Harsha issues

Results 51 issues of


                                            Harsha

fix spelling "distrubuted_learning"

bug

Add attention-unet to the models

https://arxiv.org/pdf/1804.03999.pdf or https://github.com/sabeenlohawala/tissue_labeling/blob/6a1ab8466ba6629a1d9d4e553793a26d72f2b60b/TissueLabeling/models/attention_unet.py (this is in pytorch)

model

tf.extract_volume_patches for creating blocks from volumes

Look into using [tf.extract_volume_patches](https://www.tensorflow.org/api_docs/python/tf/extract_volume_patches) for https://github.com/neuronets/nobrainer/blob/ed0d609333f9aea724c5fd45962c36dfd8a13d88/nobrainer/volume.py#L149

Add UNETR to the model API

- [UNETR: Transformers for 3D Medical Image Segmentation](https://arxiv.org/abs/2103.10504) - [Model](https://github.com/Project-MONAI/research-contributions/tree/main/UNETR) (in pytorch) - [Tensorflow Code](https://www.kaggle.com/code/usharengaraju/tensorflow-unetr-w-b)

Workflow (Guide Notebooks Regression - EC2) failing because of version upgrade in default tensorflow

- [Failed run](https://github.com/neuronets/nobrainer/actions/runs/8222757665/job/22484651746) installs `tensorflow==2.16.x` - [Successful run](https://github.com/neuronets/nobrainer/actions/runs/8203646585) installs `tensorflow==2.15.x` Solution: lock the pip dependency for tensorflow at 2.15.x for the time being (notice this will not work on openmind...

bug

Missing callbacks argument to fit method

What are you trying to accomplish? - Adding/passing callbacks to the fit method (for Segmentation) - Noticed no `callbacks` input argument in the method definition What have you tried? (TODO)...

bug

get_steps_per_epoch fails if block_shape is None

The `get_steps_per_epoch` method of the `nobrainer.dataset.Dataset` class assumes blocks are created from the input images. This method needs refactoring to handle the `block_shape = None` case. https://github.com/neuronets/nobrainer/blob/ed0d609333f9aea724c5fd45962c36dfd8a13d88/nobrainer/dataset.py#L249-L266

bug

Harsha