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        "description": "pfdicom_tagSub\n==================\n\n.. image:: https://badge.fury.io/py/pfdicom_tagSub.svg\n    :target: https://badge.fury.io/py/pfdicom_tagSub\n\n.. image:: https://travis-ci.org/FNNDSC/pfdicom_tagSub.svg?branch=master\n    :target: https://travis-ci.org/FNNDSC/pfdicom_tagSub\n\n.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg\n    :target: https://badge.fury.io/py/pfdicom_tagSub\n\n.. contents:: Table of Contents\n\n\nQuick Overview\n--------------\n\n-  ``pfdicom_tagSub`` reads/edits/saves DICOM meta information. It can be used to anonymize DICOM header data.\n\nOverview\n--------\n\n``pfdicom_tagSub`` replaces a set of ``<tag, value>`` pairs in a DICOM header with values passed in a JSON structure.\n\nThe 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.\n\nInstallation\n------------\n\nDependencies\n~~~~~~~~~~~~\n\nThe following dependencies are installed on your host system/python3 virtual env (they will also be automatically installed if pulled from pypi):\n\n-  ``pfmisc`` (various misc modules and classes for the pf* family of objects)\n-  ``pftree`` (create a dictionary representation of a filesystem hierarchy)\n-  ``pfdicom`` (handle underlying DICOM file reading)\n\nUsing ``PyPI``\n~~~~~~~~~~~~~~\n\nThe best method of installing this script and all of its dependencies is\nby fetching it from PyPI\n\n.. code:: bash\n\n        pip3 install pfdicom_tagSub\n\nCommand line arguments\n----------------------\n\n.. code:: html\n\n\n        -I|--inputDir <inputDir>\n        Input DICOM directory to examine. By default, the first file in this\n        directory is examined for its tag information. There is an implicit\n        assumption that each <inputDir> contains a single DICOM series.\n\n        -i|--inputFile <inputFile>\n        An optional <inputFile> specified relative to the <inputDir>. If \n        specified, then do not perform a directory walk, but convert only \n        this file.\n\n        -e|--extension <DICOMextension>\n        An optional extension to filter the DICOM files of interest from the \n        <inputDir>.\n\n        [-O|--outputDir <outputDir>]\n        The output root directory that will contain a tree structure identical\n        to the input directory, and each \"leaf\" node will contain the analysis\n        results.\n\n        -F|--tagFile <JSONtagFile>\n        Parse the tags and their \"subs\" from a JSON formatted <JSONtagFile>.\n\n        -T|--tagStruct <JSONtagStructure>\n        Parse the tags and their \"subs\" from a JSON formatted <JSONtagStucture>\n        passed directly in the command line.\n\n        -o|--outputFileStem <outputFileStem>\n        The output file stem to store data. This should *not* have a file\n        extension, or rather, any \".\" in the name are considered part of \n        the stem and are *not* considered extensions.\n\n        [--outputLeafDir <outputLeafDirFormat>]\n        If specified, will apply the <outputLeafDirFormat> to the output\n        directories containing data. This is useful to blanket describe\n        final output directories with some descriptive text, such as \n        'anon' or 'preview'. \n\n        This is a formatting spec, so \n\n            --outputLeafDir 'preview-%s'\n\n        where %s is the original leaf directory node, will prefix each\n        final directory containing output with the text 'preview-' which\n        can be useful in describing some features of the output set.\n\n        [--threads <numThreads>]\n        If specified, break the innermost analysis loop into <numThreads>\n        threads.\n\n        [-x|--man]\n        Show full help.\n\n        [-y|--synopsis]\n        Show brief help.\n\n        [--json]\n        If specified, output a JSON dump of final return.\n\n        [--followLinks]\n        If specified, follow symbolic links.\n\n        -v|--verbosity <level>\n        Set the app verbosity level. \n\n            0: No internal output;\n            1: Run start / stop output notification;\n            2: As with level '1' but with simpleProgress bar in 'pftree';\n            3: As with level '2' but with list of input dirs/files in 'pftree';\n            5: As with level '3' but with explicit file logging for\n                    - read\n                    - analyze\n                    - write\n                    \nExamples\n--------\n\nPerform a DICOM anonymization by processing specific tags:\n\n.. code:: bash\n\n        pfdicom_tagSub                                      \\\\\n            -I /var/www/html/normsmall -e dcm               \\\\\n            -O /var/www/html/anon                           \\\\\n            --tagStruct '\n            {\n                \"PatientName\":              \"anonymized\",\n                \"PatientID\":                \"%_md5|7_PatientID\",\n                \"AccessionNumber\":          \"%_md5|10_AccessionNumber\",\n                \"PatientBirthDate\":         \"%_strmsk|******01_PatientBirthDate\",\n                \"ReferringPhysicianName\":   \"ReferringPhysicianName\",\n                \"PhysiciansOfRecord\":       \"PhysiciansOfRecord\",\n                \"RequestingPhysician\":      \"RequestingPhysician\",\n                \"InstitutionAddress\":       \"InstitutionAddress\",\n                \"InstitutionName\":          \"InstitutionName\"\n            }\n            ' --threads 0 --printElapsedTime\n\nwhich will output only at script conclusion and will log a JSON formatted string.",
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