zipnerf / extract.py
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import logging
import os
import sys
import cv2
import numpy as np
from absl import app
import gin
from internal import configs
from internal import datasets
from internal import models
from internal import utils
from internal import coord
from internal import checkpoints
import torch
import accelerate
from tqdm import tqdm
from torch.utils._pytree import tree_map
import torch.nn.functional as F
from skimage import measure
import trimesh
import pymeshlab as pml
configs.define_common_flags()
@torch.no_grad()
def evaluate_density(model, accelerator: accelerate.Accelerator,
points, config: configs.Config, std_value=0.0):
"""
Evaluate a signed distance function (SDF) for a batch of points.
Args:
sdf: A callable function that takes a tensor of size (N, 3) containing
3D points and returns a tensor of size (N,) with the SDF values.
points: A torch tensor containing 3D points.
Returns:
A torch tensor with the SDF values evaluated at the given points.
"""
z = []
for _, pnts in enumerate(tqdm(torch.split(points, config.render_chunk_size, dim=0),
desc="Evaluating density", leave=False,
disable=not accelerator.is_main_process)):
rays_remaining = pnts.shape[0] % accelerator.num_processes
if rays_remaining != 0:
padding = accelerator.num_processes - rays_remaining
pnts = torch.cat([pnts, torch.zeros_like(pnts[-padding:])], dim=0)
else:
padding = 0
rays_per_host = pnts.shape[0] // accelerator.num_processes
start, stop = accelerator.process_index * rays_per_host, \
(accelerator.process_index + 1) * rays_per_host
chunk_means = pnts[start:stop]
chunk_stds = torch.full_like(chunk_means[..., 0], std_value)
raw_density = model.nerf_mlp.predict_density(chunk_means[:, None], chunk_stds[:, None], no_warp=True)[0]
density = F.softplus(raw_density + model.nerf_mlp.density_bias)
density = accelerator.gather(density)
if padding > 0:
density = density[: -padding]
z.append(density)
z = torch.cat(z, dim=0)
return z
@torch.no_grad()
def evaluate_color(model, accelerator: accelerate.Accelerator,
points, config: configs.Config, std_value=0.0):
"""
Evaluate a signed distance function (SDF) for a batch of points.
Args:
sdf: A callable function that takes a tensor of size (N, 3) containing
3D points and returns a tensor of size (N,) with the SDF values.
points: A torch tensor containing 3D points.
Returns:
A torch tensor with the SDF values evaluated at the given points.
"""
z = []
for _, pnts in enumerate(tqdm(torch.split(points, config.render_chunk_size, dim=0),
desc="Evaluating color",
disable=not accelerator.is_main_process)):
rays_remaining = pnts.shape[0] % accelerator.num_processes
if rays_remaining != 0:
padding = accelerator.num_processes - rays_remaining
pnts = torch.cat([pnts, torch.zeros_like(pnts[-padding:])], dim=0)
else:
padding = 0
rays_per_host = pnts.shape[0] // accelerator.num_processes
start, stop = accelerator.process_index * rays_per_host, \
(accelerator.process_index + 1) * rays_per_host
chunk_means = pnts[start:stop]
chunk_stds = torch.full_like(chunk_means[..., 0], std_value)
chunk_viewdirs = torch.zeros_like(chunk_means)
ray_results = model.nerf_mlp(False, chunk_means[:, None, None], chunk_stds[:, None, None],
chunk_viewdirs)
rgb = ray_results['rgb'][:, 0]
rgb = accelerator.gather(rgb)
if padding > 0:
rgb = rgb[: -padding]
z.append(rgb)
z = torch.cat(z, dim=0)
return z
@torch.no_grad()
def evaluate_color_projection(model, accelerator: accelerate.Accelerator, vertices, faces, config: configs.Config):
normals = auto_normals(vertices, faces.long())
viewdirs = -normals
origins = vertices - 0.005 * viewdirs
vc = []
chunk = config.render_chunk_size
model.num_levels = 1
model.opaque_background = True
for i in tqdm(range(0, origins.shape[0], chunk),
desc="Evaluating color projection",
disable=not accelerator.is_main_process):
cur_chunk = min(chunk, origins.shape[0] - i)
rays_remaining = cur_chunk % accelerator.num_processes
rays_per_host = cur_chunk // accelerator.num_processes
