ValueError: cannot convert float NaN to integer

[Khaled-Mohammed-Abdelgaber]

i am trying to get the peak of ecg signals. and for some signals i get the following error:
Cell In[7], line 42
39 Beat_loc = correctPeaks(Beat_loc, signal, 30)
41 if sign_name == 'ecg':
---> 42 minLoc = nk.ecg_process(signal , sampling_rate = 125, method='neurokit')[1]['ECG_R_Peaks']
43 Beat_loc = minLoc[1:-1]
44 Beat_loc = correctPeaks(Beat_loc, signal, 30)

File c:\Users\Khalid\anaconda3\envs\tf_gpu\lib\site-packages\neurokit2\ecg\ecg_process.py:111, in ecg_process(ecg_signal, sampling_rate, method)
106 rate = signal_rate(
107 info, sampling_rate=sampling_rate, desired_length=len(ecg_cleaned)
108 )
110 # Assess signal quality
--> 111 quality = ecg_quality(
112 ecg_cleaned, rpeaks=info["ECG_R_Peaks"], sampling_rate=sampling_rate
113 )
115 # Merge signals in a DataFrame
116 signals = pd.DataFrame(
117 {
118 "ECG_Raw": ecg_signal,
(...)
122 }
123 )

File c:\Users\Khalid\anaconda3\envs\tf_gpu\lib\site-packages\neurokit2\ecg\ecg_quality.py:105, in ecg_quality(ecg_cleaned, rpeaks, sampling_rate, method, approach)
103 # Run peak detection algorithm
104 if method in ["averageqrs"]:
--> 105 quality = _ecg_quality_averageQRS(
106 ecg_cleaned, rpeaks=rpeaks, sampling_rate=sampling_rate
107 )
108 elif method in ["zhao2018", "zhao", "SQI"]:
109 if approach is None:

File c:\Users\Khalid\anaconda3\envs\tf_gpu\lib\site-packages\neurokit2\ecg\ecg_quality.py:136, in _ecg_quality_averageQRS(ecg_cleaned, rpeaks, sampling_rate)
133 rpeaks = rpeaks["ECG_R_Peaks"]
135 # Get heartbeats
--> 136 heartbeats = ecg_segment(ecg_cleaned, rpeaks, sampling_rate)
137 data = epochs_to_df(heartbeats).pivot(
138 index="Label", columns="Time", values="Signal"
139 )
140 data.index = data.index.astype(int)

File c:\Users\Khalid\anaconda3\envs\tf_gpu\lib\site-packages\neurokit2\ecg\ecg_segment.py:64, in ecg_segment(ecg_cleaned, rpeaks, sampling_rate, show, **kwargs)
59 raise ValueError("The data length is too small to be segmented.")
61 epochs_start, epochs_end, average_hr = _ecg_segment_window(
62 rpeaks=rpeaks, sampling_rate=sampling_rate, desired_length=len(ecg_cleaned)
63 )
---> 64 heartbeats = epochs_create(
65 ecg_cleaned,
66 rpeaks,
67 sampling_rate=sampling_rate,
68 epochs_start=epochs_start,
69 epochs_end=epochs_end,
70 )
72 # Pad last heartbeats with nan so that segments are equal length
73 last_heartbeat_key = str(np.max(np.array(list(heartbeats.keys()), dtype=int)))

File c:\Users\Khalid\anaconda3\envs\tf_gpu\lib\site-packages\neurokit2\epochs\epochs_create.py:164, in epochs_create(data, events, sampling_rate, epochs_start, epochs_end, event_labels, event_conditions, baseline_correction)
162 # Find the maximum numbers of samples in an epoch
163 parameters["duration"] = list(np.array(parameters["end"]) - np.array(parameters["start"]))
--> 164 epoch_max_duration = int(max((i * sampling_rate for i in parameters["duration"])))
166 # Extend data by the max samples in epochs * NaN (to prevent non-complete data)
167 length_buffer = epoch_max_duration

ValueError: cannot convert float NaN to integer

[welcome]

Hi 👋 Thanks for reaching out and opening your first issue here! We'll try to come back to you as soon as possible. ❤️

[DerAndereJohannes]

Are you sure that your input signal itself does not contain any NaN values? Assuming your input variable signal is a pd.Series, You can check by doing something like: print(signal.isna().sum()) to see if there are any.

[geniusturtle6174]

I got the same error, and after some experiments, I guess that the error occurs when the length of the signal is too short (less than three periods).

[DerAndereJohannes]

FWIW here is a minimal example:

import neurokit2 as nk

SAMPLE_RATE=125

ecg = nk.ecg_simulate(duration=10, sampling_rate=SAMPLE_RATE, heart_rate=10)

nk.ecg_process(ecg, sampling_rate=SAMPLE_RATE)

[debaratipaul4]

I am getting the same error. My ECG sample length is 96. My code goes like below:-
_, rpeaks = nk2.ecg_peaks(ecg_signal, sampling_rate=96)
print(rpeaks['ECG_R_Peaks']) // it is getting printed as [108]
signals, waves = nk2.ecg_delineate(ecg_signal, rpeaks, sampling_rate = 24)

after this getting error
File ~/Lava_workspace/.venv/lib/python3.10/site-packages/neurokit2/epochs/epochs_create.py:164, in epochs_create(data, events, sampling_rate, epochs_start, epochs_end, event_labels, event_conditions, baseline_correction)
162 # Find the maximum numbers of samples in an epoch
163 parameters["duration"] = list(np.array(parameters["end"]) - np.array(parameters["start"]))
--> 164 epoch_max_duration = int(max((i * sampling_rate for i in parameters["duration"])))
166 # Extend data by the max samples in epochs * NaN (to prevent non-complete data)
167 length_buffer = epoch_max_duration

ValueError: cannot convert float NaN to integer

[DominiqueMakowski]

@DerAndereJohannes do you have some idea of the cause of this error?

[DerAndereJohannes]

I will take a look at it