# \_orig\_time issue with annotations

**URL:** <https://mne.discourse.group/t/orig-time-issue-with-annotations/6251>\
**Category:** Support & Discussions\
**Created:** [January 26, 2023, 4:30pm UTC](https://mne.discourse.group/t/orig-time-issue-with-annotations/6251 "2023-01-26T16:30:28Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![dsrishyla](https://avatars.discourse-cdn.com/v4/letter/d/3e96dc/32.png) [@dsrishyla](https://mne.discourse.group/u/dsrishyla)\
**Post date:** [January 26, 2023, 4:30pm UTC](https://mne.discourse.group/t/orig-time-issue-with-annotations/6251/1 "2023-01-26T16:30:28Z")

</div>

MNE version: 1.0.1  
Operating System: Windows 10

I am adding new annotations to a .fif file which already has annotations. When I re-open the plot of the file to edit or add more annotations, I find that the previous annotations have moved in time.  
I suspect this has to do with my use of \_orig\_time. However, I am unable to pinpoint the issue. So I am requesting some assistance. Here is the function I am using to add new annotations:

```python
def add_annot(raw, annot_file):
    if Path(annot_file).exists():
        annotations=mne.read_annotations(annot_file)
        annotations._orig_time = raw.annotations._orig_time
        list_annot_values = [tuple(annot.values()) for annot in annotations 
                                                   if annot["description"].lower() 
                                                   in ['saccade', 'clean']]
        onset, duration, description = list(zip(*list_annot_values))[:3]
        orig_annotations = mne.Annotations(onset,duration,description)
        raw.set_annotations(orig_annotations + raw.annotations)
        
    else:
        warnings.warn(f'Path {annot_file} not existent')

```

Let me know if I must clarify anything. Thank you for your time.

Best,  
Diksha

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<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [January 26, 2023, 5:30pm UTC](https://mne.discourse.group/t/orig-time-issue-with-annotations/6251/2 "2023-01-26T17:30:46Z")

</div>

I think you simply need to delete that line in your code that sets the private attribute \_orig\_time. Simply append annotations without an orig\_time set, and **never** manually modify private attributes (those starting with an underscore) manually unless told by a developer

Best wishes,  
Richard

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<div class="post-metadata">

**Author:** ![dsrishyla](https://avatars.discourse-cdn.com/v4/letter/d/3e96dc/32.png) [@dsrishyla](https://mne.discourse.group/u/dsrishyla)\
**Post date:** [January 26, 2023, 6:38pm UTC](https://mne.discourse.group/t/orig-time-issue-with-annotations/6251/3 "2023-01-26T18:38:17Z")

</div>

Hi Richard,  
Thanks for your suggestion. I tried that, and it still doesn’t work. For example, when I add a new annotation to the interactive window at 12s, the saved annotations file shows the onset time at 14.6 s. Any idea why this might be happening?

Best,  
Diksha

---

<div class="post-metadata">

**Author:** ![dsrishyla](https://avatars.discourse-cdn.com/v4/letter/d/3e96dc/32.png) [@dsrishyla](https://mne.discourse.group/u/dsrishyla)\
**Post date:** [January 26, 2023, 9:47pm UTC](https://mne.discourse.group/t/orig-time-issue-with-annotations/6251/4 "2023-01-26T21:47:34Z")

</div>

Hi again,  
My supervisor and I seem to have found a solution. We had to separate the annotations that were already in the file, from the new annotations being added. We did this by adding a third argument to the function:

```python
def add_annot(raw, annot_file, orig_annots):
    if Path(annot_file).exists():
        annotations=mne.read_annotations(annot_file)
        
        list_annot_values = [tuple(annot.values()) for annot in annotations 
                                                   if annot["description"].lower() 
                                                   in ['saccade','clean']]
        if len(list_annot_values)==0:
            return 
        onset, duration, description = list(zip(*list_annot_values))[:3]
        file_annots = mne.Annotations(onset,duration,description)
        raw = raw.set_annotations(file_annots + orig_annots)
else:
        warnings.warn(f'Path {annot_file} not existent')

```

Again, thanks for your time.

