The following are code examples for showing how to use . They are extracted from open source Python projects. You can vote up the examples you like or vote down the exmaples you don’t like. You can also save this page to your account.
Example 1
def compute_group(cls, data, scales, **params):
n = len(data)
if n < 3:
return pd.DataFrame()
weight = data.get('weight')
if params['trim']:
range_y = data['y'].min(), data['y'].max()
else:
range_y = scales.y.dimension()
dens = compute_density(data['y'], weight, range_y, **params)
dens['y'] = dens['x']
dens['x'] = np.mean([data['x'].min(), data['x'].max()])
# Compute width if x has multiple values
if len(np.unique(data['x'])) > 1:
dens['width'] = np.ptp(data['x']) * 0.9
return dens Example 2
def draw_group(data, panel_params, coord, ax, **params):
data = coord.transform(data, panel_params)
fill = to_rgba(data['fill'], data['alpha'])
color = to_rgba(data['color'], data['alpha'])
ranges = coord.range(panel_params)
# For perfect circles the width/height of the circle(ellipse)
# should factor in the dimensions of axes
bbox = ax.get_window_extent().transformed(
ax.figure.dpi_scale_trans.inverted())
ax_width, ax_height = bbox.width, bbox.height
factor = ((ax_width/ax_height) *
np.ptp(ranges.y)/np.ptp(ranges.x))
size = data.loc[0, 'binwidth'] * params['dotsize']
offsets = data['stackpos'] * params['stackratio']
if params['binaxis'] == 'x':
width, height = size, size*factor
xpos, ypos = data['x'], data['y'] + height*offsets
elif params['binaxis'] == 'y':
width, height = size/factor, size
xpos, ypos = data['x'] + width*offsets, data['y']
circles = []
for xy in zip(xpos, ypos):
patch = mpatches.Ellipse(xy, width=width, height=height)
circles.append(patch)
coll = mcoll.PatchCollection(circles,
edgecolors=color,
facecolors=fill)
ax.add_collection(coll) Example 3
def fit(self, X, y=None):
"""Fit it.
Parameters
----------
X : array, shape (n_epochs, n_times)
The data for one channel.
y : None
Redundant. Necessary to be compatible with sklearn
API.
"""
deltas = np.ptp(X, axis=1)
self.deltas_ = deltas
keep = deltas <= self.thresh
# XXX: actually go over all the folds before setting the min
# in skopt. Otherwise, may confuse skopt.
if self.thresh < np.min(np.ptp(X, axis=1)):
assert np.sum(keep) == 0
keep = deltas <= np.min(np.ptp(X, axis=1))
self.mean_ = _slicemean(X, keep, axis=0)
return self Example 4
def _vote_bad_epochs(self, epochs):
"""Each channel votes for an epoch as good or bad.
Parameters
----------
epochs : instance of mne.Epochs
The epochs object for which bad epochs must be found.
"""
n_epochs = len(epochs)
picks = _handle_picks(info=epochs.info, picks=self.picks)
drop_log = np.zeros((n_epochs, len(epochs.ch_names)))
bad_sensor_counts = np.zeros((len(epochs), ))
ch_names = [epochs.ch_names[p] for p in picks]
deltas = np.ptp(epochs.get_data()[:, picks], axis=-1).T
threshes = [self.threshes_[ch_name] for ch_name in ch_names]
for ch_idx, (delta, thresh) in enumerate(zip(deltas, threshes)):
bad_epochs_idx = np.where(delta > thresh)[0]
# TODO: combine for different ch types
bad_sensor_counts[bad_epochs_idx] += 1
drop_log[bad_epochs_idx, picks[ch_idx]] = 1
return drop_log, bad_sensor_counts Example 5
def extend_limits(values, fraction=0.10, tolerance=1e-2):
""" Extend the values of a list by a fractional amount """
values = np.array(values)
finite_indices = np.isfinite(values)
if np.sum(finite_indices) == 0:
raise ValueError("no finite values provided")
lower_limit, upper_limit = np.min(values[finite_indices]), np.max(values[finite_indices])
ptp_value = np.ptp([lower_limit, upper_limit])
new_limits = lower_limit - fraction * ptp_value, ptp_value * fraction + upper_limit
if np.abs(new_limits[0] - new_limits[1]) < tolerance:
if np.abs(new_limits[0]) < tolerance:
# Arbitrary limits, since we"ve just been passed zeros
offset = 1
else:
offset = np.abs(new_limits[0]) * fraction
new_limits = new_limits[0] - offset, offset + new_limits[0]
return np.array(new_limits) Example 6
def calculate_fractional_overlap(interest_range, comparison_range):
"""
Calculate how much of the range of interest overlaps with the comparison
range.
