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--- a +++ b/CHANGELOG.rst @@ -0,0 +1,956 @@ +Changelog +========= + +All notable changes to this project will be documented in this file. + +The format is based on `Keep a +Changelog <https://keepachangelog.com/en/1.1.0/>`__, and this project +adheres to `Semantic +Versioning <https://semver.org/spec/v2.0.0.html>`__. + +`Unreleased <https://github.com/DeepPSP/torch_ecg/compare/v0.0.31...HEAD>`__ +---------------------------------------------------------------------------- + +Added +~~~~~ + +Changed +~~~~~~~ + +- Make the function `remove_spikes_naive` in `torch_ecg.utils.utils_signal` + support 2D and 3D input signals. + +Deprecated +~~~~~~~~~~ + +Removed +~~~~~~~ + +Fixed +~~~~~ + +- Correctly update the `_df_metadata` attribute of the `PTBXL` database reader + classes after filtering records. +- Enhance the `save` method of the `torch_ecg.utils.utils_nn.CkptMixin` class: + non-safe items in the configs are removed before saving the model. +- Fix errors when monitor is specified while the validation dataloader is not + provided in the `torch_ecg.components.BaseTrainer` class. +- Enhance the `save_checkpoint` method of the `torch_ecg.components.BaseTrainer` class: + non-safe items in the configs are removed before saving the model. + +Security +~~~~~~~~ + +`0.0.31 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.30...v0.0.31>`__ - 2025-01-28 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add functions for downloading PhysioNet data from AWS S3. It is now made + the default way to download data from PhysioNet. +- Add ``easydict`` as a dependency for backward compatibility (loading + old models using safe-mode ``torch.load`` with ``weights_only=True``. + Extra dependencies are added with + ``torch.serialization.add_safe_globals``). + +Changed +~~~~~~~ + +- Test files (in the ``sample-data`` directory) are updated. +- Add keyword argument ``weights_only`` to ``from_checkpoint`` and + ``from_remote`` methods of the models (indeed the ``CkptMixin`` + class). The default value is ``"auto"``, which means the behavior is + the same as before. It checks if ``torch.serialization`` has + ``add_safe_globals`` attribute. If it does, it will use safe-mode + ``torch.load`` with ``weights_only=True``. Otherwise, it will use + ``torch.load`` with ``weights_only=False``. + +Deprecated +~~~~~~~~~~ + +- Support for Python 3.7, 3.8 is deprecated. The minimum supported Python + version is now 3.9. In the ``pyproject.toml`` file, the field + ``requires-python`` is updated from ``>=3.7`` to ``>=3.9``. + +Removed +~~~~~~~ + +- Restrictions on the version of ``wfdb`` and ``numpy`` packages are + removed. + +Fixed +~~~~~ + +- Fix IO issues with several PhysioNet databases. + +Security +~~~~~~~~ + +- Models are now loaded using safe-mode ``torch.load`` with + ``weights_only=True`` by default. + +`0.0.30 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.29...v0.0.30>`__ - 2024-10-10 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add support for AWS S3 in the download utility function ``http_get`` + in the ``torch_ecg.utils.download`` module. PhysioNet now provides + data download links from AWS S3, and the download utility function + can now handle these links if AWS CLI is installed. This feature is + implemented but not put into use yet. + +Changed +~~~~~~~ + +- Change the default value of the ``method`` argument of the + ``torch_ecg.utils.utils_signal.resample_irregular_timeseries`` function + from ``"spline"`` to ``"interp1d"``. The former is probably not + correctly implemented. +- Update the logger classes: add checking of the write access of the + ``log_dir``. If the directory is not writable, the default log dir + ``~/.cache/torch_ecg/logs`` is used (ref. ``torch_ecg.cfg.DEFAULTS.log_dir``). +- Update the selection mechanism of the final model for the trainer + classes: if no monitor is specified, the last model is selected by + default (previously, no model was selected and saved). +- The main part of the ``_setup_criterion`` method of the ``BaseTrainer`` + class is moved to the function ``setup_criterion`` in the + ``torch_ecg.models.loss`` module. The method is simplified and + enhanced. + +Deprecated +~~~~~~~~~~ + +- Script ``setup.py`` is deprecated. The package building system is + switched to ``hatch``. + +Removed +~~~~~~~ + +- Remove redundancy in base trainer classes: identical ``if`` blocks + are removed from the ``_setup_criterion`` method of the ``BaseTrainer`` + class. + +Fixed +~~~~~ + +- Fix potential error in getting model name in the trainer classes. +- Fix bugs in the ``CINC2020`` and ``CINC2021`` database reader classes + for parsing the header files. + +`0.0.29 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.28...v0.0.29>`__ - 2024-07-21 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add keyword argument ``with_suffix`` to function + ``torch_ecg.utils.misc.get_record_list_recursive3``. +- Add function ``_download_from_google_drive`` to the + ``torch_ecg.utils.download`` module for downloading files from Google + Drive. +- Add ``gdown`` as a dependency in the ``requirements.txt`` file. +- Add database reader class ``PTBXLPlus`` for the PTB-XL+ database in + ``torch_ecg.databases.physionet_databases``. +- Add github-release job to the publish action for creating a release + on GitHub automatically. + +Changed +~~~~~~~ + +- Improve the main training loop method of the base trainer class + ``torch_ecg.components.trainers.BaseTrainer``. +- Allow passing additional keyword arguments to pass to ``requests.head`` + in the ``url_is_reachable`` function of the ``torch_ecg.utils.download`` + module (via adding the ``**kwargs`` argument). +- Restrict version of ``numpy`` to be ``<=2.0.0`` in the + ``requirements.txt`` file. ``numpy`` version ``2.0.0`` is a breaking + update, and a large proportion of the dependencies of this project + are not compatible with it yet. +- Enhance the ``cls_to_bin`` function and rename it to ``one_hot_encode`` + in the ``torch_ecg.utils.utils_data`` module. + +Fixed +~~~~~ + +- Enhance compatibility for different ``pandas`` versions. +- Fix errors for taking length of an empty database reader class. + +Security +~~~~~~~~ + +- Fix code scanning alert - Incomplete regular expression for hostnames + `#21 <https://github.com/DeepPSP/torch_ecg/pull/21>`__. +- Fix code scanning alert - Incomplete URL substring sanitization + `#23 <https://github.com/DeepPSP/torch_ecg/pull/23>`__. + +`0.0.28 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.27...v0.0.28>`__ - 2024-04-02 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add CD workflow for the publish action with GitHub Action. +- Add an optional argument ``return_fs`` for the ``load_data`` + method for the database reader classes. If ``True``, the sampling + frequency of the record is returned along with the data as a tuple. + To keep the behavior consistent, the default value is ``False``. +- Add an optional parameter ``fs`` for the function ``compute_receptive_field`` + in the ``torch_ecg.utils.utils_nn`` module. If ``fs`` is provided, the + receptive field is computed based on the sampling frequency. +- Add method ``compute_receptive_field`` for several convolutional neural + network models (layers) in the ``torch_ecg.models._nets`` module. +- Add helper function ``make_serializable`` in the ``torch_ecg.utils.misc`` + module for making an object serializable (with the ``json`` package). + It will convert all ``numpy`` arrays to ``list`` in an object, and + also convert ``numpy`` data types to python data types in the object + recursively. +- Add helper function ``url_is_reachable`` in the ``torch_ecg.utils.download`` + module for checking if a URL is reachable. +- Add database reader class ``PTBXL`` for the PTB-XL database in + ``torch_ecg.databases.physionet_databases``. +- Add class method ``from_remote`` for ``CkptMixin`` classes. It is used + to load a model from a remote location (e.g., a URL) directly. +- Add ``sphinx-emoji-favicon`` as a dependency for generating the favicon + for the documentation. +- Add utility function ``ecg_plot`` from + `ecg-image-kit <https://github.com/alphanumericslab/ecg-image-kit/.