_glb(in_vtp: str, out_glb: str, scalar: str | None = None, point_size_frac=0.004, decimation_config=None):
    """Read a .vtp, produce a fast-to-load .glb for Gradio/three.js."""
    poly = pv.read(in_vtp)

    # Apply decimation if enabled
    if decimation_config and decimation_config.get("enabled", True):
        try:
            original_faces = poly.n_cells
            target_faces = int(original_faces * (1 - decimation_config["target_reduction"]))
            target_faces = max(decimation_config["min_faces"], min(target_faces, decimation_config["max_faces"]))
            
            if original_faces > target_faces and poly.faces.size > 0:
                print(f"🔧 Decimating VTP mesh: {original_faces} → {target_faces} faces")
                poly = poly.decimate(
                    target_reduction=decimation_config["target_reduction"],
                    preserve_topology=decimation_config["preserve_topology"]
                )
                print(f"✅ VTP decimation successful: {poly.n_cells} faces")
        except Exception as e:
            print(f"⚠️ VTP decimation failed: {e}, using original mesh")

    # If it's a triangle mesh: compute normals & color (optional), export GLB
    if poly.faces.size > 0:
        poly2 = poly.compute_normals(consistent_normals=True, auto_orient_normals=True,
                                     point_normals=True, cell_normals=False, inplace=False)
        colors = _to_vertex_colors(poly2.point_data[scalar]) if (scalar and scalar in poly2.point_data) else None
        tm_mesh = _pv_to_trimesh(poly2, colors)
        trimesh.exchange.gltf.export_glb(tm_mesh, out_glb)
        return out_glb

    # If it's a point cloud: glyph to small spheres so points are visible
    pc = pv.PolyData(poly.points)
    if scalar and scalar in poly.point_data:
        pc.point_data[scalar] = np.asarray(poly.point_data[scalar])

    # pick radius relative to bbox diagonal (tweak if needed)
    xmin, xmax, ymin, ymax, zmin, zmax = pc.bounds
    diag = np.linalg.norm([xmax - xmin, ymax - ymin, zmax - zmin])
    radius = max(1e-8, point_size_frac * diag)

    sphere = pv.Sphere(radius=radius, theta_resolution=16, phi_resolution=16)
    glyphs = pc.glyph(geom=sphere, scale=False)

    colors = None
    if scalar and scalar in glyphs.point_data:
        colors = _to_vertex_colors(glyphs.point_data[scalar])

    tm_mesh = _pv_to_trimesh(glyphs, colors)
    trimesh.exchange.gltf.export_glb(tm_mesh, out_glb)
    return out_glb


import matplotlib.pyplot as plt
from matplotlib.cm import ScalarMappable
from matplotlib.colors import Normalize

def save_colorbar_png(vmin, vmax, out_path, cmap_name="jet", units="", variable_name=""):
    # Create figure with transparent background
    fig, ax = plt.subplots(figsize=(0.1, 8.0), facecolor='none')   # transparent background
    ax.set_facecolor('none')  # transparent axis background
    
    norm = Normalize(vmin=vmin, vmax=vmax)
    sm = ScalarMappable(norm=norm, cmap=cmap_name)

    cb = plt.colorbar(sm, cax=ax, orientation="vertical")
    
    # Customize colorbar appearance
    cb.ax.set_facecolor('none')  # transparent colorbar background
    cb.ax.tick_params(colors='white', labelsize=16)  # larger font size for better visibility
    
    # Custom format function to show mantissa values only
    def format_func(x, pos):
        # Convert to scientific notation to get mantissa and exponent
        if x == 0:
            return "0.00"
        
        # Get the exponent
        exponent = int(np.floor(np.log10(abs(x))))
        # Get the mantissa
        mantissa = x / (10 ** exponent)
        
        # Format mantissa to 2 decimal places
        return f"{mantissa:.2f}"
    
    from matplotlib.ticker import FuncFormatter
    cb.ax.yaxis.set_major_formatter(FuncFormatter(format_func))
    
