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Upload 8 files
Browse files- config.py +36 -0
- dataset.py +165 -0
- eval.py +62 -0
- gui.py +92 -0
- inference.py +88 -0
- model.py +198 -0
- train.py +84 -0
- utils.py +111 -0
config.py
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import albumentations as A
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import torch
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from albumentations.pytorch import ToTensorV2
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CHECKPOINT_FILE = './checkpoints/x_ray_model.pth.tar'
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DATASET_PATH = './dataset'
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IMAGES_DATASET = './dataset/images'
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DEVICE = 'cpu'
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BATCH_SIZE = 16
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PIN_MEMORY = False
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VOCAB_THRESHOLD = 2
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FEATURES_SIZE = 1024
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EMBED_SIZE = 300
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HIDDEN_SIZE = 256
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LEARNING_RATE = 4e-5
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EPOCHS = 50
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LOAD_MODEL = True
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SAVE_MODEL = True
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basic_transforms = A.Compose([
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A.Resize(
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height=256,
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width=256
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),
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A.Normalize(
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mean=(0.485, 0.456, 0.406),
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std=(0.229, 0.224, 0.225),
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),
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ToTensorV2()
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])
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dataset.py
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import os
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import spacy
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import torch
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import config
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import utils
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import numpy as np
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import xml.etree.ElementTree as ET
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from PIL import Image
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from torch.nn.utils.rnn import pad_sequence
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from torch.utils.data import Dataset, DataLoader
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spacy_eng = spacy.load('en_core_web_sm')
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class Vocabulary:
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def __init__(self, freq_threshold):
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self.itos = {
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0: '<PAD>',
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1: '<SOS>',
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2: '<EOS>',
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3: '<UNK>',
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}
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self.stoi = {
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'<PAD>': 0,
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'<SOS>': 1,
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'<EOS>': 2,
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'<UNK>': 3,
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}
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self.freq_threshold = freq_threshold
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@staticmethod
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def tokenizer(text):
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return [tok.text.lower() for tok in spacy_eng.tokenizer(text)]
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def build_vocabulary(self, sentence_list):
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frequencies = {}
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idx = 4
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for sent in sentence_list:
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for word in self.tokenizer(sent):
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if word not in frequencies:
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frequencies[word] = 1
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else:
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frequencies[word] += 1
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if frequencies[word] == self.freq_threshold:
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self.stoi[word] = idx
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self.itos[idx] = word
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idx += 1
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def numericalize(self, text):
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tokenized_text = self.tokenizer(text)
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return [
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self.stoi[token] if token in self.stoi else self.stoi['<UNK>']
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for token in tokenized_text
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]
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def __len__(self):
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return len(self.itos)
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class XRayDataset(Dataset):
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def __init__(self, root, transform=None, freq_threshold=3, raw_caption=False):
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self.root = root
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self.transform = transform
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self.raw_caption = raw_caption
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self.vocab = Vocabulary(freq_threshold=freq_threshold)
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self.captions = []
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self.imgs = []