>`__. +- Add ``pyarrow`` as a dependency in the ``requirements.txt`` file. +- Add benchmark study ``train_crnn_cinc2023`` for the CinC2023 challenge. + +Changed +~~~~~~~ + +- Change the default value ``reset_index`` of the utility function + ``torch_ecg.utils.utils_data.stratified_train_test_split`` from + ``True`` to ``False``. +- Enhance the decorator ``torch_ecg.utils.misc.add_kwargs`` so that + the signature of the decorated function is also updated. +- Update the documentation: use ``sphinx_toolbox.collapse`` and + ``sphinxcontrib.bibtex``; add citation info in the index page. +- Make ``Dataset`` classes accept slice index for the ``__getitem__`` + method. + +Deprecated +~~~~~~~~~~ + +- Support for Python 3.6 is deprecated. The minimum supported Python + version is updated to 3.7. + +Removed +~~~~~~~ + +- Remove broken links in the docstrings of the database reader classes. +- Remove unused scripts ``formatting.sh`` and ``push2pypi.sh``. + +Fixed +~~~~~ + +- Fix errors in the decorator ``torch_ecg.utils.misc.add_kwargs`` + when a bound method is decorated. +- Fix bugs related to data overflow for preprocessor classes that + work with ``numpy`` arrays as reported in issue + `#12 <https://github.com/DeepPSP/torch_ecg/issues/12>`__. +- Fix bugs in augmentor class ``StretchCompress`` in the + ``torch_ecg.augmenters`` module. +- Fix dtype error when calling ``compute_class_weight`` from + ``sklearn.utils``. +- Fix the issue when handling nan values in in computing metrics. +- Fix errors for the ``ApneaECG`` database reader class when passing + a path that does not exist or a path that contains no records at + initialization. + +`0.0.27 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.26...v0.0.27>`__ - 2023-03-14 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add default configs for blocks of the ``ResNet`` model in the + ``torch_ecg.models.cnn`` module. +- Add ``RegNet`` model in the ``torch_ecg.models.cnn`` module. +- Add ``CutMix`` augmentor in the ``torch_ecg.augmenters`` module. +- Add support for ``torch.nn.Dropout1d`` in the models. +- Add ``.readthedocs.yml`` to the project. The documentation is + now hosted on Read the Docs besides GitHub Pages. + +Changed +~~~~~~~ + +- Move ``torch_ecg.utils.preproc`` to ``torch_ecg.utils._preproc``. +- Allow ``embed_dim`` of ``SelfAttention`` layer not divisible by + ``num_heads`` via adding a linear projection layer before the + multi-head attention layer. +- Documentation is largely improved. + +Deprecated +~~~~~~~~~~ + +- Drop compability for older versions of ``torch`` (1.5 and below). + +Removed +~~~~~~~ + +- Remove ``protobuf`` from the ``requirements.txt`` file. +- Clear unused methods in the ``CINC2020`` and ``CINC2021`` database + reader classes. +- Clear unused layers in the ``torch_ecg.models._nets`` module. +- Remove the ``torch_ecg.utils._pantompkins`` module. It contains + the implementation of the Pan-Tompkins algorithm for QRS detection, + modified from old versions of the ``wfdb`` package. It is moved to + the ``legacy`` folder of the project. +- Remove ``WandbLogger`` class from the ``torch_ecg.components.loggers`` + module. + +Fixed +~~~~~ + +- Fix bugs when passing ``units=None`` for the ``load_data`` method + of the PhysioNet database reader classes. + +`0.0.26 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.25...v0.0.26>`__ - 2022-12-25 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add a default ``load_data`` method for physionet databases reader + classes in the base class ``PhysioNetDataBase``. In most cases, + in the inherited classes, one does not need to implement the + ``load_data`` method, as the default method is sufficient. This + method is a slight improvement over ``wfdb.rdrecord``. +- Add decorator ``add_kwargs`` in the ``torch_ecg.utils.misc`` module + for adding keyword arguments to a function or method. +- Add functions ``list_databases``, ``list_datasets`` in the + ``torch_ecg.datasets`` module for listing available databases reader + classes and ``Dataset`` classes. +- Add ``save`` method for the ``CkptMixin`` class. It is used to save + the model to a file. +- Add ``_normalize_leads`` a method of the base ``_DataBase`` class + in the ``torch_ecg.databases.base`` module. It is used to normalize + the names of the ECG leads. +- Add subsampling functionality for database reader classes. +- Add benchmark study ``train_mtl_cinc2022`` for the CinC2022 challenge. +- Add ``CITATIONS.bib`` file for storing BibTeX entries of the + papers related to the project. +- Add 10 sample data from the CPSC2018 database for testing in the + ``sample-data`` directory. + +Changed +~~~~~~~ + +- Use ``CitationMixin`` from the ``bib-lookup`` package as the base + class for the ``DataBaseInfo`` class in ``torch_ecg.databases.base``. +- Use ``CitationMixin`` as one of the base classes for the models + in ``torch_ecg.models``. +- Allow dummy (empty) preprocessor managers, a warning instead of an + error is raised in such cases. +- Enhance error message for the computation of metrics. +- Add