def test_get_circle_cutout_pixels_iris_no_overlap():
header_filename = os.path.join(TESTDATA_DIR, IRIS_3D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
circle = Circle(20.0, 20.0, 0.1)
test_subject = Transform()
try:
test_subject.get_circle_cutout_pixels(circle, header, 1, 2)
assert False, 'Should raise NoContentError.'
except NoContentError:
assert True
def do_pos_circle(circle):
cutout = ['{} 140 0 0.1'.format(circle)]
test_subject = Transform()
shapes = test_subject.world_to_shape(cutout)
assert shapes is not None
assert len(shapes) == 1
circle = shapes[0]
assert isinstance(circle, Circle)
assert circle.ra == 140.0
assert circle.dec == 0.0
assert circle.radius == 0.1
def test_band_tiled_multi_chunk():
header_filename = os.path.join(TESTDATA_DIR, TILED_MULTICHUNK_HEADER)
header = fits.Header.fromtextfile(header_filename)
energy = Energy(371.0e-9, 372.0e-9)
test_subject = Transform()
pixels = test_subject.get_energy_cutout_pixels(energy, header, 3)
assert pixels is not None
assert len(pixels) == 2
# SODA returns [0][1:2724,1:3]
assert pixels[0] == 1
assert pixels[1] == 2724
def test_band_no_overlap():
header_filename = os.path.join(TESTDATA_DIR, CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
header.append(('RESTFRQ', 1.420406E9))
energy = Energy(212.0, 213.0)
test_subject = Transform()
try:
test_subject.get_energy_cutout_pixels(energy, header, 3)
assert False, 'Should raise NoContentError'
except NoContentError as e:
assert isinstance(e, NoContentError)
def test__append_world_to_circle_pixels():
cutouts = [(0, 0), (1, 256), (1, 256)]
pixels = (1, 1089, None, 1089)
header_filename = os.path.join(TESTDATA_DIR, VLASS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
test_subject = Transform()
try:
test_subject._append_world_to_circle_pixels(header, 1, 2, pixels,
cutouts)
assert False, 'Should throw NoContentError for missing value.'
except NoContentError as nce:
assert '{}'.format(nce) == 'Unable to create bounding box.', \
'Wrong message.'
def test_interval_polygon():
header_filename = os.path.join(TESTDATA_DIR, QUERY_HEADER)
header = fits.Header.fromtextfile(header_filename)
# CW winding direction
polygon = Polygon([[139.9, -0.1], [140.1, -0.1],
[140.1, 0.1], [139.9, 0.1]])
test_subject = Transform()
try:
test_subject.get_polygon_cutout_pixels(polygon, header, 1, 2)
assert False
except ValueError:
assert True
def test_get_circle_cutout_pixels_cgps_galactic():
header_filename = os.path.join(TESTDATA_DIR, CGPS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
circle = Circle(25.0, 60.0, 0.5)
test_subject = Transform()
pixels = test_subject.get_circle_cutout_pixels(circle, header, 1, 2)
# SODA returns [0][350:584,136:370]
assert pixels is not None
assert pixels[0] == 367
assert pixels[1] == 568
assert pixels[2] == 152
assert pixels[3] == 353
def test_get_circle_cutout_pixels_vlass():
header_filename = os.path.join(TESTDATA_DIR, VLASS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
circle = Circle(168.34719985367971, 76.18699791158396, 0.010)
test_subject = Transform()
pixels = test_subject.get_circle_cutout_pixels(circle, header, 1, 2)
assert pixels is not None
assert len(pixels) == 4
assert pixels[0] == 2940
assert pixels[1] == 3061
assert pixels[2] == 4193
assert pixels[3] == 4314
def test_circle():
header_filename = os.path.join(TESTDATA_DIR, QUERY_HEADER)
header = fits.Header.fromtextfile(header_filename)
circle = Circle(140.0, 0.0, 0.1)
test_subject = Transform()
pixels = test_subject.get_circle_cutout_pixels(circle, header, 1, 2)
# SODA returns [0][271:279,254:262,*]
assert pixels is not None
assert len(pixels) == 4
assert pixels[0] == 271
assert pixels[1] == 280
assert pixels[2] == 253
assert pixels[3] == 262
def test_get_polygon_cutout_pixels_vlass():
