Complexity embedding error while intervalrelated feature extraction

[melisasaygin]

Question and context
The below code works for some respiration data but not for others. Prior, I visualize the peaks and troughs and all looks okay. Then, I try to extract the features per every task I have, and for some participants' data I encounter the error below.

Below is the code

`import pandas as pd
import neurokit2 as nk

tasks = ['12.0a', '12.0b', '12.0c', '12.0d', '12.0e', '12.0f', '14.0a', '14.0b', '14.0c', '14.0d', '14.0e',
'14.0f', '16.0a', '16.0b', '16.0c', '16.0d', '16.0e', '16.0f', '18.0a', '18.0b', '18.0c', '20.0a',
'20.0b', '20.0c', '23.0a', '23.0b', '23.0c', '25.0a', '25.0b', '25.0c', '28.0a', '28.0b', '28.0c',
'30.0a', '30.0b', '30.0c', 34.0, 36.0, 38.0, 40.0, 42.0, 44.0, 47.0, 49.0, 51.0, 53.0, 55.0, 57.0, 60.0,
62.0, 64.0, 66.0, 68.0, 70.0, '75.0a', '75.0b', '75.0c', '78.0a', '78.0b', '78.0c', 83.0, 85.0, 87.0,
89.0, 91.0, 93.0]
participant_id = 25919 # Example participant ID
processed_dataframes = all_processed_data[participant_id]

Initializing empty list

interval_features_list = []

Iterate over tasks and corresponding dataframes

for task, df in processed_dataframes.items():
# Filter the dataframe for the actual task duration
task_specific_df = df[df['Task_Label_2'] == task]

# Extract interval-related features using nk.rsp_intervalrelated()
features_df = nk.rsp_intervalrelated(task_specific_df, sampling_rate=256)

# Add a column for the task label
features_df['Task_Label'] = task

# Append the features DataFrame to the list
interval_features_list.append(features_df)

Concatenate all feature DataFrames

interval_features_df = pd.concat(interval_features_list, ignore_index=True)

Display the DataFrame

interval_features_df`

Below is the error I get

`C:\Users\msa583\AppData\Local\anaconda3\lib\site-packages\neurokit2\rsp\rsp_intervalrelated.py:97: RuntimeWarning: Mean of empty slice
output["RSP_Rate_Mean"] = np.nanmean(data["RSP_Rate"].values)
C:\Users\msa583\AppData\Local\anaconda3\lib\site-packages\numpy\lib\nanfunctions.py:1878: RuntimeWarning: Degrees of freedom <= 0 for slice.
var = nanvar(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
C:\Users\msa583\AppData\Local\anaconda3\lib\site-packages\numpy\core_methods.py:265: RuntimeWarning: Degrees of freedom <= 0 for slice
ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
C:\Users\msa583\AppData\Local\anaconda3\lib\site-packages\numpy\core_methods.py:257: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)

ValueError Traceback (most recent call last)
Cell In[122], line 24
21 task_specific_df = df[df['Task_Label_2'] == task]
23 # Extract interval-related features using nk.rsp_intervalrelated()
---> 24 features_df = nk.rsp_intervalrelated(task_specific_df, sampling_rate=256)
26 # Add a column for the task label
27 features_df['Task_Label'] = task

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\rsp\rsp_intervalrelated.py:65, in rsp_intervalrelated(data, sampling_rate)
63 # If one interval dataframe
64 if isinstance(data, pd.DataFrame):
---> 65 intervals = _rsp_intervalrelated_features(data, sampling_rate)
66 intervals = pd.DataFrame.from_dict(intervals, orient="index").T
68 # If data is a dict (containing multiple intervals)

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\rsp\rsp_intervalrelated.py:98, in _rsp_intervalrelated_features(data, sampling_rate, output)
96 if "RSP_Rate" in colnames:
97 output["RSP_Rate_Mean"] = np.nanmean(data["RSP_Rate"].values)
---> 98 rrv = rsp_rrv(data, sampling_rate=sampling_rate)
99 output.update(rrv.to_dict(orient="records")[0])
101 if "RSP_Amplitude" in colnames:

