updates

.gitignore

@@ -0,0 +1,7 @@
+utils/__pycache__/*
+outputs/*
+models/MSG3D/__pycache__/*
+logs/*
+models/__pycache__/*
+data/*
+*test*

config/SiT/pretraining/mpp.yml

@@ -0,0 +1,89 @@
+# @Author: Simon Dahan
+# @Last Modified time: 2022-01-12 14:11:23
+
+SSL: mpp
+
+resolution:
+  ico: 6            ## full mesh resolution
+  sub_ico: 2        ## patching grid resolution
+
+data:
+  data_path: ../data/{}/{}
+  task: scan_age #scan_age # birth_age
+  configuration: template #template # native
+  dataset: dHCP                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
+
+logging:
+  folder_to_save_model: "../logs/SiT/"
+
+training:
+  LR: 0.0003
+  bs: 256
+  bs_val: 1
+  epochs: 100
+  gpu: 0
+  l1loss: False
+  testing: False
+  val_epoch: 10
+  load_weights_ssl: False
+  load_weights_imagenet: False
+  save_ckpt: True
+  finetuning: True
+  dataset_ssl: 'dhcp'
+
+weights: 
+  ssl_mpp: '..' # path to .pt checkpoint
+  imagenet: 'vit_tiny_patch16_224' #ViT(dim=192, depth=12, heads=3,mlp_dim=768,dim_head=64)
+  #imagenet: 'vit_small_patch16_224' #ViT(dim=384, depth=12, heads=6,mlp_dim=1536,dim_head=64)
+  #imagenet: 'vit_base_patch16_224' #ViT(dim=768, depth=12, heads=12,mlp_dim=3072,dim_head=64)
+
+transformer:
+  dim: 192 #192, 384, 768
+  depth: 12 #12, 12, 12
+  heads: 3 #3, 6, 12
+  mlp_dim: 768 #768, 1536, 3072 ## 4*dim according to DeiT
+  pool: 'cls'  # or 'mean'
+  num_classes: 1
+  num_channels: 4
+  dim_head: 64 #64
+  dropout: 0.0
+  emb_dropout: 0.0
+  model: SiT
+
+pretraining_mpp:
+  mask_prob: 0.75 #0.5
+  replace_prob: 0.8 #0.8
+  swap_prob: 0.02 #0.02
+
+optimisation:
+  optimiser: SGD
+
+Adam:
+  weight_decay: 0.
+
+AdamW:
+  weight_decay: 0.
+SGD:
+  weight_decay: 0.
+  momentum: 0.9
+  nesterov: False
+
+StepLR: 
+  stepsize: 1000
+  decay: 0.5
+
+CosineDecay:
+  T_max: 5000
+  eta_min: 0.0001
+
+sub_ico_0:
+    num_patches: 20 
+    num_vertices: 2145 
+
+sub_ico_1:
+    num_patches: 80 
+    num_vertices: 561 
+
+sub_ico_2:
+    num_patches: 320
+    num_vertices: 153 

config/SiT/training/hparams.yml

@@ -17,7 +17,7 @@ training:
   LR: 0.00001
   bs: 256
   bs_val: 1
-  epochs: 30
+  epochs: 100
   gpu: 0
   l1loss: False
   testing: False
@@ -78,7 +78,4 @@ sub_ico_1:
 
 sub_ico_2:
     num_patches: 320
-    num_vertices: 153 
-
-
-
+    num_vertices: 153 

