def calc_uvw(phase_centre,
timestamps,
antlist,
ant1,
ant2,
ant_descriptions,
refant_ind=0):
"""
Calculate uvw coordinates
Parameters
----------
phase_centre
katpoint target for phase centre position
timestamps
times, array of floats, shape(nrows)
antlist
list of antenna names - used for associating antenna descriptions with
an1 and ant2 indices, shape(nant)
ant1, ant2
array of antenna indices, shape(nrows)
antenna_descriptions
description strings for the antennas, same order as antlist, list of string
refant_ind
index of reference antenna in antlist, integer
Returns
-------
uvw
uvw coordinates numpy array, shape (3, nbl x ntimes)
"""
# use the lat-long-alt values of one of the antennas as the array reference position
refant = katpoint.Antenna(ant_descriptions[antlist[refant_ind]])
array_reference_position = katpoint.Antenna('array_position',
*refant.ref_position_wgs84)
# use the array reference position for the basis
basis = phase_centre.uvw_basis(timestamp=to_ut(timestamps),
antenna=array_reference_position)
# get enu vector for each row in MS, for each antenna in the baseline pair for that row
antenna1_uvw = np.empty([3, len(timestamps)])
antenna2_uvw = np.empty([3, len(timestamps)])
for i, [a1, a2] in enumerate(zip(ant1, ant2)):
antenna1 = katpoint.Antenna(ant_descriptions[antlist[a1]])
enu1 = np.array(antenna1.baseline_toward(array_reference_position))
antenna1_uvw[..., i] = np.tensordot(basis[..., i], enu1, ([1], [0]))
antenna2 = katpoint.Antenna(ant_descriptions[antlist[a2]])
enu2 = np.array(antenna2.baseline_toward(array_reference_position))
antenna2_uvw[..., i] = np.tensordot(basis[..., i], enu2, ([1], [0]))
# then subtract the vectors for each antenna to get the baseline vectors
baseline_uvw = np.empty([3, len(timestamps)])
for i, [a1, a2] in enumerate(zip(ant1, ant2)):
baseline_uvw[..., i] = -antenna1_uvw[..., i] + antenna2_uvw[..., i]
return baseline_uvw
def setUp(self):
self.flux_target = katpoint.Target(
'flux, radec, 0.0, 0.0, (1.0 2.0 2.0 0.0 0.0)')
self.antenna = katpoint.Antenna(
'XDM, -25:53:23.05075, 27:41:03.36453, 1406.1086, 15.0')
self.antenna2 = katpoint.Antenna(
'XDM2, -25:53:23.05075, 27:41:03.36453, 1406.1086, 15.0, 100.0 0.0 0.0'
)
self.timestamp = time.mktime(
time.strptime('2009/06/14 12:34:56', '%Y/%m/%d %H:%M:%S'))
def setUp(self):
self.target1 = katpoint.construct_azel_target('45:00:00.0',
'75:00:00.0')
self.target2 = katpoint.Target('Sun, special')
self.ant1 = katpoint.Antenna('A1, -31.0, 18.0, 0.0, 12.0, 0.0 0.0 0.0')
self.ant2 = katpoint.Antenna(
'A2, -31.0, 18.0, 0.0, 12.0, 10.0 -10.0 0.0')
self.ant3 = katpoint.Antenna(
'A3, -31.0, 18.0, 0.0, 12.0, 5.0 10.0 3.0')
self.ts = katpoint.Timestamp('2013-08-14 08:25')
self.delays = katpoint.DelayCorrection([self.ant2, self.ant3],
self.ant1, 1.285e9)
def load_antennas():
"""Return an array of katpoint antenna objects"""
antennas = []
with pkg_resources.resource_stream(__name__, 'meerkat_antennas.txt') as f:
for line in f:
antennas.append(katpoint.Antenna(line))
return antennas
def _get_ants(filename):
"""Quick look function to get the list of antennas in a data file.
This is intended to be called without createing a full katdal object.
Parameters
----------
filename : string
Data file name
Returns
-------
antennas : list of :class:'katpoint.Antenna' objects
"""
f, version = H5DataV2._open(filename)
config_group = f['MetaData/Configuration']
all_ants = [ant for ant in config_group['Antennas']]
script_ants = config_group['Observation'].attrs.get('script_ants')
script_ants = script_ants.split(',') if script_ants else all_ants
return [
katpoint.Antenna(
config_group['Antennas'][ant].attrs['description'])
for ant in script_ants if ant in all_ants
]
def fringe_correction(h5):
h5.select(corrprods='cross')
center_freqs = h5.channel_freqs
#print center_freqs.mean()
wavelengths = 3.0e8 / center_freqs
vis_set = None
# Number of turns of phase that signal B is behind signal A due to cable / receiver delay
tar = h5.catalogue.targets[0]
antlook = {}
for ant in h5.ants: antlook[ant.name] = ant # make lookup dict
tar.antenna = antlook['m024']
anttmp = antlook['m025'].description.split(',')
#anttmp[5] = "1257.713 2728.218 -7.917" #old
#anttmp[5] = "1254.75111151 2725.01575851 -9.93164 "
#anttmp[5] = "1258.828 2728.943 -7.283" # only strong sources
#anttmp[5] = "1258.862 2729.194 -7.234" # pointy sources
anttmp[5] = "1258.921 2729.124 -6.825" #best
anttmp[5] = "1258.892 2729.159 -7.029" #???
