[英]How to iterate through a directory and apply python script to multiple subfolders (not files) in that directory?
I am using a programme which converts dicom files stored in two different folders (input folders) to nifti format and saves them to a third folder (output folder).我正在使用一个程序,它将存储在两个不同文件夹(输入文件夹)中的 dicom 文件转换为 nifti 格式并将它们保存到第三个文件夹(输出文件夹)。 At the moment this programme requires me to manually specify the filepaths for these three folders.
目前这个程序需要我手动指定这三个文件夹的文件路径。
I have a directory with multiple patients/subjects in it, each containing the two (input) folders.我有一个目录,其中包含多个患者/受试者,每个都包含两个(输入)文件夹。 The third (output) folder does not exist but I have added os.makedirs to the above programme so it creates it.
第三个(输出)文件夹不存在,但我已将 os.makedirs 添加到上述程序中,以便创建它。
I would like to create a script that can automate this process so that I don't have to manually specify the 3 filepaths for each patient.我想创建一个可以自动执行此过程的脚本,这样我就不必为每个患者手动指定 3 个文件路径。 I want it to take each and every patient folder in the directory and apply the above - ie read the dicom files in the two input folders for each patient, and then save the converted nifti files to a new folder for that specific patient.
我希望它获取目录中的每个患者文件夹并应用上述内容 - 即为每个患者读取两个输入文件夹中的 dicom 文件,然后将转换后的 nifti 文件保存到该特定患者的新文件夹中。
#Importing libraries and modules:
import os
from dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs
#Next I want to create a for-loop that will walk through the directory patient folders/subfolders
#and that can then feed into the below section to automatically specify the RTstructdicom folder, the imagedicom folder
#and that can create a new folder called "Nifti" that can store the output.
for folderName, subfolders, filenames in os.walk('/Users/sh/Drive/folderC'):
#**This is where I'm stuck**
#This next section will create the specified outputfolder e.g. 'Nifti',
#Then load the RTstruct dicom from the specified folder,
#Then load the images dicoms from the specified folder,
#Then convert both to Nifti files saved in the specified output folder
RTstructdicom = ('/Users/sh/Drive/folderC/patient001/subfolder 1/RTSTRUCT_20210124_205145/RTSTRUCT/RTSTRUCT_20210124_205145.dcm')
imagedicoms = ('/Users/sh/Drive/folderC/patient001/subfolder 1/10022/DICOM')
outputfolder = ('/Users/sh/Drive/folderC/patient001/subfolder 1/10022/NIFTI')
print(list_rt_structs(RTstructdicom))
os.makedirs(outputfolder)
dcmrtstruct2nii(RTstructdicom, imagedicoms, outputfolder )
It's not clear to me what you want to do with each these multiple subfolders.我不清楚您想对这些多个子文件夹中的每一个做什么。
I hope this example will get you started.我希望这个例子能让你开始。
I did my best to我尽力了
os.walk
os.walk
遍历它I suggest learning about the Path
object from the pathlib
: https://docs.python.org/3/library/pathlib.html#basic-use我建议从 pathlib 中了解
Path
pathlib
: https://docs.python.org/3/library/pathlib.html#basic-use
I wanted to copy the contents of a subdirectory so I imported shutil.我想复制一个子目录的内容,所以我导入了shutil。
This is the sample tree I created:这是我创建的示例树:
folderC
├── patient001
│ └── subfolder 1
│ └── RTSTRUCT_085211_328790
│ └── RTSTRUCT
│ └── RTSTRUCT_085211_328790
│ └── RTSTRUCT_085211_328790.dcm
├── patient002
│ └── subfolder 2
│ └── RTSTRUCT_958381_489352
│ └── RTSTRUCT
│ └── RTSTRUCT_958381_489352
│ └── RTSTRUCT_958381_489352.dcm
└── patient003
└── subfolder 3
└── RTSTRUCT_731792_968907
└── RTSTRUCT
└── RTSTRUCT_731792_968907
└── RTSTRUCT_731792_968907.dcm
I then used the following code to to something to some particular subfolders:然后,我使用以下代码对某些特定的子文件夹进行处理:
import os
from pathlib import Path
import shutil
for root, dirnames, _ in os.walk("folderC"):
root_path = Path(root)
for dirname in dirnames:
dir_path = root_path / dirname
# Use conditionals at this point to select which directory you want to work with.
# For example.
# make a destination folder in all folders with "subfolder" in the name
if "subfolder" in dir_path.name:
destination = (dir_path / "10022" / "NIFTI")
destination.mkdir(exist_ok=True, parents=True)
# An example that copies the files from the deepest "RTSTRUCT_xxxx_xxxx" folder
# to the destination
if "RTSTRUCT_" in dir_path.name and dir_path.parent.name == "RTSTRUCT":
shutil.copytree(dir_path, destination, dirs_exist_ok=True)
This is the result.这就是结果。 You can see the files from the "RSTRUCT_xxx_xxxx" directory is in the nearly created one inside of the "subfolder x" directory.
您可以看到“RSTRUCT_xxx_xxxx”目录中的文件位于“子文件夹 x”目录中几乎创建的文件中。
folderC
├── patient001
│ └── subfolder 1
│ ├── 10022
│ │ └── NIFTI
│ │ └── RTSTRUCT_085211_328790.dcm
│ └── RTSTRUCT_085211_328790
│ └── RTSTRUCT
│ └── RTSTRUCT_085211_328790
│ └── RTSTRUCT_085211_328790.dcm
├── patient002
│ └── subfolder 2
│ ├── 10022
│ │ └── NIFTI
│ │ └── RTSTRUCT_958381_489352.dcm
│ └── RTSTRUCT_958381_489352
│ └── RTSTRUCT
│ └── RTSTRUCT_958381_489352
│ └── RTSTRUCT_958381_489352.dcm
└── patient003
└── subfolder 3
├── 10022
│ └── NIFTI
│ └── RTSTRUCT_731792_968907.dcm
└── RTSTRUCT_731792_968907
└── RTSTRUCT
└── RTSTRUCT_731792_968907
└── RTSTRUCT_731792_968907.dcm
There are some simple examples in the Python documentation as well: https://docs.python.org/3/library/os.html#os.walk Python 文档中也有一些简单的示例: https://docs.python.org/3/library/os.html#os.walk
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