cadccutout 0.4.1

Cutout library in Python

Cutout library written in Python that uses Astropy APIs.

Installation

Can be installed using pip install cadccutout in Python 2.7 or 3.X.

API

Cutouts are performed unidirectionally, meaning the library assumes an input stream that can only be read once, rather than seeking. If more than one HDU was requested, then each HDU is iterated over and compared from top to bottom. Single HDU requests are shortcircuited using the Astropy astropy.io.fits.getdata() function

Python 3.x has a potential issue when appending to an output stream where Astropy incorrectly sets a mode to prevent appending (See Astropy GitHub 7856).

Example 1

Perform a cutout of a file using the cfitsio cutout string format.

import tempfile
from cadccutout import OpenCADCCutout

test_subject = OpenCADCCutout()
output_file = tempfile.mkstemp(suffix='.fits')
input_file = '/path/to/file.fits'

# Cutouts are in cfitsio format.
cutout_region_string = '[300:800,810:1000]'  # HDU 0 along two axes.

# Needs to have 'append' flag set.  The cutout() method will write out the data.
with open(output_file, 'ab+') as output_writer, open(input_file, 'rb') as input_reader:
    test_subject.cutout(input_reader, output_writer, cutout_region_string, 'FITS')

Example 2 (CADC)

Perform a cutout from an input stream from an HTTP request.

import tempfile
from cadccutout import OpenCADCCutout
from cadcdata import CadcDataClient

test_subject = OpenCADCCutout()
anonSubject = net.Subject()
data_client = CadcDataClient(anonSubject)
output_file = tempfile.mkstemp(suffix='.fits')
archive = 'HST'
file_name = 'n8i311hiq_raw.fits'
input_stream = data_client.get_file(archive, file_name)

# Cutouts are in cfitsio format.
cutout_region_string = '[SCI,10][80:220,100:150]'  # SCI version 10, along two axes.

# Needs to have 'append' flag set.  The cutout() method will write out the data.
with open(output_file, 'ab+') as output_writer:
    test_subject.cutout(input_stream, output_writer, cutout_region_string, 'FITS')

Command Line Access

The executable cadccutout is installed by default, or the module can be run using python -m cadccutout.

Running

cadccutout -d --infile path/to/source.fits --outfile path/to/output.fits [100:400]

cadccutout -d --infile path/to/source.fits --outfile path/to/output.fits "CIRCLE=10 60 0.5"

Running in Docker

The provided Dockerfile can be used to build an image based on the desired Python version.

Build an image for Python 2.7:

docker build --build-arg PYTHON_VERSION=2.7 -t opencadc/cadccutout:2.7-alpine .

Then execute it (/usr/src/data is the location of the source files). This will send the output to standard out:

docker run --rm -v $(pwd):/usr/src/data opencadc/cadccutout:2.7-alpine cadccutout --infile /usr/src/data/myfile.fits [100:400]

or

docker run --rm --mount type=bind,source=$(pwd),target=/usr/src/data opencadc/cadccutout:2.7-alpine cadccutout --infile /usr/src/data/myfile.fits [100:400]

Build an image for Python 3.6:

docker build --build-arg PYTHON_VERSION=3.6 -t opencadc/cadccutout:3.6-alpine .

Then execute it (/usr/src/data is the location of the source files). This will send the output to a FITS file:

docker run --rm -v $(pwd):/usr/src/data opencadc/cadccutout:3.6-alpine cadccutout --infile /usr/src/data/myfile.fits --outfile /usr/src/data/mycutout_0_100_400.fits [100:400]

or

docker run --rm --mount type=bind,source=$(pwd,target=/usr/src/data opencadc/cadccutout:3.6-alpine cadccutout --infile /usr/src/data/myfile.fits --outfile /usr/src/data/mycutout_0_100_400.fits [100:400]

Testing

Docker

The easiest thing to do is to run it with docker. OpenCADC has an AstroQuery docker image available for runtime available in Python 2.7, 3.5, 3.6, and 3.7.

Run tests in Docker

You can mount the local dev directory to the image and run the python test that way. From inside the dev (working) directory:

Python 3.7:

docker run --rm -v $(pwd):/usr/src/app opencadc/astroquery:3.7-alpine python setup.py test

or

docker run --rm --mount type=bind,source=$(pwd),target=/usr/src/app opencadc/astroquery:3.7-alpine python setup.py test

Python 2.7:

docker run --rm -v $(pwd):/usr/src/app opencadc/astroquery:2.7-alpine python setup.py test

or

docker run --rm --mount type=bind,source=$(pwd),target=/usr/src/app opencadc/astroquery:2.7-alpine python setup.py test