    # Add exponent label at the top
    if vmax != 0:
        exponent = int(np.floor(np.log10(abs(vmax))))
        if exponent != 0:
            cb.ax.text(0.5, 1.05, f"×10^{exponent}", transform=cb.ax.transAxes, 
                      ha='center', va='bottom', fontsize=18, color='white', fontweight='bold')
    
    # Add units to the label if provided
    if units:
        label_text = f"{variable_name} ({units})" if variable_name else f"Value ({units})"
    else:
        label_text = variable_name if variable_name else "Value"
    
    cb.set_label(label_text, color='white', fontsize=20, fontweight='bold')
    cb.ax.yaxis.label.set_color('white')

    # Save with transparent background
    fig.savefig(out_path, bbox_inches="tight", dpi=200, facecolor='none', edgecolor='none', transparent=True)
    plt.close(fig)
    return out_path


def create_visualization_points(viz_data):
    # Apply point cloud decimation if enabled
    points = viz_data["points"]
    pred_values = viz_data["pred"]
    
    cloud = trimesh.points.PointCloud(points)
    cmap = plt.get_cmap("jet")
    v = pred_values
    vmin, vmax = float(np.min(v)), float(np.max(v))
    norm = Normalize(vmin=vmin, vmax=vmax)
    rgb = (cmap(norm(v))[:, :3] * 255).astype(np.uint8)
    cloud.visual.vertex_colors = rgb

    center = cloud.centroid
    rot_x = trimesh.transformations.rotation_matrix(np.radians(-90), [1, 0, 0], center)
    rot_z = trimesh.transformations.rotation_matrix(np.radians(180), [0, 1, 0], center)
    cloud.apply_transform(rot_z @ rot_x)
    return cloud, vmin, vmax

def create_visualization_stl(viz_data, stl_path):

    v = viz_data["pred"]
    vmin, vmax = float(np.min(v)), float(np.max(v))
    cmap = plt.get_cmap("jet")
    norm = Normalize(vmin=vmin, vmax=vmax)
    stl_mesh = trimesh.load(stl_path)
    
    stl_points = np.asarray(stl_mesh.vertices, dtype=np.float32)
    
    # Build KDTree to interpolate output on stl coordinate system
    tree = cKDTree(viz_data["points"])
    _, idx = tree.query(stl_points, k=1)  # nearest neighbor
    stl_points_pred = viz_data["pred"][idx]  
    stl_mesh.visual.vertex_colors = (cmap(norm(stl_points_pred))[:, :3] * 255).astype(np.uint8)

    # fix the orientation of the stl mesh
    center = stl_mesh.centroid
    rot_x = trimesh.transformations.rotation_matrix(
        angle=np.radians(-90),
        direction=[1, 0, 0],
        point=center
    )
    rot_z = trimesh.transformations.rotation_matrix(
        angle=np.radians(180),
        direction=[0, 1, 0],
        point=center
    )
    rotation_total = rot_z @ rot_x
    stl_mesh.apply_transform(rotation_total) 

    return stl_mesh, vmin, vmax


def create_visualization_vtp(viz_data, variable_name):
    """Create a VTP file from visualization data with scalar field"""
    # Create a PyVista point cloud
    points = viz_data["points"]
    pred_values = viz_data["pred"]
    
