def test_mosaic_detectors_gmos_binning(astrofaker, hemi, ccd):
"""
Tests that the spacing between amplifier centres for NxN binned data
is precisely N times smaller than for unbinned data when run through
mosaicDetectors()
"""
for binning in (1, 2, 4):
try:
ad = astrofaker.create('GMOS-{}'.format(hemi), ['IMAGE', ccd])
except ValueError: # No e2v for GMOS-S
pytest.skip()
ad.init_default_extensions(binning=binning, overscan=False)
for ext in ad:
shape = ext.data.shape
ext.add_star(amplitude=10000,
x=0.5 * (shape[1] - 1),
y=0.5 * (shape[0] - 1),
fwhm=0.5 * binning)
p = GMOSImage([ad])
ad = p.mosaicDetectors([ad])[0]
ad = p.detectSources([ad])[0]
x = np.array(sorted(ad[0].OBJCAT['X_IMAGE']))
if binning == 1:
unbinned_positions = x
else:
diffs = np.diff(unbinned_positions) - binning * np.diff(x)
assert np.max(abs(diffs)) < 0.01
def test_measureBG(self, ad):
p = GMOSImage([ad])
ad = p.measureBG()[0]
correct = [
726.18213, 724.36047, 727.34491, 728.49664, 728.08966, 719.83728
]
for rv, cv in zip(ad.hdr['SKYLEVEL'], correct):
assert abs(rv - cv) < 0.1, 'Wrong background level'
assert (ad.phu['SKYLEVEL'] - 727.174) < 0.1
f = open(logfilename)
for line in f.readlines():
if 'BG band' in line:
assert line.split()[6] == 'BG80', 'Wrong BG band'
ad.phu['REQBG'] = '50-percentile'
ad = p.measureBG()[0]
assert any('WARNING: BG requirement not met' in line
for line in f.readlines()), 'No BG warning'
def test_measureIQ(self):
ad = astrodata.open(
os.path.join(TESTDATAPATH, 'GMOS',
'N20150624S0106_refcatAdded.fits'))
p = GMOSImage([ad])
ad = p.measureIQ()[0]
# Try to give a reasonable-sized goal
assert abs(ad.phu['MEANFWHM'] - 0.42) < 0.02, 'Wrong FWHM'
assert abs(ad.phu['MEANELLP'] - 0.09) < 0.02, 'Wrong ellipticity'
f = open(logfilename, 'r')
for line in f.readlines():
if 'IQ range' in line:
assert line.split()[8] == 'IQ20', 'Wrong IQ band'
ad.phu['REQIQ'] = '70-percentile'
for ext in ad:
ext.OBJCAT['PROFILE_FWHM'] *= 2.5
ext.OBJCAT['PROFILE_EE50'] *= 2.5
ad = p.measureIQ()[0]
iqwarn = False
for line in f.readlines():
if 'IQ range' in line:
assert line.split()[8] == 'IQ85', 'Wrong IQ band after edit'
iqwarn |= 'WARNING: IQ requirement not met' in line
assert iqwarn, 'NO IQ warning'
def plot(ad):
"""
Displays the tiled arrays with the DQ mask for analysing the data.
Parameters
----------
ad : multi-extension data
"""
from astropy.visualization import ImageNormalize, ZScaleInterval
from copy import deepcopy
import numpy as np
import matplotlib.pyplot as plt
p = GMOSImage([deepcopy(ad)])
_ad = p.tileArrays().pop()
fig, axs = plt.subplots(num=ad.filename, ncols=len(_ad), sharey=True)
norm = ImageNormalize(
np.concatenate([ext.data.ravel()[ext.mask.ravel() == 0] for ext in _ad]),
interval=ZScaleInterval())
vmin = norm.vmin
vmax = norm.vmax
for i, ext in enumerate(_ad):
data = np.ma.masked_array(ext.data, mask=ext.mask)
cmap = plt.get_cmap('viridis')
cmap.set_bad('red', alpha='0.5')
axs[i].imshow(data, origin='lower', cmap=cmap, vmin=vmin, vmax=vmax)
