0.12.0 merged pep_benchmarking branch, algorithms now available in …

…main

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## Version 0.12.0 - January 03, 2025
+### New Features
+- Added new algorithms for pre-ejection period (PEP) computation in `biopsykit.signals`, including
+  algorithms for ECG Q-peak extraction (`biopsykit.signals.ecg`) and ICG B-point extraction (`biopsykit.signals.icg`).
+  Added further utility functions (e.g., for heartbeat segmentation) and to compute the PEP using a combination 
+  of ECG and ICG data (`biopsykit.signals.pep`).
+
 ## Version 0.11.0 - January 03, 2025
 ### Changes
 - Made `biopsykit` compatible with matplotlib >= 3.9.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopsykit"
-version = "0.11.0"
+version = "0.12.0"
 description = "A Python package for the analysis of biopsychological data."
 authors = [
     "Robert Richer <robert.richer@fau.de>",
@@ -23,7 +23,7 @@ packages = [
 python = ">=3.9,<4.0"
 numpy = "^1"
 pandas = "^1"
-matplotlib = "^3.4"
+matplotlib = "^3.9"
 seaborn = "^0"
 neurokit2 = "^0"
 pingouin = "^0.5.2"

src/biopsykit/__init__.py

@@ -30,7 +30,7 @@
     "utils",
 ]
 
-__version__ = "0.11.0"
+__version__ = "0.12.0"
 
 
 def version() -> None:

src/biopsykit/io/tfm.py

@@ -2,9 +2,10 @@
 from typing import ClassVar, Optional
 
 import pandas as pd
-from biopsykit.utils._types import path_t
 from scipy.io import loadmat
 
+from biopsykit.utils._types import path_t
+
 
 class TFMDataset:
     """Class for loading and processing Task Force Monitor (TFM) data."""

src/biopsykit/signals/__init__.py

@@ -1,4 +1,4 @@
 """Module for processing different types of biosignals."""
 from biopsykit.signals import ecg, eeg, icg, imu, rsp
 
-__all__ = ["ecg", "eeg", "imu", "rsp", "icg"]
+__all__ = ["ecg", "eeg", "icg", "imu", "rsp"]

src/biopsykit/signals/_dtypes.py

@@ -1,4 +1,5 @@
 import pandas as pd
+
 from biopsykit.utils.exceptions import ValidationError
 
 __all__ = ["assert_sample_columns_int"]

src/biopsykit/signals/ecg/__init__.py

@@ -2,4 +2,4 @@
 from biopsykit.signals.ecg import event_extraction, plotting, preprocessing, segmentation
 from biopsykit.signals.ecg.ecg import EcgProcessor
 
-__all__ = ["EcgProcessor", "plotting", "preprocessing", "segmentation", "event_extraction"]
+__all__ = ["EcgProcessor", "event_extraction", "plotting", "preprocessing", "segmentation"]

src/biopsykit/signals/ecg/event_extraction/__init__.py

@@ -9,8 +9,8 @@
 
 __all__ = [
     "BaseEcgExtraction",
-    "QPeakExtractionVanLien2013",
+    "QPeakExtractionForouzanfar2018",
     "QPeakExtractionMartinez2004Neurokit",
     "QPeakExtractionSciPyFindPeaksNeurokit",
-    "QPeakExtractionForouzanfar2018",
+    "QPeakExtractionVanLien2013",
 ]

src/biopsykit/signals/ecg/event_extraction/_q_peak_forounzafar2018.py

@@ -1,11 +1,12 @@
 import numpy as np
 import pandas as pd
+from tpcp import Parameter
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.ecg.event_extraction._base_ecg_extraction import BaseEcgExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
 from biopsykit.utils.array_handling import sanitize_input_series
-from tpcp import Parameter
 
 
 class QPeakExtractionForouzanfar2018(BaseEcgExtraction, CanHandleMissingEventsMixin):

