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WIP:Add CXR8 Dataset, Improves resource logging, Deprecates SSL, Adds tensorsboard support
This MR contains some important additions:
- Adds the CXR8 dataset and segmentations as input source for training lung segmentation on CXR, including specific versions for Idiap usage
- Fixes CPU logging (missing
recurse=True
setting) - Improves CPU/GPU logging by consulting devices in a parallel process, during the whole epoch
- Fine-tunes
train-analysis
plot, adds a plot for hardware utilisation through training - Deprecates Semi-supervised Learning (SSL) approaches due to changes in the overall re-design and infrastructural changes
- Added plumbery to support tensorboard logging
- Parallelises the evaluation procedure so it may be faster on very large datasets
- Change the flag
--multiproc-data-loading
to--parallel
as it now can be used through the whole experiment - Implements plot axes limits for the compare (portion of the experiment) script
- Adjusts the root of lung segmentation datasets (Montgomery, Shenzhen, JSRT) to make running a bit easier to reproduce remotely
- Fixes the loading of Montgomery and Shenzhen datasets to avoid resizing distortions
Edited by André Anjos
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assigned to @andre.anjos
added 1 commit
- d9af6bee - adding warning message for shenzhen/cxr8 doc
added 25 commits
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090cbe52...91db824d - 12 commits from branch
master
- 6b5ebb11 - adding cxr8 dataset files
- be167576 - reformatting with isort/black
- 25de66d7 - reformatting xtest file
- 47e85137 - fixing end of json file
- 3fb3670f - default.json end of file
- 42272231 - Updating doc for CXR8 dataset
- 98351fb1 - fixing references.rst
- 4f65919b - fix cxr8 reference class
- 06ab6f19 - include cxr8 on setup.py file
- a2def2d2 - add test for cxr8
- d9e30d8c - fix test_cxr8.py
- ec9dcd23 - adding warning message for shenzhen/cxr8 doc
- 6cecdb02 - fix trailing whitespace
Toggle commit list-
090cbe52...91db824d - 12 commits from branch
- Resolved by Matheus Armani Renzo
@arenzom: can you please check the "xtest" configuration for cxr8? It does not look right...
I'm also receiving this (possibly due to the upgrade to PyTorch-1.10.x):
remote/idiap.svm/user.active/aanjos/work/bob/bob.ip.binseg/bob/ip/binseg/engine/adabound.py:152: UserWarning: This overload of add_ is deprecated: add_(Number alpha, Tensor other) Consider using one of the following signatures instead: add_(Tensor other, *, Number alpha) (Triggered internally at /home/conda/feedstock_root/build_artifacts/pytorch-recipe_1645461916848/work/torch/csrc/utils/python_arg_parser.cpp:1050.) exp_avg.mul_(beta1).add_(1 - beta1, grad)
- Resolved by Matheus Armani Renzo
added 1 commit
- 38fef315 - fix deprecation warning for add_ and addcmul_ func
added 1 commit
- 69b6a7da - [script.train_analysis] Improve train-analysis CLI
added 1 commit
- 9db1f6f5 - [utils.resources] Fix gpu logging (fixes #11 (closed))
added 1 commit
- 85ecdccd - [utils.resources] Minor fixes to new GPU monitor
added 24 commits
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470c4b3e - 1 commit from branch
master
- 8b284c4c - adding cxr8 dataset files
- 320f5b84 - reformatting with isort/black
- 78329e03 - reformatting xtest file
- 3d52621c - fixing end of json file
- a1e1d134 - default.json end of file
- 31dcd157 - Updating doc for CXR8 dataset
- 361a272a - fixing references.rst
- 0bf2fc13 - fix cxr8 reference class
- f7d52c42 - include cxr8 on setup.py file
- 3af7d7a0 - add test for cxr8
- c4bba15e - fix test_cxr8.py
- 82ceeb52 - adding warning message for shenzhen/cxr8 doc
- 37555c08 - fix trailing whitespace
- 39d425d2 - adding cxr8 dataset to cxr8 xtest config
- 7942bd98 - fix deprecation warning for add_ and addcmul_ func
- 3b6a1acb - reformatting adabound file
- fb312749 - [cxr8] Add idiap "twist"
- 4137e847 - [cxr8] Fix identation
- 7d7ab7f2 - [utils.resources] Fix cpu logging
- 8c61b95b - [script.train_analysis] Improve train-analysis CLI
- 74da7a52 - [pre-commit] fix complaints
- 1f3a8bb1 - [utils.resources] Fix gpu logging (fixes #11 (closed))
- 9922348e - [utils.resources] Minor fixes to new GPU monitor
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470c4b3e - 1 commit from branch
added 1 commit
- 7e0d92de - [requirements] Add tensorboard as a monitoring resource
added 1 commit
- 8c59f548 - [utils.resources] Protects against zombies and gone processes during resource gathering
added 1 commit
- 278a9dd2 - [train_analysis] Adds a separate plot for hardware utilisation
added 1 commit
- 71ee7ab1 - [engine.evaluator] Parallelisation of evaluation procedure (closes #13 (closed))
added 1 commit
- 0d7c5b8c - [utils.plot] Fix axes appearance after zooming
added 1 commit
- 2d4c88b0 - [test] Change references to match new dataset organisation
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