[aaronkanzer]

TimeIntervals.add_interval (and so NWBFile.add_epoch) gives a different TimeSeriesReference for a TimeSeries with starting_time and rate than for the same samples stored as timestamps. For the rate case the reference can start one sample before start_time. If the interval starts before the series, it is stored as a missing reference. If the interval runs past the end, the reference raises IndexError when used.

import numpy as np
from pynwb import TimeSeries
from pynwb.epoch import TimeIntervals

ts_rate = TimeSeries(name="r", data=np.arange(100), unit="u", starting_time=1.0, rate=100.0)
ts_tst = TimeSeries(name="t", data=np.arange(100), unit="u", timestamps=ts_rate.get_timestamps())
for start, stop in [(1.255, 1.505), (0.5, 1.1), (1.9, 3.0)]:
    ti = TimeIntervals(name="x")
    ti.add_interval(start_time=start, stop_time=stop, timeseries=[ts_rate, ts_tst])
    print((start, stop), [(r.idx_start, r.count) for r in ti["timeseries"][0]])

Observed (pynwb 4.2.0 and dev), rate vs timestamps:

(1.255, 1.505) [(25, 25), (26, 25)]    # rate reference starts at t=1.25, before start_time
(0.5, 1.1)     [(None, None), (0, 10)] # negative idx_start, read back as a missing reference
(1.9, 3.0)     [(89, 111), (90, 10)]   # 0.9*100 = 89.999..., and count runs past the 100 samples

For the last case, ref.isvalid() raises IndexError: 'idx_start + count' out of range for timeseries 'r'.

Expected: both series give (26, 25), (0, 10) and (90, 10).

Cause: the rate branch of __calculate_idx_count uses int((t - starting_time) * rate). That truncates instead of finding the first sample at or after t, is sensitive to floating point error, and is never clipped to [0, num_samples]. The timestamps branch uses bisect_left, which has none of these problems.

Fix: compute the rate-based index the way bisect_left would on the sample times starting_time + i / rate (ceil with a one-step correction for rounding), clipped to the number of samples. Adds tests that compare the rate and timestamps results, including intervals that extend past either end.