Plugin type: 2dimage/filter

These plug-ins provide 2D image filters. Unless otherwise noted, they take a gray scale image of abitrary pixel type as input, process it and return the result as newly created 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:

adaptmed admean aniso bandpass binarize close combiner convert crop dilate distance downscale erode gauss gradnorm invert kmeans label labelmap labelscale load mask mean median mlv ngfnorm noise open pruning regiongrow sandp scale selectbig sepconv shmean sort-label sws tee thinning thresh transform ws

adaptmed

2D image adaptive median filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)2half filter width

admean

An adaptive mean filter that works like a normal mean filter, if the intensity variation within the filter mask is lower then the intensity variation in the whole image, that the uses a special formula if the local variation is higher then the image intensity variation.. Supported parameters are:

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

aniso

2D Anisotropic image filter. Supported parameters are:

NameTypeDefaultDescription
epsilonfloat in (0, inf)1iteration change threshold
iterint in [1, 10000]100number of iterations
kfloat in [0, 100]-1k the noise threshold (<=0 -> adaptive)
nset8neighbourhood Supported values are:(4, 8, )
psidicttuckey
edge stopping function
guess:test stopping function
tuckey:tukey stopping function
pm1:stopping function 1
pm2:stopping function 2

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
hintsetblacka hint at the main image content Supported values are:(black, white, )
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 2dimage/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: 2dimage/io
opfactory(required)Image combiner to be applied to the images. For supported plug-ins see Plugin type: 2dimage/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.. Supported parameters are:

NameTypeDefaultDescription
endstreamable[[-1,-1]]end of crop region
startstreamable[[0,0]]start of crop region

dilate

2d image stack dilate filter. Supported parameters are:

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

distance

2D image distance filter, evaluates the distance map for a binary mask.. (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
b2dbounds[[1,1]]blocksize
bxuint in [1, inf)1blocksize in x direction
byuint in [1, inf)1blocksize in y 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

2d image stack erode filter. Supported parameters are:

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

gauss

isotropic 2D gauss filter. Supported parameters are:

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

gradnorm

2D image to gradient norm filter. Supported parameters are:

NameTypeDefaultDescription
normalizebool0Normalize the gradient norms to range [0,1].

invert

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

kmeans

2D 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

Label connected components in a binary 2D image.. Supported parameters are:

NameTypeDefaultDescription
nfactory4nNeighborhood mask to describe connectivity.. For supported plug-ins see Plugin type: 2dimage/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-size2dbounds(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: 2dimage/io

mask

2D masking, one of the two input images must by of type bit.. Supported parameters are:

NameTypeDefaultDescription
filldictmin
fill style for pixels outside of the mask
max:set values outside the mask to the maximum value found in the image..
zero:set the values outside the mask to zero.
min:set values outside the mask to the minimum value found in the image.
inputio(input,required)second input image file name. For supported file types see Plugin type: 2dimage/io
inversebool0set to true to use the inverse of the mask for masking

mean

2D image mean filter. Supported parameters are:

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

median

2D image median filter. Supported parameters are:

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

mlv

Mean of Least Variance 2D image filter. Supported parameters are:

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

ngfnorm

2D image to normalized-gradiend-field-norm filter. (This plug-in doesn't take parameters)

noise

2D image noise filter: add additive or modulated noise to an image. Supported parameters are:

NameTypeDefaultDescription
gfactory[gauss:mu=0,sigma=10]noise generator. For supported plug-ins see Plugin type: generator/noise
modbool0additive or modulated noise

open

morphological open. Supported parameters are:

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

pruning

Morphological pruning. Pruning until convergence will erase all pixels but closed loops.. Supported parameters are:

NameTypeDefaultDescription
iterint in [1, 1000000]0Number of iterations to run, 0=until convergence

regiongrow

Region growing startin from a seed until only along increasing gradients. Supported parameters are:

NameTypeDefaultDescription
nfactory8nNeighborhood shape. For supported plug-ins see Plugin type: 2dimage/shape
seedio(input,required)seed image (bit valued). For supported file types see Plugin type: 2dimage/io

sandp

salt and pepper 3d filter. Supported parameters are:

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

scale

2D image downscale filter. Supported parameters are:

NameTypeDefaultDescription
interpfactory[bspline:d=3]interpolation method to be used . For supported plug-ins see Plugin type: 1d/splinekernel
s2dbounds[[0,0]]target size as 2D vector
sxuint in [0, inf)0target size in x direction, 0: use input size
syuint in [0, inf)0target size in y direction, 0: use input size

selectbig

2D label select biggest component filter. (This plug-in doesn't take parameters)

sepconv

2D 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

shmean

2D image filter that evaluates the mean over a given neighborhood shape. Supported parameters are:

NameTypeDefaultDescription
shapefactory8nneighborhood shape to evaluate the mean. For supported plug-ins see Plugin type: 2dimage/shape

sort-label

This plug-in sorts the labels of a gray-scale image so that the lowest label value corresponts to the lable with themost pixels. The background (0) is not touched. (This plug-in doesn't take parameters)

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: 2dimage/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: 2dimage/io

thinning

Morphological thinning. Thinning until convergence will result in a 8-connected skeleton. Supported parameters are:

NameTypeDefaultDescription
iterint in [1, 1000000]0Number of iterations to run, 0=until convergence

thresh

This filter sets all pixels of an image to zero that fall below a certain threshhold and whose neighbours in a given neighborhood shape also fall below a this threshhold. Supported parameters are:

NameTypeDefaultDescription
shapefactory4nneighborhood shape to take into account. For supported plug-ins see Plugin type: 2dimage/shape
threshdouble5The threshhold value

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: 2dtransform/io

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: 2dimage/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-2dimagefilter mia-2dimagefilterstack mia-2dsegment-fuzzyw mia-2dseries2dordermedian mia-2dseriesgradMAD mia-2dseriessmoothgradMAD mia-2dstackfilter byslice:2dstack/filter