cable_delay_turns = 0.0 # add delays correction
for compscan_no,compscan_label,target in h5.compscans():
#print compscan_no,target.description
#print "loop",compscan_no,compscan_label,target,h5.shape
vis = h5.vis[:]
# Number of turns of phase that signal B is behind signal A due to geometric delay
target.antenna = antlook['m024']
new_w =np.array(target.uvw(antenna2=katpoint.Antenna(','.join(anttmp) ),timestamp=h5.timestamps))[2,:]
w = (new_w-h5.w[:,0])
geom_delay_turns = w[:, np.newaxis, np.newaxis] / wavelengths[:, np.newaxis]
# Visibility <A, B*> has phase (A - B), therefore add (B - A) phase to stop fringes (i.e. do delay tracking)
vis *= np.exp(2j * np.pi * (geom_delay_turns + cable_delay_turns))
if vis_set is None:
vis_set = vis.copy()
else:
vis_set = np.append(vis_set,vis,axis = 0)
return vis_set
def parse_csv(filename):
""" Make an antenna object and a data array from the input csv file
update the data array with the desired flux for the give polarisation
Parameters
----------
filename : string
Filename containing the result of analyse_point_source_scans.py
first line will contain the info to construct the antenna object
Return
------
:class: katpoint Antenna object
data : heterogeneous record array
"""
antenna = katpoint.Antenna(
open(filename).readline().strip().partition('=')[2])
#Open the csv file as an array of strings without comment fields (antenna fields are comments)
data = np.loadtxt(filename, dtype='string', comments='#', delimiter=', ')
#First non-comment line is the header with fieldnames
fieldnames = data[0].tolist()
#Setup all fields as float32
formats = np.tile('float32', len(fieldnames))
#Label the string fields as input datatype
formats[[
fieldnames.index(name) for name in STRING_FIELDS if name in fieldnames
]] = data.dtype
#Save the data as a heterogeneous record array
data = np.rec.fromarrays(data[1:].transpose(),
dtype=zip(fieldnames, formats))
return data, antenna
def makeKatPointAntenna(antennaString):
antennaKat = []
for antenna in antennaString:
antkat = katpoint.Antenna(antenna)
antennaKat.append(antkat)
return antennaKat
def _get_ants(filename):
"""Quick look function to get the list of antennas in a data file.
This is intended to be called without creating a complete katdal object.
Parameters
----------
filename : string
Data file name
Returns
-------
antennas : list of :class:'katpoint.Antenna' objects
"""
f, version = H5DataV3._open(filename)
obs_params = {}
tm_group = f['TelescopeModel']
all_ants = [
ant for ant in tm_group
if tm_group[ant].attrs.get('class') == 'AntennaPositioner'
]
tm_params = tm_group['obs/params']
for obs_param in tm_params['value']:
key, val = obs_param.split(' ', 1)
obs_params[key] = np.lib.utils.safe_eval(val)
obs_ants = obs_params.get('ants')
# By default, only pick antennas that were in use by the script
obs_ants = obs_ants.split(',') if obs_ants else all_ants
return [
katpoint.Antenna(tm_group[ant].attrs['description'])
for ant in obs_ants if ant in all_ants
]
def lst2utc(req_lst, ref_location, date=None):
def get_lst_range(date):
date_timestamp = time.mktime(
date.timetuple()) # this will be local time
time_range = katpoint.Timestamp(date_timestamp).secs + \
numpy.arange(0, 24.*3600., 60)
lst_range = numpy.degrees(
target.antenna.local_sidereal_time(time_range)) / 15.
return time_range, lst_range
req_lst = float(req_lst)
cat = katpoint.Catalogue(add_specials=True)
cat.antenna = katpoint.Antenna(ref_location)
target = cat['Zenith']
if date is None: # find the best UTC for today
date = datetime.date.today()
else:
date = date.replace(hour=0, minute=0, second=0, microsecond=0)
[time_range, lst_range] = get_lst_range(date)
lst_idx = numpy.abs(lst_range - req_lst).argmin()
if lst_range[lst_idx] < req_lst:
x = lst_range[lst_idx:lst_idx + 2]
y = time_range[lst_idx:lst_idx + 2]
else:
x = lst_range[lst_idx - 1:lst_idx + 1]
y = time_range[lst_idx - 1:lst_idx + 1]
linefit = numpy.poly1d(numpy.polyfit(x, y, 1))
return datetime.datetime.utcfromtimestamp(linefit(req_lst))
def get_location(self):
"""Get the default reference location.
Calls the katpoint.Antenna object,
a MeerKAT wrapper around the PyEphem.observer object
"""
return katpoint.Antenna(self.location)
def collect_targets(kat, args):
"""Collect targets into katpoint catalogue.
Parameters
----------
kat: session kat container-like object
"""
from_names = from_strings = from_catalogues = num_catalogues = 0
catalogue = katpoint.Catalogue()
catalogue.antenna = katpoint.Antenna(_ref_location)
setobserver(catalogue.antenna.observer)
for arg in args:
try:
# First assume the string is a catalogue file name
count_before_add = len(catalogue)
try:
catalogue.add(open(arg))
except ValueError:
msg = "Catalogue {} contains bad targets".format(arg)
user_logger.warning(msg)
from_catalogues += len(catalogue) - count_before_add
num_catalogues += 1
except IOError:
# If the file failed to load,
# assume it is a name or description string
# With no comma in target string,
# assume it's the name of a target
# to be looked up in standard catalogue
if arg.find(",") < 0:
target = kat.sources[arg]
if target is None:
msg = "Unknown target or catalogue {}, skipping it".format(
arg)
user_logger.warning(msg)
else:
catalogue.add(target)
from_names += 1
else:
# Assume the argument is a target description string
try:
catalogue.add(arg)
from_strings += 1
except ValueError as err:
msg = "Invalid target {}, skipping it [{}]".format(
arg, err)
user_logger.warning(msg)
if len(catalogue) == 0:
raise ValueError("No known targets found in argument list")
msg = (
"Found {} target(s): {} from {} catalogue(s), {} from default catalogue and "
"{} as target string(s)".format(len(catalogue), from_catalogues,
num_catalogues, from_names,
from_strings))
user_logger.info(msg)
return catalogue
def _create_subarrays(self, subarray_defs):
"""
Create subarrays, setting default subarray properties
for this dataset to the first subarray.
