VQA-in-Medical-Imagery / Transformers_for_Caption.py
BigData-AI @ KSU
actual bigmed model uploaded needs sample fixing
ffb81ab
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
import copy
from typing import Optional, List
import torch
import torch.nn.functional as F
from torch import nn, Tensor
class Transformer_Caption(nn.Module):
def __init__(self, config,d_model=512, nhead=4, num_encoder_layers=1,
num_decoder_layers=2, dim_feedforward=1024, dropout=0.1,
activation="gelu", normalize_before=False,
return_intermediate_dec=False):
super().__init__()
encoder_layer = TransformerEncoderLayer(d_model, nhead, dim_feedforward,
dropout, activation, normalize_before)
encoder_norm = nn.LayerNorm(d_model) if normalize_before else None
self.encoder = TransformerEncoder(
encoder_layer, num_encoder_layers, encoder_norm)
self.embeddings = DecoderEmbeddings(config)
decoder_layer = TransformerDecoderLayer(d_model, nhead, dim_feedforward,
dropout, activation, normalize_before)
decoder_norm = nn.LayerNorm(d_model)
self.decoder = TransformerDecoder(decoder_layer, num_decoder_layers, decoder_norm,
return_intermediate=return_intermediate_dec)
print("Num decoders:")
print(num_decoder_layers)
self._reset_parameters()
self.d_model = d_model
self.nhead = nhead
def _reset_parameters(self):
for p in self.parameters():
if p.dim() > 1:
nn.init.xavier_uniform_(p)
def forward(self, src, tgt, tgt_mask):
# flatten NxCxHxW to HWxNxC
#print("HERRRRRR")
#print(src.shape)
h, bs, w = src.shape
#src = src.permute(1, 0, 2)
#print("SRCCCCCCCC")
#print(src.shape)
#pos_embed = pos_embed.flatten(2).permute(2, 0, 1)
#mask = mask.flatten(1)
#print(num_decoder_layers)
tgt = self.embeddings(tgt).permute(1, 0, 2)
query_embed = self.embeddings.position_embeddings.weight.unsqueeze(1)
query_embed = query_embed.repeat(1, bs, 1)
#print("firstmyyyyyyyyyyyyyy")
#print(tgt.shape)
#print(tgt_mask.shape)
#print(pos_embed.shape)
#print(query_embed.shape)
#print(generate_square_subsequent_mask(len(tgt)).to(tgt.device).shape)
#print(src.shape)
#memory = self.encoder(src, src_key_padding_mask=None, pos=None)
#memory = self.encoder(src)
#print("then....")
#print(tgt_mask.shape)
hs = self.decoder(tgt, src, memory_key_padding_mask=None, tgt_key_padding_mask=tgt_mask,
pos=None, query_pos=query_embed,
tgt_mask=generate_square_subsequent_mask(len(tgt)).to(tgt.device))
#hs = self.decoder(tgt, memory, tgt_key_padding_mask=tgt_mask,query_pos=query_embed,tgt_mask=generate_square_subsequent_mask(len(tgt)).to(tgt.device))
return hs
class TransformerEncoder(nn.Module):
def __init__(self, encoder_layer, num_layers, norm=None):
super().__init__()
self.layers = _get_clones(encoder_layer, num_layers)
self.num_layers = num_layers
self.norm = norm
def forward(self, src,
mask: Optional[Tensor] = None,
src_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None):
output = src
for layer in self.layers:
output = layer(output, src_mask=mask,
src_key_padding_mask=src_key_padding_mask, pos=pos)
if self.norm is not None:
output = self.norm(output)
return output
class TransformerDecoder(nn.Module):
def __init__(self, decoder_layer, num_layers, norm=None, return_intermediate=False):
super().__init__()
self.layers = _get_clones(decoder_layer, num_layers)
self.num_layers = num_layers
self.norm = norm
self.return_intermediate = return_intermediate
def forward(self, tgt, memory,
tgt_mask: Optional[Tensor] = None,
memory_mask: Optional[Tensor] = None,
tgt_key_padding_mask: Optional[Tensor] = None,
memory_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None,
query_pos: Optional[Tensor] = None):
output = tgt
intermediate = []
for layer in self.layers:
output = layer(output, memory, tgt_mask=tgt_mask,
memory_mask=memory_mask,
tgt_key_padding_mask=tgt_key_padding_mask,
