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

NAME

       mia-3dimagefilterstack - Filter a series of 3D images.

SYNOPSIS

       mia-3dimagefilterstack    -i    <in-file>    -o    <out-file>    -t    <type>    [options]
       <PLUGINS:3dimage/filter>

DESCRIPTION

       mia-3dimagefilterstack This program is used to filter and convert a  consecutive  numbered
       series  gray  of  scale  images.  File names must follow the pattern 'dataXXXX.v' (X being
       digits), i.e. the numbering comes right before the dot.

OPTIONS

              -i --in-file=(required)
                     input  image(s)   to   be   filtered    For   supported   file   types   see
                     PLUGINS:3dimage/io

              -o --out-file=(required)
                     output  file  name  base,  numbers  are  added  accorfing  to the input file
                     pattern, and the file  extension is added according to  the  'type'  option.
                     For supported file types see PLUGINS:3dimage/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: 3dimage/filter

       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 (string)
                       a hint at the main image content (black|white).

                     shape = [sphere:r=2] (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/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 in the sense that the given range is kept., supported parameters are:

                     end = [[4294967295,4294967295,4294967295]] (streamable)
                       end of cropping range, maximum = (-1,-1,-1).

                     start = [[0,0,0]] (streamable)
                       begin of cropping range.

       dilate    3d image stack dilate filter, supported parameters are:

                     hint = black (string)
                       a hint at the main image content (black|white).

                     shape = [sphere:r=2] (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/shape

       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 = [[1,1,1]] (3dbounds)
                       blocksize.

                     bx = 1 (uint)
                       blocksize in x direction.  in [1, 2147483647]

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

                     bz = 1 (uint)
                       blocksize in z direction.  in [1, 2147483647]

                     kernel = gauss (factory)
                       smoothing filter kernel to be applied (filter width is determined based on
                       the scaling factor).  For supported plug-ins see PLUGINS:1d/spacialkernel

       erode     3d image stack erode filter, supported parameters are:

                     hint = black (string)
                       a hint at the main image content (black|white).

                     shape = [sphere:r=2] (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/shape

       gauss     isotropic 3D gauss filter, supported parameters are:

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

       gradnorm  3D image to gradient norm filter

                     (no parameters)

       growmask  Use an input binary mask and a reference gray scale image to do  region  growing
                 by  adding the neighborhood pixels of an already added pixel if the have a lower
                 intensity that is above the given threshold., supported parameters are:

                     min = 1 (float)
                       lower threshold for mask growing.  in [-3.40282e+38, 3.40282e+38]

                     ref = (required, io)
                       reference image for mask region growing.  For  supported  file  types  see
                       PLUGINS:3dimage/io

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

       invert    intensity invert filter

                     (no parameters)

       isovoxel  This  filter  scales  an  image to make the voxel size isometric and its size to
                 correspond to the given value, supported parameters are:

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

                     size = 1 (float)
                       isometric target voxel size.  in [0.001, 1e+06]

       kmeans    3D  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 [0, 255]

       label     A  filter  to  label  the   connected  components  of a binary image., supported
                 parameters are:

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

       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:3dimage/io

       mask      Mask an image, one image is taken from the parameters list and  the  other  from
                 the normal filter input. Both images must be of the same dimensions and one must
                 be binary. The attributes of the image coming through the  filter  pipeline  are
                 preserved.  The  output  pixel  type  corresponds to the input image that is not
                 binary., supported parameters are:

                     input = (required, io)
                       second  input  image  file   name.    For   supported   file   types   see
                       PLUGINS:3dimage/io

       median    median 3d filter, supported parameters are:

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

       mlv       Mean of Least Variance 3D image filter, supported parameters are:

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

       open      morphological open, supported parameters are:

                     hint = black (string)
                       a hint at the main image content (black|white).

                     shape = [sphere:r=2] (factory)
                       structuring element.  For supported plug-ins see PLUGINS:3dimage/shape

       reorient  3D image reorientation filter, supported parameters are:

                     map = xyz (dict)
                       oriantation mapping to be applied.  Supported values are:
                           yzx ‐ rotate x->z->y->x
                           yxz ‐ switch x-y
                           xyz ‐ keep orientation
                           xzy ‐ switch y-z
                           zxy ‐ rotate x->y->z->x

       resize    Resize  an  image.  The  original  data is centered within the new sized image.,
                 supported parameters are:

                     size = [[0,0,0]] (streamable)
                       new size of the image a  size  0  indicates  to  keep  the  size  for  the
                       corresponding dimension..

       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     3D image filter that scales to a given target size , supported parameters are:

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

                     s = [[0,0,0]] (3dbounds)
                       target size to set all components at once  (component  0:use  input  image
                       size).

                     sx = 0 (uint)
                       target size in x direction (0:use input image size).  in [0, 4294967295]

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

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

       selectbig A  filter  that creats a binary mask representing the intensity with the highest
                 pixel count.The pixel value 0 will be ignored, and if two intensities  have  the
                 same  pixel  count,  then  the result is undefined. The input pixel must have an
                 integral pixel type.

                     (no parameters)

       sepconv   3D 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

                     kz = [gauss:w=1] (factory)
                       filter   kernel   in   z-direction.    For    supported    plug-ins    see
                       PLUGINS:1d/spacialkernel

       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:3dimage/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:3dimage/io

       thinning  3D morphological thinning,  based on: Lee and Kashyap, 'Building Skeleton Models
                 via 3-D Medial Surface/Axis Thinning Algorithms',  Graphical  Models  and  Image
                 Processing,  56(6):462-478,  1994.  This  implementation  only  supports  the 26
                 neighbourhood.

                     (no parameters)

       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:3dtransform/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:3dimage/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: 3dimage/io

       analyze   Analyze 7.5 image

                     Recognized file extensions:  .HDR, .hdr

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

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       dicom     Dicom image series as 3D

                     Recognized file extensions:  .DCM, .dcm

                     Supported element types:
                       unsigned 16 bit

       inria     INRIA image

                     Recognized file extensions:  .INR, .inr

                     Supported element types:
                       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

       mhd       MetaIO 3D image IO using the VTK implementation (experimental).

                     Recognized file extensions:  .MHA, .MHD, .mha, .mhd

                     Supported element types:
                       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

       vff       VFF Sun raster format

                     Recognized file extensions:  .VFF, .vff

                     Supported element types:
                       unsigned 8 bit, signed 16 bit

       vista     Vista 3D

                     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

       vti       3D image VTK-XML in- and output (experimental).

                     Recognized file extensions:  .VTI, .vti

                     Supported element types:
                       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

       vtk       3D VTK image legacy in- and output (experimental).

                     Recognized file extensions:  .VTK, .VTKIMAGE, .vtk, .vtkimage

                     Supported element types:
                       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: 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: 3dtransform/io

       bbs       Binary (non-portable) serialized IO of 3D transformations

                     Recognized file extensions:  .bbs

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       vista     Vista storage of 3D transformations

                     Recognized file extensions:  .v, .v3dt

       xml       XML serialized IO of 3D transformations

                     Recognized file extensions:  .x3dt

EXAMPLE

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

       mia-3dimagefilterstack -i image0000.hdr -o filtered -t hdr 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'.