"""
if not (interest_range[-1] >= comparison_range[0] \
and comparison_range[-1] >= interest_range[0]):
return 0.0 # No overlap
elif (interest_range[0] >= comparison_range[0] \
and interest_range[-1] <= comparison_range[-1]):
return 1.0 # Total overlap
else:
# Some overlap. Which side?
if interest_range[0] < comparison_range[0]:
# Left hand side
width = interest_range[-1] - comparison_range[0]
else:
# Right hand side
width = comparison_range[-1] - interest_range[0]
return width/np.ptp(interest_range) # Fractional overlap Example 7
def update_roi_xy_size(self):
""" Update the cursor size showing the optimizer scan area for the XY image.
"""
hpos = self.roi_xy.pos()[0]
vpos = self.roi_xy.pos()[1]
hsize = self.roi_xy.size()[0]
vsize = self.roi_xy.size()[1]
hcenter = hpos + 0.5 * hsize
vcenter = vpos + 0.5 * vsize
if self.adjust_cursor_roi:
newsize = self._optimizer_logic.refocus_XY_size
else:
viewrange = self.xy_image.getViewBox().viewRange()
newsize = np.sqrt(np.sum(np.ptp(viewrange, axis=1)**2)) / 20
self.roi_xy.setSize([newsize, newsize])
self.roi_xy.setPos([hcenter - newsize / 2, vcenter - newsize / 2]) Example 8
def update_roi_depth_size(self):
""" Update the cursor size showing the optimizer scan area for the X-depth image.
"""
hpos = self.roi_depth.pos()[0]
vpos = self.roi_depth.pos()[1]
hsize = self.roi_depth.size()[0]
vsize = self.roi_depth.size()[1]
hcenter = hpos + 0.5 * hsize
vcenter = vpos + 0.5 * vsize
if self.adjust_cursor_roi:
newsize_h = self._optimizer_logic.refocus_XY_size
newsize_v = self._optimizer_logic.refocus_Z_size
else:
viewrange = self.depth_image.getViewBox().viewRange()
newsize = np.sqrt(np.sum(np.ptp(viewrange, axis=1)**2)) / 20
newsize_h = newsize
newsize_v = newsize
self.roi_depth.setSize([newsize_h, newsize_v])
self.roi_depth.setPos([hcenter - newsize_h / 2, vcenter - newsize_v / 2]) Example 9
def plane_fit(points, tolerance=None):
'''
Given a set of points, find an origin and normal using least squares
Arguments
---------
points: (n,3)
tolerance: how non-planar the result can be without raising an error
Returns
---------
C: (3) point on the plane
N: (3) normal vector
'''
C = points[0]
x = points - C
M = np.dot(x.T, x)
N = np.linalg.svd(M)[0][:,-1]
if not (tolerance is None):
normal_range = np.ptp(np.dot(N, points.T))
if normal_range > tol.planar:
log.error('Points have peak to peak of %f', normal_range)
raise ValueError('Plane outside tolerance!')
return C, N Example 10
def plot_epipolar_line(p1, p2, F, show_epipole=False):
""" Plot the epipole and epipolar line F*x=0
in an image given the corresponding points.
F is the fundamental matrix and p2 are the point in the other image.
"""
lines = np.dot(F, p2)
pad = np.ptp(p1, 1) * 0.01
mins = np.min(p1, 1)
maxes = np.max(p1, 1)
# epipolar line parameter and values
xpts = np.linspace(mins[0] - pad[0], maxes[0] + pad[0], 100)
for line in lines.T:
ypts = np.asarray([(line[2] + line[0] * p) / (-line[1]) for p in xpts])
valid_idx = ((ypts >= mins[1] - pad[1]) & (ypts <= maxes[1] + pad[1]))
plt.plot(xpts[valid_idx], ypts[valid_idx], linewidth=1)
plt.plot(p1[0], p1[1], 'ro')
if show_epipole:
epipole = compute_epipole(F)
plt.plot(epipole[0] / epipole[2], epipole[1] / epipole[2], 'r*') Example 11
def startModulation(self,
radiusInMilliRad,
frequencyInHz,
centerInMilliRad):
self._origTargetPosition= centerInMilliRad
self.stopModulation()
periodInSec= 1./ frequencyInHz
assert np.ptp(self._ctrl.getWaveGeneratorTableRate()) == 0, \
"wave generator table rate must be the same for every table"
wgtr= self._ctrl.getWaveGeneratorTableRate()[0]
timestep= self._ctrl.getServoUpdateTimeInSeconds() * wgtr
lengthInPoints= periodInSec/ timestep
peakOfTheSineCurve= self._milliRadToGcsUnits(
self.getTargetPosition() + radiusInMilliRad)
offsetOfTheSineCurve= self._milliRadToGcsUnits(
self.getTargetPosition() - radiusInMilliRad)
amplitudeOfTheSineCurve= peakOfTheSineCurve - offsetOfTheSineCurve
wavelengthOfTheSineCurveInPoints= periodInSec/ timestep
startPoint= np.array([0, 0.25])* wavelengthOfTheSineCurveInPoints
curveCenterPoint= 0.5* wavelengthOfTheSineCurveInPoints
