Merge pull request #366 from HERA-Team/fix-numpy-warnings

Fix numpy warnings

Author: steven-murray

.github/workflows/ci.yml

@@ -66,5 +66,4 @@ jobs:
         env_vars: OS,PYTHON
         name: codecov-umbrella
         fail_ci_if_error: true
-        path_to_write_report: ./coverage/codecov_report.txt
         verbose: true

examples/Overview_Core_Pspec_functions.ipynb

@@ -544,7 +544,7 @@ def combine_psc_spectra(psc, groups=None, dset_split_str='_x_', ext_split_str='_
         If True, overwrite output spectra if they exist.
     """
     # Load container
-    if isinstance(psc, (str, np.str)):
+    if isinstance(psc, str):
         psc = PSpecContainer(psc, mode='rw')
     else:
         assert isinstance(psc, PSpecContainer)

hera_pspec/container.py

@@ -259,7 +259,7 @@ def average_spectra(uvp_in, blpair_groups=None, time_avg=False,
     # stat_l is a list of supplied error_fields, to sum over.
     if isinstance(error_field, (list, tuple, np.ndarray)):
         stat_l = list(error_field)
-    elif isinstance(error_field, (str, np.str)):
+    elif isinstance(error_field, str):
         stat_l = [error_field]
     else:
         stat_l = []
@@ -526,7 +526,7 @@ def average_spectra(uvp_in, blpair_groups=None, time_avg=False,
             lst_2.extend([np.mean(np.unwrap(uvp.lst_2_array[blpairts]))%(2*np.pi)])
             lst_avg_arr.extend([np.mean(np.unwrap(uvp.lst_avg_array[blpairts]))%(2*np.pi)])
         else:
-            blpair_arr.extend(np.ones_like(blpairts, np.int) * blpg[0])
+            blpair_arr.extend(np.ones_like(blpairts, int) * blpg[0])
             time_1.extend(uvp.time_1_array[blpairts])
             time_2.extend(uvp.time_2_array[blpairts])
             time_avg_arr.extend(uvp.time_avg_array[blpairts])
@@ -746,7 +746,7 @@ def spherical_average(uvp_in, kbins, bin_widths, blpair_groups=None, time_avg=Fa
         dlys_array.extend(taus)
 
         # store kbins as delay bins
-        spw_dlys_array.extend(np.ones_like(taus, dtype=np.int) * spw)
+        spw_dlys_array.extend(np.ones_like(taus, dtype=int) * spw)
 
         # iterate over blpairs
         for b, blp in enumerate(uvp.get_blpairs()):
@@ -1488,8 +1488,8 @@ def bootstrap_resampled_error(uvp, blpair_groups=None, time_avg=False, Nsamples=
     """
     from hera_pspec import UVPSpec
     # type check
-    assert isinstance(uvp, (UVPSpec, str, np.str)), "uvp must be fed as a UVPSpec object or filepath"
-    if isinstance(uvp, (str, np.str)):
+    assert isinstance(uvp, (UVPSpec, str)), "uvp must be fed as a UVPSpec object or filepath"
+    if isinstance(uvp, str):
         _uvp = UVPSpec()
         _uvp.read_hdf5(uvp)
         uvp = _uvp
@@ -1623,7 +1623,7 @@ def bootstrap_run(filename, spectra=None, blpair_groups=None, time_avg=False, Ns
     from hera_pspec import uvpspec
     from hera_pspec import PSpecContainer
     # type check
-    if isinstance(filename, (str, np.str)):
+    if isinstance(filename, str):
         # open in transactional mode
         psc = PSpecContainer(filename, mode='rw', keep_open=False, swmr=False, tsleep=0.5, maxiter=maxiter)
     elif isinstance(filename, PSpecContainer):

hera_pspec/grouping.py

@@ -94,7 +94,7 @@ def set_cosmology(self, cosmo):
         ----------
         cosmo : conversions.Cosmo_Conversions instance, or self.cosmo_params string, or dictionary
         """
-        if isinstance(cosmo, (str, np.str)):
+        if isinstance(cosmo, str):
             cosmo = ast.literal_eval(cosmo)
         if isinstance(cosmo, (dict, odict)):
             cosmo = conversions.Cosmo_Conversions(**cosmo)

hera_pspec/noise.py

@@ -69,7 +69,7 @@ def _compute_pspec_scalar(cosmo, beam_freqs, omega_ratio, pspec_freqs,
     df = np.median(np.diff(pspec_freqs))
     integration_freqs = np.linspace(pspec_freqs.min(),
                                     pspec_freqs.min() + df*len(pspec_freqs),
-                                    num_steps, endpoint=True, dtype=np.float)
+                                    num_steps, endpoint=True, dtype=float)
 
