Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Make sure peak detection works with negative signals #84

Merged
merged 1 commit into from
Oct 9, 2024
Merged

Make sure peak detection works with negative signals #84

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 10 additions & 3 deletions peakdet/operations.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -144,16 +144,23 @@ def peakfind_physio(data, *, thresh=0.2, dist=None):
data = utils.check_physio(data, ensure_fs=ensure_fs, copy=True)
# first pass peak detection to get approximate distance between peaks
cdist = data.fs // 4 if dist is None else dist
thresh = np.squeeze(np.diff(np.percentile(data, [5, 95]))) * thresh
locs, heights = signal.find_peaks(data[:], distance=cdist, height=thresh)

# check if data is negative, if so make it all positive and continue with signal
phys_signal = data.data - data.data.min() if data.data.min() < 0 else data.data
logger.debug(
f"Negative signal detected (min = {data.data.min()}), workgin with positive signal for peak detection."
)

thresh = np.squeeze(np.diff(np.percentile(phys_signal, [5, 95]))) * thresh
locs, heights = signal.find_peaks(phys_signal, distance=cdist, height=thresh)
logger.debug(
f"First peak detection iteration. Acquiring approximate distance between peaks (Number of peaks: {len(locs)})"
)

# second, more thorough peak detection
cdist = np.diff(locs).mean() // 2
heights = np.percentile(heights["peak_heights"], 1)
locs, heights = signal.find_peaks(data[:], distance=cdist, height=heights)
locs, heights = signal.find_peaks(phys_signal, distance=cdist, height=heights)
data._metadata["peaks"] = locs
logger.debug(
f"Second peak detection iteration. Acquiring more precise peak locations (Number of peaks: {len(locs)})"
Expand Down