PySDKit 0.4.55__tar.gz → 0.5.0__tar.gz

{pysdkit-0.4.55 → pysdkit-0.5.0}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: PySDKit
-Version: 0.4.55
+Version: 0.5.0
 Summary: A Python library for signal decomposition algorithms with a unified interface.
-Author: Whenxuan Wang, RuiZhe Wang, Rongkun Zhu, Kai Wu, Lei Wang, josefinez, Deeksha Manjunath, Yuan Feng, WenTong Zhao, JacktheFowler
+Author: Whenxuan Wang, RuiZhe Wang, Rongkun Zhu, Kai Wu, Lei Wang, Xinyu Wu, josefinez, Deeksha Manjunath, Yuan Feng, WenTong Zhao, JacktheFowler
 Maintainer-email: Whenxuan Wang <wwhenxuan@gmail.com>, RuiZhe Wang <3133986068@qq.com>
 License: MIT License
         
@@ -56,6 +56,7 @@ Dynamic: license-file
 # PySDKit: signal decomposition in Python
 
 [![PyPI version](https://badge.fury.io/py/PySDKit.svg)](https://pypi.org/project/PySDKit/) 
+[![Documentation Status](https://readthedocs.org/projects/pysdkit/badge/?version=latest)](https://pysdkit.readthedocs.io/en/latest/)
 ![License](https://img.shields.io/github/license/wwhenxuan/PySDKit)
 [![Python](https://img.shields.io/badge/python-3.8+-blue?logo=python)](https://www.python.org/)
 [![Downloads](https://pepy.tech/badge/pysdkit)](https://pepy.tech/project/pysdkit)
@@ -214,7 +215,10 @@ We would like to thank the researchers in signal processing for providing us wit
 
 ## Contributing 🤗
 
-This project exists thanks to all the people who contribute.
+This project exists thanks to all the people who contribute. Please read
+[CONTRIBUTING.md](CONTRIBUTING.md) for how to add an algorithm, tests, and
+gallery examples (the same guide is in the
+[documentation](https://pysdkit.readthedocs.io/en/stable/development/index.html)).
 
 <a href="https://github.com/wwhenxuan/PySDKit/graphs/contributors">
   <img src="https://contrib.rocks/image?repo=wwhenxuan/PySDKit" />

{pysdkit-0.4.55 → pysdkit-0.5.0}/PySDKit.egg-info/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: PySDKit
-Version: 0.4.55
+Version: 0.5.0
 Summary: A Python library for signal decomposition algorithms with a unified interface.
-Author: Whenxuan Wang, RuiZhe Wang, Rongkun Zhu, Kai Wu, Lei Wang, josefinez, Deeksha Manjunath, Yuan Feng, WenTong Zhao, JacktheFowler
+Author: Whenxuan Wang, RuiZhe Wang, Rongkun Zhu, Kai Wu, Lei Wang, Xinyu Wu, josefinez, Deeksha Manjunath, Yuan Feng, WenTong Zhao, JacktheFowler
 Maintainer-email: Whenxuan Wang <wwhenxuan@gmail.com>, RuiZhe Wang <3133986068@qq.com>
 License: MIT License
         
@@ -56,6 +56,7 @@ Dynamic: license-file
 # PySDKit: signal decomposition in Python
 
 [![PyPI version](https://badge.fury.io/py/PySDKit.svg)](https://pypi.org/project/PySDKit/) 
+[![Documentation Status](https://readthedocs.org/projects/pysdkit/badge/?version=latest)](https://pysdkit.readthedocs.io/en/latest/)
 ![License](https://img.shields.io/github/license/wwhenxuan/PySDKit)
 [![Python](https://img.shields.io/badge/python-3.8+-blue?logo=python)](https://www.python.org/)
 [![Downloads](https://pepy.tech/badge/pysdkit)](https://pepy.tech/project/pysdkit)
@@ -214,7 +215,10 @@ We would like to thank the researchers in signal processing for providing us wit
 
 ## Contributing 🤗
 
-This project exists thanks to all the people who contribute.
+This project exists thanks to all the people who contribute. Please read
+[CONTRIBUTING.md](CONTRIBUTING.md) for how to add an algorithm, tests, and
+gallery examples (the same guide is in the
+[documentation](https://pysdkit.readthedocs.io/en/stable/development/index.html)).
 