Parameters
----------
subarray_defs : list of dicts
List of subarray definition dictionaries
{ 'antenna' : list, 'corr_products' : list}
"""
subarrays = []
for subarray_def in subarray_defs:
try:
ants = subarray_def['antenna']
except KeyError as e:
raise KeyError("Subarray definition '%s' "
"missing '%s'" % (subarray_def, str(e)))
ants = [
a if isinstance(a, katpoint.Antenna) else katpoint.Antenna(a)
for a in ants
]
try:
corr_products = subarray_def['corr_products']
except KeyError:
# Generate correlation products for all antenna pairs
# including auto-correlations
corr_products = np.array([(a1.name + c1, a2.name + c2)
for i, a1 in enumerate(ants)
for a2 in ants[i:]
for c1 in ('h', 'v')
for c2 in ('h', 'v')])
subarrays.append(Subarray(ants, corr_products))
try:
subarray = subarrays[0]
except IndexError:
raise ValueError("No subarrays were defined in '%s'" %
subarray_defs)
self.subarrays = subarrays
self.subarray = 0
self.inputs = subarray.inputs
self.ants = subarray.ants
self.corr_products = subarray.corr_products
subarray_catdata = CategoricalData(self.subarrays, [0, self._ndumps])
subarray_index_catdata = CategoricalData([self.subarray],
[0, self._ndumps])
self.sensor['Observation/subarray'] = subarray_catdata
self.sensor['Observation/subarray_index'] = subarray_index_catdata
def setUp(self):
start_time = datetime.strptime("2018-12-07 05:00:00",
"%Y-%m-%d %H:%M:%S")
observer = ephem.Observer()
observer.date = ephem.Date(start_time)
simulate.setobserver(observer)
self.antenna = katpoint.Antenna(observatory._ref_location)
self.mock_kat = mock.Mock()
self.mock_kat.obs_params = {"durations": {"start_time": start_time}}
self.DUT = simulate.SimSession(self.mock_kat)
def makeKatPointAntenna(antennaString): ''' Takes in antenna number and returns katpoint Antenna object. ''' antennaKat = [] for antenna in antennaString: antkat = katpoint.Antenna(antenna) antennaKat.append(antkat) return antennaKat
def setUp(self):
self.tle_lines = [
'GPS BIIA-21 (PRN 09) \n',
'1 22700U 93042A %02d266.32333151 .00000012 00000-0 10000-3 0 805%1d\n'
% (YY, (YY // 10 + YY - 7 + 4) % 10),
'2 22700 55.4408 61.3790 0191986 78.1802 283.9935 2.00561720104282\n'
]
self.edb_lines = [
'HIC 13847,f|S|A4,2:58:16.03,-40:18:17.1,2.906,2000,\n'
]
self.antenna = katpoint.Antenna(
'XDM, -25:53:23.05075, 27:41:03.36453, 1406.1086, 15.0')
def get_scan_area_extents(self, test_date):
# Test Antenna: 0-m dish at lat 0:00:00.0, long 0:00:00.0, alt 0.0 m
antenna = katpoint.Antenna("Test Antenna", 0, 0, 0)
target_list = [
katpoint.Target("t1, radec, 05:16:00.0, -25:42:00.0", antenna=antenna),
katpoint.Target("t2, radec, 05:16:00.0, -35:36:00.0", antenna=antenna),
katpoint.Target("t3, radec, 06:44:00.0, -35:36:00.0", antenna=antenna),
katpoint.Target("t4, radec, 06:44:00.0, -25:42:00.0", antenna=antenna),
]
el, az_min, az_max, t_start, t_end = scans._get_scan_area_extents(target_list,
antenna,
test_date)
return el, az_min, az_max, t_start, t_end
def test_local_sidereal_time(self):
"""Test sidereal time and the use of date/time strings vs floats as timestamps."""
ant = katpoint.Antenna(self.valid_antennas[0])
utc_secs = time.mktime(
time.strptime(self.timestamp, '%Y/%m/%d %H:%M:%S')) - time.timezone
sid1 = ant.local_sidereal_time(self.timestamp)
sid2 = ant.local_sidereal_time(utc_secs)
self.assertAlmostEqual(
sid1,
sid2,
places=10,
msg='Sidereal time differs for float and date/time string')
sid3 = ant.local_sidereal_time([self.timestamp, self.timestamp])
sid4 = ant.local_sidereal_time([utc_secs, utc_secs])
assert_angles_almost_equal(sid3, sid4, decimal=12)
def lst2utc(req_lst, ref_location, date=None):
"""Find LST for given date else for Today.
