Metadata-Version: 1.0
Name: pfdicom-tagSub
Version: 1.4.0
Summary: Process DICOM tags and performs substitutions -- part of the pf* family.
Home-page: https://github.com/FNNDSC/pfdicom_tagSub
Author: FNNDSC
Author-email: dev@babymri.org
License: MIT
Description: pfdicom_tagSub
        ==================
        
        .. image:: https://badge.fury.io/py/pfdicom_tagSub.svg
            :target: https://badge.fury.io/py/pfdicom_tagSub
        
        .. image:: https://travis-ci.org/FNNDSC/pfdicom_tagSub.svg?branch=master
            :target: https://travis-ci.org/FNNDSC/pfdicom_tagSub
        
        .. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
            :target: https://badge.fury.io/py/pfdicom_tagSub
        
        .. contents:: Table of Contents
        
        
        Quick Overview
        --------------
        
        -  ``pfdicom_tagSub`` reads/edits/saves DICOM meta information. It can be used to anonymize DICOM header data.
        
        Overview
        --------
        
        ``pfdicom_tagSub`` replaces a set of ``<tag, value>`` pairs in a DICOM header with values passed in a JSON structure.
        
        The script accepts an ``<inputDir>``, and then from this point an ``os.walk()`` is performed to extract all the subdirs. Each subdir is examined for DICOM files (in the simplest sense by a file extension mapping) are passed to a processing method that reads and replaces specified DICOM tags, saving the result in a corresponding directory and filename in the output 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)
        -  pfdicom (handle underlying DICOM file reading)
        
        Installation
        ~~~~~~~~~~~~
        
        The best method of installing this script and all of its dependencies is
        by fetching it from PyPI
        
        .. code:: bash
        
                pip3 install pfdciom_tagSub
        
        Command line arguments
        ----------------------
        
        .. code:: html
        
        
                -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.
        
                -e|--extension <DICOMextension>
                An optional extension to filter the DICOM files of interest from the 
                <inputDir>.
        
                [-O|--outputDir <outputDir>]
                The output root directory that will contain a tree structure identical
                to the input directory, and each "leaf" node will contain the analysis
                results.
        
                -F|--tagFile <JSONtagFile>
                Parse the tags and their "subs" from a JSON formatted <JSONtagFile>.
        
                -T|--tagStruct <JSONtagStructure>
                Parse the tags and their "subs" from a JSON formatted <JSONtagStucture>
                passed directly in the command line.
        
                -o|--outputFileStem <outputFileStem>
                The output file stem to store data. This should *not* have a file
                extension, or rather, any "." in the name are considered part of 
                the stem and are *not* considered extensions.
        
                [--outputLeafDir <outputLeafDirFormat>]
                If specified, will apply the <outputLeafDirFormat> to the output
                directories containing data. This is useful to blanket describe
                final output directories with some descriptive text, such as 
                'anon' or 'preview'. 
        
                This is a formatting spec, so 
        
                    --outputLeafDir 'preview-%s'
        
                where %s is the original leaf directory node, will prefix each
                final directory containing output with the text 'preview-' which
                can be useful in describing some features of the output set.
        
                [--threads <numThreads>]
                If specified, break the innermost analysis loop into <numThreads>
                threads.
        
                [-x|--man]
                Show full help.
        
                [-y|--synopsis]
                Show brief help.
        
                [--json]
                If specified, output a JSON dump of final return.
        
                -v|--verbosity <level>
                Set the app verbosity level. 
        
                    0: No internal output;
                    1: Run start / stop output notification;
                    2: As with level '1' but with simpleProgress bar in 'pftree';
                    3: As with level '2' but with list of input dirs/files in 'pftree';
                    5: As with level '3' but with explicit file logging for
                            - read
                            - analyze
                            - write
                            
        Examples
        ~~~~~~~~
        
        Perform a DICOM anonymization by processing specific tags:
        
        .. code:: bash
        
                pfdicom_tagSub                                      \
                            -I /var/www/html/normsmall -e dcm       \
                            -O /var/www/html/anon                   \
                            --tagStruct '
                            {
                                "PatientName":       "anonymized",
                                "PatientID":         "%_md5|7_PatientID",
                                "AccessionNumber":   "%_md5|10_AccessionNumber",
                                "PatientBirthDate":  "%_strmsk|******01_PatientBirthDate"
                            }
                            ' --threads 0 -v 0 --json
        
        which will output only at script conclusion and will log a JSON formatted string.
         
        
Platform: UNKNOWN