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for file in os.listdir(os.path.join(self.root, 'reports')):
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if file.endswith('.xml'):
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tree = ET.parse(os.path.join(self.root, 'reports', file))
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frontal_img = ''
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findings = tree.find(".//AbstractText[@Label='FINDINGS']").text
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if findings is None:
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continue
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for x in tree.findall('parentImage'):
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if frontal_img != '':
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break
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img = x.attrib['id']
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img = os.path.join(config.IMAGES_DATASET, f'{img}.png')
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frontal_img = img
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if frontal_img == '':
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continue
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self.captions.append(findings)
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self.imgs.append(frontal_img)
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self.vocab.build_vocabulary(self.captions)
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def __getitem__(self, item):
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img = self.imgs[item]
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caption = utils.normalize_text(self.captions[item])
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img = np.array(Image.open(img).convert('L'))
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img = np.expand_dims(img, axis=-1)
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img = img.repeat(3, axis=-1)
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if self.transform is not None:
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img = self.transform(image=img)['image']
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if self.raw_caption:
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return img, caption
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numericalized_caption = [self.vocab.stoi['<SOS>']]
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numericalized_caption += self.vocab.numericalize(caption)
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numericalized_caption.append(self.vocab.stoi['<EOS>'])
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return img, torch.as_tensor(numericalized_caption, dtype=torch.long)
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def __len__(self):
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return len(self.captions)
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def get_caption(self, item):
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return self.captions[item].split(' ')
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class CollateDataset:
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def __init__(self, pad_idx):
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self.pad_idx = pad_idx
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def __call__(self, batch):
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images, captions = zip(*batch)
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images = torch.stack(images, 0)
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targets = [item for item in captions]
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targets = pad_sequence(targets, batch_first=True, padding_value=self.pad_idx)
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return images, targets
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if __name__ == '__main__':
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all_dataset = XRayDataset(
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root=config.DATASET_PATH,
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transform=config.basic_transforms,
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freq_threshold=config.VOCAB_THRESHOLD,
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)
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train_loader = DataLoader(
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dataset=all_dataset,
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batch_size=config.BATCH_SIZE,
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pin_memory=config.PIN_MEMORY,
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drop_last=True,
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shuffle=True,
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collate_fn=CollateDataset(pad_idx=all_dataset.vocab.stoi['<PAD>']),
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)
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for img, caption in train_loader:
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print(img.shape, caption.shape)
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break
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eval.py
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import config
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import utils
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import numpy as np
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from tqdm import tqdm
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from nltk.translate.bleu_score import sentence_bleu
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def check_accuracy(dataset, model):
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print('=> Testing')
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model.eval()
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bleu1_score = []
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bleu2_score = []
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bleu3_score = []
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bleu4_score = []
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for image, caption in tqdm(dataset):
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image = image.to(config.DEVICE)
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generated = model.generate_caption(image.unsqueeze(0), max_length=len(caption.split(' ')))
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bleu1_score.append(
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sentence_bleu([caption.split()], generated, weights=(1, 0, 0, 0))
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)
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bleu2_score.append(
