def test_multiple_ext_cutouts():
test_subject = OpenCADCCutout()
cutout_file_name_path = test_context.random_test_file_name_path()
cutout_regions = [
PixelCutoutHDU([(1, 100), (1, 100)], "1"),
PixelCutoutHDU([(1, 100), (1, 100)], "3")
]
with open(cutout_file_name_path, 'wb') as output_writer, \
open(target_file_name, 'rb') as input_reader:
test_subject.cutout(cutout_regions, input_reader, output_writer,
'FITS')
expected = fits.open(target_file_name, do_not_scale_image_data=True)
actual = fits.open(cutout_file_name_path, do_not_scale_image_data=True)
assert len(actual) == 3
# test primary header unchanged
assert len(expected[0].header) == len(actual[0].header)
for key in expected[0].header.keys():
assert expected[0].header[key] == actual[0].header[key]
# check BSCALE and BZERO correct in cutout file
assert expected[1].header['BSCALE'] == actual[1].header['BSCALE']
assert expected[1].header['BZERO'] == actual[1].header['BZERO']
assert expected[3].header['BSCALE'] == actual[2].header['BSCALE']
assert expected[3].header['BZERO'] == actual[2].header['BZERO']
def test_extract():
data_shape = (9, 4)
data = np.arange(36).reshape(data_shape)
test_subject = CutoutND(data)
cutout_region = PixelCutoutHDU([(4, 18)])
cutout = test_subject.extract(cutout_region.get_ranges())
expected_data = np.array([[3], [7], [11], [15], [19], [23], [27], [31],
[35]])
np.testing.assert_array_equal(expected_data, cutout.data,
'Arrays do not match.')
def test_is_extension_requested():
test_subject = FITSHelper(io.BytesIO(), io.BytesIO())
dimension = PixelCutoutHDU([(400, 800)], extension=1)
assert not test_subject._is_extension_requested('4', ('EXN', 4), dimension)
dimension = PixelCutoutHDU([(400, 800)])
assert not test_subject._is_extension_requested('4', ('NOM', 1), dimension)
dimension = PixelCutoutHDU([(400, 800)], extension=2)
assert test_subject._is_extension_requested('2', ('NOM', 7), dimension)
def test_astropy_scaling():
test_subject = OpenCADCCutout()
cutout_file_name_path = test_context.random_test_file_name_path()
cutout_regions = [PixelCutoutHDU([], "2")]
# Write out a test file with the test result FITS data.
with open(cutout_file_name_path, 'wb') as output_writer, \
open(target_file_name, 'rb') as input_reader:
test_subject.cutout(cutout_regions, input_reader, output_writer,
'FITS')
# now check that BZERO and BSCALE have not been changed
expected = fits.open(target_file_name, do_not_scale_image_data=True)
actual = fits.open(cutout_file_name_path, do_not_scale_image_data=True)
# check headers and data not changed. Except ...
# expected missing keywords from actual: PCOUNT, XTENSION and GCOUNT
# added to actual: SIMPLE
del expected[2].header['PCOUNT']
del expected[2].header['XTENSION']
del expected[2].header['GCOUNT']
assert 'SIMPLE' in actual[0].header
del actual[0].header['SIMPLE']
assert len(expected[2].header) == len(actual[0].header)
for key in expected[2].header.keys():
assert expected[2].header[key] == actual[0].header[key]
np.testing.assert_array_equal(expected[2].data, actual[0].data,
'Arrays do not match.')
# do a cutout
cutout_regions = [PixelCutoutHDU([(1, 100), (1, 100)], "3")]
# Write out a test file with the test result FITS data.
with open(cutout_file_name_path, 'wb') as output_writer, \
open(target_file_name, 'rb') as input_reader:
test_subject.cutout(cutout_regions, input_reader, output_writer,
'FITS')
# now check that BZERO and BSCALE have not been changed
expected = fits.open(target_file_name, do_not_scale_image_data=True)
actual = fits.open(cutout_file_name_path, do_not_scale_image_data=True)
# check only expected headers changed
# changed headers
del expected[3].header['PCOUNT']
del expected[3].header['XTENSION']
del expected[3].header['GCOUNT']
assert 'SIMPLE' in actual[0].header
del actual[0].header['SIMPLE']
assert len(expected[3].header) == len(actual[0].header)
for key in expected[3].header.keys():
if key == 'NAXIS1' or key == 'NAXIS2':
assert actual[0].header[key] == 100
else:
assert expected[3].header[key] == actual[0].header[key]
def test_create():
test_subject = PixelCutoutHDU([(1, 200), (305, 600)], 7)
assert test_subject.get_extension() == 7, 'Wrong extension.'
test_subject = PixelCutoutHDU([(1, 200), (30)], 'SCI,5')
assert test_subject.get_extension() == ('SCI', 5), 'Wrong extension.'
