updated unit tests

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

@@ -145,8 +145,8 @@ def extract(
             elif self.handle_missing_events == "raise":
                 raise EventExtractionError(missing_str)
 
-        is_b_point_dataframe(b_points)
         b_points = b_points.astype({"b_point_sample": "Int64", "nan_reason": "object"})
+        is_b_point_dataframe(b_points)
 
         self.points_ = b_points
         return self

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

@@ -231,8 +231,8 @@ def extract(
 
             b_points.loc[idx, "b_point_sample"] = b_point_sample
 
-        is_b_point_dataframe(b_points)
         b_points = b_points.astype({"b_point_sample": "Int64", "nan_reason": "object"})
+        is_b_point_dataframe(b_points)
 
         self.points_ = b_points
         return self

tests/test_algorithms/test_b_point_extraction_arbol2017.py

@@ -3,13 +3,15 @@
 from pathlib import Path
 
 import pandas as pd
+import pytest
 
 from biopsykit.signals.ecg.segmentation._heartbeat_segmentation import HeartbeatSegmentationNeurokit
 from biopsykit.signals.icg.event_extraction import (
     BPointExtractionArbol2017ThirdDerivative,
     CPointExtractionScipyFindPeaks,
 )
 from biopsykit.utils._datatype_validation_helper import _assert_is_dtype
+from biopsykit.utils.exceptions import ValidationError
 
 TEST_FILE_PATH = Path(__file__).parent.joinpath("../test_data/pep")
 
@@ -70,12 +72,10 @@ def test_regression_extract_series(self):
         icg_data = self.icg_data.squeeze()
         _assert_is_dtype(icg_data, pd.Series)
 
-        reference_b_points = self._get_regression_reference()
-        self.extract_algo.extract(
-            icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
-        )
-
-        self._check_b_point_equal(reference_b_points, self.extract_algo.points_)
+        with pytest.raises(ValidationError):
+            self.extract_algo.extract(
+                icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
+            )
 
     @staticmethod
     def _get_regression_reference():

tests/test_algorithms/test_b_point_extraction_debski1993.py

@@ -3,13 +3,15 @@
 from pathlib import Path
 
 import pandas as pd
+import pytest
 
 from biopsykit.signals.ecg.segmentation._heartbeat_segmentation import HeartbeatSegmentationNeurokit
 from biopsykit.signals.icg.event_extraction import (
     BPointExtractionDebski1993SecondDerivative,
     CPointExtractionScipyFindPeaks,
 )
 from biopsykit.utils._datatype_validation_helper import _assert_is_dtype
+from biopsykit.utils.exceptions import ValidationError
 
 TEST_FILE_PATH = Path(__file__).parent.joinpath("../test_data/pep")
 
@@ -70,12 +72,10 @@ def test_regression_extract_series(self):
         icg_data = self.icg_data.squeeze()
         _assert_is_dtype(icg_data, pd.Series)
 
-        reference_b_points = self._get_regression_reference()
-        self.extract_algo.extract(
-            icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
-        )
-
-        self._check_b_point_equal(reference_b_points, self.extract_algo.points_)
+        with pytest.raises(ValidationError):
+            self.extract_algo.extract(
+                icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
+            )
 
     @staticmethod
     def _get_regression_reference():

tests/test_algorithms/test_b_point_extraction_drost2022.py

@@ -3,13 +3,15 @@
 from pathlib import Path
 
 import pandas as pd
+import pytest
 
 from biopsykit.signals.ecg.segmentation._heartbeat_segmentation import HeartbeatSegmentationNeurokit
 from biopsykit.signals.icg.event_extraction import (
     BPointExtractionDrost2022,
     CPointExtractionScipyFindPeaks,
 )
 from biopsykit.utils._datatype_validation_helper import _assert_is_dtype
+from biopsykit.utils.exceptions import ValidationError
 
 TEST_FILE_PATH = Path(__file__).parent.joinpath("../test_data/pep")
 
@@ -70,12 +72,10 @@ def test_regression_extract_series(self):
         icg_data = self.icg_data.squeeze()
         _assert_is_dtype(icg_data, pd.Series)
 
-        reference_b_points = self._get_regression_reference()
-        self.extract_algo.extract(
-            icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
-        )
-
-        self._check_b_point_equal(reference_b_points, self.extract_algo.points_)
+        with pytest.raises(ValidationError):
+            self.extract_algo.extract(
+                icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
+            )
 
