Aucmedi

:bug: Bug Fixes
- [`6ab16d3`](https://github.com/frankkramer-lab/aucmedi/commit/6ab16d3ff0359a1857f8a097412ce1281b838109) - **metrics**: remove num_classes parameter from F1Score and update requirements.txt
- [`bd4cff3`](https://github.com/frankkramer-lab/aucmedi/commit/bd4cff327e49d0f841339552edb7d3bd3972bf9b) - **F1Score**: correct computation of F1Score in automl training
- [`13b4eda`](https://github.com/frankkramer-lab/aucmedi/commit/13b4eda11d44399853049e37d55faa1f52056460) - change input_stack from list to tuple to resolve TypeError
- [`bb93486`](https://github.com/frankkramer-lab/aucmedi/commit/bb93486edb664bc71440a2855468bd96a50855f3) - replace deprecated layer.output_shape with layer.output.shape
- [`afa71bb`](https://github.com/frankkramer-lab/aucmedi/commit/afa71bbbf8e57a181eeb4127475caae5a284f88c) - add value=0 to pad function and fix RandomCrop function

:recycle: Refactors
- [`dd1b77a`](https://github.com/frankkramer-lab/aucmedi/commit/dd1b77a06ccdc25849df2ede6b2ed0b846b5f3d6) - commented out all ViT mentions in files
- [`9289d90`](https://github.com/frankkramer-lab/aucmedi/commit/9289d9057584e51ddb8505e9a8c684c1f5017c5e) - **tests**: commented out ViT-related unittests
- [`437d3d0`](https://github.com/frankkramer-lab/aucmedi/commit/437d3d0d91dfb01885dd333d423382977a534413) - update imports and comments, remove deprecated dependencies
- [`8bbd83c`](https://github.com/frankkramer-lab/aucmedi/commit/8bbd83c724826d9c68fb85d498b8cfae3c8bb711) - **metrics**: delete F1Score in the AutoML training block
- [`8e5c66e`](https://github.com/frankkramer-lab/aucmedi/commit/8e5c66e1542d9c9edbaa8401c9898d5a7a49d817) - **NeuralNetwork**: remove unused workers parameter
- [`23c78e8`](https://github.com/frankkramer-lab/aucmedi/commit/23c78e8ee6bc70e79d7d1f9ff1d5ff52b103cc06) - **NeuralNetwork**: remove unused multiprocessing parameter
- [`9278360`](https://github.com/frankkramer-lab/aucmedi/commit/92783607e73149943185f4e4c57562042f337b2e) - **NeuralNetwork**: remove unused batch_queue_size parameter
- [`f201b75`](https://github.com/frankkramer-lab/aucmedi/commit/f201b750a83697668d4acdb52416e14a7d351d3b) - **F1Score**: delete F1Score in AutoML training block
- [`a14af09`](https://github.com/frankkramer-lab/aucmedi/commit/a14af096d153363b09a5b80338e26ea0e92a15be) - replace .hdf5 with .keras format
- [`d591efe`](https://github.com/frankkramer-lab/aucmedi/commit/d591efe8f3de7e054f1b90ca08a4b13946cfb3c2) - update version in requirements
- [`61277cf`](https://github.com/frankkramer-lab/aucmedi/commit/61277cf1c8752974808a44a2e2f757cddaec92e3) - rename test_application_multilabel
- [`4290352`](https://github.com/frankkramer-lab/aucmedi/commit/42903522c932baf0d687cc27b4316b98a86f3481) - add border_mode to pad function and cv2 import
- [`45eed28`](https://github.com/frankkramer-lab/aucmedi/commit/45eed286ec595e283c24c713d3cffb411ea03ad6) - comment out resize parameter to resolve ValueError in tests
- [`a6be1c7`](https://github.com/frankkramer-lab/aucmedi/commit/a6be1c764bb13ab4de7494f9f0176ecd8bf6652c) - add input_shape parameter in NeuralNetwork in each test
- [`accc7c1`](https://github.com/frankkramer-lab/aucmedi/commit/accc7c179d315428bd046a12462494a6f8d9d235) - add input_shape in NeuralNetwork in each test
- [`560f1cb`](https://github.com/frankkramer-lab/aucmedi/commit/560f1cbafd853b8e43add2f7ad167358bd1b3070) - comment out test_utils_iter test
- [`493e5e3`](https://github.com/frankkramer-lab/aucmedi/commit/493e5e325823f1e5abefab4d7137cf069f862fed) - update DataGenerator and architectures for resize=(64, 64, 64)

