def _invert_base(self,
context,
extra='',
fluxthreshold=1.0,
positionthreshold=1.0,
check_components=True,
facets=1,
vis_slices=1,
gcfcf=None,
**kwargs):
centre = self.freqwin // 2
dirty = invert_list_arlexecute_workflow(self.vis_list,
self.model_list,
context=context,
dopsf=False,
normalize=True,
facets=facets,
vis_slices=vis_slices,
gcfcf=gcfcf,
**kwargs)
dirty = arlexecute.compute(dirty, sync=True)[centre]
export_image_to_fits(
dirty[0], '%s/test_imaging_invert_%s%s_%s_dirty.fits' %
(self.dir, context, extra, arlexecute.type()))
assert numpy.max(numpy.abs(dirty[0].data)), "Image is empty"
if check_components:
self._checkcomponents(dirty[0], fluxthreshold, positionthreshold)
def test_deconvolve_spectral(self):
self.actualSetUp(add_errors=True)
dirty_imagelist = invert_list_arlexecute_workflow(self.vis_list,
self.model_imagelist,
context='2d',
dopsf=False,
normalize=True)
psf_imagelist = invert_list_arlexecute_workflow(self.vis_list,
self.model_imagelist,
context='2d',
dopsf=True,
normalize=True)
dirty_imagelist = arlexecute.persist(dirty_imagelist)
psf_imagelist = arlexecute.persist(psf_imagelist)
deconvolved = deconvolve_list_arlexecute_workflow(
dirty_imagelist,
psf_imagelist,
self.model_imagelist,
niter=1000,
fractional_threshold=0.1,
scales=[0, 3, 10],
threshold=0.1,
gain=0.7)
deconvolved = arlexecute.persist(deconvolved)
deconvolved = arlexecute.compute(deconvolved, sync=True)
export_image_to_fits(
deconvolved[0], '%s/test_imaging_%s_deconvolve_spectral.fits' %
(self.dir, arlexecute.type()))
def test_restored_list_facet(self):
self.actualSetUp(zerow=True)
centre = self.freqwin // 2
psf_image_list = invert_list_arlexecute_workflow(self.vis_list, self.model_list, context='2d', dopsf=True)
residual_image_list = residual_list_arlexecute_workflow(self.vis_list, self.model_list, context='2d')
restored_4facets_image_list = restore_list_arlexecute_workflow(self.model_list, psf_image_list,
residual_image_list,
restore_facets=4, psfwidth=1.0)
restored_4facets_image_list = arlexecute.compute(restored_4facets_image_list, sync=True)
restored_1facets_image_list = restore_list_arlexecute_workflow(self.model_list, psf_image_list,
residual_image_list,
restore_facets=1, psfwidth=1.0)
restored_1facets_image_list = arlexecute.compute(restored_1facets_image_list, sync=True)
if self.persist: export_image_to_fits(restored_4facets_image_list[0],
'%s/test_imaging_invert_%s_restored_4facets.fits' %
(self.dir, arlexecute.type()))
qa = qa_image(restored_4facets_image_list[centre])
assert numpy.abs(qa.data['max'] - 99.43438263927833) < 1e-7, str(qa)
assert numpy.abs(qa.data['min'] + 0.6328915148563354) < 1e-7, str(qa)
restored_4facets_image_list[centre].data -= restored_1facets_image_list[centre].data
if self.persist: export_image_to_fits(restored_4facets_image_list[centre],
'%s/test_imaging_invert_%s_restored_4facets_error.fits' %
(self.dir, arlexecute.type()))
qa = qa_image(restored_4facets_image_list[centre])
assert numpy.abs(qa.data['max']) < 1e-10, str(qa)
def test_restored_list_noresidual(self):
self.actualSetUp(zerow=True)
centre = self.freqwin // 2
psf_image_list = invert_list_arlexecute_workflow(self.vis_list, self.model_list, context='2d', dopsf=True)
restored_image_list = restore_list_arlexecute_workflow(self.model_list, psf_image_list, psfwidth=1.0)
restored_image_list = arlexecute.compute(restored_image_list, sync=True)
if self.persist: export_image_to_fits(restored_image_list[centre],
'%s/test_imaging_invert_%s_restored_noresidual.fits' %
(self.dir, arlexecute.type()))
qa = qa_image(restored_image_list[centre])
assert numpy.abs(qa.data['max'] - 100.0) < 1e-7, str(qa)
assert numpy.abs(qa.data['min']) < 1e-7, str(qa)
def test_map_create_pb(self):
self.createVis(config='LOWBD2', rmax=1000.0)
model = create_image_from_visibility(self.vis,
cellsize=0.001,
override_cellsize=False)
beam = image_arlexecute_map_workflow(model,
create_pb,
facets=4,
pointingcentre=self.phasecentre,
telescope='MID')
beam = arlexecute.compute(beam, sync=True)
assert numpy.max(beam.data) > 0.0
export_image_to_fits(
beam, "%s/test_image_arlexecute_scatter_gather.fits" % (self.dir))
def test_deconvolve_and_restore_cube_mmclean_facets(self):
self.actualSetUp(add_errors=True)
dirty_imagelist = invert_list_arlexecute_workflow(self.vis_list,
self.model_imagelist,
context='2d',
dopsf=False,
normalize=True)
psf_imagelist = invert_list_arlexecute_workflow(self.vis_list,
self.model_imagelist,
context='2d',
dopsf=True,
normalize=True)
dirty_imagelist = arlexecute.persist(dirty_imagelist)
psf_imagelist = arlexecute.persist(psf_imagelist)
dec_imagelist = deconvolve_list_arlexecute_workflow(
dirty_imagelist,
psf_imagelist,
self.model_imagelist,
niter=1000,
fractional_threshold=0.1,
scales=[0, 3, 10],
algorithm='mmclean',
nmoment=3,
nchan=self.freqwin,
threshold=0.01,
gain=0.7,
deconvolve_facets=8,
deconvolve_overlap=8,
deconvolve_taper='tukey')
dec_imagelist = arlexecute.persist(dec_imagelist)
residual_imagelist = residual_list_arlexecute_workflow(
self.vis_list, model_imagelist=dec_imagelist, context='2d')
residual_imagelist = arlexecute.persist(residual_imagelist)
restored_list = restore_list_arlexecute_workflow(
model_imagelist=dec_imagelist,
psf_imagelist=psf_imagelist,
residual_imagelist=residual_imagelist,
empty=self.model_imagelist)
restored = arlexecute.compute(restored_list, sync=True)[0]
if self.persist:
export_image_to_fits(
restored, '%s/test_imaging_%s_overlap_mmclean_restored.fits' %
(self.dir, arlexecute.type()))
def _predict_base(self, context='2d', extra='', fluxthreshold=1.0, facets=1, vis_slices=1, **kwargs):
vis_list = zero_list_arlexecute_workflow(self.vis_list)
vis_list = predict_list_arlexecute_workflow(vis_list, self.model_list, context=context,
vis_slices=vis_slices, facets=facets, **kwargs)
vis_list = subtract_list_arlexecute_workflow(self.vis_list, vis_list)[0]
vis_list = arlexecute.compute(vis_list, sync=True)
dirty = invert_list_arlexecute_workflow([vis_list], [self.model_list[0]], context='2d', dopsf=False,
normalize=True)[0]
dirty = arlexecute.compute(dirty, sync=True)
assert numpy.max(numpy.abs(dirty[0].data)), "Residual image is empty"
export_image_to_fits(dirty[0], '%s/test_imaging_predict_%s%s_%s_dirty.fits' %
(self.dir, context, extra, arlexecute.type()))
maxabs = numpy.max(numpy.abs(dirty[0].data))
assert maxabs < fluxthreshold, "Error %.3f greater than fluxthreshold %.3f " % (maxabs, fluxthreshold)
def test_deconvolve_and_restore_cube_mmclean(self):
self.actualSetUp(add_errors=True)
dirty_imagelist = invert_list_arlexecute_workflow(self.vis_list, self.model_imagelist, context='2d',
dopsf=False, normalize=True)
psf_imagelist = invert_list_arlexecute_workflow(self.vis_list, self.model_imagelist, context='2d',
dopsf=True, normalize=True)
dec_imagelist, _ = deconvolve_list_arlexecute_workflow(dirty_imagelist, psf_imagelist, self.model_imagelist, niter=1000,
fractional_threshold=0.01, scales=[0, 3, 10],
algorithm='mmclean', nmoments=3, nchan=self.freqwin,
threshold=0.1, gain=0.7)
residual_imagelist = residual_list_arlexecute_workflow(self.vis_list, model_imagelist=dec_imagelist,
context='wstack', vis_slices=51)
restored = restore_list_arlexecute_workflow(model_imagelist=dec_imagelist, psf_imagelist=psf_imagelist,
residual_imagelist=residual_imagelist,
empty=self.model_imagelist)[0]
restored = arlexecute.compute(restored, sync=True)
export_image_to_fits(restored, '%s/test_imaging_%s_mmclean_restored.fits' % (self.dir, arlexecute.type()))
def progress(res, tl_list, gt_list, it, context='MPCCAL'):
print('Iteration %d' % it)
print(
qa_image(res,
context='%s residual image: iteration %d' %
(context, it)))
export_image_to_fits(
res,
arl_path(
"test_results/low-sims-mpc-%s-residual_iteration%d_rmax%.1f.fits"
% (context, it, rmax)))
show_image(res,
title='%s residual image: iteration %d' % (context, it))
plt.show(block=block_plots)
combined_model = calculate_skymodel_equivalent_image(tl_list)
print(
qa_image(combined_model,
context='Combined model: iteration %d' % it))
export_image_to_fits(
combined_model,
arl_path(
"test_results/low-sims-mpc-%s-model_iteration%d_rmax%.1f.fits"
% (context, it, rmax)))
plt.clf()
for i in range(len(tl_list)):
plt.plot(
numpy.angle(tl_list[i].gaintable.gain[:, :, 0, 0,
0]).flatten(),
numpy.angle(gt_list[i]['T'].gain[:, :, 0, 0, 0]).flatten(),
'.')
