MRG, MAINT: Clean up use of bool, float, int

examples/simulation/plot_simulate_evoked_data.py

@@ -46,7 +46,7 @@
 ###############################################################################
 # Generate source time courses from 2 dipoles and the correspond evoked data
 
-times = np.arange(300, dtype=np.float) / raw.info['sfreq'] - 0.1
+times = np.arange(300, dtype=np.float64) / raw.info['sfreq'] - 0.1
 rng = np.random.RandomState(42)
 
 

examples/simulation/plot_simulated_raw_data_using_subject_anatomy.py

@@ -143,7 +143,7 @@ def data_fun(times, latency, duration):
 # event, the second is not used. The third one is the event id, which is
 # different for each of the 4 areas.
 
-times = np.arange(150, dtype=np.float) / info['sfreq']
+times = np.arange(150, dtype=np.float64) / info['sfreq']
 duration = 0.03
 rng = np.random.RandomState(7)
 source_simulator = mne.simulation.SourceSimulator(src, tstep=tstep)

examples/time_frequency/plot_time_frequency_simulated.py

@@ -43,7 +43,7 @@
 noise = rng.randn(n_epochs, len(ch_names), n_times)
 
 # Add a 50 Hz sinusoidal burst to the noise and ramp it.
-t = np.arange(n_times, dtype=np.float) / sfreq
+t = np.arange(n_times, dtype=np.float64) / sfreq
 signal = np.sin(np.pi * 2. * 50. * t)  # 50 Hz sinusoid signal
 signal[np.logical_or(t < 0.45, t > 0.55)] = 0.  # Hard windowing
 on_time = np.logical_and(t >= 0.45, t <= 0.55)

mne/beamformer/tests/test_dics.py

@@ -260,7 +260,7 @@ def test_make_dics(tmpdir, _load_forward, idx, mat_tol, vol_tol):
     assert isinstance(filters, Beamformer)
     assert isinstance(filters_read, Beamformer)
     for key in ['tmin', 'tmax']:  # deal with strictness of object_diff
-        setattr(filters['csd'], key, np.float(getattr(filters['csd'], key)))
+        setattr(filters['csd'], key, np.float64(getattr(filters['csd'], key)))
     assert object_diff(filters, filters_read) == ''
 
 

mne/bem.py

@@ -1341,7 +1341,7 @@ def _read_bem_surface(fid, this, def_coord_frame, s_id=None):
     if tag is None:
         raise ValueError('Vertex data not found')
 
-    res['rr'] = tag.data.astype(np.float)  # XXX : double because of mayavi bug
+    res['rr'] = tag.data.astype(np.float64)  # XXX : double because of mayavi
     if res['rr'].shape[0] != res['np']:
         raise ValueError('Vertex information is incorrect')
 

mne/channels/channels.py

@@ -373,7 +373,7 @@ def _set_channel_positions(self, pos, names):
         if len(pos) != len(names):
             raise ValueError('Number of channel positions not equal to '
                              'the number of names given.')
-        pos = np.asarray(pos, dtype=np.float)
+        pos = np.asarray(pos, dtype=np.float64)
         if pos.shape[-1] != 3 or pos.ndim != 2:
             msg = ('Channel positions must have the shape (n_points, 3) '
                    'not %s.' % (pos.shape,))

mne/channels/interpolation.py

@@ -136,8 +136,8 @@ def _interpolate_bads_eeg(inst, origin, verbose=None):
     inst : mne.io.Raw, mne.Epochs or mne.Evoked
         The data to interpolate. Must be preloaded.
     """
-    bads_idx = np.zeros(len(inst.ch_names), dtype=np.bool)
-    goods_idx = np.zeros(len(inst.ch_names), dtype=np.bool)
+    bads_idx = np.zeros(len(inst.ch_names), dtype=bool)
+    goods_idx = np.zeros(len(inst.ch_names), dtype=bool)
 
     picks = pick_types(inst.info, meg=False, eeg=True, exclude=[])
     inst.info._check_consistency()

mne/channels/layout.py

@@ -126,7 +126,7 @@ def _read_lout(fname):
                 name = chkind + ' ' + nb
             else:
                 cid, x, y, dx, dy, name = splits
-            pos.append(np.array([x, y, dx, dy], dtype=np.float))
+            pos.append(np.array([x, y, dx, dy], dtype=np.float64))
             names.append(name)
             ids.append(int(cid))
 