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sentence_bleu([caption.split()], generated, weights=(0.5, 0.5, 0, 0))
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)
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bleu3_score.append(
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sentence_bleu([caption.split()], generated, weights=(0.33, 0.33, 0.33, 0))
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)
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bleu4_score.append(
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sentence_bleu([caption.split()], generated, weights=(0.25, 0.25, 0.25, 0.25))
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)
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print(f'=> BLEU 1: {np.mean(bleu1_score)}')
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print(f'=> BLEU 2: {np.mean(bleu2_score)}')
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print(f'=> BLEU 3: {np.mean(bleu3_score)}')
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print(f'=> BLEU 4: {np.mean(bleu4_score)}')
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def main():
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all_dataset = utils.load_dataset(raw_caption=True)
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model = utils.get_model_instance(all_dataset.vocab)
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utils.load_checkpoint(model)
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_, test_dataset = utils.train_test_split(dataset=all_dataset)
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check_accuracy(
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test_dataset,
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model
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)
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if __name__ == '__main__':
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main()
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gui.py
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import config
|
| 2 |
+
import utils
|
| 3 |
+
import numpy as np
|
| 4 |
+
|
| 5 |
+
from tkinter import *
|
| 6 |
+
from PIL import Image, ImageTk
|
| 7 |
+
from tkinter import filedialog
|
| 8 |
+
|
| 9 |
+
|
| 10 |
+
label = None
|
| 11 |
+
image = None
|
| 12 |
+
model = None
|
| 13 |
+
|
| 14 |
+
def choose_image():
|
| 15 |
+
global label, image
|
| 16 |
+
|
| 17 |
+
path = filedialog.askopenfilename(initialdir='images', title='Select Photo')
|
| 18 |
+
|
| 19 |
+
screen = Toplevel(root)
|
| 20 |
+
screen.title('Report Generator')
|
| 21 |
+
|
| 22 |
+
ff1 = Frame(screen, bg='grey', borderwidth=6, relief=GROOVE)
|
| 23 |
+
ff1.pack(side=TOP,fill=X)
|
| 24 |
+
|
| 25 |
+
ff2 = Frame(screen, bg='grey', borderwidth=6, relief=GROOVE)
|
| 26 |
+
ff2.pack(side=TOP, fill=X)
|
| 27 |
+
|
| 28 |
+
ff4 = Frame(screen, bg='grey', borderwidth=6, relief=GROOVE)
|
| 29 |
+
ff4.pack(side=TOP, fill=X)
|
| 30 |
+
|
| 31 |
+
ff3 = Frame(screen, bg='grey', borderwidth=6, relief=GROOVE)
|
| 32 |
+
ff3.pack(side=TOP, fill=X)
|
| 33 |
+
|
| 34 |
+
Label(ff1, text='Select X-Ray', fg='white', bg='grey', font='Helvetica 16 bold').pack()
|
| 35 |
+
|
| 36 |
+
original_img = Image.open(path).convert('L')
|
| 37 |
+
|
| 38 |
+
image = np.array(original_img)
|
| 39 |
+
image = np.expand_dims(image, axis=-1)
|
| 40 |
+
image = image.repeat(3, axis=-1)
|
| 41 |
+
|
| 42 |
+
image = config.basic_transforms(image=image)['image']
|
| 43 |
+
|
| 44 |
+
photo = ImageTk.PhotoImage(original_img)
|
| 45 |
+
|
| 46 |
+
Label(ff2, image=photo).pack()
|
| 47 |
+
label = Label(ff4, text='', fg='blue', bg='gray', font='Helvetica 16 bold')
|
| 48 |
+
label.pack()
|
| 49 |
+
|
| 50 |
+
Button(ff3, text='Generate Report', bg='violet', command=generate_report, height=2, width=20, font='Helvetica 16 bold').pack(side=LEFT)
|
| 51 |
+
Button(ff3, text='Quit', bg='red', command=quit_gui, height=2, width=20, font='Helvetica 16 bold').pack()
|
| 52 |
+
|
| 53 |
+
screen.bind('<Configure>', lambda event: label.configure(wraplength=label.winfo_width()))
|
| 54 |
+
screen.mainloop()
|
| 55 |
+
|
| 56 |
+
def generate_report():
|
| 57 |
+
global label, image, model
|
| 58 |
+
|
| 59 |
+
model.eval()
|
| 60 |
+
|
| 61 |
+
image = image.to(config.DEVICE)
|
| 62 |
+
|
| 63 |
+
report = model.generate_caption(image.unsqueeze(0), max_length=25)
|
| 64 |
+
|
| 65 |
+
label.config(text=report, fg='violet', bg='green', font='Helvetica 16 bold', width=40)
|
| 66 |
+
label.update_idletasks()
|
| 67 |
+
|
| 68 |
+
def quit_gui():
|
| 69 |
+
root.destroy()
|
| 70 |
+
|
| 71 |
+
root = Tk()
|
| 72 |
+
root.title('Chest X-Ray Report Generator')
|
| 73 |
+
|
| 74 |
+
f1 = Frame(root, bg='grey', borderwidth=6, relief=GROOVE)
|
| 75 |
+
f1.pack(side=TOP, fill=X)
|
| 76 |
+
|
| 77 |
+
f2 = Frame(root, bg='grey', borderwidth=6, relief=GROOVE)
|
| 78 |
+
f2.pack(side=TOP, fill=X)
|
| 79 |
+
|
| 80 |
+
Label(f1, text='Welcome to Chest X-Ray Report Generator', fg='white', bg='grey', font='Helvetica 16 bold').pack()
|
| 81 |
+
|
| 82 |
+
btn1 = Button(root, text='Choose Chest X-Ray', command=choose_image, height=2, width=20, bg='blue', font="Helvetica 16 bold", pady=10)
|
| 83 |
+
btn1.pack()
|
| 84 |
+
|
| 85 |
+
Button(root, text='Quit', command=quit_gui, height=2, width=20, bg='violet', font='Helvetica 16 bold', pady=10).pack()
|
| 86 |
+
|
| 87 |
+
if __name__ == '__main__':
|
| 88 |
+
model = utils.get_model_instance(utils.load_dataset().vocab)
|
| 89 |
+
|
| 90 |
+
utils.load_checkpoint(model)
|
| 91 |
+
|
| 92 |
+
root.mainloop()
|
inference.py
ADDED
|
@@ -0,0 +1,88 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import os
|
| 2 |
+
import torch
|
| 3 |
+
import config
|
| 4 |
+
from utils import (
|
| 5 |
+
load_dataset,
|
| 6 |
+
get_model_instance,
|
| 7 |
+
load_checkpoint,
|
| 8 |
+
can_load_checkpoint,
|
| 9 |
+
normalize_text,
|
| 10 |
+
)
|
| 11 |
+
from PIL import Image
|
| 12 |
+
import torchvision.transforms as transforms
|
| 13 |
+
|
| 14 |
+
# Define device
|
| 15 |
+
DEVICE = 'cpu'
|
| 16 |
+
|
| 17 |
+
# Define image transformations (adjust based on training setup)
|
| 18 |
+
TRANSFORMS = transforms.Compose([
|
| 19 |
+
transforms.Resize((224, 224)), # Replace with your model's expected input size
|
| 20 |
+
transforms.ToTensor(),
|
| 21 |
+
transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),
|
| 22 |
+
])
|
| 23 |
+
|
| 24 |
+
|
| 25 |
+
def load_model():
|
| 26 |
+
"""
|
| 27 |
+
Loads the model with the vocabulary and checkpoint.
|
| 28 |
+
"""
|
| 29 |
+
print("Loading dataset and vocabulary...")
|
| 30 |
+
dataset = load_dataset() # Load dataset to access vocabulary
|
| 31 |
+
vocabulary = dataset.vocab # Assuming 'vocab' is an attribute of the dataset
|
| 32 |
+
|
| 33 |
+
print("Initializing the model...")