     # The interpolations are generally more stable in MHz
     integration_freqs_MHz = integration_freqs / 1e6
@@ -92,7 +92,7 @@ def _compute_pspec_scalar(cosmo, beam_freqs, omega_ratio, pspec_freqs,
 
     # Get B_pp = \int dnu taper^2 and Bp = \int dnu
     if taper == 'none':
-        dBpp_over_BpSq = np.ones_like(integration_freqs, np.float)
+        dBpp_over_BpSq = np.ones_like(integration_freqs, float)
     else:
         dBpp_over_BpSq = dspec.gen_window(taper, len(pspec_freqs))**2.
         dBpp_over_BpSq = interp1d(pspec_freqs, dBpp_over_BpSq, kind='nearest',
@@ -231,12 +231,12 @@ def Jy_to_mK(self, freqs, pol='pI'):
             Contains Jy -> mK factor at each frequency.
         """
         # Check input types
-        if isinstance(freqs, (np.float, float)):
+        if isinstance(freqs, float):
             freqs = np.array([freqs])
         elif not isinstance(freqs, np.ndarray):
             raise TypeError("freqs must be fed as a float ndarray")
         elif isinstance(freqs, np.ndarray) \
-            and freqs.dtype not in (float, np.float, np.float64):
+            and freqs.dtype not in (float, np.float64):
             raise TypeError("freqs must be fed as a float ndarray")
 
         # Check frequency bounds
@@ -477,7 +477,7 @@ def beam_normalized_response(self, pol='pI', freq=None, x_orientation=None):
         beam_res = self.primary_beam._interp_freq(freq) # interpolate beam in frequency, based on the data frequencies
         beam_res = beam_res[0]
 
-        if isinstance(pol, (str, np.str)):
+        if isinstance(pol, str):
             pol = uvutils.polstr2num(pol, x_orientation=x_orientation)
 
         pol_array = self.primary_beam.polarization_array
@@ -684,8 +684,8 @@ def add_pol(self, pol, OmegaP, OmegaPP):
 
         # Make sure OmegaP and OmegaPP are arrays
         try:
-            OmegaP = np.array(OmegaP).astype(np.float)
-            OmegaPP = np.array(OmegaPP).astype(np.float)
+            OmegaP = np.array(OmegaP).astype(float)
+            OmegaPP = np.array(OmegaPP).astype(float)
         except:
             raise TypeError("OmegaP and OmegaPP must both be array_like.")
 

hera_pspec/pspecbeam.py

@@ -629,7 +629,7 @@ def C_model(self, key, model='empirical', time_index=None, known_cov=None, inclu
         """
         # type check
         assert isinstance(key, tuple), "key must be fed as a tuple"
-        assert isinstance(model, (str, np.str)), "model must be a string"
+        assert isinstance(model, str), "model must be a string"
 
         # parse key
         dset, bl = self.parse_blkey(key)
@@ -720,7 +720,7 @@ def cross_covar_model(self, key1, key2, model='empirical',
         # type check
         assert isinstance(key1, tuple), "key1 must be fed as a tuple"
         assert isinstance(key2, tuple), "key2 must be fed as a tuple"
-        assert isinstance(model, (str, np.str)), "model must be a string"
+        assert isinstance(model, str), "model must be a string"
 
         # parse key
         dset1, bl1 = self.parse_blkey(key1)
@@ -1390,7 +1390,7 @@ def get_G(self, key1, key2, exact_norm=False, pol=False):
             raise ValueError("Number of delay bins should have been set"
                              "by now! Cannot be equal to None")
 
-        G = np.zeros((self.spw_Ndlys, self.spw_Ndlys), dtype=np.complex)
+        G = np.zeros((self.spw_Ndlys, self.spw_Ndlys), dtype=complex)
         R1 = self.R(key1)
         R2 = self.R(key2)
 
@@ -1489,16 +1489,16 @@ def get_H(self, key1, key2, sampling=False, exact_norm=False, pol=False):
             raise ValueError("Number of delay bins should have been set"
                              "by now! Cannot be equal to None.")
 
