---
datasets:
- danjacobellis/cell_seg_labeled
- danjacobellis/cell_seg
pipeline_tag: image-feature-extraction
tags:
- biology
- medical
---

```python
import torch
import numpy as np
from PIL import Image
from einops import repeat
from datasets import load_dataset, concatenate_datasets
from IPython.display import display, HTML
from torchvision.transforms import ToPILImage, PILToTensor, Compose
from torchvision.transforms import Resize, RandomCrop, CenterCrop, RandomHorizontalFlip, RandomVerticalFlip, RandomRotation
from vit_pytorch.mae import MAE
from vit_pytorch.simple_vit_with_register_tokens import SimpleViT
from einops.layers.torch import Rearrange
class Args: pass
```


```python
device = "cpu"
checkpoint = torch.load("v0.0.1.pt",map_location="cpu")
args = checkpoint['args']
args.crops_per_sample = 1

encoder = SimpleViT(
    image_size = args.img_dim[1],
    channels = args.img_dim[0],
    patch_size = args.patch_size,
    num_classes = args.num_classes,
    dim = args.embed_dim,
    depth = args.depth,
    heads = args.heads,
    mlp_dim = args.mlp_dim,
    dim_head = args.embed_dim//args.heads,
).to(device)

model = MAE(
    encoder=encoder,
    decoder_dim=args.embed_dim,
    masking_ratio=args.masking_ratio,
    decoder_depth=args.decoder_depth,
    decoder_heads=args.heads,
    decoder_dim_head=args.embed_dim//args.heads,
).to(device)

model.load_state_dict(checkpoint['model_state_dict'])
```




    <All keys matched successfully>




```python
dataset = load_dataset("danjacobellis/cell_synthetic_labels")
```


```python
transforms = Compose([
    RandomCrop(896),
    RandomRotation(22.5),
    CenterCrop(672),
    Resize(224, interpolation=Image.Resampling.LANCZOS),
    RandomVerticalFlip(0.5),
    RandomHorizontalFlip(0.5),
    PILToTensor(),
])

def collate_fn(batch):
    batch_size = len(batch)*args.crops_per_sample
    inputs = torch.zeros(
        (batch_size, args.img_dim[0], args.img_dim[1], args.img_dim[2]),
        dtype=torch.uint8
    )
    for i_sample, sample in enumerate(batch):
        img = sample['image']
        for i_crop in range(args.crops_per_sample):
            ind = i_sample*args.crops_per_sample + i_crop
            inputs[ind,:,:,:] = transforms(img)
    
    return inputs
```


```python
data_loader_valid = torch.utils.data.DataLoader(
    dataset['validation'],
    batch_size=8,
    shuffle=False,
    num_workers=args.num_workers,
    drop_last=False,
    pin_memory=True,
    collate_fn=collate_fn
)
```


```python
with torch.no_grad():
    x = next(iter(data_loader_valid))
    x = x.to(torch.float)
    x = x / 255
    x = x.to(device)

    patches = model.to_patch(x)
    batch, num_patches, *_ = patches.shape

    tokens = model.patch_to_emb(patches)
    tokens += model.encoder.pos_embedding.to(device, dtype=tokens.dtype) 

    num_masked = int(model.masking_ratio * num_patches)
    rand_indices = torch.rand(batch, num_patches, device = device).argsort(dim = -1)
    masked_indices, unmasked_indices = rand_indices[:, :num_masked], rand_indices[:, num_masked:]

    batch_range = torch.arange(batch, device = device)[:, None]
    tokens = tokens[batch_range, unmasked_indices]

    masked_patches = patches[batch_range, masked_indices]
    encoded_tokens = model.encoder.transformer(tokens)
    decoder_tokens = model.enc_to_dec(encoded_tokens)
    unmasked_decoder_tokens = decoder_tokens + model.decoder_pos_emb(unmasked_indices)

    mask_tokens = repeat(model.mask_token, 'd -> b n d', b = batch, n = num_masked)
    mask_tokens = mask_tokens + model.decoder_pos_emb(masked_indices)
    
    decoder_tokens = torch.zeros(batch, num_patches, model.decoder_dim, device=device)
    decoder_tokens[batch_range, unmasked_indices] = unmasked_decoder_tokens
    decoder_tokens[batch_range, masked_indices] = mask_tokens
    decoded_tokens = model.decoder(decoder_tokens)

    mask_tokens = decoded_tokens[batch_range, masked_indices]
    pred_pixel_values = model.to_pixels(mask_tokens)

    recon_loss = torch.nn.functional.mse_loss(pred_pixel_values, masked_patches)
```


```python
def reconstruct_image(self, patches, model_input, masked_indices=None, pred_pixel_values=None, patch_size=8):
    patches = patches.cpu()
    masked_indices_in = masked_indices is not None
    predicted_pixels_in = pred_pixel_values is not None
    if masked_indices_in:
        masked_indices = masked_indices.cpu()
    if predicted_pixels_in:
        pred_pixel_values = pred_pixel_values.cpu()
    patch_width = patch_height = patch_size
    reconstructed_image = patches.clone()
    if masked_indices_in or predicted_pixels_in:
        for i in range(reconstructed_image.shape[0]):
            if masked_indices_in and predicted_pixels_in:
                reconstructed_image[i, masked_indices[i].cpu()] = pred_pixel_values[i, :].cpu().float()
            elif masked_indices_in:
                reconstructed_image[i, masked_indices[i].cpu()] = 0
    invert_patch = Rearrange('b (h w) (p1 p2 c) -> b c (h p1) (w p2)', w=int(model_input.shape[3] / patch_width),
                             h=int(model_input.shape[2] / patch_height), c=model_input.shape[1],
                             p1=patch_height, p2=patch_width)
    reconstructed_image = invert_patch(reconstructed_image)
    reconstructed_image = reconstructed_image.numpy().transpose(0, 2, 3, 1)
    return reconstructed_image.transpose(0, 3, 1, 2)
```


```python
with torch.no_grad():
    reconstructed_images1 = reconstruct_image(
        model,
        patches,
        x,
        masked_indices=masked_indices,
        pred_pixel_values=pred_pixel_values,
        patch_size=16
    )
    reconstructed_images2 = reconstruct_image(
        model,
        patches,
        x,
        masked_indices=masked_indices,
        patch_size=16
    )
```


```python
for i_img, img in enumerate(x):
    rec1 = reconstructed_images1[i_img]
    rec2 = reconstructed_images2[i_img]
    display(ToPILImage()(img[0]))
    display(ToPILImage()(rec2[0]))
    display(ToPILImage()(rec1[0]))
```


    
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```python
!jupyter nbconvert --to markdown README.ipynb
```

    [NbConvertApp] Converting notebook README.ipynb to markdown
    [NbConvertApp] Support files will be in README_files/
    [NbConvertApp] Writing 7517 bytes to README.md