An Error occurred when using 'ut predict' & 'ut evaluate' （ code updated on June 21st）

[ljyljy]

I was able to run through predict.py a long time ago, but now the errors listed as follows occurred, and I am very confused about this.

The code I used was the version updated on June 21st.
When I used 'ut predict', I found the following error:
1. Report an error

TypeError: init() got an unexpected keyword argument'warnings_file'

By annotating the following code in bin/evaluate.py, I encountered the second error:
# warnings_file=warnings_name,

2. This error only occurred when using the newest code(updated on June 14 later):

Logged by: 'run_pred' in 'predict.py'

PREDICTING ON 2 STUDIES
Traceback (most recent call last):
  File "/export/ljy/U-Time/utime/dataset/sleep_study/sleep_study.py", line 410, in load
    self._load()
  File "/export/ljy/U-Time/utime/dataset/sleep_study/sleep_study.py", line 339, in _load
    self._psg, header = self._load_with_any_in(self._try_channels)
  File "/export/ljy/U-Time/utime/dataset/sleep_study/sleep_study.py", line 311, in _load_with_any_in
    header_file_path=self.header_file_path)
  File "/export/ljy/U-Time/utime/io/high_level_file_loaders.py", line 73, in load_psg
    check_duplicates=True
  File "/export/ljy/U-Time/utime/io/channels/utils.py", line 87, in get_org_include_exclude_channel_montages
    check_duplicate_channels(load_channels, channels_in_file, raise_or_warn="raise")
  File "/export/ljy/U-Time/utime/io/channels/utils.py", line 22, in check_duplicate_channels
    channels = ChannelMontageTuple(channels, relax=True)
  File "/export/ljy/U-Time/utime/io/channels/channels.py", line 166, in __new__
    channels, type(channels)))
TypeError: Input to ChannelMontageTuple should be a list, tuple or ndarray of channel names or ChannelMontage objects. Got None (type <class 'NoneType'>).

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/export/anaconda3/envs/ljy_u-sleep2/bin/ut", line 33, in <module>
    sys.exit(load_entry_point('utime', 'console_scripts', 'ut')())
  File "/export/ljy/U-Time/utime/bin/ut.py", line 71, in entry_func
    mod.entry_func(script_args + help_agrs)
  File "/export/ljy/U-Time/utime/bin/predict.py", line 394, in entry_func
    run(parser.parse_args(args))
  File "/export/ljy/U-Time/utime/bin/predict.py", line 388, in run
    logger=logger)
  File "/export/ljy/U-Time/utime/bin/predict.py", line 300, in run_pred
    seq = get_sequencer(dataset, hparams)
  File "/export/ljy/U-Time/utime/bin/evaluate.py", line 374, in get_sequencer
    require_all_loaded=False)
  File "/export/ljy/U-Time/utime/sequences/utils.py", line 82, in get_batch_sequence
    data_per_epoch, n_channels = infer_dpe_and_chans(dataset_queue)
  File "/export/ljy/U-Time/utime/sequences/utils.py", line 56, in infer_dpe_and_chans
    with dataset_queue.get_random_study() as sleep_study:
  File "/export/anaconda3/envs/ljy_u-sleep2/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/export/ljy/U-Time/utime/dataset/queue/lazy_queue.py", line 28, in get_random_study
    with study.loaded_in_context():
  File "/export/anaconda3/envs/ljy_u-sleep2/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/export/ljy/U-Time/utime/dataset/sleep_study/abc_sleep_study.py", line 157, in loaded_in_context
    self.load()
  File "/export/ljy/U-Time/utime/dataset/sleep_study/sleep_study.py", line 415, in load
    study_id=self.identifier) from e
utime.errors.CouldNotLoadError: Unexpected load error for sleep study tp026536b7_b8d5_44a5_adc6_87617520d5f2. Please refer to the above traceback.

3、Similarly, An Error occurred when using 'ut evaluate' ：

Logged by: 'run_pred_and_eval' in 'evaluate.py'

PREDICTING ON 2 STUDIES
Setting augmenter: RegionalErase({'min_region_fraction': 0.001, 'max_region_fraction': 0.33, 'log_sample': True, 'apply_prob': 0.1})
Setting augmenter: ChannelDropout({'drop_fraction': 0.5, 'apply_prob': 0.1})
Traceback (most recent call last):
  File "/export/anaconda3/envs/ljy_u-sleep2/bin/ut", line 33, in <module>
    sys.exit(load_entry_point('utime', 'console_scripts', 'ut')())
  File "/export/ljy/U-Time0/utime/bin/ut.py", line 71, in entry_func
    mod.entry_func(script_args + help_agrs)
  File "/export/ljy/U-Time0/utime/bin/evaluate.py", line 542, in entry_func
    run(parser.parse_args(args))
  File "/export/ljy/U-Time0/utime/bin/evaluate.py", line 534, in run
    logger=logger)
  File "/export/ljy/U-Time0/utime/bin/evaluate.py", line 403, in run_pred_and_eval
    dice_eval_df = get_eval_df(seq)
  File "/export/ljy/U-Time0/utime/evaluation/dataframe.py", line 6, in get_eval_df
    ids = [ss.identifier for ss in sequencer.pairs]
AttributeError: 'BatchSequence' object has no attribute 'pairs'

Could some operating errors or code problems cause the above situation?
thx a lot！

[perslev]

Hi!

Thanks for reporting these errors. I am busy these next few days, but will look into it asap. In the meantime, could you please try and remove the package and install it again according to these instructions:
https://github.com/perslev/U-Time#installation-guide

Your first error in particular seems to be related to an outdated version of the mpunet requirement.

Cheers

[ljyljy]

Thx again!!!
You may finish your work on hand first. ^^

[perslev]

Hi!

Sorry for my very late reply. I believe I have managed to solve all three issues.

1. Please install mpunet version 0.2.12 with pip install mpunet==0.2.12 --no-deps

2. Fixed in 53c7ae0.

3. Fixed in 530edb9

A few other minor changes have also been made. In all, please pull the latest version and let me know if you still experience these or any other issues :)

Cheers,
Mathias

[ljyljy]

Hi! Thank you for your reply and the code modification!
After the code is modified, the commands 'ut predict' and 'ut evaluate' have been executed successfully. ^^

In addition, I tried the 'ut extract' command and reported a minor error as follows:
(But the old version updated before June 21st can be executed successfully)

thx again!! :)

[perslev]

Great that the original issues were solved, and thanks for repoting this new error as well! I am currently on vacation, but I will look into it once as I am back in about 2 weeks.

Cheers,
Mathias

[perslev]

Nevermind, this was actually relatively straight forward and should be fixed in 492dce9.

Please let me know if that solves you issue.

Cheers,
Mathias