@@ -147,7 +147,7 @@ def _read_lay(fname):
                 name = chkind + ' ' + nb
             else:
                 cid, x, y, dx, dy, name = splits
-            pos.append(np.array([x, y, dx, dy], dtype=np.float))
+            pos.append(np.array([x, y, dx, dy], dtype=np.float64))
             names.append(name)
             ids.append(int(cid))
 

mne/chpi.py

@@ -557,7 +557,7 @@ def _fit_chpi_amplitudes(raw, time_sl, hpi):
             # loads hpi_stim channel
             chpi_data = raw[hpi['hpi_pick'], time_sl][0]
 
-        ons = (np.round(chpi_data).astype(np.int) &
+        ons = (np.round(chpi_data).astype(np.int64) &
                hpi['on'][:, np.newaxis]).astype(bool)
         n_on = ons.all(axis=-1).sum(axis=0)
         if not (n_on >= 3).all():

mne/conftest.py

@@ -88,6 +88,11 @@ def pytest_configure(config):
     ignore:.*trait.*handler.*deprecated.*:DeprecationWarning
     ignore:.*rich_compare.*metadata.*deprecated.*:DeprecationWarning
     ignore:.*In future, it will be an error for 'np.bool_'.*:DeprecationWarning
+    ignore:.*`np.bool` is a deprecated alias.*:DeprecationWarning
+    ignore:.*`np.int` is a deprecated alias.*:DeprecationWarning
+    ignore:.*`np.float` is a deprecated alias.*:DeprecationWarning
+    ignore:.*`np.object` is a deprecated alias.*:DeprecationWarning
+    ignore:.*`np.long` is a deprecated alias:DeprecationWarning
     ignore:.*Converting `np\.character` to a dtype is deprecated.*:DeprecationWarning
     ignore:.*sphinx\.util\.smartypants is deprecated.*:
     ignore:.*pandas\.util\.testing is deprecated.*:

mne/connectivity/effective.py

@@ -133,7 +133,7 @@ def phase_slope_index(data, indices=None, sfreq=2 * np.pi,
     # allocate space for output
     out_shape = list(cohy.shape)
     out_shape[freq_dim] = n_bands
-    psi = np.zeros(out_shape, dtype=np.float)
+    psi = np.zeros(out_shape, dtype=np.float64)
 
     # allocate accumulator
     acc_shape = copy.copy(out_shape)

mne/connectivity/spectral.py

@@ -980,7 +980,7 @@ def _prepare_connectivity(epoch_block, tmin, tmax, fmin, fmax, sfreq, indices,
             raise ValueError('define frequencies of interest using '
                              'cwt_freqs')
         else:
-            cwt_freqs = cwt_freqs.astype(np.float)
+            cwt_freqs = cwt_freqs.astype(np.float64)
         if any(cwt_freqs > (sfreq / 2.)):
             raise ValueError('entries in cwt_freqs cannot be '
                              'larger than Nyquist (sfreq / 2)')
@@ -1003,7 +1003,7 @@ def _prepare_connectivity(epoch_block, tmin, tmax, fmin, fmax, sfreq, indices,
                                   5. / np.min(fmin), five_cycle_freq))
 
     # create a frequency mask for all bands
-    freq_mask = np.zeros(len(freqs_all), dtype=np.bool)
+    freq_mask = np.zeros(len(freqs_all), dtype=bool)
     for f_lower, f_upper in zip(fmin, fmax):
         freq_mask |= ((freqs_all >= f_lower) & (freqs_all <= f_upper))
 

mne/cov.py

@@ -846,8 +846,8 @@ def _unpack_epochs(epochs):
         # prepare mean covs
         n_epoch_types = len(epochs)
         data_mean = [0] * n_epoch_types
-        n_samples = np.zeros(n_epoch_types, dtype=np.int)
-        n_epochs = np.zeros(n_epoch_types, dtype=np.int)
+        n_samples = np.zeros(n_epoch_types, dtype=np.int64)
+        n_epochs = np.zeros(n_epoch_types, dtype=np.int64)
 
         for ii, epochs_t in enumerate(epochs):
 