Parameters
----------
req_lst: datetime
Request LST
ref_location: `EarthLocation()`
Location on earth where LST is being measured
date: datetime
Date when LST is being measured
Returns
-------
time_range: katpoint.Timestamp
UTC date and time
lst_range: float
LST range
"""
def get_lst_range(date):
date_timestamp = time.mktime(
date.timetuple()) # this will be local time
time_range = katpoint.Timestamp(date_timestamp).secs + numpy.arange(
0, 24.0 * 3600.0, 60)
lst_range = numpy.degrees(
target.antenna.local_sidereal_time(time_range)) / 15.0
return time_range, lst_range
req_lst = float(req_lst)
cat = katpoint.Catalogue(add_specials=True)
cat.antenna = katpoint.Antenna(ref_location)
target = cat["Zenith"]
if date is None: # find the best UTC for today
date = datetime.date.today()
else:
date = date.replace(hour=0, minute=0, second=0, microsecond=0)
[time_range, lst_range] = get_lst_range(date)
lst_idx = numpy.abs(lst_range - req_lst).argmin()
if lst_range[lst_idx] < req_lst:
x = lst_range[lst_idx:lst_idx + 2]
y = time_range[lst_idx:lst_idx + 2]
else:
x = lst_range[lst_idx - 1:lst_idx + 1]
y = time_range[lst_idx - 1:lst_idx + 1]
linefit = numpy.poly1d(numpy.polyfit(x, y, 1))
return datetime.datetime.utcfromtimestamp(linefit(req_lst))
def read_offsetfile(filename):
# Load data file in one shot as an array of strings
string_fields = ['dataset', 'target', 'timestamp_ut', 'data_unit']
data = np.loadtxt(filename, dtype='string', comments='#', delimiter=', ')
# Interpret first non-comment line as header
fields = data[0].tolist()
# By default, all fields are assumed to contain floats
formats = np.tile(np.float, len(fields))
# The string_fields are assumed to contain strings - use data's string type, as it is of sufficient length
formats[[fields.index(name) for name in string_fields if name in fields]] = data.dtype
# Convert to heterogeneous record array
data = np.rec.fromarrays(data[1:].transpose(), dtype=list(zip(fields, formats)))
# Load antenna description string from first line of file and construct antenna object from it
antenna = katpoint.Antenna(file(filename).readline().strip().partition('=')[2])
# Use the pointing model contained in antenna object as the old model (if not overridden by file)
# If the antenna has no model specified, a default null model will be used
return data,antenna
def _get_ants(filename):
"""Quick look function to get the list of antennas in a data file.
This is intended to be called without creating a complete katdal object.
Parameters
----------
filename : string
Data file name
Returns
-------
antennas : list of :class:'katpoint.Antenna' objects
"""
f, version = H5DataV3._open(filename)
obs_params = {}
tm_group = f['TelescopeModel']
ants = []
for name in tm_group:
if tm_group[name].attrs.get('class') != 'AntennaPositioner':
continue
try:
ant_description = tm_group[name]['observer']['value'][0]
except KeyError:
try:
ant_description = tm_group[name].attrs['observer']
except KeyError:
ant_description = tm_group[name].attrs['description']
ants.append(katpoint.Antenna(ant_description))
cam_ants = set(ant.name for ant in ants)
# Original list of correlation products as pairs of input labels
corrprods = H5DataV3._get_corrprods(f)
# Find names of all antennas with associated correlator data
cbf_ants = set([cp[0][:-1] for cp in corrprods] + [cp[1][:-1] for cp in corrprods])
# By default, only pick antennas that were in use by the script
tm_params = tm_group['obs/params']
for obs_param in tm_params['value']:
if obs_param:
key, val = obs_param.split(' ', 1)
obs_params[key] = np.lib.utils.safe_eval(val)
obs_ants = obs_params.get('ants')
# Otherwise fall back to the list of antennas common to CAM and CBF
obs_ants = obs_ants.split(',') if obs_ants else list(cam_ants & cbf_ants)
return [ant for ant in ants if ant.name in obs_ants]
def _create_antenna_sensors(self, antenna):
"""
Create antenna sensors.
Parameters
----------
antenna : list of :class:`katpoint.Antenna`
Antenna objects
"""
for ant in antenna:
ant_catdata = CategoricalData([ant], [0, self._ndumps])
self.sensor['Antennas/%s/antenna' % (ant.name, )] = ant_catdata
# Extract array reference from first antenna (first 5 fields of description)
array_ant_fields = ['array'] + antenna[0].description.split(',')[1:5]
array_ant = katpoint.Antenna(','.join(array_ant_fields))
self.sensor['Antennas/array/antenna'] = CategoricalData(
[array_ant], [0, self._ndumps])
def check_antennas(antennas):
"""
check the type of the inputs. if they are katpoint objects,
then extract the latitude, longitude, elevation information
arguments:
antennas -- either can be a list of katpoint antenna objects or
a list of [latitude, longitude, elevation]
return:
a list of antenna geographic coordinates in the order of
[latitude, longitude, elevation]
"""
def from_katpoint_list(antennas):
antenna_list = []
for antenna in antennas:
antenna_list.append([
np.rad2deg(antenna.observer.lat),
np.rad2deg(antenna.observer.lon), antenna.observer.elev
])
return np.array(antenna_list)
antennas = np.array(antennas)
if isinstance(antennas[0], np.ndarray):
antenna_coordinates = antennas
names = ["%03d" % i for i in range(len(antennas))]
elif isinstance(antennas[0], katpoint.Antenna):
antenna_coordinates = from_katpoint_list(antennas)
names = [ant.name for ant in antennas]
elif isinstance(antennas[0], str):
katpoint_antennas = [katpoint.Antenna(i) for i in antennas]
antenna_coordinates = from_katpoint_list(katpoint_antennas)
names = [ant.name for ant in katpoint_antennas]
else:
raise Exception("Antennas are passed in unknown format")
antenna_objects = [
coord.Antenna(names[idx], coordinate)
for idx, coordinate in enumerate(antenna_coordinates)
]
return antenna_objects
def _get_ants(filename):
"""Quick look function to get the list of antennas in a data file.
This is intended to be called without creating a full katdal object.
