def solve_image(vis: Visibility,
model: Image,
components=None,
predict=predict_2d,
invert=invert_2d,
**kwargs) -> (Visibility, Image, Image):
"""Solve for image using deconvolve_cube and specified predict, invert
This is the same as a majorcycle/minorcycle algorithm. The components are removed prior to deconvolution.
See also arguments for predict, invert, deconvolve_cube functions.2d
:param vis:
:param model: Model image
:param predict: Predict function e.g. predict_2d, predict_wstack
:param invert: Invert function e.g. invert_2d, invert_wstack
:return: Visibility, model
"""
nmajor = get_parameter(kwargs, 'nmajor', 5)
log.info("solve_image: Performing %d major cycles" % nmajor)
# The model is added to each major cycle and then the visibilities are
# calculated from the full model
vispred = copy_visibility(vis)
visres = copy_visibility(vis)
vispred = predict(vispred, model, **kwargs)
if components is not None:
vispred = predict_skycomponent_visibility(vispred, components)
visres.data['vis'] = vis.data['vis'] - vispred.data['vis']
dirty, sumwt = invert(visres, model, **kwargs)
psf, sumwt = invert(visres, model, dopsf=True, **kwargs)
thresh = get_parameter(kwargs, "threshold", 0.0)
for i in range(nmajor):
log.info("solve_image: Start of major cycle %d" % i)
cc, res = deconvolve_cube(dirty, psf, **kwargs)
res = None
model.data += cc.data
vispred = predict(vispred, model, **kwargs)
visres.data['vis'] = vis.data['vis'] - vispred.data['vis']
dirty, sumwt = invert(visres, model, **kwargs)
if numpy.abs(dirty.data).max() < 1.1 * thresh:
log.info("Reached stopping threshold %.6f Jy" % thresh)
break
log.info("solve_image: End of major cycle")
log.info("solve_image: End of major cycles")
return visres, model, dirty
def _predict_base(self, context='2d', extra='', fluxthreshold=1.0):
self.modelvis = copy_visibility(self.componentvis, zero=True)
self.modelvis.data['vis'] *= 0.0
self.modelvis = predict_function(self.modelvis,
self.model,
context=context,
**self.params)
self.residualvis = copy_visibility(self.componentvis, zero=True)
self.residualvis.data['uvw'][:, 2] = 0.0
self.residualvis.data[
'vis'] = self.modelvis.data['vis'] - self.componentvis.data['vis']
self._checkdirty(self.residualvis,
'predict_%s%s' % (context, extra),
fluxthreshold=fluxthreshold)
def test_calibrate_function(self):
self.actualSetup('stokesI', 'stokesI', f=[100.0])
# Prepare the corrupted visibility data
gt = create_gaintable_from_blockvisibility(self.vis)
log.info("Created gain table: %s" % (gaintable_summary(gt)))
gt = simulate_gaintable(gt,
phase_error=10.0,
amplitude_error=0.1,
timeslice='auto')
bgt = simulate_gaintable(gt,
phase_error=0.1,
amplitude_error=0.01,
timeslice=1e5)
original = copy_visibility(self.vis)
self.vis = apply_gaintable(self.vis, bgt, timeslice=1e5)
self.vis = apply_gaintable(self.vis, gt, timeslice='auto')
# Now get the control dictionary and calibrate
controls = create_calibration_controls()
controls['T']['first_selfcal'] = 0
controls['B']['first_selfcal'] = 0
calibrated_vis, gaintables = calibrate_function(self.vis,
original,
context='TB',
controls=controls)
residual = numpy.max(gaintables['T'].residual)
assert residual < 3e-2, "Max T residual = %s" % (residual)
residual = numpy.max(gaintables['B'].residual)
assert residual < 6e-5, "Max B residual = %s" % (residual)
def predict_ignore_none(vis, model):
if vis is not None:
predicted = copy_visibility(vis)
predicted = predict_context(predicted, model, context=context, **kwargs)
return predicted
else:
return None
def predict_and_sum(vis, model, **kwargs):
if vis is not None:
predicted = copy_visibility(vis)
predicted = predict(predicted, model, **kwargs)
return predicted
else:
return None
def sum_visibility(vis: Visibility, direction: SkyCoord) -> numpy.array:
""" Direct Fourier summation in a given direction
:param vis: Visibility to be summed
:param direction: Direction of summation
:return: flux[nch,npol], weight[nch,pol]
"""
