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single_file_presto.py
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import math
from collections import OrderedDict
from copy import deepcopy
from typing import Optional, Tuple, Union, cast
import numpy as np
import torch
from einops import repeat
from torch import nn
from torch.jit import Final
from torch.nn import functional as F
BANDS_GROUPS_IDX = OrderedDict(
[
("S1", [0, 1]),
("S2_RGB", [2, 3, 4]),
("S2_Red_Edge", [5, 6, 7]),
("S2_NIR_10m", [8]),
("S2_NIR_20m", [9]),
("S2_SWIR", [10, 11]),
("ERA5", [12, 13]),
("SRTM", [14, 15]),
("NDVI", [16]),
]
)
NUM_DYNAMIC_WORLD_CLASSES = 9
class Attention(nn.Module):
# https://github.com/huggingface/pytorch-image-models/blob/main/timm/models/vision_transformer.py
fast_attn: Final[bool]
def __init__(
self,
dim,
num_heads=8,
qkv_bias=False,
qk_norm=False,
attn_drop=0.0,
proj_drop=0.0,
norm_layer=nn.LayerNorm,
):
super().__init__()
assert dim % num_heads == 0, "dim should be divisible by num_heads"
self.num_heads = num_heads
self.head_dim = dim // num_heads
self.scale = self.head_dim**-0.5
self.fast_attn = hasattr(torch.nn.functional, "scaled_dot_product_attention") # FIXME
self.qkv = nn.Linear(dim, dim * 3, bias=qkv_bias)
self.q_norm = norm_layer(self.head_dim) if qk_norm else nn.Identity()
self.k_norm = norm_layer(self.head_dim) if qk_norm else nn.Identity()
self.attn_drop = nn.Dropout(attn_drop)
self.proj = nn.Linear(dim, dim)
self.proj_drop = nn.Dropout(proj_drop)
def forward(self, x):
B, N, C = x.shape
qkv = self.qkv(x).reshape(B, N, 3, self.num_heads, self.head_dim).permute(2, 0, 3, 1, 4)
q, k, v = qkv.unbind(0)
q, k = self.q_norm(q), self.k_norm(k)
if self.fast_attn:
x = F.scaled_dot_product_attention(
q,
k,
v,
dropout_p=self.attn_drop.p,
)
else:
q = q * self.scale
attn = q @ k.transpose(-2, -1)
attn = attn.softmax(dim=-1)
attn = self.attn_drop(attn)
x = attn @ v
x = x.transpose(1, 2).reshape(B, N, C)
x = self.proj(x)
x = self.proj_drop(x)
return x
class Mlp(nn.Module):
"""MLP as used in Vision Transformer, MLP-Mixer and related networks"""
def __init__(
self,
in_features,
hidden_features=None,
out_features=None,
act_layer=nn.GELU,
bias=True,
drop=0.0,
):
super().__init__()
out_features = out_features or in_features
hidden_features = hidden_features or in_features
self.fc1 = nn.Linear(in_features, hidden_features, bias=bias)
self.act = act_layer()
self.drop1 = nn.Dropout(drop)
self.fc2 = nn.Linear(hidden_features, out_features, bias=bias)
self.drop2 = nn.Dropout(drop)
def forward(self, x):
x = self.fc1(x)
x = self.act(x)
x = self.drop1(x)
x = self.fc2(x)
x = self.drop2(x)
return x
class LayerScale(nn.Module):
def __init__(self, dim, init_values=1e-5, inplace=False):
super().__init__()
self.inplace = inplace
self.gamma = nn.Parameter(init_values * torch.ones(dim))
def forward(self, x):
return x.mul_(self.gamma) if self.inplace else x * self.gamma
class Block(nn.Module):
def __init__(
self,
dim,
num_heads,
mlp_ratio=4.0,
qkv_bias=False,
qk_norm=False,
drop=0.0,
attn_drop=0.0,
init_values=None,
act_layer=nn.GELU,
norm_layer=nn.LayerNorm,
):
super().__init__()
self.norm1 = norm_layer(dim)
self.attn = Attention(
dim,
num_heads=num_heads,
qkv_bias=qkv_bias,
qk_norm=qk_norm,
attn_drop=attn_drop,
proj_drop=drop,
norm_layer=norm_layer,
)
self.ls1 = LayerScale(dim, init_values=init_values) if init_values else nn.Identity()
self.norm2 = norm_layer(dim)
self.mlp = Mlp(
in_features=dim,
hidden_features=int(dim * mlp_ratio),