|
| 34 |
+
model = get_model_instance(vocabulary) # Initialize the model
|
| 35 |
+
|
| 36 |
+
if can_load_checkpoint():
|
| 37 |
+
print("Loading checkpoint...")
|
| 38 |
+
load_checkpoint(model)
|
| 39 |
+
else:
|
| 40 |
+
print("No checkpoint found, starting with untrained model.")
|
| 41 |
+
|
| 42 |
+
model.eval() # Set the model to evaluation mode
|
| 43 |
+
print("Model is ready for inference.")
|
| 44 |
+
return model
|
| 45 |
+
|
| 46 |
+
|
| 47 |
+
def preprocess_image(image_path):
|
| 48 |
+
"""
|
| 49 |
+
Preprocess the input image for the model.
|
| 50 |
+
"""
|
| 51 |
+
print(f"Preprocessing image: {image_path}")
|
| 52 |
+
image = Image.open(image_path).convert("RGB") # Ensure RGB format
|
| 53 |
+
image = TRANSFORMS(image).unsqueeze(0) # Add batch dimension
|
| 54 |
+
return image.to(DEVICE)
|
| 55 |
+
|
| 56 |
+
|
| 57 |
+
def generate_report(model, image_path):
|
| 58 |
+
"""
|
| 59 |
+
Generates a report for a given image using the model.
|
| 60 |
+
"""
|
| 61 |
+
image = preprocess_image(image_path)
|
| 62 |
+
|
| 63 |
+
print("Generating report...")
|
| 64 |
+
with torch.no_grad():
|
| 65 |
+
# Assuming the model has a 'generate_caption' method
|
| 66 |
+
output = model.generate_caption(image, max_length=25)
|
| 67 |
+
report = " ".join(output)
|
| 68 |
+
|
| 69 |
+
print(f"Generated report: {report}")
|
| 70 |
+
return report
|
| 71 |
+
|
| 72 |
+
|
| 73 |
+
if __name__ == "__main__":
|
| 74 |
+
# Path to the checkpoint file
|
| 75 |
+
CHECKPOINT_PATH = config.CHECKPOINT_FILE # Ensure config.CHECKPOINT_FILE is correctly set
|
| 76 |
+
|
| 77 |
+
# Path to the input image
|
| 78 |
+
IMAGE_PATH = "./dataset/images/CXR1178_IM-0121-1001.png" # Replace with your image path
|
| 79 |
+
|
| 80 |
+
# Load the model
|
| 81 |
+
model = load_model()
|
| 82 |
+
|
| 83 |
+
# Ensure the image exists before inference
|
| 84 |
+
if os.path.exists(IMAGE_PATH):
|
| 85 |
+
report = generate_report(model, IMAGE_PATH)
|
| 86 |
+
print("Final Report:", report)
|
| 87 |
+
else:
|
| 88 |
+
print(f"Image not found at path: {IMAGE_PATH}")
|
model.py
ADDED
|
@@ -0,0 +1,198 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import re
|
| 2 |
+
import torch
|
| 3 |
+
import config
|
| 4 |
+
import torch.nn as nn
|
| 5 |
+
import torch.nn.functional as F
|
| 6 |
+
import torchvision.models as models
|
| 7 |
+
|
| 8 |
+
from collections import OrderedDict
|
| 9 |
+
|
| 10 |
+
|
| 11 |
+
class DenseNet121(nn.Module):
|
| 12 |
+
def __init__(self, out_size=14, checkpoint=None):
|
| 13 |
+
super(DenseNet121, self).__init__()
|
| 14 |
+
|
| 15 |
+
self.densenet121 = models.densenet121(weights='DEFAULT')
|
| 16 |
+
num_classes = self.densenet121.classifier.in_features
|
| 17 |
+
|
| 18 |
+
self.densenet121.classifier = nn.Sequential(
|
| 19 |
+
nn.Linear(num_classes, out_size),
|
| 20 |
+
nn.Sigmoid()
|
| 21 |
+
)
|
| 22 |
+
|
| 23 |
+
if checkpoint is not None:
|
| 24 |
+
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
|
| 25 |
+
checkpoint = torch.load(checkpoint, map_location=device)
|
| 26 |
+
|
| 27 |
+
state_dict = checkpoint['state_dict']
|
| 28 |
+
new_state_dict = OrderedDict()
|
