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utils.py
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import torch
import io, os, logging, urllib
import yaml
import trimesh
import imageio
import numbers
import math
import numpy as np
from collections import OrderedDict
from plyfile import PlyData
from torch import nn
from torch.nn import functional as F
from torch.utils import model_zoo
from skimage import measure, img_as_float32
from pytorch3d.structures import Meshes
from pytorch3d.renderer import PerspectiveCameras, rasterize_meshes
from igl import adjacency_matrix, connected_components
import open3d as o3d
##################################################
# Below are functions for DPSR
def fftfreqs(res, dtype=torch.float32, exact=True):
"""
Helper function to return frequency tensors
:param res: n_dims int tuple of number of frequency modes
:return:
"""
n_dims = len(res)
freqs = []
for dim in range(n_dims - 1):
r_ = res[dim]
freq = np.fft.fftfreq(r_, d=1/r_)
freqs.append(torch.tensor(freq, dtype=dtype))
r_ = res[-1]
if exact:
freqs.append(torch.tensor(np.fft.rfftfreq(r_, d=1/r_), dtype=dtype))
else:
freqs.append(torch.tensor(np.fft.rfftfreq(r_, d=1/r_)[:-1], dtype=dtype))
omega = torch.meshgrid(freqs)
omega = list(omega)
omega = torch.stack(omega, dim=-1)
return omega
def img(x, deg=1): # imaginary of tensor (assume last dim: real/imag)
"""
multiply tensor x by i ** deg
"""
deg %= 4
if deg == 0:
res = x
elif deg == 1:
res = x[..., [1, 0]]
res[..., 0] = -res[..., 0]
elif deg == 2:
res = -x
elif deg == 3:
res = x[..., [1, 0]]
res[..., 1] = -res[..., 1]
return res
def spec_gaussian_filter(res, sig):
omega = fftfreqs(res, dtype=torch.float64) # [dim0, dim1, dim2, d]
dis = torch.sqrt(torch.sum(omega ** 2, dim=-1))
filter_ = torch.exp(-0.5*((sig*2*dis/res[0])**2)).unsqueeze(-1).unsqueeze(-1)
filter_.requires_grad = False
return filter_
def grid_interp(grid, pts, batched=True):
"""
:param grid: tensor of shape (batch, *size, in_features)
:param pts: tensor of shape (batch, num_points, dim) within range (0, 1)
:return values at query points
"""
if not batched:
grid = grid.unsqueeze(0)
pts = pts.unsqueeze(0)
dim = pts.shape[-1]
bs = grid.shape[0]
size = torch.tensor(grid.shape[1:-1]).to(grid.device).type(pts.dtype)
cubesize = 1.0 / size
ind0 = torch.floor(pts / cubesize).long() # (batch, num_points, dim)
ind1 = torch.fmod(torch.ceil(pts / cubesize), size).long() # periodic wrap-around
ind01 = torch.stack((ind0, ind1), dim=0) # (2, batch, num_points, dim)
tmp = torch.tensor([0,1],dtype=torch.long)
com_ = torch.stack(torch.meshgrid(tuple([tmp] * dim)), dim=-1).view(-1, dim)
dim_ = torch.arange(dim).repeat(com_.shape[0], 1) # (2**dim, dim)
ind_ = ind01[com_, ..., dim_] # (2**dim, dim, batch, num_points)
ind_n = ind_.permute(2, 3, 0, 1) # (batch, num_points, 2**dim, dim)
ind_b = torch.arange(bs).expand(ind_n.shape[1], ind_n.shape[2], bs).permute(2, 0, 1) # (batch, num_points, 2**dim)
# latent code on neighbor nodes
if dim == 2:
lat = grid.clone()[ind_b, ind_n[..., 0], ind_n[..., 1]] # (batch, num_points, 2**dim, in_features)
else:
lat = grid.clone()[ind_b, ind_n[..., 0], ind_n[..., 1], ind_n[..., 2]] # (batch, num_points, 2**dim, in_features)
# weights of neighboring nodes
xyz0 = ind0.type(cubesize.dtype) * cubesize # (batch, num_points, dim)
xyz1 = (ind0.type(cubesize.dtype) + 1) * cubesize # (batch, num_points, dim)
xyz01 = torch.stack((xyz0, xyz1), dim=0) # (2, batch, num_points, dim)
pos = xyz01[com_, ..., dim_].permute(2,3,0,1) # (batch, num_points, 2**dim, dim)
pos_ = xyz01[1-com_, ..., dim_].permute(2,3,0,1) # (batch, num_points, 2**dim, dim)
pos_ = pos_.type(pts.dtype)
dxyz_ = torch.abs(pts.unsqueeze(-2) - pos_) / cubesize # (batch, num_points, 2**dim, dim)
weights = torch.prod(dxyz_, dim=-1, keepdim=False) # (batch, num_points, 2**dim)
query_values = torch.sum(lat * weights.unsqueeze(-1), dim=-2) # (batch, num_points, in_features)
if not batched:
query_values = query_values.squeeze(0)
return query_values
def scatter_to_grid(inds, vals, size):
"""
Scatter update values into empty tensor of size size.