Best,  
Diksha

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<div class="post-metadata">

**Author:** ![scott-huberty](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/scott-huberty/32/2715_2.png) [@scott-huberty](https://mne.discourse.group/u/scott-huberty)\
**Post date:** [January 29, 2023, 3:07pm UTC](https://mne.discourse.group/t/orig-time-issue-with-annotations/6251/5 "2023-01-29T15:07:29Z")

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I spoke to @christian-oreilly about this, (he helped @dsrishyla troubleshoot the unexpected behavior).

Seems like when working with a raw object that has been cropped with a `tmin` \> 0, unexpected behaviour can occur with `mne.Annotations`.

1. Let’s say we have a raw file with one annotation in it.

```python
from mne.datasets import testing
import mne

egi_fpath = testing.data_path() / 'EGI' / 'test_egi.mff'

raw = mne.io.read_raw_egi(egi_fpath, preload=True)
raw.filter(1,40) # just for visualization
test_annot = mne.Annotations(onset=[2],duration=[2], description=['TEST'])
raw.set_annotations(test_annot)
raw.plot()

```

 ![Screen Shot 2023-01-28 at 6.30.58 PM](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/9/9e786c88b8f00c2d4c03718fa948ae349d28c054.png)

1. Now if I crop the file and append a new annotation at 6 seconds.

```python
raw2 = raw.copy().crop(tmin=1, tmax=11) # note that tmin is > 0
raw2.annotations.append(onset=[6], duration=[2], description=['TEST2'])
raw2.plot() # new annot TEST2 starts at 5 not 6. 

```

I set the onset of the new annotation at 6, but the onset is actually 5. 😵‍💫

 ![Screen Shot 2023-01-29 at 9.51.33 AM](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/3/3793252bad3c7ca0b71f665a0545f328e171f6bb.png)

1. Then I tried just resetting the annotations.

```python
raw2 = raw.copy().crop(tmin=1, tmax=11) 
new_annot = (onset=[6], duration=[2], description=['TEST2'])
raw2.set_annotations(test_annot + new_annot)
raw2.plot() 

```

The new annot starts at 6, as expected. The original annotation still occurs at 2 seconds, but is actually shifted 1-second to the right in relation to the signal, compared to where it originally was in the uncropped raw object.

 ![Screen Shot 2023-01-28 at 6.33.13 PM](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/5/577a81f7413c113f6ba4ed4d4470c851214cc843.png)

#2 seems like a bug

#3 maybe not a bug per se… `set.annotations` is doing what you ask - setting the first annotation at 2 seconds. But I could see why someone might try this and get tripped up, especially if `annotations.append` wasn’t working as expected like in #2. I think this is what @dsrishyla experienced!

EDIT: this example was demonstrated with mne 1.3.0

---

<div class="post-metadata">

**Author:** ![scott-huberty](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/scott-huberty/32/2715_2.png) [@scott-huberty](https://mne.discourse.group/u/scott-huberty)\
**Post date:** [January 29, 2023, 4:31pm UTC](https://mne.discourse.group/t/orig-time-issue-with-annotations/6251/6 "2023-01-29T16:31:52Z")

</div>

Follow up:

I just read the warning in the [documentation](https://mne.tools/stable/generated/mne.Annotations.html#mne.Annotations.append) for `mne.Annotations`:

> when `raw.info['meas_date'] is None` , doing `raw.set_annotations(raw.annotations)` will not alter `raw` if and only if `raw.first_samp == 0` . When it’s non-zero, `raw.set_annotations` will assume that the “new” annotations refer to the original data (with `first_samp==0` ), and will be re-referenced to the new time offset!

Seems like that could explain the unexpected (to me) behavior described in #2 above, so I must be missing something here…