@@ -1757,7 +1757,7 @@ def compute_whitener(noise_cov, info=None, picks=None, rank=None,
     nzero = (eig > 0)
     eig[~nzero] = 0.  # get rid of numerical noise (negative) ones
 
-    W = np.zeros((n_chan, 1), dtype=np.float)
+    W = np.zeros((n_chan, 1), dtype=np.float64)
     W[nzero, 0] = 1.0 / np.sqrt(eig[nzero])
     #   Rows of eigvec are the eigenvectors
     W = W * noise_cov['eigvec']  # C ** -0.5
@@ -1963,7 +1963,7 @@ def _write_cov(fid, cov):
     else:
         # Store only lower part of covariance matrix
         dim = cov['dim']
-        mask = np.tril(np.ones((dim, dim), dtype=np.bool)) > 0
+        mask = np.tril(np.ones((dim, dim), dtype=bool)) > 0
         vals = cov['data'][mask].ravel()
         write_double(fid, FIFF.FIFF_MNE_COV, vals)
 

mne/decoding/base.py

@@ -224,7 +224,7 @@ def _set_cv(cv, estimator=None, X=None, y=None):
     # Setup CV
     from sklearn import model_selection as models
     from sklearn.model_selection import (check_cv, StratifiedKFold, KFold)
-    if isinstance(cv, (int, np.int)):
+    if isinstance(cv, (int, np.int64)):
         XFold = StratifiedKFold if est_is_classifier else KFold
         cv = XFold(n_splits=cv)
     elif isinstance(cv, str):

mne/decoding/tests/test_receptive_field.py

@@ -108,7 +108,7 @@ def test_time_delay():
             _delay_time_series(X, tmin, tmax, sfreq=[1])
         # Delays must be int/float
         with pytest.raises(TypeError, match='.*complex.*'):
-            _delay_time_series(X, np.complex(tmin), tmax, 1)
+            _delay_time_series(X, np.complex128(tmin), tmax, 1)
         # Make sure swapaxes works
         start, stop = int(round(tmin * isfreq)), int(round(tmax * isfreq)) + 1
         n_delays = stop - start

mne/dipole.py

@@ -1306,7 +1306,7 @@ def fit_dipole(evoked, cov, bem, trans=None, min_dist=5., n_jobs=1,
     # cov = prepare_noise_cov(cov, info_nb, info_nb['ch_names'], verbose=False)
     # nzero = (cov['eig'] > 0)
     # n_chan = len(info_nb['ch_names'])
-    # whitener = np.zeros((n_chan, n_chan), dtype=np.float)
+    # whitener = np.zeros((n_chan, n_chan), dtype=np.float64)
     # whitener[nzero, nzero] = 1.0 / np.sqrt(cov['eig'][nzero])
     # whitener = np.dot(whitener, cov['eigvec'])
 

mne/epochs.py

@@ -904,7 +904,7 @@ def subtract_evoked(self, evoked=None):
         else:
             if self._offset is None:
                 self._offset = np.zeros((len(self.ch_names), len(self.times)),
-                                        dtype=np.float)
+                                        dtype=np.float64)
             self._offset[ep_picks] -= evoked.data[picks]
         logger.info('[done]')
 

mne/event.py

@@ -49,7 +49,7 @@ def pick_events(events, include=None, exclude=None, step=False):
     if include is not None:
         if not isinstance(include, list):
             include = [include]
-        mask = np.zeros(len(events), dtype=np.bool)
+        mask = np.zeros(len(events), dtype=bool)
         for e in include:
             mask = np.logical_or(mask, events[:, 2] == e)
             if step:
@@ -58,7 +58,7 @@ def pick_events(events, include=None, exclude=None, step=False):
     elif exclude is not None:
         if not isinstance(exclude, list):
             exclude = [exclude]
-        mask = np.ones(len(events), dtype=np.bool)
+        mask = np.ones(len(events), dtype=bool)
         for e in exclude:
             mask = np.logical_and(mask, events[:, 2] != e)
             if step:
@@ -432,7 +432,7 @@ def find_stim_steps(raw, pad_start=None, pad_stop=None, merge=0,
     if np.any(data < 0):
         warn('Trigger channel contains negative values, using absolute value.')
         data = np.abs(data)  # make sure trig channel is positive
-    data = data.astype(np.int)
+    data = data.astype(np.int64)
 
     return _find_stim_steps(data, raw.first_samp, pad_start=pad_start,
                             pad_stop=pad_stop, merge=merge)
@@ -452,9 +452,9 @@ def _find_events(data, first_samp, verbose=None, output='onset',
     else:
         merge = 0
 