Parameters
----------
filename : string
Data file name
Returns
-------
antennas : list of :class:'katpoint.Antenna' objects
"""
f, version = H5DataV1._open(filename)
ants_group = f['Antennas']
antennas = [katpoint.Antenna(to_str(ants_group[group].attrs['description']))
for group in ants_group]
return antennas
def make_uvw(args, n_time):
start = 946728000.0 # J2000, in UNIX time
dec = -np.pi / 4
target = katpoint.construct_radec_target(0, dec)
timestamps = np.arange(n_time) * args.int_time + start
ref = katpoint.Antenna('', *args.antennas[0].ref_position_wgs84)
basis = target.uvw_basis(timestamp=timestamps, antenna=ref)
antenna_uvw = []
rows = [[], [], []]
for antenna in args.antennas:
enu = np.array(ref.baseline_toward(antenna))
antenna_uvw.append(np.tensordot(basis, enu, ([1], [0])))
for i in range(len(args.antennas)):
for j in range(i):
u, v, w = antenna_uvw[j] - antenna_uvw[i]
rows[0].append(u)
rows[1].append(v)
rows[2].append(w)
uvw = np.array(rows, dtype=np.float32)
return uvw.reshape(3, uvw.shape[1] * n_time).T.copy()
def update_config_params(self):
"""
In this method parameters related to the resources assigned, are updated every time assign, release
or configure commands are executed.
:param argin: None
:return: None
"""
assigned_receptors_dict = {}
assigned_receptors = []
self.fsids_list = []
self.logger.info("Updating config parameters.")
# Load a set of antenna descriptions and construct Antenna objects from them
with importlib.resources.open_text("cspsubarrayleafnode",
"ska_antennas.txt") as f:
descriptions = f.readlines()
antennas = [katpoint.Antenna(line) for line in descriptions]
# Create a dictionary including antenna objects
antennas_dict = {ant.name: ant for ant in antennas}
antenna_keys_list = antennas_dict.keys()
for receptor in self.device_data.receptorIDList_str:
if receptor in antenna_keys_list:
assigned_receptors.append(antennas_dict[receptor])
# Create a dictionary including antennas (objects) assigned to the Subarray
assigned_receptors_dict[receptor] = antennas_dict[receptor]
# Antenna having key 'ref_ant' from antennas_dict, is referred as a reference antenna.
ref_ant = antennas_dict["ref_ant"]
# Create DelayCorrection Object
self.delay_correction_object = katpoint.DelayCorrection(
assigned_receptors, ref_ant)
self.antenna_names = list(
self.delay_correction_object.ant_models.keys())
# list of frequency slice ids
for fsp_entry in self.device_data.fsp_ids_object:
self.fsids_list.append(fsp_entry["fspID"])
self.logger.info("Completed updating config parameters.")
def test_construct_antenna(self):
"""Test construction of antennas from strings and vice versa."""
valid_antennas = [
katpoint.Antenna(descr) for descr in self.valid_antennas
]
valid_strings = [a.description for a in valid_antennas]
for descr in valid_strings:
ant = katpoint.Antenna(descr)
print('%s %s' % (str(ant), repr(ant)))
self.assertEqual(
descr, ant.description,
'Antenna description differs from original string')
self.assertEqual(ant.description, ant.format_katcp(),
'Antenna description differs from KATCP format')
for descr in self.invalid_antennas:
self.assertRaises(ValueError, katpoint.Antenna, descr)
descr = valid_antennas[0].description
self.assertEqual(descr,
katpoint.Antenna(*descr.split(', ')).description)
self.assertRaises(ValueError, katpoint.Antenna, descr,
*descr.split(', ')[1:])
# Check that description string updates when object is updated
a1 = katpoint.Antenna(
'FF1, -30:43:17.3, 21:24:38.5, 1038.0, 12.0, 18.4 -8.7 0.0')
a2 = katpoint.Antenna(
'FF2, -30:43:17.3, 21:24:38.5, 1038.0, 13.0, 18.4 -8.7 0.0, 0.1, 1.22'
)
self.assertNotEqual(a1, a2, 'Antennas should be inequal')
a1.name = 'FF2'
a1.diameter = 13.0
a1.pointing_model = katpoint.PointingModel('0.1')
a1.beamwidth = 1.22
self.assertEqual(a1.description, a2.description,
'Antenna description string not updated')
self.assertEqual(a1, a2.description,
'Antenna not equal to description string')
self.assertEqual(a1, a2, 'Antennas not equal')
self.assertEqual(a1, katpoint.Antenna(a2),
'Construction with antenna object failed')
self.assertEqual(a1, pickle.loads(pickle.dumps(a1)), 'Pickling failed')
try:
self.assertEqual(hash(a1), hash(a2), 'Antenna hashes not equal')
except TypeError:
self.fail('Antenna object not hashable')
def download_IERS_file(self):
""" This method performs one delay calculation with dummy values to download the IERS file in advanced
to the delay calcualtions at the initialization of the device ."""
