tutorial.rst
Tutorial
========
Example 1
---------
UVData: Converting between tested data formats
a) miriad (aipy) -> uvfits
**************************
::
from pyuvdata import UVData
UV = UVData()
miriad_file = 'pyuvdata/data/new.uvA'
UV.read_miriad(miriad_file) # this miriad file is known to be a drift scan
UV.write_uvfits('new.uvfits', force_phase=True, spoof_nonessential=True) # write out the uvfits file
b) uvfits -> miriad (aipy)
**************************
::
from pyuvdata import UVData
UV = UVData()
uvfits_file = 'pyuvdata/data/day2_TDEM0003_10s_norx_1src_1spw.uvfits'
UV.read_uvfits(uvfits_file)
UV.write_uvfits('day2_TDEM0003_10s_norx_1src_1spw.uv') # write out the miriad file
c) FHD -> uvfits
****************
When reading FHD format, we need to point to several files.::
from pyuvdata import UVData
UV = UVData()
fhd_prefix = 'pyuvdata/data/fhd_vis_data/1061316296_'
# Construct the list of files
fhd_files = [fhd_prefix + f for f in ['flags.sav', 'vis_XX.sav', 'params.sav',
'vis_YY.sav', 'vis_model_XX.sav',
'vis_model_YY.sav', 'settings.txt']]
UV.read_fhd(fhd_files)
UV.write_uvfits('1061316296.uvfits', spoof_nonessential=True)
d) FHD -> miriad (aipy)
****************
::
from pyuvdata import UVData
UV = UVData()
fhd_prefix = 'pyuvdata/data/fhd_vis_data/1061316296_'
# Construct the list of files
fhd_files = [fhd_prefix + f for f in ['flags.sav', 'vis_XX.sav', 'params.sav',
'vis_YY.sav', 'vis_model_XX.sav',
'vis_model_YY.sav', 'settings.txt']]
UV.read_fhd(fhd_files)
UV.write_uvfits('1061316296.uvfits')
Example 2
---------
UVData: Phasing/unphasing data::
from pyuvdata import UVData
import ephem
UV = UVData()
miriad_file = 'pyuvdata/data/new.uvA'
UV.read_miriad(miriad_file)
print(UV.phase_type) # Data is a drift scan
UV.phase_to_time(UV.time_array[0]) # Phases the data to the zenith at first time step
print(UV.phase_type) # Data should now be phased
UV.unphase_to_drift() # Undo phasing to try another phase center
UV.phase(5.23368, 0.710940, ephem.J2000) # Phase to a specific ra/dec/epoch (in radians)
Example 3
---------
UVData: Making a simple waterfall plot::
from pyuvdata import UVData
import numpy as np
import matplotlib.pyplot as plt
UV = UVData()
filename = 'pyuvdata/data/day2_TDEM0003_10s_norx_1src_1spw.uvfits'
UV.read_uvfits(filename)
print(UV.data_array.shape) # Data should have shape (Nblts, Nspws, Nfreqs, Npols)
print(UV.Ntimes) # Number of time samples in data
print(UV.Nfreqs) # Number of frequency channels in data
bl = UV.antnums_to_baseline(1, 2) # Convert antenna numbers (e.g. 1, 2) to baseline number
bl_ind = np.where(UV.baseline_array == bl)[0] # Indices corresponding to baseline
plt.imshow(np.abs(UV.data_array[bl_ind, 0, :, 0])) # Amplitude waterfall for 0th spectral window and 0th polarization
plt.show()
Example 4
---------
Selecting data (UVData): The select method lets you select specific antennas (by number or name),
antenna pairs, frequencies (in Hz or by channel number), times or polarizations
to keep in the object while removing others.
a) Select 3 antennas to keep using the antenna number.
****************
::
from pyuvdata import UVData
import numpy as np
UV = UVData()
filename = 'pyuvdata/data/day2_TDEM0003_10s_norx_1src_1spw.uvfits'
UV.read_uvfits(filename)
# print all the antennas numbers with data in the original file
print(np.unique(UV.ant_1_array.tolist() + UV.ant_2_array.tolist()))
UV.select(antenna_nums=[0, 11, 20])
# print all the antennas numbers with data after the select
print(np.unique(UV.ant_1_array.tolist() + UV.ant_2_array.tolist()))
b) Select 3 antennas to keep using the antenna names, also select 5 frequencies to keep.
****************
::
from pyuvdata import UVData
import numpy as np
UV = UVData()
filename = 'pyuvdata/data/day2_TDEM0003_10s_norx_1src_1spw.uvfits'
UV.read_uvfits(filename)
# print all the antenna names with data in the original file
unique_ants = np.unique(UV.ant_1_array.tolist() + UV.ant_2_array.tolist())
print([UV.antenna_names[np.where(UV.antenna_numbers==a)[0][0]] for a in unique_ants])
# print all the frequencies in the original file
print(UV.freq_array)
UV.select(antenna_names=['N02', 'E09', 'W06'], frequencies=UV.freq_array[0,0:4])
# print all the antenna names with data after the select
unique_ants = np.unique(UV.ant_1_array.tolist() + UV.ant_2_array.tolist())
print([UV.antenna_names[np.where(UV.antenna_numbers==a)[0][0]] for a in unique_ants])
# print all the frequencies after the select
print(UV.freq_array)
c) Select a few antenna pairs to keep
****************
::
from pyuvdata import UVData
UV = UVData()
filename = 'pyuvdata/data/day2_TDEM0003_10s_norx_1src_1spw.uvfits'
UV.read_uvfits(filename)
# print all the antenna pairs with data in the original file
print(set(zip(UV.ant_1_array, UV.ant_2_array)))
UV.select(ant_pairs_nums=[(0, 2), (6, 0), (0, 21)])
# note that order of the values in the pair does not matter
# print all the antenna pairs after the select
print(set(zip(UV.ant_1_array, UV.ant_2_array)))
Example 5
---------
Calibration files using UVCal.
a) Reading a gain calibration file.
