如果这个问题太基础了,我很抱歉,但我刚刚开始使用 PyTorch(和 Python)。
我试图一步一步地按照这里的说明进行操作: https ://pytorch.org/tutorials/beginner/finetuning_torchvision_models_tutorial.html
但是,我正在使用一些 DICOM 文件,这些文件保存在两个目录中(CANCER/NOCANCER)。我用拆分文件夹拆分它们,使其结构化以与 ImageFolder 数据集一起使用(如教程中所做的那样)。
我知道我只需要加载从 DICOM 文件中提取的 pixel_arrays,并且我编写了一些辅助函数来:
- 读取 .dcm 文件的所有路径;
- 读取它们并提取pixel_array;
- 做一点预处理。以下是辅助函数的概要:
import os
import pydicom
import cv2
import numpy as np
def createListFiles(dirName):
print("Fetching all the files in the data directory...")
lstFilesDCM =[]
for root, dir, fileList in os.walk(dirName):
for filename in fileList:
if ".dcm" in filename.lower():
lstFilesDCM.append(os.path.join( root , filename))
return lstFilesDCM
def castHeight(list):
lstHeight = []
min_height = 0
for filenameDCM in list:
readfile = pydicom.read_file(filenameDCM)
lstHeight.append(readfile.pixel_array.shape[0])
min_height = np.min(lstHeight)
return min_height
def castWidth(list):
lstWidth = []
min_Width = 0
for filenameDCM in list:
readfile = pydicom.read_file(filenameDCM)
lstWidth.append(readfile.pixel_array.shape[1])
min_Width = np.min(lstWidth)
return min_Width
def Preproc1(listDCM):
new_height, new_width = castHeight(listDCM), castWidth(listDCM)
ConstPixelDims = (len(listDCM), int(new_height), int(new_width))
ArrayDCM = np.zeros(ConstPixelDims, dtype=np.float32)
## loop through all the DICOM files
for filenameDCM in listDCM:
## read the file
ds = pydicom.read_file(filenameDCM)
mx0 = ds.pixel_array
## Standardisation
imgb = mx0.astype('float32')
imgb_stand = (imgb - imgb.mean(axis=(0, 1), keepdims=True)) / imgb.std(axis=(0, 1), keepdims=True)
## Normalisation
imgb_norm = cv2.normalize(imgb_stand, None, 0, 1, cv2.NORM_MINMAX)
## we make sure that data is saved as a data_array as a numpy array
data = np.array(imgb_norm)
## we save it into ArrayDicom and resize it based 'ConstPixelDims'
ArrayDCM[listDCM.index(filenameDCM), :, :] = cv2.resize(data, (int(new_width), int(new_height)), interpolation = cv2.INTER_CUBIC)
return ArrayDCM
那么,现在,我如何告诉数据加载器加载数据,考虑到它用于标记目的的结构,但只有在对其进行提取和预处理之后?我在文档中引用了教程的“加载数据”部分,内容如下:
# Create training and validation datasets
image_datasets = {x: datasets.ImageFolder(os.path.join(data_dir, x), data_transforms[x]) for x in ['train', 'val']}
# Create training and validation dataloaders
dataloaders_dict = {x: torch.utils.data.DataLoader(image_datasets[x], batch_size=batch_size, shuffle=True, num_workers=4) for x in ['train', 'val']}
如果它有任何意义,是否有可能做一些事情
image_datasets = {x: datasets.ImageFolder(Preproc1(os.path.join(data_dir, x)), data_transforms[x]) for x in ['train', 'val']}
?
另外,我的另一个问题是:当教程建议进行 transforms.Normalize 时,是否值得在我的预处理中进行标准化步骤?
我真的很抱歉这听起来很模糊,我已经尝试解决这个问题好几个星期了,但我无法解决。