src/biopsykit/signals/ecg/event_extraction/_q_peak_martinez2004_neurokit.py

@@ -3,6 +3,7 @@
 import neurokit2 as nk
 import numpy as np
 import pandas as pd
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.ecg.event_extraction._base_ecg_extraction import BaseEcgExtraction

src/biopsykit/signals/ecg/event_extraction/_q_peak_scipy_findpeaks_neurokit.py

@@ -3,6 +3,7 @@
 import neurokit2 as nk
 import numpy as np
 import pandas as pd
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.ecg.event_extraction._base_ecg_extraction import BaseEcgExtraction

src/biopsykit/signals/ecg/event_extraction/_q_peak_vanlien2013.py

@@ -1,11 +1,12 @@
 from typing import Optional
 
 import pandas as pd
+from tpcp import Parameter
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.ecg.event_extraction._base_ecg_extraction import BaseEcgExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
-from tpcp import Parameter
 
 
 class QPeakExtractionVanLien2013(BaseEcgExtraction, CanHandleMissingEventsMixin):

src/biopsykit/signals/ecg/segmentation/_heartbeat_segmentation.py

@@ -3,9 +3,10 @@
 import neurokit2 as nk
 import numpy as np
 import pandas as pd
+from tpcp import Parameter
+
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.ecg.segmentation._base_segmentation import BaseHeartbeatSegmentation
-from tpcp import Parameter
 
 __all__ = ["HeartbeatSegmentationNeurokit"]
 

src/biopsykit/signals/icg/__init__.py

@@ -1,4 +1,4 @@
 """Module for processing impedance cardiography (ICG) signals."""
 from biopsykit.signals.icg import event_extraction, outlier_correction, preprocessing
 
-__all__ = ["preprocessing", "event_extraction", "outlier_correction"]
+__all__ = ["event_extraction", "outlier_correction", "preprocessing"]

src/biopsykit/signals/icg/event_extraction/__init__.py

@@ -18,17 +18,17 @@
 from biopsykit.signals.icg.event_extraction._c_point_scipy_findpeaks import CPointExtractionScipyFindPeaks
 
 __all__ = [
-    "BaseBPointExtraction",
-    "BaseCPointExtraction",
-    "BPointExtractionStern1985",
-    "BPointExtractionLozano2007LinearRegression",
-    "BPointExtractionLozano2007QuadraticRegression",
     "BPointExtractionArbol2017IsoelectricCrossings",
-    "BPointExtractionArbol2017ThirdDerivative",
     "BPointExtractionArbol2017SecondDerivative",
+    "BPointExtractionArbol2017ThirdDerivative",
+    "BPointExtractionDebski1993SecondDerivative",
     "BPointExtractionDrost2022",
-    "BPointExtractionSherwood1990",
     "BPointExtractionForouzanfar2018",
-    "BPointExtractionDebski1993SecondDerivative",
+    "BPointExtractionLozano2007LinearRegression",
+    "BPointExtractionLozano2007QuadraticRegression",
+    "BPointExtractionSherwood1990",
+    "BPointExtractionStern1985",
+    "BaseBPointExtraction",
+    "BaseCPointExtraction",
     "CPointExtractionScipyFindPeaks",
 ]

src/biopsykit/signals/icg/event_extraction/_b_point_arbol2017.py

@@ -3,18 +3,19 @@
 
 import numpy as np
 import pandas as pd
+from tpcp import Parameter
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.icg.event_extraction._base_b_point_extraction import BaseBPointExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
 from biopsykit.utils.array_handling import sanitize_input_dataframe_1d
 from biopsykit.utils.exceptions import EventExtractionError
-from tpcp import Parameter
 
 __all__ = [
     "BPointExtractionArbol2017IsoelectricCrossings",
-    "BPointExtractionArbol2017ThirdDerivative",
     "BPointExtractionArbol2017SecondDerivative",
+    "BPointExtractionArbol2017ThirdDerivative",
 ]
 
 
@@ -304,7 +305,7 @@ def __init__(
         self.search_window_start_ms = search_window_start_ms
 