# axs[i].imshow(data.data, origin='lower', vmin=vmin, vmax=vmax)
plt.show()
def test_measureCC(self):
ad = astrodata.open(
os.path.join(TESTDATAPATH, 'GMOS',
'N20150624S0106_refcatAdded.fits'))
p = GMOSImage([ad])
ad = p.measureCC()[0]
correct = [28.18, 28.16, 28.14, 28.11, 28.17, 28.12]
for rv, cv in zip(ad.hdr['MEANZP'], correct):
assert abs(rv - cv) < 0.02, 'Wrong zeropoint'
f = open(logfilename, 'r')
for line in f.readlines():
if 'CC bands' in line:
assert 'CC50, CC70' in line, 'Wrong CC bands'
for ext in ad:
ext.OBJCAT['MAG_AUTO'] += 0.3
ad = p.measureCC()[0]
correct = [c - 0.3 for c in correct]
for rv, cv in zip(ad.hdr['MEANZP'], correct):
assert abs(rv - cv) < 0.02, 'Wrong zeropoint after edit'
ccwarn = False
for line in f.readlines():
if 'CC bands' in line:
assert 'CC70, CC80' in line, 'Wrong CC bands after edit'
ccwarn |= 'WARNING: CC requirement not met' in line
assert ccwarn, 'No CC warning'
def test_measureIQ(self, ad):
p = GMOSImage([ad])
ad = p.measureIQ()[0]
# Try to give a reasonable-sized goal
assert abs(ad.phu['MEANFWHM'] - 0.42) < 0.02, 'Wrong FWHM'
assert abs(ad.phu['MEANELLP'] - 0.09) < 0.02, 'Wrong ellipticity'
f = open(logfilename)
for line in f.readlines():
if 'IQ range' in line:
assert line.split()[8] == 'IQ20', 'Wrong IQ band'
ad.phu['REQIQ'] = '70-percentile'
for ext in ad:
ext.OBJCAT['PROFILE_FWHM'] *= 2.5
ext.OBJCAT['PROFILE_EE50'] *= 2.5
ad = p.measureIQ()[0]
iqwarn = False
for line in f.readlines():
if 'IQ range' in line:
assert line.split()[8] == 'IQ85', 'Wrong IQ band after edit'
iqwarn |= 'WARNING: IQ requirement not met' in line
assert iqwarn, 'NO IQ warning'
def test_add_object_mask_to_dq(astrofaker):
ad_orig = astrofaker.create('F2', 'IMAGE')
# astrodata.open(os.path.join(TESTDATAPATH, 'GMOS', 'N20150624S0106_refcatAdded.fits'))
p = GMOSImage([deepcopy(ad_orig)])
ad = p.addObjectMaskToDQ()[0]
for ext, ext_orig in zip(ad, ad_orig):
assert all(
ext.mask[ext.OBJMASK == 0] == ext_orig.mask[ext.OBJMASK == 0])
assert all(
ext.mask[ext.OBJMASK == 1] == ext_orig.mask[ext.OBJMASK == 1] | 1)
def test_add_oiwfs_runs_normally(caplog, ext_num, filename, x0, y0):
"""
Test that the primitive does not run if the input file does not have a DQ
plan.
Parameters
----------
caplog : fixture
filename : str
"""
caplog.set_level(logging.DEBUG)
file_path = download_from_archive(filename)
ad = astrodata.open(file_path)
p = GMOSImage([ad])
p.addDQ()
p.addVAR(read_noise=True)
p.addOIWFSToDQ()
# plot(p.streams['main'][0])
assert len(caplog.records) > 0
assert any("Guide star location found at" in r.message for r in caplog.records)
# Some kind of regression test
for r in caplog.records:
if r.message.startswith("Guide star location found at"):
coords = re.findall(r"\((.*?)\)", r.message).pop().split(',')
x = float(coords[0])
y = float(coords[1])
n = int(r.message.split(' ')[-1])
assert abs(x - x0) < 1
assert abs(y - y0) < 1
assert n == ext_num
def test_add_oiwfs_warns_when_wfs_if_not_in_field(caplog, filename):
"""
Test that the primitive does not run if the input file does not have a DQ
plan.