# Create an example radec target
ra = '21:08:47.92'
dec = '-88:57:22.9'
target = katpoint.Target.from_radec(ra, dec)
descriptions = '''
ref_ant, -30:42:39.8, 21:26:38.0, 1086, 13.5, 0 0 0 0 0 0,0, 0
ref_ant, -30:42:39.8, 21:26:38.0, 1086, 13.5, 0 0 0 0 0 0,0, 0
'''.strip().split('\n')
antennas = [katpoint.Antenna(line) for line in descriptions]
ref_ant = antennas[0]
ants = antennas[1:]
try:
delay_correction = katpoint.DelayCorrection(ants, ref_ant)
except Exception as delay_execption:
log_msg = f"Exception in DelayCorrection Katpoint API {delay_execption}"
self.logger.exception(log_msg)
# Get delays towards target for example timestamp
exa_time_t0 = '2021-05-04 12:54:09.686556'
time_t0_obj = datetime.strptime(exa_time_t0, '%Y-%m-%d %H:%M:%S.%f')
delays = delay_correction.delays(target, time_t0_obj)
self.logger.info("delays are: '%s'", delays)
def __init__(self, source, ref_ant='', time_offset=0.0, **kwargs):
DataSet.__init__(self, source.name, ref_ant, time_offset)
attrs = source.metadata.attrs
# ------ Extract timestamps ------
self.source = source
self.file = {}
self.version = '4.0'
self.dump_period = attrs['int_time']
num_dumps = len(source.timestamps)
source.timestamps += self.time_offset
if source.timestamps[0] < 1e9:
logger.warning(
"Data set has invalid first correlator timestamp "
"(%f)", source.timestamps[0])
half_dump = 0.5 * self.dump_period
self.start_time = katpoint.Timestamp(source.timestamps[0] - half_dump)
self.end_time = katpoint.Timestamp(source.timestamps[-1] + half_dump)
self._time_keep = np.full(num_dumps, True, dtype=np.bool_)
all_dumps = [0, num_dumps]
# Assemble sensor cache
self.sensor = SensorCache(source.metadata.sensors, source.timestamps,
self.dump_period, self._time_keep,
SENSOR_PROPS, VIRTUAL_SENSORS,
SENSOR_ALIASES)
# ------ Extract flags ------
# Internal flag mask overridden whenever _flags_keep is set via select()
self._flags_select = np.array([255], dtype=np.uint8)
self._flags_keep = 'all'
# ------ Extract observation parameters and script log ------
self.obs_params = attrs['obs_params']
# Get observation script parameters, with defaults
self.observer = self.obs_params.get('observer', '')
self.description = self.obs_params.get('description', '')
self.experiment_id = self.obs_params.get('experiment_id', '')
# Extract script log data verbatim (it is not a standard sensor anyway)
try:
self.obs_script_log = self.sensor.get(
'obs_script_log', extract=False)['value'].tolist()
except KeyError:
self.obs_script_log = []
# ------ Extract subarrays ------
# List of correlation products as pairs of input labels
corrprods = attrs['bls_ordering']
# Crash if there is mismatch between labels and data shape (bad labels?)
if source.data and (len(corrprods) != source.data.shape[2]):
raise BrokenFile('Number of baseline labels (containing expected '
'antenna names) received from correlator (%d) '
'differs from number of baselines in data (%d)' %
(len(corrprods), source.data.shape[2]))
# Find all antennas in subarray with valid katpoint Antenna objects
ants = []
for resource in attrs['sub_pool_resources'].split(','):
try:
ant_description = attrs[resource + '_observer']
ants.append(katpoint.Antenna(ant_description))
except (KeyError, ValueError):
continue
# Keep the basic list sorted as far as possible
ants = sorted(ants)
cam_ants = set(ant.name for ant in ants)
# Find names of all antennas with associated correlator data
sdp_ants = set([cp[0][:-1] for cp in corrprods] +
[cp[1][:-1] for cp in corrprods])
# By default, only pick antennas that were in use by the script
obs_ants = self.obs_params.get('ants')
# Otherwise fall back to the list of antennas common to CAM and SDP / CBF
obs_ants = obs_ants.split(',') if obs_ants else list(cam_ants
& sdp_ants)
self.ref_ant = obs_ants[0] if not ref_ant else ref_ant
self.subarrays = subs = [Subarray(ants, corrprods)]
self.sensor['Observation/subarray'] = CategoricalData(subs, all_dumps)
self.sensor['Observation/subarray_index'] = CategoricalData([0],
all_dumps)
# Store antenna objects in sensor cache too, for use in virtual sensors
for ant in ants:
sensor_name = 'Antennas/%s/antenna' % (ant.name, )
self.sensor[sensor_name] = CategoricalData([ant], all_dumps)
# ------ Extract spectral windows / frequencies ------
# Get the receiver band identity ('l', 's', 'u', 'x')
band = attrs['sub_band']
# Populate antenna -> receiver mapping and figure out noise diode
for ant in cam_ants:
# Try sanitised version of RX serial number first
rx_serial = attrs.get('%s_rsc_rx%s_serial_number' % (ant, band), 0)
self.receivers[ant] = '%s.%d' % (band, rx_serial)
nd_sensor = '%s_dig_%s_band_noise_diode' % (ant, band)
if nd_sensor in self.sensor:
# A sensor alias would be ideal for this but it only deals with suffixes ATM
new_nd_sensor = 'Antennas/%s/nd_coupler' % (ant, )
self.sensor[new_nd_sensor] = self.sensor.get(nd_sensor,
extract=False)
num_chans = attrs['n_chans']
bandwidth = attrs['bandwidth']
centre_freq = attrs['center_freq']
channel_width = bandwidth / num_chans
# Continue with different channel count, but invalidate centre freq
# (keep channel width though)
if source.data and (num_chans != source.data.shape[1]):
logger.warning(
'Number of channels reported in metadata (%d) differs'
' from actual number of channels in data (%d) - '
'trusting the latter', num_chans, source.data.shape[1])
num_chans = source.data.shape[1]
centre_freq = 0.0
product = attrs.get('sub_product', '')
sideband = 1
band_map = dict(l='L', s='S', u='UHF', x='X')
spw_params = (centre_freq, channel_width, num_chans, product, sideband,
band_map[band])
# We only expect a single spectral window within a single v4 data set
self.spectral_windows = spws = [SpectralWindow(*spw_params)]
self.sensor['Observation/spw'] = CategoricalData(spws, all_dumps)
self.sensor['Observation/spw_index'] = CategoricalData([0], all_dumps)
# ------ Extract scans / compound scans / targets ------
# Use the activity sensor of reference antenna to partition the data
# set into scans (and to set their states)
scan = self.sensor.get(self.ref_ant + '_activity')
