Merge 5582a15 into 82c0a86

docs/conf.py

@@ -25,7 +25,10 @@
 
 # Mock-import modules to allow build to complete without throwing errors
 import mock
-MOCK_MODULES = ['numpy', 'scipy', 'scipy.interpolate', 'pyuvdata', 'h5py', 'aipy', 'omnical', 'linsolve', 'hera_qm', 'uvtools', 'hera_cal', 'healpy', 'scikit-learn']
+MOCK_MODULES = ['numpy', 'scipy', 'scipy.interpolate', 'scipy.integrate', 
+                'pyuvdata', 'h5py', 'aipy', 'omnical', 'linsolve', 'hera_qm', 
+                'uvtools', 'hera_cal', 'healpy', 'scikit-learn', 'astropy', 
+                'astropy.cosmology', 'matplotlib', 'matplotlib.pyplot', 'yaml']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = mock.Mock()
 

docs/index.rst

@@ -19,6 +19,7 @@ You can find the code in the ``hera_pspec`` `GitHub repository <https://github.c
    pspecdata
    uvpspec
    container
+   plot
 
 
 Indices and tables

docs/plot.rst

@@ -0,0 +1,30 @@
+Simple plotting functions
+=========================
+
+The ``hera_pspec.plot`` module contains functions for making simple plots of delay power spectra.
+
+The following example plots the power spectra from a ``UVPSpec`` object, averaged over baseline-pairs and times.
+
+.. code-block:: python
+  
+  # Load or generate a UVPSpec object containing delay power spectra
+  uvp = ...
+  
+  # Set which baseline-pairs should be included in the plot
+  blpairs = list(uvp.blpair_array) # This includes all blpairs!
+  
+  # Plot the delay spectrum, averaged over all blpairs and times
+  # (for the spectral window with index=0, and polarization 'xx')
+  ax = hp.plot.delay_spectrum(uvp, [blpairs,], spw=0, pol='xx', 
+                              average_blpairs=True, average_times=True, 
+                              delay=False)
+  
+  # Setting delay=False plots the power spectrum in cosmological units
+  
+For a more extensive worked example, see `this example Jupyter notebook <https://github.com/HERA-Team/hera_pspec/blob/master/examples/Plotting_examples.ipynb>`_.
+
+The only plotting function currently available in the `hera_pspec.plot` module is `delay_spectrum()`.
+
+.. autofunction:: hera_pspec.plot.delay_spectrum
+
+

docs/pspec.rst

@@ -94,6 +94,7 @@ The most frequently-used methods from ``PSpecData`` are listed below. See :any:`
 
 .. autoclass:: hera_pspec.PSpecData
   :members: __init__, add, pspec, rephase_to_dset, scalar, delays, units
+  :noindex:
 
 
 ``UVPSpec``: Container for power spectra
@@ -167,6 +168,7 @@ The ``UVPSpec`` class
 The most relevant methods from ``UVPSpec`` are listed below. See :any:`uvpspec` for a full listing of all methods provided by ``UVPSpec``.
 
 .. autoclass:: hera_pspec.UVPSpec
-  :members: __init__, get_data, get_wgts, get_integrations, get_nsamples, get_dlys, get_kvecs, get_blpair_seps, select, read_hdf5, write_hdf5, generate_noise_spectra, average_spectra, fold_spectra, get_blpair_groups_from_bl_groups
+  :members: __init__, get_data, get_wgts, get_integrations, get_nsamples, get_dlys, get_kperps, get_kparas, get_blpair_seps, select, read_hdf5, write_hdf5, generate_noise_spectra, average_spectra, fold_spectra, get_blpair_groups_from_bl_groups
+  :noindex:
 
 

hera_pspec/conversions.py

@@ -4,11 +4,10 @@
 
 Cosmological and instrumental
 conversion functions for hera_pspec
-
-
 """
 import numpy as np
-from scipy import integrate
+import scipy.integrate as integrate
+
 try:
     from astropy.cosmology import LambdaCDM
     _astropy = True

hera_pspec/plot.py

@@ -30,7 +30,8 @@ def delay_spectrum(uvp, blpairs, spw, pol, average_blpairs=False,
         If True, average spectra over the time axis. Default: False.
     
     fold : bool, optional
-        Whether to fold the power spectrum in |k_parallel|. Default: False.
+        Whether to fold the power spectrum in :math:`|k_\parallel|`. 
+        Default: False.
     
     plot_noise : bool, optional
         Whether to plot noise power spectrum curves or not. Default: False.

hera_pspec/pspecbeam.py

@@ -1,14 +1,10 @@
 import numpy as np
 import os
-import aipy
-import pyuvdata
-from hera_pspec import conversions
-from scipy import __version__ as scipy_version
-from scipy import integrate
+import hera_pspec.conversions as conversions
+import scipy.integrate as integrate
 from scipy.interpolate import interp1d
+from pyuvdata import UVBeam, utils as uvutils
 import aipy
-from pyuvdata import utils as uvutils
-
 
 def _compute_pspec_scalar(cosmo, beam_freqs, omega_ratio, pspec_freqs, 
                           num_steps=5000, taper='none', little_h=True, 
@@ -241,17 +237,20 @@ def Jy_to_mK(self, freqs, pol='I'):
 
     def get_Omegas(self, pols):
         """
-        Get OmegaP and OmegaPP across beam_freqs for requested polarizatiosn
+        Get OmegaP and OmegaPP across beam_freqs for requested polarizations.
 
