Plugin type: 3dimage/filter

These plug-ins provide 3D image filters. Unless otherwise noted, they take a gray scale image of abitrary pixel type as input, process it and return the filtered result as a new image. Filters can be chained by specifying more then one filter description concated with the '+' sign. for example bandpass:min=10,max=20+median:w=3+convert:repn=ushort:map=copy' will create a filter chain that first runs a bandpass, then a median filter and a conversion to unsigned short values by a plain copy.

Plugins:

bandpass binarize close combiner convert crop dilate distance downscale erode gauss gradnorm growmask invert isovoxel kmeans label labelmap labelscale load lvdownscale mask mean median mlv msnormalizer open resize sandp scale selectbig sepconv sws tee thinning transform variance ws

bandpass

intensity bandpass filter. Supported parameters are:

NameTypeDefaultDescription
maxfloat3.40282e+38maximum of the band
minfloat0minimum of the band

binarize

image binarize filter. Supported parameters are:

NameTypeDefaultDescription
maxfloat3.40282e+38maximum of accepted range
minfloat0minimum of accepted range

close

morphological close. Supported parameters are:

NameTypeDefaultDescription
hintstringblacka hint at the main image content (black|white)
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 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:

NameTypeDefaultDescription
imageio(input,required)second image that is needed in the combiner. For supported file types see Plugin type: 3dimage/io
opfactory(required)Image combiner to be applied to the images. For supported plug-ins see Plugin type: 3dimage/combiner
reversebool0reverse the order in which the images passed to the combiner

convert

image pixel format conversion filter. Supported parameters are:

NameTypeDefaultDescription
afloat1linear conversion parameter a
bfloat0linear conversion parameter b
mapdictopt
conversion mapping
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
repndictubyte
output pixel type
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:

NameTypeDefaultDescription
endstreamable[[4294967295,4294967295,4294967295]]end of cropping range, maximum = (-1,-1,-1)
startstreamable[[0,0,0]]begin of cropping range

dilate

3d image stack dilate filter. Supported parameters are:

NameTypeDefaultDescription
hintstringblacka hint at the main image content (black|white)
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 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.. (This plug-in doesn't take 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:

NameTypeDefaultDescription
b3dbounds[[1,1,1]]blocksize
bxuint in [1, inf)1blocksize in x direction
byuint in [1, inf)1blocksize in y direction
bzuint in [1, inf)1blocksize in z direction
kernelfactorygausssmoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize.. For supported plug-ins see Plugin type: 1d/spacialkernel

erode

3d image stack erode filter. Supported parameters are:

NameTypeDefaultDescription
hintstringblacka hint at the main image content (black|white)
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 3dimage/shape

gauss

isotropic 3D gauss filter. Supported parameters are:

NameTypeDefaultDescription
wint in [0, inf)1filter width parameter

gradnorm

3D image to gradient norm filter. (This plug-in doesn't take 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:

NameTypeDefaultDescription
minfloat1lower threshold for mask growing
refio(input,required)reference image for mask region growing. For supported file types see Plugin type: 3dimage/io
shapefactory6nneighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

invert

intensity invert filter. (This plug-in doesn't take 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:

NameTypeDefaultDescription
interpfactory[bspline:d=3]interpolation kernel to be used . For supported plug-ins see Plugin type: 1d/splinekernel
sizefloat in (0, inf)1isometric 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:

NameTypeDefaultDescription
cint in [2, inf)3number of classes

label

A filter to label the connected components of a binary image.. Supported parameters are:

NameTypeDefaultDescription
nfactory6nneighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

NameTypeDefaultDescription
mapstring(input,required)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:

NameTypeDefaultDescription
out-size3dbounds(required)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:

NameTypeDefaultDescription
fileio(input,required)name of the input file to load from.. For supported file types see Plugin type: 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:

NameTypeDefaultDescription
b3dbounds[[1,1,1]]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:

NameTypeDefaultDescription
inputio(input,required)second input image file name. For supported file types see Plugin type: 3dimage/io

mean

3D image mean filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1half filter width

median

median 3d filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

mlv

Mean of Least Variance 3D image filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

msnormalizer

3D image mean-sigma normalizing filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1half filter width

open

morphological open. Supported parameters are:

NameTypeDefaultDescription
hintstringblacka hint at the main image content (black|white)
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 3dimage/shape

resize

Resize an image. The original data is centered within the new sized image.. Supported parameters are:

NameTypeDefaultDescription
sizestreamable[[0,0,0]]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:

NameTypeDefaultDescription
threshfloat in [0, inf)100thresh value
wint in [1, inf)1filter width parameter

scale

3D image filter that scales to a given target size . Supported parameters are:

NameTypeDefaultDescription
interpfactory[bspline:d=3]interpolation kernel to be used . For supported plug-ins see Plugin type: 1d/splinekernel
s3dbounds[[0,0,0]]target size to set all components at once (component 0:use input image size)
sxuint in [0, inf)0target size in x direction (0:use input image size)
syuint in [0, inf)0target size in y direction (0:use input image size)
szuint in [0, inf)0target 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.. (This plug-in doesn't take parameters)

sepconv

3D image intensity separaple convolution filter. Supported parameters are:

NameTypeDefaultDescription
kxfactory[gauss:w=1]filter kernel in x-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
kyfactory[gauss:w=1]filter kernel in y-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
kzfactory[gauss:w=1]filter kernel in z-direction. For supported plug-ins see Plugin type: 1d/spacialkernel

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

NameTypeDefaultDescription
gradbool0Interpret the input image as gradient.
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
seedstring(input,required)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:

NameTypeDefaultDescription
fileio(output,required)name of the output file to save the image too.. For supported file types see Plugin type: 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.. (This plug-in doesn't take parameters)

transform

Transform the input image with the given transformation.. Supported parameters are:

NameTypeDefaultDescription
fileio(input,required)Name of the file containing the transformation.. For supported file types see Plugin type: 3dtransform/io
imgboundaryfactory override image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory override image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

variance

3D image variance filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1half filter width

ws

basic watershead segmentation.. Supported parameters are:

NameTypeDefaultDescription
evalgradbool0Set to 1 if the input image does not represent a gradient norm image
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
threshfloat in [0, 1)0Relative 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

Plugin consumers:

mia-3dcost mia-3dimagefilter mia-3dimagefilterstack mia-3dmany2one-nonrigid mia-3dnonrigidreg mia-3dnonrigidreg-alt mia-3dprealign-nonrigid mia-3dpropose-boundingbox mia-3dserial-nonrigid mia-mesh-deformable-model maskedimage:3dimage/fullcost