# TODO: Convert to Visibility or remove?
svis = copy_visibility(vis)
l, m, n = skycoord_to_lmn(direction, svis.phasecentre)
phasor = numpy.conjugate(simulate_point(svis.uvw, l, m))
# Need to put correct mapping here
_, frequency = get_frequency_map(svis, None)
frequency = list(frequency)
nchan = max(frequency) + 1
npol = svis.polarisation_frame.npol
flux = numpy.zeros([nchan, npol])
weight = numpy.zeros([nchan, npol])
coords = svis.vis, svis.weight, phasor, list(frequency)
for v, wt, p, ic in zip(*coords):
for pol in range(npol):
flux[ic, pol] += numpy.real(wt[pol] * v[pol] * p)
weight[ic, pol] += wt[pol]
flux[weight > 0.0] = flux[weight > 0.0] / weight[weight > 0.0]
flux[weight <= 0.0] = 0.0
return flux, weight
def peel_skycomponent_blockvisibility(vis: BlockVisibility, sc: Union[Skycomponent, List[Skycomponent]], remove=True)\
-> (BlockVisibility, List[GainTable]):
""" Peel a collection of components.
Sequentially solve the gain towards each Skycomponent and optionally remove the corrupted visibility from the
observed visibility.
:param params:
:param vis: Visibility to be processed
:param sc: Skycomponent or list of Skycomponents
:return: subtracted visibility and list of GainTables
"""
assert isinstance(
vis, BlockVisibility), "vis is not a BlockVisibility: %r" % vis
if not isinstance(sc, collections.Iterable):
sc = [sc]
gtlist = []
for comp in sc:
assert comp.shape == 'Point', "Cannot handle shape %s" % comp.shape
modelvis = copy_visibility(vis, zero=True)
modelvis = predict_skycomponent_blockvisibility(modelvis, comp)
gt = solve_gaintable(vis, modelvis, phase_only=False)
modelvis = apply_gaintable(modelvis, gt)
if remove:
vis.data['vis'] -= modelvis.data['vis']
gtlist.append(gt)
return vis, gtlist
def core_solve(self,
spf,
dpf,
phase_error=0.1,
amplitude_error=0.0,
leakage=0.0,
phase_only=True,
niter=200,
crosspol=False,
residual_tol=1e-6,
f=[100.0, 50.0, -10.0, 40.0]):
self.actualSetup(spf, dpf, f=f)
gt = create_gaintable_from_blockvisibility(self.vis)
log.info("Created gain table: %s" % (gaintable_summary(gt)))
gt = simulate_gaintable(gt,
phase_error=phase_error,
amplitude_error=amplitude_error,
leakage=leakage)
original = copy_visibility(self.vis)
vis = apply_gaintable(self.vis, gt)
gtsol = solve_gaintable(self.vis,
original,
phase_only=phase_only,
niter=niter,
crosspol=crosspol,
tol=1e-6)
vis = apply_gaintable(vis, gtsol, inverse=True)
residual = numpy.max(gtsol.residual)
assert residual < residual_tol, "%s %s Max residual = %s" % (spf, dpf,
residual)
log.debug(qa_gaintable(gt))
assert numpy.max(numpy.abs(gtsol.gain - 1.0)) > 0.1
def safe_predict_list(vis_list, model, predict=predict_2d, **kwargs):
""" Predicts a list of visibilities to obtain a list of visibilities
Can be used in bag.map()
:param vis_list:
:param model:
:param predict:
:param kwargs:
:return: List of visibilities
"""
assert isinstance(vis_list, collections.Iterable
), "Visibility list is not Iterable: %s" % str(vis_list)
assert isinstance(model, Image), "Model is not an image: %s" % model
result = list()
for v in vis_list:
if v is not None:
predicted = copy_visibility(v)
result.append(predict(predicted, model, **kwargs))
assert len(
result
