mia-3dimagestatistics-in-mask

Sysnopis:

mia-3dimagestatistics-in-mask {-i io} {-m io} [ options ...]

Description:

This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values.

Options:

File-IO

-i, --image=(input, required); io

input image to be analyzed. For supported file types see Plugin type: 3dimage/io

-m, --mask=(input, required); io

mask image to use to restrict the analysis. For supported file types see Plugin type: 3dimage/io

-s, --summary=(output); string

File to write the summary statistics to as plain text.

-H, --histogram=(output); string

File to write the histogram to

Help & Info

-V, --verbose=warning; dict

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=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

--struct-name=undefined; stringSTRING

Name of the structure the statistics are evaluated for

-l, --limit=20; uint in [20, inf)

Number of pixels the mask should at least contain.

-b, --bins=8; ulong in [4, inf)

number of histogram bins to be used

--hmin=0; float

lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.

--hmax=0; float

hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.

Processing

--threads=-1; int

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).

Example:

evaluate the summary statistics on the input and a histogram with 10 bins and automtically evaluated boundaries. Save summary in summary.txt and the histogram in hist.txt

mia-3dimagestatistics-in-mask --image image.v.gz --mask mask.v.gz --summary summary.txt --histogram hist.txt

Author(s):

Gert Wollny