****************
::
from pyuvdata import UVCal
import numpy as np
import matplotlib.pyplot as plt
cal = UVCal()
filename = 'pyuvdata/data/zen.2457698.40355.xx.fitsA'
cal.read_calfits(filename)
print 'Cal Type = ', cal.cal_type # should print out 'gains'
print 'Number of jones parameters = ', cal.Njones, cal.jones_array # number of antenna polarizations and polarization type.
print 'Number of antennas with data = ', cal.Nants_data
print 'Number of frequencies = ', cal.Nfreqs
print 'Shape of the gain_array', cal.gain_array.shape # (cal.Nants_data, cal.Nfreqs, cal.Ntimes, cal.Njones)
for ant in range(cal.Nants_data):
plt.plot(cal.freq_array.flatten(), np.abs(cal.gain_array[ant, 0, :, 0, 0])) # plot abs of all gains for first time and first jones polarization.
plt.xlabel('Frequency (Hz)')
plt.ylabel('Abs(gains)')
plt.show()
b) Writing a gain calibration file.
****************
::
from pyuvdata import UVCal
import numpy as np
time_array = 2457698 + np.linspace(.2, .3, 16) # time_array in JD
Ntimes = len(time_array)
freq_array = np.linspace(1e6, 2e6, 1024) # frequency array in Hz
Nfreqs = len(freq_array)
jones_array = np.array([-5, -6]) # only 2 jones parameters.
Njones = len(jones_array)
ant_array = np.arange(19)
Nants_data = len(ant_array)
antenna_names = np.array(['ant{0}.format(ant)' for ant in ant_array])
Nspws = 1 # only 1 spw is supported
# Generate fake data
gains = (np.random.randn(Nants_data, Nspws, Nfreqs, Ntimes, Njones)
+ 1j*np.random.randn(Nants_data, Nspws, Nfreqs, Ntimes, Njones))
flags = np.ones_like(gains, dtype=np.bool)
chisq = np.random.randn(Nants_data, Nspws, Nfreqs, Ntimes, Njones)
cal = UVCal()
cal.set_gain()
cal.Nfreqs = Nfreqs
cal.Njones = Njones
cal.Ntimes = Ntimes
cal.history = 'This is an example file generated from tutorial 5b of pycaldata.'
cal.Nspws = 1
cal.freq_array = freq_array.reshape(cal.Nspws, -1)
cal.freq_range = [freq_array[0], freq_array[-1]] # valid frequencies for solutions.
cal.channel_width = np.diff(freq_array)[0]
cal.jones_array = jones_array
cal.time_array = time_array
cal.integration_time = np.diff(time_array)[0]
cal.gain_convention = 'divide' # Use this operation to apply gain solution.
cal.x_orientation = 'east' # orientation of 1st jones parameter.
cal.time_range = [time_array[0], time_array[-1]]
cal.telescope_name = 'Fake Telescope'
cal.Nants_data = Nants_data
cal.Nants_telescope = Nants_data # have solutions for all antennas in array.
cal.ant_array = ant_array
cal.antenna_names = antenna_names
cal.antenna_numbers = ant_array
cal.flag_array = flags
cal.gain_array = gains
cal.quality_array = chisq
cal.write_calfits('tutorial5b.fits')
Example 6
---------
Selecting data (UVCal): The select method lets you select specific antennas (by number or name),
frequencies (in Hz or by channel number), times or polarizations
to keep in the object while removing others.
a) Select 3 antennas to keep using the antenna number.
****************
::
from pyuvdata import UVCal
import numpy as np
cal = UVCal()
filename = 'pyuvdata/data/zen.2457698.40355.xx.fitsA'
cal.read_calfits(filename)
# print all the antennas numbers with data in the original file
print(cal.ant_array)
cal.select(antenna_nums=[9, 22, 64])
# print all the antennas numbers with data after the select
print(cal.ant_array)
b) Select 3 antennas to keep using the antenna names, also select 5 frequencies to keep.
****************
::
from pyuvdata import UVCal
import numpy as np
cal = UVCal()
filename = 'pyuvdata/data/zen.2457698.40355.xx.fitsA'
cal.read_calfits(filename)
# print all the antenna names with data in the original file
print([cal.antenna_names[np.where(cal.antenna_numbers==a)[0][0]] for a in cal.ant_array])
# print all the frequencies in the original file
print(cal.freq_array)
cal.select(antenna_names=['ant31', 'ant81', 'ant104'], freq_chans=np.arange(0, 4))
# print all the antenna names with data after the select
print([cal.antenna_names[np.where(cal.antenna_numbers==a)[0][0]] for a in cal.ant_array])
# print all the frequencies after the select
print(cal.freq_array)
