File: C:/Users/fred/anaconda3/Lib/site-packages/holoviews/operation/downsample.py
"""
Implements downsampling algorithms for large 1D datasets.
The algorithms implemented in this module have been adapted from
https://github.com/predict-idlab/plotly-resampler and are reproduced
along with the original license:
MIT License
Copyright (c) 2022 Jonas Van Der Donckt, Jeroen Van Der Donckt, Emiel Deprost.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
import math
from functools import partial
import numpy as np
import param
from ..core import NdOverlay, Overlay
from ..element.chart import Area
from .resample import ResampleOperation1D
def _argmax_area(prev_x, prev_y, avg_next_x, avg_next_y, x_bucket, y_bucket):
"""Vectorized triangular area argmax computation.
Parameters
----------
prev_x : float
The previous selected point is x value.
prev_y : float
The previous selected point its y value.
avg_next_x : float
The x mean of the next bucket
avg_next_y : float
The y mean of the next bucket
x_bucket : np.ndarray
All x values in the bucket
y_bucket : np.ndarray
All y values in the bucket
Returns
-------
int
The index of the point with the largest triangular area.
"""
return np.abs(
x_bucket * (prev_y - avg_next_y)
+ y_bucket * (avg_next_x - prev_x)
+ (prev_x * avg_next_y - avg_next_x * prev_y)
).argmax()
def _lttb_inner(x, y, n_out, sampled_x, offset):
a = 0
for i in range(n_out - 3):
o0, o1, o2 = offset[i], offset[i + 1], offset[i + 2]
a = (
_argmax_area(
x[a],
y[a],
x[o1:o2].mean(),
y[o1:o2].mean(),
x[o0:o1],
y[o0:o1],
)
+ offset[i]
)
sampled_x[i + 1] = a
# ------------ EDGE CASE ------------
# next-average of last bucket = last point
sampled_x[-2] = (
_argmax_area(
x[a],
y[a],
x[-1], # last point
y[-1],
x[offset[-2] : offset[-1]],
y[offset[-2] : offset[-1]],
)
+ offset[-2]
)
def _ensure_contiguous(x, y):
"""
Ensures the arrays are contiguous in memory (required by tsdownsample).
"""
return np.ascontiguousarray(x), np.ascontiguousarray(y)
def _lttb(x, y, n_out, **kwargs):
"""
Downsample the data using the LTTB algorithm.
Will use a Python/Numpy implementation if tsdownsample is not available.
Args:
x (np.ndarray): The x-values of the data.
y (np.ndarray): The y-values of the data.
n_out (int): The number of output points.
Returns:
np.array: The indexes of the selected datapoints.
"""
try:
from tsdownsample import LTTBDownsampler
x, y = _ensure_contiguous(x, y)
return LTTBDownsampler().downsample(x, y, n_out=n_out, **kwargs)
except ModuleNotFoundError:
pass
except Exception as e:
raise e
# Bucket size. Leave room for start and end data points
block_size = (y.shape[0] - 2) / (n_out - 2)
# Note this 'astype' cast must take place after array creation (and not with the
# aranage() its dtype argument) or it will cast the `block_size` step to an int
# before the arange array creation
offset = np.arange(start=1, stop=y.shape[0], step=block_size).astype(np.int64)
# Construct the output array
sampled_x = np.empty(n_out, dtype=np.int64)
sampled_x[0] = 0
sampled_x[-1] = x.shape[0] - 1
# View it as int64 to take the mean of it
if x.dtype.kind == 'M':
x = x.view(np.int64)
if y.dtype.kind == 'M':
y = y.view(np.int64)
_lttb_inner(x, y, n_out, sampled_x, offset)
return sampled_x
def _nth_point(x, y, n_out, **kwargs):
"""
Downsampling by selecting every n-th datapoint
Args:
x (np.ndarray): The x-values of the data.
y (np.ndarray): The y-values of the data.
n_out (int): The number of output points.
Returns:
slice: The slice of selected datapoints.
"""
n_samples = len(x)
return slice(0, n_samples, max(1, math.ceil(n_samples / n_out)))
def _viewport(x, y, n_out, **kwargs):
return slice(len(x))
def _min_max(x, y, n_out, **kwargs):
try:
from tsdownsample import MinMaxDownsampler
except ModuleNotFoundError:
raise NotImplementedError(
'The min-max downsampling algorithm requires the tsdownsample '
'library to be installed.'