| 29 |
+
|
| 30 |
+
for k, v in state_dict.items():
|
| 31 |
+
if 'module' not in k:
|
| 32 |
+
k = f'module.{k}'
|
| 33 |
+
else:
|
| 34 |
+
k = k.replace('module.densenet121.features', 'features')
|
| 35 |
+
k = k.replace('module.densenet121.classifier', 'classifier')
|
| 36 |
+
k = k.replace('.norm.1', '.norm1')
|
| 37 |
+
k = k.replace('.conv.1', '.conv1')
|
| 38 |
+
k = k.replace('.norm.2', '.norm2')
|
| 39 |
+
k = k.replace('.conv.2', '.conv2')
|
| 40 |
+
|
| 41 |
+
new_state_dict[k] = v
|
| 42 |
+
|
| 43 |
+
self.densenet121.load_state_dict(new_state_dict)
|
| 44 |
+
|
| 45 |
+
|
| 46 |
+
def forward(self, x):
|
| 47 |
+
return self.densenet121(x)
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
class EncoderCNN(nn.Module):
|
| 51 |
+
def __init__(self, checkpoint=None):
|
| 52 |
+
super(EncoderCNN, self).__init__()
|
| 53 |
+
|
| 54 |
+
self.model = DenseNet121(
|
| 55 |
+
checkpoint=checkpoint
|
| 56 |
+
)
|
| 57 |
+
|
| 58 |
+
for param in self.model.densenet121.parameters():
|
| 59 |
+
param.requires_grad_(False)
|
| 60 |
+
|
| 61 |
+
def forward(self, images):
|
| 62 |
+
features = self.model.densenet121.features(images)
|
| 63 |
+
|
| 64 |
+
batch, maps, size_1, size_2 = features.size()
|
| 65 |
+
|
| 66 |
+
features = features.permute(0, 2, 3, 1)
|
| 67 |
+
features = features.view(batch, size_1 * size_2, maps)
|
| 68 |
+
|
| 69 |
+
return features
|
| 70 |
+
|
| 71 |
+
|
| 72 |
+
class Attention(nn.Module):
|
| 73 |
+
def __init__(self, features_size, hidden_size, output_size=1):
|
| 74 |
+
super(Attention, self).__init__()
|
| 75 |
+
|
| 76 |
+
self.W = nn.Linear(features_size, hidden_size)
|
| 77 |
+
self.U = nn.Linear(hidden_size, hidden_size)
|
| 78 |
+
self.v = nn.Linear(hidden_size, output_size)
|
| 79 |
+
|
| 80 |
+
def forward(self, features, decoder_output):
|
| 81 |
+
decoder_output = decoder_output.unsqueeze(1)
|
| 82 |
+
|
| 83 |
+
w = self.W(features)
|
| 84 |
+
u = self.U(decoder_output)
|
| 85 |
+
|
| 86 |
+
scores = self.v(torch.tanh(w + u))
|
| 87 |
+
weights = F.softmax(scores, dim=1)
|
| 88 |
+
context = torch.sum(weights * features, dim=1)
|
| 89 |
+
|
| 90 |
+
weights = weights.squeeze(2)
|
| 91 |
+
|
| 92 |
+
return context, weights
|
| 93 |
+
|
| 94 |
+
|
| 95 |
+
class DecoderRNN(nn.Module):
|
| 96 |
+
def __init__(self, features_size, embed_size, hidden_size, vocab_size):
|
| 97 |
+
super(DecoderRNN, self).__init__()
|
| 98 |
+
|
| 99 |
+
self.vocab_size = vocab_size
|
| 100 |
+
|
| 101 |
+
self.embedding = nn.Embedding(vocab_size, embed_size)
|
| 102 |
+
self.lstm = nn.LSTMCell(embed_size + features_size, hidden_size)
|
| 103 |
+
|
| 104 |
+
self.fc = nn.Linear(hidden_size, vocab_size)
|
| 105 |
+
|
| 106 |
+
self.attention = Attention(features_size, hidden_size)
|
| 107 |
+
|
| 108 |
+
self.init_h = nn.Linear(features_size, hidden_size)
|
| 109 |
+
self.init_c = nn.Linear(features_size, hidden_size)
|
| 110 |
+
|
| 111 |
+
def forward(self, features, captions):
|
| 112 |
+
embeddings = self.embedding(captions)
|
| 113 |
+
|
| 114 |
+
h, c = self.init_hidden(features)
|
| 115 |
+
|
| 116 |
+
seq_len = len(captions[0]) - 1
|
| 117 |
+
