Package: kalasiris
kalasirisCalling ISIS programs from PythonThekalasirislibrary is a Python library to wrap functions and
functionality for theIntegrated Software for Imagers and Spectrometers
(ISIS).Free software: BSD-3-Clause LicenseDocumentation:https://kalasiris.readthedocs.io.FeaturesPrimarily a very lightweight wrapper around Python’s subprocess
module to allow easy calling of ISIS programs in the shell from
within Python.Calling compatibility withpysis(and emulation of return types)Works with ISIS 3.6.0 and higher.Works with Python 3.6.0 and higher.ISISThis library really only works if you already haveISISinstalled 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.Citing in your workBeyer, 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 URLQuickstartAre you new to Python? Do you just want to write something ‘real quick’
in Python and need to call some ISIS programsnow?We’ve got you covered.Need to run an ISIS program likecam2map:from kalasiris import cam2map

fromcube = 'something.cub'
tocube = 'something_mapped.cub'
cam2map(fromcube, to=tocube)Easy! Assuming you have asomething.cubfile that can be
map-projected.  The first positional argument will be assumed to be
the “from” parameter, but you could also explicitly usefrom=fromcubehere.In addition to just callingallISIS 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-05You can see that there are things like the Histogram class,
thegetkey_k()function which is part of the_k functioncollection, and much more.Read the documentation for more:https://kalasiris.readthedocs.ioInstallationYou can installkalasirisviapiporconda-forge:To installkalasirisviapip, run this command in your terminal:$pipinstallkalasirisInstallingkalasirisfrom theconda-forgechannel can be
achieved by addingconda-forgeto your channels with:conda config --add channels conda-forgeOnce theconda-forgechannel has been enabled,kalasiriscan be installed with:conda install kalasirisIt is possible to list all of the versions ofkalasirisavailable 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 thekalasirisdirectory, and copy thekalasiris.pyfile 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 (likecubenormfile.writer),
classes (likeHistogram), and syntactic sugar (the_k functions).
You don’t get them by just grabbingkalasiris.pyas described
above.However, installation via pip or conda is so easy, and you’re installing
ISIS via conda already.This repository layout was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.HistoryAll notable changes to this project will be documented in this file.The format is based onKeep a Changelog,
and this project adheres toSemantic Versioning.When updating this file, please add an entry for your change underUnreleasedand one of the following headings:Added - for new features.Changed - for changes in existing functionality.Deprecated - for soon-to-be removed features.Removed - for now removed features.Fixed - for any bug fixes.Security - in case of vulnerabilities.If the heading does not yet exist underUnreleased, then add it
as a 3rd level heading, underlined with pluses (see examples below).When preparing for a public release add a new 2nd level heading,
underlined with dashes underUnreleasedwith the version number
and the release date, in year-month-day format (see examples below).Unreleased1.10.0 (2023-12-27)AddedNew kalasiris.set_persistent_preferences() functionality so that a library user can set
a persistent preferences path rather than having to enter it with each kalasiris
function run.  Addresses Issue #11.Can now also pass parameters that do not take an argument to ISIS in a manner similar
to how you’d write them on the command line (e.g.getkey(“-help”)) in addition to
the “old” way (e.g.getkey(“help__”)).1.9.1 (2021-07-04)ChangedTesting now defaults to only running on mocks.Consolidated boolean that controls testing on “real files” to single place.Enabled GitHub Workflows for testing.FixedBug in reserved parameter handling, such that only some reserved parameters
that were given with two trailing underbars (_) would be converted to their
appropriate “-key=value” form for ISIS.  This was true for “restore” for example,
which was embarrassingly given in the documentation, but not tested!PathSet module documentation was missing the first letters of several words.1.9.0 (2020-10-13)AddedNow supports the new ISISDATA environment variable, in addition to ISIS3DATA.1.8.0 (2020-06-01)Added the ability to pass arguments tosubprocess.run()for each ISIS program.The ISIS functions now automatically log with a level of INFO.Adopted Conventional Commits pattern (https://www.conventionalcommits.org/en/v1.0.0) for commit messages.Adopted Black formatting.Minor spelling and formatting improvements.1.7.1 (2020-05-05)Corrected a readthedocs failure.1.7.0 (2020-05-05)Added some functions to read table data from cube files.Added special pixel values via specialpixels.py (implemented
as namedtuples instead of as dictionaries, as in pysis).Enabled Python 3.7 and 3.8 tests for tox.1.6.0 (2020-04-12)Provided pysis return type and exception emulation.Switched from Apache 2 to the BSD-3-Clause license.1.5.0 (2019-11-16)Did some documentation formatting.Streamlined the fromlist module.Put in a protection from accidentally adding a Path to a PathSet twice.1.4.0 (2019-10-08)Added the fromlist module.1.3.0 (2019-10-06)Added the cubeit_k() k_function.Added TravisCI tests for ISIS 3.8.1 and 3.9.0Separated tests into those that can run in-memory with mocking, and those that
need the filesystem, and ISIS, etc.1.2.0 (2019-10-04)Added a documentation section to help guide a user to choose between pysis and kalasiris.Improved the documentation for the version module a little.Added the stats_k() k_function.1.1.0 (2019-06-19)Added the version module in order to query and retrieve ISIS version
information from the ISIS system.Added TravisCI tests for ISIS 3.7.11.0.0 (2019-04-24)Removed cubenormDialect, and moved it to cubenormfile.DialectImplemented cubenormfile.writer and cubenormfile.DictWriter, to
write the fixed-width file format that ISIS cubenorm will actually read.0.2.0 (2019-03-23)Implemented a new feature: the PathSet Class.Enabled installation viaconda-forgeUpdated some documentation.Fixed it so that the module documentation appears in readthedocs0.1.2 (2019-03-04)Discovered a bug that made us platform-dependent.  Fixed.Made a variety of documentation improvements.Enabled and tested install viapip installEnabled testing via toxEnabled testing via Travis CI0.1.1 (2019-02-22)Jesse discovered that the code was incorrectly testing for
executability of the$ISISROOT/bin/xml/*xmlfiles instead of
the$ISISROOT/bin/*program files, and issued a PR that
fixed it.0.1.0 (2019-02-20)Initial creation finished. Time to share.0.0.0 (2019-02-12)Started project.Version NumberingThe kalasiris library follows theSemantic Versioning 2.0.0
specification, such that released kalasiris
version numbers follow this pattern:{major}.{minor}.{patch}.