     @staticmethod
     def _get_regression_reference():

tests/test_algorithms/test_b_point_extraction_forouzanfar2018.py

@@ -3,13 +3,15 @@
 from pathlib import Path
 
 import pandas as pd
+import pytest
 
 from biopsykit.signals.ecg.segmentation._heartbeat_segmentation import HeartbeatSegmentationNeurokit
 from biopsykit.signals.icg.event_extraction import (
     BPointExtractionForouzanfar2018,
     CPointExtractionScipyFindPeaks,
 )
 from biopsykit.utils._datatype_validation_helper import _assert_is_dtype
+from biopsykit.utils.exceptions import ValidationError
 
 TEST_FILE_PATH = Path(__file__).parent.joinpath("../test_data/pep")
 
@@ -70,12 +72,10 @@ def test_regression_extract_series(self):
         icg_data = self.icg_data.squeeze()
         _assert_is_dtype(icg_data, pd.Series)
 
-        reference_b_points = self._get_regression_reference()
-        self.extract_algo.extract(
-            icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
-        )
-
-        self._check_b_point_equal(reference_b_points, self.extract_algo.points_)
+        with pytest.raises(ValidationError):
+            self.extract_algo.extract(
+                icg=icg_data, heartbeats=self.heartbeats, c_points=self.c_points, sampling_rate_hz=self.sampling_rate_hz
+            )
 
     @staticmethod
     def _get_regression_reference():

tests/test_algorithms/test_c_point_extraction_scipy_findpeaks.py

@@ -9,6 +9,7 @@
 from biopsykit.signals.ecg.segmentation._heartbeat_segmentation import HeartbeatSegmentationNeurokit
 from biopsykit.signals.icg.event_extraction import CPointExtractionScipyFindPeaks
 from biopsykit.utils._datatype_validation_helper import _assert_is_dtype
+from biopsykit.utils.exceptions import ValidationError
 
 TEST_FILE_PATH = Path(__file__).parent.joinpath("../test_data/pep")
 
@@ -58,10 +59,8 @@ def test_regression_extract_series(self):
         icg_data = self.icg_data.squeeze()
         _assert_is_dtype(icg_data, pd.Series)
 
-        reference_c_points = self._get_regression_reference()
-        self.extract_algo.extract(icg=icg_data, heartbeats=self.heartbeats, sampling_rate_hz=self.sampling_rate_hz)
-
-        self._check_c_point_equal(reference_c_points, self.extract_algo.points_)
+        with pytest.raises(ValidationError):
+            self.extract_algo.extract(icg=icg_data, heartbeats=self.heartbeats, sampling_rate_hz=self.sampling_rate_hz)
 
     @staticmethod
     def _get_regression_reference():

tests/test_algorithms/test_heatbeat_segmentation.py

@@ -68,14 +68,11 @@ def test_regression_extract_variable_length_dataframe(self):
     def test_regression_extract_variable_length_series(self):
         self.setup()
 
-        reference_heartbeats = self._get_regression_reference("pep_test_heartbeat_reference_variable_length.csv")
-
         ecg_data = self.ecg_data["ecg"]
         _assert_is_dtype(ecg_data, pd.Series)
 
-        self.segmenter.extract(ecg=ecg_data, sampling_rate_hz=self.sampling_rate_hz)
-        # check if the first heartbeat is correct
-        self._check_heartbeats_equal(reference_heartbeats, self.segmenter.heartbeat_list_)
+        with pytest.raises(ValidationError):
+            self.segmenter.extract(ecg=ecg_data, sampling_rate_hz=self.sampling_rate_hz)
 
     def test_regression_extract_fixed_length_dataframe(self):
         self.setup()
@@ -93,34 +90,33 @@ def test_regression_extract_fixed_length_dataframe(self):
     def test_regression_extract_fixed_length_series(self):
         self.setup(variable_length=False)
 
-        reference_heartbeats = self._get_regression_reference("pep_test_heartbeat_reference_fixed_length.csv")
-
         ecg_data = self.ecg_data["ecg"]
         _assert_is_dtype(ecg_data, pd.Series)
 
-        self.segmenter.extract(ecg=ecg_data, sampling_rate_hz=self.sampling_rate_hz)
-        # check if the first heartbeat is correct
-        self._check_heartbeats_equal(reference_heartbeats, self.segmenter.heartbeat_list_)
+        with pytest.raises(ValidationError):
+            self.segmenter.extract(ecg=ecg_data, sampling_rate_hz=self.sampling_rate_hz)
 
     def test_regression_extract_fixed_length_numpy(self):
         self.setup(variable_length=False)
 