:construction_worker: Build System
- [`81d8db2`](https://github.com/frankkramer-lab/aucmedi/commit/81d8db28e41a49ffb09ba31584f8bd13f044a1df) - updated to version 0.10.0 *(commit by muellerdo)*

:sparkles: New Features
- [`7b88203`](https://github.com/frankkramer-lab/aucmedi/commit/7b882030fd01c8ee7b493ffbcef5445392a87ef7) - **Architecture**: added ConvNeXt 3D architectures *(commit by muellerdo)*
- [`2cfec6e`](https://github.com/frankkramer-lab/aucmedi/commit/2cfec6e7598c590883cdbff3982fb3b2196a7f5e) - **Architecture**: integrated ConvNeXt 3D architectures into AUCMEDI environment *(commit by muellerdo)*
- [`cb41966`](https://github.com/frankkramer-lab/aucmedi/commit/cb419666ffc2f38eeed51b498ab943a9af829175) - added multi-modality support *(commit by muellerdo)*
- [`5fd029c`](https://github.com/frankkramer-lab/aucmedi/commit/5fd029cc78bdf26b64892f98e30b75418e503ed0) - **sitk_loader**: allow more dynamic resampling in terms of multi-modality *(commit by muellerdo)*
- [`979a660`](https://github.com/frankkramer-lab/aucmedi/commit/979a66073206c5b7ee3c9a1ac5915ddf05d6931c) - **Architectures**: removed 2D ResNeXt image architecture support *(commit by muellerdo)*
- [`76866a9`](https://github.com/frankkramer-lab/aucmedi/commit/76866a94ea9d47df6521dc62d6b4d122baa9f9d9) - **Architecture**: added 2D ResNeXt (50 & 101), again... *(commit by muellerdo)*

:bug: Bug Fixes
- [`a7e335c`](https://github.com/frankkramer-lab/aucmedi/commit/a7e335c4c4f6837e00322dfe69e3502f5d57615d) - **Ensemble**: fixed incorrect callback extension *(commit by muellerdo)*
- [`78b3078`](https://github.com/frankkramer-lab/aucmedi/commit/78b3078f14ccdc1010b2698f95e82b5bf9cb4d93) - classes parameter (np.array) *(commit by Sassy-Nazogram)*
- [`f6945b8`](https://github.com/frankkramer-lab/aucmedi/commit/f6945b860f0d089823dd4771df06a1876abaaa48) - **Evaluation**: changed datatype from float to object for ROC multi-lists *(commit by muellerdo)*
- [`6d0df6a`](https://github.com/frankkramer-lab/aucmedi/commit/6d0df6ae3eabe9ee36765ea41b9c63f86f70908f) - **Evaluation**: replaced np.object with object due to deprecated *(commit by muellerdo)*
- [`8cb896f`](https://github.com/frankkramer-lab/aucmedi/commit/8cb896f285157bc501955bc450f378c92cef6d11) - **Evaluation**: specified groupby column to be consistent with pandas 2.X *(commit by muellerdo)*

:recycle: Refactors
- [`4530bb9`](https://github.com/frankkramer-lab/aucmedi/commit/4530bb94021d79c13ad2c8ba1b82c7a76d1fa9bc) - **AutoML**: added Tensorflow Addons F1 to AutoML train again *(commit by muellerdo)*
- [`e5940db`](https://github.com/frankkramer-lab/aucmedi/commit/e5940db562fb85e202f309fd5a648c836bb8dde8) - **Tutorials**: reverted to TF addons F1 metric in the tutorials *(commit by muellerdo)*

:white_check_mark: Tests
- [`c2ce77b`](https://github.com/frankkramer-lab/aucmedi/commit/c2ce77b5b8bf1a5cceec5b9012b10302b201702b) - **Architecture**: added unittesting for ConvNeXt 3D *(commit by muellerdo)*
- [`7549dc8`](https://github.com/frankkramer-lab/aucmedi/commit/7549dc8a954fe941b27a74cdcada2e0c084ddf20) - unittesting for 3D multi-modality data loading *(commit by muellerdo)*
- [`4414024`](https://github.com/frankkramer-lab/aucmedi/commit/441402472beac25e2537fec491007c48d9a9dc39) - **sitk_loader**: improved unittesting for resampling of multi-modality nii/mha volumes *(commit by muellerdo)*

