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Merge 3179c5f into aca6586
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Aaron Ewall-Wice committed Jul 17, 2019
2 parents aca6586 + 3179c5f commit bf1a088
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Showing 10 changed files with 1,612 additions and 606 deletions.
624 changes: 624 additions & 0 deletions examples/Inverse_sinc_weighting_example.ipynb
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383 changes: 242 additions & 141 deletions hera_pspec/pspecdata.py
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70 changes: 41 additions & 29 deletions hera_pspec/testing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,12 @@
from pyuvdata import UVData
from hera_cal.utils import JD2LST
from scipy import stats
import hera_pspec.uvpspec_utils as uvputils


def build_vanilla_uvpspec(beam=None):
"""
Build an example vanilla UVPSpec object from scratch, with all necessary
Build an example vanilla UVPSpec object from scratch, with all necessary
metadata.
Parameters
Expand Down Expand Up @@ -56,7 +57,7 @@ def build_vanilla_uvpspec(beam=None):
spw_freq_array = np.tile(np.arange(Nspws), Nfreqs)
spw_dly_array = np.tile(np.arange(Nspws), Ndlys)
spw_array = np.arange(Nspws)
freq_array = np.repeat(np.linspace(100e6, 105e6, Nfreqs, endpoint=False),
freq_array = np.repeat(np.linspace(100e6, 105e6, Nfreqs, endpoint=False),
Nspws)
dly_array = np.repeat(utils.get_delays(freq_array, n_dlys=Ndlys), Nspws)
polpair_array = np.array([1515,]) # corresponds to ('xx','xx')
Expand All @@ -72,6 +73,7 @@ def build_vanilla_uvpspec(beam=None):
scalar_array = np.ones((Nspws, Npols), np.float)
label1 = 'red'
label2 = 'blue'
r_params = ''
labels = np.array([label1, label2])
label_1_array = np.ones((Nspws, Nblpairts, Npols), np.int) * 0
label_2_array = np.ones((Nspws, Nblpairts, Npols), np.int) * 1
Expand All @@ -94,25 +96,25 @@ def build_vanilla_uvpspec(beam=None):
data_array[s] = np.ones((Nblpairts, Ndlys, Npols), dtype=np.complex) \
* blpair_array[:, None, None] / 1e9
wgt_array[s] = np.ones((Nblpairts, Nfreqs, 2, Npols), dtype=np.float)
# NB: The wgt_array has dimensions Nfreqs rather than Ndlys; it has the
# NB: The wgt_array has dimensions Nfreqs rather than Ndlys; it has the
# dimensions of the input visibilities, not the output delay spectra
integration_array[s] = np.ones((Nblpairts, Npols), dtype=np.float)
nsample_array[s] = np.ones((Nblpairts, Npols), dtype=np.float)
cov_array[s] =np.moveaxis(np.array([[np.identity(Ndlys,dtype=np.complex)\
for m in range(Nblpairts)]
for m in range(Nblpairts)]
for n in range(Npols)]), 0, -1)

params = ['Ntimes', 'Nfreqs', 'Nspws', 'Nspwdlys', 'Nspwfreqs', 'Nspws',
'Nblpairs', 'Nblpairts', 'Npols', 'Ndlys', 'Nbls',
'blpair_array', 'time_1_array', 'time_2_array',
params = ['Ntimes', 'Nfreqs', 'Nspws', 'Nspwdlys', 'Nspwfreqs', 'Nspws',
'Nblpairs', 'Nblpairts', 'Npols', 'Ndlys', 'Nbls',
'blpair_array', 'time_1_array', 'time_2_array',
'lst_1_array', 'lst_2_array', 'spw_array',
'dly_array', 'freq_array', 'polpair_array', 'data_array',
'wgt_array',
'dly_array', 'freq_array', 'polpair_array', 'data_array',
'wgt_array', 'r_params',
'integration_array', 'bl_array', 'bl_vecs', 'telescope_location',
'vis_units', 'channel_width', 'weighting', 'history', 'taper',
'norm', 'git_hash', 'nsample_array', 'time_avg_array',
'lst_avg_array', 'cosmo', 'scalar_array', 'labels', 'norm_units',
'labels', 'label_1_array', 'label_2_array', 'store_cov',
'vis_units', 'channel_width', 'weighting', 'history', 'taper',
'norm', 'git_hash', 'nsample_array', 'time_avg_array',
'lst_avg_array', 'cosmo', 'scalar_array', 'labels', 'norm_units',
'labels', 'label_1_array', 'label_2_array', 'store_cov',
'cov_array', 'spw_dly_array', 'spw_freq_array']