if rays_remaining != 0:
padding = accelerator.num_processes - rays_remaining
rays_per_host += 1
else:
padding = 0
start = i + accelerator.process_index * rays_per_host
stop = start + rays_per_host
batch = {
'origins': origins[start:stop],
'directions': viewdirs[start:stop],
'viewdirs': viewdirs[start:stop],
'cam_dirs': viewdirs[start:stop],
'radii': torch.full_like(origins[start:stop, ..., :1], 0.000723),
'near': torch.full_like(origins[start:stop, ..., :1], 0),
'far': torch.full_like(origins[start:stop, ..., :1], 0.01),
}
batch = accelerator.pad_across_processes(batch)
with accelerator.autocast():
renderings, ray_history = model(
False,
batch,
compute_extras=False,
train_frac=1)
rgb = renderings[-1]['rgb']
acc = renderings[-1]['acc']
rgb /= acc.clamp_min(1e-5)[..., None]
rgb = rgb.clamp(0, 1)
rgb = accelerator.gather(rgb)
rgb[torch.isnan(rgb) | torch.isinf(rgb)] = 1
if padding > 0:
rgb = rgb[: -padding]
vc.append(rgb)
vc = torch.cat(vc, dim=0)
return vc
def auto_normals(verts, faces):
i0 = faces[:, 0]
i1 = faces[:, 1]
i2 = faces[:, 2]
v0 = verts[i0, :]
v1 = verts[i1, :]
v2 = verts[i2, :]
face_normals = torch.cross(v1 - v0, v2 - v0)
# Splat face normals to vertices
v_nrm = torch.zeros_like(verts)
v_nrm.scatter_add_(0, i0[:, None].repeat(1, 3), face_normals)
v_nrm.scatter_add_(0, i1[:, None].repeat(1, 3), face_normals)
v_nrm.scatter_add_(0, i2[:, None].repeat(1, 3), face_normals)
# Normalize, replace zero (degenerated) normals with some default value
v_nrm = torch.where((v_nrm ** 2).sum(dim=-1, keepdims=True) > 1e-20, v_nrm,
torch.tensor([0.0, 0.0, 1.0], dtype=torch.float32, device=verts.device))
v_nrm = F.normalize(v_nrm, dim=-1)
return v_nrm
def clean_mesh(verts, faces, v_pct=1, min_f=8, min_d=5, repair=True, remesh=True, remesh_size=0.01, logger=None, main_process=True):
# verts: [N, 3]
# faces: [N, 3]
tbar = tqdm(total=9, desc='Clean mesh', leave=False, disable=not main_process)
_ori_vert_shape = verts.shape
_ori_face_shape = faces.shape
m = pml.Mesh(verts, faces)
ms = pml.MeshSet()
ms.add_mesh(m, 'mesh') # will copy!
# filters
tbar.set_description('Remove unreferenced vertices')
ms.meshing_remove_unreferenced_vertices() # verts not refed by any faces
tbar.update()
if v_pct > 0:
tbar.set_description('Remove unreferenced vertices')
ms.meshing_merge_close_vertices(threshold=pml.Percentage(v_pct)) # 1/10000 of bounding box diagonal
tbar.update()
tbar.set_description('Remove duplicate faces')
ms.meshing_remove_duplicate_faces() # faces defined by the same verts
tbar.update()
tbar.set_description('Remove null faces')
ms.meshing_remove_null_faces() # faces with area == 0
tbar.update()
if min_d > 0:
tbar.set_description('Remove connected component by diameter')
ms.meshing_remove_connected_component_by_diameter(mincomponentdiag=pml.Percentage(min_d))
tbar.update()
if min_f > 0:
tbar.set_description('Remove connected component by face number')
ms.meshing_remove_connected_component_by_face_number(mincomponentsize=min_f)
tbar.update()
if repair:
# tbar.set_description('Remove t vertices')
# ms.meshing_remove_t_vertices(method=0, threshold=40, repeat=True)
tbar.set_description('Repair non manifold edges')
ms.meshing_repair_non_manifold_edges(method=0)
tbar.update()
tbar.set_description('Repair non manifold vertices')
ms.meshing_repair_non_manifold_vertices(vertdispratio=0)
tbar.update()
else:
tbar.update(2)
if remesh:
# tbar.set_description('Coord taubin smoothing')
# ms.apply_coord_taubin_smoothing()
tbar.set_description('Isotropic explicit remeshing')
ms.meshing_isotropic_explicit_remeshing(iterations=3, targetlen=pml.AbsoluteValue(remesh_size))
tbar.update()
# extract mesh
m = ms.current_mesh()
verts = m.vertex_matrix()
faces = m.face_matrix()
if logger is not None:
logger.info(f'Mesh cleaning: {_ori_vert_shape} --> {verts.shape}, {_ori_face_shape} --> {faces.shape}')
return verts, faces
def decimate_mesh(verts, faces, target, backend='pymeshlab', remesh=False, optimalplacement=True, logger=None):
