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# Copyright 2020 - 2022 MONAI Consortium
# 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.
from sklearn.model_selection import KFold ## K折交叉验证
import pickle
import os
import json
import math
import numpy as np
import torch
from monai import transforms
import SimpleITK as sitk
from tqdm import tqdm
from torch.utils.data import Dataset
import glob
from light_training.dataloading.utils import unpack_dataset
import random
class MedicalDataset(Dataset):
def __init__(self, datalist, test=False) -> None:
super().__init__()
self.datalist = datalist
self.test = test
self.data_cached = []
for p in tqdm(self.datalist, total=len(self.datalist)):
info = self.load_pkl(p)
self.data_cached.append(info)
## unpacking
print(f"unpacking data ....")
# for
folder = []
for p in self.datalist:
f = os.path.dirname(p)
if f not in folder:
folder.append(f)
for f in folder:
unpack_dataset(f,
unpack_segmentation=True,
overwrite_existing=False,
num_processes=8)
print(f"data length is {len(self.datalist)}")
def load_pkl(self, data_path):
pass
properties_path = f"{data_path[:-4]}.pkl"
df = open(properties_path, "rb")
info = pickle.load(df)
return info
def post(self, batch_data):
return batch_data
def read_data(self, data_path):
image_path = data_path.replace(".npz", ".npy")
seg_path = data_path.replace(".npz", "_seg.npy")
image_data = np.load(image_path, "r+")
seg_data = None
if not self.test:
seg_data = np.load(seg_path, "r+")
return image_data, seg_data
def __getitem__(self, i):
image, seg = self.read_data(self.datalist[i])
properties = self.data_cached[i]
if seg is None:
return {
"data": image,
"properties": properties
}
else :
return {
"data": image,
"seg": seg,
"properties": properties
}
def __len__(self):
return len(self.datalist)
def get_train_test_loader_from_test_list(data_dir, test_list):
all_paths = glob.glob(f"{data_dir}/*.npz")
test_datalist = []
train_datalist = []
test_list_1 = []
for t in test_list:
test_list_1.append(t.replace(".nii.gz", ""))
test_list = test_list_1
for p in all_paths:
p2 = p.split("/")[-1].split(".")[0]
if p2 in test_list:
test_datalist.append(p)
else :
train_datalist.append(p)
print(f"training data is {len(train_datalist)}")
print(f"test data is {len(test_datalist)}", test_datalist)
train_ds = MedicalDataset(train_datalist)
test_ds = MedicalDataset(test_datalist)
loader = [train_ds, test_ds]
return loader
def get_kfold_data(data_paths, n_splits, shuffle=False):
X = np.arange(len(data_paths))
kfold = KFold(n_splits=n_splits, shuffle=shuffle) ## kfold为KFolf类的一个对象
return_res = []
for a, b in kfold.split(X):
fold_train = []
fold_val = []
for i in a:
fold_train.append(data_paths[i])
for j in b:
fold_val.append(data_paths[j])
return_res.append({"train_data": fold_train, "val_data": fold_val})
return return_res
def get_kfold_loader(data_dir, fold=0, test_dir=None):
all_paths = glob.glob(f"{data_dir}/*.npz")
fold_data = get_kfold_data(all_paths, 5)[fold]
train_datalist = fold_data["train_data"]
val_datalist = fold_data["val_data"]
print(f"training data is {len(train_datalist)}")
print(f"validation data is {len(val_datalist)}")
train_ds = MedicalDataset(train_datalist)
val_ds = MedicalDataset(val_datalist)
if test_dir is not None:
test_paths = glob.glob(f"{test_dir}/*.npz")
test_ds = MedicalDataset(test_paths, test=True)
else:
test_ds = None
loader = [train_ds, val_ds, test_ds]
return loader
def get_all_training_loader(data_dir, fold=0, test_dir=None):
## train all labeled data
## fold denote the validation data in training data
all_paths = glob.glob(f"{data_dir}/*.npz")
fold_data = get_kfold_data(all_paths, 5)[fold]
train_datalist = all_paths
val_datalist = fold_data["val_data"]
print(f"training data is {len(train_datalist)}")
