Metadata-Version: 1.0
Name: z2labelmap
Version: 1.1.6
Summary: Convert lh/rh z-score vector to FreeSurfer labelmap
Home-page: https://github.com/FNNDSC/pl-z2labelmap
Author: Rudolph Pienaar
Author-email: rudolph.pienaar@gmail.com
License: MIT
Description: pl-z2labelmap
        =============
        
        .. image:: https://badge.fury.io/py/z2labelmap.svg
            :target: https://badge.fury.io/py/z2labelmap
        
        .. image:: https://travis-ci.org/FNNDSC/z2labelmap.svg?branch=master
            :target: https://travis-ci.org/FNNDSC/z2labelmap
        
        .. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
            :target: https://badge.fury.io/py/pl-z2labelmap
        
        .. contents:: Table of Contents
        
        
        Abstract
        --------
        
        ``zlabelmap.py`` generates FreeSurfer labelmaps from z-score vector files. Essentially the script consumes an input text vector file of 
        
        .. code::
        
            <str_structureName> <float_lh_zScore> <float_rh_zScore>
        
        and creates a FreeSurfer labelmap where ``<str_structureName>`` colors correspond to the z-score (normalized between 0 and 255).
        
        Currently, only the ``aparc.a2009s`` FreeSurfer segmentation is fully supported, however future parcellation support is planned.
        
        Negative z-scores and positive z-scores are treated in the same manner but have sign-specific color specifications. Positive and negative z-Scores can be assigned some combination of the chars ``RGB`` to indicate which color dimension will reflect the z-Score. For example, a 
            
        .. code::
        
            --posColor R --negColor RG
        
        will assign positive z-scores shades of ``red`` and negative z-scores shades of ``yellow`` (Red + Green = Yellow).
        
        Synopsis
        --------
        
        .. code::
        
            python z2labelmap.py                                            \
                [-v <level>] [--verbosity <level>]                          \
                [--random]                                                  \
                [-p <f_posRange>] [--posRange <f_posRange>]                 \
                [-n <f_negRange>] [--negRange <f_negRange>]                 \
                [-P <'RGB'>] [--posColor <'RGB'>]                           \
                [-N  <'RGB'> [--negColor <'RGB'>]                           \
                [-s <f_scaleRange>] [--scaleRange <f_scaleRange>]           \
                [-l <f_lowerFilter>] [--lowerFilter <f_lowerFilter>]        \
                [-u <f_upperFilter>] [--upperFilter <f_upperFilter>]        \
                [-z <zFile>] [--zFile <zFile>]                              \
                [--version]                                                 \
                [--man]                                                     \
                [--meta]                                                    \
                <inputDir>                                                  \
                <outputDir> 
        
        Run
        ----
        
        This ``plugin`` can be run in two modes: natively as a python package or as a containerized docker image.
        
        Using PyPI
        ~~~~~~~~~~
        
        To run from PyPI, simply do a 
        
        .. code:: bash
        
            pip install z2labelmap
        
        and run with
        
        .. code:: bash
        
            z2labelmap.py --man /tmp /tmp
        
        to get inline help.
        
        
        Using ``docker run``
        ~~~~~~~~~~~~~~~~~~~~
        
        To run using ``docker``, be sure to assign an "input" directory to ``/incoming`` and an output directory to ``/outgoing``. *Make sure that the* ``$(pwd)/out`` *directory is world writable!*
        
        Now, prefix all calls with 
        
        .. code:: bash
        
            docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
                    fnndsc/pl-z2labelmap z2labelmap.py                          \
        
        Thus, getting inline help is:
        
        .. code:: bash
        
            docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
                    fnndsc/pl-z2labelmap z2labelmap.py                          \
                    --man                                                       \
                    /incoming /outgoing
        
        Examples
        --------
        
        Create a sample/random z-score file and analyze
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        * In the absense of an actual z-score file, the script can create one. This can then be used in subsequent analysis:
        
        .. code::
        
            mkdir in out
            docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing  \
                    fnndsc/pl-z2labelmap z2labelmap.py                      \
                    --random                                                \
                    --posRange 3.0 --negRange -3.0                          \
                    /incoming /outgoing
        
        or without docker
        
        .. code::
        
            mkdir in out
            z2labelmap.py                                                   \
                    --random                                                \
                    --posRange 3.0 --negRange -3.0                          \
                    /in /out
        
        
        In this example, z-scores range between 0.0 and (+/-) 3.0.
        
        Control relative brightness and lower filter low z-scores from final labelmap
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        * To analyze a file already located at ``in/zfile.csv``, apply a ``scaleRange`` and also filter out the lower 80\% of z-scores:
        
        .. code::
        
            docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing  \
                    fnndsc/pl-z2labelmap z2labelmap.py                      \
                    --scaleRange 2.0 --lowerFilter 0.8                      \
                    --negColor B --posColor R                               \
                    /incoming /outgoing
        
        This assumes a file called 'zfile.csv' in the <inputDirectory> that ranges in z-score between 0.0 and 3.0, and uses the --scaleRange to reduce the apparent brightness of the map by 50 percent. Furthermore, the lower 80 percent of z-scores are removed (this has the effect of only showing the brightest 20 percent of zscores). 
        
        Command line arguments
        ----------------------
        
        .. code::
        
                <inputDir>
                Required argument.
                Input directory for plugin.
        
                <outputDir>
                Required argument.
                Output directory for plugin.
        
                [-v <level>] [--verbosity <level>]
                Verbosity level for app. Not used currently.
        
                [--random]
                If specified, generate a z-score file based on <posRange> and <negRange>.
        
                [-p <f_posRange>] [--posRange <f_posRange>]
                Positive range for random max deviation generation.
        
                [-n <f_negRange>] [--negRange <f_negRange>]
                Negative range for random max deviation generation.
        
                [-P <'RGB'>] [--posColor <'RGB'>]
                Some combination of 'R', 'G', B' for positive heat.
        
                [-N  <'RGB'> [--negColor <'RGB'>]
                Some combination of 'R', 'G', B' for negative heat.
        
                [-s <f_scaleRange>] [--scaleRange <f_scaleRange>]
                Scale range for normalization. This has the effect of controlling the
                brightness of the map. For example, if this 1.5 the effect
                is increase the apparent range by 50% which darkens all colors values.
        
                [-l <f_lowerFilter>] [--lowerFilter <f_lowerFilter>]
                Filter all z-scores below (normalized) <lowerFilter> to 0.0.
        
                [-u <f_upperFilter>] [--upperFilter <f_upperFilter>]
                Filter all z-scores above (normalized) <upperFilter> to 0.0.
        
                [-z <zFile>] [--zFile <zFile>]
                z-score file to read (relative to input directory). Defaults to 'zfile.csv'.
        
                [--version]
                If specified, print version number. 
                
                [--man]
                If specified, print (this) man page.
        
                [--meta]
                If specified, print plugin meta data.
        
        
Platform: UNKNOWN