self._ctrl.clearWaveTableData([1, 2, 3])
self._ctrl.setSinusoidalWaveform(
1, WaveformGenerator.CLEAR, lengthInPoints,
amplitudeOfTheSineCurve[0], offsetOfTheSineCurve[0],
wavelengthOfTheSineCurveInPoints, startPoint[0], curveCenterPoint)
self._ctrl.setSinusoidalWaveform(
2, WaveformGenerator.CLEAR, lengthInPoints,
amplitudeOfTheSineCurve[1], offsetOfTheSineCurve[1],
wavelengthOfTheSineCurveInPoints, startPoint[1], curveCenterPoint)
self._ctrl.setConnectionOfWaveTableToWaveGenerator([1, 2], [1, 2])
self._ctrl.setWaveGeneratorStartStopMode([1, 1, 0])
self._modulationEnabled= True Example 12
def compute_group(cls, data, scales, **params):
labels = ['x', 'y']
X = np.array(data[labels])
res = boxplot_stats(X, whis=params['coef'], labels=labels)[1]
try:
n = data['weight'].sum()
except KeyError:
n = len(data['y'])
if len(np.unique(data['x'])) > 1:
width = np.ptp(data['x']) * 0.9
else:
width = params['width']
if pdtypes.is_categorical(data['x']):
x = data['x'].iloc[0]
else:
x = np.mean([data['x'].min(), data['x'].max()])
d = {'ymin': res['whislo'],
'lower': res['q1'],
'middle': [res['med']],
'upper': res['q3'],
'ymax': res['whishi'],
'outliers': [res['fliers']],
'notchupper': res['med']+1.58*res['iqr']/np.sqrt(n),
'notchlower': res['med']-1.58*res['iqr']/np.sqrt(n),
'x': x,
'width': width,
'relvarwidth': np.sqrt(n)}
return pd.DataFrame(d) Example 13
def test_ptp(self):
a = [3, 4, 5, 10, -3, -5, 6.0]
assert_equal(np.ptp(a, axis=0), 15.0) Example 14
def _phampcheck(self, pha, amp, axis):
"""Check phase and amplitude values."""
# Shape checking :
if pha.ndim != amp.ndim:
raise ValueError("pha and amp must have the same number of "
"dimensions.")
# Force phase / amplitude to be at least (1, N) :
if (pha.ndim == 1) and (amp.ndim == 1):
pha = pha.reshape(1, -1)
amp = amp.reshape(1, -1)
axis = 1
# Check if the phase is in radians :
if np.ptp(pha) > 2 * np.pi:
raise ValueError("Your phase is probably in degrees and should be"
" converted in radians using either np.degrees or"
" np.deg2rad.")
# Check if the phase/amplitude have the same number of points on axis:
if pha.shape[axis] != amp.shape[axis]:
phan, ampn = pha.shape[axis], amp.shape[axis]
raise ValueError("The phase (" + str(phan) + ") and the amplitude "
"(" + str(ampn) + ") do not have the same number"
" of points on the specified axis (" +
str(axis) + ").")
# Force the phase to be in [-pi, pi] :
pha = (pha + np.pi) % (2 * np.pi) - np.pi
return pha, amp, axis
###########################################################################
# PROPERTIES
###########################################################################
# ----------- IDPAC ----------- Example 15
def _postprocess_contours(self, index, times, freqs, salience):
"""Remove contours that are too short.
Parameters
----------
index : np.array
array of contour numbers
times : np.array
array of contour times
freqs : np.array
array of contour frequencies
salience : np.array
array of contour salience values
Returns
-------
index_pruned : np.array
Pruned array of contour numbers
times_pruned : np.array
Pruned array of contour times
freqs_pruned : np.array
Pruned array of contour frequencies
salience_pruned : np.array
Pruned array of contour salience values
"""
keep_index = np.ones(times.shape).astype(bool)
for i in set(index):
this_idx = (index == i)
if np.ptp(times[this_idx]) <= self.min_contour_len:
keep_index[this_idx] = False
return (index[keep_index], times[keep_index],
freqs[keep_index], salience[keep_index]) Example 16
def test_ptp(self):
a = [3, 4, 5, 10, -3, -5, 6.0]
assert_equal(np.ptp(a, axis=0), 15.0) Example 17
def fit(self, X, y=None):
"""Fit it."""
if self.n_channels is None or self.n_times is None:
raise ValueError('Cannot fit without knowing n_channels'
' and n_times')
X = X.reshape(-1, self.n_channels, self.n_times)
deltas = np.array([np.ptp(d, axis=1) for d in X])
epoch_deltas = deltas.max(axis=1)
keep = epoch_deltas <= self.thresh
self.mean_ = _slicemean(X, keep, axis=0)
return self Example 18
def _get_epochs_interpolation(self, epochs, drop_log,
ch_type, verbose='progressbar'):
"""Interpolate the bad epochs."""
