def test_calibrate_image_junk_unit_fails(self):
scanset = ScanSet('test.hdf5')
scanset.calculate_images()
with pytest.raises(ValueError) as excinfo:
images = scanset.calculate_images(calibration=self.calfile,
map_unit="junk")
assert "Unit for calibration not recognized" in str(excinfo.value)
def test_ver_images(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
scanset.remove_column('Feed0_RCP-filt')
images = scanset.calculate_images(no_offsets=True, direction=1)
img = images['Feed0_RCP']
def test_calibrate_scanset_pixel(self):
scanset = ScanSet('test.hdf5')
images_standard = scanset.calculate_images(calibration=self.calfile,
map_unit="Jy/pixel")
images = scanset.calculate_images(calibration=self.calfile,
map_unit="Jy/pixel",
calibrate_scans=True)
assert np.allclose(images['Feed0_RCP'], images_standard['Feed0_RCP'],
rtol=0.05)
def test_calibrate_image_beam(self):
scanset = ScanSet('test.hdf5')
scanset.calculate_images()
images = scanset.calculate_images(calibration=self.calfile,
map_unit="Jy/beam")
assert np.allclose(np.max(images['Feed0_RCP']), self.simulated_flux,
atol=0.1)
def test_interactive_quit(self):
scanset = ScanSet('test.hdf5')
imgsel = scanset.interactive_display('Feed0_RCP', test=True)
fake_event = type('event', (), {})()
fake_event.key = 'q'
fake_event.xdata, fake_event.ydata = (130, 30)
retval = imgsel.on_key(fake_event)
assert retval == (130, 30, 'q')
def test_barycenter_times(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
scanset.barycenter_times()
assert 'barytime' in scanset.colnames
assert np.all(np.abs(scanset['barytime'] -
scanset['time']) < 9 * 60 / 86400)
def test_global_fit_image(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
# It works with no parameters, before calculating images,
# with no_offsets
scanset.fit_full_images(no_offsets=True)
# It works after calculating images
images = scanset.calculate_images()
nx, ny = images['Feed0_RCP'].shape
excluded = [[nx // 2, ny // 2, nx // 4]]
scanset.fit_full_images(excluded=excluded, chans='Feed0_RCP')
os.path.exists("out_iter_Feed0_RCP_002.txt")
scanset.fit_full_images(excluded=excluded, chans='Feed0_LCP')
os.path.exists("out_iter_Feed0_LCP_000.txt")
if not HAS_MPL:
with pytest.raises(ImportError) as excinfo:
display_intermediate(scanset, chan="Feed0_RCP",
excluded=excluded,
parfile="out_iter_Feed0_RCP_002.txt")
assert "display_intermediate: matplotlib" in str(excinfo.value)
else:
display_intermediate(scanset, chan="Feed0_RCP",
excluded=excluded,
parfile="out_iter_Feed0_RCP_002.txt")
os.path.exists("out_iter_Feed0_LCP_002.png")
def test_find_scan_through_invalid_pixel(self):
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
ysize, xsize = images['Feed0_RCP'].shape
_, _, _, _, _, _, _, coord = \
scanset.find_scans_through_pixel(xsize//2, -2, test=True)
assert coord == {}
_, _, _, _, _, _, _, coord = \
scanset.find_scans_through_pixel(xsize//2, ysize + 2, test=True)
assert coord == {}
def test_global_fit_image_using_ds9_region(self):
scanset = ScanSet('test.hdf5')
# It works after calculating images
images = scanset.calculate_images()
nx, ny = images['Feed0_RCP'].shape
regstr = 'image;circle({},{},{})'.format(nx // 2, ny // 2, nx // 4)
with open('region.reg', 'w') as fobj:
print(regstr, file=fobj)
main_imager('test.hdf5 -g --exclude region.reg'.split())
os.unlink('region.reg')
def test_imager_global_fit_valid(self):
'''Test image production.'''
# Get information on images
scanset = ScanSet('test.hdf5')
scanset.fit_full_images(no_offsets=True)
# It works after calculating images
images = scanset.calculate_images()
nx, ny = images['Feed0_RCP'].shape
excluded = [[nx//2, ny//2, nx//4]]
main_imager('test.hdf5 -g '
'-e {} {} {}'.format(*(excluded[0])).split(' '))
def test_apply_user_filt(self):
'''Test apply user filts.'''