    # Create PyVista PolyData from points
    point_cloud = pv.PolyData(points)
    
    # Add the predicted values as scalar data
    point_cloud[variable_name] = pred_values
    
    # # Also add target values if available
    # if "tgt" in viz_data:
    #     point_cloud[f"{variable_name}_target"] = viz_data["tgt"]
    
    return point_cloud


def camera_from_bounds(bounds, distance_scale=2.2):
    xmin, xmax, ymin, ymax, zmin, zmax = bounds
    center = np.array([(xmin+xmax)/2, (ymin+ymax)/2, (zmin+zmax)/2], dtype=float)
    ext = np.array([xmax-xmin, ymax-ymin, zmax-zmin], dtype=float)
    diag = float(np.linalg.norm(ext) or 1.0)
    dir_vec = np.array([1.0, 1.0, 1.0]) / np.sqrt(3.0)
    return (center + distance_scale * diag * dir_vec).tolist()


def bounds_from_points(points: np.ndarray):
    mins = points.min(axis=0)
    maxs = points.max(axis=0)
    return (mins[0], maxs[0], mins[1], maxs[1], mins[2], maxs[2])


# ========================== Example Loading Handlers ==========================
def convert_vtp_to_glb(vtp_path, output_dir):
    """Convert VTP file to GLB format"""
    try:
        # Read VTP file with pyvista
        mesh = pv.read(vtp_path)
        mesh = mesh.triangulate()
        
        
        # Convert to trimesh format
        print(" 🔄 Converting VTP to GLB...")
        if mesh.n_points == mesh.n_cells or mesh.get_cell(0).type == 1:
            # Point cloud -> GLB via trimesh
            print(" 🔄 Point cloud -> GLB via trimesh")
            tmesh = trimesh.points.PointCloud(mesh.points)
            tmesh.visual.vertex_colors = np.tile([190, 190, 190], (mesh.n_points, 1))      
            center = tmesh.centroid
            rot_x = trimesh.transformations.rotation_matrix(np.radians(-90), [1, 0, 0], center)
            rot_z = trimesh.transformations.rotation_matrix(np.radians(180), [0, 1, 0], center)
            tmesh.apply_transform(rot_z @ rot_x)
            # Save as GLB
            glb_path = os.path.join(output_dir, f"{os.path.basename(vtp_path)}.glb")
            tmesh.export(glb_path)
            return glb_path
        else:
            # Triangular mesh -> GLB via trimesh
            print(" 🔄 Triangular mesh -> GLB via trimesh")
            mesh = mesh.triangulate()
            mesh_fixed = mesh.compute_normals(
                consistent_normals=True, auto_orient_normals=True,
                point_normals=True, cell_normals=False, inplace=False
            )
            tmesh = _pv_to_trimesh(mesh_fixed)
            glb_path = os.path.join(output_dir, f"{os.path.basename(vtp_path)}.glb")
            tmesh.export(glb_path)
            return glb_path
        
    except Exception as e:
        print(f"Error converting VTP to GLB: {str(e)}")
        return None


def convert_vtp_to_stl(vtp_path, output_dir, decimation_config=None):
    """Convert VTP file to STL format"""
    try:
        # Read VTP file with pyvista
        mesh = pv.read(vtp_path)
        mesh = mesh.triangulate()
        
        # Apply decimation if enabled
        if decimation_config and decimation_config.get("enabled", True):
            try:
                original_faces = mesh.n_cells
                target_faces = int(original_faces * (1 - decimation_config["target_reduction"]))
                target_faces = max(decimation_config["min_faces"], min(target_faces, decimation_config["max_faces"]))
                
                if original_faces > target_faces and mesh.faces.size > 0:
                    print(f"🔧 Decimating VTP mesh: {original_faces} → {target_faces} faces")
                    mesh = mesh.decimate(
                        target_reduction=decimation_config["target_reduction"]
                        # preserve_topology=decimation_config["preserve_topology"]
                    )
                    print(f"✅ VTP decimation successful: {mesh.n_cells} faces")
            except Exception as e:
                print(f"⚠️ VTP decimation failed: {e}, using original mesh")
        
        # Convert to trimesh format 
        mesh_fixed = mesh.compute_normals(
            consistent_normals=True, auto_orient_normals=True,
            point_normals=True, cell_normals=False, inplace=False
        )
        
        geom_path = os.path.join(output_dir, f"{os.path.basename(vtp_path)}.stl")
        mesh_fixed.save(geom_path)
        return geom_path

    except Exception as e:
        print(f"Error converting VTP to STL: {str(e)}")
        return None