:param inds: (#values, dims)
:param vals: (#values)
:param size: tuple for size. len(size)=dims
"""
dims = inds.shape[1]
assert(inds.shape[0] == vals.shape[0])
assert(len(size) == dims)
dev = vals.device
# result = torch.zeros(*size).view(-1).to(dev).type(vals.dtype) # flatten
# # flatten inds
result = torch.zeros(*size, device=dev).view(-1).type(vals.dtype) # flatten
# flatten inds
fac = [np.prod(size[i+1:]) for i in range(len(size)-1)] + [1]
fac = torch.tensor(fac, device=dev).type(inds.dtype)
inds_fold = torch.sum(inds*fac, dim=-1) # [#values,]
result.scatter_add_(0, inds_fold, vals)
result = result.view(*size)
return result
def point_rasterize(pts, vals, size):
"""
:param pts: point coords, tensor of shape (batch, num_points, dim) within range (0, 1)
:param vals: point values, tensor of shape (batch, num_points, features)
:param size: len(size)=dim tuple for grid size
:return rasterized values (batch, features, res0, res1, res2)
"""
dim = pts.shape[-1]
assert(pts.shape[:2] == vals.shape[:2])
assert(pts.shape[2] == dim)
size_list = list(size)
size = torch.tensor(size).to(pts.device).float()
cubesize = 1.0 / size
bs = pts.shape[0]
nf = vals.shape[-1]
npts = pts.shape[1]
dev = pts.device
ind0 = torch.floor(pts / cubesize).long() # (batch, num_points, dim)
ind1 = torch.fmod(torch.ceil(pts / cubesize), size).long() # periodic wrap-around
ind01 = torch.stack((ind0, ind1), dim=0) # (2, batch, num_points, dim)
tmp = torch.tensor([0,1],dtype=torch.long)
com_ = torch.stack(torch.meshgrid(tuple([tmp] * dim)), dim=-1).view(-1, dim)
dim_ = torch.arange(dim).repeat(com_.shape[0], 1) # (2**dim, dim)
ind_ = ind01[com_, ..., dim_] # (2**dim, dim, batch, num_points)
ind_n = ind_.permute(2, 3, 0, 1) # (batch, num_points, 2**dim, dim)
# ind_b = torch.arange(bs).expand(ind_n.shape[1], ind_n.shape[2], bs).permute(2, 0, 1) # (batch, num_points, 2**dim)
ind_b = torch.arange(bs, device=dev).expand(ind_n.shape[1], ind_n.shape[2], bs).permute(2, 0, 1) # (batch, num_points, 2**dim)
# weights of neighboring nodes
xyz0 = ind0.type(cubesize.dtype) * cubesize # (batch, num_points, dim)
xyz1 = (ind0.type(cubesize.dtype) + 1) * cubesize # (batch, num_points, dim)
xyz01 = torch.stack((xyz0, xyz1), dim=0) # (2, batch, num_points, dim)
pos = xyz01[com_, ..., dim_].permute(2,3,0,1) # (batch, num_points, 2**dim, dim)
pos_ = xyz01[1-com_, ..., dim_].permute(2,3,0,1) # (batch, num_points, 2**dim, dim)
pos_ = pos_.type(pts.dtype)
dxyz_ = torch.abs(pts.unsqueeze(-2) - pos_) / cubesize # (batch, num_points, 2**dim, dim)
weights = torch.prod(dxyz_, dim=-1, keepdim=False) # (batch, num_points, 2**dim)
ind_b = ind_b.unsqueeze(-1).unsqueeze(-1) # (batch, num_points, 2**dim, 1, 1)
ind_n = ind_n.unsqueeze(-2) # (batch, num_points, 2**dim, 1, dim)
ind_f = torch.arange(nf, device=dev).view(1, 1, 1, nf, 1) # (1, 1, 1, nf, 1)
# ind_f = torch.arange(nf).view(1, 1, 1, nf, 1) # (1, 1, 1, nf, 1)
ind_b = ind_b.expand(bs, npts, 2**dim, nf, 1)