# 1: bad segment, # 2: interpolated
fix_log = drop_log.copy()
ch_names = epochs.ch_names
non_picks = np.setdiff1d(range(epochs.info['nchan']), self.picks)
interp_channels = list()
n_interpolate = self.n_interpolate[ch_type]
for epoch_idx in range(len(epochs)):
n_bads = drop_log[epoch_idx, self.picks].sum()
if n_bads == 0:
continue
else:
if n_bads <= n_interpolate:
interp_chs_mask = drop_log[epoch_idx] == 1
else:
# get peak-to-peak for channels in that epoch
data = epochs[epoch_idx].get_data()[0]
peaks = np.ptp(data, axis=-1)
peaks[non_picks] = -np.inf
# find channels which are bad by rejection threshold
interp_chs_mask = drop_log[epoch_idx] == 1
# ignore good channels
peaks[~interp_chs_mask] = -np.inf
# find the ordering of channels amongst the bad channels
sorted_ch_idx_picks = np.argsort(peaks)[::-1]
# then select only the worst n_interpolate channels
interp_chs_mask[
sorted_ch_idx_picks[n_interpolate:]] = False
fix_log[epoch_idx][interp_chs_mask] = 2
interp_chs = np.where(interp_chs_mask)[0]
interp_chs = [ch_name for idx, ch_name in enumerate(ch_names)
if idx in interp_chs]
interp_channels.append(interp_chs)
return interp_channels, fix_log Example 19
def normalizeData(X):
mean = []
data_range = []
mean.append(np.mean(X[:,1]))
mean.append(np.mean(X[:,2]))
data_range = np.ptp(X,axis=0)[-2:]
#print(mean,data_range)
for i in range(len(X)):
X[:,1][i] = (X[:,1][i] - float(mean[0]))/float(data_range[0])
X[:,2][i] = (X[:,2][i] - float(mean[1]))/float(data_range[1])
return X Example 20
def normalizeData(X):
mean = []
data_range = []
mean.append(np.mean(X[:,1]))
mean.append(np.mean(X[:,2]))
data_range = np.ptp(X,axis=0)[-2:]
#print(mean,data_range)
for i in range(len(X)):
X[:,1][i] = (X[:,1][i] - float(mean[0]))/float(data_range[0])
X[:,2][i] = (X[:,2][i] - float(mean[1]))/float(data_range[1])
return X Example 21
def FeatureScaling(X):
mean = []
data_range = []
X1 = np.zeros((len(X),X.shape[1]))
mean.append(np.mean(X[:,1]))
mean.append(np.mean(X[:,2]))
data_range = np.ptp(X,axis=0)[-2:]
#print(mean)
print(data_range)
for i in range(len(X)):
X1[:,0][i] = (X[:,0][i] - mean[0])/data_range[0]
X1[:,1][i] = (X[:,1][i] - mean[1])/data_range[1]
return X1 Example 22
def neighbours(self, effective_temperature, surface_gravity, metallicity, N,
scales=None):
"""
Return indices of the `N`th-nearest neighbours in the grid. The three
parameters are scaled by the peak-to-peak range in the grid, unless
`scales` are indicates.
:param effective_temperature:
The effective temperature of the star.
:param surface_gravity:
The surface gravity of the star.
:param metallicity:
The metallicity of the star.
:param N:
The number of neighbouring indices to return.
:returns:
An array of length `N` that contains the indices of the closest
neighbours in the grid.
"""
point = np.array([effective_temperature, surface_gravity, metallicity])
if scales is None:
scales = np.ptp(self._grid, axis=0)
distance = np.sum(((self._grid - point)/scales)**2, axis=1)
return np.argsort(distance)[:N] Example 23
def nearest_neighbours(self, point, n):
"""
Return the indices of the n nearest neighbours to the point.
"""
stellar_parameters = _recarray_to_array(self.stellar_parameters)
distances = np.sum(((point - stellar_parameters) \
/ np.ptp(stellar_parameters, axis=0))**2, axis=1)
return distances.argsort()[:n] Example 24
def figure_mouse_pick(self, event):
"""
Trigger for when the mouse is used to select an item in the figure.
:param event:
The matplotlib event.
