Note
Go to the end to download the full example code
Optimization Info#
Tpcp is focused on “running” pipelines and less on the “optimization” step.
This is great for traditional algorithms and algorithms will complex return values, as you can easily store multiple
parameters as attributes on the object during run.
However, for optimization, you are limited to modifying input parameters. This works well in many cases, but sometimes, you need additional information from the optimization. For example, you might want to extract the loss decay of an iterative learning algorithms. This information is something that you wouldn’t want to store in the input parameters (usually).
For these cases tpcp provides the self_optimize_with_info method.
This is basically identical to self_optimize, but is expected to provide two return values: the optimized instance
AND an arbitrary additional object containing any information you like.
Methods that get optimizable pipelines as input (e.g. Optimize are aware of these method and
will call self_optimize_with_info if available and store the additional info as result objects.
The OptimizablePipeline base-class is implemented in a way that you only need to worry about
implementing either the self_optimize_with_info or the self_optimize method.
The other will be available automatically (the additional info will be NOTHING, if the method is not implemented).
If you are implementing a new Algorithm (instead of a pipeline), we don’t provide this additional support, but it is relatively simple to implement yourself.
In the following we will show how all of this works by expanding the QRS detection algorithm implemented in the other examples to return additional information from the optimization.
import numpy as np
import pandas as pd
from sklearn.metrics import roc_curve
from typing_extensions import Self
from examples.algorithms.algorithms_qrs_detection_final import (
QRSDetector,
match_events_with_reference,
)
from examples.datasets.datasets_final_ecg import ECGExampleData
from tpcp import HyperParameter, OptimizableParameter, OptimizablePipeline, Parameter, cf, make_optimize_safe
from tpcp.optimize import Optimize
In the algorithm class below, we basically reimplemented the OptimizableQrsDetector from the algorithm example.
However, instead of the self_optimize method, we implemented the self_optimize_with_info method and added
additional information from the threshold selection process to the output of the optimization.
To ensure interface compatibility with other algorithms, we also provided a self_optimize method, that simply calls
self_optimize_with_info under the hood.
class OptimizableQrsDetectorWithInfo(QRSDetector):
min_r_peak_height_over_baseline: OptimizableParameter[float]
r_peak_match_tolerance_s: HyperParameter[float]
def __init__(
self,
max_heart_rate_bpm: float = 200.0,
min_r_peak_height_over_baseline: float = 1.0,
r_peak_match_tolerance_s: float = 0.01,
high_pass_filter_cutoff_hz: float = 1,
):
self.r_peak_match_tolerance_s = r_peak_match_tolerance_s
super().__init__(
max_heart_rate_bpm=max_heart_rate_bpm,
min_r_peak_height_over_baseline=min_r_peak_height_over_baseline,
high_pass_filter_cutoff_hz=high_pass_filter_cutoff_hz,
)
@make_optimize_safe
def self_optimize_with_info(
self, ecg_data: list[pd.Series], r_peaks: list[pd.Series], sampling_rate_hz: float
) -> tuple[Self, dict[str, np.ndarray]]:
all_labels = []
all_peak_heights = []
for d, p in zip(ecg_data, r_peaks):
filtered = self._filter(d.to_numpy().flatten(), sampling_rate_hz)
# Find all potential peaks without the height threshold
potential_peaks = self._search_strategy(filtered, sampling_rate_hz, use_height=False)
# Determine the label for each peak, by matching them with our ground truth
labels = np.zeros(potential_peaks.shape)
matches = match_events_with_reference(
events=np.atleast_2d(potential_peaks).T,
reference=np.atleast_2d(p.to_numpy().astype(int)).T,
tolerance=self.r_peak_match_tolerance_s * sampling_rate_hz,
)
tp_matches = matches[(~np.isnan(matches)).all(axis=1), 0].astype(int)
labels[tp_matches] = 1
labels = labels.astype(bool)
all_labels.append(labels)
all_peak_heights.append(filtered[potential_peaks])
all_labels = np.hstack(all_labels)
all_peak_heights = np.hstack(all_peak_heights)
# We "brute-force" a good cutoff by testing a bunch of thresholds and then calculating the Youden Index for
# each.
fpr, tpr, thresholds = roc_curve(all_labels, all_peak_heights)
youden_index = tpr - fpr
# The best Youden index gives us a balance between sensitivity and specificity.
self.min_r_peak_height_over_baseline = thresholds[np.argmax(youden_index)]
# Here we create the additional infor object:
additional_info = {"all_youden_index": youden_index, "all_thresholds": thresholds}
return self, additional_info
def self_optimize(self, ecg_data: list[pd.Series], r_peaks: list[pd.Series], sampling_rate_hz: float) -> Self:
return self.self_optimize_with_info(ecg_data=ecg_data, r_peaks=r_peaks, sampling_rate_hz=sampling_rate_hz)[0]
To use this algorithm in an optimization, we need a pipeline to wrap it. Below we can find a reimplementation of the pipline from the “Optimizable Pipeline” example.
However, instead of implementing self_optimize method, we implemented the self_optimize_with_info method and
also called the self_optimize_with_info of our algorithm under the hood.