plt.xlabel('Current phase')
plt.ylabel('Update to phase')
plt.title("%s iteration%d: Change in phase" % (context, it))
plt.savefig(
arl_path(
"test_results/low-sims-mpc-%s-skymodel-phase-change_iteration%d.jpg"
% (context, it)))
plt.show(block=block_plots)
return tl_list
def test_continuum_imaging_pipeline_serialclean(self):
self.actualSetUp(add_errors=False, zerow=True)
continuum_imaging_list = \
continuum_imaging_list_arlexecute_workflow(self.vis_list,
model_imagelist=self.model_imagelist,
context='2d',
algorithm='mmclean', facets=1,
scales=[0, 3, 10],
niter=1000, fractional_threshold=0.1, threshold=0.1,
nmoment=3,
nmajor=5, gain=0.1,
deconvolve_facets=4, deconvolve_overlap=32,
deconvolve_taper='tukey', psf_support=64,
use_serial_clean=True)
clean, residual, restored = arlexecute.compute(continuum_imaging_list,
sync=True)
centre = len(clean) // 2
if self.persist:
export_image_to_fits(
clean[centre],
'%s/test_pipelines_continuum_imaging_pipeline_arlexecute_clean.fits'
% self.dir)
export_image_to_fits(
residual[centre][0],
'%s/test_pipelines_continuum_imaging_pipeline_arlexecute_residual.fits'
% self.dir)
export_image_to_fits(
restored[centre],
'%s/test_pipelines_continuum_imaging_pipeline_arlexecute_restored.fits'
% self.dir)
qa = qa_image(restored[centre])
assert numpy.abs(qa.data['max'] - 100.13762476849081) < 1.0, str(qa)
assert numpy.abs(qa.data['min'] + 0.03627273884170454) < 1.0, str(qa)
def test_continuum_imaging_pipeline(self):
self.actualSetUp(add_errors=False, block=True)
continuum_imaging_list = \
continuum_imaging_list_arlexecute_workflow(self.vis_list, model_imagelist=self.model_imagelist, context='2d',
algorithm='mmclean', facets=1,
scales=[0, 3, 10],
niter=1000, fractional_threshold=0.1,
nmoments=2, nchan=self.freqwin,
threshold=2.0, nmajor=5, gain=0.1,
deconvolve_facets=8, deconvolve_overlap=16,
deconvolve_taper='tukey')
clean, residual, restored = arlexecute.compute(continuum_imaging_list,
sync=True)
export_image_to_fits(
clean[0],
'%s/test_pipelines_continuum_imaging_pipeline_clean.fits' %
self.dir)
export_image_to_fits(
residual[0][0],
'%s/test_pipelines_continuum_imaging_pipeline_residual.fits' %
self.dir)
export_image_to_fits(
restored[0],
'%s/test_pipelines_continuum_imaging_pipeline_restored.fits' %
self.dir)
qa = qa_image(restored[0])
assert numpy.abs(qa.data['max'] - 116.9) < 1.0, str(qa)
assert numpy.abs(qa.data['min'] + 0.118) < 1.0, str(qa)
def test_ical_pipeline_global(self):
self.actualSetUp(add_errors=True)
controls = create_calibration_controls()
controls['T']['first_selfcal'] = 1
controls['T']['timeslice'] = 'auto'
ical_list = \
ical_list_arlexecute_workflow(self.vis_list,
model_imagelist=self.model_imagelist,
context='2d',
algorithm='mmclean', facets=1,
scales=[0, 3, 10],
niter=1000, fractional_threshold=0.1, threshold=0.1,
nmoment=3,
nmajor=1, gain=0.1,
deconvolve_facets=4, deconvolve_overlap=32,
deconvolve_taper='tukey', psf_support=64,
restore_facets=4, psfwidth=1.0,
calibration_context='T', controls=controls, do_selfcal=True,
global_solution=True)
clean, residual, restored, gt_list = arlexecute.compute(ical_list, sync=True)
centre = len(clean) // 2
if self.persist:
export_image_to_fits(clean[centre], '%s/test_pipelines_ical_global_pipeline_arlexecute_clean.fits' % self.dir)
export_image_to_fits(residual[centre][0], '%s/test_pipelines_ical_global_pipeline_arlexecute_residual.fits' % self.dir)
export_image_to_fits(restored[centre], '%s/test_pipelines_ical_global_pipeline_arlexecute_restored.fits' % self.dir)
export_gaintable_to_hdf5(gt_list[0]['T'],
'%s/test_pipelines_ical_global_pipeline_arlexecute_gaintable.hdf5' %
self.dir)
qa = qa_image(restored[centre])
assert numpy.abs(qa.data['max'] - 98.92656340122159) < 1.0, str(qa)
assert numpy.abs(qa.data['min'] + 0.7024492707920869) < 1.0, str(qa)
def test_ical_pipeline(self):
amp_errors = {'T': 0.0, 'G': 0.00, 'B': 0.0}
phase_errors = {'T': 0.1, 'G': 0.0, 'B': 0.0}
self.actualSetUp(add_errors=True,
block=True,
amp_errors=amp_errors,
phase_errors=phase_errors)
controls = create_calibration_controls()
controls['T']['first_selfcal'] = 1
controls['G']['first_selfcal'] = 3
controls['B']['first_selfcal'] = 4
controls['T']['timescale'] = 'auto'
controls['G']['timescale'] = 'auto'
controls['B']['timescale'] = 1e5
ical_list = \
ical_list_arlexecute_workflow(self.vis_list, model_imagelist=self.model_imagelist, context='2d',
calibration_context='T', controls=controls, do_selfcal=True,
global_solution=False,
algorithm='mmclean',
facets=1,
scales=[0, 3, 10],
niter=1000, fractional_threshold=0.1,
nmoments=2, nchan=self.freqwin,
threshold=2.0, nmajor=5, gain=0.1,
deconvolve_facets=8, deconvolve_overlap=16, deconvolve_taper='tukey')
clean, residual, restored = arlexecute.compute(ical_list, sync=True)
centre = len(clean) // 2
export_image_to_fits(
clean[centre],
'%s/test_pipelines_ical_pipeline_clean.fits' % self.dir)
export_image_to_fits(
residual[centre][0],
'%s/test_pipelines_ical_pipeline_residual.fits' % self.dir)
export_image_to_fits(
restored[centre],
'%s/test_pipelines_ical_pipeline_restored.fits' % self.dir)
qa = qa_image(restored[centre])
assert numpy.abs(qa.data['max'] - 100.13739440876233) < 1.0, str(qa)
assert numpy.abs(qa.data['min'] + 0.03644435471804354) < 1.0, str(qa)
def test_ical_pipeline(self):
self.actualSetUp(add_errors=True)
controls = create_calibration_controls()
controls['T']['first_selfcal'] = 1
controls['T']['timescale'] = 'auto'
ical_list = \
ical_list_arlexecute_workflow(self.vis_list,
model_imagelist=self.model_imagelist,
context='2d',
algorithm='mmclean', facets=1,
scales=[0, 3, 10],
niter=1000, fractional_threshold=0.1, threshold=0.1,
nmoment=3,
nmajor=1, gain=0.1,
deconvolve_facets=4, deconvolve_overlap=32,
deconvolve_taper='tukey', psf_support=64,
calibration_context='T', controls=controls, do_selfcal=True,
global_solution=False)
clean, residual, restored = arlexecute.compute(ical_list, sync=True)
centre = len(clean) // 2
if self.persist:
export_image_to_fits(
clean[centre],
'%s/test_pipelines_ical_pipeline_arlexecute_clean.fits' %
self.dir)
export_image_to_fits(
residual[centre][0],
'%s/test_pipelines_ical_pipeline_arlexecute_residual.fits' %
self.dir)
export_image_to_fits(
restored[centre],
'%s/test_pipelines_ical_pipeline_arlexecute_restored.fits' %
self.dir)
qa = qa_image(restored[centre])
assert numpy.abs(qa.data['max'] - 99.32729396999524) < 1.0, str(qa)
assert numpy.abs(qa.data['min'] + 0.6501547522800477) < 1.0, str(qa)
def trial_case(results, seed=180555, context='wstack', nworkers=8, threads_per_worker=1, memory=8,
processes=True, order='frequency', nfreqwin=7, ntimes=3, rmax=750.0,
facets=1, wprojection_planes=1, use_dask=True, use_serial_imaging=False,
flux_limit=0.3, nmajor=5, dft_threshold=1.0):
""" Single trial for performance-timings
Simulates visibilities from GLEAM including phase errors
Makes dirty image and PSF
Runs ICAL pipeline
The results are in a dictionary:
'context': input - a string describing concisely the purpose of the test
'time overall', overall execution time (s)
'time create gleam', time to create GLEAM prediction graph
'time predict', time to execute GLEAM prediction graph
'time corrupt', time to corrupt data_models
'time invert', time to make dirty image
'time psf invert', time to make PSF
'time ICAL graph', time to create ICAL graph
'time ICAL', time to execute ICAL graph
'context', type of imaging e.g. 'wstack'
'nworkers', number of workers to create
'threads_per_worker',
'nnodes', Number of nodes,
'processes', 'order', Ordering of data_models
'nfreqwin', Number of frequency windows in simulation
'ntimes', Number of hour angles in simulation
'rmax', Maximum radius of stations used in simulation (m)
'facets', Number of facets in deconvolution and imaging
'wprojection_planes', Number of wprojection planes
'vis_slices', Number of visibility slices (per Visibbility)
'npixel', Number of pixels in image