"""
ycol = "abundance"
xcol = {
self.ax_excitation_twin: "expot",
self.ax_line_strength_twin: "reduced_equivalent_width"
}[event.inaxes]
xscale = np.ptp(event.inaxes.get_xlim())
yscale = np.ptp(event.inaxes.get_ylim())
try:
distance = np.sqrt(
((self._state_transitions[ycol] - event.ydata)/yscale)**2 \
+ ((self._state_transitions[xcol] - event.xdata)/xscale)**2)
except AttributeError:
# Stellar parameters have not been measured yet
return None
index = np.nanargmin(distance)
# Because the state transitions are linked to the parent source model of
# the table view, we will have to get the proxy index.
proxy_index = self.table_view.model().mapFromSource(
self.proxy_spectral_models.sourceModel().createIndex(index, 0)).row()
self.table_view.selectRow(proxy_index)
return None Example 25
def normalize(vec):
"""
Given an input vector normalize the vector
Parameters
==========
vec : array_like
input vector to normalize
Returns
=======
out : array_like
normalized vector
Examples
========
>>> import spacepy.toolbox as tb
>>> tb.normalize([1,2,3])
[0.0, 0.5, 1.0]
"""
# check to see if vec is numpy array, this is fastest
if isinstance(vec, np.ndarray):
out = (vec - vec.min())/np.ptp(vec)
else:
vecmin = np.min(vec)
ptp = np.ptp(vec)
out = [(val - vecmin)/ptp for val in vec]
return out Example 26
def test_ptp(self):
N = 1000
arr = np.random.randn(N)
ser = Series(arr)
self.assertEqual(np.ptp(ser), np.ptp(arr))
# GH11163
s = Series([3, 5, np.nan, -3, 10])
self.assertEqual(s.ptp(), 13)
self.assertTrue(pd.isnull(s.ptp(skipna=False)))
mi = pd.MultiIndex.from_product([['a', 'b'], [1, 2, 3]])
s = pd.Series([1, np.nan, 7, 3, 5, np.nan], index=mi)
expected = pd.Series([6, 2], index=['a', 'b'], dtype=np.float64)
self.assert_series_equal(s.ptp(level=0), expected)
expected = pd.Series([np.nan, np.nan], index=['a', 'b'])
self.assert_series_equal(s.ptp(level=0, skipna=False), expected)
with self.assertRaises(ValueError):
s.ptp(axis=1)
s = pd.Series(['a', 'b', 'c', 'd', 'e'])
with self.assertRaises(TypeError):
s.ptp()
with self.assertRaises(NotImplementedError):
s.ptp(numeric_only=True) Example 27
def _get_indice(cls, w, flux, blue, red, band=None, unit='ew', degree=1,
**kwargs):
""" compute spectral index after continuum subtraction
Parameters
----------
w: ndarray (nw, )
array of wavelengths in AA
flux: ndarray (N, nw)
array of flux values for different spectra in the series
blue: tuple(2)
selection for blue continuum estimate
red: tuple(2)
selection for red continuum estimate
band: tuple(2), optional
select region in this band only.
default is band = (min(blue), max(red))
unit: str
`ew` or `mag` wether equivalent width or magnitude
degree: int (default 1)
degree of the polynomial fit to the continuum
Returns
-------
ew: ndarray (N,)
equivalent width array
"""
wi, fi = cls.continuum_normalized_region_around_line(w, flux, blue,
red, band=band,
degree=degree)
if unit in (0, 'ew', 'EW'):
return np.trapz(1. - fi, wi, axis=-1)
else:
m = np.trapz(fi, wi, axis=-1)
m = -2.5 * np.log10(m / np.ptp(wi))
return m Example 28
def test_basic(self):
a = [3, 4, 5, 10, -3, -5, 6.0]
assert_equal(np.ptp(a, axis=0), 15.0)
b = [[3, 6.0, 9.0],
[4, 10.0, 5.0],
[8, 3.0, 2.0]]
assert_equal(np.ptp(b, axis=0), [5.0, 7.0, 7.0])
assert_equal(np.ptp(b, axis=-1), [6.0, 6.0, 6.0]) Example 29
def plot_cdf(x, copy=True, fractional=True, **kwargs):
"""
Add a log-log CCDF plot to the current axes.
Arguments
---------
x : array_like
The data to plot
copy : boolean
copy input array in a new object before sorting it. If data is a *very*
large, the copy can avoided by passing False to this parameter.
fractional : boolean
compress the data by means of fractional ranking. This collapses the
ranks from multiple, identical observations into their midpoint, thus
producing smaller figures. Note that the resulting plot will NOT be the
exact CCDF function, but an approximation.
Additional keyword arguments are passed to `matplotlib.pyplot.loglog`.
Returns a matplotlib axes object.
