# coding=utf-8 from __future__ import absolute_import, division, print_function import copy import logging import math from collections import OrderedDict from os.path import join as pjoin import ml_collections import numpy as np import torch import torch.nn as nn import torch.nn.functional as F from scipy import ndimage from torch.nn import (Conv2d, CrossEntropyLoss, Dropout, LayerNorm, Linear, Softmax) from torch.nn.modules.utils import _pair def np2th(weights, conv=False): """Possibly convert HWIO to OIHW.""" if conv: weights = weights.transpose([3, 2, 0, 1]) return torch.from_numpy(weights) class StdConv2d(nn.Conv2d): def forward(self, x): w = self.weight v, m = torch.var_mean(w, dim=[1, 2, 3], keepdim=True, unbiased=False) w = (w - m) / torch.sqrt(v + 1e-5) return F.conv2d(x, w, self.bias, self.stride, self.padding, self.dilation, self.groups) def conv3x3(cin, cout, stride=1, groups=1, bias=False): return StdConv2d(cin, cout, kernel_size=3, stride=stride, padding=1, bias=bias, groups=groups) def conv1x1(cin, cout, stride=1, bias=False): return StdConv2d(cin, cout, kernel_size=1, stride=stride, padding=0, bias=bias) class PreActBottleneck(nn.Module): """Pre-activation (v2) bottleneck block. """ def __init__(self, cin, cout=None, cmid=None, stride=1): super().__init__() cout = cout or cin cmid = cmid or cout // 4 self.gn1 = nn.GroupNorm(32, cmid, eps=1e-6) self.conv1 = conv1x1(cin, cmid, bias=False) self.gn2 = nn.GroupNorm(32, cmid, eps=1e-6) self.conv2 = conv3x3(cmid, cmid, stride, bias=False) # Original code has it on conv1!! self.gn3 = nn.GroupNorm(32, cout, eps=1e-6) self.conv3 = conv1x1(cmid, cout, bias=False) self.relu = nn.ReLU(inplace=True) if (stride != 1 or cin != cout): # Projection also with pre-activation according to paper. self.downsample = conv1x1(cin, cout, stride, bias=False) self.gn_proj = nn.GroupNorm(cout, cout) def forward(self, x): # Residual branch residual = x if hasattr(self, 'downsample'): residual = self.downsample(x) residual = self.gn_proj(residual) # Unit's branch y = self.relu(self.gn1(self.conv1(x))) y = self.relu(self.gn2(self.conv2(y))) y = self.gn3(self.conv3(y)) y = self.relu(residual + y) return y def load_from(self, weights, n_block, n_unit): conv1_weight = np2th(weights[pjoin(n_block, n_unit, "conv1/kernel")], conv=True) conv2_weight = np2th(weights[pjoin(n_block, n_unit, "conv2/kernel")], conv=True) conv3_weight = np2th(weights[pjoin(n_block, n_unit, "conv3/kernel")], conv=True) gn1_weight = np2th(weights[pjoin(n_block, n_unit, "gn1/scale")]) gn1_bias = np2th(weights[pjoin(n_block, n_unit, "gn1/bias")]) gn2_weight = np2th(weights[pjoin(n_block, n_unit, "gn2/scale")]) gn2_bias = np2th(weights[pjoin(n_block, n_unit, "gn2/bias")]) gn3_weight = np2th(weights[pjoin(n_block, n_unit, "gn3/scale")]) gn3_bias = np2th(weights[pjoin(n_block, n_unit, "gn3/bias")]) self.conv1.weight.copy_(conv1_weight) self.conv2.weight.copy_(conv2_weight) self.conv3.weight.copy_(conv3_weight) self.gn1.weight.copy_(gn1_weight.view(-1)) self.gn1.bias.copy_(gn1_bias.view(-1)) self.gn2.weight.copy_(gn2_weight.view(-1)) self.gn2.bias.copy_(gn2_bias.view(-1)) self.gn3.weight.copy_(gn3_weight.view(-1)) self.gn3.bias.copy_(gn3_bias.view(-1)) if hasattr(self, 'downsample'): proj_conv_weight = np2th(weights[pjoin(n_block, n_unit, "conv_proj/kernel")], conv=True) proj_gn_weight = np2th(weights[pjoin(n_block, n_unit, "gn_proj/scale")]) proj_gn_bias = np2th(weights[pjoin(n_block, n_unit, "gn_proj/bias")]) self.downsample.weight.copy_(proj_conv_weight) self.gn_proj.weight.copy_(proj_gn_weight.view(-1)) self.gn_proj.bias.copy_(proj_gn_bias.view(-1)) class ResNetV2(nn.Module): """Implementation of Pre-activation (v2) ResNet mode.""" def __init__(self, block_units, width_factor): super().