Provided by: mia-tools_2.4.6-4ubuntu2_amd64 bug

NAME

       ('mia\-2dseriessmoothgradMAD',)  -  Evaluate  pixel-wise  time-intensity  gradient of a 2D
       image series.

SYNOPSIS

       mia-2dseriessmoothgradMAD -i <in-file> -o <out-file> [options] <PLUGINS:2dimage/filter>

DESCRIPTION

       mia-2dseriessmoothgradMAD Given a set  of  images  of  temporal  sucession,  evaluate  the
       temporal  pixel-wise  gaussian and evaluate pixel-wise its MAD.A spacial pre-filtering may
       be applied by specifying additional plugins (filter/2dimage)

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 beginning

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

              -c --crop
                     crop image before running statistics

              -g --gauss=1
                     gauss filter width for moothing the gradient

   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).

PLUGINS: 1d/spacialkernel

       cdiff     Central difference filter kernel, mirror boundary conditions are used.

                     (no parameters)

       gauss     spacial Gauss filter kernel, supported parameters are:

                     w = 1; uint in [0, inf)
                       half filter width.

       scharr    This plugin provides the 1D folding kernel for the Scharr gradient filter

                     (no parameters)

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/combiner

       absdiff   Image combiner 'absdiff'

                     (no parameters)

       add       Image combiner 'add'

                     (no parameters)

       div       Image combiner 'div'

                     (no parameters)

       mul       Image combiner 'mul'

                     (no parameters)

       sub       Image combiner 'sub'

                     (no parameters)

PLUGINS: 2dimage/filter

       adaptmed  2D image adaptive median filter, supported parameters are:

                     w = 2; int in [1, inf)
                       half filter width.

       admean    An  adaptive  mean filter that works like a normal mean filter, if the intensity
                 variation within the filter mask is lower then the intensity  variation  in  the
                 whole  image,  that  the uses a special formula if the local variation is higher
                 then the image intensity variation., supported parameters are:

                     w = 1; int in [1, inf)
                       half filter width.

       aniso     2D Anisotropic image filter, supported parameters are:

                     epsilon = 1; float in (0, inf)
                       iteration change threshold.

                     iter = 100; int in [1, 10000]
                       number of iterations.

                     k = -1; float in [0, 100]
                       k the noise threshold (<=0 -> adaptive).

                     n = 8; set
                       neighbourhood.  Supported values are:( 4, 8, )

                     psi = tuckey; dict
                       edge stopping function.  Supported values are:
                           guess ‐ test stopping function
                           tuckey ‐ tukey stopping function
                           pm1 ‐ stopping function 1
                           pm2 ‐ stopping function 2

       bandpass  intensity bandpass filter, supported parameters are:

                     max = 3.40282e+38; float
                       maximum of the band.

                     min = 0; float
                       minimum of the band.

       binarize  image binarize filter, supported parameters are:

                     max = 3.40282e+38; float
                       maximum of accepted range.

                     min = 0; float
                       minimum of accepted range.

       close     morphological close, supported parameters are:

                     hint = black; set
                       a hint at the main image content.  Supported values are:( black, white, )

                     shape = [sphere:r=2]; factory
                       structuring element.  For supported plug-ins see PLUGINS:2dimage/shape

       combiner  Combine two images with the given combiner operator.  if  'reverse'  is  set  to
                 false,  the  first operator is the image passed through the filter pipeline, and
                 the second image is loaded from the file given with the  'image'  parameter  the
                 moment the filter is run., supported parameters are:

                     image =(input, required, io)
                       second image that is needed in the combiner.  For supported file types see
                       PLUGINS:2dimage/io

                     op =(required, factory)
                       Image combiner to be applied to the images.  For  supported  plug-ins  see
                       PLUGINS:2dimage/combiner

                     reverse = 0; bool
                       reverse the order in which the images passed to the combiner.

       convert   image pixel format conversion filter, supported parameters are:

                     a = 1; float
                       linear conversion parameter a.