-        H = np.zeros((self.spw_Ndlys, self.spw_Ndlys), dtype=np.complex)
+        H = np.zeros((self.spw_Ndlys, self.spw_Ndlys), dtype=complex)
         R1 = self.R(key1)
         R2 = self.R(key2)
         if not sampling:
             nfreq=np.sum(self.filter_extension) + self.spw_Nfreqs
             sinc_matrix = np.zeros((nfreq, nfreq))
             for i in range(nfreq):
                 for j in range(nfreq):
-                    sinc_matrix[i,j] = np.float(i - j)
-            sinc_matrix = np.sinc(sinc_matrix / np.float(nfreq))
+                    sinc_matrix[i,j] = float(i - j)
+            sinc_matrix = np.sinc(sinc_matrix / float(nfreq))
 
         iR1Q1, iR2Q2 = {}, {}
         if (exact_norm):
@@ -1582,7 +1582,7 @@ def get_unnormed_E(self, key1, key2, exact_norm=False, pol=False):
                              "by now! Cannot be equal to None")
         nfreq = self.spw_Nfreqs + np.sum(self.filter_extension)
         E_matrices = np.zeros((self.spw_Ndlys, nfreq, nfreq),
-                               dtype=np.complex)
+                               dtype=complex)
         R1 = self.R(key1)
         R2 = self.R(key2)
         if (exact_norm):
@@ -2227,7 +2227,7 @@ def get_Q_alt(self, mode, allow_fft=True, include_extension=False):
         else:
             phase_correction = 0.
         if (self.spw_Ndlys == nfreq) and (allow_fft == True):
-            _m = np.zeros((nfreq,), dtype=np.complex)
+            _m = np.zeros((nfreq,), dtype=complex)
             _m[mode] = 1. # delta function at specific delay mode
             # FFT to transform to frequency space
             m = np.fft.fft(np.fft.ifftshift(_m))
@@ -2426,9 +2426,9 @@ def broadcast_dset_flags(self, spw_ranges=None, time_thresh=0.2,
                         Nfreqs = float(flags.shape[1])
                         # get time- and freq-continguous flags
                         freq_contig_flgs = np.sum(flags, axis=1) / Nfreqs > 0.999999
-                        Ntimes_noncontig = np.sum(~freq_contig_flgs, dtype=np.float)
+                        Ntimes_noncontig = np.sum(~freq_contig_flgs, dtype=float)
                         # get freq channels where non-contiguous flags exceed threshold
-                        exceeds_thresh = np.sum(flags[~freq_contig_flgs], axis=0, dtype=np.float) / Ntimes_noncontig > time_thresh
+                        exceeds_thresh = np.sum(flags[~freq_contig_flgs], axis=0, dtype=float) / Ntimes_noncontig > time_thresh
                         # flag channels for all times that exceed time_thresh
                         dset.flag_array[bl_inds, :, np.where(exceeds_thresh)[0][:, None], i] = True
                         # for pixels that have flags but didn't meet broadcasting limit
@@ -2695,9 +2695,9 @@ def validate_pol(self, dsets, pol_pair):
         x_orientation = self.dsets[0].x_orientation
 
         # convert elements to integers if fed as strings
-        if isinstance(pol_pair[0], (str, np.str)):
+        if isinstance(pol_pair[0], str):
             pol_pair = (uvutils.polstr2num(pol_pair[0], x_orientation=x_orientation), pol_pair[1])
-        if isinstance(pol_pair[1], (str, np.str)):
+        if isinstance(pol_pair[1], str):
             pol_pair = (pol_pair[0], uvutils.polstr2num(pol_pair[1], x_orientation=x_orientation))
 