act_layer=act_layer,
drop=drop,
)
self.ls2 = LayerScale(dim, init_values=init_values) if init_values else nn.Identity()
def forward(self, x):
x = x + self.ls1(self.attn(self.norm1(x)))
x = x + self.ls2(self.mlp(self.norm2(x)))
return x
def get_sinusoid_encoding_table(positions, d_hid, T=1000):
"""Sinusoid position encoding table
positions: int or list of integer, if int range(positions)"""
if isinstance(positions, int):
positions = list(range(positions))
def cal_angle(position, hid_idx):
return position / np.power(T, 2 * (hid_idx // 2) / d_hid)
def get_posi_angle_vec(position):
return [cal_angle(position, hid_j) for hid_j in range(d_hid)]
sinusoid_table = np.array([get_posi_angle_vec(pos_i) for pos_i in positions])
sinusoid_table[:, 0::2] = np.sin(sinusoid_table[:, 0::2]) # dim 2i
sinusoid_table[:, 1::2] = np.cos(sinusoid_table[:, 1::2]) # dim 2i+1
if torch.cuda.is_available():
return torch.FloatTensor(sinusoid_table).cuda()
else:
return torch.FloatTensor(sinusoid_table)
def get_month_encoding_table(d_hid):
"""Sinusoid month encoding table, for 12 months indexed from 0-11"""
assert d_hid % 2 == 0
angles = np.arange(0, 13) / (12 / (2 * np.pi))
sin_table = np.sin(np.stack([angles for _ in range(d_hid // 2)], axis=-1))
cos_table = np.cos(np.stack([angles for _ in range(d_hid // 2)], axis=-1))
month_table = np.concatenate([sin_table[:-1], cos_table[:-1]], axis=-1)
if torch.cuda.is_available():
return torch.FloatTensor(month_table).cuda()
else:
return torch.FloatTensor(month_table)
def month_to_tensor(
month: Union[torch.Tensor, int], batch_size: int, seq_len: int, device: torch.device
):
if isinstance(month, int):
assert cast(int, month) < 12
else:
assert max(cast(torch.Tensor, month.flatten())) < 12
if isinstance(month, int):
# >>> torch.fmod(torch.tensor([9., 10, 11, 12, 13, 14]), 12)
# tensor([ 9., 10., 11., 0., 1., 2.])
month = (
torch.fmod(torch.arange(month, month + seq_len, dtype=torch.long), 12)
.expand(batch_size, seq_len)
.to(device)
)
elif len(month.shape) == 1:
month = torch.stack(
[torch.fmod(torch.arange(m, m + seq_len, dtype=torch.long), 12) for m in month]
).to(device)
return month
class Encoder(nn.Module):
def __init__(
self,
embedding_size: int = 128,
channel_embed_ratio: float = 0.25,
month_embed_ratio: float = 0.25,
depth=2,
mlp_ratio=2,
num_heads=8,
max_sequence_length=24,
):
super().__init__()
self.band_groups = BANDS_GROUPS_IDX
self.embedding_size = embedding_size
# this is used for the channel embedding
self.band_group_to_idx = {
group_name: idx for idx, (group_name, _) in enumerate(self.band_groups.items())
}
self.band_group_to_idx["dynamic_world"] = max(self.band_group_to_idx.values()) + 1
self.eo_patch_embed = nn.ModuleDict(
{
group_name: nn.Linear(len(group), embedding_size)
for group_name, group in self.band_groups.items()
}
)
self.dw_embed = nn.Embedding(
num_embeddings=NUM_DYNAMIC_WORLD_CLASSES + 1, embedding_dim=embedding_size
)
self.latlon_embed = nn.Linear(3, embedding_size)
self.blocks = nn.ModuleList(
[
Block(
embedding_size,
num_heads,
mlp_ratio,
qkv_bias=True,
norm_layer=nn.LayerNorm,
)
for _ in range(depth)
]
)
self.norm = nn.LayerNorm(embedding_size)
# the positional + monthly + channel embedding
self.max_sequence_length = max_sequence_length
pos_embedding_size = int(embedding_size * (1 - (channel_embed_ratio + month_embed_ratio)))
channel_embedding_size = int(embedding_size * channel_embed_ratio)
month_embedding_size = int(embedding_size * month_embed_ratio)
