SYNOPSIS

mia-2dseries2dordermedian -i <in-file> -o <out-file> [options] <PLUGINS:2dimage/filter>

DESCRIPTION

mia-2dseries2dordermedian This program evaluates the pixel-wise median of the absolute values of the gauss filtered 2nd order temporal derivative of a series of images. In addition, it can be used to output the time-intensity curve of a given pixel.The program supports slice-wise spacial pre-filtering by giving additional filters as free parameters (filter/2dimage).

OPTIONS

-i --in-file=(input,required)

input segmentation set

-o --out-file=(output,required)

output image name For supported file types see PLUGINS:2dimage/io

-k --skip=0

Skip files at the beginning

-e --enlarge-boundary=5

Enlarge cropbox by number of pixels

-c --crop

crop image before running statistics

-g --gauss=1

gauss filter width for moothing the gradient

--itc-file=

intensity time curve output file

--itc-loc=[0,0]

intensity time curve output pixel coordinates

Help & Info

-V --verbose=warning

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

info \(hy Low level messages

trace \(hy Function call trace

fail \(hy Report test failures

warning \(hy Warnings

error \(hy Report errors

debug \(hy Debug output

message \(hy Normal messages

fatal \(hy 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).

PLUGINS: 1d/spacialkernel

gauss

spacial Gauss filter kernel, supported parameters are:

w = 1 (int)

half filter width. in [0, 2147483647]

PLUGINS: 1d/splinekernel

bspline

B-spline kernel creation , supported parameters are:

d = 3 (int)

Spline degree. in [0, 5]

omoms

OMoms-spline kernel creation, supported parameters are:

d = 3 (int)

Spline degree. in [3, 3]

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)

half filter width. in [0, 2147483647]

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)

half filter width. in [0, 2147483647]

aniso

2D Anisotropic image filter, supported parameters are:

epsilon = 1 (float)

iteration change threshold. in [0.001, 100]

iter = 100 (int)

number of iterations. in [1, 10000]

k = -1 (float)

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

n = 8 (set)

neighbourhood. Supported values are:( 4, 8, )

psi = tuckey (dict)

edge stopping function. Supported values are:

guess \(hy test stopping function

tuckey \(hy tukey stopping function

pm1 \(hy stopping function 1

pm2 \(hy stopping function 2

bandpass

intensity bandpass filter, supported parameters are:

max = 3.40282e+38 (float)

maximum of the band. in [-3.40282e+38, 3.40282e+38]

min = 0 (float)

minimum of the band. in [-3.40282e+38, 3.40282e+38]

binarize

image binarize filter, supported parameters are:

max = 3.40282e+38 (float)

maximum of accepted range. in [0, 3.40282e+38]

min = 0 (float)

minimum of accepted range. in [0, 3.40282e+38]

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, io)

second image that is needed in the combiner. For supported file types see PLUGINS:2dimage/io

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. in [-3.40282e+38, 3.40282e+38]

b = 0 (float)

linear conversion parameter b. in [-3.40282e+38, 3.40282e+38]

map = opt (dict)

conversion mapping. Supported values are:

opt \(hy apply a linear transformation that maps the real input range to the full output range

range \(hy apply linear transformation that maps the input data type range to the output data type range

copy \(hy copy data when converting

linear \(hy apply linear transformation x -> a*x+b

optstat \(hy 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:

float \(hy floating point 32 bit

sbyte \(hy signed 8 bit

double \(hy floating point 64 bit

sint \(hy signed 32 bit

ushort \(hy unsigned 16 bit

sshort \(hy signed 16 bit

uint \(hy unsigned 32 bit

bit \(hy binary data

ubyte \(hy 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)

blocksize in x direction. in [1, 2147483647]

by = 1 (uint)

blocksize in y direction. in [1, 2147483647]

kernel = gauss (factory)

smoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize.. For supported plug-ins see PLUGINS:1d/spacialkernel

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)

filter width parameter. in [0, 2147483647]

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)

number of classes. in [2, 255]

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

2D image filter to remap label id's., supported parameters are:

map =(input,required, string)

Label mapping file.

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, io)

name of the input file to load from.. For supported file types see PLUGINS:2dimage/io

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 \(hy set values outside the mask to the maximum value found in the image..

zero \(hy set the values outside the mask to zero.

min \(hy set values outside the mask to the minimum value found in the image.

input =(input,required, io)

second input image file name. For supported file types see PLUGINS:2dimage/io

inverse = 0 (bool)

set to true to use the inverse of the mask for masking.

mean

2D image mean filter, supported parameters are:

w = 1 (int)

half filter width. in [0, 2147483647]

median

2D image median filter, supported parameters are:

w = 1 (int)

half filter width. in [0, 2147483647]

mlv

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

w = 1 (int)

filter width parameter. in [0, 2147483647]

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)

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

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, io)

seed image (bit valued). For supported file types see PLUGINS:2dimage/io

sandp

salt and pepper 3d filter, supported parameters are:

thresh = 100 (float)

thresh value. in [0, 3.40282e+38]

w = 1 (int)

filter width parameter. in [0, 2147483647]

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)

target size in x direction, 0: use input size. in [0, 4294967295]

sy = 0 (uint)

target size in y direction, 0: use input size. in [0, 4294967295]

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

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, io)

name of the output file to save the image too.. For supported file types see PLUGINS:2dimage/io

thinning

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

iter = 0 (int)

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

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:

shape = 4n (factory)

neighborhood shape to take into account. For supported plug-ins see PLUGINS:2dimage/shape

thresh = 5 (double)

The threshhold value. in [-1.79769e+308, 1.79769e+308]

transform

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

file =(input,required, io)

Name of the file containing the transformation.. For supported file types see PLUGINS:2dtransform/io

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)

Relative 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. in [0, 1]

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)

height of rectangle. in [0, 2147483647]

width = 2 (int)

width of rectangle. in [0, 2147483647]

sphere

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

r = 2 (float)

sphere radius. in [0, 3.40282e+38]

square

square shape mask creator, supported parameters are:

fill = 1 (bool)

create a filled shape.

width = 2 (int)

width of rectangle. in [0, 2147483647]

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. in [-3.40282e+38, 3.40282e+38]

seed = 0 (uint)

set random seed (0=init based on system time). in [0, 4294967295]

sigma = 1 (float)

standard derivation of distribution. in [0, 3.40282e+38]

uniform

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

a = 0 (float)

lower bound if noise range. in [-3.40282e+38, 3.40282e+38]

b = 1 (float)

higher bound if noise range. in [-3.40282e+38, 3.40282e+38]

seed = 0 (uint)

set random seed (0=init based on system time). in [0, 4294967295]

EXAMPLE

Evaluate the median of the 2nd order derivative of the series given in segmentation set segment.set after filtering with a Gaussian of width 3. In addition write the time intensity curve of pixel <128,64> to curve.txt. mia-2dseries2dordermedian -i segment.set -o gradmedian.exr -g 1 --itc-file curve.txt --itc-loc "<128,64>"

AUTHOR(s)

Gert Wollny

COPYRIGHT

This software is Copyright (c) 1999\(hy2013 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'.