Parameters
----------
caplog : fixture
filename : str
"""
caplog.set_level(logging.DEBUG)
file_path = download_from_archive(filename)
ad = astrodata.open(file_path)
p = GMOSImage([ad])
p.addDQ()
p.addVAR(read_noise=True)
p.addOIWFSToDQ()
# plot(p.streams['main'][0])
print(caplog.records)
assert any("No good rows in" in r.message for r in caplog.records)
assert any("Cannot distinguish probe region from sky for"
in r.message for r in caplog.records)
def test_gmos_wcs_stability(raw_ad_path, do_prepare, do_overscan_correct,
tile_all):
raw_ad = astrodata.open(raw_ad_path)
# Ensure it's tagged IMAGE so we can get an imaging WCS and can use SkyCoord
raw_ad.phu['GRATING'] = 'MIRROR'
# Check the reference extension is what we think and find the middle
ref_index = find_reference_extension(raw_ad)
assert ref_index == (len(raw_ad) - 1) // 2 # works for GMOS
y, x = [length // 2 for length in raw_ad[ref_index].shape]
c0 = SkyCoord(*raw_ad[ref_index].wcs(x, y), unit="deg")
p = GMOSImage([raw_ad]) # TODO: support for other instruments
geotable = import_module('.geometry_conf', p.inst_lookups)
chip_gaps = geotable.tile_gaps[raw_ad.detector_name()]
# Test that prepare keeps the reference extenion's WCS intact
if do_prepare:
p.prepare()
c = SkyCoord(*raw_ad[ref_index].wcs(x, y), unit="deg")
assert c0.separation(c) < 1e-10 * u.arcsec
# Test that slicing the NDData keeps the WCS valid
if do_overscan_correct:
xshift, _, yshift, _ = raw_ad[ref_index].data_section()
p.overscanCorrect()
x -= xshift
y -= yshift
c = SkyCoord(*raw_ad[ref_index].wcs(x, y), unit="deg")
assert c0.separation(c) < 1e-10 * u.arcsec
# Test that tiling doesn't affect the reference extension's WCS
new_ref_index = 0 if (
tile_all or raw_ad.detector_roi_setting() == 'Central Stamp') else 1
p.tileArrays(tile_all=tile_all)
ad = p.streams['main'][0]
first = 0 if tile_all else (len(raw_ad) //
3) # index of first raw extension
# These extension widths are either overscan-trimmed or not, as
# required and so no alternative logic is required
x += sum([ext.shape[1] for ext in raw_ad[first:ref_index]])
if tile_all and raw_ad.detector_roi_setting() != 'Central Stamp':
x += chip_gaps // raw_ad.detector_x_bin()
c = SkyCoord(*ad[new_ref_index].wcs(x, y), unit="deg")
assert c0.separation(c) < 1e-10 * u.arcsec
# Now write the file to disk and read it back in and check WCS stability
ad.write(TEMPFILE, overwrite=True)
ad = astrodata.open(TEMPFILE)
c = SkyCoord(*ad[new_ref_index].wcs(x, y), unit="deg")
assert c0.separation(c) < 1e-9 * u.arcsec
os.remove(TEMPFILE)
def test_add_object_mask_to_dq():
try:
import AstroFaker
except ImportError:
pytest.skip("AstroFaker not installed")
ad_orig = AstroFaker.create('F2', 'IMAGE')
#astrodata.open(os.path.join(TESTDATAPATH, 'GMOS', 'N20150624S0106_refcatAdded.fits'))
p = GMOSImage([deepcopy(ad_orig)])
ad = p.addObjectMaskToDQ()[0]
for ext, ext_orig in zip(ad, ad_orig):
assert all(
ext.mask[ext.OBJMASK == 0] == ext_orig.mask[ext.OBJMASK == 0])
assert all(
ext.mask[ext.OBJMASK == 1] == ext_orig.mask[ext.OBJMASK == 1] | 1)
def test_oiwfs_not_used_in_observation(caplog, filename):
"""
Test that nothing happens when the input file does not use the OIWFS.
Parameters
----------
caplog : fixture
filename : str
"""
caplog.set_level(logging.DEBUG)
file_path = download_from_archive(filename)
ad = astrodata.open(file_path)
p = GMOSImage([ad])
p.addOIWFSToDQ()
print(caplog.records)
assert len(caplog.records) > 0
assert any("OIWFS not used for image" in r.message for r in caplog.records)
def test_warn_if_dq_does_not_exist(caplog, filename):
"""
Test that the primitive does not run if the input file does not have a DQ
plan.