def user_fun(scanset):
return scanset['barytime'] - np.floor(scanset['barytime'])
scanset = ScanSet('test.hdf5')
scanset.barycenter_times()
phase_in_sec = scanset.apply_user_filter(user_fun, 'Phase_in_sec')
assert np.min(phase_in_sec) >= 0
assert np.max(phase_in_sec) <= 1
assert np.all(phase_in_sec == scanset['Phase_in_sec'])
def test_rough_image_nooffsets_nofilt(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
scanset.remove_column('Feed0_RCP-filt')
images = scanset.calculate_images(no_offsets=True)
img = images['Feed0_RCP']
if HAS_MPL:
fig = plt.figure('img')
plt.imshow(img, origin='lower')
plt.colorbar()
plt.savefig('img_nooff_nofilt.png')
plt.close(fig)
def test_destripe(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
scanset.destripe_images(calibration=self.calfile,
map_unit="Jy/pixel", npix_tol=10)
images = scanset.images
img = images['Feed0_RCP']
center = img.shape[0] // 2, img.shape[1] // 2
shortest_side = np.min(img.shape)
X, Y = np.meshgrid(np.arange(img.shape[1]), np.arange(img.shape[0]))
good = (X-center[1])**2 + (Y-center[0])**2 <= (shortest_side//4)**2
assert np.isclose(np.sum(images['Feed0_RCP'][good]),
self.simulated_flux, rtol=0.1)
def test_rough_image(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
img = images['Feed0_RCP']
if HAS_MPL:
fig = plt.figure('img')
plt.imshow(img, origin='lower')
plt.colorbar()
plt.savefig('img.png')
plt.close(fig)
def test_calibrate_image_pixel(self):
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images(calibration=self.calfile,
map_unit="Jy/pixel")
img = images['Feed0_RCP']
center = img.shape[0] // 2, img.shape[1] // 2
shortest_side = np.min(img.shape)
X, Y = np.meshgrid(np.arange(img.shape[1]), np.arange(img.shape[0]))
good = (X-center[1])**2 + (Y-center[0])**2 <= (shortest_side//4)**2
rtol = 0.1 if HAS_STATSM else 0.15
assert np.isclose(np.sum(images['Feed0_RCP'][good]),
self.simulated_flux, rtol=rtol)
def test_image_stdev(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
img = images['Feed0_RCP-Sdev']
if HAS_MPL:
fig = plt.figure('log(img-Sdev)')
plt.imshow(np.log10(img), origin='lower')
plt.colorbar()
plt.ioff()
plt.savefig('img_sdev.png')
plt.close(fig)
def test_rough_image_altaz(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images(altaz=True)
img = images['Feed0_RCP']
if HAS_MPL:
fig = plt.figure('img_altaz')
plt.imshow(img, origin='lower')
plt.colorbar()
plt.savefig('img_altaz.png')
scanset.save_ds9_images(save_sdev=True, altaz=True)
plt.close(fig)
def test_find_scan_through_pixel0(self):
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
ysize, xsize = images['Feed0_RCP'].shape
_, _, _, _, _, _, _, coord = \
scanset.find_scans_through_pixel(xsize//2, ysize-1, test=True)
dec_scan = os.path.join(self.obsdir_dec,
self.dec_scans[self.n_dec_scans // 2])
assert dec_scan in coord
assert coord[dec_scan] == 'dec'
ra_scan = os.path.join(self.obsdir_ra,
self.ra_scans[self.n_ra_scans - 1])
assert ra_scan in coord
assert coord[ra_scan] == 'ra'
def test_meta_saved_and_loaded_correctly(self):
scanset = ScanSet('test.hdf5')
for k in scanset.meta.keys():
assert np.all(scanset.meta[k] == self.scanset.meta[k])
assert sorted(scanset.meta.keys()) == sorted(self.scanset.meta.keys())
assert scanset.scan_list == self.scanset.scan_list
assert sorted(scanset.meta['calibrator_directories']) == \
sorted(list(set(scanset.meta['calibrator_directories'])))
assert sorted(scanset.meta['list_of_directories']) == \
sorted(list(set(scanset.meta['list_of_directories'])))
def test_interactive_scans_all_calibrated_channels(self, capsys):
scanset = ScanSet('test.hdf5')
scanset.calibrate_images(calibration=self.calfile)
images = scanset.images
ysize, xsize = images['Feed0_RCP'].shape
imgsel = scanset.interactive_display(test=True)
fake_event = type('event', (), {})()
fake_event.key = 'a'
fake_event.xdata, fake_event.ydata = (xsize//2, ysize-1)
imgsel.on_key(fake_event)
fake_event.key = 'h'
fake_event.xdata, fake_event.ydata = (xsize//2, ysize-1)
out, err = capsys.readouterr()
assert "a open a window to filter all" in out
imgsel.on_key(fake_event)
fake_event.key = 'v'
fake_event.xdata, fake_event.ydata = (xsize//2, ysize-1)
imgsel.on_key(fake_event)
def test_update_scan_zap(self):
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