     # @make_action_safe
-    def extract(  # noqa: PLR0915
+    def extract(
         self,
         *,
         icg: Union[pd.Series, pd.DataFrame],

src/biopsykit/signals/icg/event_extraction/_b_point_debski1993.py

@@ -3,14 +3,15 @@
 
 import numpy as np
 import pandas as pd
+from scipy.signal import find_peaks
+from tpcp import Parameter
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.icg.event_extraction._base_b_point_extraction import BaseBPointExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
 from biopsykit.utils.array_handling import sanitize_input_dataframe_1d
 from biopsykit.utils.exceptions import EventExtractionError
-from scipy.signal import find_peaks
-from tpcp import Parameter
 
 __all__ = ["BPointExtractionDebski1993SecondDerivative"]
 

src/biopsykit/signals/icg/event_extraction/_b_point_drost2022.py

@@ -3,13 +3,14 @@
 
 import numpy as np
 import pandas as pd
+from tpcp import Parameter
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.icg.event_extraction._base_b_point_extraction import BaseBPointExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
 from biopsykit.utils.array_handling import sanitize_input_dataframe_1d
 from biopsykit.utils.exceptions import EventExtractionError
-from tpcp import Parameter
 
 __all__ = ["BPointExtractionDrost2022"]
 

src/biopsykit/signals/icg/event_extraction/_b_point_forouzanfar2018.py

@@ -3,14 +3,15 @@
 
 import numpy as np
 import pandas as pd
+from scipy.signal import argrelmin
+from tpcp import Parameter
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.icg.event_extraction._base_b_point_extraction import BaseBPointExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
 from biopsykit.utils.array_handling import sanitize_input_dataframe_1d
 from biopsykit.utils.exceptions import EventExtractionError
-from scipy.signal import argrelmin
-from tpcp import Parameter
 
 __all__ = ["BPointExtractionForouzanfar2018"]
 

src/biopsykit/signals/icg/event_extraction/_b_point_lozano2007.py

@@ -2,11 +2,12 @@
 
 import numpy as np
 import pandas as pd
+from tpcp import Parameter
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.icg.event_extraction._base_b_point_extraction import BaseBPointExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
-from tpcp import Parameter
 
 __all__ = ["BPointExtractionLozano2007LinearRegression", "BPointExtractionLozano2007QuadraticRegression"]
 

src/biopsykit/signals/icg/event_extraction/_b_point_sherwood1990.py

@@ -3,6 +3,7 @@
 
 import numpy as np
 import pandas as pd
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.icg.event_extraction._base_b_point_extraction import BaseBPointExtraction

src/biopsykit/signals/icg/event_extraction/_b_point_stern1985.py

@@ -3,13 +3,14 @@
 
 import numpy as np
 import pandas as pd
+from scipy.signal import find_peaks
+
 from biopsykit.signals._base_extraction import HANDLE_MISSING_EVENTS, CanHandleMissingEventsMixin
 from biopsykit.signals._dtypes import assert_sample_columns_int
 from biopsykit.signals.icg.event_extraction._base_b_point_extraction import BaseBPointExtraction
 from biopsykit.utils._datatype_validation_helper import _assert_has_columns, _assert_is_dtype
 from biopsykit.utils.array_handling import sanitize_input_dataframe_1d
 from biopsykit.utils.exceptions import EventExtractionError
-from scipy.signal import find_peaks
 
 __all__ = ["BPointExtractionStern1985"]
 

src/biopsykit/signals/icg/event_extraction/_base_b_point_extraction.py

@@ -1,6 +1,7 @@
 from typing import Optional
 
 import pandas as pd
+
 from biopsykit.signals._base_extraction import BaseExtraction
 
 __all__ = ["BaseBPointExtraction"]

src/biopsykit/signals/icg/event_extraction/_base_c_point_extraction.py

@@ -1,6 +1,7 @@
 from typing import Optional
 
 import pandas as pd
+
 from biopsykit.signals._base_extraction import BaseExtraction
 
 __all__ = ["BaseCPointExtraction"]