memory_key_padding_mask=memory_key_padding_mask,
pos=pos, query_pos=query_pos)
if self.return_intermediate:
intermediate.append(self.norm(output))
if self.norm is not None:
output = self.norm(output)
if self.return_intermediate:
intermediate.pop()
intermediate.append(output)
if self.return_intermediate:
return torch.stack(intermediate)
return output
class TransformerEncoderLayer(nn.Module):
def __init__(self, d_model, nhead, dim_feedforward=2048, dropout=0.1,
activation="relu", normalize_before=False):
super().__init__()
self.self_attn = nn.MultiheadAttention(d_model, nhead, dropout=dropout)
# Implementation of Feedforward model
self.linear1 = nn.Linear(d_model, dim_feedforward)
self.dropout = nn.Dropout(dropout)
self.linear2 = nn.Linear(dim_feedforward, d_model)
self.norm1 = nn.LayerNorm(d_model)
self.norm2 = nn.LayerNorm(d_model)
self.dropout1 = nn.Dropout(dropout)
self.dropout2 = nn.Dropout(dropout)
self.activation = _get_activation_fn(activation)
self.normalize_before = normalize_before
def with_pos_embed(self, tensor, pos: Optional[Tensor]):
return tensor if pos is None else tensor + pos
def forward_post(self,
src,
src_mask: Optional[Tensor] = None,
src_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None):
q = k = self.with_pos_embed(src, pos)
src2 = self.self_attn(q, k, value=src, attn_mask=src_mask,
key_padding_mask=src_key_padding_mask)[0]
src = src + self.dropout1(src2)
src = self.norm1(src)
src2 = self.linear2(self.dropout(self.activation(self.linear1(src))))
src = src + self.dropout2(src2)
src = self.norm2(src)
return src
def forward_pre(self, src,
src_mask: Optional[Tensor] = None,
src_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None):
src2 = self.norm1(src)
q = k = self.with_pos_embed(src2, pos)
src2 = self.self_attn(q, k, value=src2, attn_mask=src_mask,
key_padding_mask=src_key_padding_mask)[0]
src = src + self.dropout1(src2)
src2 = self.norm2(src)
src2 = self.linear2(self.dropout(self.activation(self.linear1(src2))))
src = src + self.dropout2(src2)
return src
def forward(self, src,
src_mask: Optional[Tensor] = None,
src_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None):
if self.normalize_before:
return self.forward_pre(src, src_mask, src_key_padding_mask, pos)
return self.forward_post(src, src_mask, src_key_padding_mask, pos)
class TransformerDecoderLayer(nn.Module):
def __init__(self, d_model, nhead, dim_feedforward=2048, dropout=0.1,
activation="relu", normalize_before=False):
super().__init__()
self.self_attn = nn.MultiheadAttention(d_model, nhead, dropout=dropout)
self.multihead_attn = nn.MultiheadAttention(
d_model, nhead, dropout=dropout)
# Implementation of Feedforward model
self.linear1 = nn.Linear(d_model, dim_feedforward)
self.dropout = nn.Dropout(dropout)
self.linear2 = nn.Linear(dim_feedforward, d_model)
self.norm1 = nn.LayerNorm(d_model)
self.norm2 = nn.LayerNorm(d_model)
self.norm3 = nn.LayerNorm(d_model)
self.dropout1 = nn.Dropout(dropout)
self.dropout2 = nn.Dropout(dropout)
self.dropout3 = nn.Dropout(dropout)
self.activation = _get_activation_fn(activation)
self.normalize_before = normalize_before
def with_pos_embed(self, tensor, pos: Optional[Tensor]):
return tensor if pos is None else tensor + pos
def forward_post(self, tgt, memory,
tgt_mask: Optional[Tensor] = None,
memory_mask: Optional[Tensor] = None,
tgt_key_padding_mask: Optional[Tensor] = None,
memory_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None,
query_pos: Optional[Tensor] = None):
#print(tgt.shape)
#print(query_pos.shape)
q = k = self.with_pos_embed(tgt, query_pos)
tgt2 = self.self_attn(q, k, value=tgt, attn_mask=tgt_mask,
key_padding_mask=tgt_key_padding_mask)[0]
tgt = tgt + self.dropout1(tgt2)
tgt = self.norm1(tgt)