self.pos_embed = nn.Parameter(
torch.zeros(1, max_sequence_length, pos_embedding_size), requires_grad=False
)
month_tab = get_month_encoding_table(month_embedding_size)
self.month_embed = nn.Embedding.from_pretrained(month_tab, freeze=True)
self.channel_embed = nn.Embedding(
num_embeddings=len(self.band_groups) + 1, embedding_dim=channel_embedding_size
)
self.initialize_weights()
def initialize_weights(self):
pos_embed = get_sinusoid_encoding_table(self.pos_embed.shape[1], self.pos_embed.shape[-1])
self.pos_embed.data.copy_(pos_embed)
# initialize nn.Linear and nn.LayerNorm
self.apply(self._init_weights)
def _init_weights(self, m):
if isinstance(m, nn.Linear):
# we use xavier_uniform following official JAX ViT:
torch.nn.init.xavier_uniform_(m.weight)
if isinstance(m, nn.Linear) and m.bias is not None:
nn.init.constant_(m.bias, 0)
elif isinstance(m, nn.LayerNorm):
nn.init.constant_(m.bias, 0)
nn.init.constant_(m.weight, 1.0)
@staticmethod
def cartesian(latlons: torch.Tensor) -> torch.Tensor:
with torch.no_grad():
# an embedding is calculated for all timesteps. This is then expanded
# for each timestep in the sequence
latlon_radians = latlons * math.pi / 180
lats, lons = latlon_radians[:, 0], latlon_radians[:, 1]
x = torch.cos(lats) * torch.cos(lons)
y = torch.cos(lats) * torch.sin(lons)
z = torch.sin(lats)
return torch.stack([x, y, z], dim=-1)
@staticmethod
def mask_tokens(x, mask):
summed = mask.sum(
dim=(1, 2)
) # summed tells me the number of masked elements per batch idx
assert summed.max() == summed.min(), f"{summed.max()}, {summed.min()}"
batch_size = x.shape[0]
removed_elements_per_batch = int(summed.max() / mask.shape[2])
kept_elements_per_batch = x.shape[1] - removed_elements_per_batch
embedding_dim = x.shape[-1]
# we want the mask to just be the indices of the masked tokens
indices = repeat(torch.arange(0, x.shape[1]).long().to(x.device), "d -> b d", b=x.shape[0])
x = x[~mask.bool()].view(batch_size, kept_elements_per_batch, embedding_dim)
mask = mask[:, :, 0]
kept_indices = indices[~mask.bool()].view(batch_size, kept_elements_per_batch)
removed_indices = indices[mask.bool()].view(batch_size, removed_elements_per_batch)
return x, kept_indices, removed_indices
def forward(
self,
x: torch.Tensor,
dynamic_world: torch.Tensor,
latlons: torch.Tensor,
mask: Optional[torch.Tensor] = None,
month: Union[torch.Tensor, int] = 0,
eval_task: bool = True,
):
device = x.device
if mask is None:
mask = torch.zeros_like(x, device=x.device).float()
months = month_to_tensor(month, x.shape[0], x.shape[1], device)
month_embedding = self.month_embed(months)
positional_embedding = repeat(
self.pos_embed[:, : x.shape[1], :], "b t d -> (repeat b) t d", repeat=x.shape[0]
)
# we assume the number of masked patches is the same
# for all items in the batch. Otherwise things become a headache
all_tokens, all_masks = [], []
for channel_group, channel_idxs in self.band_groups.items():
tokens = self.eo_patch_embed[channel_group](x[:, :, channel_idxs])
channel_embedding = self.channel_embed(
torch.tensor(self.band_group_to_idx[channel_group]).long().to(device)
)
channel_embedding = repeat(channel_embedding, "d -> b t d", b=x.shape[0], t=x.shape[1])
if channel_group == "SRTM":
# for SRTM, we reduce it to a single token instead of
# a token per timestep
channel_wise_positional_embedding = torch.cat(
(
torch.zeros_like(month_embedding[:, 0:1]),
channel_embedding[:, 0:1],
torch.zeros_like(positional_embedding[:, 0:1]),
),