-    data = data.astype(np.int)
+    data = data.astype(np.int64)
     if uint_cast:
-        data = data.astype(np.uint16).astype(np.int)
+        data = data.astype(np.uint16).astype(np.int64)
     if data.min() < 0:
         warn('Trigger channel contains negative values, using absolute '
              'value. If data were acquired on a Neuromag system with '

mne/evoked.py

@@ -746,7 +746,7 @@ def __init__(self, data, info, tmin=0., comment='', nave=1, kind='average',
         self.first = int(round(tmin * info['sfreq']))
         self.last = self.first + np.shape(data)[-1] - 1
         self.times = np.arange(self.first, self.last + 1,
-                               dtype=np.float) / info['sfreq']
+                               dtype=np.float64) / info['sfreq']
         self.info = info.copy()  # do not modify original info
         self.nave = nave
         self.kind = kind
@@ -1111,7 +1111,7 @@ def _read_evoked(fname, condition=None, kind='average', allow_maxshield=False):
         else:
             # Put the old style epochs together
             data = np.concatenate([e.data[None, :] for e in epoch], axis=0)
-        data = data.astype(np.float)
+        data = data.astype(np.float64)
 
         if first_time is not None and nsamp is not None:
             times = first_time + np.arange(nsamp) / info['sfreq']
@@ -1280,7 +1280,7 @@ def _get_peak(data, times, tmin=None, tmax=None, mode='abs'):
         raise ValueError('The tmin must be smaller or equal to tmax')
 
     time_win = (times >= tmin) & (times <= tmax)
-    mask = np.ones_like(data).astype(np.bool)
+    mask = np.ones_like(data).astype(bool)
     mask[:, time_win] = False
 
     maxfun = np.argmax

mne/filter.py

@@ -179,7 +179,7 @@ def _overlap_add_filter(x, h, n_fft=None, phase='zero', picks=None,
             # cost function based on number of multiplications
             N = 2 ** np.arange(np.ceil(np.log2(min_fft)),
                                np.ceil(np.log2(max_fft)) + 1, dtype=int)
-            cost = (np.ceil(n_x / (N - len(h) + 1).astype(np.float)) *
+            cost = (np.ceil(n_x / (N - len(h) + 1).astype(np.float64)) *
                     N * (np.log2(N) + 1))
 
             # add a heuristic term to prevent too-long FFT's which are slow
@@ -2005,7 +2005,7 @@ def resample(self, sfreq, npad='auto', window='boxcar', n_jobs=1,
         lowpass = self.info.get('lowpass')
         lowpass = np.inf if lowpass is None else lowpass
         self.info['lowpass'] = min(lowpass, sfreq / 2.)
-        new_times = (np.arange(self._data.shape[-1], dtype=np.float) /
+        new_times = (np.arange(self._data.shape[-1], dtype=np.float64) /
                      sfreq + self.times[0])
         # adjust indirectly affected variables
         if isinstance(self, BaseEpochs):

mne/fixes.py

@@ -93,14 +93,14 @@ def _read_geometry(filepath, read_metadata=False, read_stamp=False):
             nvert = _fread3(fobj)
             nquad = _fread3(fobj)
             (fmt, div) = (">i2", 100.) if magic == QUAD_MAGIC else (">f4", 1.)
-            coords = np.fromfile(fobj, fmt, nvert * 3).astype(np.float) / div
+            coords = np.fromfile(fobj, fmt, nvert * 3).astype(np.float64) / div
             coords = coords.reshape(-1, 3)
             quads = _fread3_many(fobj, nquad * 4)
             quads = quads.reshape(nquad, 4)
             #
             #   Face splitting follows
             #
-            faces = np.zeros((2 * nquad, 3), dtype=np.int)
+            faces = np.zeros((2 * nquad, 3), dtype=np.int64)
             nface = 0
             for quad in quads:
                 if (quad[0] % 2) == 0:
@@ -127,7 +127,7 @@ def _read_geometry(filepath, read_metadata=False, read_stamp=False):
         else:
             raise ValueError("File does not appear to be a Freesurfer surface")
 