if beam is not None:
Expand All @@ -127,9 +129,9 @@ def build_vanilla_uvpspec(beam=None):
return uvp, cosmo


def uvpspec_from_data(data, bl_grps, data_std=None, spw_ranges=None,
beam=None, taper='none', cosmo=None, n_dlys=None,
verbose=False):
def uvpspec_from_data(data, bl_grps, data_std=None, spw_ranges=None,
beam=None, taper='none', cosmo=None, n_dlys=None,
r_params = None, verbose=False):
"""
Build an example UVPSpec object from a visibility file and PSpecData.
Expand All @@ -139,16 +141,16 @@ def uvpspec_from_data(data, bl_grps, data_std=None, spw_ranges=None,
This can be a UVData object or a string filepath to a miriad file.
bl_grps : list
This is a list of baseline groups (e.g. redundant groups) to form
This is a list of baseline groups (e.g. redundant groups) to form
blpairs from.
Ex: [[(24, 25), (37, 38), ...], [(24, 26), (37, 39), ...], ... ]
data_std: UVData object or str, optional
Can be UVData object or a string filepath to a miriad file.
Can be UVData object or a string filepath to a miriad file.
Default: None.
spw_ranges : list, optional
List of spectral window tuples. See PSpecData.pspec docstring for
List of spectral window tuples. See PSpecData.pspec docstring for
details. Default: None.
beam : PSpecBeamBase subclass or str, optional
Expand All @@ -160,11 +162,22 @@ def uvpspec_from_data(data, bl_grps, data_std=None, spw_ranges=None,
cosmo : Cosmo_Conversions object
Cosmology object.
n_dlys : int, optional
Number of delay bins to use. Default: None (uses as many delay bins as
Number of delay bins to use. Default: None (uses as many delay bins as
frequency channels).
r_params: dictionary with parameters for weighting matrix.
Proper fields
and formats depend on the mode of data_weighting.
data_weighting == 'sinc_downweight':
dictionary with fields
'filter_centers', list of floats (or float) specifying the (delay) channel numbers
at which to center filtering windows. Can specify fractional channel number.
'filter_widths', list of floats (or float) specifying the width of each
filter window in (delay) channel numbers. Can specify fractional channel number.
'filter_factors', list of floats (or float) specifying how much power within each filter window
is to be suppressed.
verbose : bool, optional
if True, report feedback to standard output. Default: False.
Expand Down Expand Up @@ -201,7 +214,7 @@ def uvpspec_from_data(data, bl_grps, data_std=None, spw_ranges=None,
beam.cosmo = cosmo

# instantiate pspecdata
ds = pspecdata.PSpecData(dsets=[uvd, uvd], dsets_std=[uvd_std, uvd_std],
ds = pspecdata.PSpecData(dsets=[uvd, uvd], dsets_std=[uvd_std, uvd_std],
wgts=[None, None], labels=['d1', 'd2'], beam=beam)

# get blpair groups
Expand All @@ -213,16 +226,16 @@ def uvpspec_from_data(data, bl_grps, data_std=None, spw_ranges=None,
"bl_grps must be fed as a list of lists of tuples"
bls1, bls2 = [], []
for blgrp in bl_grps:
_bls1, _bls2, _ = utils.construct_blpairs(blgrp, exclude_auto_bls=True,
_bls1, _bls2, _ = utils.construct_blpairs(blgrp, exclude_auto_bls=True,
exclude_permutations=True)
bls1.extend(_bls1)
bls2.extend(_bls2)

# run pspec
uvp = ds.pspec(bls1, bls2, (0, 1), (pol, pol), input_data_weight='identity',
spw_ranges=spw_ranges, taper=taper, verbose=verbose,
store_cov=store_cov, n_dlys=n_dlys)
uvp = ds.pspec(bls1, bls2, (0, 1), (pol, pol), input_data_weight='identity',
spw_ranges=spw_ranges, taper=taper, verbose=verbose,
store_cov=store_cov, n_dlys=n_dlys, r_params = r_params)

return uvp


Expand Down Expand Up @@ -292,7 +305,7 @@ def noise_sim(data, Tsys, beam=None, Nextend=0, seed=None, inplace=False,
if beam is not None:
if isinstance(beam, (str, np.str)):
beam = pspecbeam.PSpecBeamUV(beam)
assert isinstance(beam, pspecbeam.PSpecBeamBase)
assert isinstance(beam, pspecbeam.PSpecBeamBase)

# Extend times
Nextend = int(Nextend)
Expand Down Expand Up @@ -342,4 +355,3 @@ def noise_sim(data, Tsys, beam=None, Nextend=0, seed=None, inplace=False,

if not inplace:
return data

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