"""
N = float(len(x))
if copy:
x = x.copy()
x.sort()
if fractional:
t = []
for x, chunk in groupby(enumerate(x, 1), itemgetter(1)):
xranks, _ = zip(*list(chunk))
t.append((float(x), xranks[0] + np.ptp(xranks) / 2.0))
t = np.asarray(t)
else:
t = np.c_[np.asfarray(x), np.arange(N) + 1]
if 'ax' not in kwargs:
ax = plt.gca()
else:
ax = kwargs.pop('ax')
ax.loglog(t[:, 0], (N - t[:, 1]) / N, 'ow', **kwargs)
return ax Example 30
def test_integrate():
subslice = slice(100,200)
wvln = np.linspace(1000., 4000., 1024)
flux = np.zeros_like(wvln)
flux[subslice] = 1./np.ptp(wvln[subslice]) # so the integral is 1
s = Spectrum(wvln*u.angstrom, flux*u.erg/u.cm**2/u.angstrom)
# the integration grid is a sub-section of the full wavelength array
wvln_grid = s.wavelength[subslice]
i_flux = s.integrate(wvln_grid)
assert np.allclose(i_flux.value, 1.) # "close" because this is float comparison Example 31
def is_circle(points, scale, verbose=True):
'''
Given a set of points, quickly determine if they represent
a circle or not.
'''
# make sure input is a numpy array
points = np.asanyarray(points)
scale = float(scale)
# can only be a circle if the first and last point are the
# same (AKA is a closed path)
if np.linalg.norm(points[0] - points[-1]) > tol.merge:
return None
box = points.ptp(axis=0)
# the bounding box size of the points
# check aspect ratio as an early exit if the path is not a circle
aspect = np.divide(*box)
if np.abs(aspect - 1.0) > tol.aspect_frac:
return None
# fit a circle with tolerance checks
CR = fit_circle_check(points, scale=scale)
if CR is None:
return None
# return the circle as three control points
control = angles_to_threepoint([0,np.pi*.5], *CR)
return control Example 32
def test_ptp(self):
a = [3, 4, 5, 10, -3, -5, 6.0]
assert_equal(np.ptp(a, axis=0), 15.0) Example 33
def print_confidence_interval(ci, tabs=''):
"""Pretty print confidence interval information"""
ci = list(ci)
ci += [np.ptp(ci)]
print(tabs + 'Value: {1:.04f}'.format(*ci))
print(tabs + '95% Confidence Interval: ({0:.04f}, {2:.04f})'.format(*ci))
print(tabs + '\tCI Width: {3:.05f}'.format(*ci)) Example 34
def test_ptp(self):
a = [3, 4, 5, 10, -3, -5, 6.0]
assert_equal(np.ptp(a, axis=0), 15.0) Example 35
def ptp(a, axis=None, out=None):
"""
Range of values (maximum - minimum) along an axis.
The name of the function comes from the acronym for 'peak to peak'.
Parameters
----------
a : array_like
Input values.
axis : int, optional
Axis along which to find the peaks. By default, flatten the
array.
out : array_like
Alternative output array in which to place the result. It must
have the same shape and buffer length as the expected output,
but the type of the output values will be cast if necessary.
Returns
-------
ptp : ndarray
A new array holding the result, unless `out` was
specified, in which case a reference to `out` is returned.
Examples
--------
>>> x = np.arange(4).reshape((2,2))
>>> x
array([[0, 1],
[2, 3]])
>>> np.ptp(x, axis=0)
array([2, 2])
>>> np.ptp(x, axis=1)
array([1, 1])
"""
return _wrapfunc(a, 'ptp', axis=axis, out=out) Example 36
def test_scalar(self):
"""
Should return 0 for all scalar
"""
x = scalar('x')
p = ptp(x)
f = theano.function([x], p)
y = numpy.asarray(rand() * 2000 - 1000, dtype=config.floatX)
result = f(y)
numpyResult = numpy.ptp(y)
self.assertTrue(numpy.array_equal(result, numpyResult)) Example 37
def test_vector(self):
x = vector('x')
p = ptp(x, 0)
f = theano.function([x], p)
y = rand_ranged(-1000, 1000, [100])
result = f(y)
numpyResult = numpy.ptp(y, 0)
self.assertTrue(numpy.array_equal(result, numpyResult)) Example 38
def test_matrix_first_axis(self):
x = matrix('x')
p = ptp(x, 1)
f = theano.function([x], p)
y = rand_ranged(-1000, 1000, [100, 100])
result = f(y)
numpyResult = numpy.ptp(y, 1)
self.assertTrue(numpy.array_equal(result, numpyResult)) Example 39
def test_matrix_second_axis(self):
x = matrix('x')
p = ptp(x, 0)
f = theano.function([x], p)
y = rand_ranged(-1000, 1000, [100, 100])
result = f(y)
numpyResult = numpy.ptp(y, 0)
self.assertTrue(numpy.array_equal(result, numpyResult)) Example 40
def test_matrix_neg_axis(self):
x = matrix('x')
p = ptp(x, -1)
f = theano.function([x], p)
y = rand_ranged(-1000, 1000, [100, 100])
result = f(y)