Parameters
----------
caplog : fixture
filename : str
"""
caplog.set_level(logging.DEBUG)
file_path = download_from_archive(filename)
ad = astrodata.open(file_path)
p = GMOSImage([ad])
p.addOIWFSToDQ()
assert len(caplog.records) > 0
assert any("No DQ plane for" in r.message for r in caplog.records)
def test_measureBG(self):
ad = astrodata.open(
os.path.join(TESTDATAPATH, 'GMOS',
'N20150624S0106_refcatAdded.fits'))
p = GMOSImage([ad])
ad = p.measureBG()[0]
correct = [
726.18213, 724.36047, 727.34491, 728.49664, 728.08966, 719.83728
]
for rv, cv in zip(ad.hdr['SKYLEVEL'], correct):
assert abs(rv - cv) < 0.1, 'Wrong background level'
assert (ad.phu['SKYLEVEL'] - 727.174) < 0.1
f = open(logfilename, 'r')
for line in f.readlines():
if 'BG band' in line:
assert line.split()[6] == 'BG80', 'Wrong BG band'
ad.phu['REQBG'] = '50-percentile'
ad = p.measureBG()[0]
assert any('WARNING: BG requirement not met' in line
for line in f.readlines()), 'No BG warning'
def test_inverse_transform_gmos(astrofaker, binning):
# Creates GMOS images with stars at predefined points
ad = astrofaker.create('GMOS-N')
ad.init_default_extensions(binning=binning, overscan=False)
for ext in ad:
ext.add(np.random.randn(*ext.shape))
for ystar, xstar in GMOS_STAR_LOCATIONS:
ext.add_star(amplitude=10000, x=xstar / binning, y=ystar / binning)
adg = transform.create_mosaic_transform(ad, geotable)
admos = adg.transform(attributes=None, order=1)
adout = adg.inverse_transform(admos, order=3)
p = GMOSImage([adout])
p.detectSources()
adout = p.streams['main'][0]
xbin, ybin = ad.detector_x_bin(), ad.detector_y_bin()
for ext in adout:
objcat = ext.OBJCAT
objcat.sort(['Y_IMAGE'])
for row, location in zip(objcat, GMOS_STAR_LOCATIONS):
# OBJCAT is 1-indexed
assert abs(row['Y_IMAGE'] - location[0] / ybin - 1) < 0.1
assert abs(row['X_IMAGE'] - location[1] / xbin - 1) < 0.1
def test_measureCC(self, ad):
p = GMOSImage([ad])
ad = p.measureCC()[0]
correct = [28.18, 28.16, 28.14, 28.11, 28.17, 28.12]
for rv, cv in zip(ad.hdr['MEANZP'], correct):
assert abs(rv - cv) < 0.02, 'Wrong zeropoint'
f = open(logfilename)
for line in f.readlines():
if 'CC bands' in line:
assert 'CC50, CC70' in line, 'Wrong CC bands'
for ext in ad:
ext.OBJCAT['MAG_AUTO'] += 0.3
ad = p.measureCC()[0]
correct = [c - 0.3 for c in correct]
for rv, cv in zip(ad.hdr['MEANZP'], correct):
assert abs(rv - cv) < 0.02, 'Wrong zeropoint after edit'
ccwarn = False
for line in f.readlines():
if 'CC bands' in line:
assert 'CC70, CC80' in line, 'Wrong CC bands after edit'
ccwarn |= 'WARNING: CC requirement not met' in line
assert ccwarn, 'No CC warning'
def test_plot_spectra_for_qa(input_ads):
for i, ad in enumerate(input_ads):
# Plot single frame
p = primitives_visualize.Visualize([])
p.plotSpectraForQA(adinputs=[ad])
# Gives some time to page refresh
time.sleep(10)
# Plot Stack
if i >= 1:
print('Reducing stack')
stack_ad = GMOSImage([]).stackFrames(adinputs=input_ads[:i + 1])[0]
p.plotSpectraForQA(adinputs=[stack_ad])
# Gives some time to page refresh
time.sleep(10)
def test_fit_continuum_slit_image(fname, fwhm, change_working_dir):
with change_working_dir():
log_file = 'log_{}.log'.format(fname.replace('.fits', ''))
logutils.config(file_name=log_file)
ad = astrodata.open(astrodata.testing.download_from_archive(fname))
p = GMOSImage([ad])
p.prepare(attach_mdf=True)
p.addDQ()
p.trimOverscan()
p.ADUToElectrons()
p.mosaicDetectors()
tbl = gt.fit_continuum(p.streams['main'][0])[0]
assert isinstance(tbl, Table)
assert len(tbl) == 1
assert abs(tbl['fwhm_arcsec'].data[0] - fwhm) < 0.05
def test_fit_continuum_slit_image(path_to_inputs):
results = {'N20180118S0344': 1.32}
for fname, fwhm in results.items():
ad = astrodata.open(
os.path.join(path_to_inputs, 'gt/slit_images',
'{}.fits'.format(fname)))
p = GMOSImage([ad])
p.prepare(attach_mdf=True)
p.addDQ()
p.trimOverscan()
p.ADUToElectrons()
p.mosaicDetectors()
tbl = gt.fit_continuum(p.streams['main'][0])[0]
assert isinstance(tbl, Table)
assert len(tbl) == 1
assert abs(tbl['fwhm_arcsec'].data[0] - fwhm) < 0.05