Running speed incorrectly calculated.

[colleenjg]

Describe the bug
2 errors introduced by latest commit to allensdk/brain_observatory/extract_running_speed/__main__.py in extract_running_speeds().

1. The if/else statements (line 62-65) are reversed: median duration is not used if use_median_duration is True, and is used otherwise.
2. In the else statement, angular_velocity is accidentally set to the median duration due to a = instead of a / on line 65. As a result, the running velocity array is set entirely to a single repeating value, namely the median duration.

allensdk version 2.3.0

---

FIX:

if use_median_duration:
    angular_velocity = dx_rad / durations
else:
    angular_velocity = dx_rad = np.median(durations)

should be

if use_median_duration:
    angular_velocity = dx_rad / np.median(durations)
else:
    angular_velocity = dx_rad / durations

[kschelonka]

Hi Colleen, thanks for the report. Looks like we overlooked this module in our update.

Edit:
@colleenjg Can you clarify how recent commits have affected this? I don't see any changes in the past year, or any dependencies on the running speed code that was updated recently. I agree that what you're describing are bugs but it seems like they're longstanding, not recent.

[kschelonka]

Regardless, this seems pretty cut and dry to me. You're welcome to make a PR if you'd like, otherwise we'll add it to our sprint schedule for fixing. 👍

[colleenjg]

@kschelonka right, that wasn't very clear. I meant that the bug was introduced in the most recent commit where this specific script was modified. But you are right, that commit was made back in Sept 2019, so it is a longstanding bug.
And great, I'll make a PR ASAP :)