Aucmedi Versions Save

a framework for Automated Classification of Medical Images

v0.9.0

3 months ago

:sparkles: New Features

  • 7b88203 - Architecture: added ConvNeXt 3D architectures (commit by @muellerdo)
  • 2cfec6e - Architecture: integrated ConvNeXt 3D architectures into AUCMEDI environment (commit by @muellerdo)
  • cb41966 - added multi-modality support (commit by @muellerdo)
  • 5fd029c - sitk_loader: allow more dynamic resampling in terms of multi-modality (commit by @muellerdo)
  • 979a660 - Architectures: removed 2D ResNeXt image architecture support (commit by @muellerdo)
  • 76866a9 - Architecture: added 2D ResNeXt (50 & 101), again... (commit by @muellerdo)

:bug: Bug Fixes

  • a7e335c - Ensemble: fixed incorrect callback extension (commit by @muellerdo)
  • 78b3078 - classes parameter (np.array) (commit by @Sassy-Nazogram)
  • f6945b8 - Evaluation: changed datatype from float to object for ROC multi-lists (commit by @muellerdo)
  • 6d0df6a - Evaluation: replaced np.object with object due to deprecated (commit by @muellerdo)
  • 8cb896f - Evaluation: specified groupby column to be consistent with pandas 2.X (commit by @muellerdo)

:recycle: Refactors

  • 4530bb9 - AutoML: added Tensorflow Addons F1 to AutoML train again (commit by @muellerdo)
  • e5940db - Tutorials: reverted to TF addons F1 metric in the tutorials (commit by @muellerdo)

:white_check_mark: Tests

  • c2ce77b - Architecture: added unittesting for ConvNeXt 3D (commit by @muellerdo)
  • 7549dc8 - unittesting for 3D multi-modality data loading (commit by @muellerdo)
  • 4414024 - sitk_loader: improved unittesting for resampling of multi-modality nii/mha volumes (commit by @muellerdo)

:construction_worker: Build System

  • 800713b - increased package version 3D-classification-models to 1.0.7 (commit by @muellerdo)
  • 4caf08d - Updated to version 0.8.2 (commit by @muellerdo)
  • 7750c96 - Tensorflow: incrased package version to 2.11.1 (commit by @muellerdo)
  • 8837e06 - Tensorflow-Addons: removed TF-addon and keras-applications support (commit by @muellerdo)
  • 2ce29b2 - updated dependency list (commit by @muellerdo)
  • 8b7da52 - Python: dropped Python3.8 for CI and added 3.9 & 3.10 (commit by @muellerdo)
  • 6cbe6e9 - Python: removed Python 3.12 again from CI as there is no TF1.4 support there (commit by @muellerdo)
  • 2de4ba3 - Tensorflow-Addons: added TFaddons back due to requirements for Keras ViT.. (commit by @muellerdo)
  • fc11a51 - Keras-Applications: added also back Keras Applications (and 2D ResNeXt) as classification-models-3D require it... (commit by @muellerdo)
  • 6990dd5 - Python: converted python version to strings to be 3.10 instead of 3.1 (commit by @muellerdo)
  • 7152f87 - plotnine: upgraded plotnine to version 0.12.0 (commit by @muellerdo)
  • 5db39c1 - plotnine: fixed version to 0.12.4 (commit by @muellerdo)
  • c48c4c9 - scikit: updated scikit-learn & scikit-image (commit by @muellerdo)
  • ba40783 - Pillow: updated Pillow to 10.2.0 for security (commit by @muellerdo)
  • da8c660 - updated to version 0.9.0 (commit by @muellerdo)

:memo: Documentation Changes

  • 812bb88 - Tutorials: fixed incorrect link - solves #200 (commit by @muellerdo)

:wrench: Chores

  • 444c11d - updated copyright to 2023 (commit by @muellerdo)
  • 729a275 - merged dev branch to ConvNeXt3D PR (commit by @muellerdo)
  • 22d5415 - updated copyright to 2024 (commit by @muellerdo)
  • a155af8 - updated copyright on website (commit by @muellerdo)

v0.8.1

1 year ago

:recycle: Refactors

  • 80566ed - DataGenerator: removed overlooked debugging sys.out print (commit by @muellerdo)

:construction_worker: Build System

  • ecef046 - Updated to version 0.8.1 (commit by @muellerdo)

v0.8.0

1 year ago

:sparkles: New Features

  • 2e8f2a9 - DataGenerator: rework deprecated keras.Iterator to keras.Sequence - Closes #76,#189 (commit by @muellerdo)