keyword argument ``requires_grad`` and ``include_buffers`` to + the ``torch_ecg.utils.utils_nn.compute_module_size`` function. + The ``dtype`` argument is removed as the data type of the model + is now inferred from the model itself. +- Improve several database reader classes: ``CPSC2018``, ``CPSC2021``, + ``CINC2017``, ``ApneaECG``, ``MITDB``, ``SPH``. +- Add asymmetric zero pad for convolution layers, so that when + ``stride = 1`` and ``kernel_size`` is even, strict ``"same"`` + padding is conducted. +- Use loggers instead of ``print`` in database reader classes. +- Integrate code coverage into the CI workflow. The coverage report + is generated and uploaded to Codecov. +- More unit tests are added, and the existing ones are updated. + Code coverage is largely improved. + +Deprecated +~~~~~~~~~~ + +- Drop compatibility for ``tqdm`` < 4.29.1 + +Removed +~~~~~~~ + +- Remove unused rpeaks detection methods in the ``torch_ecg.utils.rpeaks`` + module. +- Remove ``_normalize_leads`` method in ``LUDB`` database reader class. +- Remove unused functions in the file of the ``CPSC2020`` database reader + class. + +Fixed +~~~~~ + +- Fix bugs in the config class ``torch_ecg.cfg.CFG``. +- Fix errors in the ``plot`` method of ``CINC2020`` and ``CINC2021`` + database reader classes. + +Security +~~~~~~~~ + +- `CVE-2007-4559 <https://github.com/advisories/GHSA-gw9q-c7gh-j9vm>`__ + patch: Fix a potential security vulnerability in the + ``torch_ecg.utils.download.http_get`` function. + +`0.0.25 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.23...v0.0.25>`__ - 2022-10-08 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add docstring utility function ``remove_parameters_returns_from_docstring`` + in ``torch_ecg.utils.misc``. +- Add abstract property ``database_info`` to the base class ``_DataBase`` in + ``torch_ecg.databases.base`` so that when implementing a new database reader + class that inherits from the base class, its ``DataBaseInfo`` must be + implemented and assigned to the property. +- Add method ``get_citation`` to the base abstract class ``_DataBase`` in + ``torch_ecg.databases.base`` which enhances the process for getting citations + for the databases. +- Add database reader class ``CACHET_CADB`` for the CACHET-CADB database in + ``torch_ecg.databases.other_databases``. +- Add ``download`` method for the base abstract class ``CPSCDataBase`` in + ``torch_ecg.databases.base``. + +Changed +~~~~~~~ + +- Improve the warning message for passing an non-existing path when + initializing a database reader class. +- Change the default behavior of the ``download`` method for + ``PhysioNetDataBase`` class: default to download the compressed + version of the database. +- Update the ``README`` file in the ``torch_ecg/databases`` directory. + +Fixed +~~~~~ + +- Use ``register_buffer`` in custom loss classes for constant tensors + to avoid potential device mismatch issues. +- Rename and update the data file ``physionet_dbs.csv.tar.gz`` to + ``physionet_dbs.csv.gz`` to comply with the changement of the + ``pandas.read_csv`` function from version 1.4.x to 1.5.x. +- Fix the incorrect usage of ``NoReturn`` type hints. It is replaced + with ``None`` to indicate that the function/method does not return + anything. + +0.0.24 - 2022-08-13 [YANKED] +----------------------------- + +This release was yanked. + +`0.0.23 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.22...v0.0.23>`__ - 2022-08-09 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add ``collate_fn`` as an optional argument for ``BaseTrainer`` class + in ``torch_ecg.components.trainers``. + +Changed +~~~~~~~ + +- Let ``db_dir`` attribute of the database reader classes be absolute + when instantiated, to avoid potential ``pathlib`` errors. +- Update utility function `torch_ecg.utils.utils_nn.adjust_cnn_filter_lengths``: + avoid assigning unnecessary fs to dict-type config items; change default + value of the ``pattern`` argument from ``"filter_length|filt_size"`` to + ``"filter_length|filter_size"`` to avoid unintended changement of configs + for ``BlurPool`` (in ``torch_ecg.models._nets``). +- Enhance error message for ``BlurPool`` in ``torch_ecg.models._nets``. + +`0.0.22 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.21...v0.0.22>`__ - 2022-08-05 +---------------------------------------------------------------------------------------- + +Changed +~~~~~~~ + +- Make utility function ``torch_ecg.utils.utils_data.default_collate_fn`` + support ``dict`` type batched data. +- Update docstrings of several metrics utility functions in + ``torch_ecg.utils.utils_metrics``. + +`0.0.21 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.20...v0.0.21>`__ - 2022-08-01 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add utility function ``get_kwargs`` in ``torch_ecg.utils.misc`` for + getting (keyword) arguments from a function/method. +- Add AHA diagnosis statements in ``torch_ecg.databases.aux_data``. +- Add argument ``reset_index`` to the utility function + ``torch_ecg.utils.utils_data.stratified_train_test_split``. +- Add ``typing-extensions`` as a dependency in the ``requirements.txt`` + file. +- Add database reader class ``QTDB`` for the QTDB database in + ``torch_ecg.databases.physionet_databases``. + +Changed +~~~~~~~ + +- Enhance data handling (typicall when using the ``load_data`` method of + the database reader classes) with precise dtypes via + ``torch_ecg.cfg.DEFAUTLS``. +- Update the setup of optimizer for the base trainer class + ``torch_ecg.components.trainers.BaseTrainer``. +- Update the ``DataBaseInfo`` class for the ``SPH`` database. +- Update the ``README`` file in the ``torch_ecg/databases`` directory. +- Update plotted figures of the benchmark studies. +- Rename ``SequenceLabelingOutput`` to ``SequenceLabellingOutput`` + (typo fixed) in the ``torch_ecg.components.outputs`` module. +- Enhance docstring of ``LUDB`` database reader class via updating its + ``DataBaseInfo`` class. +- Append the ``_ls_rec`` method as the last step in the ``download`` + method of the database reader classes. +- Change ``torch_ecg.utils.utils_data.ECGWaveForm`` from a ``namedtuple`` + to a ``dataclass``. + +Removed +~~~~~~~ + +- ``bib_lookup.py`` is removed from the project. It is now delivered in + an isolated package ``bib_lookup`` published on PyPI, and added as a + dependency in the ``requirements.txt`` file. +- Remove unnecessary script ``exec_git.py``. +- Remove ``joblib`` in the ``requirements.txt`` file. + +`0.0.20 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.19...v0.0.20>`__ - 2022-06-15 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add database reader class ``SPH`` for the SPH database in + ``torch_ecg.databases.other_databases``. +- Add ``dataclass`` ``DataBaseInfo`` for storing information of a + database. It has attributes ``title``, ``about``, ``note``, + ``usage``, ``issues``, ``reference``, etc., and has a method + ``format_database_docstring`` for formatting the docstring of a + database reader class. The generated docstring can be assigned to + corresponding database reader class via the ``add_docstring`` + decorator (in ``torch_ecg.utils.misc``). +- Add default cache directory ``~/.cache/torch_ecg`` for storing + downloaded data files, model weight files, etc. +- Add helper function ``is_compressed_file`` for checking if a file is + compressed in ``torch_ecg.utils.download``. + +`0.0.19 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.18...v0.0.19>`__ - 2022-06-09 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add argument ``relative`` to the utility function ``get_record_list_recursive3``. +- Add attribute ``_df_records`` to the database reader classes. The attribute + stores the DataFrame of the records of the database, containing paths to the + records and other information (labels, demographics, etc.). + +Fixed +~~~~~ + +- Fix bugs in the download utility function ``http_get``. +- Fix bugs in the database reader classe ``CPSC2021``. + +`0.0.18 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.16...v0.0.18>`__ - 2022-06-05 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add property ``in_channels`` for the models.The number of input channels + is stored as a private attribute ``_in_channels``, and the property + ``in_channels`` makes it easier to access the value. +- Add warning message to the ``download`` method of the ``CPSC2019`` database + reader class. +- Add ``get_absolute_path`` method for the database reader classes to + uniformly handle the path operations. + +Changed +~~~~~~~ + +- All all absolute imports are replaced with relative imports. +- Update citation and images for several benchmark studies +- Update the ``downlaod`` link for the ``CPSC2019`` database reader class + (ref. property ``torch_ecg.databases.CPSC2019.url``). + +Removed +~~~~~~~ + +- Remove the ``torch_ecg.utils.misc.deprecate_kwargs`` decorator. It is + delivered in an isolated package ``deprecate_kwargs`` published on PyPI, + and added as a dependency in the ``requirements.txt`` file. + +Fixed +~~~~~ + +- Fix errors in the ``_ls_rec`` method of the ``CPSC2019`` database reader + class. +- Fix bugs in the ``torch_ecg.utils.misc.deprecate_kwargs`` decorator. +- Fix the issue that ``tensorboardX`` is incompatible with the latest version + of ``protobuf``. + +0.0.17 - 2022-05-03 [YANKED] +----------------------------- + +This release was yanked. + +`0.0.16 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.15...v0.0.16>`__ - 2022-04-28 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add method ``_categorize_records`` for the ``MITDB`` database reader class, + categorize records by specific attributes. Related helper properties + ``beat_types_records`` and ``rhythm_types_records`` are added. +- Add method ``_aggregate_stats`` for the ``MITDB`` database reader class. + Related helper properties ``df_stats`` and ``db_stats`` are added. +- Add function ``cls_to_bin`` for converting categorical (typically multi-label) + class labels to binary class labels (2D array with 0/1 values). +- Add context manager ``torch_ecg.utils.misc.timeout`` for setting a timeout for + a block of code. +- Add context manager ``torch_ecg.utils.misc.Timer`` to time the execution of + a block of code. +- Add module ``torch_ecg.components.inputs`` for input data classes. +- Add class ``Spectrogram`` (in ``torch_ecg.utils``) for generating spectrogram + input data. This class is modified from the ``torchaudio.transforms.Spectrogram``. +- Add decorator ``torch_ecg.utils.misc.deprecate_kwargs`` for deprecating keyword + arguments of a function/method. +- Top-level module ``torch_ecg.ssl`` for self-supervised learning methods and + models is introduced, but not implemented yet. +- Add helper function ``torch_ecg.utils.utils_nn.compute_sequential_output_shape`` + to simplify the computation of output shape of sequential models. +- ``mobilenet_v3`` model is added to the ``torch_ecg.models`` module. It is + now available as a cnn backbone choice for the ``ECG_CRNN`` model (and for other + downstream task models). + +Changed +~~~~~~~ + +- Use ``numpy``'s default ``rng`` for random number generation in place + of ``np.random`` and Python built-in ``random`` module. +- Update the ``README`` file. +- Move the function ``generate_weight_mask`` from ``CPSC2021`` dataset + to ``torch_ecg.utils.utils_data``. +- Database reader ``MITDB`` is enhanced: add properties ``df_stats_expanded``; + add arguments ``beat_types`` and ``rhythm_types`` to the data and annotation + loading methods. +- Downloading function ``http_get`` is enhanced to support downloading + normal files other than compressed files. +- Update ``__init__`` file of the ``torch_ecg.utils`` module. +- Database reader class ``CinC2017`` is updated: add property ``_validation_set``. +- The ``ECG_UNET`` model is simplified by removing the unnecessary zero padding + along the channel axis. +- Update the ``README`` file. + +Deprecated +~~~~~~~~~~ + +- Keyword argument ``batch_norm`` in model building blocks (ref. ``torch_ecg.models``) + is deprecated. Use ``norm`` instead. + +Removed +~~~~~~~ + +- Redundant functions in ``torch_ecg.utils.utils_interval`` are removed: + ``diff_with_step``, ``mask_to_intervals``. + +Fixed +~~~~~ + +- Remove redudant code for the ``ECG_UNET`` model which might cause error in + computing output shapes. + +`0.0.15 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.14...v0.0.15>`__ - 2022-04-14 +---------------------------------------------------------------------------------------- + +Changed +~~~~~~~ + +- Use ``pathlib.Path.parents`` instead of sequence of ``pathlib.Path..parent`` + to get the parent directory of a file path. +- Type hints and docstrings of some database reader classes are enhanced: + ``ApneaECG``, ``CINC2020``, ``CINC2021``. +- Update the ``README`` file: add citation information for the package. + +`0.0.14 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.13...v0.0.14>`__ - 2022-04-10 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Implements the lead-wise mechanism (as a method ``_assign_weights_lead_wise``) + for the ``Conv_Bn_Activation`` layer in the ``torch_ecg.models._nets`` module. +- Implements ``assign_weights_lead_wise`` for model ``MultiScopicCNN`` + (in ``torch_ecg.models``). +- Zenodo configuration file ``.zenodo.json`` is added. + +Changed +~~~~~~~ + +- Update the ``README`` file: add ``:point_right: [Back to TOC](#torch_ecg)`` + to the end of long sections. + +Fixed +~~~~~ + +- Fix errors in the computation of classification metrics. + +`0.0.13 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.12...v0.0.13>`__ - 2022-04-09 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add metrics computation class ``WaveDelineationMetrics`` for evaluating the + performance of ECG wave delineation models. +- Add methods for computing the metrics to the output classes (in the module + ``torch_ecg.components.outputs``). +- Add script ``push2pypi.sh`` for pushing the package to PyPI. +- Add attribute ``global_pool_size`` to the configuration of the classification + models (``torch_ecg.models.ECG_CRNN``). + +Changed +~~~~~~~ + +- ``flake8`` check ignore list is updated. +- ``README`` is updated. + +Removed +~~~~~~~ + +- Usage of ``easydict`` is removed. Now we use ``torch_ecg.cfg.CFG`` for + configuration. + +Fixed +~~~~~ + +- Computation of the metric of `mean_error` for ECG wave delineation is corrected. +- Fix bugs in ``SpaceToDepth`` layer (``torch_ecg.models.resnet``). + +`0.0.12 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.11...v0.0.12>`__ - 2022-04-05 +---------------------------------------------------------------------------------------- + +Changed +~~~~~~~ + +- Some out-of-date ``sample-data`` files are updated, unnecessary files + are removed. +- Passing a path that does not exist to a database reader class now raises + no error, but a warning is issued instead. +- Include ``isort`` and ``flake8`` in the code formatting and linting steps. + Code are reformatted and linted. + +`0.0.11 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.10...v0.0.11>`__ - 2022-04-03 +---------------------------------------------------------------------------------------- + +Changed +~~~~~~~ + +- Docstrings are cleaned up. +- Unit tests are updated. + +`0.0.10 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.9...v0.0.10>`__ - 2022-04-01 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add ``BibLookup`` class for looking up BibTeX entries from DOIs + of papers related to datasets and models. +- Add ``RPeaksDetectionMetrics`` class to the ``torch_ecg.components.metrics`` + module for evaluating the performance of R-peaks detection models. +- Add CI workflow for running tests via GitHub Actions. + +Changed +~~~~~~~ + +- The loading methods (``load_data``, ``load_ann``, etc.) of the database + reader classes are enhanced to accept ``int`` type record name argument + (``rec``), which redirects to the record with the corresponding index + in the ``all_records`` attribute of the database reader class. + +`0.0.9 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.8...v0.0.9>`__ - 2023-03-30 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add decorator ``add_docstring`` for adding/modifying docstrings of functions + and classes. +- Add method ``append`` for the ``BaseOutput`` class. +- Add several metrics computation functions in ``torch_ecg/utils/utils_metrics.py``: + - ``confusion_matrix`` + - ``ovr_confusion_matrix`` + - ``auc`` + - ``accuracy`` + - ``f_measure`` + - ``QRS_score`` +- Add top-level module ``torch_ecg.components``. +- Add classes for metrics computation to the ``torch_ecg.components.metrics`` module. + +Changed +~~~~~~~ + +- ``Dataset`` classes and corresponding config classes are added to the + ``__init__.py`` file of the ``torch_ecg.databases.dataset`` module + so that they can be imported directly from the module. +- Logger classes, output classes, and trainer classes are moved to the new + module ``torch_ecg.components``. +- Callbacks in ``BaseTrainer`` are enhanced, allowing empty monitor, and allowing + non-positive number of checkpoints to be saved (i.e., no checkpoint is saved). + +`0.0.8 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.7...v0.0.8>`__ - 2022-03-29 +---------------------------------------------------------------------------------------- + +Fixed +~~~~~ + +- Bugs in extracting compressed files in the ``http_get`` function + of the ``utils.download`` module. + +Security +~~~~~~~~ + +`0.0.7 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.6...v0.0.7>`__ - 2022-03-28 +---------------------------------------------------------------------------------------- + +Fixed +~~~~~ + +- Import errors for early versions of pytorch. +- Cached table of PhysioNet databases is added as ``package_data`` in + ``setup.py`` to avoid the error of missing the table file when + installing the package. + +Security +~~~~~~~~ + +`0.0.6 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.5...v0.0.6>`__ - 2022-03-28 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add methods ``__len__`` and ``__getitem__`` for the base class + ``torch_ecg.databases.base._DataBase``. + +Changed +~~~~~~~ + +- The base class of ``CPSC2021`` is changed from ``CPSCDataBase`` to + ``PhysioNetDataBase``. +- Function ``compute_output_shape`` is enhanced to support different + paddings in two ends of the input signal. +- ``README`` is updated. +- Docstrings of many classes and functions are updated. +- ``black`` is used for code formatting. + +`0.0.5 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.4...v0.0.5>`__ - 2022-03-27 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add cached table of PhysioNet databases as a data file + stored in the package. +- Add ``requests`` as a dependency in the ``requirements.txt`` file. + +Changed +~~~~~~~ + +- An optional argument ``btype`` is added to the function + ``butter_bandpass_filter`` to specify the type of the filter: + ``"lohi"``, ``"hilo"``. +- A ``compressed`` argument is added to the ``download`` method of the + ``PhysioNetDataBase`` class to specify whether to download the + compressed version of the database. + +Fixed +~~~~~ + +- Fix bugs in the function ``preprocess_multi_lead_signal``. + +`0.0.4 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.2...v0.0.4>`__ - 2022-03-26 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add ``ReprMixin`` class for better representation of the classes + (e.g., models, preprocessors, database readers, etc.). +- Added model_dir to default config. +- Add ``Dataset`` classes for generating input data for the models: + - ``CINC2020`` + - ``CINC2021`` + - ``CPSC2019`` + - ``CPSC2021`` + - ``LUDB`` +- Add ``sample-data`` directory for storing sample data for testing. +- Add ``url`` property to the database classes. +- Add utility functions for the computation of metrics. +- Add ``BeatAnn`` class for better annotation of ECG beats. +- Add download utility functions. +- Add ``Output`` classes for the models. The output classes are used to + store the output of the models and provide methods for post-processing. + +Changed +~~~~~~~ + +- Manipulation of custom preprocessor classes is enhanced. +- ``SizeMixin`` class is improved for better computation of the sizes of the models. +- Replace ``os`` with ``pathlib``, which is more flexible for path operations. +- Several database reader classes are updated: mitdb, ltafdb. +- Improve ``PhysioNetDataBase`` by using wfdb built-in methods of + getting database version string and downloading the database. +- Update the ``README`` file. + +Removed +~~~~~~~ + +- Unnecessary imports are removed. + +Fixed +~~~~~ + +- Fix bugs in the ``flush`` method of the ``TxtLogger``. + +0.0.3 - 2022-03-24 [YANKED] +----------------------------- + +This release was yanked. + +`0.0.2 <https://github.com/DeepPSP/torch_ecg/releases/tag/v0.0.2>`__ - 2022-03-04 +---------------------------------------------------------------------------------------- + +Added +~~~~~ + +- Add ``Preprocessor`` classes for ECG data preprocessing (ref. + ``torch_ecg.preprocessors``). +- Add ``Augmenter`` classes for ECG data augmentation (ref. + ``torch_ecg.augmenters``). +- Add database reader classes for reading ECG data from different + sources (ref. ``torch_ecg.databases``). +- Add model classes for ECG signal analysis, including classification, + segmentation (R-peak detection, wave delineation, etc., ref. + ``torch_ecg.models``). +- Add several benchmark studies for ECG signal analysis tasks: + + - CinC2020, multi-label classification. + - CinC2021, multi-label classification. + - CPSC2019, QRS detection. + - CPSC2020, single-label classification. + - CPSC2021, single-label classification. + - LUDB, wave delineation. + + ref. the ``benchmarks`` directory of the project. +- Add documentation for the project (ref. ``docs`` directory). +- Add CodeQL action for security analysis (ref. ``.github/workflows``). +- Add unit tests for the project (ref. ``test`` directory). + +0.0.1 - 2022-03-03 [YANKED] +----------------------------- + +This release was yanked.