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

NAME

       ('mia\-3dpropose\-boundingbox',) - Evaluate a bounding box for the image.

SYNOPSIS

       mia-3dpropose-boundingbox -i <in-file> [options]

DESCRIPTION

       mia-3dpropose-boundingbox  This  program evaluates a box that contains all the pixels of a
       given mask image. If the input image is not a binary image, a pre-filter must  be  applied
       that converts the imput image into a mask.

OPTIONS

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

   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

   Parameters
              -f --filter=
                     Filter to be applied to the image before the bounding box is evaluated. Must
                     return a bit-valued image.
                      For supported plugins see PLUGINS:3dimage/filter

              -p --padding=0; uint in [0, inf)
                     Padding of boundaries.

   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/splinebc

       mirror    Spline interpolation boundary conditions that mirror on the boundary

                     (no parameters)

       repeat    Spline interpolation boundary conditions that repeats the value at the boundary

                     (no parameters)

       zero      Spline interpolation boundary conditions that assumes zero for values outside

                     (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: 3dimage/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: 3dimage/filter

       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; 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

       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:3dimage/io

                     op =(required, factory)
                       Image  combiner  to  be applied to the images.  For supported plug-ins see
                       PLUGINS:3dimage/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 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

       distance  Evaluate the 3D distance transform of an image. If the image is a  binary  mask,
                 then result of the distance transform in each point corresponds to the Euclidian
                 distance to the mask. If the input image is of a scalar pixel  value,  then  the
                 this  scalar  is  interpreted  as heighfield and the per pixel value adds to the
                 distance.

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

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

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

                     bz = 1; uint in [1, inf)
                       blocksize in z 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     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 in [0, inf)
                       filter width parameter.

       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.

                     ref =(input, 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 in (0, inf)
                       isometric target voxel size.

       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 in [2, inf)
                       number of classes.

       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

       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, 3dbounds)
                       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:3dimage/io

       lvdownscale
                 This is a label voting downscale filter. It adownscales a 3D  image  by  blocks.
                 For  each  block  the  (non-zero)  label that appears most times in the block is
                 issued as output pixel in the target image. If two labels appear the same number
                 of times, the one with the lower absolute value wins., supported parameters are:

                     b = [[1,1,1]]; 3dbounds
                       blocksize for the downscaling. Each block will be represented by one pixel
                       in the target image..

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

       mean      3D image mean filter, supported parameters are:

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

       median    median 3d filter, supported parameters are:

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

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

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

       msnormalizer
                 3D image mean-sigma normalizing filter, supported parameters are:

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

       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:
                           p-zxy ‐ permutate x->y->z->x
                           r-x180 ‐ rotate around x-axis clockwise 180 degree
                           xyz ‐ keep orientation
                           p-yzx ‐ permutate x->z->y->x
                           r-z180 ‐ rotate around z-axis clockwise 180 degree
                           r-y270 ‐ rotate around y-axis clockwise 270 degree
                           f-xz ‐ flip x-z
                           f-yz ‐ flip y-z
                           r-x90 ‐ rotate around x-axis clockwise 90 degree
                           r-y90 ‐ rotate around y-axis clockwise 90 degree
                           r-x270 ‐ rotate around x-axis clockwise 270 degree
                           r-z270 ‐ rotate around z-axis clockwise 270 degree
                           r-z90 ‐ rotate around z-axis clockwise 90 degree
                           f-xy ‐ flip x-y
                           r-y180 ‐ rotate around y-axis clockwise 180 degree

       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 in [0, inf)
                       thresh value.

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

       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 in [0, inf)
                       target size in x direction (0:use input image size).

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

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

       scharr    The 3D Scharr 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
                           z ‐ gradient in z-direction

       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

       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
                           z ‐ gradient in z-direction

       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 =(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: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 =(input, required, io)
                       Name of the file containing the transformation..  For supported file types
                       see PLUGINS:3dtransform/io

                     imgboundary = ; factory
                       override image interpolation boundary conditions.  For supported  plug-ins
                       see PLUGINS:1d/splinebc

                     imgkernel = ; factory
                       override   image   interpolator   kernel.    For  supported  plug-ins  see
                       PLUGINS:1d/splinekernel

       variance  3D image variance filter, supported parameters are:

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

       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 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: 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:
                       signed 16 bit, unsigned 16 bit

       hdf5      HDF5 3D image IO

                     ('Recognized file extensions: ', '.H5, .h5')

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

       nifti     NIFTI-1 3D image IO. The orientation is transformed in the same way like  it  is
                 done with 'dicomtonifti --no-reorder' from the vtk-dicom package.

                     ('Recognized file extensions: ', '.NII, .nii')

                     Supported element types:
                       signed  8  bit,  unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
                       bit, unsigned 32 bit, signed 64 bit, unsigned 64 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 in (0, inf)
                       sphere radius.

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

       Evaluate a bounding box with boundary padding of 5 of a mask resulting from a binarization
       with a minimum value 10.10 and a boundary padding of 5 from image image.v .

       mia-3dpropose-boundingbox -i image.v -f binarize:min=10 -p 5

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'.