changed "pseudo_stokes" to just "stokes" across the repo

hera_pspec/noise.py

@@ -96,7 +96,6 @@ def calc_scalar(self, freqs, stokes, num_steps=5000, little_h=True):
         self.stokes : str, stokes polarization used to calculate self.scalar
         """
         # parse stokes
-        if stokes == 'I': stokes = 'pseudo_I'
         self.scalar = self.beam.compute_pspec_scalar(freqs.min(), freqs.max(), len(freqs), num_steps=num_steps, 
                                                      stokes=stokes, little_h=little_h, noise_scalar=True)
         self.subband = freqs

hera_pspec/pspecbeam.py

@@ -101,15 +101,15 @@ def __init__(self, cosmo=None):
         else:
             self.cosmo = conversions.Cosmo_Conversions()
 
-    def compute_pspec_scalar(self, lower_freq, upper_freq, num_freqs, num_steps=5000, stokes='pseudo_I',
+    def compute_pspec_scalar(self, lower_freq, upper_freq, num_freqs, num_steps=5000, stokes='I',
                              taper='none', little_h=True, noise_scalar=False):
         """
         Computes the scalar function to convert a power spectrum estimate
         in "telescope units" to cosmological units
 
         See arxiv:1304.4991 and HERA memo #27 for details.
 
-        Currently, only the "pseudo Stokes I", "XX" and "YY" beam are supported.
+        Currently, only the Stokes "I", "XX" and "YY" beam are supported.
         See Equations 4 and 5 of Moore et al. (2017) ApJ 836, 154
         or arxiv:1502.05072 for details.
 
@@ -133,9 +133,9 @@ def compute_pspec_scalar(self, lower_freq, upper_freq, num_freqs, num_steps=5000
 
         stokes: str, optional
                 Which Stokes parameter's to compute the beam scalar for.
-                'pseudo_I', 'pseudo_Q', 'pseudo_U', 'pseudo_V', 'XX', 'YY', 'XY', 'YX', although 
-                currently only 'pseudo_I' and linear dipole pol (e.g. 'XX') are implemented.
-                Default: 'pseudo_I'
+                'I', 'Q', 'U', 'V', 'XX', 'YY', 'XY', 'YX', although 
+                currently only 'I' and linear dipole pol (e.g. 'XX') are implemented.
+                Default: 'I'
 
         taper : str, optional
                 Whether a tapering function (e.g. Blackman-Harris) is being
@@ -171,7 +171,7 @@ def compute_pspec_scalar(self, lower_freq, upper_freq, num_freqs, num_steps=5000
 
         return scalar
 
-    def Jy_to_mK(self, freqs, stokes='pseudo_I'):
+    def Jy_to_mK(self, freqs, stokes='I'):
         """
         Return the multiplicative factor, M [mK / Jy], to convert a visibility from Jy -> mK,
 
@@ -188,9 +188,9 @@ def Jy_to_mK(self, freqs, stokes='pseudo_I'):
 
         stokes: str, optional
                 Which Stokes parameter's to compute the beam scalar for.
-                'pseudo_I', 'pseudo_Q', 'pseudo_U', 'pseudo_V', 'XX', 'YY', 'XY', 'YX', although 
-                currently only 'pseudo_I' and linear dipole pol (e.g. 'XX') are implemented.
-                Default: 'pseudo_I'
+                'I', 'Q', 'U', 'V', 'XX', 'YY', 'XY', 'YX', although 
+                currently only 'I' and linear dipole pol (e.g. 'XX') are implemented.
+                Default: 'I'
 
         Returns
         -------
@@ -233,7 +233,7 @@ def __init__(self, fwhm, beam_freqs, cosmo=None):
         else:
             self.cosmo = conversions.Cosmo_Conversions()
 
-    def power_beam_int(self, stokes='pseudo_I'):
+    def power_beam_int(self, stokes='I'):
         """
         Computes the integral of the beam over solid angle to give
         a beam area (in sr). Uses analytic formula that the answer
@@ -242,25 +242,25 @@ def power_beam_int(self, stokes='pseudo_I'):
         Trivially this returns an array (i.e., a function of frequency),
         but the results are frequency independent.
 
-        Currently, only the "pseudo Stokes I", "XX" and "YY" beam are supported.
+        Currently, only the Stokes "I", "XX" and "YY" beam are supported.
         See Equations 4 and 5 of Moore et al. (2017) ApJ 836, 154
         or arxiv:1502.05072 for details.
 