dim=-1,
)
indices = slice(0, 1)
else:
channel_wise_positional_embedding = torch.cat(
(month_embedding, channel_embedding, positional_embedding), dim=-1
)
indices = slice(None)
tokens = tokens[:, indices]
tokens += channel_wise_positional_embedding
all_tokens.append(tokens)
group_mask = repeat(
torch.max(mask[:, indices, channel_idxs], dim=-1)[0],
"b t -> b t d",
d=tokens.shape[-1],
)
all_masks.append(group_mask)
# then, dynamic world
tokens = self.dw_embed(dynamic_world)
channel_embedding = self.channel_embed(
torch.tensor(self.band_group_to_idx["dynamic_world"]).long().to(device)
)
channel_embedding = repeat(channel_embedding, "d -> b t d", b=x.shape[0], t=x.shape[1])
positional_embedding = torch.cat(
(month_embedding, channel_embedding, positional_embedding), dim=-1
)
tokens += positional_embedding
all_tokens.append(tokens)
# now we calculate the mask for these [b, t] tokens
group_mask = repeat(
dynamic_world == NUM_DYNAMIC_WORLD_CLASSES, "b t -> b t d", d=tokens.shape[-1]
)
all_masks.append(group_mask)
x = torch.cat(all_tokens, dim=1) # [batch, timesteps, embedding_dim]
mask = torch.cat(all_masks, dim=1) # [batch, timesteps, embedding_dim]
x, kept_indices, removed_indices = self.mask_tokens(x, mask)
# append latlon tokens
latlon_tokens = self.latlon_embed(self.cartesian(latlons)).unsqueeze(1)
x = torch.cat((latlon_tokens, x), dim=1)
# apply Transformer blocks
for blk in self.blocks:
x = blk(x)
# mask will be a boolean of shape [batch, total_num_tokens]
if eval_task:
return self.norm(x.mean(dim=1))
return self.norm(x), kept_indices, removed_indices
class Decoder(nn.Module):
def __init__(
self,
channel_embeddings: nn.Embedding,
encoder_embed_dim=128,
decoder_embed_dim=128,
decoder_depth=2,
decoder_num_heads=8,
mlp_ratio=2,
max_sequence_length=24,
):
super().__init__()
self.band_groups = BANDS_GROUPS_IDX
# this is used for the channel embedding
self.band_group_to_idx = {
group_name: idx for idx, (group_name, _) in enumerate(self.band_groups.items())
}
self.band_group_to_idx["dynamic_world"] = max(self.band_group_to_idx.values()) + 1
self.decoder_embed = nn.Linear(encoder_embed_dim, decoder_embed_dim, bias=True)
self.mask_token = nn.Parameter(torch.zeros(decoder_embed_dim))
self.decoder_blocks = nn.ModuleList(
[
Block(
decoder_embed_dim,
decoder_num_heads,
mlp_ratio,
qkv_bias=True,
norm_layer=nn.LayerNorm,
)
for _ in range(decoder_depth)
]
)
self.decoder_norm = nn.LayerNorm(decoder_embed_dim)
self.eo_decoder_pred = nn.ModuleDict(
{
group_name: nn.Linear(decoder_embed_dim, len(group))
for group_name, group in self.band_groups.items()
}
)
self.dw_decoder_pred = nn.Linear(decoder_embed_dim, NUM_DYNAMIC_WORLD_CLASSES)
self.channel_embeddings = channel_embeddings
channel_embedding_dims = channel_embeddings.weight.shape[-1]
remaining_embeddings = decoder_embed_dim - channel_embedding_dims
# the positional + monthly + channel embedding
self.max_sequence_length = max_sequence_length
self.pos_embed = nn.Parameter(
torch.zeros(1, max_sequence_length, int(remaining_embeddings) // 2),
requires_grad=False,
)
month_tab = get_month_encoding_table(int(remaining_embeddings) // 2)
self.month_embed = nn.Embedding.from_pretrained(month_tab, freeze=True)
self.initialize_weights()
def initialize_weights(self):
pos_embed = get_sinusoid_encoding_table(self.pos_embed.shape[1], self.pos_embed.shape[-1])
self.pos_embed.data.copy_(pos_embed)
# initialize nn.Linear and nn.LayerNorm
self.apply(self._init_weights)
def _init_weights(self, m):