# If the antenna starts slewing on the second dump, incorporate the
# first dump into the slew too. This scenario typically occurs when the
# first target is only set after the first dump is received.
# The workaround avoids putting the first dump in a scan by itself,
# typically with an irrelevant target.
if len(scan) > 1 and scan.events[1] == 1 and scan[1] == 'slew':
scan.events, scan.indices = scan.events[1:], scan.indices[1:]
scan.events[0] = 0
# Use labels to partition the data set into compound scans
try:
label = self.sensor.get('obs_label')
except KeyError:
label = CategoricalData([''], all_dumps)
# Discard empty labels (typically found in raster scans, where first
# scan has proper label and rest are empty) However, if all labels are
# empty, keep them, otherwise whole data set will be one pathological
# compscan...
if len(label.unique_values) > 1:
label.remove('')
# Create duplicate scan events where labels are set during a scan
# (i.e. not at start of scan)
# ASSUMPTION: Number of scans >= number of labels
# (i.e. each label should introduce a new scan)
scan.add_unmatched(label.events)
self.sensor['Observation/scan_state'] = scan
self.sensor['Observation/scan_index'] = CategoricalData(
range(len(scan)), scan.events)
# Move proper label events onto the nearest scan start
# ASSUMPTION: Number of labels <= number of scans
# (i.e. only a single label allowed per scan)
label.align(scan.events)
# If one or more scans at start of data set have no corresponding label,
# add a default label for them
if label.events[0] > 0:
label.add(0, '')
self.sensor['Observation/label'] = label
self.sensor['Observation/compscan_index'] = CategoricalData(
range(len(label)), label.events)
# Use the target sensor of reference antenna to set target for each scan
target = self.sensor.get(self.ref_ant + '_target')
# Remove initial blank target (typically because antenna starts stopped)
if len(target) > 1 and target[0] == 'Nothing, special':
target.events, target.indices = target.events[1:], target.indices[
1:]
target.events[0] = 0
# Move target events onto the nearest scan start
# ASSUMPTION: Number of targets <= number of scans
# (i.e. only a single target allowed per scan)
target.align(scan.events)
self.sensor['Observation/target'] = target
self.sensor['Observation/target_index'] = CategoricalData(
target.indices, target.events)
# Set up catalogue containing all targets in file, with reference
# antenna as default antenna
self.catalogue.add(target.unique_values)
ref_sensor = 'Antennas/%s/antenna' % (self.ref_ant, )
self.catalogue.antenna = self.sensor.get(ref_sensor)[0]
# Ensure that each target flux model spans all frequencies
# in data set if possible
self._fix_flux_freq_range()
# Apply default selection and initialise all members that depend
# on selection in the process
self.select(spw=0, subarray=0, ants=obs_ants)
def __init__(self,
filename,
ref_ant='',
time_offset=0.0,
mode='r',
**kwargs):
DataSet.__init__(self, filename, ref_ant, time_offset)
# Load file
self.file, self.version = H5DataV1._open(filename, mode)
f = self.file
# Load main HDF5 groups
ants_group, corr_group, data_group = f['Antennas'], f['Correlator'], f[
'Scans']
# Get observation script parameters, with defaults
self.observer = self.obs_params['observer'] = f.attrs.get(
'observer', '')
self.description = self.obs_params['description'] = f.attrs.get(
'description', '')
self.experiment_id = self.obs_params['experiment_id'] = f.attrs.get(
'experiment_id', '')
# Collect all groups below data group that fit the description of a scan group
scan_groups = []
def register_scan_group(name, obj):
"""A scan group is defined as a group named 'Scan*' with non-empty timestamps and data."""
if isinstance(obj, h5py.Group) and name.split('/')[-1].startswith('Scan') and \
'data' in obj and 'timestamps' in obj and len(obj['timestamps']) > 0:
scan_groups.append(obj)
data_group.visititems(register_scan_group)
# Sort scan groups in chronological order via 'decorate-sort-undecorate' (DSU) idiom
decorated_scan_groups = [(s['timestamps'][0], s) for s in scan_groups]
decorated_scan_groups.sort()
self._scan_groups = [s[-1] for s in decorated_scan_groups]
# ------ Extract timestamps ------
self.dump_period = 1.0 / corr_group.attrs['dump_rate_hz']
self._segments = np.cumsum(
[0] + [len(s['timestamps']) for s in self._scan_groups])
num_dumps = self._segments[-1]
self._time_keep = np.ones(num_dumps, dtype=np.bool)
data_timestamps = self.timestamps
if data_timestamps[0] < 1e9:
logger.warning(
"File '%s' has invalid first correlator timestamp (%f)" % (
filename,
data_timestamps[0],
))