__init__() width = int(64 * width_factor) self.width = width self.root = nn.Sequential(OrderedDict([ ('conv', StdConv2d(3, width, kernel_size=7, stride=2, bias=False, padding=3)), ('gn', nn.GroupNorm(32, width, eps=1e-6)), ('relu', nn.ReLU(inplace=True)), # ('pool', nn.MaxPool2d(kernel_size=3, stride=2, padding=0)) ])) self.body = nn.Sequential(OrderedDict([ ('block1', nn.Sequential(OrderedDict( [('unit1', PreActBottleneck(cin=width, cout=width * 4, cmid=width))] + [(f'unit{i:d}', PreActBottleneck(cin=width * 4, cout=width * 4, cmid=width)) for i in range(2, block_units[0] + 1)], ))), ('block2', nn.Sequential(OrderedDict( [('unit1', PreActBottleneck(cin=width * 4, cout=width * 8, cmid=width * 2, stride=2))] + [(f'unit{i:d}', PreActBottleneck(cin=width * 8, cout=width * 8, cmid=width * 2)) for i in range(2, block_units[1] + 1)], ))), ('block3', nn.Sequential(OrderedDict( [('unit1', PreActBottleneck(cin=width * 8, cout=width * 16, cmid=width * 4, stride=2))] + [(f'unit{i:d}', PreActBottleneck(cin=width * 16, cout=width * 16, cmid=width * 4)) for i in range(2, block_units[2] + 1)], ))), ])) def forward(self, x): features = [] b, c, in_size, _ = x.size() x = self.root(x) features.append(x) x = nn.MaxPool2d(kernel_size=3, stride=2, padding=0)(x) for i in range(len(self.body) - 1): x = self.body[i](x) right_size = int(in_size / 4 / (i + 1)) if x.size()[2] != right_size: pad = right_size - x.size()[2] assert pad < 3 and pad > 0, "x {} should {}".format(x.size(), right_size) feat = torch.zeros((b, x.size()[1], right_size, right_size), device=x.device) feat[:, :, 0:x.size()[2], 0:x.size()[3]] = x[:] else: feat = x features.append(feat) x = self.body[-1](x) return x, features[::-1] def get_b16_config(): """Returns the ViT-B/16 configuration.""" config = ml_collections.ConfigDict() config.patches = ml_collections.ConfigDict({'size': (16, 16)}) config.hidden_size = 768 config.transformer = ml_collections.ConfigDict() config.transformer.mlp_dim = 3072 config.transformer.num_heads = 12 config.transformer.num_layers = 12 config.transformer.attention_dropout_rate = 0.0 config.transformer.dropout_rate = 0.1 config.n_skip = 3 config.classifier = 'seg' config.representation_size = None config.resnet_pretrained_path = None config.pretrained_path = '/home/Bigdata/mtt_distillation_ckpt/ViT-B_16.npz' config.patch_size = 16 config.decoder_channels = (256, 128, 64, 16) config.n_classes = 1 config.activation = 'softmax' return config def get_r50_b16_config(): """Returns the Resnet50 + ViT-B/16 configuration.""" config = get_b16_config() config.patches.grid = (16, 16) config.resnet = ml_collections.ConfigDict() config.resnet.num_layers = (3, 4, 9) config.resnet.width_factor = 1 config.classifier = 'seg' config.pretrained_path = '/home/Bigdata/mtt_distillation_ckpt/R50+ViT-B_16.npz' config.decoder_channels = (256, 128, 64, 16) config.skip_channels = [512, 256, 64, 16] config.n_classes = 1 config.n_skip = 3 config.activation = 'softmax' return config