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dataloader_pth.py
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dataloader_pth.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
CODE RELEASE TO SUPPORT RESEARCH.
COMMERCIAL USE IS NOT PERMITTED.
#==============================================================================
An implementation based on:
***
C.I. Nwoye, T. Yu, C. Gonzalez, B. Seeliger, P. Mascagni, D. Mutter, J. Marescaux, N. Padoy.
Rendezvous: Attention Mechanisms for the Recognition of Surgical Action Triplets in Endoscopic Videos.
Medical Image Analysis, 78 (2022) 102433.
***
Created on Thu Oct 21 15:38:36 2021
#==============================================================================
Copyright 2021 The Research Group CAMMA Authors All Rights Reserved.
(c) Research Group CAMMA, University of Strasbourg, France
@ Laboratory: CAMMA - ICube
@ Author: Chinedu Innocent Nwoye
@ Website: http://camma.u-strasbg.fr
#==============================================================================
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
#==============================================================================
"""
import os
import random
import numpy as np
from PIL import Image
import torchvision.transforms as transforms
from torch.utils.data import Dataset, ConcatDataset, DataLoader
class CholecT50():
def __init__(self,
dataset_dir,
dataset_variant="cholect45-crossval",
test_fold=1,
augmentation_list=['original', 'vflip', 'hflip', 'contrast', 'rot90'],
normalize=True):
""" Args
dataset_dir : common path to the dataset (excluding videos, output)
list_video : list video IDs, e.g: ['VID01', 'VID02']
aug : data augumentation style
split : data split ['train', 'val', 'test']
Call
batch_size: int,
shuffle: True or False
Return
tuple ((image), (tool_label, verb_label, target_label, triplet_label))
"""
self.normalize = normalize
self.dataset_dir = dataset_dir
self.list_dataset_variant = {
"cholect45-crossval": "for CholecT45 dataset variant with the official cross-validation splits.",
"cholect50-crossval": "for CholecT50 dataset variant with the official cross-validation splits",
"cholect50-challenge": "for CholecT50 dataset variant as used in CholecTriplet challenge",
"cholect50": "for the CholecT50 dataset with original splits used in rendezvous paper",
"cholect45": "a pointer to cholect45-crossval",
"cholect50-subset": "specially created for EDU4SDS summer school"
}
assert dataset_variant in self.list_dataset_variant.keys(), print(dataset_variant, "is not a valid dataset variant")
video_split = self.split_selector(case=dataset_variant)
train_videos = sum([v for k,v in video_split.items() if k!=test_fold], []) if 'crossval' in dataset_variant else video_split['train']
test_videos = sum([v for k,v in video_split.items() if k==test_fold], []) if 'crossval' in dataset_variant else video_split['test']
if 'crossval' in dataset_variant:
val_videos = train_videos[-5:]
train_videos = train_videos[:-5]
else:
val_videos = video_split['val']
self.train_records = ['VID{}'.format(str(v).zfill(2)) for v in train_videos]
self.val_records = ['VID{}'.format(str(v).zfill(2)) for v in val_videos]
self.test_records = ['VID{}'.format(str(v).zfill(2)) for v in test_videos]
self.augmentations = {
'original': self.no_augumentation,
'vflip': transforms.RandomVerticalFlip(0.4),
'hflip': transforms.RandomHorizontalFlip(0.4),
'contrast': transforms.ColorJitter(brightness=0.1, contrast=0.2, saturation=0, hue=0),
'rot90': transforms.RandomRotation(90,expand=True),
'brightness': transforms.RandomAdjustSharpness(sharpness_factor=1.6, p=0.5),
'contrast': transforms.RandomAutocontrast(p=0.5),
}
self.augmentation_list = []
for aug in augmentation_list:
self.augmentation_list.append(self.augmentations[aug])
trainform, testform = self.transform()
self.build_train_dataset(trainform)
self.build_val_dataset(trainform)
self.build_test_dataset(testform)
def list_dataset_variants(self):
print(self.list_dataset_variant)
def list_augmentations(self):
print(self.augmentations.keys())
def split_selector(self, case='cholect50'):
switcher = {
'cholect50': {
'train': [1, 15, 26, 40, 52, 65, 79, 2, 18, 27, 43, 56, 66, 92, 4, 22, 31, 47, 57, 68, 96, 5, 23, 35, 48, 60, 70, 103, 13, 25, 36, 49, 62, 75, 110],
'val' : [8, 12, 29, 50, 78],
'test' : [6, 51, 10, 73, 14, 74, 32, 80, 42, 111]