-    coords = coords.astype(np.float)  # XXX: due to mayavi bug on mac 32bits
+    coords = coords.astype(np.float64)  # XXX: due to mayavi bug on mac 32bits
 
     ret = (coords, faces)
     if read_metadata:

mne/forward/_make_forward.py

@@ -690,7 +690,7 @@ def make_forward_dipole(dipole, bem, info, trans=None, n_jobs=1, verbose=None):
     # Check for omissions due to proximity to inner skull in
     # make_forward_solution, which will result in an exception
     if fwd['src'][0]['nuse'] != len(pos):
-        inuse = fwd['src'][0]['inuse'].astype(np.bool)
+        inuse = fwd['src'][0]['inuse'].astype(bool)
         head = ('The following dipoles are outside the inner skull boundary')
         msg = len(head) * '#' + '\n' + head + '\n'
         for (t, pos) in zip(times[np.logical_not(inuse)],

mne/forward/forward.py

@@ -175,12 +175,12 @@ def _block_diag(A, n):
     if na % n > 0:
         raise ValueError('Width of matrix must be a multiple of n')
 
-    tmp = np.arange(ma * bdn, dtype=np.int).reshape(bdn, ma)
+    tmp = np.arange(ma * bdn, dtype=np.int64).reshape(bdn, ma)
     tmp = np.tile(tmp, (1, n))
     ii = tmp.ravel()
 
-    jj = np.arange(na, dtype=np.int)[None, :]
-    jj = jj * np.ones(ma, dtype=np.int)[:, None]
+    jj = np.arange(na, dtype=np.int64)[None, :]
+    jj = jj * np.ones(ma, dtype=np.int64)[:, None]
     jj = jj.T.ravel()  # column indices foreach sparse bd
 
     bd = sparse.coo_matrix((A.T.ravel(), np.c_[ii, jj].T)).tocsc()
@@ -994,7 +994,7 @@ def compute_orient_prior(forward, loose=0.2, verbose=None):
     if not (0 <= loose <= 1):
         raise ValueError('loose value should be between 0 and 1, '
                          'got %s.' % (loose,))
-    orient_prior = np.ones(n_sources, dtype=np.float)
+    orient_prior = np.ones(n_sources, dtype=np.float64)
     if loose > 0.:
         if is_fixed_ori:
             raise ValueError('loose must be 0. with forward operator '

mne/inverse_sparse/_gamma_map.py

@@ -51,7 +51,7 @@ def _gamma_map_opt(M, G, alpha, maxit=10000, tol=1e-6, update_mode=1,
     M = M.copy()
 
     if gammas is None:
-        gammas = np.ones(G.shape[1], dtype=np.float)
+        gammas = np.ones(G.shape[1], dtype=np.float64)
 
     eps = np.finfo(float).eps
 
@@ -132,7 +132,7 @@ def denom_fun(x):
             gammas = np.repeat(gammas_comb / group_size, group_size)
 
         # compute convergence criterion
-        gammas_full = np.zeros(n_sources, dtype=np.float)
+        gammas_full = np.zeros(n_sources, dtype=np.float64)
         gammas_full[active_set] = gammas
 
         err = (np.sum(np.abs(gammas_full - gammas_full_old)) /

mne/inverse_sparse/mxne_inverse.py

@@ -403,7 +403,7 @@ def mixed_norm(evoked, forward, noise_cov, alpha, loose='auto', depth=0.8,
     M_estimated = np.dot(gain[:, active_set], X)
 
     if mask is not None:
-        active_set_tmp = np.zeros(len(mask), dtype=np.bool)
+        active_set_tmp = np.zeros(len(mask), dtype=bool)
         active_set_tmp[mask] = active_set
         active_set = active_set_tmp
         del active_set_tmp
@@ -662,7 +662,7 @@ def tf_mixed_norm(evoked, forward, noise_cov,
     M_estimated = np.dot(gain[:, active_set], X)
 
     if mask is not None:
-        active_set_tmp = np.zeros(len(mask), dtype=np.bool)
+        active_set_tmp = np.zeros(len(mask), dtype=bool)
         active_set_tmp[mask] = active_set
         active_set = active_set_tmp
         del active_set_tmp