# ========================== Unit Conversion Utilities ==========================
def mph_to_ms(mph):
    """Convert miles per hour to meters per second"""
    return mph * 0.44704  # 1 mph = 0.44704 m/s

def ms_to_mph(ms):
    """Convert meters per second to miles per hour"""
    return ms / 0.44704

def time_function(func_name=None):
    """Decorator to time function execution"""
    def decorator(func):
        @wraps(func)
        def wrapper(*args, **kwargs):
            name = func_name or func.__name__
            start_time = time.time()
            print(f"⏱️  Starting {name}...")
            try:
                result = func(*args, **kwargs)
                elapsed = time.time() - start_time
                print(f"✅ {name} completed in {elapsed:.3f} seconds")
                return result
            except Exception as e:
                elapsed = time.time() - start_time
                print(f"❌ {name} failed after {elapsed:.3f} seconds: {str(e)}")
                raise
        return wrapper
    return decorator

def print_timing(message, start_time=None):
    """Print timing information"""
    if start_time is None:
        return time.time()
    else:
        elapsed = time.time() - start_time
        print(f"⏱️  {message}: {elapsed:.3f} seconds")
        return time.time()


def vtk_to_np(arr):
    if isinstance(arr, np.ndarray):
        return arr
    try:
        return np.asarray(arr)
    except Exception:
        return nps.vtk_to_numpy(arr)



def mesh_get_variable(mesh: pv.DataSet, var_name: str, npts: int):
    if var_name in mesh.point_data:
        v = vtk_to_np(mesh.point_data[var_name]).reshape(-1)
    elif var_name in mesh.cell_data:
        mesh2 = mesh.cell_data_to_point_data()
        v = vtk_to_np(mesh2.point_data[var_name]).reshape(-1)
    elif var_name in mesh.field_data:
        v0 = vtk_to_np(mesh.field_data[var_name]).ravel()
        v = np.full(npts, float(v0[0]), dtype=np.float32) if v0.size == 1 else np.zeros(npts, np.float32)
    else:
        v = np.zeros(npts, np.float32)
    return v.astype(np.float32, copy=False)




def get_boundary_conditions_text(dataset):
    """Generate boundary conditions display text for the UI"""
    if dataset == "Incompressible flow inside artery":
        return ""
    elif dataset == "Incompressible flow over car":
        return """
**Reference Density:** 1.225 kg/m³

**Reference Viscosity:** 1.789e-5 Pa·s

**Operating Pressure:** 101325 Pa"""
    elif dataset == "Compressible flow over plane":
        return """
**Reference Density:** 0.36 kg/m³

**Reference viscosity:** 1.716e-05 kg/(m·s)

**Operating Pressure:** 23842 Pa

---

**Ambient Temperature:** 218 K

**Cruising velocity:** 250.0 m/s or 560 mph
"""
    elif dataset == "Vehicle crash analysis":
        return ""
    else:
        return "**📋 Boundary Conditions:** Not specified"

def get_boundary_conditions_left(dataset):
    """Generate left column boundary conditions for plane dataset"""
    if dataset == "Compressible flow over plane":
        return """
**Reference Density:** 0.36 kg/m³

**Reference viscosity:** 1.716e-05 kg/(m·s)

**Operating Pressure:** 23842 Pa
"""
    else:
        return ""

def get_boundary_conditions_right(dataset):
    """Generate right column boundary conditions for plane dataset"""
    if dataset == "Compressible flow over plane":
        return """
**Ambient Temperature:** 218 K

**Cruising velocity:** 250.0 m/s or 560 mph
"""
    else:
        return ""


### utils to compute cosine score
def get_points(mesh, max_points=5000):
    """Extract and subsample point cloud from VTP file."""
    try:
        points = mesh.points
        if len(points) > max_points:
            indices = np.random.choice(len(points), max_points, replace=False)
            points = points[indices]
        return points
    except Exception as e:
        raise ValueError(f"Error reading {mesh}: {e}")



def compute_cosine_score(mesh, dataset, smooth_sigma=1):
    """
    Compute Cosine similarity score for a single VTP file against saved training distribution.
    