logger = logging.getLogger(__name__) ATTENTION_Q = "MultiHeadDotProductAttention_1/query" ATTENTION_K = "MultiHeadDotProductAttention_1/key" ATTENTION_V = "MultiHeadDotProductAttention_1/value" ATTENTION_OUT = "MultiHeadDotProductAttention_1/out" FC_0 = "MlpBlock_3/Dense_0" FC_1 = "MlpBlock_3/Dense_1" ATTENTION_NORM = "LayerNorm_0" MLP_NORM = "LayerNorm_2" def np2th(weights, conv=False): """Possibly convert HWIO to OIHW.""" if conv: weights = weights.transpose([3, 2, 0, 1]) return torch.from_numpy(weights) def swish(x): return x * torch.sigmoid(x) ACT2FN = {"gelu": torch.nn.functional.gelu, "relu": torch.nn.functional.relu, "swish": swish} class Attention(nn.Module): def __init__(self, config, vis): super(Attention, self).__init__() self.vis = vis self.num_attention_heads = config.transformer["num_heads"] self.attention_head_size = int(config.hidden_size / self.num_attention_heads) self.all_head_size = self.num_attention_heads * self.attention_head_size self.query = Linear(config.hidden_size, self.all_head_size) self.key = Linear(config.hidden_size, self.all_head_size) self.value = Linear(config.hidden_size, self.all_head_size) self.out = Linear(config.hidden_size, config.hidden_size) self.attn_dropout = Dropout(config.transformer["attention_dropout_rate"]) self.proj_dropout = Dropout(config.transformer["attention_dropout_rate"]) self.softmax = Softmax(dim=-1) def transpose_for_scores(self, x): new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size) x = x.view(*new_x_shape) return x.permute(0, 2, 1, 3) def forward(self, hidden_states): mixed_query_layer = self.query(hidden_states) mixed_key_layer = self.key(hidden_states) mixed_value_layer = self.value(hidden_states) query_layer = self.transpose_for_scores(mixed_query_layer) key_layer = self.transpose_for_scores(mixed_key_layer) value_layer = self.transpose_for_scores(mixed_value_layer) attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2)) attention_scores = attention_scores / math.sqrt(self.attention_head_size) attention_probs = self.softmax(attention_scores) weights = attention_probs if self.vis else None attention_probs = self.attn_dropout(attention_probs) context_layer = torch.matmul(attention_probs, value_layer) context_layer = context_layer.permute(0, 2, 1, 3).contiguous() new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,) context_layer = context_layer.view(*new_context_layer_shape) attention_output = self.out(context_layer) attention_output = self.proj_dropout(attention_output) return attention_output, weights class Mlp(nn.Module): def __init__(self, config): super(Mlp, self).__init__() self.fc1 = Linear(config.hidden_size, config.transformer["mlp_dim"]) self.fc2 = Linear(config.transformer["mlp_dim"], config.hidden_size) self.act_fn = ACT2FN["gelu"] self.dropout = Dropout(config.transformer["dropout_rate"]) self._init_weights() def _init_weights(self): nn.init.xavier_uniform_(self.fc1.weight) nn.init.xavier_uniform_(self.fc2.weight) nn.init.normal_(self.fc1.bias, std=1e-6) nn.init.normal_(self.fc2.bias, std=1e-6) def forward(self, x): x = self.fc1(x) x = self.act_fn(x) x = self.dropout(x) x = self.fc2(x) x = self.dropout(x) return x class Embeddings(nn.Module): """Construct the embeddings from patch, position embeddings. """ def __init__(self, config, img_size, in_channels=3): super(Embeddings, self).