Calling ISIS programs from Python
The kalasiris library is a Python library to wrap functions and functionality for the Integrated Software for Imagers and Spectrometers (ISIS).
- Free software: BSD-3-Clause License
- Documentation: https://kalasiris.readthedocs.io.
- Primarily a very lightweight wrapper around Python's subprocess module to allow easy calling of ISIS programs in the shell from within Python.
- Calling compatibility with pysis (and emulation of return types)
- Works with ISIS 3.6.0 and higher.
- Works with Python 3.6.0 and higher.
This library really only works if you already have ISIS installed and working properly. Quirks of working with where and how ISIS is loaded in your environment and how to use kalasiris with it, can be found in the documentation.
Beyer, R. A. 2020. Kalasiris, a Python Library for Calling ISIS Programs. 51st Lunar and Planetary Science Conference, not held due to COVID-19, Abstract #2441. ADS URL
Are you new to Python? Do you just want to write something 'real quick' in Python and need to call some ISIS programs now?
We've got you covered.
Need to run an ISIS program like cam2map:
from kalasiris import cam2map fromcube = 'something.cub' tocube = 'something_mapped.cub' cam2map(fromcube, to=tocube)
Easy! Assuming you have a something.cub file that can be
map-projected. The first positional argument will be assumed to be
the "from" parameter, but you could also explicitly use from=fromcube
here.
In addition to just calling all ISIS programs this way, you can do other fun things like this:
import kalasiris as isis img = 'PSP_010502_2090_RED5_0.IMG' hicube = 'PSP_010502_2090_RED5_0.cub' histfile = 'PSP_010502_2090_RED5_0.hist' isis.hi2isis(img, to=hicube) InsID = isis.getkey_k(hicube, 'Instrument', 'InstrumentId') print(InsID) # prints HIRISE isis.hist(hicube, to=histfile) h = isis.Histogram(histfile) print(h) # prints the hist file header info print(h['Std Deviation']) # prints 166.739 print(h[1]) # prints the second row of the histogram: # HistRow(DN=3924.0, Pixels=1.0, CumulativePixels=2.0, Percent=4.88281e-05, CumulativePercent=9.76563e-05) print(h[1][3]) print(h[1].Percent) # both of the above print 4.88281e-05
You can see that there are things like the Histogram class,
the getkey_k() function which is part of the _k function collection, and much more.
Read the documentation for more: https://kalasiris.readthedocs.io
You can install kalasiris via pip or conda-forge:
To install kalasiris via pip, run this command in your terminal:
$ pip install kalasirisInstalling kalasiris from the conda-forge channel can be
achieved by adding conda-forge to your channels with:
conda config --add channels conda-forgeOnce the conda-forge channel has been enabled, kalasiris can be installed with:
conda install kalasirisIt is possible to list all of the versions of kalasiris available on your platform with:
conda search kalasiris --channel conda-forgeIf for some reason you don't want to use conda or pip, you could do one of these two things (but really, just use conda or pip):
The core functionality is contained in a single file. Just go into the
kalasiris directory, and copy the kalasiris.py
file into the same directory where your own program is. It doesn't
depend on anything that isn't already part of Python, so you can
just use it.
Just grabbing this one file gets you the ability to call ISIS
programs from your Python programs. There are other parts of this
package that provide helper functions (like cubenormfile.writer),
classes (like Histogram), and syntactic sugar (the _k functions).
You don't get them by just grabbing kalasiris.py as described
above.
However, installation via pip or conda is so easy, and you're installing ISIS via conda already.
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