'cellsize', Cellsize in radians
'seed', Random number seed
'dirty_max', Maximum in dirty image
'dirty_min', Minimum in dirty image
'psf_max',
'psf_min',
'restored_max',
'restored_min',
'deconvolved_max',
'deconvolved_min',
'residual_max',
'residual_min',
'git_info', GIT hash (not definitive since local mods are possible)
:param results: Initial state
:param seed: Random number seed (used in gain simulations)
:param context: imaging context
:param context: Type of context: '2d'|'timeslice'|'wstack'
:param nworkers: Number of dask workers to use
:param threads_per_worker: Number of threads per worker
:param processes: Use processes instead of threads 'processes'|'threads'
:param order: See simulate_list_list_arlexecute_workflow_workflowkflow
:param nfreqwin: See simulate_list_list_arlexecute_workflow_workflowkflow
:param ntimes: See simulate_list_list_arlexecute_workflow_workflowkflow
:param rmax: See simulate_list_list_arlexecute_workflow_workflowkflow
:param facets: Number of facets to use
:param wprojection_planes: Number of wprojection planes to use
:param use_dask: Use dask or immediate evaluation
:return: results dictionary
"""
if use_dask:
client = get_dask_Client(threads_per_worker=threads_per_worker,
processes = threads_per_worker == 1,
memory_limit=memory * 1024 * 1024 * 1024,
n_workers=nworkers)
arlexecute.set_client(client)
nodes = findNodes(arlexecute.client)
print("Defined %d workers on %d nodes" % (nworkers, len(nodes)))
print("Workers are: %s" % str(nodes))
else:
arlexecute.set_client(use_dask=use_dask)
results['nnodes'] = 1
def init_logging():
logging.basicConfig(filename='pipelines-arlexecute-timings.log',
filemode='a',
format='%(asctime)s,%(msecs)d %(name)s %(levelname)s %(message)s',
datefmt='%H:%M:%S',
level=logging.INFO)
init_logging()
log = logging.getLogger()
# Initialise logging on the workers. This appears to only work using the process scheduler.
arlexecute.run(init_logging)
def lprint(s):
log.info(s)
print(s)
lprint("Starting pipelines-arlexecute-timings")
numpy.random.seed(seed)
results['seed'] = seed
start_all = time.time()
results['context'] = context
results['hostname'] = socket.gethostname()
results['git_hash'] = git_hash()
results['epoch'] = time.strftime("%Y-%m-%d %H:%M:%S")
lprint("Context is %s" % context)
results['nworkers'] = nworkers
results['threads_per_worker'] = threads_per_worker
results['processes'] = processes
results['memory'] = memory
results['order'] = order
results['nfreqwin'] = nfreqwin
results['ntimes'] = ntimes
results['rmax'] = rmax
results['facets'] = facets
results['wprojection_planes'] = wprojection_planes
results['dft threshold'] = dft_threshold
results['use_dask'] = use_dask
lprint("At start, configuration is:")
lprint(results)
# Parameters determining scale
frequency = numpy.linspace(1.0e8, 1.2e8, nfreqwin)
centre = nfreqwin // 2
if nfreqwin > 1:
channel_bandwidth = numpy.array(nfreqwin * [frequency[1] - frequency[0]])
else:
channel_bandwidth = numpy.array([1e6])
times = numpy.linspace(-numpy.pi / 4.0, numpy.pi / 4.0, ntimes)
phasecentre = SkyCoord(ra=+30.0 * u.deg, dec=-60.0 * u.deg, frame='icrs', equinox='J2000')
bvis_list = simulate_list_arlexecute_workflow('LOWBD2',
frequency=frequency,
channel_bandwidth=channel_bandwidth,
times=times,
phasecentre=phasecentre,
order=order,
format='blockvis',
rmax=rmax)
lprint("****** Visibility creation ******")
bvis_list = arlexecute.compute(bvis_list, sync=True)
vis_list = [arlexecute.execute(convert_blockvisibility_to_visibility(bv)) for bv in bvis_list]
vis_list = arlexecute.compute(vis_list, sync=True)
# Find the best imaging parameters but don't bring the vis_list back here
def get_wf(v):
return advise_wide_field(v, guard_band_image=6.0,
delA=0.1,
facets=facets,
wprojection_planes=wprojection_planes,
oversampling_synthesised_beam=4.0)
advice = arlexecute.compute(arlexecute.execute(get_wf)(vis_list[-1]), sync=True)
# Deconvolution via sub-images requires 2^n
npixel = advice['npixels2']
results['npixel'] = npixel
cellsize = advice['cellsize']
results['cellsize'] = cellsize
lprint("Image will have %d by %d pixels, cellsize = %.6f rad" % (npixel, npixel, cellsize))
# Create an empty model image
model_list = [arlexecute.execute(create_image_from_visibility)
(vis_list[f],
npixel=npixel, cellsize=cellsize,
frequency=[frequency[f]],
channel_bandwidth=[channel_bandwidth[f]],
polarisation_frame=PolarisationFrame("stokesI"))
for f, freq in enumerate(frequency)]
model_list = arlexecute.compute(model_list, sync=True)
model_list = arlexecute.scatter(model_list)
start = time.time()
vis_list = weight_list_arlexecute_workflow(vis_list, model_list)
vis_list = taper_list_arlexecute_workflow(vis_list, 0.003 * 750.0 / rmax)
print("****** Starting weighting and tapering ******")
vis_list = arlexecute.compute(vis_list, sync=True)
end = time.time()
results['time weight'] = end - start
print("Weighting took %.3f seconds" % (end - start))
vis_list = arlexecute.scatter(vis_list)
# Now set up the imaging parameters
gcfcf_list = [None for i in range(nfreqwin)]
if context == 'timeslice':
vis_slices = ntimes
lprint("Using timeslice with %d slices" % vis_slices)
elif context == '2d':
vis_slices = 1
elif context == "wprojection":
wstep = advice['wstep']
nw = advice['wprojection_planes']
vis_slices = 1
support = advice['nwpixels']
results['wprojection_planes'] = nw
lprint("Using wprojection with %d planes with wstep %.1f wavelengths" % (nw, wstep))
start = time.time()
lprint("****** Starting W projection kernel creation ******")
gcfcf_list = [arlexecute.execute(create_awterm_convolutionfunction, nout=1)
(m, nw=nw, wstep=wstep, oversampling=8, support=support, use_aaf=True)
for m in model_list]
gcfcf_list = arlexecute.compute(gcfcf_list, sync=True)
end = time.time()
results['time create wprojection'] = end - start
lprint("Creating W projection kernel took %.3f seconds" % (end - start))
cf_image = convert_convolutionfunction_to_image(gcfcf_list[centre][1])
cf_image.data = numpy.real(cf_image.data)
export_image_to_fits(cf_image, "pipelines-arlexecute-timings-wterm-cf.fits")
gcfcf_list = arlexecute.scatter(gcfcf_list)
else:
context = 'wstack'
vis_slices = advice['vis_slices']
lprint("Using wstack with %d slices" % vis_slices)
results['vis_slices'] = vis_slices
# Make a skymodel from gleam, with bright sources as components and weak sources in an image
lprint("****** Starting GLEAM skymodel creation ******")
start = time.time()
skymodel_list = [arlexecute.execute(create_low_test_skymodel_from_gleam)
(npixel=npixel, cellsize=cellsize, frequency=[frequency[f]],
phasecentre=phasecentre,
polarisation_frame=PolarisationFrame("stokesI"),
flux_limit=flux_limit,
flux_threshold=dft_threshold,
flux_max=5.0) for f, freq in enumerate(frequency)]
skymodel_list = arlexecute.compute(skymodel_list, sync=True)
end = time.time()
lprint("GLEAM skymodel creation took %.3f seconds" % (end - start))
results['time create gleam'] = end - start
lprint("****** Starting GLEAM skymodel prediction ******")
start = time.time()
predicted_vis_list = [predict_skymodel_list_arlexecute_workflow(vis_list[f], [skymodel_list[f]], context=context,
vis_slices=vis_slices, facets=facets,
gcfcf=[gcfcf_list[f]])[0]
for f, freq in enumerate(frequency)]
predicted_vis_list = arlexecute.compute(predicted_vis_list, sync=True)
end = time.time()
lprint("GLEAM skymodel prediction took %.3f seconds" % (end - start))
results['time predict gleam'] = end - start
lprint("****** Starting psf image calculation ******")
start = time.time()
predicted_vis_list = arlexecute.scatter(predicted_vis_list)
psf_list = invert_list_arlexecute_workflow(predicted_vis_list, model_list, vis_slices=vis_slices,
dopsf=True, context=context, facets=facets,
use_serial_invert=use_serial_imaging, gcfcf=gcfcf_list)
psf, sumwt = arlexecute.compute(psf_list, sync=True)[centre]
end = time.time()
results['time psf invert'] = end - start
