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(Python) Base module for parsing DICOM files in the pf* family.

Project description

Quick Overview

  • pfdicom is primarily a base module for other, more specialized classes. It typically is never used on its own.

Overview

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.

Dependencies

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)

Installation

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.

Examples

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

Project details


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1.2.2

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1.1.2

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Filename, size & hash SHA256 hash help File type Python version Upload date
pfdicom-1.2.2.tar.gz (8.6 kB) Copy SHA256 hash SHA256 Source None Jul 19, 2018

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