mia-3dimagefilterstack(1) 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=(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: [email protected]

 
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: [email protected]

 
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'.