 <a href="https://github.com/wwhenxuan/PySDKit/graphs/contributors">
   <img src="https://contrib.rocks/image?repo=wwhenxuan/PySDKit" />

{pysdkit-0.4.55 → pysdkit-0.5.0}/PySDKit.egg-info/SOURCES.txt

@@ -101,41 +101,48 @@ pysdkit/data/_loaders.py
 pysdkit/data/_models.py
 pysdkit/data/_test_univariate.py
 pysdkit/data/_time_series.py
-pysdkit/data/apitmemd_section_2b.npy
-pysdkit/data/apitmemd_section_3a.npy
-pysdkit/data/apitmemd_section_3b.npy
-pysdkit/data/deconv_sig1.npy
-pysdkit/data/deconv_sig2.npy
-pysdkit/data/deconv_sig3.npy
-pysdkit/data/dual_signal_noise.npy
-pysdkit/data/ecg_055m.npy
-pysdkit/data/fast_kurtogram_x.npy
-pysdkit/data/fmd_demo.npy
-pysdkit/data/gearbox_fault_snippet.npy
-pysdkit/data/input_sig.npy
-pysdkit/data/map2.npy
-pysdkit/data/memd_syn_12channel.npy
-pysdkit/data/memd_syn_16channel.npy
-pysdkit/data/memd_syn_hex.npy
-pysdkit/data/memd_taichi_hex.npy
-pysdkit/data/oemd_ecg.npy
-pysdkit/data/prefixed_double_filter.npy
-pysdkit/data/set_batdata2.npy
-pysdkit/data/set_vibdata.npy
-pysdkit/data/single_nsignal.npy
-pysdkit/data/sst_doppler.npy
-pysdkit/data/sst_float.npy
 pysdkit/data/texture.txt
-pysdkit/data/vmd_example.npy
+pysdkit/data/real_world/apitmemd_section_2b.npy
+pysdkit/data/real_world/apitmemd_section_3a.npy
+pysdkit/data/real_world/apitmemd_section_3b.npy
+pysdkit/data/real_world/bmemd_source02.npy
+pysdkit/data/real_world/bmemd_source09.npy
+pysdkit/data/real_world/bss_beam.npy
+pysdkit/data/real_world/bss_yk9.npy
+pysdkit/data/real_world/deconv_sig1.npy
+pysdkit/data/real_world/deconv_sig2.npy
+pysdkit/data/real_world/deconv_sig3.npy
+pysdkit/data/real_world/dual_signal_noise.npy
+pysdkit/data/real_world/ecg_055m.npy
+pysdkit/data/real_world/fast_kurtogram_x.npy
+pysdkit/data/real_world/fmd_demo.npy
+pysdkit/data/real_world/gearbox_fault_snippet.npy
+pysdkit/data/real_world/input_sig.npy
+pysdkit/data/real_world/map2.npy
+pysdkit/data/real_world/memd_syn_12channel.npy
+pysdkit/data/real_world/memd_syn_16channel.npy
+pysdkit/data/real_world/memd_syn_hex.npy
+pysdkit/data/real_world/memd_taichi_hex.npy
+pysdkit/data/real_world/oemd_ecg.npy
+pysdkit/data/real_world/prefixed_double_filter.npy
+pysdkit/data/real_world/set_batdata2.npy
+pysdkit/data/real_world/set_vibdata.npy
+pysdkit/data/real_world/single_nsignal.npy
+pysdkit/data/real_world/sst_doppler.npy
+pysdkit/data/real_world/sst_float.npy
+pysdkit/data/real_world/vmd_example.npy
 pysdkit/entropy/__init__.py
-pysdkit/entropy/_approxiamte_entropy.py
+pysdkit/entropy/_approximate_entropy.py
+pysdkit/entropy/_coarse_grain.py
+pysdkit/entropy/_dispersion_entropy.py
+pysdkit/entropy/_distribution_entropy.py
+pysdkit/entropy/_fuzzy_entropy.py
+pysdkit/entropy/_increment_entropy.py
 pysdkit/entropy/_permutation_entropy.py
 pysdkit/entropy/_sample_entropy.py
-pysdkit/models/__init__.py
-pysdkit/models/_base.py
-pysdkit/models/_kmeans.py
-pysdkit/models/_knn.py
-pysdkit/models/_pca.py
+pysdkit/entropy/_slope_entropy.py
+pysdkit/entropy/_spectral_entropy.py
+pysdkit/entropy/_symbolic_dynamic_entropy.py
 pysdkit/plot/__init__.py
 pysdkit/plot/_fourier_spectra.py
 pysdkit/plot/_functions.py
@@ -152,6 +159,7 @@ pysdkit/tests/test_apmd.py
 pysdkit/tests/test_avncmd.py
 pysdkit/tests/test_baacmd.py
 pysdkit/tests/test_bmemd.py
+pysdkit/tests/test_bss.py
 pysdkit/tests/test_ceemdan.py
 pysdkit/tests/test_cvmd2d.py
 pysdkit/tests/test_ddacmd.py
@@ -160,6 +168,7 @@ pysdkit/tests/test_eemd.py
 pysdkit/tests/test_efd.py
 pysdkit/tests/test_emd.py
 pysdkit/tests/test_emd2d.py
+pysdkit/tests/test_entropy.py
 pysdkit/tests/test_esmd.py
 pysdkit/tests/test_ewt.py
 pysdkit/tests/test_ewt2d.py
@@ -208,9 +217,6 @@ pysdkit/tests/data/test_generator_cube.py
 pysdkit/tests/data/test_generator_image.py
 pysdkit/tests/data/test_generator_signal.py
 pysdkit/tests/data/test_generator_univariate_signal.py
-pysdkit/tests/models/__init__.py
-pysdkit/tests/models/test_knn.py
-pysdkit/tests/models/test_pca.py
 pysdkit/tsa/__init__.py
 pysdkit/tsa/_dtw.py
 pysdkit/tsa/_moving_decomp.py
@@ -230,6 +236,10 @@ pysdkit/utils/_mirror.py
 pysdkit/utils/_pca.py
 pysdkit/utils/_process.py
 pysdkit/utils/_smooth1d.py
+pysdkit/utils/bss/__init__.py
+pysdkit/utils/bss/_bss.py
+pysdkit/utils/bss/_modal.py
+pysdkit/utils/bss/_stft.py
 pysdkit/utils/deconvolution/__init__.py
 pysdkit/utils/deconvolution/_acycbd.py
 pysdkit/utils/deconvolution/_common.py