) > 0, "Visibility after concatenation is empty, input list is %s" % str(
vis_list)
return result
def calibrate_visibility(vt: Visibility,
model: Image = None,
components=None,
predict=predict_2d,
**kwargs) -> Visibility:
""" calibrate Visibility with respect to model and optionally components
:param vt: Visibility
:param model: Model image
:param components: Sky components
:return: Calibrated visibility
"""
assert model is not None or components is not None, "calibration requires a model or skycomponents"
vtpred = copy_visibility(vt, zero=True)
if model is not None:
vtpred = predict(vtpred, model, **kwargs)
if components is not None:
vtpred = predict_skycomponent_visibility(vtpred, components)
else:
vtpred = predict_skycomponent_visibility(vtpred, components)
bvt = decoalesce_visibility(vt)
bvtpred = decoalesce_visibility(vtpred)
gt = solve_gaintable(bvt, bvtpred, **kwargs)
bvt = apply_gaintable(bvt,
gt,
inverse=get_parameter(kwargs, "inverse", False))
return convert_blockvisibility_to_visibility(bvt)
def calibrate_blockvisibility(bvt: BlockVisibility,
model: Image = None,
components=None,
predict=predict_2d,
**kwargs) -> BlockVisibility:
""" calibrate BlockVisibility with respect to model and optionally components
:param bvt: BlockVisibility
:param model: Model image
:param components: Sky components
:return: Calibrated BlockVisibility
"""
assert model is not None or components is not None, "calibration requires a model or skycomponents"
if model is not None:
vtpred = convert_blockvisibility_to_visibility(bvt)
vtpred = predict(vtpred, model, **kwargs)
bvtpred = decoalesce_visibility(vtpred)
if components is not None:
bvtpred = predict_skycomponent_blockvisibility(bvtpred, components)
else:
bvtpred = copy_visibility(bvt, zero=True)
bvtpred = predict_skycomponent_blockvisibility(bvtpred, components)
gt = solve_gaintable(bvt, bvtpred, **kwargs)
return apply_gaintable(bvt, gt, **kwargs)
def subtract_visibility(vis, model_vis, inplace=False):
""" Subtract model_vis from vis, returning new visibility
:param vis:
:param model_vis:
:return:
"""
if isinstance(vis, Visibility):
assert isinstance(model_vis, Visibility), model_vis
elif isinstance(vis, BlockVisibility):
assert isinstance(model_vis, BlockVisibility), model_vis
else:
raise RuntimeError("Types of vis and model visibility are invalid")
assert vis.vis.shape == model_vis.vis.shape, "Observed %s and model visibilities %s have different shapes"\
% (vis.vis.shape, model_vis.vis.shape)
if inplace:
vis.data['vis'] = vis.data['vis'] - model_vis.data['vis']
return vis
else:
residual_vis = copy_visibility(vis)
residual_vis.data[
'vis'] = residual_vis.data['vis'] - model_vis.data['vis']
return residual_vis
def zerovis(vis):
if vis is not None:
zerovis = copy_visibility(vis)
zerovis.data['vis'][...] = 0.0
return zerovis
else:
return None
def predict_facets_and_accumulate(vis, model, **kwargs):
if vis is not None:
predicted = copy_visibility(vis)
predicted = predict(predicted, model, **kwargs)
return predicted
else:
return None
def subtract_vis(vis, model_vis):
if vis is not None and model_vis is not None:
assert vis.vis.shape == model_vis.vis.shape
subvis = copy_visibility(vis)
subvis.data['vis'][...] -= model_vis.data['vis'][...]