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\rsp\rsp_rrv.py:118, in rsp_rrv(rsp_rate, troughs, sampling_rate, show, silent)
114 rrv.update(_rsp_rrv_time(bbi))
115 rrv.update(
116 _rsp_rrv_frequency(rsp_period, sampling_rate=sampling_rate, show=show, silent=silent)
117 )
--> 118 rrv.update(rsp_rrv_nonlinear(bbi))
120 rrv = pd.DataFrame.from_dict(rrv, orient="index").T.add_prefix("RRV")
122 if show:

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\rsp\rsp_rrv.py:224, in _rsp_rrv_nonlinear(bbi)
214 out["SD2SD1"] = out["SD2"] / out["SD1"]
216 # CSI / CVI
217 # T = 4 * out["SD1"]
218 # L = 4 * out["SD2"]
(...)
222
223 # Entropy
--> 224 out["ApEn"] = entropy_approximate(bbi, dimension=2)[0]
225 out["SampEn"] = entropy_sample(bbi, dimension=2, tolerance=0.2 * np.std(bbi, ddof=1))[0]
227 # DFA

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\complexity\entropy_approximate.py:102, in entropy_approximate(signal, delay, dimension, tolerance, corrected, **kwargs)
98 # Compute index
99 if corrected is False:
100 # ApEn is implemented in 'utils_entropy.py' to avoid circular imports
101 # as one of the method for optimizing tolerance relies on ApEn
--> 102 out, _ = _entropy_apen(signal, delay, dimension, info["Tolerance"], **kwargs)
103 else:
104 out = _entropy_capen(signal, delay, dimension, info["Tolerance"], **kwargs)

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\complexity\utils_entropy.py:14, in _entropy_apen(signal, delay, dimension, tolerance, **kwargs)
13 def _entropy_apen(signal, delay, dimension, tolerance, **kwargs):
---> 14 phi, info = _phi(
15 signal,
16 delay=delay,
17 dimension=dimension,
18 tolerance=tolerance,
19 approximate=True,
20 **kwargs,
21 )
23 return np.abs(np.subtract(phi[0], phi[1])), info

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\complexity\utils_entropy.py:57, in _phi(signal, delay, dimension, tolerance, distance, approximate, fuzzy, kdtree1, kdtree2, **kwargs)
45 # Embed signal at m and m+1
46 embedded1, count1, kdtree1 = _get_count(
47 signal,
48 delay,
(...)
54 kdtree=kdtree1,
55 )
---> 57 embedded2, count2, kdtree2 = _get_count(
58 signal,
59 delay,
60 dimension + 1,
61 tolerance,
62 distance=distance,
63 approximate=True,
64 fuzzy=fuzzy,
65 kdtree=kdtree2,
66 )
68 # Initialize phi
69 phi = np.zeros(2)

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\complexity\utils_entropy.py:123, in _get_count(signal, delay, dimension, tolerance, distance, approximate, fuzzy, kdtree, n, **kwargs)
115 """
116 This is usually the bottleneck for several complexity methods, in particular in the counting.
117 That's why we allow the possibility of giving kdtrees as pre-computed (used in the optimization
118 of tolerance via MaxApEn which computes iteratively the value with multiple tolerances).
119 However, more improvements are welcome!
120 """
121 # Get embedded
122 # -------------------
--> 123 embedded = complexity_embedding(signal, delay=delay, dimension=dimension)
124 if approximate is False:
125 embedded = embedded[:-1] # Removes the last line

File ~\AppData\Local\anaconda3\lib\site-packages\neurokit2\complexity\utils_complexity_embedding.py:141, in complexity_embedding(signal, delay, dimension, show, **kwargs)
139 dimension = int(dimension)
140 if dimension * delay > N:
--> 141 raise ValueError(
142 "NeuroKit error: complexity_embedding(): dimension * delay should be lower than",
143 " the length of the signal.",
144 )
145 if delay < 1:
146 raise ValueError("NeuroKit error: complexity_embedding(): 'delay' has to be at least 1.")

ValueError: ('NeuroKit error: complexity_embedding(): dimension * delay should be lower than', ' the length of the signal.')`

Do you know how I can resolve this?

[stale]

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[melisasaygin]

I am still interested in the answer (e.g., what causes complexity embedding error) so I can include it as a reasoning in a paper.

[stale]

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.