{pysdkit-0.4.55 → pysdkit-0.5.0}/README.md

@@ -3,6 +3,7 @@
 # PySDKit: signal decomposition in Python
 
 [![PyPI version](https://badge.fury.io/py/PySDKit.svg)](https://pypi.org/project/PySDKit/) 
+[![Documentation Status](https://readthedocs.org/projects/pysdkit/badge/?version=latest)](https://pysdkit.readthedocs.io/en/latest/)
 ![License](https://img.shields.io/github/license/wwhenxuan/PySDKit)
 [![Python](https://img.shields.io/badge/python-3.8+-blue?logo=python)](https://www.python.org/)
 [![Downloads](https://pepy.tech/badge/pysdkit)](https://pepy.tech/project/pysdkit)
@@ -161,7 +162,10 @@ We would like to thank the researchers in signal processing for providing us wit
 
 ## Contributing 🤗
 
-This project exists thanks to all the people who contribute.
+This project exists thanks to all the people who contribute. Please read
+[CONTRIBUTING.md](CONTRIBUTING.md) for how to add an algorithm, tests, and
+gallery examples (the same guide is in the
+[documentation](https://pysdkit.readthedocs.io/en/stable/development/index.html)).
 
 <a href="https://github.com/wwhenxuan/PySDKit/graphs/contributors">
   <img src="https://contrib.rocks/image?repo=wwhenxuan/PySDKit" />

{pysdkit-0.4.55 → pysdkit-0.5.0}/pyproject.toml

@@ -15,6 +15,7 @@ authors = [
     { name = "Rongkun Zhu" },
     { name = "Kai Wu" },
     { name = "Lei Wang" },
+    { name = "Xinyu Wu"},
     { name = "josefinez" },
     { name = "Deeksha Manjunath" },
     { name = "Yuan Feng" },
@@ -67,4 +68,4 @@ where = ["."]
 include = ["pysdkit*"]
 
 [tool.setuptools.package-data]
-"pysdkit.data" = ["*.npy", "*.txt"]
+"pysdkit.data" = ["*.txt", "real_world/*.npy"]