:bug: Bug Fixes

  • 8f1a2e8 - Evaluation: updated deprecated np.int to np.int8 for boolean to integer matrix conversion (commit by @muellerdo)

:white_check_mark: Tests

  • c70fc4c - NeuralNetwork: testing for repeatition capabilities in datagenerators (commit by @muellerdo)
  • 5568cfa - DataGenerator: added iteration & repetition testing as well as batch access (commit by @muellerdo)

:construction_worker: Build System

  • c27c7f1 - Codecov: added config file with threshold of 1% (commit by @muellerdo)
  • dc264bf - Updated to version 0.8.0 (commit by @muellerdo)

:memo: Documentation Changes

  • 973ff46 - README: fixed package build status badge (commit by @muellerdo)

v0.7.3

1 year ago

:boom: BREAKING CHANGES

  • due to b38dd6d - updated various package versions (commit by @muellerdo):

    updated various package versions

:sparkles: New Features

  • 82c3e3d - Architecture: added ConvNeXt - closes #101 (commit by @muellerdo)
  • 5d94fbe - Architecture: added ConvNeXt to architecture library (commit by @muellerdo)

:white_check_mark: Tests

  • b379dc2 - Architecture: added unittesting for ConvNeXt (commit by @muellerdo)

:construction_worker: Build System

  • 34dc3ca - TensorFlow: increased tensorflow to at least v2.10 (commit by @muellerdo)
  • b38dd6d - updated various package versions (commit by @muellerdo)
  • d089d88 - TensorFlow-Addons: fixed typo in version (commit by @muellerdo)
  • efb6297 - Updated to version 0.7.3 (commit by @muellerdo)

:memo: Documentation Changes

  • 1e96578 - Example: removed template pipeline of standardized framework example (commit by @muellerdo)
  • 6985b72 - Example: added link to Medium blog article (commit by @muellerdo)
  • a3781fa - Example: added manuscripts to framework examples (commit by @muellerdo)
  • e867b34 - Reference: added ref to application preprint paper (commit by @muellerdo)

v0.7.2

1 year ago

:construction_worker: Build System

:memo: Documentation Changes

v0.7.1

1 year ago

:sparkles: New Features

  • f02195e - Evaluation: added show option for dataset evaluation plots (commit by @muellerdo)

:bug: Bug Fixes

:white_check_mark: Tests

  • ed10587 - Evaluation: added edge case support of non-complete data for confusion matrix (commit by @muellerdo)
  • c6dae5d - XAI: added test for xai_decoder with directory interface (commit by @muellerdo)

:construction_worker: Build System

:memo: Documentation Changes

v0.7.0

1 year ago

:sparkles: New Features

:bug: Bug Fixes

  • ea04aad - Ensemble: Added missing library import in Stacking & Bagging (commit by @muellerdo)
  • cc53a57 - AutoML: changed incorrect grayscale parameter of DataGenerator in training function block (commit by @muellerdo)
  • 8b973d2 - AutoML: some hotfixes for AutoML XAI support (commit by @muellerdo)
  • 7c78357 - AutoML: incorrect output path as directory creation (commit by @muellerdo)
  • 4a23572 - AutoML: added more config parsing for CLI (3D shape, input and output path) (commit by @muellerdo)
  • c31355d - Evaluation: catch no-possible AUROC computation (commit by @muellerdo)
  • f4b165c - AutoML: fixed multiple architecture passing for advanced training (commit by @muellerdo)
  • 6729798 - Evaluation: fixed unequal length of training epochs by multi model pipelines (commit by @muellerdo)
  • c5f9712 - AutoML: forget to exluce yaml parser function in main runner (commit by @muellerdo)
  • 05169cf - XAI: added missing inverse of occlusion sensitivity heatmap (commit by @muellerdo)
  • 87e3f9d - evaluation: fix evaluate training charts (commit by @SherlockMones)
  • e474282 - Evaluation: added support for only transfer learning epochs in evaluate_fitting() (commit by @muellerdo)

