(Python) Base module for parsing DICOM files in the pf* family.
- pfdicom is primarily a base module for other, more specialized classes. It typically is never used on its own.
pfdicom in and of itself provides minimal end value. This module/class is intended to be a building block for deeper functionality. Its purpose is to probe a given directory filesystem for DICOM files and construct a tree representation (using pftree), and then, for each directory provide the means to read in a given DICOM file (using pydicom) to provide some minimal tag extraction and output file templating.
Most importantly, derived classes of this parent class can provide detailed and powerful methods to process the directories containing DICOM files, saving results to an output file tree.
The following dependencies are installed on your host system/python3 virtual env (they will also be automatically installed if pulled from pypi):
- pfmisc (various misc modules and classes for the pf* family of objects)
- pftree (create a dictionary representation of a filesystem hierarchy)
The best method of installing this script and all of its dependencies is by fetching it from PyPI
pip3 install pfdciom
Command line arguments
-I|--inputDir <inputDir> Input DICOM directory to examine. By default, the first file in this directory is examined for its tag information. There is an implicit assumption that each <inputDir> contains a single DICOM series. -i|--inputFile <inputFile> An optional <inputFile> specified relative to the <inputDir>. If specified, then do not perform a directory walk, but convert only this file. [-O|--outputDir <outputDir>] The directory to contain all output files. -e|--extension <DICOMextension> An optional extension to filter the DICOM files of interest from the <inputDir>. [-t|--threads <numThreads>] If specified, break the innermost analysis loop into <numThreads> threads. Please note the following caveats: * Only thread if you have a high CPU analysis loop. Since most of the operations of this module will entail reading and writing DICOM files, and since these operations are the bulk of the execution time, adding threading will not really help. * Threading will change the nature of the innermost looping across the problem domain, with the result that *all* of the problem data will be read into memory! That means all of DICOMs across all of the subdirs! In non-threading mode, only DICOMs from a single directory at a time are read and then discarded. This flag is less applicable to this base class. It is here to provide fall-through compatibility with derived classes. [-x|--man] Show full help. [-y|--synopsis] Show brief help. -v|--verbosity <level> Set the app verbosity level. -1: No internal output. 0: All internal output.
Run on a target tree, exploring the space of all possible targets.
pfdicom -I /var/www/html \ -O /tmp \ -o %PatientID-%PatientAge \ -e dcm \ --printElapsedTime