-        reference_heartbeats = self._get_regression_reference("pep_test_heartbeat_reference_fixed_length.csv")
-
         ecg_data = self.ecg_data["ecg"].to_numpy()
         _assert_is_dtype(ecg_data, np.ndarray)
 
-        self.segmenter.extract(ecg=ecg_data, sampling_rate_hz=self.sampling_rate_hz)
-        # check if the first heartbeat is correct
-        estimated_heartbeats = self.segmenter.heartbeat_list_.drop(columns="start_time")
-        reference_heartbeats = reference_heartbeats.drop(columns="start_time")
-
-        self._check_heartbeats_equal(reference_heartbeats, estimated_heartbeats)
+        with pytest.raises(ValidationError):
+            self.segmenter.extract(ecg=ecg_data, sampling_rate_hz=self.sampling_rate_hz)
 
     @staticmethod
     def _get_regression_reference(file_path):
         data = pd.read_csv(TEST_FILE_PATH.joinpath(file_path), index_col=0, parse_dates=True)
-        data = data.convert_dtypes(infer_objects=True)
+        data = data.astype(
+            {
+                "start_sample": "Int64",
+                "end_sample": "Int64",
+                "r_peak_sample": "Int64",
+                "rr_interval_sample": "Int64",
+                "rr_interval_ms": "Float64",
+            }
+        )
         data["start_time"] = pd.to_datetime(data["start_time"]).dt.tz_convert("Europe/Berlin")
         return data
 
@@ -131,8 +127,8 @@ def _check_heartbeats_equal(reference_heartbeats, extracted_heartbeats):
     @pytest.mark.parametrize(
         ("data", "expected"),
         [
-            (None, pytest.raises(ValueError)),
-            (pd.Series([], dtype="Float64"), pytest.raises(ValueError)),
+            (None, pytest.raises(ValidationError)),
+            (pd.Series([], dtype="Float64"), pytest.raises(ValidationError)),
             (pd.DataFrame(), pytest.raises(ValidationError)),
         ],
     )

tests/test_algorithms/test_q_peak_extraction.py

@@ -9,6 +9,7 @@
 from biopsykit.signals.ecg.event_extraction import QPeakExtractionMartinez2004Neurokit, QPeakExtractionVanLien2013
 from biopsykit.signals.ecg.segmentation._heartbeat_segmentation import HeartbeatSegmentationNeurokit
 from biopsykit.utils._datatype_validation_helper import _assert_is_dtype
+from biopsykit.utils.exceptions import ValidationError
 
 TEST_FILE_PATH = Path(__file__).parent.joinpath("../test_data/pep")
 
@@ -57,10 +58,8 @@ def test_regression_extract_series(self):
         ecg_data = self.ecg_data.squeeze()
         _assert_is_dtype(ecg_data, pd.Series)
 
-        reference_q_peaks = self._get_regression_reference()
-        self.extract_algo.extract(ecg=ecg_data, heartbeats=self.heartbeats, sampling_rate_hz=self.sampling_rate_hz)
-
-        self._check_q_peaks_equal(reference_q_peaks, self.extract_algo.points_)
+        with pytest.raises(ValidationError):
+            self.extract_algo.extract(ecg=ecg_data, heartbeats=self.heartbeats, sampling_rate_hz=self.sampling_rate_hz)
 
     @staticmethod
     def _get_regression_reference():
@@ -126,9 +125,8 @@ def test_regression_extract_series(self, time_interval_ms):
         ecg_data = self.ecg_data.squeeze()
         _assert_is_dtype(ecg_data, pd.Series)
 
-        reference_q_peaks = self._get_regression_reference(time_interval_ms)
-        self.extract_algo.extract(ecg=ecg_data, heartbeats=self.heartbeats, sampling_rate_hz=self.sampling_rate_hz)
-        self._check_q_peaks_equal(reference_q_peaks, self.extract_algo.points_)
+        with pytest.raises(ValidationError):
+            self.extract_algo.extract(ecg=ecg_data, heartbeats=self.heartbeats, sampling_rate_hz=self.sampling_rate_hz)
 
     def _get_regression_reference(self, time_interval_ms: int = 40):
         data = pd.read_csv(