test_subject = PixelCutoutHDU(extension='5')
assert test_subject.get_extension() == 5, 'Wrong extension.'
def test__check_hdu_list():
in_io = io.BytesIO(b'TEST STRING HERE')
out_io = io.BytesIO()
test_subject = FITSHelper(in_io, out_io)
dimensions = [PixelCutoutHDU([(20, 35), (40, 50)], extension=1)]
hdu_list = _create_hdu_list()
assert test_subject._check_hdu_list(dimensions, hdu_list), 'Should match.'
def test_construct():
test_subject = OpenCADCCutout()
with pytest.raises(ValueError) as ve:
test_subject.cutout([])
assert '{}'.format(ve) == 'No Cutout regions specified.', \
'Wrong error message.'
with pytest.raises(ValueError) as ve:
test_subject.cutout([PixelCutoutHDU([(8, 10)])], input_reader=None)
assert '{}'.format(ve) == 'No input source specified.', \
'Wrong error message.'
with pytest.raises(ValueError) as ve:
test_subject.cutout([PixelCutoutHDU([(8, 10)])], output_writer=None)
assert '{}'.format(ve) == 'No output target specified.', \
'Wrong error message.'
def test_construct():
test_subject = OpenCADCCutout()
with pytest.raises(ValueError) as ve:
test_subject.cutout([])
assert str(ve.value) == 'No Cutout regions specified.', \
'Wrong error message.'
with pytest.raises(FileNotFoundError):
test_subject.cutout([PixelCutoutHDU([(8, 10)])],
input_reader=open('/no/such/file'))
def test__check_hdu_list():
in_io = io.BytesIO(b'TEST STRING HERE')
out_io = io.BytesIO()
test_subject = FITSHelper(in_io, out_io)
dimensions = [PixelCutoutHDU([(20, 35), (40, 50)], extension=1)]
hdu_list = _create_hdu_list()
has_match = test_subject._check_hdu_list(dimensions, hdu_list)
logging.debug('Output from _check_hdu_list() is {}'.format(has_match))
assert has_match, 'Should match.'
def test_get_shape():
test_subject = PixelCutoutHDU([(1, 200), (305, 600)])
shape = test_subject.get_shape()
assert shape == (200, 296), 'Wrong shape output.'
test_subject = PixelCutoutHDU([(10, 20), (30)])
shape = test_subject.get_shape()
assert shape == (11, 1), 'Wrong shape output.'
def test_get_position():
test_subject = PixelCutoutHDU([(1, 200), (305, 360), (400, 1000)])
position = test_subject.get_position()
assert position == (99, 331, 699), 'Wrong position output.'
test_subject = PixelCutoutHDU([(10, 20), (30), (400, 406)])
position = test_subject.get_position()
assert position == (14, 29, 402), 'Wrong position output.'
def test_get_ranges():
test_subject = PixelCutoutHDU([(1, 200), (305, 600)])
ranges = test_subject.get_ranges()
assert ranges == [(1, 200), (305, 600)], 'Wrong ranges output.'
test_subject = PixelCutoutHDU([(10, 20), (30)])
ranges = test_subject.get_ranges()
assert ranges == [(10, 20), (30, 30)], 'Wrong ranges output.'
def test_multiple_cutouts_single_ext():
test_subject = OpenCADCCutout()
cutout_file_name_path = test_context.random_test_file_name_path()
cutout_regions = [
PixelCutoutHDU([(1, 100), (1, 100)], "1"),
PixelCutoutHDU([(200, 300), (2, 300)], "1")
]
with open(cutout_file_name_path, 'wb') as output_writer, \
open(target_file_name, 'rb') as input_reader:
test_subject.cutout(cutout_regions, input_reader, output_writer,
'FITS')
expected = fits.open(target_file_name, do_not_scale_image_data=True)
actual = fits.open(cutout_file_name_path, do_not_scale_image_data=True)
# cutouts in the same extension => no extra primary HDU
assert len(actual) == 2
# test primary header changed
assert len(expected[0].header) != len(actual[0].header)
# check BSCALE and BZERO correct in cutout file
assert expected[1].header['BSCALE'] == actual[0].header['BSCALE']
assert expected[1].header['BZERO'] == actual[0].header['BZERO']
assert expected[1].header['BSCALE'] == actual[1].header['BSCALE']
assert expected[1].header['BZERO'] == actual[1].header['BZERO']
def test_simple_cutout():
test_subject = OpenCADCCutout()
cutout_file_name_path = test_context.random_test_file_name_path()
logger.info('Testing with {}'.format(cutout_file_name_path))
cutout_regions = [PixelCutoutHDU([(300, 800), (810, 1000)])]
# Write out a test file with the test result FITS data.
with open(cutout_file_name_path, 'ab+') as output_writer, \
open(target_file_name, 'rb') as input_reader:
test_subject.cutout(cutout_regions, input_reader, output_writer,
'FITS')
with fits.open(expected_cutout_file_name, mode='readonly') \
as expected_hdu_list, \
fits.open(cutout_file_name_path, mode='readonly') \
as result_hdu_list:
fits_diff = fits.FITSDiff(expected_hdu_list, result_hdu_list)
np.testing.assert_array_equal(
(), fits_diff.diff_hdu_count, 'HDU count diff should be empty.')
