index error when mode=None in detect_badsegments

[yingjoeyzhou]

The following config

config = """
    preproc:
    - filter: {l_freq: 0.25, h_freq: 125, method: iir, iir_params: {order: 5, ftype: butter}}
    - notch_filter: {freqs: 50 100}
    - resample: {sfreq: 250}
    - bad_segments: {segment_len: 500, picks: mag, significance_level: 0.1}
    - bad_segments: {segment_len: 500, picks: grad, significance_level: 0.1}
    - bad_segments: {segment_len: 500, picks: mag, mode: diff, significance_level: 0.1}
    - bad_segments: {segment_len: 500, picks: grad, mode: diff, significance_level: 0.1}
    - bad_channels: {picks: mag, significance_level: 0.1}
    - bad_channels: {picks: grad, significance_level: 0.1}
    - ica_raw: {picks: meg, n_components: 0.99}
    - ica_autoreject: {picks: meg, ecgmethod: ctps, eogthreshold: auto}
    - interpolate_bads: {}
"""

returned the following error

index 167749 is out of bounds for axis 0 with size 153001
  File "/home/zhouj/osl/osl/preprocessing/batch.py", line 737, in run_proc_chain
    dataset = func(dataset, userargs)
  File "/home/zhouj/osl/osl/preprocessing/osl_wrappers.py", line 355, in run_osl_bad_segments
    dataset["raw"] = detect_badsegments(dataset["raw"], **userargs)
  File "/home/zhouj/osl/osl/preprocessing/osl_wrappers.py", line 177, in detect_badsegments
    onsets_secs = raw.first_samp/raw.info["sfreq"] + XX_times[onsets.astype(int)]

And I tried running the same code with this config (i.e., removed the bad segment detection using mode=None)

config = """
    preproc:
    - filter: {l_freq: 0.25, h_freq: 125, method: iir, iir_params: {order: 5, ftype: butter}}
    - notch_filter: {freqs: 50 100}
    - resample: {sfreq: 250}
    - bad_segments: {segment_len: 500, picks: mag, mode: diff, significance_level: 0.1}
    - bad_segments: {segment_len: 500, picks: grad, mode: diff, significance_level: 0.1}
    - bad_channels: {picks: mag, significance_level: 0.1}
    - bad_channels: {picks: grad, significance_level: 0.1}
    - ica_raw: {picks: meg, n_components: 0.99}
    - ica_autoreject: {picks: meg, ecgmethod: ctps, eogthreshold: auto}
    - interpolate_bads: {}
"""

the preprocessing was successful!

I have slacked @matsvanes and the data to reproduce this bug is in a temporal folder 4Mats under knobre on hbaws.

[cgohil8]

Looks like this issue has been resolved in the latest code. @yingjoeyzhou try git pull to get the latest code and reopen this issue if you're still getting an error. If not, please delete

/ohba/pi/knobre/4Mats