Installation and setup

pylidc works on Linux, Mac, and Windows, and on Python 2 and 3.

The package can be installed via pip:

pip install pylidc

Dicom file directory configuration

While pylidc has many functions for analyzing and querying only annotation data (which do not require DICOM image data access), pylidc also has many functions that do require access to the DICOM files associated with the LIDC dataset. pylidc looks for a special configuration file that tells it where DICOM data is located on your system. You can use pylidc without creating this configuration file, but of course, any functions that depend on CT image data will not be usable.

pylidc looks in your home folder for a configuration file called, .pylidcrc on Mac and Linux, or pylidc.conf on Windows. You must create this file. On Linux and Mac, the file should be located at /home/[user]/.pylidcrc. On Windows, the file should be located at C:Users[User]pylidc.conf.

The configuration file should be formatted as follows:

path = /path/to/big_external_drive/datasets/LIDC-IDRI
warn = True

If you want to use pylidc without utilizing the DICOM data (for say, querying annotation attributes, etc.), you can remove path and set warn to False and leave the path undefined, i.e.,:

warn = False

and the module won’t bother you about it each time you import the module.

The DICOM files should be stored in a folder with corresponding PatientID (i.e., a string of the form LIDC-IDRI-dddd, where dddd is a string of 4 integers). pylidc looks for a subfolder within:


for DICOM files that match the SeriesInstanceUID and StudyInstanceUID of the particular scan being requested.