Metadata-Version: 1.0
Name: pfdicomtag
Version: 1.0.0
Summary: (Python) utility to extract meta data from trees of organized DICOM files.
Home-page: https://github.com/FNNDSC/med2image
Author: FNNDSC
Author-email: dev@babymri.org
License: MIT
Description-Content-Type: UNKNOWN
Description: pfdicomtag
        ==========
        
        Quick Overview
        --------------
        
        -  Extract DICOM tags.
        
        Overview
        --------
        
        pfdicomtag is a dir-based DICOM file tag extractor. By 'dir-based' is understood that input DICOMs exist in a nested directory tree, and results of the tag extraction are written an output tree. This tree mimics the structure of the input data tree.
        
        Dependencies
        ------------
        
        Make sure that the following dependencies are installed on your host
        system/python3 virtual env:
        
        -  pydicom (to read DICOM files)
        -  matplotlib (to save data in various image formats)
        -  pillow (to save data in jpg format)
        
        Installation
        ~~~~~~~~~~~~
        
        The best method of installing this script and all of its dependencies is
        by fetching it from PyPI
        
        .. code:: bash
        
                pip3 install pydicomtag
        
        You migh get an error about `python3-tk` not installed. So you should install that package.
        For example on Ubuntu:
        
        .. code:: bash
        
                sudo apt-get update
                sudo apt-get install -y python3-tk
        
        
        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.
        
                -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.
        
                NOTE: If neither -F nor -T are specified, a '-r raw' is
                assumed.
        
                -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>.
        
                -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
        
                [-p|--printToScreen]
                If specified, will print tags to screen.
        
                [-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
        ~~~~~~~~
        
        Replicate a tree and for each DICOM series dir, create multiple reports, including an html output with an embedded image of the center (middle file) of the series:
        
        .. code:: bash
        
                pfdicomtag  -I /var/www/html/normative      \
                            -m m:out.jpg -e dcm             \
                            -o %PatientAge-%md5PatientID    \
                            -O /var/www/html/tag            \
                            -t raw,json,col,csv,html,dict
        
        
Platform: UNKNOWN