for extension, result_hdu in enumerate(result_hdu_list):
expected_hdu = expected_hdu_list[extension]
expected_wcs = WCS(header=expected_hdu.header)
result_wcs = WCS(header=result_hdu.header)
np.testing.assert_array_equal(
expected_wcs.wcs.crpix, result_wcs.wcs.crpix,
'Wrong CRPIX values.')
np.testing.assert_array_equal(
expected_wcs.wcs.crval, result_wcs.wcs.crval,
'Wrong CRVAL values.')
assert expected_hdu.header['NAXIS1'] \
== result_hdu.header['NAXIS1'], 'Wrong NAXIS1 values.'
assert expected_hdu.header['NAXIS2'] \
== result_hdu.header['NAXIS2'], 'Wrong NAXIS2 values.'
assert expected_hdu.header.get(
'CHECKSUM') is None, 'Should not contain CHECKSUM.'
assert expected_hdu.header.get(
'DATASUM') is None, 'Should not contain DATASUM.'
np.testing.assert_array_equal(
np.squeeze(expected_hdu.data), result_hdu.data,
'Arrays do not match.')
def test_create():
test_subject = PixelCutoutHDU([(1, 200), (305, 600)], 7)
assert test_subject.get_extension() == 7, 'Wrong extension.'
test_subject = PixelCutoutHDU([(1, 200), (30)], 'SCI,5')
assert test_subject.get_extension() == ('SCI', 5), 'Wrong extension.'
test_subject = PixelCutoutHDU([(99, 101), (44, 66)], 'AMS ,2')
assert test_subject.get_extension() == ('AMS', 2), \
'Wrong extension (didn' 't filter out spaces)'
test_subject = PixelCutoutHDU([(12, 30)], 'EXT,0')
assert test_subject.get_extension() == ('EXT', 1)
with pytest.raises(ValueError,
match=r"Specifying XTENSION return type "
r"is not supported\."):
PixelCutoutHDU([(23, 67), (23, 89)], extension='SCI, 3, i')
test_subject = PixelCutoutHDU(extension='5')
assert test_subject.get_extension() == 5, 'Wrong extension.'
test_subject = PixelCutoutHDU([()])
assert test_subject.get_extension() == 0
def parse(self, pixel_range_input_str):
"""
Parse a string range.
:param pixel_range_input_str: The string to parse.
:return List of PixelCutoutHDU instances
Example:
rp = PixelRangeInputParser()
rp.parse('[0][1]')
=> [PixelCutoutHDU((1,1), extension='0')]
rp.parse('[99:112]')
=> [PixelCutoutHDU((99,112), extension='0')]
rp.parse('[SCI][99:112][5]')
=> [PixelCutoutHDU((99,112), extension=SCI),
PixelCutoutHDU(extension='5')]
rp.parse('[IMG,2][100:112][6][300:600]')
=> [PixelCutoutHDU((100,112), extension='IMG,2'),
PixelCutoutHDU((300,600), extension='6')]
"""
rs = pixel_range_input_str.strip()
if not self.is_pixel_cutout(rs):
raise PixelRangeInputParserError(
'Not a valid pixel cutout string "{}".'.format(rs))
# List of ranges in format [ext][pixel ranges]
ranges = re.findall(self.match_pattern, rs)
if not ranges:
raise PixelRangeInputParserError(
'Invalid range specified. Should be in the format of {} \
(i.e.[0][8:35]), or single digit(i.e. 9). '.format(
self.match_pattern))
parsed_items = []
for r in ranges:
pixel_ranges = []
extension = '0'
split_items = list(
map(lambda x: x.split('[')[1], list(filter(None,
r.split(']')))))
l_items = len(split_items)
if l_items == 2:
extension = split_items[0]
pixel_ranges = list(
map(
self._to_range_tuple,
list(filter(None,
split_items[1].split(self.separator)))))
elif l_items == 1:
item = split_items[0]
if item.count(self.delimiter) > 0:
pixel_ranges = list(
map(self._to_range_tuple,
list(filter(None, item.split(self.separator)))))
else:
extension = item
else:
raise PixelRangeInputParserError(
'Nothing usable for range {}'.format(r))
parsed_items.append(
PixelCutoutHDU(dimension_ranges=pixel_ranges,
extension=extension))
return parsed_items