if isinstance(m, nn.Linear):
# we use xavier_uniform following official JAX ViT:
torch.nn.init.xavier_uniform_(m.weight)
if isinstance(m, nn.Linear) and m.bias is not None:
nn.init.constant_(m.bias, 0)
elif isinstance(m, nn.LayerNorm):
nn.init.constant_(m.bias, 0)
nn.init.constant_(m.weight, 1.0)
def add_masked_tokens(self, x, kept_indices, removed_indices):
mask_tokens = repeat(
self.mask_token, "d -> b t d", b=x.shape[0], t=removed_indices.shape[1]
)
x = torch.cat([x, mask_tokens], dim=1)
# sort according to their indices. Shape is [batch, index]
combined_indices = torch.cat([kept_indices, removed_indices], dim=1) + 1
# 0 for latlon index
combined_indices = torch.sort(
torch.cat([torch.zeros_like(combined_indices[:, 0:1]), combined_indices], dim=1)
)[1]
# and then tile for each dimension
combined_indices = repeat(combined_indices, "b t -> b t d", d=x.shape[-1])
x = torch.gather(x, 1, combined_indices)
return x
def add_embeddings(self, x, month: Union[torch.Tensor, int]):
num_channel_groups = len(self.band_group_to_idx)
# -2 since we remove srtm and latlon, and -1 since the srtm
# channel group doesn't have timesteps
num_timesteps = int((x.shape[1] - 2) / (num_channel_groups - 1))
srtm_index = self.band_group_to_idx["SRTM"] * num_timesteps
months = month_to_tensor(month, x.shape[0], num_timesteps, x.device)
# when we expand the encodings, each channel_group gets num_timesteps
# encodings. However, there is only one SRTM token so we remove the
# excess SRTM encodings
remove_mask = torch.full(size=(num_timesteps * num_channel_groups,), fill_value=False)
remove_mask[torch.arange(num_timesteps - 1) + srtm_index] = True
month_embedding = repeat(
self.month_embed(months), "b t d -> b (repeat t) d", repeat=num_channel_groups
)
month_embedding = month_embedding[:, ~remove_mask]
month_embedding[:, srtm_index] = 0
positional_embedding = repeat(
self.pos_embed[:, :num_timesteps, :],
"b t d -> (b2 b) (t2 t) d",
b2=x.shape[0],
t2=num_channel_groups,
)
positional_embedding = positional_embedding[:, ~remove_mask]
positional_embedding[:, srtm_index] = 0
channel_embeddings = torch.repeat_interleave(
self.channel_embeddings.weight, repeats=num_timesteps, dim=0
)
channel_embeddings = repeat(channel_embeddings, "c d -> b c d", b=x.shape[0])
channel_embeddings = channel_embeddings[:, ~remove_mask]
positional_embedding = torch.cat(
(month_embedding, channel_embeddings, positional_embedding), dim=-1
)
# add the zero embedding for the latlon token
positional_embedding = torch.cat(
[torch.zeros_like(positional_embedding[:, 0:1, :]), positional_embedding], dim=1
)
x += positional_embedding
return x
def reconstruct_inputs(self, x) -> Tuple[torch.Tensor, torch.Tensor]:
# remove the latlon token
x = x[:, 1:, :]
# split into channel groups
num_channel_groups = len(self.band_group_to_idx) - 1
num_timesteps = int((x.shape[1] - 1) / num_channel_groups)
srtm_index = self.band_group_to_idx["SRTM"] * num_timesteps
srtm_token = x[:, srtm_index : srtm_index + 1, :]
mask = torch.full((x.shape[1],), True, device=x.device)
mask[torch.tensor(srtm_index)] = False
x = x[:, mask]
x = x.view(x.shape[0], num_channel_groups, num_timesteps, x.shape[-1])
eo_output, dw_output = [], None
for group_name, idx in self.band_group_to_idx.items():
if group_name == "SRTM":
eo_output.append(
repeat(
self.eo_decoder_pred[group_name](srtm_token),
"b t d -> b (t2 t) d",
t2=num_timesteps,
)
)
else:
if idx > self.band_group_to_idx["SRTM"]:
idx -= 1
