cloome.py

import numpy as np
import pandas as pd
import streamlit as st
from PIL import Image

import sys
import io
import os
import glob
import json
import zipfile
from tqdm import tqdm
from itertools import chain

import torch
from torch.utils.data import DataLoader
from torch.utils.tensorboard import SummaryWriter

import clip.clip as clip
from clip.clip import _transform
from training.datasets import CellPainting
from clip.model import convert_weights, CLIPGeneral

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
from rdkit.Chem import DataStructs




basepath = os.path.dirname(__file__)

MODEL_PATH = os.path.join(basepath, "epoch_55.pt")
CLOOME_PATH = "/home/ana/gitrepos/hti-cloob"
npzs = os.path.join(basepath, "npzs")
imgname = "I1"
molecule_features = "all_molecule_cellpainting_features.pkl"
image_features = "subset_image_cellpainting_features.pkl"
images_arr = "subset_npzs_dict_200.npz"

device = "cuda" if torch.cuda.is_available() else "cpu"
model_type = "RN50"
image_resolution = 520

######### CLOOME FUNCTIONS #########
def convert_models_to_fp32(model):
    for p in model.parameters():
        p.data = p.data.float()
        if p.grad:
            p.grad.data = p.grad.data.float()


def load(model_path, device, model, image_resolution):
    state_dict = torch.load(model_path, map_location="cpu")
    state_dict = state_dict["state_dict"]

    model_config_file = f"{model.replace('/', '-')}.json"
    print('Loading model from', model_config_file)
    assert os.path.exists(model_config_file)
    with open(model_config_file, 'r') as f:
        model_info = json.load(f)
    model = CLIPGeneral(**model_info)
    convert_weights(model)
    convert_models_to_fp32(model)

    if str(device) == "cpu":
        model.float()
    print(device)

    new_state_dict = {k[len('module.'):]: v for k,v in state_dict.items()}

    model.load_state_dict(new_state_dict)
    model.to(device)
    model.eval()

    return model


def get_features(dataset, model, device):
    all_image_features = []
    all_text_features = []
    all_ids = []

    print(f"get_features {device}")
    print(len(dataset))

    with torch.no_grad():
        for batch in tqdm(DataLoader(dataset, num_workers=1, batch_size=64)):
            if type(batch) is dict:
                imgs = batch
                text_features = None
                mols = None
            elif type(batch) is torch.Tensor:
                mols = batch
                imgs = None
            else:
                imgs, mols = batch

            if mols is not None:
                text_features = model.encode_text(mols.to(device))
                text_features = text_features / text_features.norm(dim=-1, keepdim=True)
                all_text_features.append(text_features)
                molecules_exist = True

            if imgs is not None:
                images = imgs["input"]
                ids = imgs["ID"]

                img_features = model.encode_image(images.to(device))
                img_features = img_features / img_features.norm(dim=-1, keepdim=True)
                all_image_features.append(img_features)

                all_ids.append(ids)


        all_ids = list(chain.from_iterable(all_ids))

    if imgs is not None and mols is not None:
        return torch.cat(all_image_features), torch.cat(all_text_features), all_ids
    elif imgs is not None:
        return torch.cat(all_image_features), all_ids
    elif mols is not None:
        return torch.cat(all_text_features), all_ids
    return


def read_array(file):
    t = torch.load(file)
    features = t["mol_features"]
    ids = t["mol_ids"]
    return features, ids


def main(df, model_path, model, img_path=None, mol_path=None, image_resolution=None):
    # Load the model
    device = "cuda" if torch.cuda.is_available() else "cpu"
    print(torch.cuda.device_count())

    model = load(model_path, device, model, image_resolution)

    preprocess_val = _transform(image_resolution, image_resolution, is_train=False, normalize="dataset", preprocess="downsize")

    # Load the dataset
    val = CellPainting(df,
                       img_path,
                       mol_path,
                       transforms = preprocess_val)

