pysis package

Subpackages

• pysis.binning package
  • Submodules
  • pysis.binning.abstract module
  • pysis.binning.bounded module
  • pysis.binning.const_width module
  • pysis.binning.geometric module
  • Module contents
• pysis.labels package
  • Submodules
  • pysis.labels.decoder module
  • pysis.labels.encoder module
  • pysis.labels.stream module
  • Module contents
• pysis.util package
  • Submodules
  • pysis.util.file_manipulation module
  • Module contents

Submodules

pysis.cubefile module

class pysis.cubefile.CubeFile(stream_or_fname, filename=None)

Bases: object

A Isis Cube file reader.

BYTE_ORDERS = {'Lsb': '<', 'Msb': '>', 'NoByteOrder': '='}

PIXEL_TYPES = {'Real': dtype('float32'), 'SignedWord': dtype('int16'), 'UnsignedByte': dtype('uint8'), 'Double': dtype('float64'), 'UnsignedInteger': dtype('uint32'), 'SignedInteger': dtype('int32'), 'SignedByte': dtype('int8'), 'UnsignedWord': dtype('uint16')}

SPECIAL_PIXELS = {'Real': {'His': -3.4028233e+38, 'Min': -3.4028225e+38, 'Max': 3.4028235e+38, 'Hrs': -3.4028235e+38, 'Lrs': -3.4028229e+38, 'Lis': -3.4028231e+38, 'Null': -3.4028227e+38}, 'UnsignedByte': {'His': 255, 'Min': 1, 'Max': 254, 'Hrs': 255, 'Lrs': 0, 'Lis': 0, 'Null': 0}, 'Double': {'His': -1.7976931348623155e+308, 'Min': -1.7976931348623147e+308, 'Max': 1.7976931348623157e+308, 'Hrs': -1.7976931348623157e+308, 'Lrs': -1.7976931348623151e+308, 'Lis': -1.7976931348623153e+308, 'Null': -1.7976931348623149e+308}, 'SignedWord': {'His': -32765, 'Min': -32752, 'Max': 32767, 'Hrs': -32764, 'Lrs': -32767, 'Lis': -32766, 'Null': -32768}, 'SignedInteger': {'His': -8388610, 'Min': -8388614, 'Max': 2147483647, 'Hrs': -8388609, 'Lrs': -8388612, 'Lis': -8388611, 'Null': -8388613}, 'UnsignedWord': {'His': 65534, 'Min': 3, 'Max': 65522, 'Hrs': 65535, 'Lrs': 1, 'Lis': 2, 'Null': 0}}

apply_numpy_specials(copy=True)

Convert isis special pixel values to numpy special pixel values.

Isis	Numpy
Null	nan
Lrs	-inf
Lis	-inf
His	inf
Hrs	inf

Parameters:copy – whether to apply the new special values to a copy of the pixel data and leave the orginial unaffected Returns:a numpy array with special values converted to numpy’s nan, inf and -inf

apply_scaling(copy=True)

Scale pixel values to there true DN.

Parameters:copy – whether to apply the scalling to a copy of the pixel data and leave the orginial unaffected Returns:a scalled version of the pixel data

bands

Number of image bands.

base

An additive factor by which to offset pixel DN.

data = None

A numpy array representing the image data.

dtype

Pixel data type.

filename = None

The filename if given, otherwise none.

format

get_image_array()

Create an array for use in making an image.

Creates a linear stretch of the image and scales it to between 0 and 255. Null, Lis and Lrs pixels are set to 0. His and Hrs pixels are set to 255.

Usage:

from pysis import CubeFile
from PIL import Image

# Read in the image and create the image data
image = CubeFile.open('test.cub')
data = image.get_image_array()

# Save the first band to a new file
Image.fromarray(data[0]).save('test.png')

Returns:A uint8 array of pixel values.

label = None

The parsed label header in dictionary form.

lines

Number of lines per band.

multiplier

A multiplicative factor by which to scale pixel DN.

classmethod open(filename)

Read an Isis Cube file from disk.

Parameters:filename – name of file to read as an isis file

samples

Number of samples per line.

shape

Tuple of images bands, lines and samples.

size

Total number of pixels.

specials

specials_mask()

Create a pixel map for special pixels.

Returns:an array where the value is False if the pixel is special and True otherwise

start_byte

Index of the start of the image data (zero indexed).

tile_lines

Number of lines per tile.

tile_samples

Number of samples per tile.

pysis.env module

pysis.env.require_isis_version(major, minor=0, patch=0, build=0)

Decorator that ensures a function is called with a minimum isis version.

pysis.exceptions module

This module contains the set of Pysis exceptions.

exception pysis.exceptions.IsisException

Bases: exceptions.Exception

Base exception for isis errors.

exception pysis.exceptions.ProcessError(returncode, cmd, stdout, stderr)

Bases: pysis.exceptions.IsisException

This exception is raised when an isis process returns a non-zero exit status.

exception pysis.exceptions.VersionError

Bases: pysis.exceptions.IsisException

The wrong version of isis is being used.

pysis.isis module

pysis.isiscommand module

class pysis.isiscommand.Isis(strict=False, path=None)

Bases: object

class pysis.isiscommand.IsisCommand(name)

Bases: object

call(**kwargs)

cmd(**kwargs)

to_string(**kwargs)

pysis.isispool module

class pysis.isispool.IsisPool(strict=False, *args, **kwargs)

Bases: pysis.isiscommand.Isis

Multiprocessing pool for ISIS commands.

Example for running the following isis script in parallel for a list of images.