{pysdkit-0.4.55 → pysdkit-0.5.0}/pysdkit/__init__.py

@@ -2,7 +2,7 @@
 A Python library for signal decomposition algorithms.
 """
 
-__version__ = "0.4.55"
+__version__ = "0.5.0"
 
 # Empirical Mode Decomposition
 from ._emd import EMD
@@ -337,7 +337,6 @@ __all__ = [
     "Moving_Decomp",
     "STL",
     "MSTL",
-    "models",
     "data",
     "entropy",
     "HHT",

{pysdkit-0.4.55 → pysdkit-0.5.0}/pysdkit/_vmd/base.py

@@ -35,6 +35,7 @@ class Base(object):
         Implements a signal mirroring expansion function.
         This function mirrors 'sym' elements at both the beginning and the end of the given array 'ts',
         to create a new extended array.
+
         :param ts: The one-dimensional numpy array to be mirrored.
         :param sym: The number of elements to mirror from both the start and the end of the array 'ts'.
                     This value must be less than or equal to half the length of the array.

{pysdkit-0.4.55 → pysdkit-0.5.0}/pysdkit/data/__init__.py

@@ -55,6 +55,10 @@ __all__ = [
     "load_imckd_sig1",
     "load_acycbd_sig2",
     "load_smhd_sig3",
+    "load_bss_beam",
+    "load_bss_yk9",
+    "load_bmemd_source02",
+    "load_bmemd_source09",
 ]
 
 # A series of functions for generating 1D NumPy signals
@@ -149,4 +153,8 @@ from ._loaders import (
     load_imckd_sig1,
     load_acycbd_sig2,
     load_smhd_sig3,
+    load_bss_beam,
+    load_bss_yk9,
+    load_bmemd_source02,
+    load_bmemd_source09,
 )

pysdkit-0.5.0/pysdkit/data/_assets.py

@@ -0,0 +1,40 @@
+# -*- coding: utf-8 -*-
+"""Resolve packaged array / text assets under ``pysdkit/data``."""
+
+from pathlib import Path
+
+DATA_DIR = Path(__file__).resolve().parent
+REAL_WORLD_DIR = DATA_DIR / "real_world"
+
+
+def data_file(name: str) -> Path:
+    """
+    Return the path to a file shipped in ``pysdkit/data``.
+
+    ``.npy`` records live in ``pysdkit/data/real_world``.  Other assets
+    (e.g. ``texture.txt``) stay at the package root.  ``name`` may be a
+    bare file name or a path relative to ``pysdkit/data``.
+
+    :param name: File name relative to ``pysdkit/data``.
+    :return: Absolute path to the packaged file.
+    :raises FileNotFoundError: If the asset is missing from the install.
+    """
+    relative = Path(name)
+    candidates = []
+    if relative.suffix.lower() == ".npy":
+        candidates.append(REAL_WORLD_DIR / relative.name)
+        candidates.append(DATA_DIR / relative)
+        if relative.parts and relative.parts[0] != "real_world":
+            candidates.append(DATA_DIR / "real_world" / relative)
+    else:
+        candidates.append(DATA_DIR / relative)
+
+    for path in candidates:
+        if path.is_file():
+            return path
+
+    tried = ", ".join(str(path) for path in candidates)
+    raise FileNotFoundError(
+        "Missing packaged data: {}. Reinstall PySDKit or restore "
+        "pysdkit/data (looked in: {})".format(name, tried)
+    )