         assert isinstance(pol_pair[0], (int, np.integer)), err_msg
@@ -3081,9 +3081,9 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
                 # Convert string to pol-integer pair
                 p = (uvutils.polstr2num(p, x_orientation=self.dsets[0].x_orientation),
                      uvutils.polstr2num(p, x_orientation=self.dsets[0].x_orientation))
-            if isinstance(p[0], (str, np.str)):
+            if isinstance(p[0], str):
                 p = (uvutils.polstr2num(p[0], x_orientation=self.dsets[0].x_orientation), p[1])
-            if isinstance(p[1], (str, np.str)):
+            if isinstance(p[1], str):
                 p = (p[0], uvutils.polstr2num(p[1], x_orientation=self.dsets[0].x_orientation))
             _pols.append(p)
         pols = _pols
@@ -3285,7 +3285,7 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
                     # the diagonal norm matrix mode (i.e., norm = 'I')
                     if norm == 'I' and not(exact_norm):
                         sa = self.scalar_delay_adjustment(Gv=Gv, Hv=Hv)
-                        if isinstance(sa, (np.float, float)):
+                        if isinstance(sa, float):
                             pv *= sa
                         else:
                             pv = np.atleast_2d(sa).T * pv
@@ -3305,7 +3305,7 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
                             cov_imag = cov_imag * (scalar)**2.
 
                         if norm == 'I' and not(exact_norm):
-                            if isinstance(sa, (np.float, float)):
+                            if isinstance(sa, float):
                                 cov_real = cov_real * (sa)**2.
                                 cov_imag = cov_imag * (sa)**2.
                             else:
@@ -3386,7 +3386,7 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
                         lst2.extend(dset2.lst_array[inds2])
 
                         # insert blpair info
-                        blp_arr.extend(np.ones_like(inds1, np.int) \
+                        blp_arr.extend(np.ones_like(inds1, int) \
                                        * uvputils._antnums_to_blpair(blp))
 
                 # insert into data and wgts integrations dictionaries
@@ -3458,7 +3458,7 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
         uvp.Nspwdlys = len(uvp.spw_dly_array)
         uvp.Nspwfreqs = len(uvp.spw_freq_array)
         uvp.Nfreqs = len(np.unique(freqs))
-        uvp.polpair_array = np.array(spw_polpair, np.int)
+        uvp.polpair_array = np.array(spw_polpair, int)
         uvp.Npols = len(spw_polpair)
         uvp.scalar_array = np.array(sclr_arr)
         uvp.channel_width = dset1.channel_width  # all dsets validated to agree
@@ -3473,11 +3473,11 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
         label1 = self.labels[self.dset_idx(dsets[0])]
         label2 = self.labels[self.dset_idx(dsets[1])]
         uvp.labels = sorted(set([label1, label2]))
-        uvp.label_1_array = np.ones((uvp.Nspws, uvp.Nblpairts, uvp.Npols), np.int) \
+        uvp.label_1_array = np.ones((uvp.Nspws, uvp.Nblpairts, uvp.Npols), int) \
                             * uvp.labels.index(label1)
-        uvp.label_2_array = np.ones((uvp.Nspws, uvp.Nblpairts, uvp.Npols), np.int) \
+        uvp.label_2_array = np.ones((uvp.Nspws, uvp.Nblpairts, uvp.Npols), int) \
                             * uvp.labels.index(label2)
-        uvp.labels = np.array(uvp.labels, np.str)
+        uvp.labels = np.array(uvp.labels, str)
         uvp.r_params = uvputils.compress_r_params(r_params)
         uvp.taper = taper
         if not return_q:
@@ -3507,7 +3507,7 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
         uvp.integration_array = integration_array
         uvp.wgt_array = wgt_array
         uvp.nsample_array = dict(
-                        [ (k, np.ones_like(uvp.integration_array[k], np.float))
+                        [ (k, np.ones_like(uvp.integration_array[k], float))
                          for k in uvp.integration_array.keys() ] )
 
         # covariance
@@ -4030,7 +4030,7 @@ def pspec_run(dsets, filename, dsets_std=None, cals=None, cal_flag=True,
 
     # parse psname
     if psname_ext is not None:
-        assert isinstance(psname_ext, (str, np.str))
+        assert isinstance(psname_ext, str)
     else:
         psname_ext = ''
 
@@ -4132,7 +4132,7 @@ def pspec_run(dsets, filename, dsets_std=None, cals=None, cal_flag=True,
     assert len(pol_pairs) > 0, "no pol_pairs specified"
 
     # load beam
-    if isinstance(beam, (str, np.str)):
+    if isinstance(beam, str):
         beam = pspecbeam.PSpecBeamUV(beam, cosmo=cosmo)
 
     # beam and cosmology check
@@ -4472,7 +4472,7 @@ def _load_dsets(fnames, bls=None, pols=None, logf=None, verbose=True,
 
         # read data
         uvd = UVData()
-        if isinstance(dset, (str, np.str)):
+        if isinstance(dset, str):
             dfiles = glob.glob(dset)
         else:
             dfiles = dset
@@ -4510,7 +4510,7 @@ def _load_cals(cnames, logf=None, verbose=True):
 