# optimalplacement: default is True, but for flat mesh must turn False to prevent spike artifect.
_ori_vert_shape = verts.shape
_ori_face_shape = faces.shape
if backend == 'pyfqmr':
import pyfqmr
solver = pyfqmr.Simplify()
solver.setMesh(verts, faces)
solver.simplify_mesh(target_count=target, preserve_border=False, verbose=False)
verts, faces, normals = solver.getMesh()
else:
m = pml.Mesh(verts, faces)
ms = pml.MeshSet()
ms.add_mesh(m, 'mesh') # will copy!
# filters
# ms.meshing_decimation_clustering(threshold=pml.Percentage(1))
ms.meshing_decimation_quadric_edge_collapse(targetfacenum=int(target), optimalplacement=optimalplacement)
if remesh:
# ms.apply_coord_taubin_smoothing()
ms.meshing_isotropic_explicit_remeshing(iterations=3, targetlen=pml.Percentage(1))
# extract mesh
m = ms.current_mesh()
verts = m.vertex_matrix()
faces = m.face_matrix()
if logger is not None:
logger.info(f'Mesh decimation: {_ori_vert_shape} --> {verts.shape}, {_ori_face_shape} --> {faces.shape}')
return verts, faces
def main(unused_argv):
config = configs.load_config()
config.compute_visibility = True
config.exp_path = os.path.join("exp", config.exp_name)
config.mesh_path = os.path.join("exp", config.exp_name, "mesh")
config.checkpoint_dir = os.path.join(config.exp_path, 'checkpoints')
os.makedirs(config.mesh_path, exist_ok=True)
# accelerator for DDP
accelerator = accelerate.Accelerator()
device = accelerator.device
# setup logger
logging.basicConfig(
format="%(asctime)s: %(message)s",
datefmt="%Y-%m-%d %H:%M:%S",
force=True,
handlers=[logging.StreamHandler(sys.stdout),
logging.FileHandler(os.path.join(config.exp_path, 'log_extract.txt'))],
level=logging.INFO,
)
sys.excepthook = utils.handle_exception
logger = accelerate.logging.get_logger(__name__)
logger.info(config)
logger.info(accelerator.state, main_process_only=False)
config.world_size = accelerator.num_processes
config.global_rank = accelerator.process_index
accelerate.utils.set_seed(config.seed, device_specific=True)
# setup model and optimizer
model = models.Model(config=config)
model = accelerator.prepare(model)
step = checkpoints.restore_checkpoint(config.checkpoint_dir, accelerator, logger)
model.eval()
module = accelerator.unwrap_model(model)
visibility_path = os.path.join(config.mesh_path, 'visibility_mask_{:.1f}.pt'.format(config.mesh_radius))
visibility_resolution = config.visibility_resolution
if not os.path.exists(visibility_path):
logger.info('Generate visibility mask...')