ysize, xsize = images['Feed0_RCP'].shape
ra_xs, ra_ys, dec_xs, dec_ys, scan_ids, ra_masks, dec_masks, coord = \
scanset.find_scans_through_pixel(xsize//2, 0, test=True)
sname = sorted(list(dec_xs.keys()))[0]
s = Scan(sname)
info = {sname: copy.copy(self.stdinfo)}
info[sname]['zap'].xs = [np.float(s['dec'][0]), np.float(s['dec'][10])]
sid = scan_ids[sname]
mask = scanset['Scan_id'] == sid
before = scanset['Feed0_RCP-filt'][mask]
scanset.update_scan(sname, scan_ids[sname], coord[sname],
info[sname]['zap'],
info[sname]['fitpars'], info[sname]['FLAG'],
test=True)
after = scanset['Feed0_RCP-filt'][mask]
assert np.all(before[:10] != after[:10])
s = Scan(sname)
assert np.all(np.array(after, dtype=bool) ==
np.array(s['Feed0_RCP-filt'], dtype=bool))
def test_image_scrunch(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
scanset.calculate_images()
images = scanset.scrunch_images()
img = images['TOTAL']
if HAS_MPL:
fig = plt.figure('img - scrunched')
plt.imshow(img, origin='lower')
plt.colorbar()
img = images['TOTAL-Sdev']
plt.savefig('img_scrunch.png')
plt.close(fig)
fig = plt.figure('img - scrunched - sdev')
plt.imshow(img, origin='lower')
plt.colorbar()
plt.ioff()
plt.savefig('img_scrunch_sdev.png')
plt.close(fig)
def test_find_scan_through_pixel_bad_scan(self, logger, caplog):
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
ysize, xsize = images['Feed0_RCP'].shape
x, y = xsize // 2, 0
good_entries = np.logical_and(
np.abs(scanset['x'][:, 0] - x) < 1,
np.abs(scanset['y'][:, 0] - y) < 1)
sids = list(set(scanset['Scan_id'][good_entries]))
scanset.scan_list[sids[0]] = 'skd'
scanset.find_scans_through_pixel(x, y, test=True)
assert "Errors while opening scan skd" in caplog.text
def test_calibrate_image_sr(self):
scanset = ScanSet('test.hdf5')
scanset.calculate_images()
images = scanset.calculate_images(calibration=self.calfile,
map_unit="Jy/sr")
images_pix = scanset.calculate_images(calibration=self.calfile,
map_unit="Jy/pixel")
pixel_area = scanset.meta['pixel_size'] ** 2
assert np.allclose(images['Feed0_RCP'],
images_pix['Feed0_RCP'] / pixel_area.to(u.sr).value,
rtol=0.05)
def test_find_scan_through_pixel1(self):
scanset = ScanSet('test.hdf5')
for i in scanset.chan_columns:
scanset.remove_column(i + '-filt')
images = scanset.calculate_images()
ysize, xsize = images['Feed0_RCP'].shape
_, _, _, _, _, _, _, coord = \
scanset.find_scans_through_pixel(xsize//2, 0, test=True)
dec_scan = os.path.join(self.obsdir_dec,
self.dec_scans[self.n_dec_scans // 2])
assert dec_scan in coord
assert coord[dec_scan] == 'dec'
ra_scan = os.path.join(self.obsdir_ra, 'Ra0.fits')
assert ra_scan in coord
assert coord[ra_scan] == 'ra'
def test_update_scan_invalid(self):
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
ysize, xsize = images['Feed0_RCP'].shape
ra_xs, ra_ys, dec_xs, dec_ys, scan_ids, ra_masks, dec_masks, coord = \
scanset.find_scans_through_pixel(xsize//2, 0, test=True)
sname = 'xkd'
coord['xkd'] = None
scan_ids['xkd'] = None
info = {sname: copy.copy(self.stdinfo)}
info[sname]['FLAG'] = True
with pytest.warns(UserWarning):
scanset.update_scan(sname, scan_ids[sname], coord[sname],
info[sname]['zap'],
info[sname]['fitpars'], info[sname]['FLAG'],
test=True)
def test_update_scan_fit(self):
scanset = ScanSet('test.hdf5')
images = scanset.calculate_images()
ysize, xsize = images['Feed0_RCP'].shape
ra_xs, ra_ys, dec_xs, dec_ys, scan_ids, ra_masks, dec_masks, coord = \
scanset.find_scans_through_pixel(xsize//2, 0, test=True)
sname = list(scan_ids.keys())[0]
info = {sname: copy.copy(self.stdinfo)}
info[sname]['fitpars'] = np.array([0.1, 0.3])
sid = scan_ids[sname]
mask = scanset['Scan_id'] == sid
before = scanset['Feed0_RCP'][mask]
scanset.update_scan(sname, scan_ids[sname], coord[sname],
info[sname]['zap'],
info[sname]['fitpars'], info[sname]['FLAG'],
test=True)
after = scanset['Feed0_RCP'][mask]
assert np.all(before != after)
s = Scan(sname)
assert np.all(after == s['Feed0_RCP'])
def test_import_scanset():
from srttools.imager import ScanSet
s = ScanSet()
assert isinstance(s, Table)
def test_ds9_image_not_save_sdev(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
scanset.save_ds9_images(save_sdev=False)
def test_ds9_image_destripe(self):
'''Test image production.'''
scanset = ScanSet('test.hdf5')
scanset.save_ds9_images(destripe=True)