         Parameters
         ----------
         stokes: str, optional
                 Which Stokes parameter's to compute the beam scalar for.
-                'pseudo_I', 'pseudo_Q', 'pseudo_U', 'pseudo_V', 'XX', 'YY', 'XY', 'YX', although 
-                currently only 'pseudo_I' and linear dipole pol (e.g. 'XX') are implemented.
-                Default: 'pseudo_I'
+                'I', 'Q', 'U', 'V', 'XX', 'YY', 'XY', 'YX', although 
+                currently only 'I' and linear dipole pol (e.g. 'XX') are implemented.
+                Default: 'I'
 
         Returns
         -------
         primary beam area: float, array-like
         """
         return np.ones_like(self.beam_freqs) * 2. * np.pi * self.fwhm**2 / (8. * np.log(2.))
 
-    def power_beam_sq_int(self, stokes='pseudo_I'):
+    def power_beam_sq_int(self, stokes='I'):
         """
         Computes the integral of the beam**2 over solid angle to give
         a beam area (in str). Uses analytic formula that the answer
@@ -269,17 +269,17 @@ def power_beam_sq_int(self, stokes='pseudo_I'):
         Trivially this returns an array (i.e., a function of frequency),
         but the results are frequency independent.
 
-        Currently, only the "pseudo Stokes I", "XX" and "YY" beam are supported.
+        Currently, only the Stokes "I", "XX" and "YY" beam are supported.
         See Equations 4 and 5 of Moore et al. (2017) ApJ 836, 154
         or arxiv:1502.05072 for details.
 
         Parameters
         ----------
         stokes: str, optional
                 Which Stokes parameter's to compute the beam scalar for.
-                'pseudo_I', 'pseudo_Q', 'pseudo_U', 'pseudo_V', 'XX', 'YY', 'XY', 'YX', although 
-                currently only 'pseudo_I' and linear dipole pol (e.g. 'XX') are implemented.
-                Default: 'pseudo_I'
+                'I', 'Q', 'U', 'V', 'XX', 'YY', 'XY', 'YX', although 
+                currently only 'I' and linear dipole pol (e.g. 'XX') are implemented.
+                Default: 'I'
 
         Returns
         -------
@@ -310,23 +310,23 @@ def __init__(self, beam_fname, cosmo=None):
         else:
             self.cosmo = conversions.Cosmo_Conversions()
 
-    def power_beam_int(self, stokes='pseudo_I'):
+    def power_beam_int(self, stokes='I'):
         """
         Computes the integral of the beam over solid angle to give
         a beam area (in str) as a function of frequency. Uses function
         in pyuvdata.
 
-        Currently, only the "pseudo Stokes I", "XX" and "YY" beam are supported.
+        Currently, only the Stokes "I", "XX" and "YY" beam are supported.
         See Equations 4 and 5 of Moore et al. (2017) ApJ 836, 154
         or arxiv:1502.05072 for details.
 
         Parameters
         ----------
         stokes: str, optional
                 Which Stokes parameter's to compute the beam scalar for.
-                'pseudo_I', 'pseudo_Q', 'pseudo_U', 'pseudo_V', 'XX', 'YY', 'XY', 'YX', although 
-                currently only 'pseudo_I' and linear dipole pol (e.g. 'XX') are implemented.
-                Default: 'pseudo_I'
+                'I', 'Q', 'U', 'V', 'XX', 'YY', 'XY', 'YX', although 
+                currently only 'I' and linear dipole pol (e.g. 'XX') are implemented.
+                Default: 'I'
 
         Returns
         -------
@@ -337,23 +337,23 @@ def power_beam_int(self, stokes='pseudo_I'):
         else:
             raise NotImplementedError("Outdated version of pyuvdata.")
 
-    def power_beam_sq_int(self, stokes='pseudo_I'):
+    def power_beam_sq_int(self, stokes='I'):
         """
         Computes the integral of the beam**2 over solid angle to give
         a beam**2 area (in str) as a function of frequency. Uses function
         in pyuvdata.
 
-        Currently, only the "pseudo Stokes I", "XX" and "YY" beam are supported.
+        Currently, only the Stokes "I", "XX" and "YY" beam are supported.
         See Equations 4 and 5 of Moore et al. (2017) ApJ 836, 154
         or arxiv:1502.05072 for details.
 
