Cookbook¶

This is a collection of tips and tricks that can be useful when working with pylinac.

Combining DICOM files into a single file¶

There are cases when multiple DICOM files are related and should be treated as a single file.

from pylinac.image import load_multiples, load

files = ["file1.dcm", "file2.dcm", "file3.dcm"]
combined_img = load_multiples(files, method="mean", stretch_each=True, loader=load)
# save to a new DICOM file
combined_img.save("combined.dcm")
# plot, etc
combined_img.plot()

See load_multiples() for more information.

Filtering DICOM files from a directory¶

This will return only DICOM files from a directory, assuming there are other files (PDFs, text files, etc) in the directory.

Looking for DICOM files only at the root directory¶

import glob
from pathlib import Path

from pylinac.core.io import is_dicom

dicom_files = [
    f for f in glob.glob("my_directory") if Path(f).is_file() and is_dicom(f)
]

Looking for DICOM files in this and all subdirectories¶

 import glob
 from pathlib import Path
 from pylinac.core.io import is_dicom

 dicom_files = [
     f
     for f in glob.glob("my_directory/**", recursive=True)
     if Path(f).is_file() and is_dicom(f)
 ]

See is_dicom() for more information.

Filtering DICOM images only¶

This will find DICOM files that are images specifically. E.g. pulling out RT images from amongst RT plans, etc.

import glob
from pathlib import Path
from pylinac.core.io import is_dicom_image

dicom_image_files = [
    f
    for f in glob.glob("my_directory/**", recursive=True)
    if Path(f).is_file() and is_dicom_image(f)
]

See is_dicom_image() for more information.

Temporarily Unzip Files¶

It’s quite common that you may want to analyze files inside a zip archive. Assuming that no modification is required and that you want to leave the zip archive as you found it, you can use the following code to perform actions in a temporary directory:

from pathlib import Path
from pylinac.core.io import TemporaryZipDirectory

zip_file = "my_stuff.zip"
# contains a.dcm and b.txt
with TemporaryZipDirectory(zip_file) as zip_dir:
    pf = PicketFence(Path(zip_dir / "a.dcm"))
    ...

Converting TIFF to DICOM¶

See TIFF to DICOM.

Manipulating a DICOM file and saving back¶

This use case is to modify a DICOM file and save it back to disk. This might be to apply known corrections before analysis, etc.

from pylinac.image import DicomImage

img = DicomImage("my_dicom.dcm")
img.rotate(45)
img.normalize()
img.filter()
img.save("my_modified_dicom.dcm")
# my_modified_dicom.dcm can be treated like any other DICOM file

See How data is loaded and DicomImage for available manipulations.