__init__() self.hybrid = None self.config = config img_size = _pair(img_size) if config.patches.get("grid") is not None: # ResNet grid_size = config.patches["grid"] patch_size = (img_size[0] // 16 // grid_size[0], img_size[1] // 16 // grid_size[1]) patch_size_real = (patch_size[0] * 16, patch_size[1] * 16) n_patches = (img_size[0] // patch_size_real[0]) * (img_size[1] // patch_size_real[1]) self.hybrid = True else: patch_size = _pair(config.patches["size"]) n_patches = (img_size[0] // patch_size[0]) * (img_size[1] // patch_size[1]) self.hybrid = False if self.hybrid: self.hybrid_model = ResNetV2(block_units=config.resnet.num_layers, width_factor=config.resnet.width_factor) in_channels = self.hybrid_model.width * 16 self.patch_embeddings = Conv2d(in_channels=in_channels, out_channels=config.hidden_size, kernel_size=patch_size, stride=patch_size) self.position_embeddings = nn.Parameter(torch.zeros(1, n_patches, config.hidden_size)) self.dropout = Dropout(config.transformer["dropout_rate"]) def forward(self, x): if self.hybrid: x, features = self.hybrid_model(x) else: features = None x = self.patch_embeddings(x) # (B, hidden. n_patches^(1/2), n_patches^(1/2)) x = x.flatten(2) x = x.transpose(-1, -2) # (B, n_patches, hidden) embeddings = x + self.position_embeddings embeddings = self.dropout(embeddings) return embeddings, features class Block(nn.Module): def __init__(self, config, vis): super(Block, self).__init__() self.hidden_size = config.hidden_size self.attention_norm = LayerNorm(config.hidden_size, eps=1e-6) self.ffn_norm = LayerNorm(config.hidden_size, eps=1e-6) self.ffn = Mlp(config) self.attn = Attention(config, vis) def forward(self, x): h = x x = self.attention_norm(x) x, weights = self.attn(x) x = x + h h = x x = self.ffn_norm(x) x = self.ffn(x) x = x + h return x, weights def load_from(self, weights, n_block): ROOT = f"Transformer/encoderblock_{n_block}" with torch.no_grad(): query_weight = np2th(weights[pjoin(ROOT, ATTENTION_Q, "kernel")]).view(self.hidden_size, self.hidden_size).t() key_weight = np2th(weights[pjoin(ROOT, ATTENTION_K, "kernel")]).view(self.hidden_size, self.hidden_size).t() value_weight = np2th(weights[pjoin(ROOT, ATTENTION_V, "kernel")]).view(self.hidden_size, self.hidden_size).t() out_weight = np2th(weights[pjoin(ROOT, ATTENTION_OUT, "kernel")]).view(self.hidden_size, self.hidden_size).t() query_bias = np2th(weights[pjoin(ROOT, ATTENTION_Q, "bias")]).view(-1) key_bias = np2th(weights[pjoin(ROOT, ATTENTION_K, "bias")]).view(-1) value_bias = np2th(weights[pjoin(ROOT, ATTENTION_V, "bias")]).view(-1) out_bias = np2th(weights[pjoin(ROOT, ATTENTION_OUT, "bias")]).view(-1) self.attn.query.weight.copy_(query_weight) self.attn.key.weight.copy_(key_weight) self.attn.value.weight.copy_(value_weight) self.attn.out.weight.copy_(out_weight) self.attn.query.bias.copy_(query_bias) self.attn.key.bias.copy_(key_bias) self.attn.value.bias.copy_(value_bias) self.attn.out.bias.copy_(out_bias) mlp_weight_0 = np2th(weights[pjoin(ROOT, FC_0, "kernel")]).t() mlp_weight_1 = np2th(weights[pjoin(ROOT, FC_1, "kernel")]).t() mlp_bias_0 = np2th(weights[pjoin(ROOT, FC_0, "bias")]).t() mlp_bias_1 = np2th(weights[pjoin(ROOT, FC_1, "bias")]).t() self.ffn.fc1.weight.copy_(mlp_weight_0) self.ffn.fc2.weight.copy_(mlp_weight_1) self.ffn.fc1.bias.copy_(mlp_bias_0) self.ffn.fc2.bias.copy_(mlp_bias_1) self.attention_norm.weight.copy_(np2th(weights[pjoin(ROOT, ATTENTION_NORM, "scale")])) self.attention_norm.bias.copy_(np2th(weights[pjoin(ROOT, ATTENTION_NORM, "bias")])) self.ffn_norm.weight.copy_(np2th(weights[pjoin(ROOT, MLP_NORM, "scale")])) self.ffn_norm.bias.copy_(np2th(weights[pjoin(ROOT, MLP_NORM, "bias")])) class Encoder(nn.Module): def __init__(self, config, vis): super(Encoder, self).