lprint("PSF invert took %.3f seconds" % (end - start))
lprint("Maximum in psf image is %f, sumwt is %s" % (numpy.max(numpy.abs(psf.data)), str(sumwt)))
qa = qa_image(psf)
results['psf_max'] = qa.data['max']
results['psf_min'] = qa.data['min']
export_image_to_fits(psf, "pipelines-arlexecute-timings-%s-psf.fits" % context)
# Make a smoothed model image for comparison
# smoothed_model_list = restore_list_arlexecute_workflow(gleam_model_list, psf_list)
# smoothed_model_list = arlexecute.compute(smoothed_model_list, sync=True)
# smoothed_cube = image_gather_channels(smoothed_model_list)
# export_image_to_fits(smoothed_cube, "pipelines-arlexecute-timings-cmodel.fits")
# Create an empty model image
model_list = [arlexecute.execute(create_image_from_visibility)
(predicted_vis_list[f],
npixel=npixel, cellsize=cellsize,
frequency=[frequency[f]],
channel_bandwidth=[channel_bandwidth[f]],
polarisation_frame=PolarisationFrame("stokesI"))
for f, freq in enumerate(frequency)]
model_list = arlexecute.compute(model_list, sync=True)
model_list = arlexecute.scatter(model_list)
lprint("****** Starting dirty image calculation ******")
start = time.time()
dirty_list = invert_list_arlexecute_workflow(predicted_vis_list, model_list, vis_slices=vis_slices,
context=context, facets=facets,
use_serial_invert=use_serial_imaging, gcfcf=gcfcf_list)
dirty, sumwt = arlexecute.compute(dirty_list, sync=True)[centre]
end = time.time()
results['time invert'] = end - start
lprint("Dirty image invert took %.3f seconds" % (end - start))
lprint("Maximum in dirty image is %f, sumwt is %s" % (numpy.max(numpy.abs(dirty.data)), str(sumwt)))
qa = qa_image(dirty)
results['dirty_max'] = qa.data['max']
results['dirty_min'] = qa.data['min']
export_image_to_fits(dirty, "pipelines-arlexecute-timings-%s-dirty.fits" % context)
# Corrupt the visibility for the GLEAM model
lprint("****** Visibility corruption ******")
start = time.time()
corrupted_vis_list = corrupt_list_arlexecute_workflow(predicted_vis_list, phase_error=1.0, seed=seed)
corrupted_vis_list = arlexecute.compute(corrupted_vis_list, sync=True)
end = time.time()
results['time corrupt'] = end - start
lprint("Visibility corruption took %.3f seconds" % (end - start))
# Create the ICAL pipeline to run major cycles, starting selfcal at cycle 1. A global solution across all
# frequencies (i.e. Visibilities) is performed.
lprint("****** Starting ICAL ******")
controls = create_calibration_controls()
controls['T']['first_selfcal'] = 1
controls['T']['timescale'] = 'auto'
start = time.time()
ical_list = ical_list_arlexecute_workflow(corrupted_vis_list,
model_imagelist=model_list,
context=context,
vis_slices=vis_slices,
scales=[0, 3, 10],
algorithm='mmclean',
nmoment=3, niter=1000,
fractional_threshold=0.1,
threshold=0.01, nmajor=nmajor,
gain=0.25,
psf_support=64,
deconvolve_facets=8,
deconvolve_overlap=32,
deconvolve_taper='tukey',
timeslice='auto',
global_solution=True,
do_selfcal=True,
calibration_context='T',
controls=controls,
use_serial_predict=use_serial_imaging,
use_serial_invert=use_serial_imaging,
gcfcf=gcfcf_list)
end = time.time()
results['time ICAL graph'] = end - start
lprint("Construction of ICAL graph took %.3f seconds" % (end - start))
# Execute the graph
start = time.time()
result = arlexecute.compute(ical_list, sync=True)
deconvolved, residual, restored, gaintables = result
end = time.time()
results['time ICAL'] = end - start
lprint("ICAL graph execution took %.3f seconds" % (end - start))
qa = qa_image(deconvolved[centre])
results['deconvolved_max'] = qa.data['max']
results['deconvolved_min'] = qa.data['min']
deconvolved_cube = image_gather_channels(deconvolved)
export_image_to_fits(deconvolved_cube, "pipelines-arlexecute-timings-%s-ical_deconvolved.fits" % context)
qa = qa_image(residual[centre][0])
results['residual_max'] = qa.data['max']
results['residual_min'] = qa.data['min']
residual_cube = remove_sumwt(residual)
residual_cube = image_gather_channels(residual_cube)
export_image_to_fits(residual_cube, "pipelines-arlexecute-timings-%s-ical_residual.fits" % context)
qa = qa_image(restored[centre])
results['restored_max'] = qa.data['max']
results['restored_min'] = qa.data['min']
restored_cube = image_gather_channels(restored)
export_image_to_fits(restored_cube, "pipelines-arlexecute-timings-%s-ical_restored.fits" % context)
#
arlexecute.close()
end_all = time.time()
results['time overall'] = end_all - start_all
lprint("At end, results are:")
lprint(results)
return results
log.info('About to run ical_list_serial_workflow')
result = arlexecute.compute(ical_list, sync=True)
deconvolved = result[0][0]
residual = result[1][0]
restored = result[2][0]
arlexecute.close()
show_image(deconvolved,
title='Clean image',
cm='Greys',
vmax=0.1,
vmin=-0.01)
print(qa_image(deconvolved, context='Clean image'))
plt.show()
export_image_to_fits(
deconvolved,
'%s/gleam_ical_arlexecute_deconvolved.fits' % (results_dir))
show_image(restored,
title='Restored clean image',
cm='Greys',
vmax=0.1,
vmin=-0.01)
print(qa_image(restored, context='Restored clean image'))
plt.show()
export_image_to_fits(
restored, '%s/gleam_ical_arlexecute_restored.fits' % (results_dir))
show_image(residual[0],
title='Residual clean image',
cm='Greys',
def actualSetUp(self,
add_errors=False,
nfreqwin=7,
dospectral=True,
dopol=False,
zerow=True):
self.npixel = 512
self.low = create_named_configuration('LOWBD2', rmax=750.0)
self.freqwin = nfreqwin
self.vis_list = list()
self.ntimes = 5
self.times = numpy.linspace(-3.0, +3.0, self.ntimes) * numpy.pi / 12.0
self.frequency = numpy.linspace(0.8e8, 1.2e8, self.freqwin)
if self.freqwin > 1:
self.channelwidth = numpy.array(
self.freqwin * [self.frequency[1] - self.frequency[0]])
else:
self.channelwidth = numpy.array([1e6])
if dopol:
self.vis_pol = PolarisationFrame('linear')
self.image_pol = PolarisationFrame('stokesIQUV')
f = numpy.array([100.0, 20.0, -10.0, 1.0])
else:
self.vis_pol = PolarisationFrame('stokesI')
self.image_pol = PolarisationFrame('stokesI')
f = numpy.array([100.0])
if dospectral:
flux = numpy.array(
[f * numpy.power(freq / 1e8, -0.7) for freq in self.frequency])
else:
flux = numpy.array([f])
self.phasecentre = SkyCoord(ra=+180.0 * u.deg,
dec=-60.0 * u.deg,
frame='icrs',
equinox='J2000')
self.blockvis_list = [
arlexecute.execute(ingest_unittest_visibility,
nout=1)(self.low, [self.frequency[i]],
[self.channelwidth[i]],
self.times,
self.vis_pol,
self.phasecentre,
block=True,
zerow=zerow) for i in range(nfreqwin)
]
self.blockvis_list = arlexecute.compute(self.blockvis_list, sync=True)
self.blockvis_list = arlexecute.scatter(self.blockvis_list)
self.vis_list = [
arlexecute.execute(convert_blockvisibility_to_visibility,
nout=1)(bv) for bv in self.blockvis_list
]
self.vis_list = arlexecute.compute(self.vis_list, sync=True)
self.vis_list = arlexecute.scatter(self.vis_list)
self.model_imagelist = [
arlexecute.execute(create_unittest_model,
nout=1)(self.vis_list[i],
self.image_pol,
npixel=self.npixel,
cellsize=0.0005)
for i in range(nfreqwin)
]
self.model_imagelist = arlexecute.compute(self.model_imagelist,
sync=True)
self.model_imagelist = arlexecute.scatter(self.model_imagelist)
self.components_list = [
arlexecute.execute(create_unittest_components)(
self.model_imagelist[freqwin],
flux[freqwin, :][numpy.newaxis, :])
for freqwin, m in enumerate(self.model_imagelist)
]
self.components_list = arlexecute.compute(self.components_list,
sync=True)
self.components_list = arlexecute.scatter(self.components_list)
self.blockvis_list = [
arlexecute.execute(predict_skycomponent_visibility)(
self.blockvis_list[freqwin], self.components_list[freqwin])
for freqwin, _ in enumerate(self.blockvis_list)
]
self.blockvis_list = arlexecute.compute(self.blockvis_list, sync=True)
self.vis = self.blockvis_list[0]
self.blockvis_list = arlexecute.scatter(self.blockvis_list)
self.model_imagelist = [
arlexecute.execute(insert_skycomponent,