Note, that for pipelines, we don’t need to implement a dummy self_optimize method.
Our baseclass already takes care of that.
class MyPipeline(OptimizablePipeline[ECGExampleData]):
algorithm: Parameter[OptimizableQrsDetectorWithInfo]
algorithm__min_r_peak_height_over_baseline: OptimizableParameter[float]
r_peak_positions_: pd.Series
def __init__(self, algorithm: OptimizableQrsDetectorWithInfo = cf(OptimizableQrsDetectorWithInfo())):
self.algorithm = algorithm
@make_optimize_safe
def self_optimize_with_info(self, dataset: ECGExampleData, **kwargs):
ecg_data = [d.data["ecg"] for d in dataset]
r_peaks = [d.r_peak_positions_["r_peak_position"] for d in dataset]
# Note: We need to clone the algorithm instance, to make sure we don't leak any data between runs.
algo = self.algorithm.clone()
# Here we call the `self_optimize_with_info` method!
self.algorithm, additional_data = algo.self_optimize_with_info(ecg_data, r_peaks, dataset.sampling_rate_hz)
return self, additional_data
def run(self, datapoint: ECGExampleData):
# Note: We need to clone the algorithm instance, to make sure we don't leak any data between runs.
algo = self.algorithm.clone()
algo.detect(datapoint.data["ecg"], datapoint.sampling_rate_hz)
self.r_peak_positions_ = algo.r_peak_positions_
return self
Let’s test this class!
However, first we need some test data
from pathlib import Path
from sklearn.model_selection import train_test_split
try:
HERE = Path(__file__).parent
except NameError:
HERE = Path().resolve()
data_path = HERE.parent.parent / "example_data/ecg_mit_bih_arrhythmia/data"
example_data = ECGExampleData(data_path)
train_set, test_set = train_test_split(example_data, train_size=0.7, random_state=0)
# We only want a single dataset in the test set
test_set = test_set[0]
With the train data we can try out the optimization
optimized_pipe, info = MyPipeline().self_optimize_with_info(train_set)
info
{'all_youden_index': array([0.00000000e+00, 6.19540301e-05, 1.52512466e-05, 8.86714683e-02,
8.86247656e-02, 1.01263388e-01, 1.01216685e-01, 1.07040364e-01,
1.06993661e-01, 1.07489293e-01, 1.07442590e-01, 1.07752361e-01,
1.07705658e-01, 1.23751752e-01, 1.23705049e-01, 1.24076773e-01,
1.24030070e-01, 1.29915703e-01, 1.29869000e-01, 1.30302678e-01,
1.30255976e-01, 1.31185286e-01, 1.31138583e-01, 1.36714446e-01,
1.36667743e-01, 1.36915559e-01, 1.36868857e-01, 1.39161156e-01,
1.39114453e-01, 1.40973074e-01, 1.40926371e-01, 1.42227406e-01,
1.42180703e-01, 1.43729554e-01, 1.43682851e-01, 1.57932278e-01,
1.57885575e-01, 2.48152597e-01, 2.48105894e-01, 2.48477618e-01,
2.48430916e-01, 2.49917812e-01, 2.49871109e-01, 2.50180880e-01,
2.50134177e-01, 2.51744982e-01, 2.51698279e-01, 2.52441727e-01,
2.52395024e-01, 2.53324335e-01, 2.53230929e-01, 2.53850470e-01,
2.53803767e-01, 2.55290664e-01, 2.55243961e-01, 2.57969938e-01,
2.57923235e-01, 2.59410132e-01, 2.59363429e-01, 2.59797107e-01,
2.59750405e-01, 2.60493853e-01, 2.60447150e-01, 2.60633012e-01,
2.60586310e-01, 2.61949298e-01, 2.61902595e-01, 2.63017768e-01,
2.62971065e-01, 2.63838422e-01, 2.63791719e-01, 2.65278616e-01,
2.65185210e-01, 2.68035095e-01, 2.67988393e-01, 2.70652416e-01,
2.70605713e-01, 2.71473070e-01, 2.71426367e-01, 2.72665447e-01,
2.72618745e-01, 2.72742653e-01, 2.72695950e-01, 2.75917559e-01,
2.75870857e-01, 2.76924075e-01, 2.76877372e-01, 2.77806683e-01,
2.77759980e-01, 2.77883888e-01, 2.77837185e-01, 2.78456726e-01,
2.78410023e-01, 2.79339333e-01, 2.79292630e-01, 2.79478493e-01,
2.79431790e-01, 2.88353170e-01, 2.88306467e-01, 2.92023709e-01,
