Merge pull request #37 from NERC-CEH/bioclip-exp

BioCLIP WIP notebook

notebooks/BioclipExperiment.md

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+---
+jupyter:
+  jupytext:
+    formats: ipynb,md
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.3'
+      jupytext_version: 1.16.4
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
+---
+
+# Joe experiments with BioCLIP
+
+```python
+import logging
+import warnings
+
+from PIL import Image
+import torch
+import open_clip
+
+# Get clues about what's happening upstream
+logging.basicConfig(level=logging.INFO)
+
+warnings.filterwarnings(action="ignore", category=FutureWarning)
+```
+
+<!-- #region -->
+## Loading and inspecting the model
+
+I am following the (very minimal) instructions for loading the BioCLIP from the [BioCLIP huggingface page](https://huggingface.co/imageomics/bioclip#how-to-get-started-with-the-model
+), and the more generic ones from the [`open_clip` README](https://github.com/mlfoundations/open_clip?tab=readme-ov-file#usage).
+
+The first step is
+
+```python
+model, preprocess_train, preprocess_val = open_clip.create_model_and_transforms('hf-hub:imageomics/bioclip')
+```
+
+I am looking at the logic inside [`open_clip.create_model_and_transforms`](https://github.com/mlfoundations/open_clip/blob/main/src/open_clip/factory.py#L375) and it's quite messy/confusing and sparsely documented, with defaults silently overriden. Probably best to just treat this as a black box! Most importantly, it returns three things:
+
+1. an instance of [`open_clip.model.CLIP`](https://github.com/mlfoundations/open_clip/blob/main/src/open_clip/model.py#L220) (a subclass of `torch.nn.Module`) with loaded weights
+2. an instance of [`torchvision.transforms.transforms.Compose`](https://pytorch.org/vision/main/generated/torchvision.transforms.Compose.html) that performs the image preprocessing for training
+3. another `Compose` for validation
+<!-- #endregion -->
+
+```python
+model, preprocess_train, preprocess_val = open_clip.create_model_and_transforms('hf-hub:imageomics/bioclip')
+model.eval()
+print(type(model), type(preprocess_train), type(preprocess_val))
+```
+
+### Unpacking CLIP
+
+The `forward` pass of `CLIP` transforms both image and text inputs (if both are provided).
+
+#### Images
+Images are passed to the `visual` submodule, which is an instance of [`VisionTransformer`](https://github.com/mlfoundations/open_clip/blob/main/src/open_clip/transformer.py#L434) (You can get an idea for what a `VisionTransformer` contains/does from the `repr` below, but see [source code](https://github.com/mlfoundations/open_clip/blob/main/src/open_clip/transformer.py#L434) for more details.)
+The outputs of the transformer are then [normalised](https://pytorch.org/docs/stable/generated/torch.nn.functional.normalize.html) (by dividing by the $\ell_2$ norm). 
+
+#### Text
+Text goes through the following stages:
+
+1. Token embedding (`token_embedding`)
+2. Transformer (`transformer`)
+3. Layer norm (`ln_final1`)
+4. Normalise (another division by the $\ell_2$ norm, functional so not listed as a module)
+
+```python
+model
+```
+
+### Preprocessing
+
+The preprocessing for training and validation are slightly different: during training [`torchvision.transforms.RandomResizedCrop`](https://pytorch.org/vision/main/generated/torchvision.transforms.RandomResizedCrop.html) is used to crop a random portion of the image and resize it to (224, 224), whereas in validation the image is resized so that the *smaller* edge is 224 pixels, before a center crop is applied to make the resulting image square.
+
+Note that [`torchvision.transforms.CenterCrop`](https://pytorch.org/vision/main/generated/torchvision.transforms.CenterCrop.html#torchvision.transforms.CenterCrop.forward) pads any dimensions that are smaller than the give center size with zeros.
+
+```python
+preprocess_train.transforms
+```
+
+```python
+preprocess_val.transforms
+```
+
+**TODO:** demo the preprocessors on our images
+
+
+### Tokenizer
+
+```python
+tokenizer = open_clip.get_tokenizer('hf-hub:imageomics/bioclip')
+```
+
+## Plankton images
+
+```python
+import os
+from cyto_ml.models.scivision import prepare_image
+from intake_xarray import ImageSource
+from dotenv import load_dotenv
+