                     b = 0; float
                       linear conversion parameter b.

                     map = opt; dict
                       conversion mapping.  Supported values are:
                           opt  ‐ apply a linear transformation that maps the real input range to
                           the full output range
                           range ‐ apply linear transformation that  maps  the  input  data  type
                           range to the output data type range
                           copy ‐ copy data when converting
                           linear ‐ apply linear transformation x -> a*x+b
                           optstat  ‐  apply a linear transform that maps based on input mean and
                           variation to the full output range

                     repn = ubyte; dict
                       output pixel type.  Supported values are:
                           none ‐ no pixel type defined
                           float ‐ floating point 32 bit
                           sbyte ‐ signed 8 bit
                           ulong ‐ unsigned 64 bit
                           double ‐ floating point 64 bit
                           sint ‐ signed 32 bit
                           ushort ‐ unsigned 16 bit
                           sshort ‐ signed 16 bit
                           uint ‐ unsigned 32 bit
                           slong ‐ signed 64 bit
                           bit ‐ binary data
                           ubyte ‐ unsigned 8 bit

       crop      Crop a region of an image, the region is always clamped to  the  original  image
                 size., supported parameters are:

                     end = [[-1,-1]]; streamable
                       end of crop region.

                     start = [[0,0]]; streamable
                       start of crop region.

       dilate    2d image stack dilate filter, supported parameters are:

                     hint = black; set
                       a hint at the main image content.  Supported values are:( black, white, )

                     shape = [sphere:r=2]; factory
                       structuring element.  For supported plug-ins see PLUGINS:2dimage/shape

       distance  2D image distance filter, evaluates the distance map for a binary mask.

                     (no parameters)

       downscale Downscale  the  input  image by using a given block size to define the downscale
                 factor. Prior to scaling  the  image  is  filtered  by  a  smoothing  filter  to
                 eliminate   high   frequency  data  and  avoid  aliasing  artifacts.,  supported
                 parameters are:

                     b = [[1,1]]; 2dbounds
                       blocksize.

                     bx = 1; uint in [1, inf)
                       blocksize in x direction.

                     by = 1; uint in [1, inf)
                       blocksize in y direction.

                     kernel = gauss; factory
                       smoothing filter kernel to be applied, the size of the filter is estimated
                       based     on    the    blocksize..     For    supported    plug-ins    see
                       PLUGINS:1d/spacialkernel

       erode     2d image stack erode filter, supported parameters are:

                     hint = black; set
                       a hint at the main image content.  Supported values are:( black, white, )

                     shape = [sphere:r=2]; factory
                       structuring element.  For supported plug-ins see PLUGINS:2dimage/shape

       gauss     isotropic 2D gauss filter, supported parameters are:

                     w = 1; int in [0, inf)
                       filter width parameter.

       gradnorm  2D image to gradient norm filter, supported parameters are:

                     normalize = 0; bool
                       Normalize the gradient norms to range [0,1]..

       invert    intensity invert filter

                     (no parameters)

       kmeans    2D image k-means filter. In the output image  the  pixel  value  represents  the
                 class  membership  and  the class centers are stored as attribute in the image.,
                 supported parameters are:

                     c = 3; int in [2, inf)
                       number of classes.

       label     Label connected components in a binary 2D image., supported parameters are:

                     n = 4n; factory
                       Neighborhood mask to describe connectivity..  For supported  plug-ins  see
                       PLUGINS:2dimage/shape

       labelmap  Image  filter to remap label id's. Only applicable to images with integer valued
                 intensities/labels., supported parameters are:

                     map =(input, required, string)
                       Label mapping file.

       labelscale
                 A filter that only creates output voxels that are already created in  the  input
                 image.  Scaling  is  done  by  using a voting algorithms that selects the target
                 pixel value based on  the  highest  pixel  count  of  a  certain  label  in  the
                 corresponding  source  region.  If the region comprises two labels with the same
                 count, the one with the lower number wins., supported parameters are:

                     out-size =(required, 2dbounds)
                       target size given as two coma separated values.