{pysdkit-0.4.55 → pysdkit-0.5.0}/pysdkit/data/_image.py

@@ -165,6 +165,7 @@ def test_image_1(
     Generate a single image test sample 1
     the symbol function comes from:
     https://www.mathworks.com/matlabcentral/fileexchange/71270-fast-and-adaptive-multivariate-and-multidimensional-emd
+
     :param low: Minimum value of grid matrix
     :param high: Maximum value of grid matrix
     :param sampling_rate: The sampling rate of the grid matrix, which is the number of points in the matrix
@@ -254,6 +255,7 @@ def test_image_4(
     Generate a single image test sample 4
     the symbol function comes from:
     https://www.mathworks.com/matlabcentral/fileexchange/71270-fast-and-adaptive-multivariate-and-multidimensional-emd
+
     :param low: Minimum value of grid matrix
     :param high: Maximum value of grid matrix
     :param sampling_rate: The sampling rate of the grid matrix, which is the number of points in the matrix
@@ -283,6 +285,7 @@ def test_image_5(
     Generate a single image test sample 5
     the symbol function comes from:
     https://www.mathworks.com/matlabcentral/fileexchange/71270-fast-and-adaptive-multivariate-and-multidimensional-emd
+
     :param low: Minimum value of grid matrix
     :param high: Maximum value of grid matrix
     :param sampling_rate: The sampling rate of the grid matrix, which is the number of points in the matrix
@@ -312,6 +315,7 @@ def test_image_6(
     Generate a single image test sample 6
     the symbol function comes from:
     https://www.mathworks.com/matlabcentral/fileexchange/71270-fast-and-adaptive-multivariate-and-multidimensional-emd
+
     :param low: Minimum value of grid matrix
     :param high: Maximum value of grid matrix
     :param sampling_rate: The sampling rate of the grid matrix, which is the number of points in the matrix
@@ -341,6 +345,7 @@ def test_uni_image_7(
     Generate a single image test sample 7
     the symbol function comes from:
     https://www.mathworks.com/matlabcentral/fileexchange/71270-fast-and-adaptive-multivariate-and-multidimensional-emd
+
     :param low: Minimum value of grid matrix
     :param high: Maximum value of grid matrix
     :param sampling_rate: The sampling rate of the grid matrix, which is the number of points in the matrix

{pysdkit-0.4.55 → pysdkit-0.5.0}/pysdkit/data/_loaders.py

@@ -2,9 +2,9 @@
 """
 Load packaged demo arrays and related example files.
 
-All ``.npy`` assets live under ``pysdkit/data``. Algorithm modules should
-import these helpers from here (or from ``pysdkit.data``) rather than
-resolving files themselves.
+All ``.npy`` assets live under ``pysdkit/data/real_world``. Algorithm
+modules should import these helpers from here (or from ``pysdkit.data``)
+rather than resolving files themselves.
 """
 
 from __future__ import annotations
@@ -371,6 +371,109 @@ def load_acycbd_sig2() -> Dict[str, Union[np.ndarray, float]]:
     return {"signal": signal, "fs": fs, "t": t, "bpfi": 47.0}
 
