NAME
mia-2dseriesgradvariation - Evaluate the time-intensity gradient variation in a series of images.
SYNOPSIS
mia-2dseriesgradvariation -i <in-file> -o <out-file> [options]
DESCRIPTION
mia-2dseriesgradvariation Given a set of images of temporal sucession, this program evaluates the gradient variation of the pixel-wise time-intensity curves of this series. If the input image set provides a segmentation, then this segmentation can be used to create a bounding box and restrict evaluation to this box.
OPTIONS
- -i --in-file=(input, required); string
-
input segmentation set
- -o --out-file=(required, output); io
-
output file 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
Help & Info
- -V --verbose=warning
-
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
trace ‐ Function call trace
debug ‐ Debug output
info ‐ Low level messages
message ‐ Normal messages
warning ‐ Warnings
fail ‐ Report test failures
error ‐ Report errors
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).
PLUGINS: 2dimage/io
- bmp
-
BMP 2D-image input/output support. The plug-in supports reading and writing of binary images and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. The color table is ignored and the pixel values are taken as literal gray scale values.
Recognized file extensions: .BMP, .bmp
Supported element types:
binary data, unsigned 8 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
EXAMPLE
Evaluate the gradient-variation image of the bounding box surrounding the segmentation from a series 'segment.set'. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.
mia-2dseriesgradvariation -i segment.set -o gradvar.exr -c -e 3
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'.