header_filename = os.path.join(TESTDATA_DIR, VLASS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
polygon = Polygon([[168.34, 76.18], [168.34, 76.19], [168.35, 76.19]])
test_subject = Transform()
pixels = test_subject.get_polygon_cutout_pixels(polygon, header, 1, 2)
# SODA returns cutout=[0][2997:3011,4211:4272,*,*]
assert pixels is not None
assert len(pixels) == 4
assert pixels[0] == 2996
assert pixels[1] == 3012
assert pixels[2] == 4211
assert pixels[3] == 4272
def test_get_energy_cutout_pixels_jcmt():
header_filename = os.path.join(TESTDATA_DIR, JCMT_3D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
# cdelt3 from caom2: 3.05140426249E-5
header.append(('CDELT3', 3.05140426249E-5))
energy = Energy(0.00091067, 0.00091012)
test_subject = Transform()
pixels = test_subject.get_energy_cutout_pixels(energy, header, 3)
# caom2ops returns cutout=[0][*,*,290:6810]&cutout=[1][*,*,290:6810]
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 290
assert pixels[1] == 6810
def test_get_circle_cutout_pixels_iris_all_overlap():
header_filename = os.path.join(TESTDATA_DIR, IRIS_3D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
circle = Circle(140.0, 0.0, 10.0)
test_subject = Transform()
pixels = test_subject.get_circle_cutout_pixels(circle, header, 1, 2)
# cutout pixels: -125:676, -143:659
# cutout returning entire image returns empty list
assert pixels is not None
assert len(pixels) == 4
assert pixels[0] == 1
assert pixels[1] == 500
assert pixels[2] == 1
assert pixels[3] == 500
def test_pos_band():
header_filename = os.path.join(TESTDATA_DIR, CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
header.append(('RESTFRQ', 1.420406E9))
world = ['circle 25.0 60.0 0.5', 'BAND 211.0e-3 211.05e-3']
test_subject = Transform()
pixel_cutout_hdu = test_subject.world_to_pixels(world, header)
# SODA returns [0][350:584,136:370,91:177,*]
assert pixel_cutout_hdu is not None
ranges = pixel_cutout_hdu.get_ranges()
assert len(ranges) == 4
assert ranges[0] == (367, 568)
assert ranges[1] == (152, 353)
assert ranges[2] == (91, 178)
assert ranges[3] == (1, 1)
def test_polygon():
header_filename = os.path.join(TESTDATA_DIR, QUERY_HEADER)
header = fits.Header.fromtextfile(header_filename)
# CCW winding direction
polygon = Polygon([[139.9, 0.1], [140.1, 0.1],
[140.1, -0.1], [139.9, -0.1]])
test_subject = Transform()
pixels = test_subject.get_polygon_cutout_pixels(polygon, header, 1, 2)
# SODA returns [0][271:279,254:262,*]
assert pixels is not None
assert len(pixels) == 4
assert pixels[0] == 271
assert pixels[1] == 280
assert pixels[2] == 253
assert pixels[3] == 263
def test_get_energy_cutout_pixels_cgps_raises_error():
"""
CPGS cube lacks rest wavelength or frequency for wcslib
to do the transform from VELO-LFR to WAVE-???, and the
python wcslib wrapper will raise a ValueError.
"""
header_filename = os.path.join(TESTDATA_DIR, CGPS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
energy = Energy(211.0e-3, 211.05e-3)
test_subject = Transform()
try:
test_subject.get_energy_cutout_pixels(energy, header, 3)
assert False, 'Should raise ValueError.'
except ValueError:
assert True
def test_get_energy_cutout_pixels_vlass():
"""
BAND 0.04456576 0.11662493
cutout=[1:2]
"""
header_filename = os.path.join(TESTDATA_DIR, VLASS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
energy = Energy(0.04456576, 0.11662493)
test_subject = Transform()
pixels = test_subject.get_energy_cutout_pixels(energy, header, 3)
# SODA returns cutout=[0][*,*,1:2,*]
# library returns (before clipping) [2.79849082, 0.79277332] pixels
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 1
assert pixels[1] == 3
def test_get_polarization_cutout_pixels_cgps():
"""
CTYPE4 = 'STOKES ' / 4TH COORDINATE TYPE
CRVAL4 = 1.000000000000E+00 / REF. COORD. 1-4=I,Q,U,V
CRPIX4 = 1.00 / REF. PIXEL
CDELT4 = 1.0000000E+00 / DELTA COORD.