__init__() self.vis = vis self.layer = nn.ModuleList() self.encoder_norm = LayerNorm(config.hidden_size, eps=1e-6) for _ in range(config.transformer["num_layers"]): layer = Block(config, vis) self.layer.append(copy.deepcopy(layer)) def forward(self, hidden_states): attn_weights = [] for layer_block in self.layer: hidden_states, weights = layer_block(hidden_states) if self.vis: attn_weights.append(weights) encoded = self.encoder_norm(hidden_states) return encoded, attn_weights class Transformer(nn.Module): def __init__(self, config, img_size, vis): super(Transformer, self).__init__() self.embeddings = Embeddings(config, img_size=img_size) self.encoder = Encoder(config, vis) def forward(self, input_ids): embedding_output, features = self.embeddings(input_ids) encoded, attn_weights = self.encoder(embedding_output) # (B, n_patch, hidden) return encoded, attn_weights, features class Conv2dReLU(nn.Sequential): def __init__( self, in_channels, out_channels, kernel_size, padding=0, stride=1, use_batchnorm=True, ): conv = nn.Conv2d( in_channels, out_channels, kernel_size, stride=stride, padding=padding, bias=not (use_batchnorm), ) relu = nn.ReLU(inplace=True) bn = nn.BatchNorm2d(out_channels) super(Conv2dReLU, self).__init__(conv, bn, relu) class DecoderBlock(nn.Module): def __init__( self, in_channels, out_channels, skip_channels=0, use_batchnorm=True, ): super().__init__() self.conv1 = Conv2dReLU( in_channels + skip_channels, out_channels, kernel_size=3, padding=1, use_batchnorm=use_batchnorm, ) self.conv2 = Conv2dReLU( out_channels, out_channels, kernel_size=3, padding=1, use_batchnorm=use_batchnorm, ) self.up = nn.UpsamplingBilinear2d(scale_factor=2) def forward(self, x, skip=None): x = self.up(x) if skip is not None: x = torch.cat([x, skip], dim=1) x = self.conv1(x) x = self.conv2(x) return x class SegmentationHead(nn.Sequential): def __init__(self, in_channels, out_channels, kernel_size=3, upsampling=1): conv2d = nn.Conv2d(in_channels, out_channels, kernel_size=kernel_size, padding=kernel_size // 2) upsampling = nn.UpsamplingBilinear2d(scale_factor=upsampling) if upsampling > 1 else nn.Identity() super().__init__(conv2d, upsampling) class DecoderCup(nn.Module): def __init__(self, config): super().__init__() self.config = config head_channels = 512 self.conv_more = Conv2dReLU( config.hidden_size, head_channels, kernel_size=3, padding=1, use_batchnorm=True, ) decoder_channels = config.decoder_channels in_channels = [head_channels] + list(decoder_channels[:-1]) out_channels = decoder_channels if self.config.n_skip != 0: skip_channels = self.config.skip_channels for i in range(4 - self.config.n_skip): # re-select the skip channels according to n_skip skip_channels[3 - i] = 0 else: skip_channels = [0, 0, 0, 0] blocks = [ DecoderBlock(in_ch, out_ch, sk_ch) for in_ch, out_ch, sk_ch in zip(in_channels, out_channels, skip_channels) ] self.blocks = nn.ModuleList(blocks) def forward(self, hidden_states, features=None): B, n_patch, hidden = hidden_states.size() # reshape