return subvis
else:
return None
def predict_facets_and_accumulate(vis, model, **kwargs):
if vis is not None:
predicted = copy_visibility(vis)
predicted = predict(predicted, model, **kwargs)
vis.data['vis'] += predicted.data['vis']
return vis
else:
return None
def test_copy_visibility(self):
self.vis = create_visibility(self.lowcore, self.times, self.frequency,
channel_bandwidth=self.channel_bandwidth, phasecentre=self.phasecentre, weight=1.0,
polarisation_frame=PolarisationFrame("stokesIQUV"))
vis = copy_visibility(self.vis)
self.vis.data['vis'] = 0.0
vis.data['vis'] = 1.0
assert (vis.data['vis'][0, 0].real == 1.0)
assert (self.vis.data['vis'][0, 0].real == 0.0)
def test_apply_gaintable_null(self):
for spf, dpf in[('stokesI', 'stokesI'), ('stokesIQUV', 'linear'), ('stokesIQUV', 'circular')]:
self.actualSetup(spf, dpf)
gt = create_gaintable_from_blockvisibility(self.vis, timeslice='auto')
gt.data['gain']*=0.0
original = copy_visibility(self.vis)
vis = apply_gaintable(self.vis, gt, inverse=True, timeslice='auto')
error = numpy.max(numpy.abs(vis.vis[:,0,1,...] - original.vis[:,0,1,...]))
assert error < 1e-12, "Error = %s" % (error)
def test_create_gaintable_from_visibility(self):
for spf, dpf in [('stokesIQUV', 'linear'), ('stokesIQUV', 'circular')]:
self.actualSetup(spf, dpf)
gt = create_gaintable_from_blockvisibility(self.vis)
log.info("Created gain table: %s" % (gaintable_summary(gt)))
gt = simulate_gaintable(gt, phase_error=0.1)
original = copy_visibility(self.vis)
vis = apply_gaintable(self.vis, gt)
assert numpy.max(numpy.abs(vis.vis - original.vis)) > 0.0
def test_apply_gaintable_only(self):
for spf, dpf in[('stokesI', 'stokesI'), ('stokesIQUV', 'linear'), ('stokesIQUV', 'circular')]:
self.actualSetup(spf, dpf)
gt = create_gaintable_from_blockvisibility(self.vis, timeslice='auto')
log.info("Created gain table: %s" % (gaintable_summary(gt)))
gt = simulate_gaintable(gt, phase_error=0.1, amplitude_error=0.01, timeslice='auto')
original = copy_visibility(self.vis)
vis = apply_gaintable(self.vis, gt, timeslice='auto')
error = numpy.max(numpy.abs(vis.vis - original.vis))
assert error > 10.0, "Error = %f" % (error)
def test_apply_gaintable_and_inverse_both(self):
for spf, dpf in [('stokesIQUV', 'linear'), ('stokesIQUV', 'circular')]:
self.actualSetup(spf, dpf)
gt = create_gaintable_from_blockvisibility(self.vis)
log.info("Created gain table: %s" % (gaintable_summary(gt)))
gt = simulate_gaintable(gt, phase_error=0.1, amplitude_error=0.1)
original = copy_visibility(self.vis)
vis = apply_gaintable(self.vis, gt)
vis = apply_gaintable(self.vis, gt, inverse=True)
error = numpy.max(numpy.abs(vis.vis - original.vis))
assert error < 1e-12, "Error = %s" % (error)
def test_solve_gaintable_scalar(self):
self.actualSetup('stokesI', 'stokesI', f=[100.0])
gt = create_gaintable_from_blockvisibility(self.vis)
log.info("Created gain table: %s" % (gaintable_summary(gt)))
gt = simulate_gaintable(gt, phase_error=10.0, amplitude_error=0.0)
original = copy_visibility(self.vis)
self.vis = apply_gaintable(self.vis, gt)
gtsol = solve_gaintable(self.vis, original, phase_only=True, niter=200)
residual = numpy.max(gtsol.residual)
assert residual < 3e-8, "Max residual = %s" % (residual)
assert numpy.max(numpy.abs(gtsol.gain - 1.0)) > 0.1
def test_create_gaintable_from_visibility_interval(self):
for timeslice in [10.0, 'auto', 1e5]:
for spf, dpf in[('stokesIQUV', 'linear')]:
self.actualSetup(spf, dpf)
gt = create_gaintable_from_blockvisibility(self.vis, timeslice=timeslice)
log.info("Created gain table: %s" % (gaintable_summary(gt)))
gt = simulate_gaintable(gt, phase_error=1.0, timeslice=timeslice)
original = copy_visibility(self.vis)
vis = apply_gaintable(self.vis, gt, timeslice=timeslice)
assert numpy.max(numpy.abs(original.vis)) > 0.0
assert numpy.max(numpy.abs(vis.vis)) > 0.0
assert numpy.max(numpy.abs(vis.vis - original.vis)) > 0.0
def test_predict_2d(self):