CROTA4 = 0.00 / ROTATION ANGLE (DEG)
"""
header_filename = os.path.join(TESTDATA_DIR, CGPS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
polarization = Polarization([PolarizationState.I])
test_subject = Transform()
pixels = test_subject.get_polarization_cutout_pixels(
polarization, header, 4)
# SODA returns [*,*,*,1:1]
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 1
assert pixels[1] == 1
def test_band():
header_filename = os.path.join(TESTDATA_DIR, CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
header.append(('RESTFRQ', 1.420406E9))
# energy from caom2
# bandpassName: 21 cm
# resolvingPower: null
# specsys: LSRK
# ssysobs: null
# restfrq: 1.420406E9
# restwav: null
# velosys: null
# zsource: null
# ssyssrc: null
# velang: null
# ctype: VRAD
# cunit: m/s
# syser:
# rnder:
# naxis: 272
# crpix: 145.0
# crval: -60000.0
# cdelt: -824.46002
# bounds: null
# range: null
energy = Energy(211.0e-3, 211.05e-3)
test_subject = Transform()
pixels = test_subject.get_energy_cutout_pixels(energy, header, 3)
assert pixels is not None
assert len(pixels) == 2
# SODA returns [0][*,*,91:177,*]
assert pixels[0] == 91
assert pixels[1] == 178
def test_parse_world():
test_subject = Transform()
world = 'CIRCLE 1.0 2.0 3.0'
circle = test_subject.parse_world(world)
assert circle is not None
assert isinstance(circle, Circle)
assert circle.ra == 1.0
assert circle.dec == 2.0
assert circle.radius == 3.0
world = 'POLYGON 1.0 2.0 3.0 4.0 5.0 6.0'
polygon = test_subject.parse_world(world)
assert polygon is not None
assert isinstance(polygon, Polygon)
vertices = polygon.vertices
assert len(vertices) == 3
assert vertices[0][0] == 1.0
assert vertices[0][1] == 2.0
assert vertices[1][0] == 3.0
assert vertices[1][1] == 4.0
assert vertices[2][0] == 5.0
assert vertices[2][1] == 6.0
world = 'BAND 1.0 2.0'
energy = test_subject.parse_world(world)
assert energy is not None
assert isinstance(energy, Energy)
assert energy.lower == 1.0
assert energy.upper == 2.0
world = 'TIME 1.0 2.0'
time = test_subject.parse_world(world)
assert time is not None
assert isinstance(time, Time)
assert time.lower == 1.0
assert time.upper == 2.0
world = 'POL I V'
polarization = test_subject.parse_world(world)
assert polarization is not None
assert isinstance(polarization, Polarization)
states = polarization.states
assert len(states) == 2
assert states[0] == PolarizationState.I
assert states[1] == PolarizationState.V
def test_world_to_pixels_vlass():
"""
CIRCLE 168.34719985367971 76.18699791158396 0.01
BAND 0.04456576 0.11662493 POL I
cutout=[0][2938:3062,4191:4316,1:2,1:1]
"""
header_filename = os.path.join(TESTDATA_DIR, VLASS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
world = [
'circle 168.34719985367971 76.18699791158396 0.01',
'BAND 0.04456576 0.11662493', 'POL I'
]
test_subject = Transform()
pixel_cutout_hdu = test_subject.world_to_pixels(world, header)
assert pixel_cutout_hdu is not None
ranges = pixel_cutout_hdu.get_ranges()
assert len(ranges) == 4
# assert ranges[0] == (2940, 3061)
assert ranges[1] == (4193, 4314)
assert ranges[2] == (1, 3)
assert ranges[3] == (1, 1)
def _check_hdu_list(self, cutout_dimensions, hdu_list):
has_match = False
pixel_matches_left = len(cutout_dimensions)
for curr_extension_idx, hdu in enumerate(hdu_list):
# If we encounter a PrimaryHDU, write it at the top and continue.
if isinstance(hdu, PrimaryHDU) and hdu.data is None:
logger.debug('Appending Primary from index {}'.format(
curr_extension_idx))
fits.append(filename=self.output_writer,
header=hdu.header,
data=None,
overwrite=False,
output_verify='silentfix',
checksum='remove')
elif hdu.is_image:
header = hdu.header
ext_name = header.get('EXTNAME')
ext_ver = header.get('EXTVER', 0)
curr_ext_name_ver = None
if ext_name is not None:
curr_ext_name_ver = (ext_name, ext_ver)
try:
if isinstance(cutout_dimensions[0], PixelCutoutHDU):
for cutout_dimension in cutout_dimensions:
if self._is_extension_requested(
curr_extension_idx, curr_ext_name_ver,
cutout_dimension):
logger.debug(
'*** Extension {} does match ({} | {})'.
format(cutout_dimension.get_extension(),
curr_extension_idx,
curr_ext_name_ver))
pixel_matches_left -= 1
self._pixel_cutout(header, hdu.data,
cutout_dimension)
has_match = True
if pixel_matches_left == 0:
return has_match
else:
logger.debug('Handling WCS transform.')