    Args:
        mesh: PyVista mesh
        dataset: Dataset name
        smooth_sigma: Gaussian smoothing parameter
    
    Returns:
        float: Cosine similarity score (0-1), higher means closer to training distribution
    """
    # Load the saved training distribution
    train_dist_path = os.path.join("configs/app_configs/" , dataset, "train_dist.npz")
    if not os.path.exists(train_dist_path):
        raise ValueError(f"Training distribution file not found: {train_dist_path}")
    
    data = np.load(train_dist_path)
    train_hist = data['hist']
    bin_edges = [data['edges0'], data['edges1'], data['edges2']]
    
    
    # Get test points from VTP file
    test_points = get_points(mesh)
    
    # Create 3D histogram for test points using same bins as training
    test_hist, _ = np.histogramdd(test_points, bins=bin_edges, density=True)
    test_hist = gaussian_filter(test_hist, sigma=smooth_sigma)
    
    # Flatten and normalize
    test_hist = test_hist.flatten()
    test_hist /= test_hist.sum()
    
    # Add small epsilon to avoid zero values
    epsilon = 1e-12
    train_hist_safe = train_hist + epsilon
    test_hist_safe = test_hist + epsilon
    
    # Compute Cosine similarity (1 - cosine distance)
    cosine_distance = cosine(train_hist_safe, test_hist_safe)
    cosine_similarity = 1 - cosine_distance
    
    print(f"Cosine Score for {dataset}: {cosine_similarity:.6f}")
    return cosine_similarity


js_func = """
function refresh() {
    const url = new URL(window.location);

    if (url.searchParams.get('__theme') !== 'dark') {
        url.searchParams.set('__theme', 'dark');
        window.location.href = url.href;
    }
}
"""




# ========================== Mesh Decimation Utilities ==========================
def decimate_mesh(mesh, config=None):
    """
    Decimate a PyVista mesh for faster visualization while preserving important features.
    
    Args:
        mesh: PyVista mesh object
        config: Decimation configuration dict (uses DECIMATION_CONFIG if None)
    
    Returns:
        Decimated PyVista mesh
    """
    
    try:
        # Skip decimation for point clouds
        if mesh.n_cells == 0 or mesh.n_points == mesh.n_cells or mesh.get_cell(0).type == 1:
            print("☁️ Skipping decimation for point cloud")
            return mesh
        

        ## triangulate mesh
        mesh = mesh.triangulate()

        original_faces = mesh.n_cells
        original_points = mesh.n_points
        
        # Calculate target number of faces
        target_faces = int(original_faces * (1 - config["target_reduction"]))
        target_faces = max(config["min_faces"], min(target_faces, config["max_faces"]))
        
        # Skip if already small enough
        if original_faces <= target_faces:
            print(f"📊 Mesh already small enough: {original_faces} faces")
            return mesh
        
        print(f"🔧 Decimating mesh: {original_faces} → {target_faces} faces ({original_points} → ~{target_faces*2} points)")
        
        # Use PyVista's decimation
        decimated = mesh.decimate(
            target_reduction=config["target_reduction"]
            # preserve_topology=config["preserve_topology"]
        )
        
        # Ensure we don't go below minimum faces
        if decimated.n_cells < config["min_faces"]:
            print(f"⚠️ Decimation resulted in too few faces ({decimated.n_cells}), using original mesh")
            return mesh
        
        print(f"✅ Decimation successful: {decimated.n_cells} faces, {decimated.n_points} points")
        return decimated
        
    except Exception as e:
        print(f"⚠️ Decimation failed: {e}, using original mesh")
        return mesh