+load_dotenv()  # sets our object store endpoint and credentials from the .env file
+
+from intake import open_catalog
+```
+
+```python
+dataset = open_catalog(f"{os.environ.get('ENDPOINT', '')}/metadata/intake.yml")
+imgs = dataset.test_image().to_dask()
+imgs.to_numpy().shape
+```
+
+```python
+index_df = dataset.plankton().to_dask().compute()  # intake-xarray is not sensible here - to_dask.compute() seems silly
+index_df
+```
+
+<!-- #raw -->
+image_data = [
+    ImageSource(row).to_dask().to_numpy() for row in index_df["Filename"].iloc[:100]  # take first 100, 535 too many!
+]
+image_data[0].shape
+<!-- #endraw -->
+
+```python
+from tqdm.autonotebook import tqdm
+
+fnames = index_df["Filename"]
+
+images = []
+
+for row in tqdm(fnames):
+    try:
+        image = ImageSource(row).to_dask().to_numpy()
+    except OSError as e: # I think one of these is a csv not an image!
+        print(e)
+    else:
+        images.append(image)
+```
+
+```python
+import matplotlib.pyplot as plt
+
+plt.imshow(images[0])
+```
+
+```python
+from IPython.display import display
+print(images[0].shape)
+im = Image.fromarray(images[0], "RGB")
+display(im)
+```
+
+```python
+for i in images[10:50]:
+    display(Image.fromarray(i, "RGB"))
+```
+
+```python
+images[0].shape
+```
+
+```python
+dimensions = [image.shape[:-1] for image in images]
+plt.scatter(*zip(*dimensions), s=3)
+```
+
+```python
+test = preprocess_val(Image.fromarray(images[0], "RGB"))
+print(test.shape)
+print(test.min(), test.max())
+test
+
+testim = test.permute(2, 1, 0).numpy()
+print(testim.shape)
+im = Image.fromarray(test.permute(1, 2, 0).numpy(), "RGB")
+display(im)
+```
+
+```python
+#resize, crop, totensor, norm = preprocess_val.transforms
+
+test_image = Image.fromarray(images[16], "RGB")
+
+for transform in preprocess_val.transforms:
+    print("transform: ", transform)
+    test_image = transform(test_image)
+    print("new type: ", type(test_image))
+
+
+    if isinstance(test_image, Image.Image):
+        display(test_image)
+
+    elif isinstance(test_image, torch.Tensor):
+        plt.imshow(test_image.transpose(2, 0))
+        print(test_image.min(), test_image.max())
+
+    else:
+        print(type(test_image))
+```
+
+```python
+from torchvision.transforms.v2.functional import to_image
+
+test_image = Image.fromarray(images[16], "RGB")
+
+poo = to_image(test_image)
+poo.min(), poo.max()
+```
+
+## Put in the thing
+
+```python
+test_image = Image.fromarray(images[16], "RGB")
+
+display(test_image)
+```
+
+```python
+in_tensor = preprocess_val(test_image)
+in_tensor.shape
+```
+
+```python
+image_features, text_features, scale = model(in_tensor.unsqueeze(0))
+```
+
+```python
+image_features.shape
+```
+
+### One at a time or it cries
+
+```python
+from pathlib import Path
+from tqdm.autonotebook import tqdm
+assert Path("features").is_dir()
+
+for i, image in tqdm(enumerate(images)):
+    image_tensor = preprocess_val(Image.fromarray(image, "RGB"))
+    out_feature, _, _ = model(image_tensor.unsqueeze(0))
+    torch.save(out_feature, f"features/feature_{i}.pt") 
+```
+
+```python
+features = torch.cat(
+    [torch.load(f"features/feature_{i}.pt") for i in range(len(images))]
+)
+features.shape
+```
+
+```python
+!pip install scikit-learn
+```
+
+```python
+from sklearn.manifold import TSNE
+
+t_sne = TSNE()
+
+embedded = t_sne.fit_transform(features.detach().numpy())
+```
+
+```python
+embedded.shape
+```
+
+```python
+plt.scatter(*zip(*embedded))
+```
+
+```python
+
+```
+
+## Resources
+
+### CLIP
+
+- [GitHub repo](https://github.com/mlfoundations/open_clip/)
+- [Class definition](https://github.com/mlfoundations/open_clip/blob/main/src/open_clip/model.py#L220)
+- 
+
+### BioCLIP 
+
+- [arXiv paper](https://arxiv.org/pdf/2311.18803)
+- [GitHub repo](https://github.com/Imageomics/bioclip)
+- [Model card](https://huggingface.co/imageomics/bioclip)
+- [Evaluation using t-SNE](https://imageomics.github.io/bioclip/#intrinsic)
+
+### Evaluation
+
+- [Scikit Learn TSNE class](https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#tsne)
+- [t-SNE from the original author](https://lvdmaaten.github.io/tsne/)
+- [Demo about manifold learning](https://scikit-learn.org/stable/auto_examples/manifold/plot_compare_methods.html#)
+
+```python
+
+```