DICOMpiler

dicompiler.py

""" 
DICOMpiler 
Splits a folder of DICOM files in one folder into subfolders by series UID
Warning: will throw an error if there are non-DICOM files in the folder

If you want to split the files according to another identifier, change 0x0020000e into the DICOM tag that you want.

Some useful tags to sort by:
0x00200011 Series Number
0x0020000e Series Instance UID

0x00100020 Patient ID

0x00080022 Acquisition Date
0x00080032 Acquisition Time            
0x00081030 Study Description        
0x0008103e Series Description
"""

from pathlib import Path
import pydicom

# specify the paths here
image_path = r"/source/of/your/images"
output_path = r"/destination/of/your/subfolders/output"

# looks for files in the folder - not recursive, and ignores all file extensions
# if the files are mixed and some have extensions, change the "*" to "*.dcm" or something
images = [im for im in Path(image_path).glob("*")]

# print the series IDs of the images
# print({pydicom.dcmread(im).get(0x0020000e).value for im in images})

# group images by series uid
series_grp = {}
for im in images:
    series_uid = pydicom.dcmread(im).get(0x0020000e).value
    if series_uid not in series_grp:
        series_grp[series_uid] = []
    series_grp[series_uid].append(im.relative_to(image_path))

# copy the files into the folders
import shutil
for series_uid, images in series_grp.items():
    series_path = Path(output_path) / series_uid
    series_path.mkdir(exist_ok=True, parents=True)
    for im in images:
        shutil.copy(Path(image_path) / im, series_path / im.name)

print("DONE")

dicomverter.py

"""
DICOMverter
Takes the output folders of DICOMpiler and turns it into .nii.gz files. 
Will ignore folders that can't be read by SimpleITK
"""

from pathlib import Path
import SimpleITK as sitk

# read the folders in the output folder
for folder in Path("output").glob("*"):
    try:
        reader = sitk.ImageSeriesReader()
        dicom_names = reader.GetGDCMSeriesFileNames(str(folder))
        reader.SetFileNames(dicom_names)
        image = reader.Execute()
        sitk.WriteImage(image, str(folder) + ".nii.gz")
    except Exception as e:
        print(folder)
        print(e)
        continue

print("DONE")