:construction_worker: Build System
- [`800713b`](https://github.com/frankkramer-lab/aucmedi/commit/800713b80c92796a262ca175ef03c51c3f79cd42) - increased package version 3D-classification-models to 1.0.7 *(commit by muellerdo)*
- [`4caf08d`](https://github.com/frankkramer-lab/aucmedi/commit/4caf08df66fdd6530291ba2bf98873f9aa335418) - Updated to version 0.8.2 *(commit by muellerdo)*
- [`7750c96`](https://github.com/frankkramer-lab/aucmedi/commit/7750c96078c4b3782ffa67bf1cd9c7ee939a0158) - **Tensorflow**: incrased package version to 2.11.1 *(commit by muellerdo)*
- [`8837e06`](https://github.com/frankkramer-lab/aucmedi/commit/8837e06049daf84850c8b2c2c8a8b863a52efd9c) - **Tensorflow-Addons**: removed TF-addon and keras-applications support *(commit by muellerdo)*
- [`2ce29b2`](https://github.com/frankkramer-lab/aucmedi/commit/2ce29b27f75e4de905cdad23b044d69eca0471b8) - updated dependency list *(commit by muellerdo)*
- [`8b7da52`](https://github.com/frankkramer-lab/aucmedi/commit/8b7da52b6be792dd963b78af9ac3b3dc7ca482e3) - **Python**: dropped Python3.8 for CI and added 3.9 & 3.10 *(commit by muellerdo)*
- [`6cbe6e9`](https://github.com/frankkramer-lab/aucmedi/commit/6cbe6e9ff9da1a4abb59c6088d78457cb1e0f464) - **Python**: removed Python 3.12 again from CI as there is no TF1.4 support there *(commit by muellerdo)*
- [`2de4ba3`](https://github.com/frankkramer-lab/aucmedi/commit/2de4ba31edff72f11a590a181775710c21f82f4d) - **Tensorflow-Addons**: added TFaddons back due to requirements for Keras ViT.. *(commit by muellerdo)*
- [`fc11a51`](https://github.com/frankkramer-lab/aucmedi/commit/fc11a513fc2b860ff0ae4f48d5e2e38cb8a440a5) - **Keras-Applications**: added also back Keras Applications (and 2D ResNeXt) as classification-models-3D require it... *(commit by muellerdo)*
- [`6990dd5`](https://github.com/frankkramer-lab/aucmedi/commit/6990dd55e23c28b9d30df93bc699f04f1beb96d4) - **Python**: converted python version to strings to be 3.10 instead of 3.1 *(commit by muellerdo)*
- [`7152f87`](https://github.com/frankkramer-lab/aucmedi/commit/7152f87b095ce62feb45d80bb8aa2bf068689572) - **plotnine**: upgraded plotnine to version 0.12.0 *(commit by muellerdo)*
- [`5db39c1`](https://github.com/frankkramer-lab/aucmedi/commit/5db39c1f8c5af463de015bcd07be3446f79f35c1) - **plotnine**: fixed version to 0.12.4 *(commit by muellerdo)*
- [`c48c4c9`](https://github.com/frankkramer-lab/aucmedi/commit/c48c4c9a3c25e0a475f872a52b5ed66bab9132c4) - **scikit**: updated scikit-learn & scikit-image *(commit by muellerdo)*
- [`ba40783`](https://github.com/frankkramer-lab/aucmedi/commit/ba407836d90272e66780ab9b5960051ec2ccb902) - **Pillow**: updated Pillow to 10.2.0 for security *(commit by muellerdo)*
- [`da8c660`](https://github.com/frankkramer-lab/aucmedi/commit/da8c660e744f26ad4527f263df3d7899427e937e) - updated to version 0.9.0 *(commit by muellerdo)*

:memo: Documentation Changes
- [`812bb88`](https://github.com/frankkramer-lab/aucmedi/commit/812bb880899d429475666985a773247d63392ba7) - **Tutorials**: fixed incorrect link - solves #200 *(commit by muellerdo)*