features_size = features.size(1)
|
| 118 |
+
batch_size = captions.size(0)
|
| 119 |
+
|
| 120 |
+
outputs = torch.zeros(batch_size, seq_len, self.vocab_size).to(config.DEVICE)
|
| 121 |
+
atten_weights = torch.zeros(batch_size, seq_len, features_size).to(config.DEVICE)
|
| 122 |
+
|
| 123 |
+
for i in range(seq_len):
|
| 124 |
+
context, attention = self.attention(features, h)
|
| 125 |
+
|
| 126 |
+
inputs = torch.cat((embeddings[:, i, :], context), dim=1)
|
| 127 |
+
|
| 128 |
+
h, c = self.lstm(inputs, (h, c))
|
| 129 |
+
h = F.dropout(h, p=0.5)
|
| 130 |
+
|
| 131 |
+
output = self.fc(h)
|
| 132 |
+
|
| 133 |
+
outputs[:, i, :] = output
|
| 134 |
+
atten_weights[:, i, :] = attention
|
| 135 |
+
|
| 136 |
+
return outputs, atten_weights
|
| 137 |
+
|
| 138 |
+
def init_hidden(self, features):
|
| 139 |
+
features = torch.mean(features, dim=1)
|
| 140 |
+
|
| 141 |
+
h = self.init_h(features)
|
| 142 |
+
c = self.init_c(features)
|
| 143 |
+
|
| 144 |
+
return h, c
|
| 145 |
+
|
| 146 |
+
|
| 147 |
+
class EncoderDecoderNet(nn.Module):
|
| 148 |
+
def __init__(self, features_size, embed_size, hidden_size, vocabulary, encoder_checkpoint=None):
|
| 149 |
+
super(EncoderDecoderNet, self).__init__()
|
| 150 |
+
|
| 151 |
+
self.vocabulary = vocabulary
|
| 152 |
+
|
| 153 |
+
self.encoder = EncoderCNN(
|
| 154 |
+
checkpoint=encoder_checkpoint
|
| 155 |
+
)
|
| 156 |
+
self.decoder = DecoderRNN(
|
| 157 |
+
features_size=features_size,
|
| 158 |
+
embed_size=embed_size,
|
| 159 |
+
hidden_size=hidden_size,
|
| 160 |
+
vocab_size=len(self.vocabulary)
|
| 161 |
+
)
|
| 162 |
+
|
| 163 |
+
def forward(self, images, captions):
|
| 164 |
+
features = self.encoder(images)
|
| 165 |
+
outputs, _ = self.decoder(features, captions)
|
| 166 |
+
|
| 167 |
+
return outputs
|
| 168 |
+
|
| 169 |
+
def generate_caption(self, image, max_length=25):
|
| 170 |
+
caption = []
|
| 171 |
+
|
| 172 |
+
with torch.no_grad():
|
| 173 |
+
features = self.encoder(image)
|
| 174 |
+
h, c = self.decoder.init_hidden(features)
|
| 175 |
+
|
| 176 |
+
word = torch.tensor(self.vocabulary.stoi['<SOS>']).view(1, -1).to(config.DEVICE)
|
| 177 |
+
embeddings = self.decoder.embedding(word).squeeze(0)
|
| 178 |
+
|
| 179 |
+
for _ in range(max_length):
|
| 180 |
+
context, _ = self.decoder.attention(features, h)
|
| 181 |
+
|
| 182 |
+
inputs = torch.cat((embeddings, context), dim=1)
|
| 183 |
+
|
| 184 |
+
h, c = self.decoder.lstm(inputs, (h, c))
|
| 185 |
+
|
| 186 |
+
output = self.decoder.fc(F.dropout(h, p=0.5))
|
| 187 |
+
output = output.view(1, -1)
|
| 188 |
+
|
| 189 |
+
predicted = output.argmax(1)
|
| 190 |
+
|
| 191 |
+
if self.vocabulary.itos[predicted.item()] == '<EOS>':
|
| 192 |
+
break
|
| 193 |
+
|
| 194 |
+
caption.append(predicted.item())
|
| 195 |
+
|
| 196 |
+
embeddings = self.decoder.embedding(predicted)
|
| 197 |
+
|
| 198 |
+
return [self.vocabulary.itos[idx] for idx in caption]
|
train.py
ADDED
|
@@ -0,0 +1,84 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import config
|
| 2 |
+
import utils
|
| 3 |
+
import torch.nn as nn
|
| 4 |
+
import torch.optim as optim
|
| 5 |
+
import numpy as np