) from None
x, y = _ensure_contiguous(x, y)
return MinMaxDownsampler().downsample(x, y, n_out=n_out, **kwargs)
def _min_max_lttb(x, y, n_out, **kwargs):
try:
from tsdownsample import MinMaxLTTBDownsampler
except ModuleNotFoundError:
raise NotImplementedError(
'The minmax-lttb downsampling algorithm requires the tsdownsample '
'library to be installed.'
) from None
x, y = _ensure_contiguous(x, y)
return MinMaxLTTBDownsampler().downsample(x, y, n_out=n_out, **kwargs)
def _m4(x, y, n_out, **kwargs):
try:
from tsdownsample import M4Downsampler
except ModuleNotFoundError:
raise NotImplementedError(
'The m4 downsampling algorithm requires the tsdownsample '
'library to be installed.'
) from None
x, y = _ensure_contiguous(x, y)
n_out = n_out - (n_out % 4) # n_out must be a multiple of 4
return M4Downsampler().downsample(x, y, n_out=n_out, **kwargs)
_ALGORITHMS = {
'lttb': _lttb,
'nth': _nth_point,
'viewport': _viewport,
'minmax': _min_max,
'minmax-lttb': _min_max_lttb,
'm4': _m4,
}
class downsample1d(ResampleOperation1D):
"""
Implements downsampling of a regularly sampled 1D dataset.
If available uses the `tsdownsample` library to perform massively
accelerated downsampling.
"""
algorithm = param.Selector(default='lttb', objects=list(_ALGORITHMS), doc="""
The algorithm to use for downsampling:
- `lttb`: Largest Triangle Three Buckets downsample algorithm.
- `nth`: Selects every n-th point.
- `viewport`: Selects all points in a given viewport.
- `minmax`: Selects the min and max value in each bin (requires tsdownsample).
- `m4`: Selects the min, max, first and last value in each bin (requires tsdownsample).
- `minmax-lttb`: First selects n_out * minmax_ratio min and max values,
then further reduces these to n_out values using the
Largest Triangle Three Buckets algorithm (requires tsdownsample).""")
parallel = param.Boolean(default=False, doc="""
The number of threads to use (if tsdownsample is available).""")
minmax_ratio = param.Integer(default=4, bounds=(0, None), doc="""
For the minmax-lttb algorithm determines the ratio of candidate
values to generate with the minmax algorithm before further
downsampling with LTTB.""")
neighbor_points = param.Boolean(default=None, doc="""
Whether to add the neighbor points to the range before downsampling.
By default this is only enabled for the viewport algorithm.""")
def _process(self, element, key=None, shared_data=None):
if isinstance(element, (Overlay, NdOverlay)):
# Shared data is so we only slice the given data once
kwargs = {'key': key, 'shared_data': {}}
_process = partial(self._process, **kwargs)
if isinstance(element, Overlay):
elements = [v.map(_process) for v in element]
else:
elements = {k: v.map(_process) for k, v in element.items()}
return element.clone(elements)
if self.p.x_range:
key = (id(element.data), str(element.kdims[0]))
if shared_data is not None and key in shared_data:
element = element.clone(shared_data[key])
else:
mask = self._compute_mask(element)
element = element[mask]
if shared_data is not None:
shared_data[key] = element.data
if len(element) <= self.p.width:
return element
xs, ys = (element.dimension_values(i) for i in range(2))
if ys.dtype == np.bool_:
ys = ys.astype(np.int8)
downsample = _ALGORITHMS[self.p.algorithm]
kwargs = {}
if "lttb" in self.p.algorithm and isinstance(element, Area):
raise NotImplementedError(
"LTTB algorithm is not implemented for hv.Area"
)
elif self.p.algorithm == "minmax-lttb":
kwargs['minmax_ratio'] = self.p.minmax_ratio
samples = downsample(xs, ys, self.p.width, parallel=self.p.parallel, **kwargs)
return element.iloc[samples]
def _compute_mask(self, element):
"""
Computes the mask to apply to the element before downsampling.
"""
neighbor_enabled = (
self.p.neighbor_points
if self.p.neighbor_points is not None
else self.p.algorithm == "viewport"
)
if not neighbor_enabled:
return slice(*self.p.x_range)
try:
mask = element.dataset.interface._select_mask_neighbor(
element.dataset, {element.kdims[0]: self.p.x_range}
)
except NotImplementedError:
mask = slice(*self.p.x_range)
except Exception as e:
self.param.warning(f"Could not apply neighbor mask to downsample1d: {e}")
mask = slice(*self.p.x_range)
return mask