2.91977006e-01, 2.95880110e-01, 2.95833407e-01, 3.01223408e-01,
3.01176705e-01, 3.02415786e-01, 3.02369083e-01, 3.02740807e-01,
3.02694105e-01, 3.13164336e-01, 3.13117633e-01, 3.42297981e-01,
3.42251278e-01, 3.46588060e-01, 3.46541358e-01, 3.47470668e-01,
3.47423965e-01, 3.51265115e-01, 3.51218412e-01, 3.59644160e-01,
3.59597458e-01, 3.66350447e-01, 3.66303744e-01, 3.85571447e-01,
3.85524745e-01, 3.94941757e-01, 3.94895054e-01, 4.04374021e-01,
4.04327318e-01, 4.12691112e-01, 4.12644410e-01, 4.30982802e-01,
4.30936100e-01, 4.36264146e-01, 4.36217444e-01, 4.46006180e-01,
4.45959477e-01, 4.49243041e-01, 4.49196338e-01, 4.52851626e-01,
4.52804923e-01, 4.54167912e-01, 4.54121209e-01, 4.55793968e-01,
4.55747265e-01, 4.55995081e-01, 4.55948379e-01, 4.63073092e-01,
4.63026389e-01, 4.63212251e-01, 4.63165549e-01, 4.63599227e-01,
4.63552524e-01, 4.64667696e-01, 4.64620994e-01, 4.64744902e-01,
4.64698199e-01, 4.74177166e-01, 4.74130463e-01, 4.74378279e-01,
4.74331576e-01, 4.78172726e-01, 4.78126023e-01, 4.78187977e-01,
4.78141274e-01, 4.86071390e-01, 4.86024688e-01, 5.16320208e-01,
5.16273505e-01, 5.22840633e-01, 5.22793930e-01, 5.23165654e-01,
5.23118951e-01, 5.24729756e-01, 5.24683053e-01, 5.27966617e-01,
5.27919914e-01, 5.28911179e-01, 5.28864476e-01, 5.29917694e-01,
5.29870992e-01, 5.31357888e-01, 5.31311185e-01, 5.31744864e-01,
5.31698161e-01, 5.41796668e-01, 5.41749965e-01, 5.47511690e-01,
5.47464987e-01, 5.47526941e-01, 5.47480238e-01, 5.52622423e-01,
5.52575720e-01, 5.56231008e-01, 5.56184305e-01, 5.59343961e-01,
5.59297258e-01, 5.62394959e-01, 5.62348256e-01, 5.64206877e-01,
5.64160175e-01, 5.71470750e-01, 5.71424047e-01, 5.73344622e-01,
5.73297920e-01, 5.89158151e-01, 5.89111448e-01, 5.89235356e-01,
5.89188654e-01, 5.89808194e-01, 5.89761491e-01, 5.97257929e-01,
5.97211226e-01, 5.98760077e-01, 5.98713374e-01, 6.00571995e-01,
6.00478589e-01, 6.05001234e-01, 6.04954531e-01, 6.14805222e-01,
6.14758519e-01, 6.15440013e-01, 6.15393310e-01, 6.16384575e-01,
6.16337872e-01, 6.19373620e-01, 6.19326917e-01, 6.20689905e-01,
6.20643203e-01, 6.22563778e-01, 6.22517075e-01, 6.23508339e-01,
6.23461636e-01, 6.26063706e-01, 6.26017003e-01, 6.28866888e-01,
6.28820186e-01, 6.41210992e-01, 6.41164289e-01, 6.44200036e-01,
6.44153333e-01, 6.45454368e-01, 6.45407665e-01, 6.46027206e-01,
6.45980503e-01, 6.47777170e-01, 6.47730467e-01, 6.51943341e-01,
6.51896638e-01, 6.52392270e-01, 6.52345568e-01, 6.52841200e-01,
6.52794497e-01, 6.59733348e-01, 6.59686646e-01, 6.64147336e-01,
6.64100633e-01, 6.65277760e-01, 6.65231057e-01, 6.66779908e-01,
6.66733205e-01, 6.70326539e-01, 6.70279836e-01, 6.72757997e-01,
6.72711294e-01, 6.77233938e-01, 6.77187236e-01, 6.80532753e-01,
6.80486050e-01, 6.82096855e-01, 6.82050152e-01, 6.82236015e-01,
6.82189312e-01, 6.82313220e-01, 6.82266517e-01, 6.83195828e-01,
6.83149125e-01, 6.90335792e-01, 6.90289089e-01, 7.03547252e-01,
7.03500549e-01, 7.05173308e-01, 7.05126605e-01, 7.07480858e-01,
7.07434155e-01, 7.11151397e-01, 7.11104695e-01, 7.11662281e-01,
7.11615578e-01, 7.11677532e-01, 7.11630829e-01, 7.12126461e-01,
7.12079759e-01, 7.15673092e-01, 7.15579687e-01, 7.18057848e-01,
7.18011145e-01, 7.21418617e-01, 7.21371914e-01, 7.22734903e-01,
7.22688200e-01, 7.24422913e-01, 7.24376210e-01, 7.26234831e-01,
7.26188128e-01, 7.26250082e-01, 7.26203379e-01, 7.27132690e-01,
7.27085987e-01, 7.27395757e-01, 7.27349055e-01, 7.28464227e-01,
7.28417524e-01, 7.33745571e-01, 7.33698868e-01, 7.39336685e-01,
7.39289982e-01, 7.41644235e-01, 7.41597532e-01, 7.42464889e-01,
7.42418186e-01, 7.45330025e-01, 7.45283323e-01, 7.46646311e-01,
