Provided by: mia-tools_2.0.13-1_amd64 bug

NAME

       mia-2dstackfilter - Filter a series of 2D images in a 3D fashion.

SYNOPSIS

       mia-2dstackfilter -i <in-file> -o <out-file> -t <type> [options] <PLUGINS:2dstack/filter>

DESCRIPTION

       mia-2dstackfilter  This  program  is  used to filter and convert a series of 2D gray scale
       images in a 3D fashion by running filters (filter/2dimage) as given on the command line.

OPTIONS

              -i --in-file=(required)
                     input  image(s)   to   be   filtered    For   supported   file   types   see
                     PLUGINS:2dimage/io

              -o --out-file=(required)
                     output file name base, the actual names is created by adding the file number
                     based on output order and the extension bysed on the 'type'  parameter   For
                     supported file types see PLUGINS:2dimage/io

              -t --type=(required)
                     output file type

                 --help-plugins
                     give some help about the filter plugins

   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
                        warning ‐ Warnings
                        error ‐ Report errors
                        fail ‐ Report test failures
                        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

       gauss     spacial Gauss filter kernel, supported parameters are:

                     w = 1 (int)
                       half filter width.  in [0, 2147483647]

PLUGINS: 1d/splinekernel

       bspline   B-spline kernel creation , supported parameters are:

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

       omoms     OMoms-spline kernel creation, supported parameters are:

                     d = 3 (int)
                       Spline degree.  in [3, 3]

PLUGINS: 2dimage/filter

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

                     w = 2 (int)
                       half filter width.  in [0, 2147483647]

       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)
                       half filter width.  in [0, 2147483647]

       aniso     2D Anisotropic image filter, supported parameters are:

                     epsilon = 1 (float)
                       iteration change threshold.  in [0.001, 100]

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

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

                     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.  in [-3.40282e+38, 3.40282e+38]

                     min = 0 (float)
                       minimum of the band.  in [-3.40282e+38, 3.40282e+38]

       binarize  image binarize filter, supported parameters are:

                     max = 3.40282e+38 (float)
                       maximum of accepted range.  in [0, 3.40282e+38]

                     min = 0 (float)
                       minimum of accepted range.  in [0, 3.40282e+38]

       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

       convert   image pixel format conversion filter, supported parameters are:

                     a = 1 (float)
                       linear conversion parameter a.  in [-3.40282e+38, 3.40282e+38]

                     b = 0 (float)
                       linear conversion parameter b.  in [-3.40282e+38, 3.40282e+38]

                     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:
                           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)
                       blocksize in x direction.  in [1, 2147483647]

                     by = 1 (uint)
                       blocksize in y direction.  in [1, 2147483647]

                     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)
                       filter width parameter.  in [0, 2147483647]

       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)
                       number of classes.  in [2, 255]

       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  2D image filter to remap label id's., supported parameters are:

                     map = (required, string)
                       Label mapping file.

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

                     file = (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 = (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.

       mean      2D image mean filter, supported parameters are:

                     w = 0 (int)
                       half filter width.  in [0, 2147483647]

       median    2D image median filter, supported parameters are:

                     w = 0 (int)
                       half filter width.  in [0, 2147483647]

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

                     w = 1 (int)
                       filter width parameter.  in [0, 2147483647]

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

       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 = (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)
                       thresh value.  in [0, 3.40282e+38]

                     w = 1 (int)
                       filter width parameter.  in [0, 2147483647]

       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)
                       target size in x direction, 0: use input size.  in [0, 4294967295]

                     sy = 0 (uint)
                       target size in y direction, 0: use input size.  in [0, 4294967295]

       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

       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 = (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 = (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)
                       Number of iterations to run, 0=until convergence.  in [1, 1000000]

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

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

                     thresh = 5 (double)
                       The threshhold value.  in [-1.79769e+308, 1.79769e+308]

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

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

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:
                       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)
                       height of rectangle.  in [0, 2147483647]

                     width = 2 (int)
                       width of rectangle.  in [0, 2147483647]

