mne-tools / mne-tools/mne-python
Annotation times cannot be used to get corresponding data
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- Python
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Description
Description of the problem
I have some (manually-created) annotations for a raw file. I want to pull out the data from a particular channel, from the start to the end of that annotation. Either I'm making a really dumb mistake, or this is surprisingly difficult to do. It's clear that the problem has to do with first_samp (and I could subtract raw.first_samp somewhere in my code to get the right result) but it feels like this should be easier / "just work".
Steps to reproduce
import matplotlib.pyplot as plt
import mne
import numpy as np
fname = mne.datasets.sample.data_path() / "MEG" / "sample" / "sample_audvis_raw.fif"
raw = mne.io.read_raw_fif(fname)
annot = mne.Annotations(onset=3, duration=1, description="test")
raw.set_annotations(annot)
ann = raw.annotations[0]
data = raw.get_data(picks=[0], tmin=ann["onset"], tmax=ann["onset"] + ann["duration"])[0]
plt.ion()
fig, ax = plt.subplots(layout="constrained")
ax.plot(np.arange(len(data)), data)
raw.plot(picks=[0], start=ann["onset"], duration=ann["duration"])
Link to data
No response
Expected results
- when I call
raw.plot(start=raw.annotations[0]["onset"], duration=raw.annotations[0]["duration"])I would really like to see the data corresponding to that annotation span - when I call
raw.get_data(tmin=raw.annotations[0]["onset"], tmax=raw.annotations[0]["onset"] + raw.annotations[0]["duration"])I would really like to obtain the data corresponding to the annotation span
Actual results
NB: although sys_info() below says I'm on 1.11.0, I get the same results on main --- just happened to be in a project venv when I stumbled on this.
Additional information
Platform Linux-6.8.0-45-generic-x86_64-with-glibc2.39
Python 3.13.12 | packaged by conda-forge | (main, Feb 5 2026, 05:53:46) [GCC 14.3.0]
Executable /home/drmccloy/Documents/academics/research/ilabs/prism/.pixi/envs/analysis/bin/python3.13
CPU Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz (16 cores)
Memory 125.7 GiB
Core
├☒ mne 1.11.0 (outdated, release 1.12.1 is available!)
├☑ numpy 2.4.2 (OpenBLAS 0.3.30 with 8 threads)
├☑ scipy 1.17.1
└☑ matplotlib 3.10.8 (backend=qtagg)
Numerical (optional)
├☑ sklearn 1.8.0
├☑ numba 0.64.0
├☑ nibabel 5.4.0
├☑ nilearn 0.13.1
├☑ dipy 1.11.0
├☑ openmeeg 2.5.16
├☑ pandas 3.0.1
├☑ h5io 0.2.5
├☑ h5py 3.15.1
└☐ unavailable cupy
Visualization (optional)
├☑ pyvista 0.47.1 (OpenGL 4.5.0 NVIDIA 595.58.03 via NVIDIA GeForce RTX 2060/PCIe/SSE2)
├☑ pyvistaqt 0.11.3
├☑ vtk 9.5.0
├☑ qtpy 2.4.3 (PySide6=6.9.2)
├☑ pyqtgraph 0.14.0
├☑ mne-qt-browser 0.7.4
├☑ ipywidgets 8.1.8
├☑ trame_client 3.11.3
├☑ trame_server 3.10.0
├☑ trame_vtk 2.11.1
├☑ trame_vuetify 3.2.1
└☐ unavailable ipympl
Ecosystem (optional)
├☑ mne-bids 0.18.0
├☑ mne-icalabel 0.8.1
├☑ mne-bids-pipeline 1.10.0.dev167+g18af7ca2d
├☑ eeglabio 0.1.3
├☑ edfio 0.4.13
├☑ curryreader 0.1.2
├☑ mffpy 0.10.0
├☑ pybv 0.7.6
├☑ antio 0.6.1
├☑ defusedxml 0.7.1
└☐ unavailable mne-nirs, mne-features, mne-connectivity, neo
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the provided script, then inspect the Raw.get_data and Raw.plot entry points for how they interpret annotation onsets alongside first_samp. Trace the resulting sample ranges and verify that both APIs select and display the data covered by the annotation without requiring callers to adjust the onset.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data, data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100