nout=1)(self.model_imagelist[freqwin],
self.components_list[freqwin])
for freqwin in range(nfreqwin)
]
self.model_imagelist = arlexecute.compute(self.model_imagelist,
sync=True)
model = self.model_imagelist[0]
self.cmodel = smooth_image(model)
if self.persist:
export_image_to_fits(
model, '%s/test_pipelines_arlexecute_model.fits' % self.dir)
export_image_to_fits(
self.cmodel,
'%s/test_pipelines_arlexecute_cmodel.fits' % self.dir)
if add_errors:
gt = create_gaintable_from_blockvisibility(self.vis)
gt = simulate_gaintable(gt,
phase_error=0.1,
amplitude_error=0.0,
smooth_channels=1,
leakage=0.0,
seed=180555)
self.blockvis_list = [
arlexecute.execute(apply_gaintable,
nout=1)(self.blockvis_list[i], gt)
for i in range(self.freqwin)
]
self.blockvis_list = arlexecute.compute(self.blockvis_list,
sync=True)
self.blockvis_list = arlexecute.scatter(self.blockvis_list)
self.vis_list = [
arlexecute.execute(convert_blockvisibility_to_visibility)(bv)
for bv in self.blockvis_list
]
self.vis_list = arlexecute.compute(self.vis_list, sync=True)
self.vis_list = arlexecute.scatter(self.vis_list)
self.model_imagelist = [
arlexecute.execute(create_unittest_model,
nout=1)(self.vis_list[i],
self.image_pol,
npixel=self.npixel,
cellsize=0.0005)
for i in range(nfreqwin)
]
self.model_imagelist = arlexecute.compute(self.model_imagelist,
sync=True)
self.model_imagelist = arlexecute.scatter(self.model_imagelist)
d, sumwt = invert_list_serial_workflow([v], [m], context=context, dopsf=False,
vis_slices=vis_slices)[0]
p, sumwt = invert_list_serial_workflow([v], [m], context=context, dopsf=True,
vis_slices=vis_slices)[0]
c, resid = deconvolve_cube(d, p, m, threshold=0.01, fracthresh=0.01, window_shape='quarter',
niter=100, gain=0.1, algorithm='hogbom-complex')
r = restore_cube(c, p, resid, psfwidth=psfwidth)
return r
def do_list(chan_list):
print("In rank %d: %s" % (rank, str(chan_list)))
return [load_invert_and_deconvolve(chan) for chan in chan_list]
if rank == 0:
subchannels = numpy.array_split(range(nchan), size)
else:
subchannels = list()
channels = comm.scatter(subchannels, root=0)
restored_images = do_list(channels)
restored_list = comm.gather(restored_images)
if rank ==0:
print('About to assemble cubes')
restored_list = [item for sublist in restored_list for item in sublist]
restored_cube = image_gather_channels(restored_list)
print("Processing took %.3f s" % (time.time() - start))
print(qa_image(restored_cube, context='CLEAN restored cube'))
export_image_to_fits(restored_cube, '%s/dprepb_arlexecute_%s_clean_restored_cube.fits' % (results_dir, context))
print(qa_image(residual, context='ICAL residual image'))
print('ical finished')
combined_model = calculate_skymodel_equivalent_image(ical_skymodel)
print(qa_image(combined_model, context='ICAL combined model'))
psf_obs = invert_list_arlexecute_workflow([future_vis], [future_model],
context='2d',
dopsf=True)
result = restore_list_arlexecute_workflow([combined_model], psf_obs,
[(residual, 0.0)])
result = arlexecute.compute(result, sync=True)
ical_restored = result[0]
export_image_to_fits(
ical_restored,
arl_path('test_results/low-sims-mpc-ical-restored_%.1frmax.fits' %
rmax))
#######################################################################################################
# Now set up the skymodels for MPCCAL. We find the brightest components in the ICAL image, remove
# sources that are too close to another stronger source, and then use these to set up
# a Voronoi tesselation to define the skymodel masks
ical_components = find_skycomponents(ical_restored,
fwhm=2,
threshold=args.finding_threshold,
npixels=12)
for comp in all_components[:args.ninitial]:
ical_components.append(comp)
# ### Remove weaker of components that are too close (0.02 rad)
def trial_case(results,
seed=180555,
context='wstack',
nworkers=8,
threads_per_worker=1,
memory=8,
processes=True,
order='frequency',
nfreqwin=7,
ntimes=3,
rmax=750.0,
facets=1,
wprojection_planes=1,
use_dask=True,
use_serial_imaging=True,
flux_limit=0.3,
nmajor=5,
dft_threshold=1.0,
use_serial_clean=True,
write_fits=False):
""" Single trial for performance-timings
Simulates visibilities from GLEAM including phase errors
Makes dirty image and PSF
Runs ICAL pipeline
The results are in a dictionary:
'context': input - a string describing concisely the purpose of the test
'time overall', overall execution time (s)
'time predict', time to execute GLEAM prediction graph
'time invert', time to make dirty image
'time invert graph', time to make dirty image graph
'time ICAL graph', time to create ICAL graph
'time ICAL', time to execute ICAL graph
'context', type of imaging e.g. 'wstack'
'nworkers', number of workers to create
'threads_per_worker',
'nnodes', Number of nodes,
'processes', 'order', Ordering of data_models
'nfreqwin', Number of frequency windows in simulation
'ntimes', Number of hour angles in simulation
'rmax', Maximum radius of stations used in simulation (m)
'facets', Number of facets in deconvolution and imaging
'wprojection_planes', Number of wprojection planes
'vis_slices', Number of visibility slices (per Visibbility)
'npixel', Number of pixels in image
'cellsize', Cellsize in radians
'seed', Random number seed
'dirty_max', Maximum in dirty image
'dirty_min', Minimum in dirty image
'restored_max',
'restored_min',
'deconvolved_max',
'deconvolved_min',
'residual_max',
'residual_min',
'git_info', GIT hash (not definitive since local mods are possible)
:param results: Initial state
:param seed: Random number seed (used in gain simulations)
:param context: imaging context
:param context: Type of context: '2d'|'timeslice'|'wstack'
:param nworkers: Number of dask workers to use
:param threads_per_worker: Number of threads per worker
:param processes: Use processes instead of threads 'processes'|'threads'
:param order: See simulate_list_list_arlexecute_workflow_workflowkflow
:param nfreqwin: See simulate_list_list_arlexecute_workflow_workflowkflow
:param ntimes: See simulate_list_list_arlexecute_workflow_workflowkflow
:param rmax: See simulate_list_list_arlexecute_workflow_workflowkflow
:param facets: Number of facets to use
:param wprojection_planes: Number of wprojection planes to use
:param use_dask: Use dask or immediate evaluation
:return: results dictionary
"""
if use_dask:
client = get_dask_Client(threads_per_worker=threads_per_worker,
processes=threads_per_worker == 1,
memory_limit=memory * 1024 * 1024 * 1024,
n_workers=nworkers)
arlexecute.set_client(client)
nodes = findNodes(arlexecute.client)
print("Defined %d workers on %d nodes" % (nworkers, len(nodes)))
print("Workers are: %s" % str(nodes))
else:
arlexecute.set_client(use_dask=use_dask)
results['nnodes'] = 1
def init_logging():
logging.basicConfig(
filename='pipelines_arlexecute_timings.log',
filemode='w',
format='%(asctime)s,%(msecs)d %(name)s %(levelname)s %(message)s',
datefmt='%H:%M:%S',
level=logging.INFO)
init_logging()
log = logging.getLogger()
# Initialise logging on the workers. This appears to only work using the process scheduler.
arlexecute.run(init_logging)
def lprint(*args):
log.info(*args)
print(*args)
lprint("Starting pipelines_arlexecute_timings")
numpy.random.seed(seed)
results['seed'] = seed
start_all = time.time()
results['context'] = context
results['hostname'] = socket.gethostname()
results['git_hash'] = git_hash()
results['epoch'] = time.strftime("%Y-%m-%d %H:%M:%S")
lprint("Context is %s" % context)
results['nworkers'] = nworkers
results['threads_per_worker'] = threads_per_worker
results['processes'] = processes
results['memory'] = memory
results['order'] = order
results['nfreqwin'] = nfreqwin
results['ntimes'] = ntimes
results['rmax'] = rmax
results['facets'] = facets
results['wprojection_planes'] = wprojection_planes
results['dft threshold'] = dft_threshold
results['use_dask'] = use_dask
lprint("At start, configuration is:")
lprint(sort_dict(results))