|
| 6 |
+
|
| 7 |
+
from tqdm import tqdm
|
| 8 |
+
from torch.utils.data import DataLoader
|
| 9 |
+
from dataset import CollateDataset
|
| 10 |
+
|
| 11 |
+
|
| 12 |
+
def train_epoch(loader, model, optimizer, loss_fn, epoch):
|
| 13 |
+
model.train()
|
| 14 |
+
|
| 15 |
+
losses = []
|
| 16 |
+
|
| 17 |
+
loader = tqdm(loader)
|
| 18 |
+
|
| 19 |
+
for img, captions in loader:
|
| 20 |
+
img = img.to(config.DEVICE)
|
| 21 |
+
captions = captions.to(config.DEVICE)
|
| 22 |
+
|
| 23 |
+
output = model(img, captions)
|
| 24 |
+
|
| 25 |
+
loss = loss_fn(
|
| 26 |
+
output.reshape(-1, output.shape[2]),
|
| 27 |
+
captions[:, 1:].reshape(-1)
|
| 28 |
+
)
|
| 29 |
+
|
| 30 |
+
optimizer.zero_grad()
|
| 31 |
+
loss.backward()
|
| 32 |
+
optimizer.step()
|
| 33 |
+
|
| 34 |
+
loader.set_postfix(loss=loss.item())
|
| 35 |
+
|
| 36 |
+
losses.append(loss.item())
|
| 37 |
+
|
| 38 |
+
if config.SAVE_MODEL:
|
| 39 |
+
utils.save_checkpoint({
|
| 40 |
+
'state_dict': model.state_dict(),
|
| 41 |
+
'optimizer': optimizer.state_dict(),
|
| 42 |
+
'epoch': epoch,
|
| 43 |
+
'loss': np.mean(losses)
|
| 44 |
+
})
|
| 45 |
+
|
| 46 |
+
print(f'Epoch[{epoch}]: Loss {np.mean(losses)}')
|
| 47 |
+
|
| 48 |
+
|
| 49 |
+
def main():
|
| 50 |
+
all_dataset = utils.load_dataset()
|
| 51 |
+
|
| 52 |
+
train_dataset, _ = utils.train_test_split(dataset=all_dataset)
|
| 53 |
+
|
| 54 |
+
train_loader = DataLoader(
|
| 55 |
+
dataset=train_dataset,
|
| 56 |
+
batch_size=config.BATCH_SIZE,
|
| 57 |
+
pin_memory=config.PIN_MEMORY,
|
| 58 |
+
drop_last=False,
|
| 59 |
+
shuffle=True,
|
| 60 |
+
collate_fn=CollateDataset(pad_idx=all_dataset.vocab.stoi['<PAD>']),
|
| 61 |
+
)
|
| 62 |
+
|
| 63 |
+
model = utils.get_model_instance(all_dataset.vocab)
|
| 64 |
+
|
| 65 |
+
optimizer = optim.Adam(model.parameters(), lr=config.LEARNING_RATE)
|
| 66 |
+
loss_fn = nn.CrossEntropyLoss(ignore_index=all_dataset.vocab.stoi['<PAD>'])
|
| 67 |
+
|
| 68 |
+
starting_epoch = 1
|
| 69 |
+
|
| 70 |
+
if utils.can_load_checkpoint():
|
| 71 |
+
starting_epoch = utils.load_checkpoint(model, optimizer)
|
| 72 |
+
|
| 73 |
+
for epoch in range(starting_epoch, config.EPOCHS):
|
| 74 |
+
train_epoch(
|
| 75 |
+
train_loader,
|
| 76 |
+
model,
|
| 77 |
+
optimizer,
|
| 78 |
+
loss_fn,
|
| 79 |
+
epoch
|
| 80 |
+
)
|
| 81 |
+
|
| 82 |
+
|
| 83 |
+
if __name__ == '__main__':
|
| 84 |
+
main()
|
utils.py
ADDED
|
@@ -0,0 +1,111 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import os
|
| 2 |
+
import re
|
| 3 |
+
import html
|
| 4 |
+
import string
|
| 5 |
+
import torch
|
| 6 |
+
import config
|
| 7 |
+
import unicodedata
|
| 8 |
+
from nltk.tokenize import word_tokenize
|
| 9 |
+
|
| 10 |
+
from dataset import XRayDataset
|
| 11 |
+
from model import EncoderDecoderNet
|
| 12 |
+
from torch.utils.data import Subset
|
| 13 |
+
from sklearn.model_selection import train_test_split as sklearn_train_test_split
|
| 14 |
+
|
| 15 |
+
|
| 16 |
+
def load_dataset(raw_caption=False):
|
| 17 |
+
return XRayDataset(
|
| 18 |
+
root=config.DATASET_PATH,
|
| 19 |
+
transform=config.basic_transforms,
|
| 20 |
+
freq_threshold=config.VOCAB_THRESHOLD,