},
'cholect50-challenge': {
'train': [1, 15, 26, 40, 52, 79, 2, 27, 43, 56, 66, 4, 22, 31, 47, 57, 68, 23, 35, 48, 60, 70, 13, 25, 49, 62, 75, 8, 12, 29, 50, 78, 6, 51, 10, 73, 14, 32, 80, 42],
'val': [5, 18, 36, 65, 74],
'test': [92, 96, 103, 110, 111]
},
'cholect45-crossval': {
1: [79, 2, 51, 6, 25, 14, 66, 23, 50,],
2: [80, 32, 5, 15, 40, 47, 26, 48, 70,],
3: [31, 57, 36, 18, 52, 68, 10, 8, 73,],
4: [42, 29, 60, 27, 65, 75, 22, 49, 12,],
5: [78, 43, 62, 35, 74, 1, 56, 4, 13,],
},
'cholect50-crossval': {
1: [79, 2, 51, 6, 25, 14, 66, 23, 50, 111],
2: [80, 32, 5, 15, 40, 47, 26, 48, 70, 96],
3: [31, 57, 36, 18, 52, 68, 10, 8, 73, 103],
4: [42, 29, 60, 27, 65, 75, 22, 49, 12, 110],
5: [78, 43, 62, 35, 74, 1, 56, 4, 13, 92],
},
}
return switcher.get(case)
def no_augumentation(self, x):
return x
def transform(self):
normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])
op_test = [transforms.Resize((256, 448)), transforms.ToTensor(), ]
op_train = [transforms.Resize((256, 448))] + self.augmentation_list + [transforms.Resize((256, 448)), transforms.ToTensor()]
if self.normalize:
op_test.append(normalize)
op_train.append(normalize)
testform = transforms.Compose(op_test)
trainform = transforms.Compose(op_train)
return trainform, testform
def build_train_dataset(self, transform):
iterable_dataset = []
for video in self.train_records:
dataset = T50(img_dir = os.path.join(self.dataset_dir, 'data', video),
triplet_file = os.path.join(self.dataset_dir, 'triplet', '{}.txt'.format(video)),
tool_file = os.path.join(self.dataset_dir, 'instrument', '{}.txt'.format(video)),
verb_file = os.path.join(self.dataset_dir, 'verb', '{}.txt'.format(video)),
target_file = os.path.join(self.dataset_dir, 'target', '{}.txt'.format(video)),
transform=transform)
iterable_dataset.append(dataset)
self.train_dataset = ConcatDataset(iterable_dataset)
def build_val_dataset(self, transform):
iterable_dataset = []
for video in self.val_records:
dataset = T50(img_dir = os.path.join(self.dataset_dir, 'data', video),
triplet_file = os.path.join(self.dataset_dir, 'triplet', '{}.txt'.format(video)),
tool_file = os.path.join(self.dataset_dir, 'instrument', '{}.txt'.format(video)),
verb_file = os.path.join(self.dataset_dir, 'verb', '{}.txt'.format(video)),
target_file = os.path.join(self.dataset_dir, 'target', '{}.txt'.format(video)),
transform=transform)
iterable_dataset.append(dataset)
self.val_dataset = ConcatDataset(iterable_dataset)
def build_test_dataset(self, transform):
iterable_dataset = []
for video in self.test_records:
dataset = T50(img_dir = os.path.join(self.dataset_dir, 'data', video),
triplet_file = os.path.join(self.dataset_dir, 'triplet', '{}.txt'.format(video)),
tool_file = os.path.join(self.dataset_dir, 'instrument', '{}.txt'.format(video)),
verb_file = os.path.join(self.dataset_dir, 'verb', '{}.txt'.format(video)),
target_file = os.path.join(self.dataset_dir, 'target', '{}.txt'.format(video)),
transform=transform)
iterable_dataset.append(dataset)
self.test_dataset = iterable_dataset
def build(self):
return (self.train_dataset, self.val_dataset, self.test_dataset)
class T50(Dataset):
def __init__(self, img_dir, triplet_file, tool_file, verb_file, target_file, transform=None, target_transform=None):
self.triplet_labels = np.loadtxt(triplet_file, dtype=np.int, delimiter=',',)
self.tool_labels = np.loadtxt(tool_file, dtype=np.int, delimiter=',',)
self.verb_labels = np.loadtxt(verb_file, dtype=np.int, delimiter=',',)
self.target_labels = np.loadtxt(target_file, dtype=np.int, delimiter=',',)
self.img_dir = img_dir
self.transform = transform
self.target_transform = target_transform
def __len__(self):
return len(self.triplet_labels)
def __getitem__(self, index):
triplet_label = self.triplet_labels[index, 1:]
tool_label = self.tool_labels[index, 1:]
verb_label = self.verb_labels[index, 1:]
target_label = self.target_labels[index, 1:]
basename = "{}.png".format(str(self.triplet_labels[index, 0]).zfill(6))
img_path = os.path.join(self.img_dir, basename)
image = Image.open(img_path)
if self.transform:
image = self.transform(image)
if self.target_transform:
triplet_label = self.target_transform(triplet_label)
return image, (tool_label, verb_label, target_label, triplet_label)
if __name__ == "__main__":
print("Refers to https://github.com/CAMMA-public/cholect45 for the usage guide.")