 
+def load_bss_beam() -> Dict[str, Union[np.ndarray, float]]:
+    """
+    Load the packaged three-sensor beam record used by BSS Example 2.
+
+    MATLAB ``data_test.mat`` from Yu, Shock and Vibration 2019
+    (experiment 1 / Yang et al. SCA paper): channels ``x1, x2, x3``,
+    first 1280 samples, linearly detrended as in ``Example_2.m``.
+    Sampling rate 2560 Hz.  Stored as ``bss_beam.npy`` with layout
+    ``(3, 1280)``.
+
+    :return: dict with ``signal``, ``fs``, ``t``, ``mode_shape``
+    """
+    signal = np.asarray(np.load(data_file("bss_beam.npy")), dtype=np.float64)
+    if signal.ndim != 2 or signal.shape[0] != 3:
+        raise ValueError("bss_beam.npy must have shape (3, n_samples)")
+    fs = 2560.0
+    t = np.arange(signal.shape[1], dtype=float) / fs
+    mode_shape = np.array(
+        [
+            [1.0, 1.0, 1.0, 1.0],
+            [0.7625, 0.0747, -0.5937, -1.238],
+            [0.0025, -0.5344, 1.0722, -1.3099],
+        ],
+        dtype=float,
+    )
+    return {"signal": signal, "fs": fs, "t": t, "mode_shape": mode_shape}
+
+
+def load_bss_yk9() -> Dict[str, Union[np.ndarray, float]]:
+    """
+    Load the packaged cantilever record used by BSS Example 3.
+
+    MATLAB ``yk9_mean.mat`` from Yu, Shock and Vibration 2019
+    (experiment 2): displacement channels ``d_1, d_2, d_5``, first
+    1000 samples as in ``Example_3.m``.  Sampling rate is
+    ``8142 / (t_end - t_start)``.  Stored as ``bss_yk9.npy`` with
+    layout ``(3, 1000)``.
+
+    :return: dict with ``signal``, ``fs``, ``t``, ``mode_shape``
+    """
+    signal = np.asarray(np.load(data_file("bss_yk9.npy")), dtype=np.float64)
+    if signal.ndim != 2 or signal.shape[0] != 3:
+        raise ValueError("bss_yk9.npy must have shape (3, n_samples)")
+    fs = 8142.0 / (5.33 - 0.03252)
+    t = np.arange(signal.shape[1], dtype=float) / fs
+    mode_shape_full = np.array(
+        [
+            [1.0, 1.0, 1.0, 1.0, 1.0],
+            [0.1244, 0.1804, 0.3119, 0.9233, -0.3431],
+            [2.1046, 1.1760, 0.0262, -1.4827, -0.1384],
+            [3.8569, 0.5650, -0.8170, 0.8732, 0.6237],
+            [8.5515, -1.5033, 0.4697, -0.0618, -0.5077],
+        ],
+        dtype=float,
+    )
+    return {
+        "signal": signal,
+        "fs": fs,
+        "t": t,
+        "mode_shape": mode_shape_full[[0, 1, 4], :],
+        "mode_shape_full": mode_shape_full,
+    }
+
+
+def load_bmemd_source02() -> Dict[str, Union[np.ndarray, Tuple[str, str]]]:
+    """
+    Load the packaged BMEMD multi-focus pair ``source02_1`` / ``source02_2``.
+
+    Xia et al., IEEE Access 2019 (MATLAB ``IMG/source02_*.tif``).  Two
+    grayscale 224×224 frames stored as ``bmemd_source02.npy`` with layout
+    ``(2, 224, 224)`` uint8.
+
+    :return: dict with ``signal`` in ``[0, 1]`` of shape ``(2, H, W)``
+        and ``names``
+    """
+    raw = np.asarray(np.load(data_file("bmemd_source02.npy")))
+    if raw.ndim != 3 or raw.shape[0] != 2:
+        raise ValueError("bmemd_source02.npy must have shape (2, H, W)")
+    signal = raw.astype(np.float64)
+    if signal.max() > 1.0:
+        signal = signal / 255.0
+    return {"signal": signal, "names": ("source02_1", "source02_2")}
+
+
+def load_bmemd_source09() -> Dict[str, Union[np.ndarray, Tuple[str, str]]]:
+    """
+    Load the packaged BMEMD pair ``source09_1`` / ``source09_2``.
+
+    Xia et al., IEEE Access 2019 (MATLAB ``IMG/source09_*.tif``).  Stored
+    as ``bmemd_source09.npy`` with layout ``(2, 204, 268)`` uint8.
+
+    :return: dict with ``signal`` in ``[0, 1]`` of shape ``(2, H, W)``
+        and ``names``
+    """
+    raw = np.asarray(np.load(data_file("bmemd_source09.npy")))
+    if raw.ndim != 3 or raw.shape[0] != 2:
+        raise ValueError("bmemd_source09.npy must have shape (2, H, W)")
+    signal = raw.astype(np.float64)
+    if signal.max() > 1.0:
+        signal = signal / 255.0
+    return {"signal": signal, "names": ("source09_1", "source09_2")}
+
+
 def load_smhd_sig3() -> Dict[str, Union[np.ndarray, float]]:
     """
     Load the packaged SMHD demo record (Miao et al., Meas. Sci. Technol. 2016).

pysdkit-0.5.0/pysdkit/entropy/__init__.py

@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+"""
+Entropy measures for time series.
+"""
+
+from ._permutation_entropy import permutation_entropy
+from ._permutation_entropy import multiscale_permutation_entropy
+
+from ._sample_entropy import sample_entropy
+from ._sample_entropy import multiscale_sample_entropy
+from ._sample_entropy import composite_multiscale_sample_entropy
+from ._sample_entropy import refined_composite_multiscale_sample_entropy
+
+from ._approximate_entropy import approximate_entropy
+
+from ._fuzzy_entropy import fuzzy_entropy
+from ._fuzzy_entropy import multiscale_fuzzy_entropy
+
+from ._dispersion_entropy import dispersion_entropy
+from ._dispersion_entropy import multiscale_dispersion_entropy
+
+from ._spectral_entropy import spectral_entropy
+
+from ._distribution_entropy import distribution_entropy
+
+from ._increment_entropy import increment_entropy
+
+from ._slope_entropy import slope_entropy
+
+from ._symbolic_dynamic_entropy import symbolic_dynamic_entropy

