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Toolkit for using USGS Isis in Python.

Project description

Toolkit for using USGS Isis in Python.

How to install

At the command line:

$ easy_install pysis

Or, if you have virtualenvwrapper installed:

$ mkvirtualenv pysis
$ pip install pysis


For working with ISIS commands, you must firts have USGS ISIS 3 installed on your machine. See the ISIS 3 installation guide for further instructions. Remember to set your environmental variables (see step 4 of USGS ISIS guide) so Pysis knows where your installation is.

Quickstart Guide

How to write ISIS 3 code in python using Pysis.

Using ISIS 3 at the command line you might want to run the following basic commands (examples for the MDIS camera on the MESSENGER mission):

mdis2isis from=filename.IMG to=filename.cub
spiceinit from=filename.cub
mdiscal from=filename.cub

using Pysis the syntax is:

from pysis.isis import mdis2isis, spiceinit, mdiscal
from pysis.util import file_variations

def calibrate_mids(img_name):
    (cub_name, cal_name) = file_variations(img_name, ['.cub', '.cal.cub'])

    mdis2isis(from_=img_name, to=cub_name)
    mdiscal(from_=cub_name, to=cal_name)

You will notice that we use the keyword from_ when we call a command because from is a reserved word in python.

Numerical and String Arguments

Here is an example of the maptemplate and cam2map commands in Pysis:

from pysis import isis

isis.maptemplate(map='', projection='equirectangular',
                 clon=0.0, clat=0.0, resopt='mpp', resolution=1000,
                 rngopt='user', minlat=-10.0, maxlat=10.0, minlon=-10.0,

isis.cam2map(from_=cal_name, to=proj_name, pixres='map',

Getting values from ISIS commands

Pysis commands will return the command’s STDOUT as a byte string. If the command returns a nonzero exit code, a ProcessError will be thrown. This example command uses getkey to receive values from the label of an ISIS cube:

from pysis.isis import getkey

value = getkey(from_='',
               keyword='minimumringradius', grp='mapping')

Catching ProcessingErrors

Pysis supports catching ISIS processing errors like so:

from pysis.exceptions import ProcessError
from pysis.isis import hi2sis

    hi2isis(from_=filein, to=fileout)
except ProcessError as e:
    print("STDOUT:", e.stdout)
    print("STDERR:", e.stderr)

Multiprocessing Isis Commands with IsisPool

Pysis has built-in support to make multiprocessing isis commands simple. To run the above MDIS calibration script for multiple images in multiple processes we could rewrite the function as so:

from pysis import IsisPool
from pysis.util import ImageName

def calibrate_mdis(images):
    images = [ImageName(filename) for filename in images]

    with IsisPool() as isis_pool:
        for filename in images:
            isis_pool.mdis2isis(from_=filename.IMG, to=filename.cub)

    with IsisPool() as isis_pool:
        for filename in images:

    with IsisPool() as isis_pool:
        for filename in images:

When using IsisPool we can’t determine which order commands will be executed in so we much run each command for all the files as a group before moving to the next command and creating a new IsisPool.


0.6.0 (2016-05-22)

  • Support filenames in image constructor. (thanks @michaelaye)
  • Use pvl for label decoding.

0.5.2 (2015-05-30)

  • Relicense as BSD.

0.5.1 (2015-05-18)

  • Add support for line comments.
  • Fix packages in (thanks @michaelaye)

0.5.0 (2015-04-18)

  • Add support for python 2.6/3.3/3.4
  • Simplified command api.
  • Labels package now shares the json module api.
  • Label parser now fully conforms to the PVL spec.
  • Add label encoder.

0.4.0 (2015-03-21)

  • First release on PyPI.

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