    # Calculate the image features
    print("getting_features")
    result = get_features(val, model, device)

    if len(result) > 2:
        val_img_features, val_text_features, val_ids = result
        return val_img_features, val_text_features, val_ids
    else:
        val_img_features, val_ids = result
        return val_img_features, val_ids

    #val_img_features, val_ids = get_features(val, model, device)

    #return val_img_features, val_text_features, val_ids

def img_to_numpy(file):
    img = Image.open(file)
    arr = np.array(img)
    return arr


def illumination_threshold(arr, perc=0.0028):
    """ Return threshold value to not display a percentage of highest pixels"""

    perc = perc/100

    h = arr.shape[0]
    w = arr.shape[1]

    # find n pixels to delete
    total_pixels = h * w
    n_pixels = total_pixels * perc
    n_pixels = int(np.around(n_pixels))

    # find indexes of highest pixels
    flat_inds = np.argpartition(arr, -n_pixels, axis=None)[-n_pixels:]
    inds = np.array(np.unravel_index(flat_inds, arr.shape)).T

    max_values = [arr[i, j] for i, j in inds]

    threshold = min(max_values)

    return threshold


def process_image(arr):
    threshold = illumination_threshold(arr)
    scaled_img = sixteen_to_eight_bit(arr, threshold)
    return scaled_img


def sixteen_to_eight_bit(arr, display_max, display_min=0):
    threshold_image = ((arr.astype(float) - display_min) * (arr > display_min))

    scaled_image = (threshold_image * (256. / (display_max - display_min)))
    scaled_image[scaled_image > 255] = 255

    scaled_image = scaled_image.astype(np.uint8)

    return scaled_image


def process_image(arr):
    threshold = illumination_threshold(arr)
    scaled_img = sixteen_to_eight_bit(arr, threshold)
    return scaled_img


def process_sample(imglst, channels, filenames, outdir, outfile):
    sample = np.zeros((520, 696, 5), dtype=np.uint8)

    filenames_dict, channels_dict = {}, {}

    for i, (img, channel, fname) in enumerate(zip(imglst, channels, filenames)):
        print(channel)
        arr = img_to_numpy(img)
        arr = process_image(arr)

        sample[:,:,i] = arr

        channels_dict[i] = channel
        filenames_dict[channel] = fname

    sample_dict = dict(sample=sample,
                  channels=channels_dict,
                  filenames=filenames_dict)

    outfile = outfile + ".npz"
    outpath = os.path.join(outdir, outfile)

    np.savez(outpath, sample=sample, channels=channels, filenames=filenames)

    return sample_dict, outpath


def display_cellpainting(sample):
    arr = sample["sample"]
    r = arr[:, :, 0].astype(np.float32)
    g = arr[:, :, 3].astype(np.float32)
    b = arr[:, :, 4].astype(np.float32)

    rgb_arr = np.dstack((r, g, b))

    im = Image.fromarray(rgb_arr.astype("uint8"))
    im_rgb = im.convert("RGB")
    return im_rgb


def morgan_from_smiles(smiles, radius=3, nbits=1024, chiral=True):
    mol = Chem.MolFromSmiles(smiles)
    fp = AllChem.GetMorganFingerprintAsBitVect(mol, radius=3, nBits=nbits, useChirality=chiral)
    arr = np.zeros((0,), dtype=np.int8)
    DataStructs.ConvertToNumpyArray(fp,arr)
    return arr


def save_hdf(fps, index, outfile_hdf):
    ids = [i for i in range(len(fps))]
    columns = [str(i) for i in range(fps[0].shape[0])]
    df = pd.DataFrame(fps, index=ids, columns=columns)
    df.to_hdf(outfile_hdf, key="df", mode="w")
    return outfile_hdf


def create_index(outdir, ids, filename):
    filepath = os.path.join(outdir, filename)
    if type(ids) is str:
        values = [ids]
    else:
        values = ids
    data = {"SAMPLE_KEY": values}
    print(data)
    df = pd.DataFrame(data)
    df.to_csv(filepath)
    return filepath