         # read data
         uvc = UVCal()
-        if isinstance(cfile, (str, np.str)):
+        if isinstance(cfile, str):
             uvc.read_calfits(glob.glob(cfile))
         else:
             uvc.read_calfits(cfile)

hera_pspec/pspecdata.py

@@ -104,9 +104,9 @@ def _combine_pol(uvd1, uvd2, pol1, pol2, pstokes='pI', x_orientation=None):
         "uvd2 must be a pyuvdata.UVData instance"
 
     # convert pol1 and/or pol2 to integer if fed as a string
-    if isinstance(pol1, (str, np.str)):
+    if isinstance(pol1, str):
         pol1 = pyuvdata.utils.polstr2num(pol1, x_orientation=x_orientation)
-    if isinstance(pol2, (str, np.str)):
+    if isinstance(pol2, str):
         pol2 = pyuvdata.utils.polstr2num(pol2, x_orientation=x_orientation)
 
     # extracting data array from the UVData objects
@@ -121,7 +121,7 @@ def _combine_pol(uvd1, uvd2, pol1, pol2, pstokes='pI', x_orientation=None):
     flag = np.logical_or(flag1, flag2)
 
     # convert pStokes to polarization integer if a string
-    if isinstance(pstokes, (str, np.str)):
+    if isinstance(pstokes, str):
         pstokes = pyuvdata.utils.polstr2num(pstokes, x_orientation=x_orientation)
 
     # get string form of polarizations
@@ -144,7 +144,7 @@ def _combine_pol(uvd1, uvd2, pol1, pol2, pstokes='pI', x_orientation=None):
     uvdS = copy.deepcopy(uvd1)
     uvdS.data_array = stdata  # pseudo-stokes data
     uvdS.flag_array = flag  # flag array
-    uvdS.polarization_array = np.array([pstokes], dtype=np.int) # polarization number
+    uvdS.polarization_array = np.array([pstokes], dtype=int) # polarization number
     uvdS.nsample_array = uvd1.nsample_array + uvd2.nsample_array # nsamples
 
     uvdS.history = "Merged into pseudo-stokes vis with hera_pspec version {}\n{}" \
@@ -220,15 +220,15 @@ def construct_pstokes(dset1, dset2, pstokes='pI', run_check=True, antenna_nums=N
     """
     # convert dset1 and dset2 to UVData objects if they are miriad files
     if isinstance(dset1, pyuvdata.UVData) == False:
-        assert isinstance(dset1, (str, np.str)), \
+        assert isinstance(dset1, str), \
             "dset1 must be fed as a string or UVData object"
         uvd1 = miriad2pyuvdata(dset1, antenna_nums=antenna_nums, bls=bls,
                                polarizations=polarizations, ant_str=ant_str,
                                time_range=time_range)
     else:
         uvd1 = dset1
     if isinstance(dset2, pyuvdata.UVData) == False:
-        assert isinstance(dset2, (str, np.str)), \
+        assert isinstance(dset2, str), \
             "dset2 must be fed as a string or UVData object"
         uvd2 = miriad2pyuvdata(dset2, antenna_nums=antenna_nums, bls=bls,
                                polarizations=polarizations, ant_str=ant_str,
@@ -237,7 +237,7 @@ def construct_pstokes(dset1, dset2, pstokes='pI', run_check=True, antenna_nums=N
         uvd2 = dset2
 
     # convert pstokes to integer if fed as a string
-    if isinstance(pstokes, (str, np.str)):
+    if isinstance(pstokes, str):
         pstokes = pyuvdata.utils.polstr2num(pstokes, x_orientation=dset1.x_orientation)
 
     # check if dset1 and dset2 habe the same spectral window
@@ -326,7 +326,7 @@ def filter_dset_on_stokes_pol(dsets, pstokes):
     pols = [d.polarization_array[0] for d in dsets]
 
     # convert pstokes to integer if a string
-    if isinstance(pstokes, (str, np.str)):
+    if isinstance(pstokes, str):
         pstokes = pyuvdata.utils.polstr2num(pstokes, x_orientation=dsets[0].x_orientation)
     assert pstokes in [1, 2, 3, 4], \
         "pstokes must be fed as a pseudo-Stokes parameter"