models/mpp.py

@@ -0,0 +1,135 @@
+# -*- coding: utf-8 -*-
+# @Author: Your name
+# @Date:   1970-01-01 01:00:00
+# @Last Modified by:   Your name
+# @Last Modified time: 2022-02-14 17:50:22
+#
+# Created on Mon Oct 18 2021
+#
+# by Simon Dahan @SD3004
+#
+# Copyright (c) 2021 MeTrICS Lab
+#
+
+
+import math
+from random import random
+
+import torch
+import torch.nn as nn
+import torch.nn.functional as F 
+
+from einops import rearrange, repeat
+
+
+def get_mask_from_prob(inputs, prob):
+    '''
+    This function creates a mask on the sequence of tokens, per sample
+    Based on the probability of masking. 
+    return: a boolean mask of the shape of the inputs. 
+    '''
+    batch, seq_len, _, device = *inputs.shape, inputs.device
+    max_masked = math.ceil(prob * seq_len)
+
+    rand = torch.rand((batch, seq_len), device=device)
+    _, sampled_indices = rand.topk(max_masked, dim=-1)
+
+    new_mask = torch.zeros((batch, seq_len), device=device)
+    new_mask.scatter_(1, sampled_indices, 1)
+    return new_mask.bool()
+
+def prob_mask_like(inputs, prob):
+    batch, seq_length, _ = inputs.shape
+    return torch.zeros((batch, seq_length)).float().uniform_(0, 1) < prob
+
+
+class masked_patch_pretraining(nn.Module):
+
+    def __init__(
+        self,
+        transformer,
+        dim_in,
+        dim_out,
+        device,
+        mask_prob=0.15,
+        replace_prob=0.5,
+        swap_prob=0.3,
+        channels=4,
+        num_vertices=561,):
+
+        super().__init__()
+        self.transformer = transformer
+
+        self.dim_out = dim_out
+        self.dim_in = dim_in
+
+        self.to_original = nn.Linear(dim_in,dim_out)
+        self.to_original.to(device)
+
+        self.mask_prob = mask_prob
+        self.replace_prob = replace_prob
+        self.swap_prob = swap_prob
+
+        # token ids
+        self.mask_token = nn.Parameter(torch.randn(1, 1, channels * num_vertices))
+
+
+    def forward(self, batch, **kwargs):
+
+        transformer = self.transformer
+
+        # clone original image for loss
+        batch = rearrange(batch,
+                        'b c n v  -> b n (v c)')
+
+        corrupted_sequence = get_mask_from_prob(batch, self.mask_prob)
+
+        corrupted_batch = batch.clone().detach()
+
+        #randomly swap patches in the sequence
+        if self.swap_prob > 0:
+            random_patch_sampling_prob = self.swap_prob / (
+                1 - self.replace_prob)
+
+            random_patch_prob = prob_mask_like(batch,
+                                               random_patch_sampling_prob).to(corrupted_sequence.device)
+
+            bool_random_patch_prob = corrupted_sequence * (random_patch_prob == True)
+
+            random_patches = torch.randint(0,
+                                           batch.shape[1],
+                                           (batch.shape[0], batch.shape[1]),
+                                           device=batch.device)
+            #shuffle entierely masked_batch                               
+            randomized_input = corrupted_batch[
+                torch.arange(corrupted_batch.shape[0]).unsqueeze(-1),
+                random_patches]
+            corrupted_batch[bool_random_patch_prob] = randomized_input[bool_random_patch_prob]
+
+        tokens_to_mask = prob_mask_like(batch, self.replace_prob).to(corrupted_sequence.device)
+
+        bool_mask_replace = (corrupted_sequence * tokens_to_mask) == True
+        corrupted_batch[bool_mask_replace] = self.mask_token.to(corrupted_sequence.device)
+
+        # linear embedding of patches
+        corrupted_batch = transformer.to_patch_embedding[-1](corrupted_batch)
+        emb_masked_sequence = corrupted_batch.clone().detach()
+
+        # add cls token to input sequence
+        b, n, _ = corrupted_batch.shape
+        cls_tokens = repeat(transformer.cls_token, '() n d -> b n d', b=b)
+        corrupted_batch = torch.cat((cls_tokens, corrupted_batch), dim=1)
+
+        # add positional embeddings to input
+        corrupted_batch += transformer.pos_embedding[:, :(n + 1)]
+        corrupted_batch = transformer.dropout(corrupted_batch)
+
+        # get generator output and get mpp loss
+        batch_out = transformer.transformer(corrupted_batch, **kwargs)
+        batch_out = self.to_original(batch_out[:,1:,:])        
+
+        # compute loss 
+        mpp_loss = F.mse_loss(batch_out[corrupted_sequence], batch[corrupted_sequence])
+
+        return mpp_loss, batch_out
+