|
| 21 |
+
raw_caption=raw_caption
|
| 22 |
+
)
|
| 23 |
+
|
| 24 |
+
|
| 25 |
+
def get_model_instance(vocabulary):
|
| 26 |
+
model = EncoderDecoderNet(
|
| 27 |
+
features_size=config.FEATURES_SIZE,
|
| 28 |
+
embed_size=config.EMBED_SIZE,
|
| 29 |
+
hidden_size=config.HIDDEN_SIZE,
|
| 30 |
+
vocabulary=vocabulary,
|
| 31 |
+
encoder_checkpoint='./weights/chexnet.pth.tar'
|
| 32 |
+
)
|
| 33 |
+
model = model.to(config.DEVICE)
|
| 34 |
+
|
| 35 |
+
return model
|
| 36 |
+
|
| 37 |
+
def train_test_split(dataset, test_size=0.25, random_state=44):
|
| 38 |
+
train_idx, test_idx = sklearn_train_test_split(
|
| 39 |
+
list(range(len(dataset))),
|
| 40 |
+
test_size=test_size,
|
| 41 |
+
random_state=random_state
|
| 42 |
+
)
|
| 43 |
+
|
| 44 |
+
return Subset(dataset, train_idx), Subset(dataset, test_idx)
|
| 45 |
+
|
| 46 |
+
|
| 47 |
+
def save_checkpoint(checkpoint):
|
| 48 |
+
print('=> Saving checkpoint')
|
| 49 |
+
|
| 50 |
+
torch.save(checkpoint, config.CHECKPOINT_FILE)
|
| 51 |
+
|
| 52 |
+
|
| 53 |
+
def load_checkpoint(model, optimizer=None):
|
| 54 |
+
print('=> Loading checkpoint')
|
| 55 |
+
|
| 56 |
+
checkpoint = torch.load(config.CHECKPOINT_FILE, map_location=torch.device('cpu'))
|
| 57 |
+
model.load_state_dict(checkpoint['state_dict'])
|
| 58 |
+
|
| 59 |
+
if optimizer is not None:
|
| 60 |
+
optimizer.load_state_dict(checkpoint['optimizer'])
|
| 61 |
+
|
| 62 |
+
return checkpoint['epoch']
|
| 63 |
+
|
| 64 |
+
|
| 65 |
+
def can_load_checkpoint():
|
| 66 |
+
return os.path.exists(config.CHECKPOINT_FILE) and config.LOAD_MODEL
|
| 67 |
+
|
| 68 |
+
|
| 69 |
+
def remove_special_chars(text):
|
| 70 |
+
re1 = re.compile(r' +')
|
| 71 |
+
x1 = text.lower().replace('#39;', "'").replace('amp;', '&').replace('#146;', "'").replace(
|
| 72 |
+
'nbsp;', ' ').replace('#36;', '$').replace('\\n', "\n").replace('quot;', "'").replace(
|
| 73 |
+
'<br />', "\n").replace('\\"', '"').replace('<unk>', 'u_n').replace(' @.@ ', '.').replace(
|
| 74 |
+
' @-@ ', '-').replace('\\', ' \\ ')
|
| 75 |
+
|
| 76 |
+
return re1.sub(' ', html.unescape(x1))
|
| 77 |
+
|
| 78 |
+
|
| 79 |
+
def remove_non_ascii(text):
|
| 80 |
+
return unicodedata.normalize('NFKD', text).encode('ascii', 'ignore').decode('utf-8', 'ignore')
|
| 81 |
+
|
| 82 |
+
|
| 83 |
+
def to_lowercase(text):
|
| 84 |
+
return text.lower()
|
| 85 |
+
|
| 86 |
+
|
| 87 |
+
def remove_punctuation(text):
|
| 88 |
+
translator = str.maketrans('', '', string.punctuation)
|
| 89 |
+
return text.translate(translator)
|
| 90 |
+
|
| 91 |
+
|
| 92 |
+
def replace_numbers(text):
|
| 93 |
+
return re.sub(r'\d+', '', text)
|
| 94 |
+
|
| 95 |
+
|
| 96 |
+
def text2words(text):
|
| 97 |
+
return word_tokenize(text)
|
| 98 |
+
|
| 99 |
+
|
| 100 |
+
def normalize_text( text):
|
| 101 |
+
text = remove_special_chars(text)
|
| 102 |
+
text = remove_non_ascii(text)
|
| 103 |
+
text = remove_punctuation(text)
|
| 104 |
+
text = to_lowercase(text)
|
| 105 |
+
text = replace_numbers(text)
|
| 106 |
+
|
| 107 |
+
return text
|
| 108 |
+
|
| 109 |
+
|
| 110 |
+
def normalize_corpus(corpus):
|
| 111 |
+
return [normalize_text(t) for t in corpus]
|