# load dataset
dataset = datasets.load_dataset('train', config.data_dir, config)
dataloader = torch.utils.data.DataLoader(np.arange(len(dataset)),
num_workers=4,
shuffle=True,
batch_size=1,
collate_fn=dataset.collate_fn,
persistent_workers=True,
)
visibility_mask = torch.ones(
(1, 1, visibility_resolution, visibility_resolution, visibility_resolution), requires_grad=True
).to(device)
visibility_mask.retain_grad()
tbar = tqdm(dataloader, desc='Generating visibility grid', disable=not accelerator.is_main_process)
for index, batch in enumerate(tbar):
batch = accelerate.utils.send_to_device(batch, accelerator.device)
rendering = models.render_image(model, accelerator,
batch, False, 1, config,
verbose=False, return_weights=True)
coords = rendering['coord'].reshape(-1, 3)
weights = rendering['weights'].reshape(-1)
valid_points = coords[weights > config.valid_weight_thresh]
valid_points /= config.mesh_radius
# update mask based on ray samples
with torch.enable_grad():
out = torch.nn.functional.grid_sample(visibility_mask,
valid_points[None, None, None],
align_corners=True)
out.sum().backward()
tbar.set_postfix({"visibility_mask": (visibility_mask.grad > 0.0001).float().mean().item()})
# if index == 10:
# break
visibility_mask = (visibility_mask.grad > 0.0001).float()
if accelerator.is_main_process:
torch.save(visibility_mask.detach().cpu(), visibility_path)
else:
logger.info('Load visibility mask from {}'.format(visibility_path))
visibility_mask = torch.load(visibility_path, map_location=device)
space = config.mesh_radius * 2 / (config.visibility_resolution - 1)
logger.info("Extract mesh from visibility mask...")
visibility_mask_np = visibility_mask[0, 0].permute(2, 1, 0).detach().cpu().numpy()
verts, faces, normals, values = measure.marching_cubes(
volume=-visibility_mask_np,
level=-0.5,
spacing=(space, space, space))
verts -= config.mesh_radius
if config.extract_visibility:
meshexport = trimesh.Trimesh(verts, faces)
meshexport.export(os.path.join(config.mesh_path, "visibility_mask_{}.ply".format(config.mesh_radius)), "ply")
logger.info("Extract visibility mask done.")
# Initialize variables
crop_n = 512
grid_min = verts.min(axis=0)
grid_max = verts.max(axis=0)
space = ((grid_max - grid_min).prod() / config.mesh_voxels) ** (1 / 3)
world_size = ((grid_max - grid_min) / space).astype(np.int32)
Nx, Ny, Nz = np.maximum(1, world_size // crop_n)
crop_n_x, crop_n_y, crop_n_z = world_size // [Nx, Ny, Nz]
xs = np.linspace(grid_min[0], grid_max[0], Nx + 1)
ys = np.linspace(grid_min[1], grid_max[1], Ny + 1)
zs = np.linspace(grid_min[2], grid_max[2], Nz + 1)
# Initialize meshes list
meshes = []
# Iterate over the grid
for i in range(Nx):
for j in range(Ny):
for k in range(Nz):
logger.info(f"Process grid cell ({i + 1}/{Nx}, {j + 1}/{Ny}, {k + 1}/{Nz})...")
# Calculate grid cell boundaries
x_min, x_max = xs[i], xs[i + 1]
y_min, y_max = ys[j], ys[j + 1]
z_min, z_max = zs[k], zs[k + 1]
# Create point grid
x = np.linspace(x_min, x_max, crop_n_x)
y = np.linspace(y_min, y_max, crop_n_y)
z = np.linspace(z_min, z_max, crop_n_z)
xx, yy, zz = np.meshgrid(x, y, z, indexing="ij")
points = torch.tensor(np.vstack([xx.ravel(), yy.ravel(), zz.ravel()]).T,
dtype=torch.float,
device=device)
# Construct point pyramids
points_tmp = points.reshape(crop_n_x, crop_n_y, crop_n_z, 3)[None]
points_tmp /= config.mesh_radius
current_mask = torch.nn.functional.grid_sample(visibility_mask, points_tmp, align_corners=True)
current_mask = (current_mask > 0.0).cpu().numpy()[0, 0]
pts_density = evaluate_density(module, accelerator, points,
config, std_value=config.std_value)
# bound the vertices
points_world = coord.inv_contract(2 * points)
pts_density[points_world.norm(dim=-1) > config.mesh_max_radius] = 0.0
z = pts_density.detach().cpu().numpy()
# Skip if no surface found
valid_z = z.reshape(crop_n_x, crop_n_y, crop_n_z)[current_mask]
if valid_z.shape[0] <= 0 or (
np.min(valid_z) > config.isosurface_threshold or np.max(
valid_z) < config.isosurface_threshold
):
continue
if not (np.min(z) > config.isosurface_threshold or np.max(z) < config.isosurface_threshold):
# Extract mesh
logger.info('Extract mesh...')
z = z.astype(np.float32)
verts, faces, _, _ = measure.marching_cubes(
volume=-z.reshape(crop_n_x, crop_n_y, crop_n_z),
level=-config.isosurface_threshold,
spacing=(
(x_max - x_min) / (crop_n_x - 1),
(y_max - y_min) / (crop_n_y - 1),
(z_max - z_min) / (crop_n_z - 1),
),
mask=current_mask,
)
verts = verts + np.array([x_min, y_min, z_min])
meshcrop = trimesh.Trimesh(verts, faces)
logger.info('Extract vertices: {}, faces: {}'.format(meshcrop.vertices.shape[0],
meshcrop.faces.shape[0]))
meshes.append(meshcrop)
# Save mesh
logger.info('Concatenate mesh...')
combined_mesh = trimesh.util.concatenate(meshes)
# from https://github.com/ashawkey/stable-dreamfusion/blob/main/nerf/renderer.py
# clean
logger.info('Clean mesh...')
vertices = combined_mesh.vertices.astype(np.float32)
faces = combined_mesh.faces.astype(np.int32)
vertices, faces = clean_mesh(vertices, faces,
remesh=False, remesh_size=0.01,
logger=logger, main_process=accelerator.is_main_process)
v = torch.from_numpy(vertices).contiguous().float().to(device)
v = coord.inv_contract(2 * v)
vertices = v.detach().cpu().numpy()
f = torch.from_numpy(faces).contiguous().int().to(device)
# decimation
if config.decimate_target > 0 and faces.shape[0] > config.decimate_target:
logger.info('Decimate mesh...')
vertices, triangles = decimate_mesh(vertices, faces, config.decimate_target, logger=logger)
# import ipdb; ipdb.set_trace()
if config.vertex_color:
# batched inference to avoid OOM
logger.info('Evaluate mesh vertex color...')
if config.vertex_projection:
rgbs = evaluate_color_projection(module, accelerator, v, f, config)
else:
rgbs = evaluate_color(module, accelerator, v,
config, std_value=config.std_value)
rgbs = (rgbs * 255).detach().cpu().numpy().astype(np.uint8)
if accelerator.is_main_process:
logger.info('Export mesh (vertex color)...')
mesh = trimesh.Trimesh(vertices, faces,
vertex_colors=rgbs,
process=False) # important, process=True leads to seg fault...
mesh.export(os.path.join(config.mesh_path, 'mesh_{}.ply'.format(config.mesh_radius)))
logger.info('Finish extracting mesh.')
return
def _export(v, f, h0=2048, w0=2048, ssaa=1, name=''):
logger.info('Export mesh (atlas)...')
# v, f: torch Tensor
device = v.device
v_np = v.cpu().numpy() # [N, 3]
f_np = f.cpu().numpy() # [M, 3]
# unwrap uvs
import xatlas
import nvdiffrast.torch as dr
from sklearn.neighbors import NearestNeighbors
from scipy.ndimage import binary_dilation, binary_erosion
logger.info(f'Running xatlas to unwrap UVs for mesh: v={v_np.shape} f={f_np.shape}')
atlas = xatlas.Atlas()
atlas.add_mesh(v_np, f_np)
chart_options = xatlas.ChartOptions()
chart_options.max_iterations = 4 # for faster unwrap...
