Plugin type: 3dimage/filter
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## 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 reorient resize sandp scale scharr selectbig sepconv sobel sws tee thinning transform variance ws

##### bandpass

intensity bandpass filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
max | float | 3.40282e+38 | maximum of the band
min | float | 0 | minimum of the band

##### binarize

image binarize filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
max | float | 3.40282e+38 | maximum of accepted range
min | float | 0 | minimum of accepted range

##### close

morphological close. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
hint | string | black | a hint at the main image content (black|white)
shape | factory | [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:

Name | Type | Default | Description
--- | --- | --- | ---
image | io | (input,required) | second image that is needed in the combiner. For supported file types see Plugin type: 3dimage/io
op | factory | (required) | Image combiner to be applied to the images. For supported plug-ins see Plugin type: 3dimage/combiner
reverse | bool | 0 | reverse the order in which the images passed to the combiner

##### convert

image pixel format conversion filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
a | float | 1 | linear conversion parameter a
b | float | 0 | linear conversion parameter b

map

dict

opt

conversion mapping
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

dict

ubyte

output pixel type
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:

Name | Type | Default | Description
--- | --- | --- | ---
end | streamable | [[4294967295,4294967295,4294967295]] | end of cropping range, maximum = (-1,-1,-1)
start | streamable | [[0,0,0]] | begin of cropping range

##### dilate

3d image stack dilate filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
hint | string | black | a hint at the main image content (black|white)
shape | factory | [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:

Name | Type | Default | Description
--- | --- | --- | ---
b | 3dbounds | [[1,1,1]] | blocksize
bx | uint in [1, inf) | 1 | blocksize in x direction
by | uint in [1, inf) | 1 | blocksize in y direction
bz | uint in [1, inf) | 1 | blocksize in z direction
kernel | factory | gauss | smoothing 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:

Name | Type | Default | Description
--- | --- | --- | ---
hint | string | black | a hint at the main image content (black|white)
shape | factory | [sphere:r=2] | structuring element. For supported plug-ins see Plugin type: 3dimage/shape

##### gauss

isotropic 3D gauss filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [0, inf) | 1 | filter 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:

Name | Type | Default | Description
--- | --- | --- | ---
min | float | 1 | lower threshold for mask growing
ref | io | (input,required) | reference image for mask region growing. For supported file types see Plugin type: 3dimage/io
shape | factory | 6n | neighborhood 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:

Name | Type | Default | Description
--- | --- | --- | ---
interp | factory | [bspline:d=3] | interpolation kernel to be used . For supported plug-ins see Plugin type: 1d/splinekernel
size | float in (0, inf) | 1 | 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:

Name | Type | Default | Description
--- | --- | --- | ---
c | int in [2, inf) | 3 | number of classes

##### label

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

Name | Type | Default | Description
--- | --- | --- | ---
n | factory | 6n | neighborhood 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:

Name | Type | Default | Description
--- | --- | --- | ---
map | string | (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:

Name | Type | Default | Description
--- | --- | --- | ---
out-size | 3dbounds | (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:

Name | Type | Default | Description
--- | --- | --- | ---
file | io | (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:

Name | Type | Default | Description
--- | --- | --- | ---
b | 3dbounds | [[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:

Name | Type | Default | Description
--- | --- | --- | ---
input | io | (input,required) | second input image file name. For supported file types see Plugin type: 3dimage/io

##### mean

3D image mean filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | half filter width

##### median

median 3d filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | filter width parameter

##### mlv

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

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | filter width parameter

##### msnormalizer

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

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | half filter width

##### open

morphological open. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
hint | string | black | a hint at the main image content (black|white)
shape | factory | [sphere:r=2] | structuring element. For supported plug-ins see Plugin type: 3dimage/shape

##### reorient

3D image reorientation filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---

map

dict

xyz

oriantation mapping to be applied
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:

Name | Type | Default | Description
--- | --- | --- | ---
size | streamable | [[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:

Name | Type | Default | Description
--- | --- | --- | ---
thresh | float in [0, inf) | 100 | thresh value
w | int in [1, inf) | 1 | filter width parameter

##### scale

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

Name | Type | Default | Description
--- | --- | --- | ---
interp | factory | [bspline:d=3] | interpolation kernel to be used . For supported plug-ins see Plugin type: 1d/splinekernel
s | 3dbounds | [[0,0,0]] | target size to set all components at once (component 0:use input image size)
sx | uint in [0, inf) | 0 | target size in x direction (0:use input image size)
sy | uint in [0, inf) | 0 | target size in y direction (0:use input image size)
sz | uint in [0, inf) | 0 | 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:

Name | Type | Default | Description
--- | --- | --- | ---

dir

dict

x

Gradient direction
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.. (This plug-in doesn't take parameters)

##### sepconv

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

Name | Type | Default | Description
--- | --- | --- | ---
kx | factory | [gauss:w=1] | filter kernel in x-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
ky | factory | [gauss:w=1] | filter kernel in y-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
kz | factory | [gauss:w=1] | filter kernel in z-direction. For supported plug-ins see Plugin type: 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:

Name | Type | Default | Description
--- | --- | --- | ---

dir

dict

x

Gradient direction
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:

Name | Type | Default | Description
--- | --- | --- | ---
grad | bool | 0 | Interpret the input image as gradient.
mark | bool | 0 | Mark the segmented watersheds with a special gray scale value
n | factory | [sphere:r=1] | Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
seed | string | (input,required) | 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:

Name | Type | Default | Description
--- | --- | --- | ---
file | io | (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:

Name | Type | Default | Description
--- | --- | --- | ---
file | io | (input,required) | Name of the file containing the transformation.. For supported file types see Plugin type: 3dtransform/io
imgboundary | factory |  | override image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory |  | override image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

##### variance

3D image variance filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | half filter width

##### ws

basic watershead segmentation.. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
evalgrad | bool | 0 | Set to 1 if the input image does not represent a gradient norm image
mark | bool | 0 | Mark the segmented watersheds with a special gray scale value
n | factory | [sphere:r=1] | Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
thresh | float in [0, 1) | 0 | 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

#### 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

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