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        "description": "pfdicom_tagExtract\n==================\n\n.. image:: https://badge.fury.io/py/pfdicom_tagExtract.svg\n    :target: https://badge.fury.io/py/pfdicom_tagExtract\n\n.. image:: https://travis-ci.org/FNNDSC/pfdicom_tagExtract.svg?branch=master\n    :target: https://travis-ci.org/FNNDSC/pfdicom_tagExtract\n\n.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg\n    :target: https://badge.fury.io/py/pfdicom_tagExtract\n\n.. contents:: Table of Contents\n\n\nQuick Overview\n--------------\n\n-  ``pfdicom_tagExtract`` generates reports in various formats (txt, html, etc) based on parsing DICOM meta data (i.e. DICOM tags).\n\nOverview\n--------\n\n``pfdicom_tagExtract`` extracts the header information of DICOM files and echoes to stdout as well as to an output report-type file -- this can be a raw output, a json-type output, or html-type output.\n\nThe script accepts an ``<inputDir>``, and then from this point a recursive ``os.walk()``  is performed to probe all subdirs containing files to process. Each subdir is examined for DICOM files (in the simplest sense by a file extension mapping) and either the head, tail, middle (or other indexed) file is examined for its tag information.\n\nOptionally, the tag list can be constrained either by passing a ``<tagFile>`` containing a line-by-line list of tags to query, or by passing a comma separated list of tags directly.\n\nFinally, an image conversion can also be performed (and embedded within the output html file, if an html conversion is specified).\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-  ``matplotlib`` (handle saving / conversion to image formats for html reports)\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_tagExtract\n\nCommand line arguments\n----------------------\n\n.. code:: html\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 directory to contain all output files.\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        -F|--tagFile <tagFile>\n        Read the tags, one-per-line in <tagFile>, and print the\n        corresponding tag information in the DICOM <inputFile>.\n\n        -T|--tagList <tagList>\n        Read the list of comma-separated tags in <tagList>, and print the\n        corresponding tag information parsed from the DICOM <inputFile>.\n\n        -m|--image <[<index>:]imageFile>\n        If specified, also convert the <inputFile> to <imageFile>. If the\n        name is preceded by an index and colon, then convert this indexed \n        file in the particular <inputDir>.\n\n        [-s|--imageScale <factor:interpolation>]\n        If an image conversion is specified, this flag will scale the image\n        by <factor> and use an interpolation <order>. This is useful in \n        increasing the size of images for the html output.\n\n        Note that certain interpolation choices can result in a significant\n        slowdown!\n\n            interpolation order:\n            \n            'none', 'nearest', 'bilinear', 'bicubic', 'spline16',\n            'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric',\n            'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos'\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        [-t|--outputFileType <outputFileType>]\n        A comma specified list of output types. These can be:\n\n            o <type>    <ext>       <desc>\n            o raw       -raw.txt    the raw internal dcm structure to string\n            o json      .json       a json representation\n            o html      .html       an html representation with optional image\n            o dict      -dict.txt   a python dictionary\n            o col       -col.txt    a two-column text representation (tab sep)\n            o csv       .csv        a csv representation\n\n        Note that if not specified, a default type of 'raw' is assigned.\n\n        [-p|--printToScreen]\n        If specified, will print tags to screen.\n\n        [-x|--man]\n        Show full help.\n\n        [-y|--synopsis]\n        Show brief help.\n\n        [--version]\n        If specified, print the version number and exit.\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\nRun on a target tree and output some detail and stats\n\n.. code:: bash\n\n        pfdicom_tagExtract                                      \\\n                    -I /var/www/html/normsmall -e dcm           \\\n                    -O /var/www/html/tag                        \\\n                    -o '%_md5|6_PatientID-%PatientAge'          \\\n                    -m 'm:%_nospc|-_ProtocolName.jpg'           \\\n                    -s 3:none                                   \\\n                    --useIndexhtml                              \\\n                    -t raw,json,html,dict,col,csv               \\\n                    --threads 0 -v 0 --json\n \nwhich will output only at script conclusion and will log a JSON formatted string.",
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