group_tokens = x[:, idx]
if group_name == "dynamic_world":
dw_output = self.dw_decoder_pred(group_tokens)
else:
eo_output.append(self.eo_decoder_pred[group_name](group_tokens))
# we can just do this concatenation because the BANDS_GROUP_IDX
# is ordered
return torch.cat(eo_output, dim=-1), cast(torch.Tensor, dw_output)
def forward(self, x, kept_indices, removed_indices, month):
x = self.decoder_embed(x)
x = self.add_masked_tokens(x, kept_indices, removed_indices)
x = self.add_embeddings(x, month)
# apply Transformer blocks
for blk in self.decoder_blocks:
x = blk(x)
x = self.decoder_norm(x)
return self.reconstruct_inputs(x)
class PrestoFineTuningModel(nn.Module):
def __init__(self, encoder, head):
super().__init__()
self.encoder: Encoder = deepcopy(encoder)
# make sure the model is trainable, since we can call
# this having called requires_grad_(False)
self.encoder.requires_grad_(True)
# but don't unfreeze the position encoder, which
# shouldn't be trainable
self.encoder.pos_embed.requires_grad_(False)
self.encoder.month_embed.requires_grad_(False)
self.head = head
def forward(
self,
x: torch.Tensor,
dynamic_world: torch.Tensor,
latlons: torch.Tensor,
mask: Optional[torch.Tensor] = None,
month: Union[torch.Tensor, int] = 0,
) -> torch.Tensor:
return self.head(
self.encoder(
x=x,
dynamic_world=dynamic_world,
latlons=latlons,
mask=mask,
month=month,
eval_task=True,
)
)
class FinetuningHead(nn.Module):
def __init__(self, hidden_size: int, num_outputs: int, regression: bool) -> None:
super().__init__()
self.hidden_size = hidden_size
self.num_outputs = num_outputs
self.regression = regression
self.linear = nn.Linear(hidden_size, num_outputs)
def forward(self, x: torch.Tensor):
x = self.linear(x)
if (not self.regression) & (self.num_outputs == 1):
x = torch.sigmoid(x)
return x
class Presto(nn.Module):
def __init__(self, encoder, decoder):
super().__init__()
self.encoder: Encoder = encoder
self.decoder: Decoder = decoder
def forward(
self,
x: torch.Tensor,
dynamic_world: torch.Tensor,
latlons: torch.Tensor,
mask: Optional[torch.Tensor] = None,
month: Union[torch.Tensor, int] = 0,
) -> torch.Tensor:
x, kept_indices, removed_indices = self.encoder(
x=x,
dynamic_world=dynamic_world,
latlons=latlons,
mask=mask,
month=month,
eval_task=False,
)
return self.decoder(x, kept_indices, removed_indices, month)
@classmethod
def construct(
cls,
encoder_embedding_size: int = 128,
channel_embed_ratio: float = 0.25,
month_embed_ratio: float = 0.25,
encoder_depth=2,
mlp_ratio=4,
encoder_num_heads=8,
decoder_embedding_size=128,
decoder_depth=2,
decoder_num_heads=8,
max_sequence_length=24,
):
encoder = Encoder(
embedding_size=encoder_embedding_size,
channel_embed_ratio=channel_embed_ratio,
month_embed_ratio=month_embed_ratio,
depth=encoder_depth,
mlp_ratio=mlp_ratio,
num_heads=encoder_num_heads,
max_sequence_length=max_sequence_length,
)
decoder = Decoder(
channel_embeddings=encoder.channel_embed,
encoder_embed_dim=encoder_embedding_size,
decoder_embed_dim=decoder_embedding_size,
decoder_depth=decoder_depth,
decoder_num_heads=decoder_num_heads,
mlp_ratio=mlp_ratio,
max_sequence_length=max_sequence_length,
)
return cls(encoder, decoder)
def construct_finetuning_model(
self,
num_outputs: int,
regression: bool = False,
):
head = FinetuningHead(
num_outputs=num_outputs,
hidden_size=self.encoder.embedding_size,
regression=regression,
)
model = PrestoFineTuningModel(self.encoder, head).to(self.encoder.pos_embed.device)
model.train()
return model