:zap: Performance Improvements

  • c79110f - Ensemble: Replaced python built-in multiprocessing to pathos multiprocessing (commit by @muellerdo)
  • 816fea3 - Ensemble: Re-initialize NeuralNetworks in processes to allow custom loss functions (commit by @muellerdo)
  • ab6c0bc - Ensemble: allow dumping of ensemble output into already existing directories (commit by @muellerdo)
  • d3988a5 - AutoML: Various improvements of the function block training (commit by @muellerdo)
  • e5b8ae2 - AutoML: added sanity checks for multi_label supported metalearners (commit by @muellerdo)
  • 2b9b355 - Evaluation: call explicit categorical parsing of class names for omnious class names (numbers) (commit by @muellerdo)
  • 834799e - AutoML: switched csvlogger to append mode (commit by @muellerdo)
  • 850a6a1 - AutoML: adjusted training hyperparameters of early stopping & dynamicLR (commit by @muellerdo)
  • e3fe4ff - AutoML: increased batch size from 12 to 24 (commit by @muellerdo)
  • 3db0252 - AutoML: increased sensitivity for help page hook (commit by @muellerdo)
  • 2dea1e1 - NeuralNetwork: increased default number of transfer learning epochs to 10 (commit by @muellerdo)

:recycle: Refactors

:white_check_mark: Tests

:construction_worker: Build System

:memo: Documentation Changes

  • 6183d72 - Website: Modified relatives pathes of Home page for gh-pages (commit by @muellerdo)
  • 5fcf2fe - Website: fixes contribution image on website (commit by @muellerdo)
  • 7787ff8 - Reference: added Zenodo link (commit by @muellerdo)
  • 5e9041d - PyPI-README: Fixed broken link of logo (commit by @muellerdo)
  • 3049080 - Website: fixed incorrect getting started link from README (commit by @muellerdo)
  • e9f160e - Website: added site_url to mkdocs.yml - fixes broken 404 pages (commit by @muellerdo)
  • b72e728 - Website: Moved workflow figure to separate nav tab (commit by @muellerdo)
  • 8c3408e - Evaluate: Fix incorrect example in Comparison (commit by @muellerdo)
  • 0fdab3a - Reference: Added ORCID for Simone Mayer (commit by @muellerdo)
  • 1edb7fb - AutoML: fixed incorrect comment in training block function (commit by @muellerdo)
  • 4ed4995 - AutoML: Added docstrings to train and predict function blocks (commit by @muellerdo)
  • 4522abe - AutoML: improved cli help documentation for prediction (commit by @muellerdo)
  • 1b8f2bd - DataGenerator: enhanced warning info of passing expected DataGenerator parameters (commit by @muellerdo)
  • 8ecce74 - DataGenerator: added passing of model meta parameters to DataGenerator examples - closes #149 (commit by @muellerdo)
  • 2d3a589 - AutoML: added documentation base structure for AutoML (commit by @muellerdo)
  • faf7d26 - README: Updated README quick start example (commit by @muellerdo)
  • 1604fa1 - AutoML: started on AutoML quick start docs (commit by @muellerdo)
  • 333677d - AutoML: added AutoML Quick Start & updated framework Quick Start (commit by @muellerdo)
  • fcebb7b - AutoML: refactoring AutoML docs structure (commit by @muellerdo)
  • 045c1c9 - Roadmap: updated status by adding AutoML support (commit by @muellerdo)
  • fbffc3b - AutoML: updated installation docs (commit by @muellerdo)
  • 75b724d - AutoML: added Dataset description for AutoML (commit by @muellerdo)
  • 07debab - AutoML: fixed a broken image link in AutoML Dataset (commit by @muellerdo)
  • 5ed641a - AutoML: added AutoML overview page (commit by @muellerdo)
  • 813cae2 - AutoML: added docs for AutoML parameters (commit by @muellerdo)
  • 6e66125 - AutoML: implemented introductions to AutoML interfaces Docker & CLI (commit by @muellerdo)
  • bdd4581 - Metaleaner: added warning about multi-label support to Metalearner submodule (commit by @muellerdo)
  • e6348e5 - Ensemble: added warnings for automatic DataGenerator parameter estimation in Stacking & Composite (commit by @muellerdo)
  • b569043 - AutoML: added usage page for AutoML CLI (commit by @muellerdo)
  • 6a42c24 - AutoML: changed code block formats (commit by @muellerdo)
  • 729fc1b - AutoML: implemented AutoML usage docs for Docker (commit by @muellerdo)
  • 4421c99 - AutoML: changed file structure visualization in AutoML usage docs for CLI (commit by @muellerdo)
  • b4048dc - Examples: updated docs for examples (commit by @muellerdo)
  • 1be3a93 - AutoML: added documentation for AutoML API reference (commit by @muellerdo)
  • 3593d79 - Roadmap: checked AutoML docs as milestone on roadmap (commit by @muellerdo)
  • fe557d1 - IO_Loader: fixed mapping of io loader to description in table (commit by @muellerdo)

