SYNOPSIS

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

DESCRIPTION

mia-3dimagefilter This program is used to filter and convert gray scale 3D images.

OPTIONS

-i --in-file=(input,required)

input image(s) to be filtered For supported file types see PLUGINS:3dimage/io

-o --out-file=(output,required)

output image(s) that have been filtered For supported file types see PLUGINS:3dimage/io

--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 \(hy Low level messages

trace \(hy Function call trace

fail \(hy Report test failures

warning \(hy Warnings

error \(hy Report errors

debug \(hy Debug output

message \(hy Normal messages

fatal \(hy 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/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)

Spline degree. in [0, 5]

omoms

OMoms-spline kernel creation, supported parameters are:

d = 3 (int)

Spline degree. in [3, 3]

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. 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

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. 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 \(hy apply a linear transformation that maps the real input range to the full output range

range \(hy apply linear transformation that maps the input data type range to the output data type range

copy \(hy copy data when converting

linear \(hy apply linear transformation x -> a*x+b

optstat \(hy 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 \(hy floating point 32 bit

sbyte \(hy signed 8 bit

double \(hy floating point 64 bit

sint \(hy signed 32 bit

ushort \(hy unsigned 16 bit

sshort \(hy signed 16 bit

uint \(hy unsigned 32 bit

bit \(hy binary data

ubyte \(hy 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)

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, 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)

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 =(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)

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 =(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)

half filter width. in [1, 2147483647]

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]

msnormalizer

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

w = 1 (int)

half filter width. in [1, 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

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 =(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)

half filter width. in [1, 2147483647]

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:

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, 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

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, 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:

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: 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 input.v, then run a 5-class k-means classification and binarize by selecting the 4th class. mia-3dimagefilter -i image.v -o filtered.v mlv:w=2 kmeans:c=5 binarize:min=4,max=4

AUTHOR(s)

Gert Wollny

COPYRIGHT

This software is Copyright (c) 1999\(hy2013 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'.