Command Line Usage

Image analysis usually relies on different softwares in different platform. The traditional command line based interface is still useful in this purpose.

impy also supports command line usage.

Basic Usage

The most basic one is:

impy --input path/to/image.tif --output path/to/output.tif --method gaussian_filter --sigma 2

or --input and --output can be omitted like:

impy path/to/image.tif path/to/output.tif --method gaussian_filter --sigma 2

You have to specify --method or -m to let impy know what method you’d like to run. Method names should match those in ImgArray. The last --sigma option is characteristic to gaussian_filter so that it may differ with other method. Those commands above are equivalent to following Python code.

import impy as ip
img = ip.imread("path/to/image.tif")
out = img.gaussian_filter(sigma=2)
out.imsave("path/to/output.tif")

Advanced Usage

Sometimes you may want to apply multiple filters in tandem to an image. Classically it was usually done by saving intermediate files, but here we should take advantage of IPython.

Instead of parsing --output, you can use -i flag to launch IPython interpreter with namespace ip and img. ip is an alias of impy as usual, and img is an ImgArray object that is created by reading the --input argument.

impy path/to/image.tif -i

>>> arr = ip.random.random((100, 120))  # "ip" is already available
>>> out = img + arr  # img = ip.imread("path/to/image.tif")
>>> out.imsave("path/to/output.tif")

Another option is -n, which send namespace including input image to napari viewer and console.

impy path/to/image.tif -n