Error in "Import MARS Annotation" #383
Comments
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Thanks @sara-xinyue-liang for reporting this, much appreciated. Let's fix this bug. Sorry the BENTO annotation append code, is a little outdated. I haven't touch it for some years, partly as I don't have any BENTO data at hand no more, so don't know expected input and if it has changed. Would you be willing to share your annotation file in the original format, perhaps zip it up and drag and drop it into this thread? And I will make sure Simba can handle it. |
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Hi @sronilsson , would this work? Let me know if I can provide anything else that could help! Sara Liang |
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Thanks @sara-xinyue-liang ! That's all I need for now. I will check this over and get back to you. |
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PS. There is another method for appending BENTO/MARS that was written a little more recently if you use this menu:
It is documented HERE. Not sure if it runs yet on your data but if you have time you can try it and let me know if you see the same error. |
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PS again :) Don't try the above, it won't work. These files look slightly different from what I have seen in the past. As I fix the code I want to make sure I don't brake it for people that have other formatted |
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Thank you for your help! I am using the BENTO I installed in May 2024 from "https://github.com/neuroethology/bentoMAT" I am unable to find what version it is though. Also, I wonder could you point out the difference between this annot file and the other bento file you have seen in the past? Perhaps sharing an example file? I wonder if I change the file to make them look like the one you have seen whether that will make simba recognize it. I checked the example annot file from https://github.com/sgoldenlab/simba/blob/master/misc/bento_example.annot, but the only difference I noticed is the unit. (and I hope simba can work for both units) but if there is something else that is different, I would like to see if modifying the annot file will make simba recognize it. Sincerely, |
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Quick follow up on that. I quickly tested whether changing unit from frames into seconds can make simba work. Unfortunately I still see the same error: (simba) saraliang@dhcp-10-29-170-104 ~ % simba
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Yes they were rather subtle the differences: (i) The file example file on github has a little Ch1---------- delimiter row that marks the split between the meta data and the actual annotation data. I was using that row, thinking it was always there, but that delimiter does not appear in your file so it will fail. (ii) The file is not But I have to come back to this and step away from the computer. One question though: Does BENTO allow you to choose to export the annotation in time or frame format, can they be either? |
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Hi @sronilsson , "Does BENTO allow you to choose to export the annotation in time or frame format, can they be either?" |
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Thanks @sara-xinyue-liang very helpful I didn't know this, only examples I've seen where is seconds. What I could do in the code is to check if all the annotation values are exact integers. If they are integers I will assume that the annotations are provided in frame numbers. If they are float values, then I will assume the annotations are provided in seconds. I think this could work.. there may be some issues if you record less than 1 fps like 0.25 fps videos but I will skip those odd cases for now. EDIT: But please let me know if you can see some issues with that |
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See above, but if you could give it ago with the latest version of SimBA and let me know how it runs? You can install it with I think that you might be working fish? Just a heads up, many of the features being calculated out-of-box can be improved for shape shifters like fish, see this thread for an example discussion. I'm happy to help should you want to use your own feature extraction class in simba as documented here, but lets check if the append works first. |
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Hi @sronilsson, I am able to append the label data from Bento using the updated script! Sara Liang |
Describe the bug
When I was using simba to import the behaviors labeled in BENTO, the main simba page showed the message "Appending BENTO annotation to video 20240812_crumpling3..." and then it was stuck there. At the same time, some error message showed up in my terminal.
To Reproduce
Steps to reproduce the behavior:
"Appending BENTO annotation to video 20240812_crumpling3..."
(simba) saraliang@dhcp-10-29-170-104 ~ % simba
warning||SimBA is not extensively tested beyond python 3.6. You are using python 3.10. If you encounter errors in python>3.6, please report them on GitHub or Gitter (links in the help toolbar) and we will work together to fix the issues!
warning||SimBA could not find a FFMPEG installation on computer (as evaluated by "ffmpeg" returning None). SimBA works best with FFMPEG and it is recommended to install it on your computer
Exception in thread Thread-1 (run):
Traceback (most recent call last):
File "/Users/saraliang/anaconda3/envs/simba/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
self.run()
File "/Users/saraliang/anaconda3/envs/simba/lib/python3.10/threading.py", line 953, in run
self._target(*self._args, **self._kwargs)
File "/Users/saraliang/anaconda3/envs/simba/lib/python3.10/site-packages/simba/third_party_label_appenders/BENTO_appender.py", line 74, in run
annotation_df = pd.read_csv(
File "/Users/saraliang/anaconda3/envs/simba/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/Users/saraliang/anaconda3/envs/simba/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 626, in _read
return parser.read(nrows)
File "/Users/saraliang/anaconda3/envs/simba/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1923, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/Users/saraliang/anaconda3/envs/simba/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 239, in read
data = self._reader.read(nrows)
File "parsers.pyx", line 820, in pandas._libs.parsers.TextReader.read
File "parsers.pyx", line 914, in pandas._libs.parsers.TextReader._read_rows
File "parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
File "parsers.pyx", line 2061, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 3 fields in line 5, saw 4
Bento annotation file
Movie file(s):
Stimulus name:
Annotation start time: 3.333333e-02
Annotation stop time: 1.807000e+02
Annotation framerate: 30.000000
List of channels:
fish1
List of annotations:
crumpling
margin_folding
quiescence
swimming
tacoing
fish1----------
Screenshots
Desktop (please complete the following information):
Thank you!
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