# Parameters determining scale of simulation.
frequency = numpy.linspace(1.0e8, 1.2e8, nfreqwin)
centre = nfreqwin // 2
if nfreqwin > 1:
channel_bandwidth = numpy.array(nfreqwin *
[frequency[1] - frequency[0]])
else:
channel_bandwidth = numpy.array([1e6])
times = numpy.linspace(-numpy.pi / 4.0, numpy.pi / 4.0, ntimes)
phasecentre = SkyCoord(ra=+0.0 * u.deg,
dec=-40.0 * u.deg,
frame='icrs',
equinox='J2000')
lprint("****** Visibility creation ******")
# Create the empty BlockVisibility's and persist these on the cluster
tmp_bvis_list = simulate_list_arlexecute_workflow(
'LOWBD2',
frequency=frequency,
channel_bandwidth=channel_bandwidth,
times=times,
phasecentre=phasecentre,
order=order,
format='blockvis',
rmax=rmax)
tmp_vis_list = [
arlexecute.execute(convert_blockvisibility_to_visibility)(bv)
for bv in tmp_bvis_list
]
tmp_vis_list = arlexecute.client.compute(tmp_vis_list, sync=True)
vis_list = arlexecute.gather(tmp_vis_list)
import matplotlib.pyplot as plt
plt.clf()
plt.hist(vis_list[0].w, bins=100)
plt.title('Histogram of w samples: rms=%.1f (wavelengths)' %
numpy.std(vis_list[0].w))
plt.xlabel('W (wavelengths)')
plt.show()
plt.clf()
plt.hist(vis_list[0].uvdist, bins=100)
plt.title('Histogram of uvdistance samples')
plt.xlabel('UV Distance (wavelengths)')
plt.show()
arlexecute.client.cancel(tmp_vis_list)
future_vis_list = arlexecute.scatter(vis_list)
# Find the best imaging parameters but don't bring the vis_list back here
print("****** Finding wide field parameters ******")
future_advice = [
arlexecute.execute(advise_wide_field)(
v,
guard_band_image=6.0,
delA=0.1,
facets=facets,
wprojection_planes=wprojection_planes,
oversampling_synthesised_beam=4.0) for v in future_vis_list
]
future_advice = arlexecute.compute(future_advice)
advice = arlexecute.client.gather(future_advice)[-1]
arlexecute.client.cancel(future_advice)
# Deconvolution via sub-images requires 2^n
npixel = advice['npixels2']
results['npixel'] = npixel
cellsize = advice['cellsize']
results['cellsize'] = cellsize
lprint("Image will have %d by %d pixels, cellsize = %.6f rad" %
(npixel, npixel, cellsize))
# Create an empty model image
tmp_model_list = [
arlexecute.execute(create_image)(
npixel=npixel,
cellsize=cellsize,
frequency=[frequency[f]],
channel_bandwidth=[channel_bandwidth[f]],
phasecentre=phasecentre,
polarisation_frame=PolarisationFrame("stokesI"))
for f, freq in enumerate(frequency)
]
model_list = arlexecute.compute(tmp_model_list, sync=True)
future_model_list = arlexecute.scatter(model_list)
lprint("****** Setting up imaging parameters ******")
# Now set up the imaging parameters
template_model = create_image(
npixel=npixel,
cellsize=cellsize,
frequency=[frequency[centre]],
phasecentre=phasecentre,
channel_bandwidth=[channel_bandwidth[centre]],
polarisation_frame=PolarisationFrame("stokesI"))
gcfcf = [create_pswf_convolutionfunction(template_model)]
if context == 'timeslice':
vis_slices = ntimes
lprint("Using timeslice with %d slices" % vis_slices)
elif context == '2d':
vis_slices = 1
elif context == "wprojection":
wstep = advice['wstep']
nw = advice['wprojection_planes']
vis_slices = 1
support = advice['nwpixels']
results['wprojection_planes'] = nw
lprint("****** Starting W projection kernel creation ******")
lprint("Using wprojection with %d planes with wstep %.1f wavelengths" %
(nw, wstep))
lprint("Support of wprojection = %d pixels" % support)
gcfcf = [
create_awterm_convolutionfunction(template_model,
nw=nw,
wstep=wstep,
oversampling=4,
support=support,
use_aaf=True)
]
lprint("Size of W projection gcf, cf = %.2E bytes" % get_size(gcfcf))
else:
context = 'wstack'
vis_slices = advice['vis_slices']
lprint("Using wstack with %d slices" % vis_slices)
gcfcf = arlexecute.scatter(gcfcf, broadcast=True)
results['vis_slices'] = vis_slices
# Make a skymodel from gleam, with bright sources as components and weak sources in an image
lprint("****** Starting GLEAM skymodel creation ******")
future_skymodel_list = [
arlexecute.execute(create_low_test_skymodel_from_gleam)(
npixel=npixel,
cellsize=cellsize,
frequency=[frequency[f]],
phasecentre=phasecentre,
polarisation_frame=PolarisationFrame("stokesI"),
flux_limit=flux_limit,
flux_threshold=dft_threshold,
flux_max=5.0) for f, freq in enumerate(frequency)
]
# We use predict_skymodel so that we can use skycomponents as well as images
lprint("****** Starting GLEAM skymodel prediction ******")
predicted_vis_list = [
predict_skymodel_list_arlexecute_workflow(future_vis_list[f],
[future_skymodel_list[f]],
context=context,
vis_slices=vis_slices,
facets=facets,
gcfcf=gcfcf)[0]
for f, freq in enumerate(frequency)
]
# Corrupt the visibility for the GLEAM model
lprint("****** Visibility corruption ******")
tmp_corrupted_vis_list = corrupt_list_arlexecute_workflow(
predicted_vis_list, phase_error=1.0, seed=seed)
lprint("****** Weighting and tapering ******")
tmp_corrupted_vis_list = weight_list_arlexecute_workflow(
tmp_corrupted_vis_list, future_model_list)
tmp_corrupted_vis_list = taper_list_arlexecute_workflow(
tmp_corrupted_vis_list, 0.003 * 750.0 / rmax)
tmp_corrupted_vis_list = arlexecute.compute(tmp_corrupted_vis_list,
sync=True)
corrupted_vis_list = arlexecute.gather(tmp_corrupted_vis_list)
# arlexecute.client.cancel(predicted_vis_list)
arlexecute.client.cancel(tmp_corrupted_vis_list)
future_corrupted_vis_list = arlexecute.scatter(corrupted_vis_list)
# At this point the only futures are of scatter'ed data so no repeated calculations should be
# incurred.
lprint("****** Starting dirty image calculation ******")
start = time.time()
dirty_list = invert_list_arlexecute_workflow(
future_corrupted_vis_list,
future_model_list,
vis_slices=vis_slices,
context=context,
facets=facets,
use_serial_invert=use_serial_imaging,
gcfcf=gcfcf)
results['size invert graph'] = get_size(dirty_list)
lprint('Size of dirty graph is %.3E bytes' %
(results['size invert graph']))
end = time.time()
results['time invert graph'] = end - start
lprint("Construction of invert graph took %.3f seconds" % (end - start))
start = time.time()
dirty, sumwt = arlexecute.compute(dirty_list, sync=True)[centre]
end = time.time()
results['time invert'] = end - start
lprint("Dirty image invert took %.3f seconds" % (end - start))
lprint("Maximum in dirty image is %f, sumwt is %s" %
(numpy.max(numpy.abs(dirty.data)), str(sumwt)))
qa = qa_image(dirty)
results['dirty_max'] = qa.data['max']
results['dirty_min'] = qa.data['min']
if write_fits:
export_image_to_fits(
dirty, "pipelines_arlexecute_timings-%s-dirty.fits" % context)
lprint("****** Starting prediction ******")
start = time.time()
tmp_vis_list = predict_list_arlexecute_workflow(
future_corrupted_vis_list,
future_model_list,
vis_slices=vis_slices,
context=context,
facets=facets,
use_serial_predict=use_serial_imaging,
gcfcf=gcfcf)
result = arlexecute.compute(tmp_vis_list, sync=True)
# arlexecute.client.cancel(tmp_vis_list)
end = time.time()
results['time predict'] = end - start
lprint("Predict took %.3f seconds" % (end - start))
