SYNOPSISmia-2dsegmentcropbox -i <in-file> -o <out-file> [options]
DESCRIPTIONmia-2dsegmentcropbox This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined.
- -i --in-file=(input, required); string
- input segmentation set
- -p --override-imagepath
- Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory
- -o --out-file=(output, required); string
- output segmentation set
- -c --cropped-base=crop
- Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering.
- -e --enlarge=5
- Enlarge the area around the obtained sbounding box by this number of pixels in each directionEnlarge the area around the obtained sbounding box by this number of pixels in each direction
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
- print copyright information
- -h --help
- print this help
- -? --usage
- print a short help
- print the version number and exit
- 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).
EXAMPLEEvaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3 pixels. Store the resulting set in the file cropped.set.
- mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3
COPYRIGHTThis 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'.