       load      Load the input image from a file and use it to replace the current image in  the
                 pipeline., supported parameters are:

                     file =(input, required, io)
                       name  of  the  input  file  to  load  from..  For supported file types see
                       PLUGINS:2dimage/io

       mask      2D masking, one of the  two  input  images  must  by  of  type  bit.,  supported
                 parameters are:

                     fill = min; dict
                       fill style for pixels outside of the mask.  Supported values are:
                           max  ‐  set  values outside the mask to the maximum value found in the
                           image..
                           zero ‐ set the values outside the mask to zero.
                           min ‐ set values outside the mask to the minimum value  found  in  the
                           image.

                     input =(input, required, io)
                       second   input   image   file   name.    For   supported  file  types  see
                       PLUGINS:2dimage/io

                     inverse = 0; bool
                       set to true to use the inverse of the mask for masking.

       maxflow   This  filter  implements  the  uses  the  max-flow  min-cut  algorithmfor  image
                 segmentation, supported parameters are:

                     sink-flow =(input, required, io)
                       Image  of  float  type  to  define  the  per-pixel  flow to the sink.  For
                       supported file types see PLUGINS:2dimage/io

                     source-flow =(input, required, io)
                       Image of float type to define the  per-pixel  flow  to  the  source.   For
                       supported file types see PLUGINS:2dimage/io

       mean      2D image mean filter, supported parameters are:

                     w = 1; int in [1, inf)
                       half filter width.

       meanvar   Filter  that evaluates simultaniously the pixel wise mean and the variance of an
                 image in a given window. Pixel intensities below the  given  threshold  will  be
                 ignored and at their loctions the output mean and variation are set to zero. The
                 mean intensity image is directly passed as float  image  to  the  pipeline,  the
                 variation  image is saved to a file given with the varfile parameter., supported
                 parameters are:

                     thresh = 0; double in [0, inf)
                       Intensity thresholding  parameter:  Pixels  with  intensities  below  this
                       threshold  will be set to zero, and also not used when evaluating mean and
                       variation.

                     varfile =(output, required, io)
                       name of the output file to save the variation image too..   For  supported
                       file types see PLUGINS:2dimage/io

                     w = 1; uint in [1, inf)
                       filter width parameter.

       median    2D image median filter, supported parameters are:

                     w = 1; int in [1, inf)
                       half filter width.

       medianmad Filter  that  evaluates  simultaniously  the  pixel  wise  median and the median
                 absolute deviation (MAD) of an image in a given window. Pixel intensities  below
                 the  given threshold will be ignored and at their loctions the output median and
                 MAD are set to zero. The median  intensity  image  is  directly  passed  to  the
                 pipeline,  the  variation  image  is  saved  to  a  file  given with the varfile
                 parameter. Both output images have the same pixel type like  the  input  image.,
                 supported parameters are:

                     madfile =(output, required, io)
                       name  of the output file to save the median absolute deviation image too..
                       For supported file types see PLUGINS:2dimage/io

                     thresh = 0; double in [0, inf)
                       Intensity thresholding  parameter:  Pixels  with  intensities  below  this
                       threshold  will be set to zero, and also not used when evaluating mean and
                       variation.

                     w = 1; uint in [1, inf)
                       filter width parameter.

       mlv       Mean of Least Variance 2D image filter, supported parameters are:

                     w = 1; int in [1, inf)
                       filter width parameter.

       ngfnorm   2D image to normalized-gradiend-field-norm filter

                     (no parameters)

       noise     2D image noise filter: add additive or modulated noise to  an  image,  supported
                 parameters are:

                     g = [gauss:mu=0,sigma=10]; factory
                       noise generator.  For supported plug-ins see PLUGINS:generator/noise

                     mod = 0; bool
                       additive or modulated noise.