numpyResult = numpy.ptp(y, -1)
self.assertTrue(numpy.array_equal(result, numpyResult)) Example 41
def test_interface(self):
x = matrix('x')
p = x.ptp(1)
f = theano.function([x], p)
y = rand_ranged(-1000, 1000, [100, 100])
result = f(y)
numpyResult = numpy.ptp(y, 1)
self.assertTrue(numpy.array_equal(result, numpyResult)) Example 42
def has_constant(x):
"""
Parameters
----------
x: ndarray
Array to be checked for a constant (n,k)
Returns
-------
const : bool
Flag indicating whether x contains a constant or has column span with
a constant
loc : int
Column location of constant
"""
if np.any(np.all(x == 1, axis=0)):
loc = np.argwhere(np.all(x == 1, axis=0))
return True, int(loc)
if np.any((np.ptp(x, axis=0) == 0) & ~np.all(x == 0, axis=0)):
loc = np.any((np.ptp(x, axis=0) == 0) & ~np.all(x == 0, axis=0))
loc = np.argwhere(loc)
return True, int(loc)
n = x.shape[0]
aug_rank = matrix_rank(np.c_[np.ones((n, 1)), x])
rank = matrix_rank(x)
has_const = bool(aug_rank == rank)
loc = None
if has_const:
out = np.linalg.lstsq(x, np.ones((n, 1)))
beta = out[0].ravel()
loc = np.argmax(np.abs(beta) * x.var(0))
return has_const, loc Example 43
def test_ids(panel):
data = PanelData(panel)
eids = data.entity_ids
assert eids.shape == (77, 1)
assert len(np.unique(eids)) == 11
for i in range(0, len(eids), 7):
assert np.ptp(eids[i:i + 7]) == 0
assert np.all((eids[i + 8:] - eids[i]) != 0)
tids = data.time_ids
assert tids.shape == (77, 1)
assert len(np.unique(tids)) == 7
for i in range(0, 11):
assert np.ptp(tids[i::7]) == 0 Example 44
def test_neighbors_accuracy_with_n_candidates():
# Checks whether accuracy increases as `n_candidates` increases.
n_candidates_values = np.array([.1, 50, 500])
n_samples = 100
n_features = 10
n_iter = 10
n_points = 5
rng = np.random.RandomState(42)
accuracies = np.zeros(n_candidates_values.shape[0], dtype=float)
X = rng.rand(n_samples, n_features)
for i, n_candidates in enumerate(n_candidates_values):
lshf = LSHForest(n_candidates=n_candidates)
ignore_warnings(lshf.fit)(X)
for j in range(n_iter):
query = X[rng.randint(0, n_samples)].reshape(1, -1)
neighbors = lshf.kneighbors(query, n_neighbors=n_points,
return_distance=False)
distances = pairwise_distances(query, X, metric='cosine')
ranks = np.argsort(distances)[0, :n_points]
intersection = np.intersect1d(ranks, neighbors).shape[0]
ratio = intersection / float(n_points)
accuracies[i] = accuracies[i] + ratio
accuracies[i] = accuracies[i] / float(n_iter)
# Sorted accuracies should be equal to original accuracies
assert_true(np.all(np.diff(accuracies) >= 0),
msg="Accuracies are not non-decreasing.")
# Highest accuracy should be strictly greater than the lowest
assert_true(np.ptp(accuracies) > 0,
msg="Highest accuracy is not strictly greater than lowest.") Example 45
def test_neighbors_accuracy_with_n_estimators():
# Checks whether accuracy increases as `n_estimators` increases.
n_estimators = np.array([1, 10, 100])
n_samples = 100
n_features = 10
n_iter = 10
n_points = 5
rng = np.random.RandomState(42)
accuracies = np.zeros(n_estimators.shape[0], dtype=float)
X = rng.rand(n_samples, n_features)
for i, t in enumerate(n_estimators):
lshf = LSHForest(n_candidates=500, n_estimators=t)
ignore_warnings(lshf.fit)(X)
for j in range(n_iter):
query = X[rng.randint(0, n_samples)].reshape(1, -1)
neighbors = lshf.kneighbors(query, n_neighbors=n_points,
return_distance=False)
distances = pairwise_distances(query, X, metric='cosine')
ranks = np.argsort(distances)[0, :n_points]
intersection = np.intersect1d(ranks, neighbors).shape[0]
ratio = intersection / float(n_points)
accuracies[i] = accuracies[i] + ratio
accuracies[i] = accuracies[i] / float(n_iter)
# Sorted accuracies should be equal to original accuracies
assert_true(np.all(np.diff(accuracies) >= 0),
msg="Accuracies are not non-decreasing.")
# Highest accuracy should be strictly greater than the lowest
assert_true(np.ptp(accuracies) > 0,
msg="Highest accuracy is not strictly greater than lowest.") Example 46
def test_ptp(self):
a = [3, 4, 5, 10, -3, -5, 6.0]
assert_equal(np.ptp(a, axis=0), 15.0) Example 47
def ptp(a, axis=None, out=None):
"""
Range of values (maximum - minimum) along an axis.
The name of the function comes from the acronym for 'peak to peak'.
