[WIP] Support Deepgrow 2D/3D Training

[SachidanandAlle]

Fixes # .

Description

Support Deegrow 2D/3D training (training example will be added into Tutorials)

Status

Work in progress

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh --codeformat --coverage.
• Quick tests passed locally by running ./runtests.sh --quick.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[wyli]

thanks! i put a few todos here for discussion:

• the transforms should inherit monai.transforms.Transform so that the dataset caching could work properly https://github.com/Project-MONAI/MONAI/blob/master/monai/transforms/compose.py#L26
• ideally the core functionality should only rely on numpy and torch, the other packages should be imported with the optional_import method

  MONAI/monai/utils/module.py

  Line 114 in 4907f39

  def optional_import(

• make_grid_with_titles looks nice, it could be in the visualize folder (is it possible to avoid cv2, and add support for https://pytorch.org/docs/stable/tensorboard.html#torch.utils.tensorboard.writer.SummaryWriter.add_image)
• scipy.ndimage.filters.gaussian_filter could be replaced by

  MONAI/monai/networks/layers/simplelayers.py

  Line 133 in 4907f39

  class GaussianFilter(nn.Module):

  example:

  MONAI/monai/data/utils.py

  Line 522 in 4f2df00

  pt_gaussian = GaussianFilter(len(patch_size), sigmas).to(device=device, dtype=torch.float)

• some normalisation could be replaced by monai.transforms.ScaleIntensityRange

  MONAI/monai/transforms/intensity/array.py

  Line 282 in 4907f39

  class ScaleIntensityRange(Transform):

• DeepgrowStatsHandler implements quite a few features might need another iteration to split it into smaller/specific event handlers.
• some overview docs/links about how deepgrow works

I feel it's important to set up some regression tests before any of these refactorings it'll also be very helpful for other people that continue maintaining this module

cc @Nic-Ma

[tvercaut]

Interesting. I couldn't see a paper reference within the code. Is this a re-implementation of https://arxiv.org/abs/1903.08205?

Having some documentation, and maybe even an exemplar tutorial / example use case would be great.

[SachidanandAlle]

Refer: #1395