       open      morphological open, supported parameters are:

                     hint = black; set
                       a hint at the main image content.  Supported values are:( black, white, )

                     shape = [sphere:r=2]; factory
                       structuring element.  For supported plug-ins see PLUGINS:2dimage/shape

       pruning   Morphological  pruning.  Pruning  until  convergence  will  erase all pixels but
                 closed loops., supported parameters are:

                     iter = 0; int in [1, 1000000]
                       Number of iterations to run, 0=until convergence.

       regiongrow
                 Region growing startin from  a  seed  until  only  along  increasing  gradients,
                 supported parameters are:

                     n = 8n; factory
                       Neighborhood shape.  For supported plug-ins see PLUGINS:2dimage/shape

                     seed =(input, required, io)
                       seed image (bit valued).  For supported file types see PLUGINS:2dimage/io

       sandp     salt and pepper  3d filter, supported parameters are:

                     thresh = 100; float in (0, inf)
                       thresh value.

                     w = 1; int in [1, inf)
                       filter width parameter.

       scale     2D image downscale filter, supported parameters are:

                     interp = [bspline:d=3]; factory
                       interpolation   method   to   be   used  .   For  supported  plug-ins  see
                       PLUGINS:1d/splinekernel

                     s = [[0,0]]; 2dbounds
                       target size as 2D vector.

                     sx = 0; uint in [0, inf)
                       target size in x direction, 0: use input size.

                     sy = 0; uint in [0, inf)
                       target size in y direction, 0: use input size.

       selectbig 2D label select biggest component filter

                     (no parameters)

       sepconv   2D image intensity separaple convolution filter, supported parameters are:

                     kx = [gauss:w=1]; factory
                       filter   kernel   in   x-direction.    For    supported    plug-ins    see
                       PLUGINS:1d/spacialkernel

                     ky = [gauss:w=1]; factory
                       filter    kernel    in    y-direction.    For   supported   plug-ins   see
                       PLUGINS:1d/spacialkernel

       shmean    2D image filter that  evaluates  the  mean  over  a  given  neighborhood  shape,
                 supported parameters are:

                     shape = 8n; factory
                       neighborhood  shape  to  evaluate  the  mean.   For supported plug-ins see
                       PLUGINS:2dimage/shape

       sobel     The 2D Sobel filter for gradient evaluation. Note that the output pixel type  of
                 the  filtered image is the same as the input pixel type, so converting the input
                 beforehand to  a  floating  point  valued  image  is  recommendable.,  supported
                 parameters are:

                     dir = x; dict
                       Gradient direction.  Supported values are:
                           y ‐ gradient in y-direction
                           x ‐ gradient in x-direction

       sort-label
                 This  plug-in  sorts  the  labels of a gray-scale image so that the lowest label
                 value corresponts to the lable with themost pixels. The background  (0)  is  not
                 touched

                     (no parameters)

       sws       seeded  watershead.  The  algorithm extracts exactly so many reagions as initial
                 labels are given in the seed image., supported parameters are:

                     grad = 0; bool
                       Interpret the input image as gradient. .

                     mark = 0; bool
                       Mark the segmented watersheds with a special gray scale value.

                     n = [sphere:r=1]; factory
                       Neighborhood for watershead region growing.  For  supported  plug-ins  see
                       PLUGINS:2dimage/shape

                     seed =(input, required, string)
                       seed input image containing the lables for the initial regions.

       tee       Save  the  input  image  to  a file and also pass it through to the next filter,
                 supported parameters are:

                     file =(output, required, io)
                       name of the output file to save the image too..  For supported file  types
                       see PLUGINS:2dimage/io

       thinning  Morphological  thinning. Thinning until convergence will result in a 8-connected
                 skeleton, supported parameters are:

                     iter = 0; int in [1, 1000000]
                       Number of iterations to run, 0=until convergence.

