Provided by: mia-tools_2.4.6-5build3_amd64 bug

NAME

       mia-2dcost - Evaluate the similarity between two 2D images.

SYNOPSIS

       mia-2dcost [options] <PLUGINS:2dimage/fullcost>

DESCRIPTION

       mia-2dcost  This  program is used to evaluate the cost between two images by using a given
       cost function.

OPTIONS

   Help & Info
              -V --verbose=warning
                     verbosity of output, print messages of given level  and  higher  priorities.
                     Supported priorities starting at lowest level are:

                        trace ‐ Function call trace
                        debug ‐ Debug output
                        info ‐ Low level messages
                        message ‐ Normal messages
                        warning ‐ Warnings
                        fail ‐ Report test failures
                        error ‐ Report errors
                        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).

PLUGINS: 1d/splinekernel

       bspline   B-spline kernel creation , supported parameters are:

                     d = 3; int in [0, 5]
                       Spline degree.

       omoms     OMoms-spline kernel creation, supported parameters are:

                     d = 3; int in [3, 3]
                       Spline degree.

PLUGINS: 2dimage/cost

       lncc      local  normalized  cross correlation with masking support., supported parameters
                 are:

                     w = 5; uint in [1, 256]
                       half  width  of  the  window  used  for  evaluating  the  localized  cross
                       correlation.

       lsd       Least-Squares Distance measure

                     (no parameters)

       mi        Spline parzen based mutual information., supported parameters are:

                     cut = 0; float in [0, 40]
                       Percentage  of  pixels  to  cut  at  high  and  low  intensities to remove
                       outliers.

                     mbins = 64; uint in [1, 256]
                       Number of histogram bins used for the moving image.

                     mkernel = [bspline:d=3]; factory
                       Spline kernel for moving image parzen hinstogram.  For supported  plug-ins
                       see PLUGINS:1d/splinekernel

                     rbins = 64; uint in [1, 256]
                       Number of histogram bins used for the reference image.

                     rkernel = [bspline:d=0]; factory
                       Spline  kernel for reference image parzen hinstogram.  For supported plug-
                       ins see PLUGINS:1d/splinekernel

       ncc       normalized cross correlation.

                     (no parameters)

       ngf       This function evaluates  the  image  similarity  based  on  normalized  gradient
                 fields. Various evaluation kernels are available., supported parameters are:

                     eval = ds; dict
                       plugin subtype.  Supported values are:
                           sq ‐ square of difference
                           ds ‐ square of scaled difference
                           dot ‐ scalar product kernel
                           cross ‐ cross product kernel

       ssd       2D imaga cost: sum of squared differences, supported parameters are:

                     autothresh = 0; float in [0, 1000]
                       Use automatic masking of the moving image by only takeing intensity values
                       into accound that are larger than the given threshold.

                     norm = 0; bool
                       Set whether the metric should be normalized by the number of image pixels.

       ssd-automask
                 2D image cost: sum of squared  differences,  with  automasking  based  on  given
                 thresholds, supported parameters are:

                     rthresh = 0; double
                       Threshold intensity value for reference image.

                     sthresh = 0; double
                       Threshold intensity value for source image.

PLUGINS: 2dimage/fullcost

       image     Generalized  image  similarity  cost function that also handles multi-resolution
                 processing.  The  actual  similarity  measure  is  given  es  extra  parameter.,
                 supported parameters are:

                     cost = ssd; factory
                       Cost function kernel.  For supported plug-ins see PLUGINS:2dimage/cost

                     debug = 0; bool
                       Save intermediate resuts for debugging.

                     ref =(input, io)
                       Reference image.  For supported file types see PLUGINS:2dimage/io

                     src =(input, io)
                       Study image.  For supported file types see PLUGINS:2dimage/io

                     weight = 1; float
                       weight of cost function.

       labelimage
                 Similarity  cost  function  that  maps  labels  of two images and handles label-
                 preserving multi-resolution processing., supported parameters are:

                     debug = 0; int in [0, 1]
                       write the distance transforms to a 3D image.

                     maxlabel = 256; int in [2, 32000]
                       maximum number of labels to consider.

                     ref =(input, io)
                       Reference image.  For supported file types see PLUGINS:2dimage/io

                     src =(input, io)
                       Study image.  For supported file types see PLUGINS:2dimage/io

                     weight = 1; float
                       weight of cost function.

       maskedimage
                 Generalized masked image similarity  cost  function  that  also  handles  multi-
                 resolution  processing.  The  provided  masks should be densly filled regions in
                 multi-resolution procesing because otherwise the mask information may  get  lost
                 when  downscaling  the image. The reference mask and the transformed mask of the
                 study image are combined by binary AND. The actual similarity measure  is  given
                 es extra parameter., supported parameters are:

                     cost = ssd; factory
                       Cost      function     kernel.      For     supported     plug-ins     see
                       PLUGINS:2dimage/maskedcost

                     ref =(input, io)
                       Reference image.  For supported file types see PLUGINS:2dimage/io

                     ref-mask =(input, io)
                       Reference  image  mask   (binary).    For   supported   file   types   see
                       PLUGINS:2dimage/io

                     src =(input, io)
                       Study image.  For supported file types see PLUGINS:2dimage/io

                     src-mask =(input, io)
                       Study    image    mask   (binary).    For   supported   file   types   see
                       PLUGINS:2dimage/io

                     weight = 1; float
                       weight of cost function.

PLUGINS: 2dimage/io

       bmp       BMP 2D-image input/output support. The plug-in supports reading and  writing  of
                 binary  images  and  8-bit  gray scale images. read-only support is provided for
                 4-bit gray scale images. The color table is ignored and  the  pixel  values  are
                 taken as literal gray scale values.

                     Recognized file extensions:  .BMP, .bmp

                     Supported element types:
                       binary data, unsigned 8 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

PLUGINS: 2dimage/maskedcost

       lncc      local  normalized  cross correlation with masking support., supported parameters
                 are:

                     w = 5; uint in [1, 256]
                       half  width  of  the  window  used  for  evaluating  the  localized  cross
                       correlation.

       mi        Spline parzen based mutual information with masking., supported parameters are:

                     cut = 0; float in [0, 40]
                       Percentage  of  pixels  to  cut  at  high  and  low  intensities to remove
                       outliers.

                     mbins = 64; uint in [1, 256]
                       Number of histogram bins used for the moving image.

                     mkernel = [bspline:d=3]; factory
                       Spline kernel for moving image parzen hinstogram.  For supported  plug-ins
                       see PLUGINS:1d/splinekernel

                     rbins = 64; uint in [1, 256]
                       Number of histogram bins used for the reference image.

                     rkernel = [bspline:d=0]; factory
                       Spline  kernel for reference image parzen hinstogram.  For supported plug-
                       ins see PLUGINS:1d/splinekernel

       ncc       normalized cross correlation with masking support.

                     (no parameters)

       ssd       Sum of squared differences with masking.

                     (no parameters)

EXAMPLE

       Evaluate the SSD cost function between image1.png and image2.png

       mia-2dcost image:src=image1.png,ref=image2.png,cost=ssd

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'.