v0.6.1

1 year ago

:construction_worker: Build System

  • bc2104f - Unittesting: Renamed GitHub Action workflow for package building (commit by @muellerdo)
  • bc34d09 - Code-Quality: Refactored code coverage GitHub Action workflow (commit by @muellerdo)
  • 34bde90 - Code-Quality: Added GitHub Action commitlint for commit convention checking (commit by @muellerdo)
  • f226d89 - Code-Quality: currently disabling commitlint (commit by @muellerdo)
  • 43f6c8a - Code-Quality: added configuration file for commitlint (commit by @muellerdo)
  • 67c6d9b - Updated to version 0.6.1 for Zenodo release (commit by @muellerdo)

v0.6.0

1 year ago

:sparkles: New Features

  • de02965 - Bagging: Implemented training process for Bagging (also closes #121) (commit by @muellerdo)
  • c7cbc8e - Bagging: Implemented Bagging training in separate Processes to avoid any garbage collection issues (commit by @muellerdo)
  • c9ed177 - Bagging: Implemented Bagging inference functionality (commit by @muellerdo)
  • f78bba3 - Bagging: Implemented Bagging dump (result storage) functionality (commit by @muellerdo)
  • 41c4114 - Bagging: Implemented Bagging load (re-using result directory) functionality (commit by @muellerdo)
  • 7014130 - Metalearner: Started working on Metalearners for later usage in Stacking (commit by @muellerdo)
  • cdf9f54 - Metalearner: Implemented abstract base class for Metalearner (commit by @muellerdo)
  • 168116f - Stacking: Implemented ensemble learning technique Stacking (commit by @muellerdo)
  • 633af82 - Metalearner: Implemented Metalearner Logistic Regression (commit by @muellerdo)
  • 726c6f2 - Metalearner: Implemented Metalearner: Naive Bayes (commit by @muellerdo)
  • b7d5548 - Metalearner: Added Metalearner Support Vector Machine (commit by @muellerdo)
  • d07b12d - Metalearner: Added Metalearner Gaussian Process (commit by @muellerdo)
  • 85b861b - Metalearner: Added Metalearner Decision Tree (commit by @muellerdo)
  • 54d6f4e - Metalearner: Added Metalearner Best Model (commit by @muellerdo)
  • 162b977 - Metalearner: Added Metalearner Weighted Mean (commit by @muellerdo)
  • be429f6 - Metalearner: Added Random Forest - Contributes to #129 (commit by @muellerdo)
  • 817e02d - Metalearner: Added k-Nearest Neighbors - Contributes to #129 (commit by @muellerdo)
  • b66de88 - Metalearner: Added MLP Neural Network - Contributes to #129 (commit by @muellerdo)
  • 205dd12 - Aggregate: Added Global Argmax - Contributes to #129 (commit by @muellerdo)
  • 09d4b13 - Classifier: Removed two_dim parameter from Classifier (commit by @muellerdo)
  • 2c8f13a - Architectures: Started working on Vision Transformer (commit by @muellerdo)
  • 33068ac - Architectures: Implemented Vision Transformer Architecture (commit by @muellerdo)
  • 32a43d1 - Utils: Added utility function for parsing CSVLogger fitting file to fitting dictionary (commit by @muellerdo)
  • da69ac2 - Evaluation: Implemented fitting curve plotting (commit by @muellerdo)
  • 393274f - Evaluation: Started implementing performance evaluation (commit by @muellerdo)
  • 2962aa3 - Evaluation: Fully implemented performance evaluation (commit by @muellerdo)
  • 1c80fdd - Evaluation: Added unittesting for performance evaluation (commit by @muellerdo)
  • 0cdc6bd - Evaluation: Implemented comparison evaluation function (commit by @muellerdo)
  • 4f90c5c - Ensemble: Added return_ensemble feature for Stacking and Bagging predictions. (commit by @muellerdo)
  • c2c1a33 - Evaluation: Added returning merged and gain dataframe in Comparison Evaluation (commit by @muellerdo)
  • 8da7c53 - Evaluation: Added dataset analysis evaluation function (commit by @muellerdo)