# Test if the 2D prediction works
#
# Set w=0 so that the two-dimensional transform should agree exactly with the component transform.
# Good check on the grid correction in the image->vis direction
# Set all w to zero
self.actualSetUp()
self.componentvis.data['uvw'][:, 2] = 0.0
# Predict the visibility using direct evaluation
self.componentvis.data['vis'][...] = 0.0
self.componentvis = predict_skycomponent_visibility(
self.componentvis, self.components)
self.modelvis = copy_visibility(self.componentvis, zero=True)
self.modelvis.data['uvw'][:, 2] = 0.0
self.modelvis = predict_2d(self.modelvis, self.model, **self.params)
self.residualvis = copy_visibility(self.componentvis, zero=True)
self.residualvis.data['uvw'][:, 2] = 0.0
self.residualvis.data[
'vis'] = self.modelvis.data['vis'] - self.componentvis.data['vis']
self._checkdirty(self.residualvis, 'predict_2d')
def sum_predict_results(results):
""" Sum a set of predict results
:param results: List of visibilities to be summed
:return: summed visibility
"""
sum_results = None
for result in results:
if result is not None:
if sum_results is None:
sum_results = copy_visibility(result)
else:
sum_results.data['vis'] += result.data['vis']
return sum_results
def residual_image(vis: Visibility, model: Image, invert_residual=invert_2d, predict_residual=predict_2d,
**kwargs) -> Image:
"""Calculate residual image and visibility
:param vis: Visibility to be inverted
:param im: image template (not changed)
:param invert: invert to be used (default invert_2d)
:param predict: predict to be used (default predict_2d)
:return: residual visibility, residual image, sum of weights
"""
visres = copy_visibility(vis, zero=True)
visres = predict_residual(visres, model, **kwargs)
visres.data['vis'] = vis.data['vis'] - visres.data['vis']
dirty, sumwt = invert_residual(visres, model, dopsf=False, **kwargs)
return visres, dirty, sumwt
def subtract_visibility(vis, model_vis, inplace=False):
""" Subtract model_vis from vis, returning new visibility
:param vis:
:param model_vis:
:return:
"""
assert isinstance(vis, Visibility) or isinstance(vis, BlockVisibility), vis
if inplace:
vis.data['vis'] = vis.data['vis'] - model_vis.data['vis']
return vis
else:
residual_vis = copy_visibility(vis)
residual_vis.data['vis'] = residual_vis.data['vis'] - model_vis.data['vis']
return residual_vis
def spectral_line_imaging(vis: Visibility,
model: Image,
continuum_model: Image = None,
continuum_components=None,
predict=predict_2d,
invert=invert_2d,
deconvolve_spectral=False,
**kwargs) -> (Image, Image, Image):
"""Spectral line imaging from calibrated (DIE) data
A continuum model can be subtracted, and deconvolution is optional.
If deconvolve_spectral is True then the solve_image is used to deconvolve.
