code examples of MONAI input data pipeline #14
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Nic-Ma
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Jun 26, 2020
* adds network * adds basic training * update loading * working prototype * update validation set * [MONAI] Add author; paper info; PDDCA18 (#6) + Author + Early accept + PDDCA18 link * Update README.md * adds network * adds basic training * update loading * working prototype * update validation set * [MONAI] Update TRAIN_PATH, VAL_PATH (#8) + Update TRAIN_PATH, VAL_PATH * [MONAI] Add data link (#7) + Add data link https://drive.google.com/file/d/1A2zpVlR3CkvtkJPvtAF3-MH0nr1WZ2Mn/view?usp=sharing * fixes typos * tested new dataset * print more infor, checked new dataset * [MONAI] Add paper link (#9) Add paper link https://arxiv.org/abs/2006.12575 * [MONAI] Use dice loss + focal loss to train (#10) Use dice loss + focal loss to train * [MONAI] Support non-one-hot ground truth (#11) Support non-one-hot ground truth * fixes format and docstrings, adds argparser options * resume the focal_loss * adds tests * [MONAI] Support non-one-hot ground truth (#11) Support non-one-hot ground truth * adds tests * update docstring * [MONAI] Keep track of best validation scores (#12) Keep track of best validation scores * model saving * adds window sampling * update readme * update docs * fixes flake8 error * update window sampling * fixes model name * fixes channel size issue * [MONAI] Update --pretrain, --lr (#13) + lr from 5e-4 to 1e-3 because we use mean for class channel instead of sum for class channel. + pretrain path is consistent with current model_name. * [MONAI] Pad image; elastic; best class model (#14) * [MONAI] Pad image; elastic; best class model + Pad image bigger than crop_size, avoid potential issues in RandCropByPosNegLabeld + Use Rand3DElasticd + Save best model for each class * Update train.py Co-authored-by: Wenqi Li <wenqil@nvidia.com> * flake8 fixes * removes -1 cropsize deform * testing commands * fixes unit tests * update spatial padding * [MONAI] Add full image deform augmentation (#15) + Add full image deform augmentation by Rand3DElasticd + Please use latest MONAI in #623 * Adding py.typed * updating setup.py to comply with black * update based on comments * excluding research from packaging * update tests * update setup.py Co-authored-by: Wentao Zhu <wentaozhu1991@gmail.com> Co-authored-by: Neil Tenenholtz <ntenenz@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com>
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