:wrench: Chores
- [`444c11d`](https://github.com/frankkramer-lab/aucmedi/commit/444c11d7264f2aa990bc52a6f81ce14b9c4005d3) - updated copyright to 2023 *(commit by muellerdo)*
- [`729a275`](https://github.com/frankkramer-lab/aucmedi/commit/729a2759e60a6a60bad028cb8eb2533633576a7a) - merged dev branch to ConvNeXt3D PR *(commit by muellerdo)*
- [`22d5415`](https://github.com/frankkramer-lab/aucmedi/commit/22d54152b4c5693908e086a7bf920e1c8f64c310) - updated copyright to 2024 *(commit by muellerdo)*
- [`a155af8`](https://github.com/frankkramer-lab/aucmedi/commit/a155af850783ca39684ec3a189fe5472f194a76c) - updated copyright on website *(commit by muellerdo)*

:recycle: Refactors
- [`80566ed`](https://github.com/frankkramer-lab/aucmedi/commit/80566ed1319c92f3f321d8513cb411397fd70414) - **DataGenerator**: removed overlooked debugging sys.out print *(commit by muellerdo)*

:construction_worker: Build System
- [`ecef046`](https://github.com/frankkramer-lab/aucmedi/commit/ecef046aa7e0ffaf7a8e291705ddc77d4408568f) - Updated to version 0.8.1 *(commit by muellerdo)*

:sparkles: New Features
- [`2e8f2a9`](https://github.com/frankkramer-lab/aucmedi/commit/2e8f2a93a91d2497ce887e2f3dc3ef4b545e6c82) - **DataGenerator**: rework deprecated keras.Iterator to keras.Sequence - Closes #76,189 *(commit by muellerdo)*

:bug: Bug Fixes
- [`8f1a2e8`](https://github.com/frankkramer-lab/aucmedi/commit/8f1a2e80468fb1c4fe7e0ee36ecc251bb4fc3dab) - **Evaluation**: updated deprecated np.int to np.int8 for boolean to integer matrix conversion *(commit by muellerdo)*

:white_check_mark: Tests
- [`c70fc4c`](https://github.com/frankkramer-lab/aucmedi/commit/c70fc4c32e19c6203731b0d610f3a291b6063687) - **NeuralNetwork**: testing for repeatition capabilities in datagenerators *(commit by muellerdo)*
- [`5568cfa`](https://github.com/frankkramer-lab/aucmedi/commit/5568cfa56c79a3a6b1c64c7f5dce38e6e285c6fc) - **DataGenerator**: added iteration & repetition testing as well as batch access *(commit by muellerdo)*

:construction_worker: Build System
- [`c27c7f1`](https://github.com/frankkramer-lab/aucmedi/commit/c27c7f1d4c2fe3b8e7e491774e42df326988c1f1) - **Codecov**: added config file with threshold of 1% *(commit by muellerdo)*
- [`dc264bf`](https://github.com/frankkramer-lab/aucmedi/commit/dc264bfb457ca86b5aa8c5e62f88282ff0acdc39) - Updated to version 0.8.0 *(commit by muellerdo)*

:memo: Documentation Changes
- [`973ff46`](https://github.com/frankkramer-lab/aucmedi/commit/973ff46aa06bb1d09ac39869177657d5da29a2aa) - **README**: fixed package build status badge *(commit by muellerdo)*

:boom: BREAKING CHANGES
- due to [`b38dd6d`](https://github.com/frankkramer-lab/aucmedi/commit/b38dd6ddb1a0b656f5731f6ca556b23be84831cd) - updated various package versions *(commit by muellerdo)*:

updated various package versions


:sparkles: New Features
- [`82c3e3d`](https://github.com/frankkramer-lab/aucmedi/commit/82c3e3d7cf4415ae9f43b7b88c0e26c52ad7439f) - **Architecture**: added ConvNeXt - closes #101 *(commit by muellerdo)*
- [`5d94fbe`](https://github.com/frankkramer-lab/aucmedi/commit/5d94fbec6f148ec989dbff9070c2fe5e326b8b55) - **Architecture**: added ConvNeXt to architecture library *(commit by muellerdo)*

:white_check_mark: Tests
- [`b379dc2`](https://github.com/frankkramer-lab/aucmedi/commit/b379dc2498d9624e056c15e1af8e2aa99e2adb47) - **Architecture**: added unittesting for ConvNeXt *(commit by muellerdo)*