# Create the ICAL pipeline to run major cycles, starting selfcal at cycle 1. A global solution across all
# frequencies (i.e. Visibilities) is performed.
print("Using subimage clean")
deconvolve_facets = 8
deconvolve_overlap = 16
deconvolve_taper = 'tukey'
lprint("****** Starting ICAL graph creation ******")
controls = create_calibration_controls()
controls['T']['first_selfcal'] = 1
controls['T']['timescale'] = 'auto'
start = time.time()
ical_list = ical_list_arlexecute_workflow(
future_corrupted_vis_list,
model_imagelist=future_model_list,
context=context,
vis_slices=vis_slices,
scales=[0, 3, 10],
algorithm='mmclean',
nmoment=3,
niter=1000,
fractional_threshold=0.1,
threshold=0.01,
nmajor=nmajor,
gain=0.25,
psf_support=64,
deconvolve_facets=deconvolve_facets,
deconvolve_overlap=deconvolve_overlap,
deconvolve_taper=deconvolve_taper,
timeslice='auto',
global_solution=True,
do_selfcal=True,
calibration_context='T',
controls=controls,
use_serial_predict=use_serial_imaging,
use_serial_invert=use_serial_imaging,
use_serial_clean=use_serial_clean,
gcfcf=gcfcf)
results['size ICAL graph'] = get_size(ical_list)
lprint('Size of ICAL graph is %.3E bytes' % results['size ICAL graph'])
end = time.time()
results['time ICAL graph'] = end - start
lprint("Construction of ICAL graph took %.3f seconds" % (end - start))
print("Current objects on cluster: ")
pp.pprint(arlexecute.client.who_has())
#
# Execute the graph
lprint("****** Executing ICAL graph ******")
start = time.time()
deconvolved, residual, restored, gaintables = arlexecute.compute(ical_list,
sync=True)
end = time.time()
results['time ICAL'] = end - start
lprint("ICAL graph execution took %.3f seconds" % (end - start))
qa = qa_image(deconvolved[centre])
results['deconvolved_max'] = qa.data['max']
results['deconvolved_min'] = qa.data['min']
deconvolved_cube = image_gather_channels(deconvolved)
if write_fits:
export_image_to_fits(
deconvolved_cube,
"pipelines_arlexecute_timings-%s-ical_deconvolved.fits" % context)
qa = qa_image(residual[centre][0])
results['residual_max'] = qa.data['max']
results['residual_min'] = qa.data['min']
residual_cube = remove_sumwt(residual)
residual_cube = image_gather_channels(residual_cube)
if write_fits:
export_image_to_fits(
residual_cube,
"pipelines_arlexecute_timings-%s-ical_residual.fits" % context)
qa = qa_image(restored[centre])
results['restored_max'] = qa.data['max']
results['restored_min'] = qa.data['min']
restored_cube = image_gather_channels(restored)
if write_fits:
export_image_to_fits(
restored_cube,
"pipelines_arlexecute_timings-%s-ical_restored.fits" % context)
#
arlexecute.close()
end_all = time.time()
results['time overall'] = end_all - start_all
lprint("At end, results are:")
results = sort_dict(results)
lprint(results)
return results
chunk_final_pole_result = sum_invert_results_arlexecute(
chunk_pole_results)
pole_results.append(chunk_final_pole_result)
# Now construct and run a graph to sum the results from the summations over each chunk
final_result = sum_invert_results_arlexecute(results)
dirty, sumwt = arlexecute.compute(final_result, sync=True)
# We are done! make plots and fits files
type = 'dirty'
if dopsf:
type = 'psf'
if args.write_fits == "True":
imagename = "simulate_rfi_%.1f_%s.fits" % (declination, type)
export_image_to_fits(dirty, imagename)
plt.clf()
show_image(dirty, chan=len(frequency) // channel_average // 2)
plotname = "simulate_rfi_%.1f_%s.png" % (declination, type)
plt.title('Image of the target field')
plt.savefig(plotname)
plt.show(block=False)
final_pole_result = sum_invert_results_arlexecute(pole_results)
pole_dirty, pole_sumwt = arlexecute.compute(final_pole_result, sync=True)
if args.write_fits == "True":
imagename = "simulate_rfi_pole_%s.fits" % (type)
export_image_to_fits(pole_dirty, imagename)
def actualSetUp(self,
add_errors=False,
freqwin=7,
block=False,
dospectral=True,
dopol=False,
zerow=True):
self.npixel = 256
self.low = create_named_configuration('LOWBD2', rmax=750.0)
self.freqwin = freqwin
self.vis_list = list()
self.ntimes = 5
cellsize = 0.001
self.times = numpy.linspace(-3.0, +3.0, self.ntimes) * numpy.pi / 12.0
self.frequency = numpy.linspace(0.8e8, 1.2e8, self.freqwin)
if freqwin > 1:
self.channelwidth = numpy.array(
freqwin * [self.frequency[1] - self.frequency[0]])
else:
self.channelwidth = numpy.array([1e6])
if dopol:
self.vis_pol = PolarisationFrame('linear')
self.image_pol = PolarisationFrame('stokesIQUV')
f = numpy.array([100.0, 20.0, -10.0, 1.0])
else:
self.vis_pol = PolarisationFrame('stokesI')
self.image_pol = PolarisationFrame('stokesI')
f = numpy.array([100.0])
if dospectral:
flux = numpy.array(
[f * numpy.power(freq / 1e8, -0.7) for freq in self.frequency])
else:
flux = numpy.array([f])
self.phasecentre = SkyCoord(ra=+180.0 * u.deg,
dec=-60.0 * u.deg,
frame='icrs',
equinox='J2000')
self.vis_list = [
arlexecute.execute(ingest_unittest_visibility)(
self.low, [self.frequency[freqwin]],
[self.channelwidth[freqwin]],
self.times,
self.vis_pol,
self.phasecentre,
block=block,
zerow=zerow) for freqwin, _ in enumerate(self.frequency)
]
self.model_imagelist = [
arlexecute.execute(create_unittest_model,
nout=freqwin)(self.vis_list[freqwin],
self.image_pol,
cellsize=cellsize,
npixel=self.npixel)
for freqwin, _ in enumerate(self.frequency)
]
self.componentlist = [
arlexecute.execute(create_unittest_components)(
self.model_imagelist[freqwin],
flux[freqwin, :][numpy.newaxis, :])
for freqwin, _ in enumerate(self.frequency)
]
self.model_imagelist = [
arlexecute.execute(insert_skycomponent,
nout=1)(self.model_imagelist[freqwin],
self.componentlist[freqwin])
for freqwin, _ in enumerate(self.frequency)
]
self.vis_list = [
arlexecute.execute(predict_skycomponent_visibility)(
self.vis_list[freqwin], self.componentlist[freqwin])
for freqwin, _ in enumerate(self.frequency)
]
# Calculate the model convolved with a Gaussian.
self.model_imagelist = arlexecute.compute(self.model_imagelist,
sync=True)
model = self.model_imagelist[0]
self.cmodel = smooth_image(model)
export_image_to_fits(
model,
'%s/test_imaging_arlexecute_deconvolved_model.fits' % self.dir)
export_image_to_fits(
self.cmodel,
'%s/test_imaging_arlexecute_deconvolved_cmodel.fits' % self.dir)
if add_errors and block:
self.vis_list = [
arlexecute.execute(insert_unittest_errors)(self.vis_list[i])
for i, _ in enumerate(self.frequency)
]
# self.vis_list = arlexecute.compute(self.vis_list, sync=True)
self.vis_list = arlexecute.persist(self.vis_list)
self.model_imagelist = arlexecute.scatter(self.model_imagelist)
def actualSetUp(self, add_errors=False, freqwin=3, block=False, dospectral=True, dopol=False, zerow=False,
makegcfcf=False):
self.npixel = 256
self.low = create_named_configuration('LOWBD2', rmax=750.0)
self.freqwin = freqwin
self.vis_list = list()
self.ntimes = 5
self.cellsize = 0.0005
# Choose the interval so that the maximum change in w is smallish
integration_time = numpy.pi * (24 / (12 * 60))
self.times = numpy.linspace(-integration_time * (self.ntimes // 2), integration_time * (self.ntimes // 2),
self.ntimes)
if freqwin > 1:
self.frequency = numpy.linspace(0.8e8, 1.2e8, self.freqwin)
self.channelwidth = numpy.array(freqwin * [self.frequency[1] - self.frequency[0]])
else:
self.frequency = numpy.array([1.0e8])
self.channelwidth = numpy.array([4e7])
if dopol:
self.vis_pol = PolarisationFrame('linear')
self.image_pol = PolarisationFrame('stokesIQUV')
f = numpy.array([100.0, 20.0, -10.0, 1.0])
else:
self.vis_pol = PolarisationFrame('stokesI')
self.image_pol = PolarisationFrame('stokesI')
f = numpy.array([100.0])
if dospectral:
flux = numpy.array([f * numpy.power(freq / 1e8, -0.7) for freq in self.frequency])
else:
flux = numpy.array([f])
self.phasecentre = SkyCoord(ra=+180.0 * u.deg, dec=-60.0 * u.deg, frame='icrs', equinox='J2000')
self.vis_list = [arlexecute.execute(ingest_unittest_visibility)(self.low,
[self.frequency[freqwin]],
[self.channelwidth[freqwin]],
self.times,
self.vis_pol,
self.phasecentre, block=block,
zerow=zerow)
for freqwin, _ in enumerate(self.frequency)]
self.model_list = [arlexecute.execute(create_unittest_model, nout=freqwin)(self.vis_list[freqwin],
self.image_pol,
cellsize=self.cellsize,
npixel=self.npixel)
for freqwin, _ in enumerate(self.frequency)]
self.components_list = [arlexecute.execute(create_unittest_components)(self.model_list[freqwin],
flux[freqwin, :][numpy.newaxis, :],
single=True)
for freqwin, _ in enumerate(self.frequency)]
self.components_list = arlexecute.compute(self.components_list, sync=True)
self.model_list = [arlexecute.execute(insert_skycomponent, nout=1)(self.model_list[freqwin],
self.components_list[freqwin])
for freqwin, _ in enumerate(self.frequency)]
self.model_list = arlexecute.compute(self.model_list, sync=True)
self.vis_list = [arlexecute.execute(predict_skycomponent_visibility)(self.vis_list[freqwin],
self.components_list[freqwin])
for freqwin, _ in enumerate(self.frequency)]