Parameters
----------
a : array_like
Input values.
axis : int, optional
Axis along which to find the peaks. By default, flatten the
array.
out : array_like
Alternative output array in which to place the result. It must
have the same shape and buffer length as the expected output,
but the type of the output values will be cast if necessary.
Returns
-------
ptp : ndarray
A new array holding the result, unless `out` was
specified, in which case a reference to `out` is returned.
Examples
--------
>>> x = np.arange(4).reshape((2,2))
>>> x
array([[0, 1],
[2, 3]])
>>> np.ptp(x, axis=0)
array([2, 2])
>>> np.ptp(x, axis=1)
array([1, 1])
"""
try:
ptp = a.ptp
except AttributeError:
return _wrapit(a, 'ptp', axis, out)
return ptp(axis, out) Example 48
def ptp(a, axis=None, out=None):
"""
Range of values (maximum - minimum) along an axis.
The name of the function comes from the acronym for 'peak to peak'.
Parameters
----------
a : array_like
Input values.
axis : int, optional
Axis along which to find the peaks. By default, flatten the
array.
out : array_like
Alternative output array in which to place the result. It must
have the same shape and buffer length as the expected output,
but the type of the output values will be cast if necessary.
Returns
-------
ptp : ndarray
A new array holding the result, unless `out` was
specified, in which case a reference to `out` is returned.
Examples
--------
>>> x = np.arange(4).reshape((2,2))
>>> x
array([[0, 1],
[2, 3]])
>>> np.ptp(x, axis=0)
array([2, 2])
>>> np.ptp(x, axis=1)
array([1, 1])
"""
try:
ptp = a.ptp
except AttributeError:
return _wrapit(a, 'ptp', axis, out)
return ptp(axis, out) Example 49
def _plot_histogram(params):
"""Function for plotting histogram of peak-to-peak values."""
import matplotlib.pyplot as plt
epochs = params['epochs']
p2p = np.ptp(epochs.get_data(), axis=2)
types = list()
data = list()
if 'eeg' in params['types']:
eegs = np.array([p2p.T[i] for i,
x in enumerate(params['types']) if x == 'eeg'])
data.append(eegs.ravel())
types.append('eeg')
if 'mag' in params['types']:
mags = np.array([p2p.T[i] for i,
x in enumerate(params['types']) if x == 'mag'])
data.append(mags.ravel())
types.append('mag')
if 'grad' in params['types']:
grads = np.array([p2p.T[i] for i,
x in enumerate(params['types']) if x == 'grad'])
data.append(grads.ravel())
types.append('grad')
params['histogram'] = plt.figure()
scalings = _handle_default('scalings')
units = _handle_default('units')
titles = _handle_default('titles')
colors = _handle_default('color')
for idx in range(len(types)):
ax = plt.subplot(len(types), 1, idx + 1)
plt.xlabel(units[types[idx]])
plt.ylabel('count')
color = colors[types[idx]]
rej = None
if epochs.reject is not None and types[idx] in epochs.reject.keys():
rej = epochs.reject[types[idx]] * scalings[types[idx]]
rng = [0., rej * 1.1]
else:
rng = None
plt.hist(data[idx] * scalings[types[idx]], bins=100, color=color,
range=rng)
if rej is not None:
ax.plot((rej, rej), (0, ax.get_ylim()[1]), color='r')
plt.title(titles[types[idx]])
params['histogram'].suptitle('Peak-to-peak histogram', y=0.99)
params['histogram'].subplots_adjust(hspace=0.6)
try:
params['histogram'].show(warn=False)
except Exception:
pass
if params['fig_proj'] is not None:
params['fig_proj'].canvas.draw() Example 50
def relim_axes(axes, percent=20):
"""
Generate new axes for a matplotlib axes based on the collections present.
:param axes:
The matplotlib axes.
:param percent: [optional]
The percent of the data to extend past the minimum and maximum data
points.
:returns:
A two-length tuple containing the lower and upper limits in the x- and
y-axis, respectively.
"""
data = np.vstack([item.get_offsets() for item in axes.collections \
if isinstance(item, PathCollection)])
if data.size == 0:
return (None, None)
data = data.reshape(-1, 2)
x, y = data[:,0], data[:, 1]
# Only use finite values.
finite = np.isfinite(x*y)
x, y = x[finite], y[finite]
if x.size > 1:
xlim = [
np.min(x) - np.ptp(x) * percent/100.,
np.max(x) + np.ptp(x) * percent/100.,
]
elif x.size == 0:
xlim = None
else:
xlim = (x[0] - 1, x[0] + 1)
if y.size > 1:
ylim = [
np.min(y) - np.ptp(y) * percent/100.,
np.max(y) + np.ptp(y) * percent/100.
]
elif y.size == 0:
ylim = None
else:
ylim = (y[0] - 1, y[0] + 1)
axes.set_xlim(xlim)
axes.set_ylim(ylim)
return (xlim, ylim) 