pysdkit-0.5.0/pysdkit/entropy/_approximate_entropy.py

@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+"""
+Approximate entropy of a 1-D series (Pincus 1991).
+"""
+
+import numpy as np
+from typing import Optional
+
+from pysdkit.entropy._coarse_grain import as_1d, embed
+
+
+def approximate_entropy(
+    y: np.ndarray,
+    m: Optional[int] = 2,
+    r: Optional[float] = 0.2,
+    tau: int = 1,
+) -> float:
+    """
+    Approximate entropy (ApEn) of a 1-D series.
+
+    Unlike sample entropy, each template is compared with **all** templates
+    of the same length, including itself.  The radius is ``r * std(y)``.
+
+    Pincus, S. M. (1991). Approximate entropy as a measure of system
+    complexity. Proceedings of the National Academy of Sciences, 88(6),
+    2297-2301.
+
+    :param y: 1-D input series.
+    :param m: Embedding dimension (must be < ``len(y)``).
+    :param r: Tolerance as a fraction of the series standard deviation.
+    :param tau: Time delay between embedding coordinates.
+    :return: ApEn = Phi(m) - Phi(m + 1).
+    """
+    y = as_1d(y)
+    n = len(y)
+    if n < 2:
+        raise ValueError("Signal must have at least two points.")
+    if m < 1 or m >= n:
+        raise ValueError("Embedding dimension must satisfy 1 <= m < N.")
+    if tau < 1:
+        raise ValueError("tau must be a positive integer.")
+
+    sigma = np.std(y)
+    radius = r * sigma if sigma > 0 else 0.0
+    phi_m = _phi(y, m, radius, tau)
+    phi_m1 = _phi(y, m + 1, radius, tau)
+    return float(phi_m - phi_m1)
+
+
+def _phi(y: np.ndarray, m: int, radius: float, tau: int) -> float:
+    """Mean log of the fraction of Chebyshev matches, including self-matches."""
+    templates = embed(y, m, tau)
+    n_vec = templates.shape[0]
+    delta = np.max(np.abs(templates[:, None, :] - templates[None, :, :]), axis=2)
+    counts = np.sum(delta <= radius, axis=1)
+    frac = counts / n_vec
+    frac = np.maximum(frac, np.finfo(float).tiny)
+    return float(np.mean(np.log(frac)))

pysdkit-0.5.0/pysdkit/entropy/_coarse_grain.py

@@ -0,0 +1,53 @@
+# -*- coding: utf-8 -*-
+"""
+Costa coarse-graining for multiscale entropy.
+"""
+
+import numpy as np
+
+
+def as_1d(y: np.ndarray) -> np.ndarray:
+    """Flatten ``y`` to a 1-D float array."""
+    return np.asarray(y, dtype=float).ravel()
+
+
+def shannon(prob: np.ndarray) -> float:
+    """Natural-log Shannon entropy of a probability vector (zeros ignored)."""
+    p = np.asarray(prob, dtype=float)
+    p = p[p > 0]
+    if p.size == 0:
+        return 0.0
+    return float(-np.sum(p * np.log(p)))
+
+
+def embed(y: np.ndarray, m: int, tau: int = 1) -> np.ndarray:
+    """Delay-embed ``y`` into shape ``(n_vectors, m)``."""
+    y = as_1d(y)
+    n_vec = len(y) - (m - 1) * tau
+    if n_vec < 1:
+        raise ValueError(
+            "Not enough samples for embedding dimension m=%d and delay tau=%d."
+            % (m, tau)
+        )
+    return np.column_stack([y[i * tau : i * tau + n_vec] for i in range(m)])
+
+
+def coarse_grain(x: np.ndarray, scale: int, offset: int = 0) -> np.ndarray:
+    """
+    Non-overlapping mean blocks (Costa coarse-graining).
+
+    :param x: 1-D series.
+    :param scale: Block length (scale factor), integer >= 1.
+    :param offset: Start index; used for composite / phase-shifted grains.
+    :return: Coarse-grained series of length ``(len(x) - offset) // scale``.
+    """
+    x = as_1d(x)
+    if scale < 1:
+        raise ValueError("scale must be an integer >= 1.")
+    if offset < 0:
+        raise ValueError("offset must be >= 0.")
+    x = x[offset:]
+    n_blocks = len(x) // scale
+    if n_blocks < 1:
+        return np.empty(0, dtype=float)
+    return x[: n_blocks * scale].reshape(n_blocks, scale).mean(axis=1)