# Handle WCS transform.
transform = Transform()
transformed_cutout_dimension = \
transform.world_to_pixels(cutout_dimensions, header)
logger.debug('Transformed {} into {}'.format(
cutout_dimensions, transformed_cutout_dimension))
self._pixel_cutout(header, hdu.data,
transformed_cutout_dimension)
has_match = True
except NoContentError:
# Skip for now as we're iterating the loop.
logger.debug('No overlap with extension {}'.format(
curr_extension_idx))
logger.debug('Finished extension {}'.format(curr_extension_idx))
logger.debug('Has match in list? -- {}'.format(has_match))
return has_match
def test_get_polarization_cutout_pixels_vlass():
"""
Polarization states for header are I, Q, U, V (1, 2, 3, 4)
"""
header_filename = os.path.join(TESTDATA_DIR, VLASS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
polarization = Polarization([PolarizationState.I])
test_subject = Transform()
pixels = test_subject.get_polarization_cutout_pixels(
polarization, header, 4)
# SODA returns [*,*,*,1:1]
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 1
assert pixels[1] == 1
polarization = Polarization([PolarizationState.I, PolarizationState.Q])
pixels = test_subject.get_polarization_cutout_pixels(
polarization, header, 4)
# should return [1:2]
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 1
assert pixels[1] == 2
polarization = Polarization(
[PolarizationState.I, PolarizationState.Q, PolarizationState.U])
pixels = test_subject.get_polarization_cutout_pixels(
polarization, header, 4)
# should return [1:3]
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 1
assert pixels[1] == 3
polarization = Polarization([
PolarizationState.I, PolarizationState.Q, PolarizationState.U,
PolarizationState.V
])
pixels = test_subject.get_polarization_cutout_pixels(
polarization, header, 4)
# should return [1:4]
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 1
assert pixels[1] == 4
polarization = Polarization([PolarizationState.I, PolarizationState.V])
pixels = test_subject.get_polarization_cutout_pixels(
polarization, header, 4)
# should return [1:4]
assert pixels is not None
assert len(pixels) == 2
assert pixels[0] == 1
assert pixels[1] == 4
def test_world_to_shape():
test_subject = Transform()
world = ['CIRCLE 1.0 2.0 3.0', 'CIRCLE 4.0 5.0 6.0']
try:
shapes = test_subject.world_to_shape(world)
assert False, 'Should raise ValueError'
except ValueError:
assert True
world = ['CIRCLE 1.0 2.0 3.0', 'POLYGON 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0']
try:
shapes = test_subject.world_to_shape(world)
assert False, 'Should raise ValueError'
except ValueError:
assert True
world = [
'POLYGON 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0',
'POLYGON 1.5 2.5 3.5 4.5 5.5 6.5 7.5 8.5'
]
try:
shapes = test_subject.world_to_shape(world)
assert False, 'Should raise ValueError'
except ValueError:
assert True
world = ['BAND 1.0 2.0 3.0', 'BAND 4.0 5.0 6.0']
try:
shapes = test_subject.world_to_shape(world)
assert False, 'Should raise ValueError'
except ValueError:
assert True
world = ['TIME 1.0 2.0 3.0', 'TIME 4.0 5.0 6.0']
try:
shapes = test_subject.world_to_shape(world)
assert False, 'Should raise ValueError'
except ValueError:
assert True
world = ['POL I V', 'POL Q U']
try:
shapes = test_subject.world_to_shape(world)
assert False, 'Should raise ValueError'
except ValueError:
assert True
world = ['CIRCLE 1.0 2.0 3.0', 'BAND 4.0 5.0', 'TIME 6.0 7.0', 'POL I V']
shapes = test_subject.world_to_shape(world)
assert shapes is not None
assert len(shapes) == 4
circle = shapes[0]
assert circle is not None
assert isinstance(circle, Circle)
assert circle.ra == 1.0
assert circle.dec == 2.0
assert circle.radius == 3.0
energy = shapes[1]
assert energy is not None
assert isinstance(energy, Energy)
assert energy.lower == 4.0
assert energy.upper == 5.0
time = shapes[2]
assert time is not None
assert isinstance(time, Time)
assert time.lower == 6.0
assert time.upper == 7.0
polarization = shapes[3]
assert polarization is not None
assert isinstance(polarization, Polarization)
states = polarization.states
assert len(states) == 2
assert states[0] == PolarizationState.I
assert states[1] == PolarizationState.V
world = [
