mia-2dimagefilterstack - Online in the Cloud

PROGRAM:

NAME

mia-2dimagefilterstack - Run filters on a series of 2D images.

SYNOPSIS

mia-2dimagefilterstack -i <in-file> -o <out-file> [options] <PLUGINS:2dimage/filter>

DESCRIPTION

mia-2dimagefilterstack This program runs a series filters on a series of consecutive
numbered input image. The filters are given as extra parameters on the command line and
are run in the order in which they are given.

OPTIONS

File IO
-i --in-file=(input, required); io
input image(s) to be filtered For supported file types see
PLUGINS:2dimage/io

-o --out-file=(output, required); io
output file name base, the file type is set accurding to the 'type' option
For supported file types see PLUGINS:2dimage/io

-t --type=
output file type, if not given the input type is used
Supported values are:( @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW,
TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif,
tiff, v, vista, )

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).

Processing1
-s --start=0
first possible number of file number range to be filteredfirst possible
number of file number range to be filtered

-e --end=2147483647
last possible number of file number range to be filteredlast possible number
of file number range to be filtered

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/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: 2dimage/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: 2dimage/filter

adaptmed 2D image adaptive median filter, supported parameters are:

w = 2; int in [1, inf)
half 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:

w = 1; int in [1, inf)
half filter width.

aniso 2D Anisotropic image filter, supported parameters are:

epsilon = 1; float in (0, inf)
iteration change threshold.

iter = 100; int in [1, 10000]
number of iterations.

k = -1; float in [0, 100]
k the noise threshold (<=0 -> adaptive).

n = 8; set
neighbourhood. Supported values are:( 4, 8, )

psi = tuckey; dict
edge stopping function. Supported values are:
guess ‐ test stopping function
tuckey ‐ tukey stopping function
pm1 ‐ stopping function 1
pm2 ‐ stopping function 2

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; set
a hint at the main image content. Supported values are:( black, white,
)

shape = [sphere:r=2]; factory
structuring element. For supported plug-ins see PLUGINS: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:

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:2dimage/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., supported parameters are:

end = [[-1,-1]]; streamable
end of crop region.

start = [[0,0]]; streamable
start of crop region.

dilate 2d image stack dilate filter, supported parameters are:

hint = black; set
a hint at the main image content. Supported values are:( black, white,
)

shape = [sphere:r=2]; factory
structuring element. For supported plug-ins see PLUGINS:2dimage/shape

distance 2D image distance filter, evaluates the distance map for a binary mask.

(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]]; 2dbounds
blocksize.

bx = 1; uint in [1, inf)
blocksize in x direction.

by = 1; uint in [1, inf)
blocksize in y direction.

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

erode 2d image stack erode filter, supported parameters are:

hint = black; set
a hint at the main image content. Supported values are:( black, white,
)

shape = [sphere:r=2]; factory
structuring element. For supported plug-ins see PLUGINS:2dimage/shape

gauss isotropic 2D gauss filter, supported parameters are:

w = 1; int in [0, inf)
filter width parameter.

gradnorm 2D image to gradient norm filter, supported parameters are:

normalize = 0; bool
Normalize the gradient norms to range [0,1]..

invert intensity invert filter

(no 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:

c = 3; int in [2, inf)
number of classes.

label Label connected components in a binary 2D image., supported parameters are:

n = 4n; factory
Neighborhood mask to describe connectivity.. For supported plug-ins see
PLUGINS:2dimage/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, 2dbounds)
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..

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

fill = min; dict
fill style for pixels outside of the mask. Supported values are:
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.

input =(input, required, string)
second input image file name.

inverse = 0; bool
set to true to use the inverse of the mask for masking.

maxflow This filter implements the uses the max-flow min-cut algorithmfor image
segmentation, supported parameters are:

sink-flow =(input, required, string)
Image of float type to define the per-pixel flow to the sink.

source-flow =(input, required, string)
Image of float type to define the per-pixel flow to the source.

mean 2D image mean filter, supported parameters are:

w = 1; int in [1, inf)
half filter width.

median 2D image median filter, supported parameters are:

w = 1; int in [1, inf)
half filter width.

mlv Mean of Least Variance 2D image filter, supported parameters are:

w = 1; int in [1, inf)
filter width parameter.

ngfnorm 2D image to normalized-gradiend-field-norm filter

(no parameters)

noise 2D image noise filter: add additive or modulated noise to an image, supported
parameters are:

g = [gauss:mu=0,sigma=10]; factory
noise generator. For supported plug-ins see PLUGINS:generator/noise

mod = 0; bool
additive or modulated noise.

open morphological open, supported parameters are:

hint = black; set
a hint at the main image content. Supported values are:( black, white,
)

shape = [sphere:r=2]; factory
structuring element. For supported plug-ins see PLUGINS:2dimage/shape

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

iter = 0; int in [1, 1000000]
Number of iterations to run, 0=until convergence.

regiongrow
Region growing startin from a seed until only along increasing gradients,
supported parameters are:

n = 8n; factory
Neighborhood shape. For supported plug-ins see PLUGINS:2dimage/shape

seed =(input, required, string)
seed image (bit valued).