print(f"validation data is {len(val_datalist)}")
train_ds = MedicalDataset(train_datalist)
val_ds = MedicalDataset(val_datalist)
if test_dir is not None:
test_paths = glob.glob(f"{test_dir}/*.npz")
test_ds = MedicalDataset(test_paths, test=True)
else:
test_ds = None
loader = [train_ds, val_ds, test_ds]
return loader
def get_train_val_test_loader_seperate(train_dir, val_dir, test_dir=None):
train_datalist = glob.glob(f"{train_dir}/*.npz")
val_datalist = glob.glob(f"{val_dir}/*.npz")
print(f"training data is {len(train_datalist)}")
print(f"validation data is {len(val_datalist)}")
if test_dir is not None:
test_datalist = glob.glob(f"{test_dir}/*.npz")
print(f"test data is {len(test_datalist)}")
test_ds = MedicalDataset(test_datalist, test=True)
else :
test_ds = None
train_ds = MedicalDataset(train_datalist)
val_ds = MedicalDataset(val_datalist)
loader = [train_ds, val_ds, test_ds]
return loader
def get_train_val_test_loader_from_split_json(data_dir, split_json_file):
import json
with open(split_json_file, "r") as f:
datalist = json.loads(f.read())
train_datalist = datalist["train"]
val_datalist = datalist["validation"]
test_datalist = datalist["test"]
def add_pre(datalist):
for i in range(len(datalist)):
datalist[i] = os.path.join(data_dir, datalist[i])
add_pre(train_datalist)
add_pre(val_datalist)
add_pre(test_datalist)
print(f"training data is {len(train_datalist)}")
print(f"validation data is {len(val_datalist)}")
print(f"test data is {len(test_datalist)}", sorted(test_datalist))
train_ds = MedicalDataset(train_datalist)
val_ds = MedicalDataset(val_datalist)
test_ds = MedicalDataset(test_datalist)
loader = [train_ds, val_ds, test_ds]
return loader
def get_train_val_test_loader_from_train(data_dir, train_rate=0.7, val_rate=0.1, test_rate=0.2, seed=42):
## train all labeled data
## fold denote the validation data in training data
all_paths = glob.glob(f"{data_dir}/*.npz")
# fold_data = get_kfold_data(all_paths, 5)[fold]
train_number = int(len(all_paths) * train_rate)
val_number = int(len(all_paths) * val_rate)
test_number = int(len(all_paths) * test_rate)
random.seed(seed)
# random_state = random.random
random.shuffle(all_paths)
train_datalist = all_paths[:train_number]
val_datalist = all_paths[train_number: train_number + val_number]
test_datalist = all_paths[-test_number:]
print(f"training data is {len(train_datalist)}")
print(f"validation data is {len(val_datalist)}")
print(f"test data is {len(test_datalist)}", sorted(test_datalist))
train_ds = MedicalDataset(train_datalist)
val_ds = MedicalDataset(val_datalist)
test_ds = MedicalDataset(test_datalist)
loader = [train_ds, val_ds, test_ds]
return loader
def get_train_loader_from_train(data_dir):
## train all labeled data
## fold denote the validation data in training data
all_paths = glob.glob(f"{data_dir}/*.npz")
# fold_data = get_kfold_data(all_paths, 5)[fold]
train_ds = MedicalDataset(all_paths)
return train_ds
def get_test_loader_from_test(data_dir):
all_paths = glob.glob(f"{data_dir}/*.npz")
test_ds = MedicalDataset(all_paths)
return test_ds
def get_multi_dir_training_loader(data_dir, fold=0, test_dir=None):
## train all labeled data
## fold denote the validation data in training data
all_paths = []
for p in data_dir:
paths = glob.glob(f"{p}/*.npz")
for pp in paths:
all_paths.append(pp)
# print(all_paths)
fold_data = get_kfold_data(all_paths, 5)[fold]
train_datalist = all_paths
val_datalist = fold_data["val_data"]
print(f"training data is {len(train_datalist)}")
print(f"validation data is {len(val_datalist)}")
train_ds = MedicalDataset(train_datalist)
val_ds = MedicalDataset(val_datalist)
if test_dir is not None:
test_paths = glob.glob(f"{test_dir}/*.npz")
test_ds = MedicalDataset(test_paths, test=True)
else:
test_ds = None
loader = [train_ds, val_ds, test_ds]
return loader |