         Parameters
         ----------
         stokes: str, optional
                 Which Stokes parameter's to compute the beam scalar for.
-                'pseudo_I', 'pseudo_Q', 'pseudo_U', 'pseudo_V', 'XX', 'YY', 'XY', 'YX', although 
-                currently only 'pseudo_I' and linear dipole pol (e.g. 'XX') are implemented.
-                Default: 'pseudo_I'
+                'I', 'Q', 'U', 'V', 'XX', 'YY', 'XY', 'YX', although 
+                currently only 'I' and linear dipole pol (e.g. 'XX') are implemented.
+                Default: 'I'
 
         Returns
         -------

hera_pspec/pspecdata.py

@@ -759,7 +759,7 @@ def delays(self):
             return utils.get_delays(self.freqs[self.spw_range[0]:self.spw_range[1]]) * 1e9 # convert to ns    
 
 
-    def scalar(self, stokes='pseudo_I', taper='none', little_h=True, num_steps=2000, beam=None):
+    def scalar(self, stokes='I', taper='none', little_h=True, num_steps=2000, beam=None):
         """
         Computes the scalar function to convert a power spectrum estimate
         in "telescope units" to cosmological units, using self.spw_range to set spectral window.

hera_pspec/tests/test_noise.py

@@ -41,14 +41,14 @@ def test_add(self):
 
     def test_scalar(self):
         freqs = np.linspace(150e6, 160e6, 100, endpoint=False)
-        self.sense.calc_scalar(freqs, 'pseudo_I', num_steps=5000, little_h=True)
+        self.sense.calc_scalar(freqs, 'I', num_steps=5000, little_h=True)
         nt.assert_true(np.isclose(freqs, self.sense.subband).all())
         nt.assert_true(self.sense.stokes, 'I')
 
     def test_calc_P_N(self):
         # calculate scalar
         freqs = np.linspace(150e6, 160e6, 100, endpoint=False)
-        self.sense.calc_scalar(freqs, 'pseudo_I', num_steps=5000, little_h=True)
+        self.sense.calc_scalar(freqs, 'I', num_steps=5000, little_h=True)
         # basic execution 
         k = np.linspace(0, 3, 10)
         Tsys = 500.0

hera_pspec/tests/test_pspecbeam.py

@@ -44,7 +44,7 @@ def test_UVbeam(self):
         lower_freq = 120.*10**6
         upper_freq = 128.*10**6
         num_freqs = 20
-        scalar = self.bm.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='pseudo_I', num_steps=2000)
+        scalar = self.bm.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='I', num_steps=2000)
 
         # Check that user-defined cosmology can be specified
         bm = pspecbeam.PSpecBeamUV(self.beamfile,
@@ -72,7 +72,7 @@ def test_UVbeam(self):
         self.assertAlmostEqual(scalar/567871703.75268996, 1.0, delta=1e-4)
 
         # convergence of integral
-        scalar_large_Nsteps = self.bm.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='pseudo_I', num_steps=10000) 
+        scalar_large_Nsteps = self.bm.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='I', num_steps=10000) 
         self.assertAlmostEqual(scalar / scalar_large_Nsteps, 1.0, delta=1e-5)
 
         # test taper execution
@@ -93,7 +93,7 @@ def test_UVbeam(self):
         nt.assert_raises(TypeError, self.bm.Jy_to_mK, np.array([1]))
 
         # test noise scalar
-        sclr = self.bm.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='pseudo_I', num_steps=2000, noise_scalar=True)
+        sclr = self.bm.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='I', num_steps=2000, noise_scalar=True)
         nt.assert_almost_equal(sclr, 70.983962969086235)
 
 
@@ -103,7 +103,7 @@ def test_Gaussbeam(self):
         lower_freq = 120.*10**6
         upper_freq = 128.*10**6
         num_freqs = 20
-        scalar = self.gauss.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='pseudo_I', num_steps=2000)
+        scalar = self.gauss.compute_pspec_scalar(lower_freq, upper_freq, num_freqs, stokes='I', num_steps=2000)
 
         # Check that user-defined cosmology can be specified
         bgauss = pspecbeam.PSpecBeamGauss(0.8, 

hera_pspec/uvpspec.py

@@ -962,9 +962,8 @@ def generate_noise_spectra(self, spw, pol, Tsys, blpairs=None,
         # get frequency band
         freqs = self.freq_array[self.spw_to_indices(spw)]
 
-        # calculate scalar, hard-coded to pseudo_I because that is currently all that pyuvdata supports
-        # near-future pyuvdata PR will extend support for extra polarizations
-        self.sensitivity.calc_scalar(freqs, 'pseudo_I', num_steps=num_steps, little_h=little_h)
+        # calculate scalar
+        self.sensitivity.calc_scalar(freqs, pol, num_steps=num_steps, little_h=little_h)
 
         # Get k vectors
         if form == 'DelSq':