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7.49108272e-01, 7.49294134e-01, 7.49247432e-01, 7.49371340e-01,
7.49324637e-01, 7.50068085e-01, 7.50021382e-01, 7.53986440e-01,
7.53939738e-01, 7.55054910e-01, 7.55008207e-01, 7.55194069e-01,
7.55147367e-01, 7.56200585e-01, 7.56153882e-01, 7.57083193e-01,
7.57036490e-01, 7.57408214e-01, 7.57361511e-01, 7.57485419e-01,
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7.70725484e-01, 7.70973300e-01, 7.70926597e-01, 7.74457977e-01,
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8.00287113e-01, 8.00349067e-01, 8.00302364e-01, 8.03090295e-01,
8.03043593e-01, 8.03291409e-01, 8.03198003e-01, 8.03259957e-01,
8.03213255e-01, 8.04204519e-01, 8.04157816e-01, 8.05087127e-01,
8.05040424e-01, 8.05598010e-01, 8.05551307e-01, 8.06542572e-01,
8.06495869e-01, 8.07177363e-01, 8.07130661e-01, 8.07564339e-01,
8.07517636e-01, 8.10119705e-01, 8.10073003e-01, 8.11435991e-01,
8.11389288e-01, 8.11451242e-01, 8.11404540e-01, 8.11652356e-01,
8.11558950e-01, 8.11930674e-01, 8.11883972e-01, 8.11945926e-01,
8.11899223e-01, 8.13571982e-01, 8.13525279e-01, 8.13587233e-01,
8.13540530e-01, 8.14098116e-01, 8.14051414e-01, 8.14175322e-01,
8.14128619e-01, 8.14190573e-01, 8.14143870e-01, 8.15073181e-01,
8.14979775e-01, 8.15165637e-01, 8.15118934e-01, 8.15180888e-01,
8.15134186e-01, 8.16806944e-01, 8.16760242e-01, 8.17193920e-01,
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8.22443812e-01, 8.23620939e-01, 8.23574236e-01, 8.23760098e-01,
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0.64671599, 0.64666635, 0.64548275, 0.6454153 , 0.64448791,
0.64416142, 0.64371965, 0.64354348, 0.64344275, 0.64300468,
0.64193997, 0.64171255, 0.64133969, 0.64116234, 0.64096289,
0.6409129 , 0.63952081, 0.63950827, 0.63902306, 0.6389233 ,
0.63810876, 0.63783852, 0.63612388, 0.63547062, 0.63525282,
0.6352358 , 0.63379831, 0.63365277, 0.63328088, 0.63308378,
0.63295313, 0.63290852, 0.63287906, 0.63286552, 0.63227 ,
0.63222855, 0.63221683, 0.63184702, 0.63122582, 0.63087174,
0.630557 , 0.63022362, 0.63011146, 0.63009744, 0.62971778,
0.62968969, 0.62932408, 0.62889603, 0.62797538, 0.62746714,
0.62719731, 0.62652844, 0.62395336, 0.62332224, 0.62276692,
0.62275731, 0.62205803, 0.62201743, 0.62137472, 0.62055958,
0.62018453, 0.62012921, 0.61888304, 0.61813255, 0.61765367,
0.61726459, 0.61717313, 0.61716811, 0.61702895, 0.61659888,
0.61659286, 0.61639966, 0.61627868, 0.61600207, 0.61276081,
0.61251471, 0.61229583, 0.61227858, 0.61224416, 0.61170973,
0.61081375, 0.61007074, 0.60960521, 0.60893997, 0.60807332,
0.60793793, 0.60691953, 0.60579938, 0.60138818, 0.5993801 ,
0.59928863, 0.59908586, 0.59791037, 0.5977756 , 0.59737943,
0.59573503, 0.59489916, 0.59489023, 0.59487381, 0.59473522,
0.59385356, 0.59284896, 0.5926476 , 0.59146026, 0.58956582,
0.58946917, 0.58939275, 0.58901627, 0.58871067, 0.58866832,
0.5881326 , 0.58799827, 0.58791072, 0.58785609, 0.58708307,
0.58648895, 0.58586351, 0.58498751, 0.58414999, 0.58376531,
0.58313602, 0.58264483, 0.58242003, 0.58207685, 0.58164475,
0.58117116, 0.58109385, 0.58020233, 0.58007321, 0.58001233,
0.57955434, 0.57878865, 0.5781294 , 0.57724563, 0.5771014 ,
0.57698526, 0.57695894, 0.57481346, 0.57309526, 0.5707037 ,
0.5703109 , 0.56986351, 0.56927792, 0.56755315, 0.56728743,
0.56726834, 0.56684715, 0.56684128, 0.56659215, 0.56464794,
0.56284241, 0.56283656, 0.56226535, 0.56224435, 0.56194802,
0.55939182, 0.55933155, 0.55828076, 0.55817749, 0.55459145,
0.55137933, 0.55071159, 0.55052289, 0.54967242, 0.54913999,