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

                     r = 2 (float)
                       sphere radius.  in [0, 3.40282e+38]

       square    square shape mask creator, supported parameters are:

                     fill = 1 (bool)
                       create a filled shape.

                     width = 2 (int)
                       width of rectangle.  in [0, 2147483647]

PLUGINS: 2dstack/filter

       byslice   Runs a filter on a per slice basis. In essence, this is a wrapper that makes  it
                 possible   to  add  pure  2D  filters  to  the  stack  filter  pipeline  without
                 ducplicating the implementation., supported parameters are:

                     filter = (required, factory)
                       2D   filter   to    be    applied.     For    supported    plug-ins    see
                       PLUGINS:2dimage/filter

       close     2D Stack morphological filter 'close', supported parameters are:

                     shape = 6n (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/shape

       dilate    2D Stack morphological filter 'dilate', supported parameters are:

                     shape = 6n (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/shape

       erode     2D Stack morphological filter 'erode', supported parameters are:

                     shape = 6n (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/shape

       gauss     Gauss 2D fifo filter, supported parameters are:

                     w = 1 (int)
                       filter width parameter (2*w+1).  in [0, 2147483647]

       label     Stack Label filter, supported parameters are:

                     map = (required, string)
                       Mapfile to save label numbers that are joined.

                     n = 4n (factory)
                       2D  neighbourhood  shape  to define connectedness.  For supported plug-ins
                       see PLUGINS:2dimage/shape

       median    median 2D fifo filter, supported parameters are:

                     w = 1 (int)
                       filter width parameter.  in [0, 2147483647]

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

                     w = 1 (int)
                       filter width parameter.  in [0, 2147483647]

       open      2D Stack morphological filter 'open', supported parameters are:

                     shape = 6n (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/shape

       regiongrow
                 Run a region-growing filter on a stack of images that comprise a 3D image.   The
                 region  growing  is  based  on  class  probabilities  obtained  from  a  c-means
                 classification of the pixel intensities. One seed thresh is use  to  initiate  a
                 region,  and  another  (lower)  threshold is used to stop the region growing. By
                 holding a number of 3D slices in the working memory to allow the region to  grow
                 "backwards  "  in  the  stack  a  Quasi-3D processing is achieved. However, with
                 complex structures the region growing may not properly be segmented.,  supported
                 parameters are:

                     class = 2 (int)
                       class to be segmented.  in [0, 2147483647]

                     depth = 10 (int)
                       number of slices to keep during processing.  in [5, 2147483647]

                     low = 0.5 (float)
                       low threshold for acceptance probability.  in [0, 1]

                     map = (required, string)
                       seed class map.

                     seed = 0.98 (float)
                       threshold for seed probability.  in [0, 1]

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: 3dimage/shape

       18n       18n neighborhood 3D shape creator

                     (no parameters)

       26n       26n neighborhood 3D shape creator

                     (no parameters)

       6n        6n neighborhood 3D shape creator

                     (no parameters)

       sphere    Closed  spherical  shape neighborhood including the pixels within a given radius
                 r., supported parameters are:

                     r = 2 (float)
                       sphere radius.  in [0, 3.40282e+38]

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.  in [-3.40282e+38, 3.40282e+38]

                     seed = 0 (uint)
                       set random seed (0=init based on system time).  in [0, 4294967295]

                     sigma = 1 (float)
                       standard derivation of distribution.  in [0, 3.40282e+38]

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

                     a = 0 (float)
                       lower bound if noise range.  in [-3.40282e+38, 3.40282e+38]

                     b = 1 (float)
                       higher bound if noise range.  in [-3.40282e+38, 3.40282e+38]

                     seed = 0 (uint)
                       set random seed (0=init based on system time).  in [0, 4294967295]

EXAMPLE

       Run a mean-least-varaiance filter on a series of images that follow the numbering  pattern
       imageXXXX.exr and store the output in images filteredXXXX.exr

       mia-2dstackfilter -i image0000.exr -o filtered -t exr mlv:w=2

AUTHOR(s)

       Gert Wollny

COPYRIGHT

       This  software  is  Copyright  (c) 1999‐2013 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'.