mia-3dpropose-boundingbox(1)

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:

        trace - Function call trace
        debug - Debug output
        info - Low level messages
        message - Normal messages
        warning - Warnings
        fail - Report test failures
        error - Report errors
        fatal - Report only fatal errors

    --copyright
        print copyright information

    -h --help
        print this help

    -? --usage
        print a short help

    --version
        print the version number and exit

  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:
            copy - copy data when converting
            linear - apply linear transformation x -> a*x+b
            range - apply linear transformation that maps the input data type range to the output data type range
            opt - apply a linear transformation that maps the real input range to the full output range
            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:
            bit - binary data
            sbyte - signed 8 bit
            ubyte - unsigned 8 bit
            sshort - signed 16 bit
            ushort - unsigned 16 bit
            sint - signed 32 bit
            uint - unsigned 32 bit
            slong - signed 64 bit
            ulong - unsigned 64 bit
            float - floating point 32 bit
            double - floating point 64 bit
            none - no pixel type defined

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