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Separate data config for different splits

See original GitHub issue

Subject of the issue

When predict with config labeled=true, without providing label files, error raised: WARNING:root:sample_label is not used in predict. It is True if and only if mode == ‘train’. WARNING:root:Using customized configuration.The code might break if the config doesn’t match the saved model. 2021-02-02 19:58:43.570942: W tensorflow/stream_executor/platform/default/] Could not load dynamic library ‘’; dlerror: cannot open shared object file: No such file or directory 2021-02-02 19:58:43.570972: W tensorflow/stream_executor/cuda/] failed call to cuInit: UNKNOWN ERROR (303) 2021-02-02 19:58:43.570986: I tensorflow/stream_executor/cuda/] kernel driver does not appear to be running on this host (precision7750-yhu): /proc/driver/nvidia/version does not exist Traceback (most recent call last): File “demos/paired_ct_lung/”, line 59, in <module> config_path=config_path, File “/home/yipenghu/git/DeepReg/deepreg/”, line 238, in predict repeat=False, File “/home/yipenghu/git/DeepReg/deepreg/”, line 42, in build_dataset data_loader = get_data_loader(dataset_config, mode) File “/home/yipenghu/git/DeepReg/deepreg/dataset/”, line 47, in get_data_loader config=data_loader_config, default_args=default_args File “/home/yipenghu/git/DeepReg/deepreg/”, line 262, in build_data_loader category=DATA_LOADER_CLASS, config=config, default_args=default_args File “/home/yipenghu/git/DeepReg/deepreg/”, line 141, in build_from_config return cls(**args) File “/home/yipenghu/git/DeepReg/deepreg/dataset/loader/”, line 71, in init dir_paths=data_dir_paths, name=“moving_labels”, grouped=False File “/home/yipenghu/git/DeepReg/deepreg/dataset/loader/”, line 40, in init self.set_data_structure() File “/home/yipenghu/git/DeepReg/deepreg/dataset/loader/”, line 65, in set_data_structure ), f"directory {named_dir_path} does not exist" AssertionError: directory demos/paired_ct_lung/dataset/test/moving_labels does not exist

Your environment

  • DeepReg version bd3202ace94151d657c3daf9c49ce06563fdc556

  • OS: Ubuntu 20.04

  • Python Version: 3.7

  • TensorFlow

    • TensorFlow Version 2.3

Steps to reproduce

remove fixed_labels and moving_labels in dataset/test folder of the demo, e.g. paired_ct_lung

run python demos/paired_ct_lung/

Expected behaviour

It should allow prediction without any labels

Actual behaviour

1- It only allows prediction when the config key changed to “false” - this is a confusing behaviour as the labeled key should only control the training.

2- When debugging, the docstring isn’t clear: L163 in it is not clear when labels are not provided, if the labels should be “None” or else.

3- double check: The availability of the labels should not affect the model output.

@mathpluscode can you have a look.

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:6 (6 by maintainers)

github_iconTop GitHub Comments

mathpluscodecommented, Apr 12, 2021

I will limit this issue as config change, then decouple the train/predict in a separate issue, so that we do not modify 100 files at a time.

mathpluscodecommented, Mar 7, 2021

I’m now working on this issue.

So the reality is that, we may have different availabilities of labels for

  • train/valid
  • test

I can see two options

  1. For prediction script, we can overwrite labeled flag using flags.
  2. Or alternatively, we need to change data config as
    dir: "data/test/nifti/unpaired/train" # required
    labeled: true
    dir: "data/test/nifti/unpaired/train" # required
    labeled: true
    dir: "data/test/nifti/unpaired/train" # required
    labeled: false

We can even allow mixed format like nifit/h5 in the future.

@YipengHu what do u think?

I prefer the “new” config. It is clearer. And I insist to deal with this as a bug fix as the current can be ambiguous. What do you think?

Yes, this new config unlocks more options.

Bug fix or new feature, it’s just different names 😂

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