atlas.generate(chart_options=chart_options)
vmapping, ft_np, vt_np = atlas[0] # [N], [M, 3], [N, 2]
# vmapping, ft_np, vt_np = xatlas.parametrize(v_np, f_np) # [N], [M, 3], [N, 2]
vt = torch.from_numpy(vt_np.astype(np.float32)).float().to(device)
ft = torch.from_numpy(ft_np.astype(np.int64)).int().to(device)
# render uv maps
uv = vt * 2.0 - 1.0 # uvs to range [-1, 1]
uv = torch.cat((uv, torch.zeros_like(uv[..., :1]), torch.ones_like(uv[..., :1])), dim=-1) # [N, 4]
if ssaa > 1:
h = int(h0 * ssaa)
w = int(w0 * ssaa)
else:
h, w = h0, w0
if h <= 2048 and w <= 2048:
glctx = dr.RasterizeCudaContext()
else:
glctx = dr.RasterizeGLContext()
rast, _ = dr.rasterize(glctx, uv.unsqueeze(0), ft, (h, w)) # [1, h, w, 4]
xyzs, _ = dr.interpolate(v.unsqueeze(0), rast, f) # [1, h, w, 3]
mask, _ = dr.interpolate(torch.ones_like(v[:, :1]).unsqueeze(0), rast, f) # [1, h, w, 1]
# masked query
xyzs = xyzs.view(-1, 3)
mask = (mask > 0).view(-1)
feats = torch.zeros(h * w, 3, device=device, dtype=torch.float32)
if mask.any():
xyzs = xyzs[mask] # [M, 3]
# batched inference to avoid OOM
all_feats = evaluate_color(module, accelerator, xyzs,
config, std_value=config.std_value)
feats[mask] = all_feats
feats = feats.view(h, w, -1)
mask = mask.view(h, w)
# quantize [0.0, 1.0] to [0, 255]
feats = feats.cpu().numpy()
feats = (feats * 255).astype(np.uint8)
### NN search as an antialiasing ...
mask = mask.cpu().numpy()
inpaint_region = binary_dilation(mask, iterations=3)
inpaint_region[mask] = 0
search_region = mask.copy()
not_search_region = binary_erosion(search_region, iterations=2)
search_region[not_search_region] = 0
search_coords = np.stack(np.nonzero(search_region), axis=-1)
inpaint_coords = np.stack(np.nonzero(inpaint_region), axis=-1)
knn = NearestNeighbors(n_neighbors=1, algorithm='kd_tree').fit(search_coords)
_, indices = knn.kneighbors(inpaint_coords)
feats[tuple(inpaint_coords.T)] = feats[tuple(search_coords[indices[:, 0]].T)]
feats = cv2.cvtColor(feats, cv2.COLOR_RGB2BGR)
# do ssaa after the NN search, in numpy
if ssaa > 1:
feats = cv2.resize(feats, (w0, h0), interpolation=cv2.INTER_LINEAR)
cv2.imwrite(os.path.join(config.mesh_path, f'{name}albedo.png'), feats)
# save obj (v, vt, f /)
obj_file = os.path.join(config.mesh_path, f'{name}mesh.obj')
mtl_file = os.path.join(config.mesh_path, f'{name}mesh.mtl')
logger.info(f'writing obj mesh to {obj_file}')
with open(obj_file, "w") as fp:
fp.write(f'mtllib {name}mesh.mtl \n')
logger.info(f'writing vertices {v_np.shape}')
for v in v_np:
fp.write(f'v {v[0]} {v[1]} {v[2]} \n')
logger.info(f'writing vertices texture coords {vt_np.shape}')
for v in vt_np:
fp.write(f'vt {v[0]} {1 - v[1]} \n')
logger.info(f'writing faces {f_np.shape}')
fp.write(f'usemtl mat0 \n')
for i in range(len(f_np)):
fp.write(
f"f {f_np[i, 0] + 1}/{ft_np[i, 0] + 1} {f_np[i, 1] + 1}/{ft_np[i, 1] + 1} {f_np[i, 2] + 1}/{ft_np[i, 2] + 1} \n")
with open(mtl_file, "w") as fp:
fp.write(f'newmtl mat0 \n')
fp.write(f'Ka 1.000000 1.000000 1.000000 \n')
fp.write(f'Kd 1.000000 1.000000 1.000000 \n')
fp.write(f'Ks 0.000000 0.000000 0.000000 \n')
fp.write(f'Tr 1.000000 \n')
fp.write(f'illum 1 \n')
fp.write(f'Ns 0.000000 \n')
fp.write(f'map_Kd {name}albedo.png \n')
# could be extremely slow
_export(v, f)
logger.info('Finish extracting mesh.')
if __name__ == '__main__':
with gin.config_scope('bake'):
app.run(main)