Welcome to Pysis’s documentation!¶
Pysis¶
Toolkit for using USGS Isis in Python.
- Free software: BSD license
- Documentation: http://pysis.readthedocs.org.
How to install¶
At the command line:
$ easy_install pysis
Or, if you have virtualenvwrapper installed:
$ mkvirtualenv pysis
$ pip install pysis
Dependencies¶
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 to=filename.cal.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)
spiceinit(from_=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='MDIS_eqr.map', projection='equirectangular',
clon=0.0, clat=0.0, resopt='mpp', resolution=1000,
rngopt='user', minlat=-10.0, maxlat=10.0, minlon=-10.0,
maxlon=10.0)
isis.cam2map(from_=cal_name, to=proj_name, pixres='map',
map='MDIS_eqr.map',defaultrange='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_='W1467351325_4.map.cal.cub',
keyword='minimumringradius', grp='mapping')
Catching ProcessingErrors¶
Pysis supports catching ISIS processing errors like so:
from pysis.exceptions import ProcessError
from pysis.isis import hi2sis
try:
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:
isis_pool.spiceinit(from_=filename.cub)
with IsisPool() as isis_pool:
for filename in images:
isis_pool.mdiscal(from_=filename.cub, to=filename.cal.cub)
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.