:bug: Bug Fixes

  • d764ff9 - Bagging: Force setting multiprocessing start option which solves multi-assignment (commit by @muellerdo)
  • 00cefe4 - Bagging: Removed unittests for deprecated model_list variable in Bagging initialization (commit by @muellerdo)
  • 275b0b8 - Bagging: Fixed incorrect DataGenerator parameter mapping in predict function (commit by @muellerdo)
  • 72794df - Metalearner: Fixed postprocessing of Decision Tree prediction (commit by @muellerdo)
  • 546c07b - Website: Fixed 'funky' first item on landing page - Closes #106 (commit by @muellerdo)
  • 2584e78 - Website: Hotfix of new introduced bug with previous commit (commit by @muellerdo)
  • e44916b - Architectures: Fixed incorrect input shapes for B16 and B32 Vision Transformer Architecture (commit by @muellerdo)
  • 1b554cc - Evaluation: Fixed suffix=None usage in evaluate_fitting() (commit by @muellerdo)
  • c8ce20d - Classifier: Removed deprecated two_dim parameter from unittesting (commit by @muellerdo)

:zap: Performance Improvements

  • c5d3131 - DataGenerator: Enhanced temporary dictionary management for prepare_images - Closes #120, #10 (commit by @muellerdo)

:recycle: Refactors

  • 2e25ddb - Bagging: Removed redundant deepcopy module dependency (commit by @muellerdo)
  • 8e3eaae - Metalearner: Changed Metalearner training and prediction function to train() and predict() (commit by @muellerdo)
  • d3488ca - Evaluation: Removed redundant plot submodule file (commit by @muellerdo)
  • 0a417d7 - Remove inconsistency of class naming (now following PEP8) - Closes #138 (commit by @muellerdo)

:white_check_mark: Tests

  • e87c8e9 - Bagging: Implemented unittesting for Bagging training and inference (commit by @muellerdo)
  • 2110666 - Bagging: Implemented unittesting for Bagging dump() (commit by @muellerdo)
  • efbc889 - Bagging: Implemented unittesting for Bagging load function (commit by @muellerdo)
  • 1e7056e - Stacking: Added unittesting for Stacking (commit by @muellerdo)
  • decde32 - Metalearner: Added unittesting for Metalearners - Closes #127 (commit by @muellerdo)
  • ddc6ef0 - Aggregate: Added unittesting for Global Argmax (commit by @muellerdo)
  • 384334d - Architectures: Added unittesting for Vision Transformer (commit by @muellerdo)
  • 0fb98a2 - Utils: Added unittesting for csv2history (commit by @muellerdo)
  • 182774c - Evaluation: Implemented unittesting for fitting curve plotting (commit by @muellerdo)
  • b66bab7 - Evaluation: Implemented unittesting for evaluate_comparison() (commit by @muellerdo)
  • d6fd5f3 - Evaluation: Implemented unittesting for evaluate_dataset() (commit by @muellerdo)
  • da49ee3 - Evaluation: Implemented unittesting for evaluate_dataset() (commit by @muellerdo)
  • 1b9031e - Architectures: Removed ViT architecture testing due to too heavy RAM requirements (commit by @muellerdo)
  • 4524b30 - Neural_Network: Added unittesting for model.predict() (commit by @muellerdo)

:construction_worker: Build System

  • 1f38ce5 - Architectures: Added module dependency vit-keras (commit by @muellerdo)
  • 4b6c89c - Evaluation: Added plotnine module dependency (commit by @muellerdo)
  • 3376920 - Architectures: Added Tensorflow Addons as dependency for ViT Architecture (commit by @muellerdo)
  • d0544a3 - Requirements: Set minimum and debugging version of Tensorflow Addons to 0.16.1 (commit by @muellerdo)
  • 686efc9 - Tensorflow: Added fixed version of protobuf to requirement dependencies due to global major release break (commit by @muellerdo)
  • b85e23a - Release: Added automatic CHANGELOG creation - Closes #113 (commit by @muellerdo)

:memo: Documentation Changes

:wrench: Chores

  • 20217ad - Classifier: Removed the two_dim parameter in all Classifier.build() calls (commit by @muellerdo)
  • 9cf93d2 - Package: Update to version 0.6.0 (commit by @muellerdo)

:boom: BREAKING CHANGES

  • due to 0a417d7 - Remove inconsistency of class naming (now following PEP8) - Closes #138 (commit by @muellerdo):

    Remove inconsistency of class naming (now following PEP8) - Closes #138

v0.5.2

2 years ago

Fixed metadata support for Augmenting.