[Mne_analysis] Updating raw data matrix based upon visual annotations

[Paul Fishback]

        External Email - Use Caution        

Colleagues,

My work is primarily done outside MNE, with the exception of reading in EDF
data and performing basic filtering. Yesterday I submitted a question to
the moderator and received a very helpful answer, which I was encouraged to
share with others.

The problem is essentially as follows:

Suppose I read in my EDF into a raw structure and visually annotate the
data plot. Once I perform the annotations, is there a way to obtain the
revised data matrix which is the original one with the annotations removed.
Here's a synopsis of how to do so, where all work was done on a MAC with
OSX 10.15.4, using IDLE and Python 3.7.

import mne as mn
import matplotlib.pyplot as plt
plt.switch_backend('TkAgg')
plt.ion()

raw = mn.io.read_raw_edf("/Users/fishbacp/data.edf", preload=True)

Fs=raw.info['sfreq']
data,times=raw[:,:]
raw.plot(block=True)   #At this stage we annotate our data visually. Once
the plot window is closed, all annotation data is saved in raw.annotations.

starts=[int(t*Fs) for t in raw.annotations.onset]      #The annotation
start times converted to indices using the sampling frequencies
lengths=[int(t*Fs) for t in raw.annotations.duration]     #The annotation
durations converted to indices.

#Now remove from data those columns determined by the starts and lengths
just computed. There are various means of doing so as discussed at
https://stackoverflow.com/questions/62921389/the-most-efficient-way-to-delete-columns-of-a-matrix-based-upon-lists-of-startin/62923354#62923354
.

Here's one way, where the result is stored in data_new:

cols = list(range(data.shape[1]))
remove = []
for i, s in enumerate(starts):
    remove += range(s, s+lengths[i])
saved_cols = list(set(cols).difference(set(remove)))
data_new=data[:,saved_cols]

A big thank you to the individual who provided assistance.

Best,

Paul Fishback
-- 
Professor of Mathematics, Grand Valley State University
Department of Mathematics (MAK C-2-408)
Grand Valley State University
1 Campus Dr.
Allendale, MI 49401
fishbacp at mail.gvsu.edu
616.331.2040
616.331.3120 (fax)
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