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=(input, required); io

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

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

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); set

output file typeoutput file type

Supported values are:( analyze, datapool, dicom, hdf5, inria, mhd, nifti, vff, vista, vti, vtk, )

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

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).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.

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, string)

second image that is needed in the combiner.

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; string

smoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize..

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, string)

reference image for mask region growing.

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, string)

name of the input file to load from..

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, string)

second input image file name.

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).

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, string)

name of the output file to save the image too..

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, string)

Name of the file containing the transformation..

imgboundary = ; string

override image interpolation boundary conditions.

imgkernel = ; string

override image interpolator kernel.

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

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:

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 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

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) 1999-2015 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'.