0.54759925, 0.54735771, 0.54720498, 0.54577005, 0.54359384,
0.54345838, 0.54165384, 0.54090694, 0.53980642, 0.53939542,
0.5384282 , 0.53820027, 0.53604474, 0.53531947, 0.53360005,
0.53271364, 0.52357718, 0.52207081, 0.51976737, 0.51943839,
0.50831462, 0.50815075, 0.50784908, 0.50754449, 0.49730647,
0.49701034, 0.49661627, 0.49645763, 0.49530115, 0.49518421,
0.49509224, 0.49497211, 0.49466723, 0.49448543, 0.49353372,
0.49333923, 0.49187409, 0.49169893, 0.48957056, 0.48943141,
0.488741 , 0.48860717, 0.48436627, 0.48351431, 0.4759083 ,
0.47570301, 0.46690634, 0.46679363, 0.44257288, 0.44252377,
0.42786575, 0.42765668, 0.42551195, 0.42546797, 0.42501634,
0.42499752, 0.41733453, 0.41724043, 0.40333304, 0.40315878,
0.39878492, 0.3987665 , 0.39650699, 0.39632832, 0.38491504,
0.38486632, 0.36865236, 0.36863028, 0.36407871, 0.36402918,
0.35090496, 0.35080663, 0.34914529, 0.3491028 , 0.33322126,
0.33313405, 0.27414564, 0.27394971, 0.19306236, 0.19293001,
0.17693419, 0.17684902, 0.08041446, 0.08037123, -2.03591419])}
optimized_pipe
MyPipeline(algorithm=OptimizableQrsDetectorWithInfo(high_pass_filter_cutoff_hz=1, max_heart_rate_bpm=200.0, min_r_peak_height_over_baseline=0.5816447455722318, r_peak_match_tolerance_s=0.01))
But we can also just call the auto-generated self_optimize method and don’t get the info:
optimized_pipe = MyPipeline().self_optimize(train_set)
optimized_pipe
MyPipeline(algorithm=OptimizableQrsDetectorWithInfo(high_pass_filter_cutoff_hz=1, max_heart_rate_bpm=200.0, min_r_peak_height_over_baseline=0.5816447455722318, r_peak_match_tolerance_s=0.01))
However, in most cases, we should just use the Optimize wrapper.
It will call the self_optimize_with_info method if available (you can force it to use self_optimize using the
optimize_with_info parameter) and then provide the additional info as attribute
optimizer = Optimize(MyPipeline()).optimize(train_set)
optimizer.optimization_info_
{'all_youden_index': array([0.00000000e+00, 6.19540301e-05, 1.52512466e-05, 8.86714683e-02,
8.86247656e-02, 1.01263388e-01, 1.01216685e-01, 1.07040364e-01,
1.06993661e-01, 1.07489293e-01, 1.07442590e-01, 1.07752361e-01,
1.07705658e-01, 1.23751752e-01, 1.23705049e-01, 1.24076773e-01,
1.24030070e-01, 1.29915703e-01, 1.29869000e-01, 1.30302678e-01,
1.30255976e-01, 1.31185286e-01, 1.31138583e-01, 1.36714446e-01,
1.36667743e-01, 1.36915559e-01, 1.36868857e-01, 1.39161156e-01,
1.39114453e-01, 1.40973074e-01, 1.40926371e-01, 1.42227406e-01,
1.42180703e-01, 1.43729554e-01, 1.43682851e-01, 1.57932278e-01,
1.57885575e-01, 2.48152597e-01, 2.48105894e-01, 2.48477618e-01,
2.48430916e-01, 2.49917812e-01, 2.49871109e-01, 2.50180880e-01,
2.50134177e-01, 2.51744982e-01, 2.51698279e-01, 2.52441727e-01,
2.52395024e-01, 2.53324335e-01, 2.53230929e-01, 2.53850470e-01,
2.53803767e-01, 2.55290664e-01, 2.55243961e-01, 2.57969938e-01,
2.57923235e-01, 2.59410132e-01, 2.59363429e-01, 2.59797107e-01,
2.59750405e-01, 2.60493853e-01, 2.60447150e-01, 2.60633012e-01,
2.60586310e-01, 2.61949298e-01, 2.61902595e-01, 2.63017768e-01,
2.62971065e-01, 2.63838422e-01, 2.63791719e-01, 2.65278616e-01,
2.65185210e-01, 2.68035095e-01, 2.67988393e-01, 2.70652416e-01,
2.70605713e-01, 2.71473070e-01, 2.71426367e-01, 2.72665447e-01,
2.72618745e-01, 2.72742653e-01, 2.72695950e-01, 2.75917559e-01,
2.75870857e-01, 2.76924075e-01, 2.76877372e-01, 2.77806683e-01,
2.77759980e-01, 2.77883888e-01, 2.77837185e-01, 2.78456726e-01,
2.78410023e-01, 2.79339333e-01, 2.79292630e-01, 2.79478493e-01,
2.79431790e-01, 2.88353170e-01, 2.88306467e-01, 2.92023709e-01,
