xenial (1) mia-2dseriesgradvariation.1.gz

NAME

       mia-2dseriesgradvariation - Evaluate the time-intensity gradient variation in a series of images.

SYNOPSIS

       mia-2dseriesgradvariation -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-2dseriesgradvariation  Given  a  set  of  images  of  temporal  sucession, this program evaluates the
       gradient variation of the pixel-wise time-intensity curves  of  this  series.  If  the  input  image  set
       provides  a  segmentation,  then  this  segmentation  can  be  used to create a bounding box and restrict
       evaluation to this box.

OPTIONS

              -i --in-file=(input, required); string
                     input segmentation set

              -o --out-file=(output, required); io
                     output file name  For supported file types see PLUGINS:2dimage/io

              -k --skip=0
                     Skip files at the beginningSkip files at the beginning

              -e --enlarge-boundary=5
                     Enlarge cropbox by number of pixelsEnlarge cropbox by number of pixels

              -c --crop
                     crop image before running statistics

   Help & Info
              -V --verbose=warning
                     verbosity of output, print  messages  of  given  level  and  higher  priorities.  Supported
                     priorities starting at lowest level are:
                        info ‐ Low level messages
                        trace ‐ Function call trace
                        fail ‐ Report test failures
                        warning ‐ Warnings
                        error ‐ Report errors
                        debug ‐ Debug output
                        message ‐ Normal messages
                        fatal ‐ Report only fatal errors

                 --copyright
                     print copyright information

              -h --help
                     print this help

              -? --usage
                     print a short help

                 --version
                     print the version number and exit

   Processing
                 --threads=-1
                     Maxiumum  number  of  threads to use for processing,This number should be lower or equal to
                     the number of logical processor cores in the machine. (-1:  automatic  estimation).Maxiumum
                     number  of threads to use for processing,This number should be lower or equal to the number
                     of logical processor cores in the machine. (-1: automatic estimation).

PLUGINS: 2dimage/io

       bmp       BMP 2D-image input/output support

                     Recognized file extensions:  .BMP, .bmp

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       dicom     2D image io for DICOM

                     Recognized file extensions:  .DCM, .dcm

                     Supported element types:
                       signed 16 bit, unsigned 16 bit

       exr       a 2dimage io plugin for OpenEXR images

                     Recognized file extensions:  .EXR, .exr

                     Supported element types:
                       unsigned 32 bit, floating point 32 bit

       jpg       a 2dimage io plugin for jpeg gray scale images

                     Recognized file extensions:  .JPEG, .JPG, .jpeg, .jpg

                     Supported element types:
                       unsigned 8 bit

       png       a 2dimage io plugin for png images

                     Recognized file extensions:  .PNG, .png

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit

       raw       RAW 2D-image output support

                     Recognized file extensions:  .RAW, .raw

                     Supported element types:
                       binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit,
                       unsigned 32 bit, floating point 32 bit, floating point 64 bit

       tif       TIFF 2D-image input/output support

                     Recognized file extensions:  .TIF, .TIFF, .tif, .tiff

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

       vista     a 2dimage io plugin for vista images

                     Recognized file extensions:  .V, .VISTA, .v, .vista

                     Supported element types:
                       binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit,
                       unsigned 32 bit, floating point 32 bit, floating point 64 bit

EXAMPLE

       Evaluate the gradient-variation image of the bounding box surrounding  the  segmentation  from  a  series
       'segment.set'.  The  bounding  box  will  be  enlarged  by 3 pixels in all directions. Store the image in
       OpenEXR format.

       mia-2dseriesgradvariation  -i segment.set -o gradvar.exr -c -e 3

AUTHOR(s)

       Gert Wollny

COPYRIGHT

       This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain.  It comes  with   ABSOLUTELY
       NO  WARRANTY   and   you  may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3
       (or later). For more information run the program with the option '--copyright'.