On the command line:

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

With pysis:

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)

Parameters:

• strict – when in strict mode, the isis pool will initialize its attributes with commands from the isis environment. Otherwise attributes are dynamically added as use
• **kwargs –

  additional parameters used to initialize the multiprocessing pool

close(*args, **kwarg)

close_and_wait()

Close the pool and wait for all commands to complete.

This will be automatically called if used as a context manager.

join(*args, **kwarg)

class pysis.isispool.QueuedIsisCommand(name, pool)

Bases: pysis.isiscommand.IsisCommand

pysis.specialpixels module

Constants for Isis Special Pixels.

Min: The minimum valid value for a pixel. Null: Pixel has no data available. Lis: Pixel was lower bound saturated on the instrument. His: Pixel was higher bound saturated on the instrument. Lrs: Pixel was lower bound saturated during a computation. Hrs: Pixel was higher bound saturated during a computation. Max: The maximum valid value for a pixel.

Module contents

class pysis.Isis(strict=False, path=None)

Bases: object

class pysis.IsisPool(strict=False, *args, **kwargs)

Bases: pysis.isiscommand.Isis

Multiprocessing pool for ISIS commands.

Example for running the following isis script in parallel for a list of images.

On the command line:

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

With pysis:

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)

Parameters:

• strict – when in strict mode, the isis pool will initialize its attributes with commands from the isis environment. Otherwise attributes are dynamically added as use
• **kwargs –

  additional parameters used to initialize the multiprocessing pool

close(*args, **kwarg)

close_and_wait()

Close the pool and wait for all commands to complete.

This will be automatically called if used as a context manager.

join(*args, **kwarg)

class pysis.CubeFile(stream_or_fname, filename=None)

Bases: object

A Isis Cube file reader.

BYTE_ORDERS = {'Lsb': '<', 'Msb': '>', 'NoByteOrder': '='}

PIXEL_TYPES = {'Real': dtype('float32'), 'SignedWord': dtype('int16'), 'UnsignedByte': dtype('uint8'), 'Double': dtype('float64'), 'UnsignedInteger': dtype('uint32'), 'SignedInteger': dtype('int32'), 'SignedByte': dtype('int8'), 'UnsignedWord': dtype('uint16')}

SPECIAL_PIXELS = {'Real': {'His': -3.4028233e+38, 'Min': -3.4028225e+38, 'Max': 3.4028235e+38, 'Hrs': -3.4028235e+38, 'Lrs': -3.4028229e+38, 'Lis': -3.4028231e+38, 'Null': -3.4028227e+38}, 'UnsignedByte': {'His': 255, 'Min': 1, 'Max': 254, 'Hrs': 255, 'Lrs': 0, 'Lis': 0, 'Null': 0}, 'Double': {'His': -1.7976931348623155e+308, 'Min': -1.7976931348623147e+308, 'Max': 1.7976931348623157e+308, 'Hrs': -1.7976931348623157e+308, 'Lrs': -1.7976931348623151e+308, 'Lis': -1.7976931348623153e+308, 'Null': -1.7976931348623149e+308}, 'SignedWord': {'His': -32765, 'Min': -32752, 'Max': 32767, 'Hrs': -32764, 'Lrs': -32767, 'Lis': -32766, 'Null': -32768}, 'SignedInteger': {'His': -8388610, 'Min': -8388614, 'Max': 2147483647, 'Hrs': -8388609, 'Lrs': -8388612, 'Lis': -8388611, 'Null': -8388613}, 'UnsignedWord': {'His': 65534, 'Min': 3, 'Max': 65522, 'Hrs': 65535, 'Lrs': 1, 'Lis': 2, 'Null': 0}}

apply_numpy_specials(copy=True)

Convert isis special pixel values to numpy special pixel values.

Isis	Numpy
Null	nan
Lrs	-inf
Lis	-inf
His	inf
Hrs	inf

Parameters:copy – whether to apply the new special values to a copy of the pixel data and leave the orginial unaffected Returns:a numpy array with special values converted to numpy’s nan, inf and -inf

apply_scaling(copy=True)

Scale pixel values to there true DN.

Parameters:copy – whether to apply the scalling to a copy of the pixel data and leave the orginial unaffected Returns:a scalled version of the pixel data

bands

Number of image bands.

base

An additive factor by which to offset pixel DN.

dtype

Pixel data type.

format

get_image_array()

Create an array for use in making an image.

Creates a linear stretch of the image and scales it to between 0 and 255. Null, Lis and Lrs pixels are set to 0. His and Hrs pixels are set to 255.

Usage:

from pysis import CubeFile
from PIL import Image

# Read in the image and create the image data
image = CubeFile.open('test.cub')
data = image.get_image_array()

# Save the first band to a new file
Image.fromarray(data[0]).save('test.png')

Returns:A uint8 array of pixel values.

lines

Number of lines per band.

multiplier

A multiplicative factor by which to scale pixel DN.

classmethod open(filename)

Read an Isis Cube file from disk.

Parameters:filename – name of file to read as an isis file

samples

Number of samples per line.

shape

Tuple of images bands, lines and samples.

size

Total number of pixels.

specials

specials_mask()

Create a pixel map for special pixels.

Returns:an array where the value is False if the pixel is special and True otherwise

start_byte

Index of the start of the image data (zero indexed).

tile_lines

Number of lines per tile.

tile_samples

Number of samples per tile.

pysis.check_isis_version(major, minor=0, patch=0, build=0)

Checks that the current isis version is equal to or above the suplied version.

pysis.require_isis_version(major, minor=0, patch=0, build=0)

Decorator that ensures a function is called with a minimum isis version.