2.91977006e-01, 2.95880110e-01, 2.95833407e-01, 3.01223408e-01,
3.01176705e-01, 3.02415786e-01, 3.02369083e-01, 3.02740807e-01,
3.02694105e-01, 3.13164336e-01, 3.13117633e-01, 3.42297981e-01,
3.42251278e-01, 3.46588060e-01, 3.46541358e-01, 3.47470668e-01,
3.47423965e-01, 3.51265115e-01, 3.51218412e-01, 3.59644160e-01,
3.59597458e-01, 3.66350447e-01, 3.66303744e-01, 3.85571447e-01,
3.85524745e-01, 3.94941757e-01, 3.94895054e-01, 4.04374021e-01,
4.04327318e-01, 4.12691112e-01, 4.12644410e-01, 4.30982802e-01,
4.30936100e-01, 4.36264146e-01, 4.36217444e-01, 4.46006180e-01,
4.45959477e-01, 4.49243041e-01, 4.49196338e-01, 4.52851626e-01,
4.52804923e-01, 4.54167912e-01, 4.54121209e-01, 4.55793968e-01,
4.55747265e-01, 4.55995081e-01, 4.55948379e-01, 4.63073092e-01,
4.63026389e-01, 4.63212251e-01, 4.63165549e-01, 4.63599227e-01,
4.63552524e-01, 4.64667696e-01, 4.64620994e-01, 4.64744902e-01,
4.64698199e-01, 4.74177166e-01, 4.74130463e-01, 4.74378279e-01,
4.74331576e-01, 4.78172726e-01, 4.78126023e-01, 4.78187977e-01,
4.78141274e-01, 4.86071390e-01, 4.86024688e-01, 5.16320208e-01,
5.16273505e-01, 5.22840633e-01, 5.22793930e-01, 5.23165654e-01,
5.23118951e-01, 5.24729756e-01, 5.24683053e-01, 5.27966617e-01,
5.27919914e-01, 5.28911179e-01, 5.28864476e-01, 5.29917694e-01,
5.29870992e-01, 5.31357888e-01, 5.31311185e-01, 5.31744864e-01,
5.31698161e-01, 5.41796668e-01, 5.41749965e-01, 5.47511690e-01,
5.47464987e-01, 5.47526941e-01, 5.47480238e-01, 5.52622423e-01,
5.52575720e-01, 5.56231008e-01, 5.56184305e-01, 5.59343961e-01,
5.59297258e-01, 5.62394959e-01, 5.62348256e-01, 5.64206877e-01,
5.64160175e-01, 5.71470750e-01, 5.71424047e-01, 5.73344622e-01,
5.73297920e-01, 5.89158151e-01, 5.89111448e-01, 5.89235356e-01,
5.89188654e-01, 5.89808194e-01, 5.89761491e-01, 5.97257929e-01,
5.97211226e-01, 5.98760077e-01, 5.98713374e-01, 6.00571995e-01,
6.00478589e-01, 6.05001234e-01, 6.04954531e-01, 6.14805222e-01,
6.14758519e-01, 6.15440013e-01, 6.15393310e-01, 6.16384575e-01,
6.16337872e-01, 6.19373620e-01, 6.19326917e-01, 6.20689905e-01,
6.20643203e-01, 6.22563778e-01, 6.22517075e-01, 6.23508339e-01,
6.23461636e-01, 6.26063706e-01, 6.26017003e-01, 6.28866888e-01,
6.28820186e-01, 6.41210992e-01, 6.41164289e-01, 6.44200036e-01,
6.44153333e-01, 6.45454368e-01, 6.45407665e-01, 6.46027206e-01,
6.45980503e-01, 6.47777170e-01, 6.47730467e-01, 6.51943341e-01,
6.51896638e-01, 6.52392270e-01, 6.52345568e-01, 6.52841200e-01,
6.52794497e-01, 6.59733348e-01, 6.59686646e-01, 6.64147336e-01,
6.64100633e-01, 6.65277760e-01, 6.65231057e-01, 6.66779908e-01,
6.66733205e-01, 6.70326539e-01, 6.70279836e-01, 6.72757997e-01,
6.72711294e-01, 6.77233938e-01, 6.77187236e-01, 6.80532753e-01,
6.80486050e-01, 6.82096855e-01, 6.82050152e-01, 6.82236015e-01,
6.82189312e-01, 6.82313220e-01, 6.82266517e-01, 6.83195828e-01,
6.83149125e-01, 6.90335792e-01, 6.90289089e-01, 7.03547252e-01,
7.03500549e-01, 7.05173308e-01, 7.05126605e-01, 7.07480858e-01,
7.07434155e-01, 7.11151397e-01, 7.11104695e-01, 7.11662281e-01,
7.11615578e-01, 7.11677532e-01, 7.11630829e-01, 7.12126461e-01,
7.12079759e-01, 7.15673092e-01, 7.15579687e-01, 7.18057848e-01,
7.18011145e-01, 7.21418617e-01, 7.21371914e-01, 7.22734903e-01,
7.22688200e-01, 7.24422913e-01, 7.24376210e-01, 7.26234831e-01,
7.26188128e-01, 7.26250082e-01, 7.26203379e-01, 7.27132690e-01,
7.27085987e-01, 7.27395757e-01, 7.27349055e-01, 7.28464227e-01,
7.28417524e-01, 7.33745571e-01, 7.33698868e-01, 7.39336685e-01,
7.39289982e-01, 7.41644235e-01, 7.41597532e-01, 7.42464889e-01,
