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b/common/dataset.py |
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from __future__ import print_function, division |
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import os |
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import torch |
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import pandas as pd |
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from skimage import io, transform |
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import numpy as np |
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from torch.utils.data import Dataset, DataLoader |
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from torchvision import transforms, utils |
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from PIL import Image, ImageOps |
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from random import random, randint |
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# Ignore warnings |
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import warnings |
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import pdb |
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warnings.filterwarnings("ignore") |
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def make_dataset(root,mode): |
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""" Takes in the root directory and mode(train or val or test) as inputs |
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then joins the path with the folder of the specified mode.Applies normalize |
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function to each img of the folder and returns a list of tuples containing |
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image and its corresponding mask. |
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Returns |
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------- |
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tuple : Normalized image and its annotation. |
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""" |
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assert mode in ['train', 'val', 'test'] |
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items = [] |
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if mode == 'train': |
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train_img_path = os.path.join(root, 'Train/train_image') |
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train_mask_path = os.path.join(root, 'Train/train_mask') |
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images = os.listdir(train_img_path) |
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labels = os.listdir(train_mask_path) |
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images.sort() |
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labels.sort() |
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for it_im, it_gt in zip(images, labels): |
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item = (os.path.join(train_img_path, it_im), os.path.join(train_mask_path, it_gt)) |
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items.append(item) |
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elif mode == 'val': |
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val_img_path = os.path.join(root, 'Val/val_img') |
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val_mask_path = os.path.join(root, 'Val/val_mask') |
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images = os.listdir(val_img_path) |
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labels = os.listdir(val_mask_path) |
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images.sort() |
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labels.sort() |
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for it_im, it_gt in zip(images, labels): |
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item = (os.path.join(val_img_path, it_im), os.path.join(val_mask_path, it_gt)) |
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items.append(item) |
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else: |
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test_img_path = os.path.join(root, 'Test/test_img') |
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# test_mask_path = os.path.join(root, 'Test/test_mask') |
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images = os.listdir(test_img_path) |
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#labels = os.listdir(test_mask_path) |
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images.sort() |
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#labels.sort() |
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for it_im in images: |
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item = os.path.join(test_img_path, it_im) |
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items.append(item) |
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return items |
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class MedicalImageDataset(Dataset): |
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""" GI dataset.""" |
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def __init__(self, mode, root_dir, transform=None): |
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""" |
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Args: |
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csv_file (string): Path to the csv file with annotations. |
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root_dir (string): Directory with all the images. |
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transform (callable, optional): Optional transform to be applied |
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on a sample. |
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""" |
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self.root_dir = root_dir |
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self.mode=mode |
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self.transform = transform |
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self.imgs = make_dataset(root_dir, mode) |
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def __len__(self): |
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return len(self.imgs) |
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def __getitem__(self,index): |
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if self.mode== 'test': |
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img_path=self.imgs[index] |
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img =np.array( Image.open(img_path)) |
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img_shape=np.array(img).shape |
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if self.transform: |
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augmented = self.transform(image=img) |
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image=augmented["image"] |
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return image |
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else: |
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img_path, mask_path = self.imgs[index] |
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# print("{} and {}".format(img_path,mask_path)) |
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img = np.array(Image.open(img_path)) # .convert('RGB') |
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# mask = Image.open(mask_path) # .convert('RGB') |
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# img = Image.open(img_path).convert('L') |
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mask = np.array(Image.open(mask_path).convert('L')) |
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# print('{} and {}'.format(img_path,mask_path)) |
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if self.transform: |
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augmented = self.transform(image=img,mask=mask) |
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image=augmented["image"] |
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mask=augmented["mask"] |
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return [image, mask] |