from (B, n_patch, hidden) to (B, h, w, hidden) h, w = int(np.sqrt(n_patch)), int(np.sqrt(n_patch)) x = hidden_states.permute(0, 2, 1) x = x.contiguous().view(B, hidden, h, w) x = self.conv_more(x) for i, decoder_block in enumerate(self.blocks): if features is not None: skip = features[i] if (i < self.config.n_skip) else None else: skip = None x = decoder_block(x, skip=skip) return x class VisionTransformer(nn.Module): def __init__(self, config=get_r50_b16_config(), img_size=256, num_classes=1, zero_head=False, vis=False): super(VisionTransformer, self).__init__() self.num_classes = num_classes self.zero_head = zero_head self.classifier = config.classifier self.transformer = Transformer(config, img_size, vis) self.decoder = DecoderCup(config) self.segmentation_head = SegmentationHead( in_channels=config['decoder_channels'][-1], out_channels=config['n_classes'], kernel_size=3, ) self.config = config def forward(self, x): if x.size()[1] == 1: x = x.repeat(1, 3, 1, 1) x, attn_weights, features = self.transformer(x) # (B, n_patch, hidden) x = self.decoder(x, features) logits = self.segmentation_head(x) return logits def load_from(self, weights): with torch.no_grad(): res_weight = weights self.transformer.embeddings.patch_embeddings.weight.copy_(np2th(weights["embedding/kernel"], conv=True)) self.transformer.embeddings.patch_embeddings.bias.copy_(np2th(weights["embedding/bias"])) self.transformer.encoder.encoder_norm.weight.copy_(np2th(weights["Transformer/encoder_norm/scale"])) self.transformer.encoder.encoder_norm.bias.copy_(np2th(weights["Transformer/encoder_norm/bias"])) posemb = np2th(weights["Transformer/posembed_input/pos_embedding"]) posemb_new = self.transformer.embeddings.position_embeddings if posemb.size() == posemb_new.size(): self.transformer.embeddings.position_embeddings.copy_(posemb) elif posemb.size()[1] - 1 == posemb_new.size()[1]: posemb = posemb[:, 1:] self.transformer.embeddings.position_embeddings.copy_(posemb) else: logger.info("load_pretrained: resized variant: %s to %s" % (posemb.size(), posemb_new.size())) ntok_new = posemb_new.size(1) if self.classifier == "seg": _, posemb_grid = posemb[:, :1], posemb[0, 1:] gs_old = int(np.sqrt(len(posemb_grid))) gs_new = int(np.sqrt(ntok_new)) print('load_pretrained: grid-size from %s to %s' % (gs_old, gs_new)) posemb_grid = posemb_grid.reshape(gs_old, gs_old, -1) zoom = (gs_new / gs_old, gs_new / gs_old, 1) posemb_grid = ndimage.zoom(posemb_grid, zoom, order=1) # th2np posemb_grid = posemb_grid.reshape(1, gs_new * gs_new, -1) posemb = posemb_grid self.transformer.embeddings.position_embeddings.copy_(np2th(posemb)) # Encoder whole for bname, block in self.transformer.encoder.named_children(): for uname, unit in block.named_children(): unit.load_from(weights, n_block=uname) if self.transformer.embeddings.hybrid: self.transformer.embeddings.hybrid_model.root.conv.weight.copy_( np2th(res_weight["conv_root/kernel"], conv=True)) gn_weight = np2th(res_weight["gn_root/scale"]).view(-1) gn_bias = np2th(res_weight["gn_root/bias"]).view(-1) self.transformer.embeddings.hybrid_model.root.gn.weight.copy_(gn_weight) self.transformer.embeddings.hybrid_model.root.gn.bias.copy_(gn_bias) for bname, block in self.transformer.embeddings.hybrid_model.body.named_children(): for uname, unit in block.named_children(): unit.load_from(res_weight, n_block=bname, n_unit=uname)