ind_n = ind_n.expand(bs, npts, 2**dim, nf, dim).to(dev)
ind_f = ind_f.expand(bs, npts, 2**dim, nf, 1)
inds = torch.cat([ind_b, ind_f, ind_n], dim=-1) # (batch, num_points, 2**dim, nf, 1+1+dim)
# weighted values
vals = weights.unsqueeze(-1) * vals.unsqueeze(-2) # (batch, num_points, 2**dim, nf)
inds = inds.view(-1, dim+2).permute(1, 0).long() # (1+dim+1, bs*npts*2**dim*nf)
vals = vals.reshape(-1) # (bs*npts*2**dim*nf)
tensor_size = [bs, nf] + size_list
raster = scatter_to_grid(inds.permute(1, 0), vals, [bs, nf] + size_list)
return raster # [batch, nf, res, res, res]
##################################################
# Below are the utilization functions in general
class AverageMeter(object):
"""Computes and stores the average and current value"""
def __init__(self):
self.reset()
def reset(self):
self.val = 0
self.n = 0
self.avg = 0
self.sum = 0
self.count = 0
def update(self, val, n=1):
self.val = val
self.n = n
self.sum += val * n
self.count += n
self.avg = self.sum / self.count
@property
def valcavg(self):
return self.val.sum().item() / (self.n != 0).sum().item()
@property
def avgcavg(self):
return self.avg.sum().item() / (self.count != 0).sum().item()
def load_model_manual(state_dict, model):
new_state_dict = OrderedDict()
is_model_parallel = isinstance(model, torch.nn.DataParallel)
for k, v in state_dict.items():
if k.startswith('module.') != is_model_parallel:
if k.startswith('module.'):
# remove module
k = k[7:]
else:
# add module
k = 'module.' + k
new_state_dict[k]=v
model.load_state_dict(new_state_dict)
def mc_from_psr(psr_grid, pytorchify=False, real_scale=False, zero_level=0):
'''
Run marching cubes from PSR grid
'''
batch_size = psr_grid.shape[0]
s = psr_grid.shape[-1] # size of psr_grid
psr_grid_numpy = psr_grid.squeeze().detach().cpu().numpy()
if batch_size>1:
verts, faces, normals = [], [], []
for i in range(batch_size):
verts_cur, faces_cur, normals_cur, values = measure.marching_cubes(psr_grid_numpy[i], level=0)
verts.append(verts_cur)
faces.append(faces_cur)
normals.append(normals_cur)
verts = np.stack(verts, axis = 0)
faces = np.stack(faces, axis = 0)
normals = np.stack(normals, axis = 0)
else:
try:
verts, faces, normals, values = measure.marching_cubes(psr_grid_numpy, level=zero_level)
except:
verts, faces, normals, values = measure.marching_cubes(psr_grid_numpy)
if real_scale:
verts = verts / (s-1) # scale to range [0, 1]
else:
verts = verts / s # scale to range [0, 1)
if pytorchify:
device = psr_grid.device
verts = torch.Tensor(np.ascontiguousarray(verts)).to(device)
faces = torch.Tensor(np.ascontiguousarray(faces)).to(device)
normals = torch.Tensor(np.ascontiguousarray(-normals)).to(device)
return verts, faces, normals
def calc_inters_points(verts, faces, pose, img_size, mask_gt=None):
verts = verts.squeeze()
faces = faces.squeeze()
pix_to_face, w, mask = mesh_rasterization(verts, faces, pose, img_size)
if mask_gt is not None:
#! only evaluate within the intersection
mask = mask & mask_gt