7.42418186e-01, 7.45330025e-01, 7.45283323e-01, 7.46646311e-01,
7.46599609e-01, 7.47095241e-01, 7.47048538e-01, 7.49154975e-01,
7.49108272e-01, 7.49294134e-01, 7.49247432e-01, 7.49371340e-01,
7.49324637e-01, 7.50068085e-01, 7.50021382e-01, 7.53986440e-01,
7.53939738e-01, 7.55054910e-01, 7.55008207e-01, 7.55194069e-01,
7.55147367e-01, 7.56200585e-01, 7.56153882e-01, 7.57083193e-01,
7.57036490e-01, 7.57408214e-01, 7.57361511e-01, 7.57485419e-01,
7.57438717e-01, 7.59854924e-01, 7.59808221e-01, 7.61790750e-01,
7.61744047e-01, 7.61867955e-01, 7.61821253e-01, 7.61883207e-01,
7.61836504e-01, 7.62394090e-01, 7.62347387e-01, 7.63090836e-01,
7.63044133e-01, 7.63539765e-01, 7.63493062e-01, 7.67829844e-01,
7.67783142e-01, 7.69765671e-01, 7.69718968e-01, 7.70772186e-01,
7.70725484e-01, 7.70973300e-01, 7.70926597e-01, 7.74457977e-01,
7.74364571e-01, 7.76347100e-01, 7.76300397e-01, 7.76424305e-01,
7.76377602e-01, 7.76935189e-01, 7.76888486e-01, 7.79862279e-01,
7.79815577e-01, 7.82169830e-01, 7.82123127e-01, 7.83857840e-01,
7.83811137e-01, 7.87032747e-01, 7.86986044e-01, 7.88410987e-01,
7.88364284e-01, 7.89541410e-01, 7.89494708e-01, 7.89556662e-01,
7.89509959e-01, 7.89633867e-01, 7.89587164e-01, 7.89834980e-01,
7.89788277e-01, 7.90160002e-01, 7.90113299e-01, 7.90485023e-01,
7.90438320e-01, 7.91801309e-01, 7.91754606e-01, 7.92436100e-01,
7.92389398e-01, 7.93008938e-01, 7.92962235e-01, 7.93581775e-01,
7.93535073e-01, 7.93906797e-01, 7.93860094e-01, 7.95285037e-01,
7.95238334e-01, 7.96725231e-01, 7.96678528e-01, 8.00333816e-01,
8.00287113e-01, 8.00349067e-01, 8.00302364e-01, 8.03090295e-01,
8.03043593e-01, 8.03291409e-01, 8.03198003e-01, 8.03259957e-01,
8.03213255e-01, 8.04204519e-01, 8.04157816e-01, 8.05087127e-01,
8.05040424e-01, 8.05598010e-01, 8.05551307e-01, 8.06542572e-01,
8.06495869e-01, 8.07177363e-01, 8.07130661e-01, 8.07564339e-01,
8.07517636e-01, 8.10119705e-01, 8.10073003e-01, 8.11435991e-01,
8.11389288e-01, 8.11451242e-01, 8.11404540e-01, 8.11652356e-01,
8.11558950e-01, 8.11930674e-01, 8.11883972e-01, 8.11945926e-01,
8.11899223e-01, 8.13571982e-01, 8.13525279e-01, 8.13587233e-01,
8.13540530e-01, 8.14098116e-01, 8.14051414e-01, 8.14175322e-01,
8.14128619e-01, 8.14190573e-01, 8.14143870e-01, 8.15073181e-01,
8.14979775e-01, 8.15165637e-01, 8.15118934e-01, 8.15180888e-01,
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8.22443812e-01, 8.23620939e-01, 8.23574236e-01, 8.23760098e-01,
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8.27739458e-01, 8.28792677e-01, 8.28745974e-01, 8.29737238e-01,
8.29690536e-01, 8.30433984e-01, 8.30387281e-01, 8.31936132e-01,
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8.65558123e-01, 8.67230882e-01, 8.67184179e-01, 8.72388317e-01,
8.72341615e-01, 8.75872994e-01, 8.75826291e-01, 8.83012959e-01,
8.82966256e-01, 8.89471429e-01, 8.89424727e-01, 8.90168175e-01,
8.90121472e-01, 8.90431242e-01, 8.90384540e-01, 8.96146264e-01,
8.96099562e-01, 8.96595194e-01, 8.96548491e-01, 9.04106883e-01,
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9.11958844e-01, 9.13569649e-01, 9.13522946e-01, 9.18789039e-01,
9.18742336e-01, 9.21716129e-01, 9.21669427e-01, 9.21979197e-01,
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9.26733457e-01, 9.29645296e-01, 9.29598593e-01, 9.33997330e-01,
9.33950627e-01, 9.35437524e-01, 9.35390821e-01, 9.35948407e-01,
9.35901704e-01, 9.36149520e-01, 9.36102818e-01, 9.37094082e-01,
9.37047379e-01, 9.37171287e-01, 9.37077882e-01, 9.39679951e-01,
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9.41274556e-01, 9.41584326e-01, 9.41537623e-01, 9.41723485e-01,