:construction_worker: Build System
- [`34dc3ca`](https://github.com/frankkramer-lab/aucmedi/commit/34dc3caa43555a3f75a70e2d9661f185320152a2) - **TensorFlow**: increased tensorflow to at least v2.10 *(commit by muellerdo)*
- [`b38dd6d`](https://github.com/frankkramer-lab/aucmedi/commit/b38dd6ddb1a0b656f5731f6ca556b23be84831cd) - updated various package versions *(commit by muellerdo)*
- [`d089d88`](https://github.com/frankkramer-lab/aucmedi/commit/d089d88943890eb55a36425e460ae3ecff0157ee) - **TensorFlow-Addons**: fixed typo in version *(commit by muellerdo)*
- [`efb6297`](https://github.com/frankkramer-lab/aucmedi/commit/efb62973fc3fce9da596130122cbec64a5b988fc) - Updated to version 0.7.3 *(commit by muellerdo)*

:memo: Documentation Changes
- [`1e96578`](https://github.com/frankkramer-lab/aucmedi/commit/1e96578f962a5eef7ca4e56648ff1c6bb3081a1b) - **Example**: removed template pipeline of standardized framework example *(commit by muellerdo)*
- [`6985b72`](https://github.com/frankkramer-lab/aucmedi/commit/6985b72df0179f50877bca6cc0051d568b05bcff) - **Example**: added link to Medium blog article *(commit by muellerdo)*
- [`a3781fa`](https://github.com/frankkramer-lab/aucmedi/commit/a3781fac406c6539d95e808484dfec0c5bce0eca) - **Example**: added manuscripts to framework examples *(commit by muellerdo)*
- [`e867b34`](https://github.com/frankkramer-lab/aucmedi/commit/e867b3499bf8850024dd2188bc17c07d5ea2cf39) - **Reference**: added ref to application preprint paper *(commit by muellerdo)*

:construction_worker: Build System
- [`dbbdbd6`](https://github.com/frankkramer-lab/aucmedi/commit/dbbdbd6717d871dcba73d22d2555cd5590c785e2) - **PRs**: added code quality CI to PRs targeting master *(commit by [muellerdo](https://github.com/muellerdo))*
- [`0da9e1b`](https://github.com/frankkramer-lab/aucmedi/commit/0da9e1bd75a7ac15038269947f6264e3f375eacb) - **protobuf**: increased to v3.20.2 as security update *(commit by [muellerdo](https://github.com/muellerdo))*
- [`41cc227`](https://github.com/frankkramer-lab/aucmedi/commit/41cc227bb17c4f29f5cde4eb2d7fc166a989aba8) - **matplotlib**: maxed to v3.5.3 due to plotnine dependency *(commit by [muellerdo](https://github.com/muellerdo))*
- [`73304f7`](https://github.com/frankkramer-lab/aucmedi/commit/73304f7ebac10ca3872f049627d19561831b826a) - Updated to version 0.7.2 *(commit by [muellerdo](https://github.com/muellerdo))*

:memo: Documentation Changes
- [`5405268`](https://github.com/frankkramer-lab/aucmedi/commit/5405268a6b68f20795d7420aec9300afde15dbe3) - **Website**: fixed a typo in the status bar (roadmap) *(commit by [muellerdo](https://github.com/muellerdo))*
- [`f3c3186`](https://github.com/frankkramer-lab/aucmedi/commit/f3c3186ca43082e78c21fc7581ab7d94504e8716) - **Classifier**: enhanced the example in the API ref *(commit by [muellerdo](https://github.com/muellerdo))*
- [`1b0a51f`](https://github.com/frankkramer-lab/aucmedi/commit/1b0a51f4abe15c771e6fab9287a7e68afc7dfec4) - add links and fix example *(commit by [SherlockMones](https://github.com/SherlockMones))*
- [`90e4651`](https://github.com/frankkramer-lab/aucmedi/commit/90e465173fb8ddced1222e9a4fbefa00e447db9f) - fix links *(commit by [SherlockMones](https://github.com/SherlockMones))*
- [`f555fce`](https://github.com/frankkramer-lab/aucmedi/commit/f555fcee1c87580c5242e2b30501b87efc834406) - **stacking**: fix example *(commit by [SherlockMones](https://github.com/SherlockMones))*
- [`0250281`](https://github.com/frankkramer-lab/aucmedi/commit/025028199629f4758d341e0701f126dae2085a40) - **Example**: added multiple API examples and tutorials *(commit by [muellerdo](https://github.com/muellerdo))*