# find 3D points intesected on the mesh
if True:
w_masked = w[mask]
f_p = faces[pix_to_face[mask]].long() # cooresponding faces for each pixel
# corresponding vertices for p_closest
v_a, v_b, v_c = verts[f_p[..., 0]], verts[f_p[..., 1]], verts[f_p[..., 2]]
# calculate the intersection point of each pixel and the mesh
p_inters = w_masked[..., 0, None] * v_a + \
w_masked[..., 1, None] * v_b + \
w_masked[..., 2, None] * v_c
else:
# backproject ndc to world coordinates using z-buffer
W, H = img_size[1], img_size[0]
xy = uv.to(mask.device)[mask]
x_ndc = 1 - (2*xy[:, 0]) / (W - 1)
y_ndc = 1 - (2*xy[:, 1]) / (H - 1)
z = zbuf.squeeze().reshape(H * W)[mask]
xy_depth = torch.stack((x_ndc, y_ndc, z), dim=1)
p_inters = pose.unproject_points(xy_depth, world_coordinates=True)
# if there are outlier points, we should remove it
if (p_inters.max()>1) | (p_inters.min()<-1):
mask_bound = (p_inters>=-1) & (p_inters<=1)
mask_bound = (mask_bound.sum(dim=-1)==3)
mask[mask==True] = mask_bound
p_inters = p_inters[mask_bound]
print('!!!!!find outlier!')
return p_inters, mask, f_p, w_masked
def mesh_rasterization(verts, faces, pose, img_size):
'''
Use PyTorch3D to rasterize the mesh given a camera
'''
transformed_v = pose.transform_points(verts.detach()) # world -> ndc coordinate system
if isinstance(pose, PerspectiveCameras):
transformed_v[..., 2] = 1/transformed_v[..., 2]
# find p_closest on mesh of each pixel via rasterization
transformed_mesh = Meshes(verts=[transformed_v], faces=[faces])
pix_to_face, zbuf, bary_coords, dists = rasterize_meshes(
transformed_mesh,
image_size=img_size,
blur_radius=0,
faces_per_pixel=1,
perspective_correct=False
)
pix_to_face = pix_to_face.reshape(1, -1) # B x reso x reso -> B x (reso x reso)
mask = pix_to_face.clone() != -1
mask = mask.squeeze()
pix_to_face = pix_to_face.squeeze()
w = bary_coords.reshape(-1, 3)
return pix_to_face, w, mask
def verts_on_largest_mesh(verts, faces):
'''
verts: Numpy array or Torch.Tensor (N, 3)
faces: Numpy array (N, 3)
'''
if torch.is_tensor(faces):
verts = verts.squeeze().detach().cpu().numpy()
faces = faces.squeeze().int().detach().cpu().numpy()
A = adjacency_matrix(faces)
num, conn_idx, conn_size = connected_components(A)
if num == 0:
v_large, f_large = verts, faces
else:
max_idx = conn_size.argmax() # find the index of the largest component
v_large = verts[conn_idx==max_idx] # keep points on the largest component
if True:
mesh_largest = trimesh.Trimesh(verts, faces)
connected_comp = mesh_largest.split(only_watertight=False)
mesh_largest = connected_comp[max_idx]
v_large, f_large = mesh_largest.vertices, mesh_largest.faces
v_large = v_large.astype(np.float32)
return v_large, f_large
def load_pointcloud(in_file):
plydata = PlyData.read(in_file)
vertices = np.stack([
plydata['vertex']['x'],
plydata['vertex']['y'],
plydata['vertex']['z']
], axis=1)
return vertices
# General config
def load_config(path, default_path=None):
''' Loads config file.