'POLYGON 1.0 1.5 2.0 2.5 3.0 3.5', 'BAND 4.0 5.0', 'TIME 6.0 7.0',
'POL I V'
]
shapes = test_subject.world_to_shape(world)
assert shapes is not None
assert len(shapes) == 4
polygon = shapes[0]
assert polygon is not None
assert isinstance(polygon, Polygon)
vertices = polygon.vertices
assert len(vertices) == 3
assert vertices[0][0] == 1.0
assert vertices[0][1] == 1.5
assert vertices[1][0] == 2.0
assert vertices[1][1] == 2.5
assert vertices[2][0] == 3.0
assert vertices[2][1] == 3.5
energy = shapes[1]
assert energy is not None
assert isinstance(energy, Energy)
assert energy.lower == 4.0
assert energy.upper == 5.0
time = shapes[2]
assert time is not None
assert isinstance(time, Time)
assert time.lower == 6.0
assert time.upper == 7.0
polarization = shapes[3]
assert polarization is not None
assert isinstance(polarization, Polarization)
states = polarization.states
assert len(states) == 2
assert states[0] == PolarizationState.I
assert states[1] == PolarizationState.V
def test_world_to_pixels_no_content():
header_filename = os.path.join(TESTDATA_DIR, VLASS_4D_CUBE_HEADER)
header = fits.Header.fromtextfile(header_filename)
# circle no content
query = [
'CIRCLE -168.34719985367971 -76.18699791158396 0.01',
'BAND 0.04456576 0.11662493', 'POL I'
]
test_subject = Transform()
try:
test_subject.world_to_pixels(query, header)
assert False, 'Should raise NoContentError'
except NoContentError:
assert True
# polygon no content
query = [
'POLYGON -168.34 -76.18 -168.34 -76.19 -168.35 -76.19',
'BAND 0.04456576 0.11662493', 'POL I'
]
test_subject = Transform()
try:
test_subject.world_to_pixels(query, header)
assert False, 'Should raise NoContentError'
except NoContentError:
assert True
# energy no content
query = [
'CIRCLE 168.34719985367971 76.18699791158396 0.01',
'BAND 0.14456576 0.21662493', 'POL I'
]
test_subject = Transform()
try:
test_subject.world_to_pixels(query, header)
assert False, 'Should raise NoContentError'
except NoContentError:
assert True
# polarization no content
query = [
'CIRCLE 168.34719985367971 76.18699791158396 0.01',
'BAND 0.04456576 0.11662493', 'POL LL'
]
test_subject = Transform()
try:
test_subject.world_to_pixels(query, header)
assert False, 'Should raise NoContentError'
except NoContentError:
assert True
def _check_hdu_list(self, cutout_dimensions, hdu_list):
has_match = False
len_cutout_dimensions = len(cutout_dimensions)
if len_cutout_dimensions > 0:
result_hdu_list = None
if self._require_primary_hdu(cutout_dimensions) and \
hdu_list[0].header['NAXIS'] == 0:
# add the PrimaryHDU from the original HDU list
result_hdu_list = fits.HDUList([hdu_list[0]])
# Check for a pixel cutout
if isinstance(cutout_dimensions[0], PixelCutoutHDU):
for cutout_dimension in cutout_dimensions:
ext = cutout_dimension.get_extension()
ext_idx = hdu_list.index_of(ext)
hdu = hdu_list[ext_idx]
# Entire extension was requested.
if not cutout_dimension.get_ranges():
logger.debug(
'Appending entire extension {}'.format(ext))
result_hdu_list = self._add_hdu(hdu, result_hdu_list)
has_match = True
else:
try:
result_hdu_list = self._add_hdu(
self._pixel_cutout(hdu, cutout_dimension),
result_hdu_list)
has_match = True
logger.debug(
'Successfully cutout from {} ({})'.format(
ext, ext_idx))
except NoContentError:
logger.debug(
'Skipping non-overlapping cutout {}'.format(
cutout_dimension))
else:
# Skip the primary as it should be written out already.
for hdu in hdu_list:
if hdu.is_image and hdu.data is not None:
transform = Transform()
logger.debug(
'Transforming {}'.format(cutout_dimensions))
transformed_cutout_dimension = \
transform.world_to_pixels(
cutout_dimensions, hdu.header)
logger.debug('Transformed {} into {}'.format(
cutout_dimensions, transformed_cutout_dimension))
try:
result_hdu_list = self._add_hdu(self._pixel_cutout(
hdu,
transformed_cutout_dimension), result_hdu_list)
has_match = True
except NoContentError:
logger.debug(
'Skipping non-overlapping cutout {}'.format(
cutout_dimensions))
# time to write the cutout file
result_hdu_list.writeto(
self.output_writer, output_verify='ignore', checksum='remove')
else:
raise NoContentError('No overlap found (No cutout specified).')
logger.debug('Has match in list? -- {}'.format(has_match))
return has_match