       thresh    This filter sets all pixels of an image  to  zero  that  fall  below  a  certain
                 threshold  and  whose neighbours in a given neighborhood shape also fall below a
                 this threshold, supported parameters are:

                     shape = 4n; factory
                       neighborhood shape to take  into  account.   For  supported  plug-ins  see
                       PLUGINS:2dimage/shape

                     thresh = 5; double
                       The threshold value.

       tmean     2D  image  thresholded tmean filter: The output pixel value is zero if the input
                 pixel value is below the given threshold, otherwise the pixels in the evaluation
                 windows  are  only  considered  if  the  input  pixel  intensity  is  above  the
                 threshold., supported parameters are:

                     t = 0; float
                       Threshold for pixels not to take into account.

                     w = 1; int in [1, inf)
                       half filter width.

       transform Transform the input image with the given transformation.,  supported  parameters
                 are:

                     file =(input, required, io)
                       Name of the file containing the transformation..  For supported file types
                       see PLUGINS:2dtransform/io

       ws        basic watershead segmentation., supported parameters are:

                     evalgrad = 0; bool
                       Set to 1 if the input image does not represent a gradient norm image.

                     mark = 0; bool
                       Mark the segmented watersheds with a special gray scale value.

                     n = [sphere:r=1]; factory
                       Neighborhood for watershead region growing.  For  supported  plug-ins  see
                       PLUGINS:2dimage/shape

                     thresh = 0; float in [0, 1)
                       Relative  gradient  norm  threshold.  The  actual value threshold value is
                       thresh * (max_grad - min_grad) + min_grad. Bassins separated by  gradients
                       with a lower norm will be joined.

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/shape

       1n        A shape that only contains the central point

                     (no parameters)

       4n        4n neighborhood 2D shape

                     (no parameters)

       8n        8n neighborhood 2D shape

                     (no parameters)

       rectangle rectangle shape mask creator, supported parameters are:

                     fill = 1; bool
                       create a filled shape.

                     height = 2; int in [1, inf)
                       height of rectangle.

                     width = 2; int in [1, inf)
                       width of rectangle.

       sphere    Closed spherical neighborhood shape of radius r., supported parameters are:

                     r = 2; float in (0, inf)
                       sphere radius.

       square    square shape mask creator, supported parameters are:

                     fill = 1; bool
                       create a filled shape.

                     width = 2; int in [1, inf)
                       width of rectangle.

PLUGINS: 2dtransform/io

       bbs       Binary (non-portable) serialized IO of 2D transformations

                     ('Recognized file extensions: ', '.bbs')

       datapool  Virtual IO to and from the internal data pool

                     ('Recognized file extensions: ', '.@')

       vista     Vista storage of 2D transformations

                     ('Recognized file extensions: ', '.v2dt')

       xml       XML serialized IO of 2D transformations

                     ('Recognized file extensions: ', '.x2dt')

PLUGINS: generator/noise

       gauss     This noise generator creates random values that are distributed according  to  a
                 Gaussien   distribution  by  using  the  Box-Muller  transformation.,  supported
                 parameters are:

                     mu = 0; float
                       mean of distribution.

                     seed = 0; uint in [0, inf)
                       set random seed (0=init based on system time).

                     sigma = 1; float in (0, inf)
                       standard derivation of distribution.

       uniform   Uniform noise generator using C stdlib rand(), supported parameters are:

                     a = 0; float
                       lower bound if noise range.

                     b = 1; float
                       higher bound if noise range.

                     seed = 0; uint in [0, inf)
                       set random seed (0=init based on system time).

EXAMPLE

       Evaluate the MAD-image of the bounding box surrounding  the  segmentation  from  a  series
       segment.set  after  applying  a  temporal Gaussian filter of width 5. No spacial filtering
       will be applied. The bounding box will be enlarged by 3 pixels in  all  directions.  Store
       the image in OpenEXR format.

       mia-2dseriessmoothgradMAD -i segment.set -o mad.exr -g 2 -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'.