Args:
path (str): path to config file
default_path (bool): whether to use default path
'''
# Load configuration from file itself
with open(path, 'r') as f:
cfg_special = yaml.load(f, Loader=yaml.Loader)
# Check if we should inherit from a config
inherit_from = cfg_special.get('inherit_from')
# If yes, load this config first as default
# If no, use the default_path
if inherit_from is not None:
cfg = load_config(inherit_from, default_path)
elif default_path is not None:
with open(default_path, 'r') as f:
cfg = yaml.load(f, Loader=yaml.Loader)
else:
cfg = dict()
# Include main configuration
update_recursive(cfg, cfg_special)
return cfg
def update_config(config, unknown):
# update config given args
for idx,arg in enumerate(unknown):
if arg.startswith("--"):
keys = arg.replace("--","").split(':')
assert(len(keys)==2)
k1, k2 = keys
argtype = type(config[k1][k2])
if argtype == bool:
v = unknown[idx+1].lower() == 'true'
else:
if config[k1][k2] is not None:
v = type(config[k1][k2])(unknown[idx+1])
else:
v = unknown[idx+1]
print(f'Changing {k1}:{k2} ---- {config[k1][k2]} to {v}')
config[k1][k2] = v
return config
def initialize_logger(cfg):
out_dir = cfg['train']['out_dir']
if not out_dir:
os.makedirs(out_dir)
cfg['train']['dir_model'] = os.path.join(out_dir, 'model')
os.makedirs(cfg['train']['dir_model'], exist_ok=True)
if cfg['train']['exp_mesh']:
cfg['train']['dir_mesh'] = os.path.join(out_dir, 'vis/mesh')
os.makedirs(cfg['train']['dir_mesh'], exist_ok=True)
if cfg['train']['exp_pcl']:
cfg['train']['dir_pcl'] = os.path.join(out_dir, 'vis/pointcloud')
os.makedirs(cfg['train']['dir_pcl'], exist_ok=True)
if cfg['train']['vis_rendering']:
cfg['train']['dir_rendering'] = os.path.join(out_dir, 'vis/rendering')
os.makedirs(cfg['train']['dir_rendering'], exist_ok=True)
if cfg['train']['o3d_show']:
cfg['train']['dir_o3d'] = os.path.join(out_dir, 'vis/o3d')
os.makedirs(cfg['train']['dir_o3d'], exist_ok=True)
logger = logging.getLogger("train")
logger.setLevel(logging.DEBUG)
logger.handlers = []
# ch = logging.StreamHandler()
# logger.addHandler(ch)
fh = logging.FileHandler(os.path.join(cfg['train']['out_dir'], "log.txt"))
logger.addHandler(fh)
logger.info('Outout dir: %s', out_dir)
return logger
def update_recursive(dict1, dict2):
''' Update two config dictionaries recursively.
Args:
dict1 (dict): first dictionary to be updated
dict2 (dict): second dictionary which entries should be used
'''
for k, v in dict2.items():
if k not in dict1:
dict1[k] = dict()
if isinstance(v, dict):
update_recursive(dict1[k], v)
else:
dict1[k] = v
def export_pointcloud(name, points, normals=None):
if len(points.shape) > 2:
points = points[0]
if normals is not None:
normals = normals[0]
if isinstance(points, torch.Tensor):
points = points.detach().cpu().numpy()
if normals is not None:
normals = normals.detach().cpu().numpy()
pcd = o3d.geometry.PointCloud()
pcd.points = o3d.utility.Vector3dVector(points)
if normals is not None:
pcd.normals = o3d.utility.Vector3dVector(normals)
o3d.io.write_point_cloud(name, pcd)
def export_mesh(name, v, f):
if len(v.shape) > 2:
v, f = v[0], f[0]
if isinstance(v, torch.Tensor):
v = v.detach().cpu().numpy()
f = f.detach().cpu().numpy()
mesh = o3d.geometry.TriangleMesh()
mesh.vertices = o3d.utility.Vector3dVector(v)
mesh.triangles = o3d.utility.Vector3iVector(f)
o3d.io.write_triangle_mesh(name, mesh)
def scale2onet(p, scale=1.2):
'''
Scale the point cloud from SAP to ONet range
'''
return (p - 0.5) * scale
def update_optimizer(inputs, cfg, epoch, model=None, schedule=None):
if model is not None:
if schedule is not None:
optimizer = torch.optim.Adam([
{"params": model.parameters(),
"lr": schedule[0].get_learning_rate(epoch)},
{"params": inputs,
"lr": schedule[1].get_learning_rate(epoch)}])
elif 'lr' in cfg['train']:
optimizer = torch.optim.Adam([
{"params": model.parameters(),
"lr": float(cfg['train']['lr'])},
{"params": inputs,
"lr": float(cfg['train']['lr_pcl'])}])
else:
raise Exception('no known learning rate')
else:
if schedule is not None:
optimizer = torch.optim.Adam([inputs], lr=schedule[0].get_learning_rate(epoch))
else:
optimizer = torch.optim.Adam([inputs], lr=float(cfg['train']['lr_pcl']))
return optimizer
def is_url(url):
scheme = urllib.parse.urlparse(url).scheme
return scheme in ('http', 'https')
def load_url(url):
'''Load a module dictionary from url.
