Merge pull request #1 from jefferson-bercaw/first_attempt

First attempt

Author: jefferson-bercaw

vit-classifier.py

@@ -0,0 +1,226 @@
+from __future__ import print_function
+
+import glob
+from itertools import chain
+import os
+import random
+import zipfile
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import torch.optim as optim
+from linformer import Linformer
+from PIL import Image
+# from sklearn.model_selection import train_test_split
+from torch.optim.lr_scheduler import StepLR
+from torch.utils.data import DataLoader, Dataset
+from torchvision import datasets, transforms
+from tqdm.notebook import tqdm
+
+
+from readDataFromExcel import getDataFromExcelFile
+from vit_pytorch.vit_3d import ViT
+
+
+def seed_everything(seed):
+    random.seed(seed)
+    os.environ['PYTHONHASHSEED'] = str(seed)
+    np.random.seed(seed)
+    torch.manual_seed(seed)
+    # torch.cuda.manual_seed(seed)
+    # torch.cuda.manual_seed_all(seed)
+    torch.backends.cudnn.deterministic = True
+
+
+def Img_and_Label(data_obj):
+
+    img_list = []
+    label_list = []
+    file_folder = data_obj.imgRootPath
+
+    data_dict = data_obj.excelData
+    for idx in range(len(data_dict)):
+        img_list.append(data_dict[idx]["img"])
+
+        cur_label = data_dict[idx]["label"]
+        if cur_label == '0':
+            label_float = float(0)
+        else:
+            label_float = float(1)
+        label_list.append(label_float)
+
+    uniq_names = []
+    num_images = []
+    label = []
+    label_list_short = []
+
+    for ind, name in enumerate(img_list):
+        split_name = name.split("_")
+        subj = split_name[0]
+        label.append(label_list[ind])
+
+        if subj not in uniq_names:
+            uniq_names.append(subj)
+            num_images.append(1)
+            label_list_short.append(label[-1])
+        else:
+            index = uniq_names.index(subj)
+            num_images[index] += 1
+
+    files = [[]]
+    labels = []
+    ind = 0
+    for idx, subj in enumerate(uniq_names):
+        if num_images[uniq_names.index(subj)] != 24:
+            print("Subject {} has only {} images".format(subj, num_images[uniq_names.index(subj)]))
+
+        else:
+            files.append([])
+            for img in range(24):
+                if img < 10:
+                    img_str = "000" + str(img)
+                else:
+                    img_str = "00" + str(img)
+                files[ind].append(os.path.join(file_folder, (subj + "_" + img_str + ".bmp")).replace("\\", "/"))
+            labels.append(label_list_short[ind])
+            ind += 1
+
+    files = files[0:-1]
+    # files = list(filter(None, files))
+    # labels = list(filter(None, labels))
+    return files, labels
+
+
+class MRIDataset(Dataset):
+    def __init__(self, data_obj, transform=None):
+        files, labels = Img_and_Label(data_obj)
+        self.file_list = files
+        self.label = labels
+        self.transform = transform
+
+    def __len__(self):
+        self.filelength = len(self.file_list)
+        return self.filelength
+
+    def __getitem__(self, idx):
+        imgs = self.file_list[idx]
+        img = np.zeros((224, 224, 24))
+        for idx, cur_img in enumerate(imgs):
+            img_here = np.asarray(Image.open(cur_img))
+            assert img_here.dtype == 'uint8'
+            img[:, :, idx] = img_here / (2**8)
+
+        img = np.float32(img)
+        label = np.float32(self.label)
+
+        img_transformed = self.transform(img)
+        label = self.label[idx]
+
+        return img_transformed, label
+
+
+if __name__ == '__main__':
+
+    batch_size = 12
+    epochs = 100
+    lr = 3e-5
+    gamma = 0.7
+    seed = 42
+
+    seed_everything(seed)
+
+    device = 'cpu'
+
+    n_folds = 10
+    cur_dir = os.getcwd()
+    print(f"Current Directory: {cur_dir}")
+    os.makedirs(os.path.join(cur_dir, "saved_models"), exist_ok=True)
+
+    excelFilePath = os.path.join(cur_dir,'Fold_Split.xlsx')
+    imgRootPath = "C:/Users/jrb187/PycharmProjects/FITNet/subset_data/2D_Images"
+
+    # Transforms to data
+    train_transforms = transforms.Compose(
+        [
+            transforms.ToTensor(),
+        ]
+    )
+
+    val_transforms = transforms.Compose(
+        [
+            transforms.ToTensor(),
+        ]
+    )
+
+    for fold in range(n_folds):
+
+        excel_sheet_name_train = 'train_fold' + str(fold)
+        excel_sheet_name_test = 'valid_fold' + str(fold)
+
+        train_obj = getDataFromExcelFile(excelFilePath=excelFilePath, imgRootPath=imgRootPath, excelSheetName=excel_sheet_name_train)
+        test_obj = getDataFromExcelFile(excelFilePath=excelFilePath, imgRootPath=imgRootPath, excelSheetName=excel_sheet_name_test)
+
+        train_dataset = MRIDataset(train_obj, transform=train_transforms)
+        test_dataset = MRIDataset(test_obj, transform=val_transforms)
+
+        train_loader = DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=False)
+        test_loader = DataLoader(dataset=test_dataset, batch_size=batch_size, shuffle=False)
+
+        model = ViT(image_size=224, channels =1, frames=24, image_patch_size=16, frame_patch_size=1, num_classes=2,
+                    dim=14*14*24, depth=6, heads=8, mlp_dim=2048, dropout=0.1, emb_dropout=0.1)
+
+        # Training
+        criterion = nn.CrossEntropyLoss()
+        optimizer = optim.Adam(model.parameters(), lr=lr)
+        scheduler = StepLR(optimizer, step_size=1, gamma=gamma)
+
+        for epoch in range(epochs):
+            epoch_loss = 0
+            epoch_accuracy = 0
+
+            for data, label in train_loader:
+
+                # Add 1 (channel)
+                data = data.unsqueeze(1)
+                assert data.shape == (batch_size, 1, 24, 224, 224)
+
+                data = data.to(device)
+                label = label.to(device)
+
+                output = model(data)
+                loss = criterion(output, label)
+
+                optimizer.zero_grad()
+                loss.backward()
+                optimizer.step()
+
+                acc = (output.argmax(dim=1) == label).float().mean()
+                epoch_accuracy += acc / len(train_loader)
+                epoch_loss += loss / len(train_loader)
+
+                torch.cuda.empty_cache()
+
+            with torch.no_grad():
+                epoch_val_accuracy = 0
+                epoch_val_loss = 0
+                for data, label in test_loader:
+                    data = data.to(device)
+                    label = label.to(device)
+
+                    val_output = model(data)
+                    val_loss = criterion(val_output, label)
+
+                    acc = (val_output.argmax(dim=1) == label).float().mean()
+                    epoch_val_accuracy += acc / len(test_loader)
+                    epoch_val_loss += val_loss / len(test_loader)
+
+            print(
+                f"Fold : {fold+1} - Epoch : {epoch + 1} - loss : {epoch_loss:.4f} - acc: {epoch_accuracy:.4f} - val_loss : {epoch_val_loss:.4f} - val_acc: {epoch_val_accuracy:.4f}\n"
+            )
+
+        torch.save(model.state_dict(), './saved_models/{}.pt'.format("fold" + str(fold+1)))
+