Calling ISIS programs from Python
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The kalasiris library is a Python library to wrap functions and
functionality for the Integrated Software for Imagers and Spectrometers (ISIS) <https://isis.astrogeology.usgs.gov>
_.
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 <https://ui.adsabs.harvard.edu/abs/2020LPI....51.2441B>
_
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:
.. code-block:: console
$ pip install kalasiris
Installing kalasiris
from the conda-forge
channel can be
achieved by adding conda-forge
to your channels with:
.. code-block:: console
conda config --add channels conda-forge
Once the conda-forge
channel has been enabled, kalasiris
can be installed with:
.. code-block:: console
conda install kalasiris
It is possible to list all of the versions of kalasiris
available on your platform with:
.. code-block:: console
conda search kalasiris --channel conda-forge
If 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.
This repository layout was created with Cookiecutter and the audreyr/cookiecutter-pypackage
project template.
.. _ISIS: https://isis.astrogeology.usgs.gov
.. _pysis: https://github.com/wtolson/pysis
.. Cookiecutter: https://github.com/audreyr/cookiecutter
.. audreyr/cookiecutter-pypackage
: https://github.com/audreyr/cookiecutter-pypackage