Args:
url (str): url to saved model
'''
print(url)
print('=> Loading checkpoint from url...')
state_dict = model_zoo.load_url(url, progress=True)
return state_dict
class GaussianSmoothing(nn.Module):
"""
Apply gaussian smoothing on a
1d, 2d or 3d tensor. Filtering is performed seperately for each channel
in the input using a depthwise convolution.
Arguments:
channels (int, sequence): Number of channels of the input tensors. Output will have this number of channels as well.
kernel_size (int, sequence): Size of the gaussian kernel.
sigma (float, sequence): Standard deviation of the gaussian kernel.
dim (int, optional): The number of dimensions of the data.
Default value is 2 (spatial).
"""
def __init__(self, channels, kernel_size, sigma, dim=3):
super(GaussianSmoothing, self).__init__()
if isinstance(kernel_size, numbers.Number):
kernel_size = [kernel_size] * dim
if isinstance(sigma, numbers.Number):
sigma = [sigma] * dim
# The gaussian kernel is the product of the
# gaussian function of each dimension.
kernel = 1
meshgrids = torch.meshgrid(
[
torch.arange(size, dtype=torch.float32)
for size in kernel_size
]
)
for size, std, mgrid in zip(kernel_size, sigma, meshgrids):
mean = (size - 1) / 2
kernel *= 1 / (std * math.sqrt(2 * math.pi)) * \
torch.exp(-((mgrid - mean) / std) ** 2 / 2)
# Make sure sum of values in gaussian kernel equals 1.
kernel = kernel / torch.sum(kernel)
# Reshape to depthwise convolutional weight
kernel = kernel.view(1, 1, *kernel.size())
kernel = kernel.repeat(channels, *[1] * (kernel.dim() - 1))
self.register_buffer('weight', kernel)
self.groups = channels
if dim == 1:
self.conv = F.conv1d
elif dim == 2:
self.conv = F.conv2d
elif dim == 3:
self.conv = F.conv3d
else:
raise RuntimeError(
'Only 1, 2 and 3 dimensions are supported. Received {}.'.format(dim)
)
def forward(self, input):
"""
Apply gaussian filter to input.
Arguments:
input (torch.Tensor): Input to apply gaussian filter on.
Returns:
filtered (torch.Tensor): Filtered output.
"""
return self.conv(input, weight=self.weight, groups=self.groups)
# Originally from https://github.com/amosgropp/IGR/blob/0db06b1273/code/utils/general.py
def get_learning_rate_schedules(schedule_specs):
schedules = []
for key in schedule_specs.keys():
schedules.append(StepLearningRateSchedule(
schedule_specs[key]['initial'],
schedule_specs[key]["interval"],
schedule_specs[key]["factor"],
schedule_specs[key]["final"]))
return schedules
class LearningRateSchedule:
def get_learning_rate(self, epoch):
pass
class StepLearningRateSchedule(LearningRateSchedule):
def __init__(self, initial, interval, factor, final=1e-6):
self.initial = float(initial)
self.interval = interval
self.factor = factor
self.final = float(final)
def get_learning_rate(self, epoch):
lr = np.maximum(self.initial * (self.factor ** (epoch // self.interval)), 5.0e-6)
if lr > self.final:
return lr
else:
return self.final
def adjust_learning_rate(lr_schedules, optimizer, epoch):
for i, param_group in enumerate(optimizer.param_groups):
param_group["lr"] = lr_schedules[i].get_learning_rate(epoch)