tgt2 = self.multihead_attn(query=self.with_pos_embed(tgt, query_pos),
key=self.with_pos_embed(memory, pos),
value=memory, attn_mask=memory_mask,
key_padding_mask=memory_key_padding_mask)[0]
tgt = tgt + self.dropout2(tgt2)
tgt = self.norm2(tgt)
tgt2 = self.linear2(self.dropout(self.activation(self.linear1(tgt))))
tgt = tgt + self.dropout3(tgt2)
tgt = self.norm3(tgt)
return tgt
def forward_pre(self, tgt, memory,
tgt_mask: Optional[Tensor] = None,
memory_mask: Optional[Tensor] = None,
tgt_key_padding_mask: Optional[Tensor] = None,
memory_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None,
query_pos: Optional[Tensor] = None):
tgt2 = self.norm1(tgt)
q = k = self.with_pos_embed(tgt2, query_pos)
tgt2 = self.self_attn(q, k, value=tgt2, attn_mask=tgt_mask,
key_padding_mask=tgt_key_padding_mask)[0]
tgt = tgt + self.dropout1(tgt2)
tgt2 = self.norm2(tgt)
tgt2 = self.multihead_attn(query=self.with_pos_embed(tgt2, query_pos),
key=self.with_pos_embed(memory, pos),
value=memory, attn_mask=memory_mask,
key_padding_mask=memory_key_padding_mask)[0]
tgt = tgt + self.dropout2(tgt2)
tgt2 = self.norm3(tgt)
tgt2 = self.linear2(self.dropout(self.activation(self.linear1(tgt2))))
tgt = tgt + self.dropout3(tgt2)
return tgt
def forward(self, tgt, memory,
tgt_mask: Optional[Tensor] = None,
memory_mask: Optional[Tensor] = None,
tgt_key_padding_mask: Optional[Tensor] = None,
memory_key_padding_mask: Optional[Tensor] = None,
pos: Optional[Tensor] = None,
query_pos: Optional[Tensor] = None):
if self.normalize_before:
return self.forward_pre(tgt, memory, tgt_mask, memory_mask,
tgt_key_padding_mask, memory_key_padding_mask, pos, query_pos)
return self.forward_post(tgt, memory, tgt_mask, memory_mask,
tgt_key_padding_mask, memory_key_padding_mask, pos, query_pos)
class DecoderEmbeddings(nn.Module):
def __init__(self, config):
super().__init__()
self.word_embeddings = nn.Embedding(
config.vocab_size, config.hidden_dim, padding_idx=config.pad_token_id)
self.position_embeddings = nn.Embedding(
config.max_position_embeddings, config.hidden_dim
)
self.LayerNorm = torch.nn.LayerNorm(
config.hidden_dim, eps=config.layer_norm_eps)
self.dropout = nn.Dropout(config.dropout)
def forward(self, x):
input_shape = x.size()
x=x.long()
#print(x.shape)
seq_length = input_shape[1]
device = x.device
position_ids = torch.arange(
seq_length, dtype=torch.long, device=device)
position_ids = position_ids.unsqueeze(0).expand(input_shape)
input_embeds = self.word_embeddings(x)
position_embeds = self.position_embeddings(position_ids)
embeddings = input_embeds + position_embeds
embeddings = self.LayerNorm(embeddings)
embeddings = self.dropout(embeddings)
#print(embeddings)
return embeddings
def _get_clones(module, N):
return nn.ModuleList([copy.deepcopy(module) for i in range(N)])
def _get_activation_fn(activation):
"""Return an activation function given a string"""
if activation == "relu":
return F.relu
if activation == "gelu":
return F.gelu
if activation == "glu":
return F.glu
raise RuntimeError(F"activation should be relu/gelu, not {activation}.")
def generate_square_subsequent_mask(sz):
r"""Generate a square mask for the sequence. The masked positions are filled with float('-inf').
Unmasked positions are filled with float(0.0).
"""
mask = (torch.triu(torch.ones(sz, sz)) == 1).transpose(0, 1)
mask = mask.float().masked_fill(mask == 0, float(
'-inf')).masked_fill(mask == 1, float(0.0))
return mask
def build_transformer(config):
return Transformer_Caption(
config,
d_model=config.hidden_dim,
dropout=config.dropout,
nhead=config.nheads,
dim_feedforward=config.dim_feedforward,
num_encoder_layers=config.enc_layers,
num_decoder_layers=config.dec_layers,
normalize_before=config.pre_norm,
return_intermediate_dec=False,
)