9.41676782e-01, 9.45332070e-01, 9.45285367e-01, 9.47515712e-01,
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0.63222855, 0.63221683, 0.63184702, 0.63122582, 0.63087174,
0.630557 , 0.63022362, 0.63011146, 0.63009744, 0.62971778,
0.62968969, 0.62932408, 0.62889603, 0.62797538, 0.62746714,
0.62719731, 0.62652844, 0.62395336, 0.62332224, 0.62276692,
0.62275731, 0.62205803, 0.62201743, 0.62137472, 0.62055958,
0.62018453, 0.62012921, 0.61888304, 0.61813255, 0.61765367,
0.61726459, 0.61717313, 0.61716811, 0.61702895, 0.61659888,
0.61659286, 0.61639966, 0.61627868, 0.61600207, 0.61276081,
0.61251471, 0.61229583, 0.61227858, 0.61224416, 0.61170973,
0.61081375, 0.61007074, 0.60960521, 0.60893997, 0.60807332,
0.60793793, 0.60691953, 0.60579938, 0.60138818, 0.5993801 ,
0.59928863, 0.59908586, 0.59791037, 0.5977756 , 0.59737943,
0.59573503, 0.59489916, 0.59489023, 0.59487381, 0.59473522,
0.59385356, 0.59284896, 0.5926476 , 0.59146026, 0.58956582,
0.58946917, 0.58939275, 0.58901627, 0.58871067, 0.58866832,
0.5881326 , 0.58799827, 0.58791072, 0.58785609, 0.58708307,
0.58648895, 0.58586351, 0.58498751, 0.58414999, 0.58376531,
0.58313602, 0.58264483, 0.58242003, 0.58207685, 0.58164475,
0.58117116, 0.58109385, 0.58020233, 0.58007321, 0.58001233,
0.57955434, 0.57878865, 0.5781294 , 0.57724563, 0.5771014 ,
0.57698526, 0.57695894, 0.57481346, 0.57309526, 0.5707037 ,
0.5703109 , 0.56986351, 0.56927792, 0.56755315, 0.56728743,
0.56726834, 0.56684715, 0.56684128, 0.56659215, 0.56464794,
0.56284241, 0.56283656, 0.56226535, 0.56224435, 0.56194802,
0.55939182, 0.55933155, 0.55828076, 0.55817749, 0.55459145,
0.55137933, 0.55071159, 0.55052289, 0.54967242, 0.54913999,
0.54759925, 0.54735771, 0.54720498, 0.54577005, 0.54359384,
0.54345838, 0.54165384, 0.54090694, 0.53980642, 0.53939542,
0.5384282 , 0.53820027, 0.53604474, 0.53531947, 0.53360005,
0.53271364, 0.52357718, 0.52207081, 0.51976737, 0.51943839,
0.50831462, 0.50815075, 0.50784908, 0.50754449, 0.49730647,
0.49701034, 0.49661627, 0.49645763, 0.49530115, 0.49518421,
0.49509224, 0.49497211, 0.49466723, 0.49448543, 0.49353372,
0.49333923, 0.49187409, 0.49169893, 0.48957056, 0.48943141,
0.488741 , 0.48860717, 0.48436627, 0.48351431, 0.4759083 ,
0.47570301, 0.46690634, 0.46679363, 0.44257288, 0.44252377,
0.42786575, 0.42765668, 0.42551195, 0.42546797, 0.42501634,
0.42499752, 0.41733453, 0.41724043, 0.40333304, 0.40315878,
0.39878492, 0.3987665 , 0.39650699, 0.39632832, 0.38491504,
0.38486632, 0.36865236, 0.36863028, 0.36407871, 0.36402918,
0.35090496, 0.35080663, 0.34914529, 0.3491028 , 0.33322126,
0.33313405, 0.27414564, 0.27394971, 0.19306236, 0.19293001,
0.17693419, 0.17684902, 0.08041446, 0.08037123, -2.03591419])}
optimizer.optimized_pipeline_
MyPipeline(algorithm=OptimizableQrsDetectorWithInfo(high_pass_filter_cutoff_hz=1, max_heart_rate_bpm=200.0, min_r_peak_height_over_baseline=0.5816447455722318, r_peak_match_tolerance_s=0.01))
As Optimize is aware of this and stores the info as a result attribute, the information is also available in the
output of a cross validation.
Further Notes#
Sometimes it might be a good idea to provide separate implementation of self_optimize and self_optimize_with_info.
This might be required, when collecting and calculating the additional info creates a relevant computational overhead.
However, you should make sure, that the two methods return the same optimization result otherwise.
Total running time of the script: (0 minutes 3.259 seconds)
Estimated memory usage: 14 MB