Metadata-Version: 1.0
Name: pfdicom-tagExtract
Version: 2.2.24
Summary: Extract DICOM header info -- part of the pf* family.
Home-page: https://github.com/FNNDSC/pfdicom_tagExtract
Author: FNNDSC
Author-email: dev@babymri.org
License: MIT
Description: pfdicom_tagExtract
        ==================
        
        .. image:: https://badge.fury.io/py/pfdicom_tagExtract.svg
            :target: https://badge.fury.io/py/pfdicom_tagExtract
        
        .. image:: https://travis-ci.org/FNNDSC/pfdicom_tagExtract.svg?branch=master
            :target: https://travis-ci.org/FNNDSC/pfdicom_tagExtract
        
        .. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
            :target: https://badge.fury.io/py/pfdicom_tagExtract
        
        .. contents:: Table of Contents
        
        
        Quick Overview
        --------------
        
        -  ``pfdicom_tagExtract`` generates reports in various formats (txt, html, etc) based on parsing DICOM meta data (i.e. DICOM tags).
        
        Overview
        --------
        
        ``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.
        
        The 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.
        
        Optionally, 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.
        
        Finally, an image conversion can also be performed (and embedded within the output html file, if an html conversion is specified).
        
        Installation
        ------------
        
        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)
        -  ``matplotlib`` (handle saving / conversion to image formats for html reports)
        
        Using ``PyPI``
        ~~~~~~~~~~~~~~
        
        The best method of installing this script and all of its dependencies is
        by fetching it from PyPI
        
        .. code:: bash
        
                pip3 install pfdicom_tagExtract
        
        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 directory to contain all output files.
        
                [--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.
        
                -F|--tagFile <tagFile>
                Read the tags, one-per-line in <tagFile>, and print the
                corresponding tag information in the DICOM <inputFile>.
        
                -T|--tagList <tagList>
                Read the list of comma-separated tags in <tagList>, and print the
                corresponding tag information parsed from the DICOM <inputFile>.
        
                -m|--image <[<index>:]imageFile>
                If specified, also convert the <inputFile> to <imageFile>. If the
                name is preceded by an index and colon, then convert this indexed
                file in the particular <inputDir>.
        
                [-s|--imageScale <factor:interpolation>]
                If an image conversion is specified, this flag will scale the image
                by <factor> and use an interpolation <order>. This is useful in
                increasing the size of images for the html output.
        
                Note that certain interpolation choices can result in a significant
                slowdown!
        
                    interpolation order:
        
                    'none', 'nearest', 'bilinear', 'bicubic', 'spline16',
                    'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric',
                    'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos'
        
                -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.
        
                [-t|--outputFileType <outputFileType>]
                A comma specified list of output types. These can be:
        
                    o <type>    <ext>       <desc>
                    o raw       -raw.txt    the raw internal dcm structure to string
                    o json      .json       a json representation
                    o html      .html       an html representation with optional image
                    o dict      -dict.txt   a python dictionary
                    o col       -col.txt    a two-column text representation (tab sep)
                    o csv       .csv        a csv representation
        
                Note that if not specified, a default type of 'raw' is assigned.
        
                [-p|--printToScreen]
                If specified, will print tags to screen.
        
                [-x|--man]
                Show full help.
        
                [-y|--synopsis]
                Show brief help.
        
                [--version]
                If specified, print the version number and exit.
        
                [--json]
                If specified, output a JSON dump of final return.
        
                [--followLinks]
                If specified, follow symbolic links.
        
                -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
        --------
        
        Run on a target tree and output some detail and stats
        
        .. code:: bash
        
                pfdicom_tagExtract                                      \
                            -I /var/www/html/normsmall -e dcm           \
                            -O /var/www/html/tag                        \
                            -o '%_md5|6_PatientID-%PatientAge'          \
                            -m 'm:%_nospc|-_ProtocolName.jpg'           \
                            -s 3:none                                   \
                            --useIndexhtml                              \
                            -t raw,json,html,dict,col,csv               \
                            --threads 0 -v 0 --json
        
        which will output only at script conclusion and will log a JSON formatted string.
        
Platform: UNKNOWN