         Parameters
         ----------
-        pols : list of polarization strings or integers
+        pols : list
+            List of polarization strings or integers.
 
-        Returns (OmegaP, OmegaPP)
+        Returns
         -------
-        OmegaP : ndarray containing power_beam_int, shape=(Nbeam_freqs, Npols)
+        OmegaP : array_like
+            Array containing power_beam_int, shape: (Nbeam_freqs, Npols).
 
-        OmegaPP : ndarray containing power_sq_beam_int, shape=(Nbeam_freqs, Npols)
+        OmegaPP : array_like
+            Array containing power_sq_beam_int, shape: (Nbeam_freqs, Npols).
         """
         # type check
         if isinstance(pols, (int, np.int, np.int32)):
@@ -373,7 +372,7 @@ def __init__(self, beam_fname, cosmo=None):
             Cosmology object. Uses the default cosmology object if not 
             specified. Default: None.
         """
-        self.primary_beam = pyuvdata.UVBeam()
+        self.primary_beam = UVBeam()
         self.primary_beam.read_beamfits(beam_fname)
 
         self.beam_freqs = self.primary_beam.freq_array[0]
@@ -608,7 +607,8 @@ def power_beam_sq_int(self, pol='I'):
 
         Returns
         -------
-        primary_beam_area: float, array-like
+        primary_beam_area: array_like
+            Array of floats containing the primary beam-squared area.
         """
         if pol in self.OmegaPP.keys():
             return self.OmegaPP[pol]
@@ -620,7 +620,7 @@ def power_beam_sq_int(self, pol='I'):
 
     def __str__(self):
         """
-        Print string with useful information.
+        Return a string with useful information about this object.
         """
         s = "PSpecBeamFromArray object\n"
         s += "\tFrequency range: Min. %4.4e Hz, Max. %4.4e Hz\n" \

hera_pspec/pspecdata.py

@@ -1048,8 +1048,8 @@ def pspec(self, bls1, bls2, dsets, input_data_weight='identity', norm='I',
               taper='none', little_h=True, spw_ranges=None, verbose=True, 
               history=''):
         """
-        Estimate the delay power spectrum from a pair of datasets contained in this 
-        object, using the optimal quadratic estimator from arXiv:1502.06016.
+        Estimate the delay power spectrum from a pair of datasets contained in 
+        this object, using the optimal quadratic estimator of arXiv:1502.06016.
 
         In this formulation, the power spectrum is proportional to the 
         visibility data via
@@ -1071,9 +1071,8 @@ def pspec(self, bls1, bls2, dsets, input_data_weight='identity', norm='I',
 
         Parameters
         ----------
-        bls1 : list of baseline groups, each being a list of ant-pair tuples
-
-        bls2 : list of baseline groups, each being a list of ant-pair tuples
+        bls1, bls2 : list
+            List of baseline groups, each group being a list of ant-pair tuples.
 
         dsets : length-2 tuple or list
             Contains indices of self.dsets to use in forming power spectra, 
@@ -1101,11 +1100,10 @@ def pspec(self, bls1, bls2, dsets, input_data_weight='identity', norm='I',
             A list of spectral window channel ranges to select within the total 
             bandwidth of the datasets, each of which forms an independent power 
             spectrum estimate. Example: [(220, 320), (650, 775)].
-            
             Each tuple should contain a start and stop channel used to index 
             the `freq_array` of each dataset. The default (None) is to use the 
             entire band provided in each dataset.
-
+        
         verbose : bool, optional
             If True, print progress, warnings and debugging info to stdout.
 
@@ -1119,30 +1117,41 @@ def pspec(self, bls1, bls2, dsets, input_data_weight='identity', norm='I',
 
         Examples
         --------
-        Example 1 : no grouping, i.e. each baseline is its own group, no 
-        brackets needed for each bl.
-        if
+        *Example 1:* No grouping; i.e. each baseline is its own group, no 
+        brackets needed for each bl. If::
+        
             A = (1, 2); B = (2, 3); C = (3, 4); D = (4, 5); E = (5, 6); F = (6, 7)
-        and
+        
+        and::
+        
             bls1 = [ A, B, C ]
             bls2 = [ D, E, F ]
-        then
+        
+        then::
+        
             blpairs = [ (A, D), (B, E), (C, F) ]
 
-        Example 2: grouping, blpairs come in lists of blgroups, which are considered 
-        "grouped" in OQE
-        if
+        *Example 2:* Grouping; blpairs come in lists of blgroups, which are 
+        considered "grouped" in OQE. 
+        If::
+        
             bls1 = [ [A, B], [C, D] ]
             bls2 = [ [C, D], [E, F] ]
-        then
+        
+        then::
+        
             blpairs = [ [(A, C), (B, D)], [(C, E), (D, F)] ]   
     
-        Example 3: mixed grouping, i.e. some blpairs are grouped, others are not
-        if
+        *Example 3:* Mixed grouping; i.e. some blpairs are grouped, others are 
+        not. If::
+        
             bls1 = [ [A, B], C ]
             bls2 = [ [D, E], F ]
-        then
+        
+        then::
+        
             blpairs = [ [(A, D), (B, E)], (C, F)]
+        
         """
         # Validate the input data to make sure it's sensible
         self.validate_datasets(verbose=verbose)