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 2D image downscale filter, supported parameters are:

interp = [bspline:d=3]; factory
interpolation method to be used . For supported plug-ins see
PLUGINS:1d/splinekernel

s = [[0,0]]; 2dbounds
target size as 2D vector.

sx = 0; uint in [0, inf)
target size in x direction, 0: use input size.

sy = 0; uint in [0, inf)
target size in y direction, 0: use input size.

selectbig 2D label select biggest component filter

(no parameters)

sepconv 2D 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

shmean 2D image filter that evaluates the mean over a given neighborhood shape,
supported parameters are:

shape = 8n; factory
neighborhood shape to evaluate the mean. For supported plug-ins see
PLUGINS:2dimage/shape

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:

dir = x; dict
Gradient direction. Supported values are:
y ‐ gradient in y-direction
x ‐ gradient in x-direction

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

(no parameters)

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:2dimage/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 Morphological thinning. Thinning until convergence will result in a 8-connected
skeleton, supported parameters are:

iter = 0; int in [1, 1000000]
Number of iterations to run, 0=until convergence.

thresh This filter sets all pixels of an image to zero that fall below a certain
threshold and whose neighbours in a given neighborhood shape also fall below a
this threshold, supported parameters are:

shape = 4n; factory
neighborhood shape to take into account. For supported plug-ins see
PLUGINS:2dimage/shape

thresh = 5; double
The threshold value.

transform Transform the input image with the given transformation., supported parameters
are:

file =(input, required, string)
Name of the file containing the transformation..

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:2dimage/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: 2dimage/io

bmp BMP 2D-image input/output support

Recognized file extensions: .BMP, .bmp

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

datapool Virtual IO to and from the internal data pool

Recognized file extensions: .@

dicom 2D image io for DICOM

Recognized file extensions: .DCM, .dcm

Supported element types:
signed 16 bit, unsigned 16 bit

exr a 2dimage io plugin for OpenEXR images

Recognized file extensions: .EXR, .exr

Supported element types:
unsigned 32 bit, floating point 32 bit

jpg a 2dimage io plugin for jpeg gray scale images

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

Supported element types:
unsigned 8 bit

png a 2dimage io plugin for png images

Recognized file extensions: .PNG, .png

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

raw RAW 2D-image output support

Recognized file extensions: .RAW, .raw

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

tif TIFF 2D-image input/output support

Recognized file extensions: .TIF, .TIFF, .tif, .tiff

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

vista a 2dimage io plugin for vista images

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

PLUGINS: 2dimage/shape

1n A shape that only contains the central point

(no parameters)

4n 4n neighborhood 2D shape

(no parameters)

8n 8n neighborhood 2D shape

(no parameters)

rectangle rectangle shape mask creator, supported parameters are:

fill = 1; bool
create a filled shape.

height = 2; int in [1, inf)
height of rectangle.

width = 2; int in [1, inf)
width of rectangle.

sphere Closed spherical neighborhood shape of radius r., supported parameters are:

r = 2; float in (0, inf)
sphere radius.

square square shape mask creator, supported parameters are:

fill = 1; bool
create a filled shape.

width = 2; int in [1, inf)
width of rectangle.

PLUGINS: 2dtransform/io

bbs Binary (non-portable) serialized IO of 2D transformations

Recognized file extensions: .bbs

datapool Virtual IO to and from the internal data pool

Recognized file extensions: .@

vista Vista storage of 2D transformations

Recognized file extensions: .v2dt

xml XML serialized IO of 2D transformations

Recognized file extensions: .x2dt

PLUGINS: generator/noise

gauss This noise generator creates random values that are distributed according to a
Gaussien distribution by using the Box-Muller transformation., supported
parameters are:

mu = 0; float
mean of distribution.

seed = 0; uint in [0, inf)
set random seed (0=init based on system time).

sigma = 1; float in (0, inf)
standard derivation of distribution.

uniform Uniform noise generator using C stdlib rand(), supported parameters are:

a = 0; float
lower bound if noise range.

b = 1; float
higher bound if noise range.

seed = 0; uint in [0, inf)
set random seed (0=init based on system time).

EXAMPLE

Run a kmeans classification of 5 classes on images inputXXXX.png (X being digits) and then
a binarization of the 4th class and store the result in resultXXXX.png

mia-2dimagefilterstack -i input0000.png -o result -t png kmeans:c=5 binarize:min=4,max=4

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'.

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