From 4743945a68952d05c8a97b82b1bb75a3ad5dbf71 Mon Sep 17 00:00:00 2001 From: Wenqi Li <831580+wyli@users.noreply.github.com> Date: Wed, 11 Oct 2023 15:36:14 +0100 Subject: [PATCH] update changelog and docs for v1.3 (#7110) part of https://github.com/Project-MONAI/MONAI/issues/7017 fixes #7112 ### Types of changes - [x] 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 -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li --- CHANGELOG.md | 10 +++++++++- tests/test_swin_unetr.py | 3 ++- 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1e3f952b3d..61be8f07c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). ## [Unreleased] -## [1.3.0] - 2023-10-06 +## [1.3.0] - 2023-10-12 ### Added * Intensity transforms `ScaleIntensityFixedMean` and `RandScaleIntensityFixedMean` (#6542) * `UltrasoundConfidenceMapTransform` used for computing confidence map from an ultrasound image (#6709) @@ -39,6 +39,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). * Support str type annotation to `device` in `ToTensorD` (#6737) * Improve logging message and file name extenstion in `DataAnalyzer` for `Auto3DSeg` (#6758) * Set `data_range` as a property in `SSIMLoss` (#6788) +* Unify environment variable access (#7084) * `end_lr` support in `WarmupCosineSchedule` (#6662) * Add `ClearML` as optional dependency (#6827) * `yandex.disk` support in `download_url` (#6667) @@ -52,6 +53,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). * Fix mismatched shape in `Spacing` (#6912) * Avoid FutureWarning in `CropForeground` (#6934) * Fix `Lazy=True` ignored when using `Dataset` call (#6975) +* Shape check for arbitrary types for DataStats (#7082) #### data * Fix wrong spacing checking logic in `PydicomReader` and broken link in `ITKReader` (#6660) * Fix boolean indexing of batched `MetaTensor` (#6781) @@ -65,6 +67,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). #### metrics and losses * Fixed bug in `GeneralizedDiceLoss` when `batch=True` (#6775) * Support for `BCEWithLogitsLoss` in `DiceCELoss` (#6924) +* Support for `weight` in Dice and related losses (#7098) #### networks * Use `np.prod` instead of `np.product` (#6639) * Fix dimension issue in `MBConvBlock` (#6672) @@ -87,8 +90,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). * Bundle syntax `#` as alias of `::` (#6955) * Fix bundle download naming issue (#6969, #6963) * Simplify the usage of `ckpt_export` (#6965) +* `update_kwargs` in `monai.bundle.script` for merging multiple configs (#7109) #### engines and handlers * Added int options for `iteration_log` and `epoch_log` in `TensorBoardStatsHandler` (#7027) +* Support to run validator at training start (#7108) #### misc. * Fix device fallback error in `DataAnalyzer` (#6658) * Add int check for `current_mode` in `convert_applied_interp_mode` (#6719) @@ -104,6 +109,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). * Add type check to avoid comparing a np.array with a string in `_check_kwargs_are_present` (#6624) * Fix md5 hashing with FIPS mode (#6635) * Capture failures from Auto3DSeg related subprocess calls (#6596) +* Code formatting tool for user-specified directory (#7106) +* Various docstring fixes ### Changed * Base Docker image upgraded to `nvcr.io/nvidia/pytorch:23.08-py3` from `nvcr.io/nvidia/pytorch:23.03-py3` ### Deprecated @@ -112,6 +119,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). * `workflow` in `BundleWorkflow` in favor of `workflow_type`(#6768) * `pos_embed` in `PatchEmbeddingBlock` in favor of `proj_type`(#6986) * `net_name` and `net_kwargs` in `download` in favor of `model`(#7016) +* `img_size` parameter in SwinUNETR (#7093) ### Removed * `pad_val`, `stride`, `per_channel` and `upsampler` in `OcclusionSensitivity` (#6642) * `compute_meaniou` (#7019) diff --git a/tests/test_swin_unetr.py b/tests/test_swin_unetr.py index 9197308aa5..9f6b1e7c0a 100644 --- a/tests/test_swin_unetr.py +++ b/tests/test_swin_unetr.py @@ -24,7 +24,7 @@ from monai.networks.nets.swin_unetr import PatchMerging, PatchMergingV2, SwinUNETR, filter_swinunetr from monai.networks.utils import copy_model_state from monai.utils import optional_import -from tests.utils import assert_allclose, skip_if_downloading_fails, skip_if_quick, testing_data_config +from tests.utils import assert_allclose, skip_if_downloading_fails, skip_if_no_cuda, skip_if_quick, testing_data_config einops, has_einops = optional_import("einops") @@ -108,6 +108,7 @@ def test_patch_merging(self): @parameterized.expand(TEST_CASE_FILTER) @skip_if_quick + @skip_if_no_cuda def test_filter_swinunetr(self, input_param, key, value): with skip_if_downloading_fails(): with tempfile.TemporaryDirectory() as tempdir: