#! /usr/bin/env python
"""Tests for the ``preview_image`` module.
Authors
-------
- Johannes Sahlmann
- Lauren Chambers
Use
---
These tests can be run via the command line (omit the ``-s`` to
suppress verbose output to ``stdout``):
::
pytest -s test_preview_image.py
"""
import glob
import numpy as np
import os
import pytest
import shutil
from astropy.io import fits
from jwst.datamodels import dqflags
from jwql.utils.preview_image import PreviewImage, crop_to_subarray
from jwql.utils.constants import ON_GITHUB_ACTIONS, ON_READTHEDOCS
from jwql.utils.utils import get_config, ensure_dir_exists
[docs]
def test_crop_to_subarray():
"""Test that the code correctly crops larger arrays down to
the requested subarray
"""
# Set up a small DQ array that shows the location of reference pixels on 2 sides
dq = np.ones((10, 10), dtype=int)
dq[0:3, :] = 0
dq[:, 0:3] = 0
# Set up a fits header
h = fits.ImageHDU([0])
h.header['FILENAME'] = 'myfile_uncal.fits'
# Specify that we are cropping the DQ array down to a 5x5 subarray
xdim = 5
ydim = 5
# First test the case where the header has no info on subarray location
c = crop_to_subarray(dq, h.header, xdim, ydim)
expected = np.ones((ydim, xdim), dtype=int)
assert np.all(c == expected)
# Next test the case where the header does include subarray location info
h.header['SUBSTRT1'] = 2
h.header['SUBSTRT2'] = 4
h.header['SUBSIZE1'] = 5
h.header['SUBSIZE2'] = 5
c = crop_to_subarray(dq, h.header, xdim, ydim)
expected = np.ones((5, 5), dtype=int)
expected[:, 0:2] = 0
assert np.all(c == expected)
# Tweak the y location and try again
h.header['SUBSTRT2'] = 1
c = crop_to_subarray(dq, h.header, xdim, ydim)
expected = np.zeros((5, 5), dtype=int)
expected[3:, 2:] = 1
assert np.all(c == expected)
[docs]
def get_test_fits_files():
"""Get a list of the FITS files on central storage to make preview images.
Returns
-------
filenames : list
List of filepaths to FITS files
"""
# Get the files from central store
if not ON_GITHUB_ACTIONS and not ON_READTHEDOCS:
filenames = glob.glob(os.path.join(get_config()['test_dir'], '*.fits'))
assert len(filenames) > 0
return filenames
# Or return an empty list
else:
return []
[docs]
def test_get_nonsci_map():
"""Test the retrieval of the dq data from an HDUList
"""
# Create HDUList. Start with the case where there is no DQ extension
h0 = fits.PrimaryHDU([0])
h1 = fits.ImageHDU(np.zeros((10, 10), dtype=int))
hdulist = fits.HDUList([h0, h1])
extensions = ['PRIMARY', 'ERR']
xd = 10
yd = 10
dq = PreviewImage.get_nonsci_map(0, hdulist, extensions, xd, yd)
expected = np.ones((10, 10), dtype=bool)
assert np.all(dq == expected)
# Now test the case where there is a DQ extension. And insert some
# NON_SCIENCE and REFERENCE_PIXEL flags
h1.header['EXTNAME'] = 'DQ'
extensions[1] = 'DQ'
hdulist['DQ'].data[1, 1] = dqflags.pixel['REFERENCE_PIXEL']
hdulist['DQ'].data[3, 3] = dqflags.pixel['NON_SCIENCE']
hdulist['DQ'].data[5, 5] = dqflags.pixel['HOT']
hdulist['DQ'].data[7, 7] = dqflags.pixel['REFERENCE_PIXEL'] + dqflags.pixel['NON_SCIENCE']
hdulist['DQ'].data[9, 9] = dqflags.pixel['REFERENCE_PIXEL'] + dqflags.pixel['DEAD']
dq = PreviewImage.get_nonsci_map(0, hdulist, extensions, xd, yd)
expected = np.ones((10, 10), dtype=bool)
expected[1, 1] = expected[3, 3] = expected[7, 7] = expected[9, 9] = 0
assert np.all(dq == expected)
[docs]
@pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Requires access to central storage.')
@pytest.mark.parametrize('filename', get_test_fits_files())
def test_make_image(tmp_path, filename):
"""Use PreviewImage.make_image to create preview images of a sample
JWST exposure.
Assert that the number of JPGs created corresponds to the number of
integrations.
Parameters
----------
tmp_path : pathlib.Path
Temporary directory to write to
filename : str
Path of FITS image to generate preview of
"""
test_directory = str(tmp_path)
header = fits.getheader(filename)
# Create and save the preview image or thumbnail
for create_thumbnail in [False, True]:
try:
image = PreviewImage(filename, "SCI")
image.clip_percent = 0.01
image.scaling = 'log'
image.cmap = 'viridis'
image.output_format = 'jpg'
image.thumbnail_output_directory = test_directory
image.preview_output_directory = test_directory
image.make_image(create_thumbnail=create_thumbnail)
except ValueError as error:
print(error)
if create_thumbnail:
extension = 'thumb'
n_img = 1
else:
extension = 'jpg'
n_img = header['NINTS']
# list of preview images
preview_image_filenames = glob.glob(
os.path.join(test_directory, '*.{}'.format(extension)))
assert len(preview_image_filenames) == n_img
# clean up: delete preview images
for file in preview_image_filenames:
os.remove(file)