def draw_molecules(smiles_lst):
    mols = [Chem.MolFromSmiles(s) for s in smiles_lst]
    mol_imgs = [Chem.Draw.MolToImage(m) for m in mols]
    return mol_imgs


def reshape_image(arr):
    c, h, w = arr.shape
    reshaped_image = np.empty((h, w, c))

    reshaped_image[:,:,0] = arr[0]
    reshaped_image[:,:,1] = arr[1]
    reshaped_image[:,:,2] = arr[2]

    reshaped_pil = Image.fromarray(reshaped_image.astype("uint8"))

    return reshaped_pil


# missing functions: save morgan to to_hdf, create index, load features, calculate similarities


#model = load(MODEL_PATH, device, model_type, image_resolution)

##### STREAMLIT FUNCTIONS ######
st.title('CLOOME: Contrastive Learning for Molecule Representation with Microscopy Images and Chemical Structures')


def main_page():
    st.markdown(
    """
    Contrastive learning for self-supervised representation learning has brought a
    strong improvement to many application areas, such as computer vision and natural
    language processing. With the availability of large collections of unlabeled data in
    vision and language, contrastive learning of language and image representations
    has shown impressive results. The contrastive learning methods CLIP and CLOOB
    have demonstrated that the learned representations are highly transferable to a
    large set of diverse tasks when trained on multi-modal data from two different
    domains. In drug discovery, similar large, multi-modal datasets comprising both
    cell-based microscopy images and chemical structures of molecules are available.

    However, contrastive learning has not yet been used for this type of multi-modal data,
    although transferable representations could be a remedy for the
    time-consuming and cost-expensive label acquisition in this domain. In this work,
    we present a contrastive learning method for image-based and structure-based
    representations of small molecules for drug discovery.

    Our method, Contrastive Leave One Out boost for Molecule Encoders (CLOOME), is based on CLOOB
    and comprises an encoder for microscopy data, an encoder for chemical structures
    and a contrastive learning objective. On the benchmark dataset ”Cell Painting”,
    we demonstrate the ability of our method to learn transferable representations by
    performing linear probing for activity prediction tasks. Additionally, we show that
    the representations could also be useful for bioisosteric replacement tasks.
    """
    )


def molecules_from_image():
    ## TODO: Check if expander can be automatically collapsed
    exp = st.expander("Upload a microscopy image")
    with exp:
        channels = ['Mito', 'ERSyto', 'ERSytoBleed', 'Ph_golgi', 'Hoechst']
        imglst, filenames = [], []

        for c in channels:
            file_obj = st.file_uploader(f'Choose a TIF image for {c}:', ".tif")
            if file_obj is not None:
                imglst.append(file_obj)
                filenames.append(file_obj.name)


    if imglst:
        if not os.path.isdir(npzs):
            os.mkdir(npzs)

        sample_dict, imgpath = process_sample(imglst, channels, filenames, npzs, imgname)
        print(imglst)


        i = display_cellpainting(sample_dict)
        st.image(i)

    uploaded_file = st.file_uploader("Choose a molecule file to retrieve from (optional)")

    if imglst:
        if uploaded_file is not None:
            molecule_df = pd.read_csv(uploaded_file)
            smiles = molecule_df["SMILES"].tolist()
            morgan = [morgan_from_smiles(s) for s in smiles]
            molnames = [f"M{i}" for i in range(len(morgan))]
            mol_index_fname = "mol_index.csv"
            mol_index = create_index(basepath, molnames, mol_index_fname)
            molpath = os.path.join(basepath, "mols.hdf")
            fps_fname = save_hdf(morgan, molnames, molpath)
            mol_imgs = draw_molecules(smiles)
            mol_features, mol_ids = main(mol_index, MODEL_PATH, model_type, mol_path=molpath, image_resolution=image_resolution)
            predefined_features = False
        else:
            mol_index = pd.read_csv("cellpainting-unique-molecule.csv")
            mol_features_torch = torch.load("all_molecule_cellpainting_features.pkl")
            mol_features = mol_features_torch["mol_features"]
            mol_ids = mol_features_torch["mol_ids"]
            print(len(mol_ids))
            predefined_features = True