# Estimate timestamps by assuming they are uniformly spaced (much quicker than loading them from file).
# This is useful for the purpose of segmenting data set, where accurate timestamps are not that crucial.
# The real timestamps are still loaded when the user explicitly asks for them.
# Do quick test for uniform spacing of timestamps (necessary but not sufficient).
if abs((data_timestamps[-1] - data_timestamps[0]) / self.dump_period +
1 - num_dumps) < 0.01:
# Estimate the timestamps as being uniformly spaced
data_timestamps = data_timestamps[
0] + self.dump_period * np.arange(num_dumps)
else:
# Load the real timestamps instead and warn the user, as this is anomalous
data_timestamps = data_timestamps[:]
expected_dumps = (data_timestamps[-1] -
data_timestamps[0]) / self.dump_period + 1
logger.warning((
"Irregular timestamps detected in file '%s':"
"expected %.3f dumps based on dump period and start/end times, got %d instead"
) % (filename, expected_dumps, num_dumps))
self.start_time = katpoint.Timestamp(data_timestamps[0] -
0.5 * self.dump_period)
self.end_time = katpoint.Timestamp(data_timestamps[-1] +
0.5 * self.dump_period)
# ------ Extract sensors ------
# Populate sensor cache with all HDF5 datasets below antennas group that fit the description of a sensor
cache = {}
def register_sensor(name, obj):
if isinstance(obj, h5py.Dataset) and obj.shape != (
) and obj.dtype.names == ('timestamp', 'value', 'status'):
# Assume sensor dataset name is AntennaN/Sensors/dataset and rename it to Antennas/{ant}/dataset
ant_name = obj.parent.parent.attrs['description'].split(',')[0]
standardised_name = 'Antennas/%s/%s' % (ant_name,
name.split('/')[-1])
cache[standardised_name] = SensorData(obj, standardised_name)
ants_group.visititems(register_sensor)
# Use estimated data timestamps for now, to speed up data segmentation
# This will linearly interpolate pointing coordinates to correlator data timestamps (on access)
# As long as azimuth is in natural antenna coordinates, no special angle interpolation required
self.sensor = SensorCache(cache,
data_timestamps,
self.dump_period,
keep=self._time_keep,
props=SENSOR_PROPS,
virtual=VIRTUAL_SENSORS,
aliases=SENSOR_ALIASES)
# ------ Extract subarrays ------
ants = [
katpoint.Antenna(ants_group[group].attrs['description'])
for group in ants_group
]
self.ref_ant = ants[0].name if not ref_ant else ref_ant
# Map from (old-style) DBE input label (e.g. '0x') to the new antenna-based input label (e.g. 'ant1h')
input_label = dict([(ants_group[group]['H'].attrs['dbe_input'],
ant.name + 'h')
for ant, group in zip(ants, ants_group.keys())
if 'H' in ants_group[group]])
input_label.update(
dict([(ants_group[group]['V'].attrs['dbe_input'], ant.name + 'v')
for ant, group in zip(ants, ants_group.keys())
if 'V' in ants_group[group]]))
# Split DBE input product string into its separate inputs
split_product = re.compile(r'(\d+[xy])(\d+[xy])')
# Iterate over map from correlation product index to DBE input product string and convert
# the latter to pairs of input labels (this assumes that the corrprod indices are sorted)
corrprods = []
for corrind, product in corr_group['input_map']:
match = split_product.match(product)
if match is None:
raise BrokenFile(
"Unknown DBE input product '%s' in input map (expected e.g. '0x1y')"
% (product, ))
corrprods.append(
tuple([input_label[inp] for inp in match.groups()]))
data_cp_len = len(self._scan_groups[0]['data'].dtype)
if len(corrprods) != data_cp_len:
raise BrokenFile(
'Number of baseline labels received from correlator '
'(%d) differs from number of baselines in data (%d)' %
(len(corrprods), data_cp_len))
self.subarrays = [Subarray(ants, corrprods)]
self.sensor['Observation/subarray'] = CategoricalData(
self.subarrays, [0, len(data_timestamps)])
self.sensor['Observation/subarray_index'] = CategoricalData(
[0], [0, len(data_timestamps)])
# Store antenna objects in sensor cache too, for use in virtual sensor calculations
for ant in ants:
self.sensor['Antennas/%s/antenna' %
(ant.name, )] = CategoricalData(
[ant], [0, len(data_timestamps)])
# ------ Extract spectral windows / frequencies ------
centre_freq = corr_group.attrs['center_frequency_hz']
num_chans = corr_group.attrs['num_freq_channels']
data_num_chans = self._scan_groups[0]['data'].shape[1]
if num_chans != data_num_chans:
raise BrokenFile(
'Number of channels received from correlator '
'(%d) differs from number of channels in data (%d)' %
(num_chans, data_num_chans))
channel_width = corr_group.attrs['channel_bandwidth_hz']
self.spectral_windows = [
SpectralWindow(centre_freq, channel_width, num_chans, 'poco')
]
self.sensor['Observation/spw'] = CategoricalData(
self.spectral_windows, [0, len(data_timestamps)])
self.sensor['Observation/spw_index'] = CategoricalData(
[0], [0, len(data_timestamps)])
# ------ Extract scans / compound scans / targets ------
# Fringe Finder augment does not store antenna activity sensors - use scan + compscan labels as a guess
scan_labels = [s.attrs.get('label', '') for s in self._scan_groups]
compscan_labels = [
s.parent.attrs.get('label', '') for s in self._scan_groups
]
scan_states = [
_labels_to_state(s, cs)
for s, cs in zip(scan_labels, compscan_labels)
]
# The scans are already partitioned into groups - use corresponding segments as start events
self.sensor['Observation/scan_state'] = CategoricalData(
scan_states, self._segments)
self.sensor['Observation/scan_index'] = CategoricalData(
range(len(scan_states)), self._segments)
# Group scans together based on compscan group name and have one label per compound scan
compscan = CategoricalData([s.parent.name for s in self._scan_groups],
self._segments)
compscan.remove_repeats()
label = CategoricalData(compscan_labels, self._segments)
label.align(compscan.events)
self.sensor['Observation/label'] = label
self.sensor['Observation/compscan_index'] = CategoricalData(
range(len(label)), label.events)
# Extract targets from compscan groups, replacing empty or bad descriptions with dummy target
target = CategoricalData([
_robust_target(s.parent.attrs.get('target', ''))
for s in self._scan_groups
], self._segments)
target.align(compscan.events)
self.sensor['Observation/target'] = target
self.sensor['Observation/target_index'] = CategoricalData(
target.indices, target.events)
# Set up catalogue containing all targets in file, with reference antenna as default antenna
self.catalogue.add(target.unique_values)
self.catalogue.antenna = self.sensor['Antennas/%s/antenna' %
(self.ref_ant, )][0]
# Ensure that each target flux model spans all frequencies in data set if possible
self._fix_flux_freq_range()
# Restore original (slow) timestamps so that subsequent sensors (e.g. pointing) will have accurate values
self.sensor.timestamps = self.timestamps
# Apply default selection and initialise all members that depend on selection in the process
self.select(spw=0, subarray=0)