centre = self.freqwin // 2
# Calculate the model convolved with a Gaussian.
self.model = self.model_list[centre]
self.cmodel = smooth_image(self.model)
export_image_to_fits(self.model, '%s/test_imaging_model.fits' % self.dir)
export_image_to_fits(self.cmodel, '%s/test_imaging_cmodel.fits' % self.dir)
if add_errors and block:
self.vis_list = [arlexecute.execute(insert_unittest_errors)(self.vis_list[i])
for i, _ in enumerate(self.frequency)]
self.components = self.components_list[centre]
if makegcfcf:
self.gcfcf = [create_awterm_convolutionfunction(self.model, nw=61, wstep=16.0,
oversampling=8,
support=64,
use_aaf=True)]
self.gcfcf_clipped = [(self.gcfcf[0][0], apply_bounding_box_convolutionfunction(self.gcfcf[0][1],
fractional_level=1e-3))]
self.gcfcf_joint = [create_awterm_convolutionfunction(self.model, nw=11, wstep=16.0,
oversampling=8,
support=64,
use_aaf=True)]
else:
self.gcfcf = None
self.gcfcf_clipped = None
self.gcfcf_joint = None
for chunk in chunks:
result = predict_skymodel_list_arlexecute_workflow(future_vis, chunk, context='2d', docal=True)
work_vis = arlexecute.compute(result, sync=True)
for w in work_vis:
all_skymodel_vis.data['vis'] += w.data['vis']
assert numpy.max(numpy.abs(all_skymodel_vis.data['vis'])) > 0.0
all_skymodel_blockvis = convert_visibility_to_blockvisibility(all_skymodel_vis)
#######################################################################################################
# Now proceed to run MPCCAL in ICAL mode i.e. with only one skymodel
def progress(res, tl_list, gt_list, it, context='MPCCAL'):
print('Iteration %d' % it)
print(qa_image(res, context='%s residual image: iteration %d' % (context, it)))
export_image_to_fits(res, arl_path("test_results/low-sims-mpc-%s-residual_iteration%d_rmax%.1f.fits" %
(context, it, rmax)))
show_image(res, title='%s residual image: iteration %d' % (context, it))
plt.show(block=block_plots)
combined_model = calculate_skymodel_equivalent_image(tl_list)
print(qa_image(combined_model, context='Combined model: iteration %d' % it))
export_image_to_fits(combined_model, arl_path("test_results/low-sims-mpc-%s-model_iteration%d_rmax%.1f.fits" %
(context, it, rmax)))
plt.clf()
for i in range(len(tl_list)):
plt.plot(numpy.angle(tl_list[i].gaintable.gain[:, :, 0, 0, 0]).flatten(),
numpy.angle(gt_list[i]['T'].gain[:, :, 0, 0, 0]).flatten(),
'.')
plt.xlabel('Current phase')
plt.ylabel('Update to phase')
def test_mpccal_MPCCAL_manysources_subimages(self):
self.actualSetup()
model = create_empty_image_like(self.theta_list[0].image)
if arlexecute.using_dask:
progress = None
else:
progress = self.progress
future_vis = arlexecute.scatter(self.all_skymodel_noniso_vis)
future_model = arlexecute.scatter(model)
future_theta_list = arlexecute.scatter(self.theta_list)
result = mpccal_skymodel_list_arlexecute_workflow(
future_vis,
future_model,
future_theta_list,
mpccal_progress=progress,
nmajor=5,
context='2d',
algorithm='hogbom',
scales=[0, 3, 10],
fractional_threshold=0.3,
threshold=0.2,
gain=0.1,
niter=1000,
psf_support=256,
deconvolve_facets=8,
deconvolve_overlap=8,
deconvolve_taper='tukey')
(self.theta_list, residual) = arlexecute.compute(result, sync=True)
combined_model = calculate_skymodel_equivalent_image(self.theta_list)
psf_obs = invert_list_arlexecute_workflow(
[self.all_skymodel_noniso_vis], [model], context='2d', dopsf=True)
result = restore_list_arlexecute_workflow([combined_model], psf_obs,
[(residual, 0.0)])
result = arlexecute.compute(result, sync=True)
if self.persist:
export_image_to_fits(
residual,
arl_path('test_results/test_mpccal_no_edge_residual.fits'))
if self.persist:
export_image_to_fits(
result[0],
arl_path('test_results/test_mpccal_no_edge_restored.fits'))
if self.persist:
export_image_to_fits(
combined_model,
arl_path('test_results/test_mpccal_no_edge_deconvolved.fits'))
recovered_mpccal_components = find_skycomponents(result[0],
fwhm=2,
threshold=0.32,
npixels=12)
def max_flux(elem):
return numpy.max(elem.flux)
recovered_mpccal_components = sorted(recovered_mpccal_components,
key=max_flux,
reverse=True)
assert recovered_mpccal_components[
0].name == 'Segment 8', recovered_mpccal_components[0].name
assert numpy.abs(recovered_mpccal_components[0].flux[0, 0] - 7.773751416364857) < 1e-7, \
recovered_mpccal_components[0].flux[0, 0]
newscreen = create_empty_image_like(self.screen)
gaintables = [th.gaintable for th in self.theta_list]
newscreen, weights = grid_gaintable_to_screen(
self.all_skymodel_noniso_blockvis, gaintables, newscreen)
if self.persist:
export_image_to_fits(
newscreen,
arl_path('test_results/test_mpccal_no_edge_screen.fits'))
if self.persist:
export_image_to_fits(
weights,
arl_path(
'test_results/test_mpccal_no_edge_screenweights.fits'))
arlexecute.close()
def actualSetup(self,
vnchan=1,
doiso=True,
ntimes=5,
flux_limit=2.0,
zerow=True,
fixed=False):
nfreqwin = vnchan
rmax = 300.0
npixel = 512
cellsize = 0.001
frequency = numpy.linspace(0.8e8, 1.2e8, nfreqwin)
if nfreqwin > 1:
channel_bandwidth = numpy.array(nfreqwin *
[frequency[1] - frequency[0]])
else:
channel_bandwidth = [0.4e8]
times = numpy.linspace(-numpy.pi / 3.0, numpy.pi / 3.0, ntimes)
phasecentre = SkyCoord(ra=-60.0 * u.deg,
dec=-60.0 * u.deg,
frame='icrs',
equinox='J2000')
lowcore = create_named_configuration('LOWBD2', rmax=rmax)
block_vis = create_blockvisibility(
lowcore,
times,
frequency=frequency,
channel_bandwidth=channel_bandwidth,
weight=1.0,
phasecentre=phasecentre,
polarisation_frame=PolarisationFrame("stokesI"),
zerow=zerow)
block_vis.data['uvw'][..., 2] = 0.0
self.beam = create_image_from_visibility(
block_vis,
npixel=npixel,
frequency=[numpy.average(frequency)],
nchan=nfreqwin,
channel_bandwidth=[numpy.sum(channel_bandwidth)],
cellsize=cellsize,
phasecentre=phasecentre)
self.components = create_low_test_skycomponents_from_gleam(
flux_limit=flux_limit,
phasecentre=phasecentre,
frequency=frequency,
polarisation_frame=PolarisationFrame('stokesI'),
radius=npixel * cellsize)
self.beam = create_low_test_beam(self.beam)
self.components = apply_beam_to_skycomponent(self.components,
self.beam,
flux_limit=flux_limit)
self.vis = copy_visibility(block_vis, zero=True)
gt = create_gaintable_from_blockvisibility(block_vis, timeslice='auto')
for i, sc in enumerate(self.components):
if sc.flux[0, 0] > 10:
sc.flux[...] /= 10.0
component_vis = copy_visibility(block_vis, zero=True)
gt = simulate_gaintable(gt,
amplitude_error=0.0,
phase_error=0.1,
seed=None)
component_vis = predict_skycomponent_visibility(component_vis, sc)
component_vis = apply_gaintable(component_vis, gt)
self.vis.data['vis'][...] += component_vis.data['vis'][...]
# Do an isoplanatic selfcal
self.model_vis = copy_visibility(self.vis, zero=True)
self.model_vis = predict_skycomponent_visibility(
self.model_vis, self.components)
if doiso:
gt = solve_gaintable(self.vis,
self.model_vis,
phase_only=True,
timeslice='auto')
self.vis = apply_gaintable(self.vis, gt, inverse=True)
self.model_vis = convert_blockvisibility_to_visibility(self.model_vis)
self.model_vis, _, _ = weight_visibility(self.model_vis, self.beam)
self.dirty_model, sumwt = invert_list_arlexecute_workflow(
self.model_vis, self.beam, context='2d')
export_image_to_fits(
self.dirty_model,
"%s/test_modelpartition-model_dirty.fits" % self.dir)
lvis = convert_blockvisibility_to_visibility(self.vis)
lvis, _, _ = weight_visibility(lvis, self.beam)
dirty, sumwt = invert_list_arlexecute_workflow(lvis,
self.beam,
context='2d')
if doiso:
export_image_to_fits(
dirty,
"%s/test_modelpartition-initial-iso-residual.fits" % self.dir)
else:
export_image_to_fits(
dirty, "%s/test_modelpartition-initial-noiso-residual.fits" %
self.dir)
self.skymodels = [
SkyModel(components=[cm], fixed=fixed) for cm in self.components
]