        img_index_fname = "img_index.csv"
        img_index = create_index(basepath, imgname, img_index_fname)
        img_features, img_ids = main(img_index, MODEL_PATH, model_type, img_path=npzs, image_resolution=image_resolution)

        print(img_features.shape)
        print(mol_features.shape)

        logits = img_features @ mol_features.T
        mol_probs = (30.0 * logits).softmax(dim=-1)
        top_probs, top_labels = mol_probs.cpu().topk(5, dim=-1)

        # Delete this if want to allow retrieval for multiple images
        top_probs = torch.flatten(top_probs)
        top_labels = torch.flatten(top_labels)

        print(top_probs.shape)
        print(top_labels.shape)

        if predefined_features:
            mol_index.set_index(["SAMPLE_KEY"], inplace=True)
            top_ids = [mol_ids[i] for i in top_labels]
            smiles = mol_index.loc[top_ids]["SMILES"].tolist()
            mol_imgs = draw_molecules(smiles)

        with st.container():
            #st.write("Ranking of most similar molecules")
            columns = st.columns(len(top_probs))
            for i, col in enumerate(columns):
                if predefined_features:
                    image_id = i
                else:
                    image_id = top_labels[i]
                index = i+1
                col.image(mol_imgs[image_id], width=140, caption=index)

        print(mol_probs.sum(dim=-1))
        print((top_probs, top_labels))

def images_from_molecule():
    smiles = st.text_input("Enter a SMILES string", value="CC(=O)OC1=CC=CC=C1C(=O)O", placeholder="CC(=O)OC1=CC=CC=C1C(=O)O")
    if smiles:
        smiles = [smiles]
        morgan = [morgan_from_smiles(s) for s in smiles]
        molnames = [f"M{i}" for i in range(len(morgan))]
        mol_index_fname = "mol_index.csv"
        mol_index = create_index(basepath, molnames, mol_index_fname)
        molpath = os.path.join(basepath, "mols.hdf")
        fps_fname = save_hdf(morgan, molnames, molpath)
        mol_imgs = draw_molecules(smiles)

        mol_features, mol_ids = main(mol_index, MODEL_PATH, model_type, mol_path=molpath, image_resolution=image_resolution)

        col1, col2, col3 = st.columns(3)

        with col1:
            st.write("")

        with col2:
            st.image(mol_imgs, width = 140)

        with col3:
            st.write("")


        img_features_torch = torch.load(image_features)
        img_features = img_features_torch["img_features"]
        img_ids = img_features_torch["img_ids"]

        logits = mol_features @ img_features.T
        img_probs = (30.0 * logits).softmax(dim=-1)
        top_probs, top_labels = img_probs.cpu().topk(5, dim=-1)

        top_probs = torch.flatten(top_probs)
        top_labels = torch.flatten(top_labels)

        img_index = pd.read_csv("cellpainting-all-imgpermol.csv")
        img_index.set_index(["SAMPLE_KEY"], inplace=True)
        top_ids = [img_ids[i] for i in top_labels]

        images_dict = np.load(images_arr, allow_pickle = True)

        with st.container():
            columns = st.columns(len(top_probs))
            for i, col in enumerate(columns):
                id = top_ids[i]
                id = f"{id}.npz"
                image = images_dict[id]

                ## TODO: generalize and functionalize
                im = reshape_image(image)

                index = i+1
                col.image(im, caption=index)


page_names_to_funcs = {
    "-": main_page,
    "Molecules from a microscopy image": molecules_from_image,
    "Microscopy images from a molecule": images_from_molecule,
}


selected_page = st.sidebar.selectbox("What would you like to retrieve?", page_names_to_funcs.keys())
page_names_to_funcs[selected_page]()

# print(img_features.shape)
# print(img_ids)