If deconvolve_spectral is False then the residual image after continuum subtraction is calculated
:param vis: Visibility
:param continuum_model: model continuum image to be subtracted
:param continuum_components: mode components to be subtracted
:param spectral_model: model spectral image
:param predict: Predict fumction e.g. predict_2d
:param invert: Invert function e.g. invert_wprojection
:return: Residual visibility, spectral model image, spectral residual image
"""
vis_no_continuum = copy_visibility(vis)
if continuum_model is not None:
vis_no_continuum = predict(vis_no_continuum, continuum_model, **kwargs)
if continuum_components is not None:
vis_no_continuum = predict_skycomponent_visibility(
vis_no_continuum, continuum_components)
vis_no_continuum.data[
'vis'] = vis.data['vis'] - vis_no_continuum.data['vis']
if deconvolve_spectral:
log.info(
"spectral_line_imaging: Deconvolving continuum subtracted visibility"
)
vis_no_continuum, spectral_model, spectral_residual = solve_image(
vis_no_continuum, model, **kwargs)
else:
log.info(
"spectral_line_imaging: Making dirty image from continuum subtracted visibility"
)
spectral_model, spectral_residual = \
invert(vis_no_continuum, model, **kwargs)
return vis_no_continuum, spectral_model, spectral_residual
def decoalesce_visibility(vis: Visibility, overwrite=False) -> BlockVisibility:
""" Decoalesce the visibilities to the original values (opposite of coalesce_visibility)
This relies upon the block vis and the index being part of the vis.
'uv': Needs the original image used in coalesce_visibility
'tb': Needs the index generated by coalesce_visibility
:param vis: (Coalesced visibility)
:return: BlockVisibility with vis and weight columns overwritten
"""
# 去合并，元数据不变，vis按照cindex填入
assert type(vis) is Visibility, "vis is not a Visibility: %r" % vis
assert type(vis.blockvis) is BlockVisibility, "No blockvisibility in vis"
assert vis.cindex is not None, "No reverse index in Visibility"
if overwrite:
log.debug(
'decoalesce_visibility: Created new Visibility for decoalesced data'
)
decomp_vis = copy_visibility(vis.blockvis)
else:
log.debug(
'decoalesce_visibility: Filled decoalesced data into template')
decomp_vis = vis.blockvis
vshape = decomp_vis.data['vis'].shape
npol = vshape[-1]
dvis = numpy.zeros(vshape, dtype='complex')
assert numpy.max(vis.cindex) < dvis.size
# print(vis.cindex)
# TODO 感觉此处逻辑有误
# for i in range(dvis.size // npol):
# decomp_vis.data['vis'].flat[i:i + npol] = vis.data['vis'][vis.cindex[i]]
# 修改后
for i in range(dvis.size // npol):
decomp_vis.data['vis'].flat[i * npol:i * npol +
npol] = vis.data['vis'][vis.cindex[i]]
log.debug('decoalesce_visibility: Coalesced %s, decoalesced %s' %
(vis_summary(vis), vis_summary(decomp_vis)))
return decomp_vis
def predict_wstack_single(vis, model, remove=True, **kwargs) -> Visibility:
""" Predict using a single w slices.
This processes a single w plane, rotating out the w beam for the average w
:param vis: Visibility to be predicted
:param model: model image
:return: resulting visibility (in place works)
"""
if not isinstance(vis, Visibility):
log.debug("predict_wstack_single: Coalescing")
avis = coalesce_visibility(vis, **kwargs)
else:
avis = vis
log.debug("predict_wstack_single: predicting using single w slice")
avis.data['vis'] *= 0.0
# We might want to do wprojection so we remove the average w
w_average = numpy.average(avis.w)
avis.data['uvw'][..., 2] -= w_average
tempvis = copy_visibility(avis)
# Calculate w beam and apply to the model. The imaginary part is not needed
workimage = copy_image(model)
w_beam = create_w_term_like(model, w_average, vis.phasecentre)
# Do the real part
workimage.data = w_beam.data.real * model.data
avis = predict_2d_base(avis, workimage, **kwargs)
# and now the imaginary part
workimage.data = w_beam.data.imag * model.data
tempvis = predict_2d_base(tempvis, workimage, **kwargs)
avis.data['vis'] -= 1j * tempvis.data['vis']
if not remove:
avis.data['uvw'][..., 2] += w_average
if isinstance(vis, BlockVisibility) and isinstance(avis, Visibility):
log.debug("imaging.predict decoalescing post prediction")
return decoalesce_visibility(avis)
else:
return avis