Global options

-u

This options disables compression of output files. This is useful when fast file writing (and subsequent reading) is required, given that compressing and decompressing data upon file writing and reading induces a computational cost that can be significant with large images. This option is also useful when writing images that are intended to be loaded into other software that are not very efficient in loading compressed TIF files.

-f

This option allows BIP to overwrite existing files. This is useful when calling BIP repeatedly on the same inputs, for example when testing different pipelines or operator values. By default, BIP will not overwrite any existing file and will generate an error when attempting to write over an existing file.

In the example below, the second call generates an error because an output file has already been created in the current directory by the first call:

bip gaussian-filter 1.0 ../input/image.tif
bip gaussian-filter 1.0 ../input/image.tif
*** error: Exception raised:
  What: File already exists
  Where: void ImageWriter::write(...)
  Calls: [0] void ImageWriter::write(...)
  Filename: image-gaussian-filter.tif

With the -f option, the file created upon the first call is silently overwritten:

bip gaussian-filter 1.0 ../input/image.tif
bip -f gaussian-filter 1.0 ../input/image.tif

-b, --no-suffix

This option removes the suffix (name of applied operator) that is automatically added to filenames when writing output files (-b stands for “bare”). Hence, using this option results in having identical filenames for input and for output images. Beware that using this option together with the -f option can be very dangerous, as permanent loss of files may result. To avoid loosing precious data, it is highly recommended to never run BIP within a folder containing input images.

--long-suffix

This option asks BIP to use long suffixes instead of just operator names as suffixes. Long suffixes typically contain values of operator values. This is useful for example to store the results obtained with different parameter settings for a given operator. Without this option, only one output could be stored without further file manipulation.

For example, the second call below generates an error:

bip median-filter ball 1 ../input/image.tif
bip median-filter ball 2 ../input/image.tif
*** error: Exception raised:
    What: File already exists
    Where: void ImageWriter::write(...)
    Calls: [0] void ImageWriter::write(...)
    Filename: image-median-filter.tif

Using --long-suffix, no error is generated:

bip --long-suffix median-filter ball 1 ../input/image.tif
bip --long-suffix median-filter ball 2 ../input/image.tif

Indeed, two distinct files have been created:

image-median-filter-ball-1.tif
image-median-filter-ball-2.tif

--gen-completion-script

(Linux) With this option set, BIP generates a bash completion script and immediately returns. The generated file is to be moved to, or copied into, the .bash_completion file in the user home directory. This provides the tab-completion functionality on BIP operator names.

-B <background>

This option sets the background value for many operators that rely on a distinction between background and foreground. Examples include thresholding operators and operators for binary mathematical morphology.

The default background value is 0.

-F <foreground>

This option sets the foreground value for many operators that rely on a distinction between background and foreground. Examples include thresholding operators and operators for binary mathematical morphology.

The default foreground value is 1.