PyPI - careamics - Versions diffs - 0.0.19__py3-none-any.whl - Mend

careamics 0.0.19__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (279) hide show

careamics/__init__.py +24 -0
careamics/careamist.py +961 -0
careamics/cli/__init__.py +5 -0
careamics/cli/conf.py +394 -0
careamics/cli/main.py +234 -0
careamics/cli/utils.py +27 -0
careamics/config/__init__.py +66 -0
careamics/config/algorithms/__init__.py +21 -0
careamics/config/algorithms/care_algorithm_config.py +122 -0
careamics/config/algorithms/hdn_algorithm_config.py +103 -0
careamics/config/algorithms/microsplit_algorithm_config.py +103 -0
careamics/config/algorithms/n2n_algorithm_config.py +115 -0
careamics/config/algorithms/n2v_algorithm_config.py +296 -0
careamics/config/algorithms/pn2v_algorithm_config.py +301 -0
careamics/config/algorithms/unet_algorithm_config.py +91 -0
careamics/config/algorithms/vae_algorithm_config.py +178 -0
careamics/config/architectures/__init__.py +7 -0
careamics/config/architectures/architecture_config.py +37 -0
careamics/config/architectures/lvae_config.py +262 -0
careamics/config/architectures/unet_config.py +125 -0
careamics/config/configuration.py +367 -0
careamics/config/configuration_factories.py +2400 -0
careamics/config/data/__init__.py +27 -0
careamics/config/data/data_config.py +472 -0
careamics/config/data/inference_config.py +237 -0
careamics/config/data/ng_data_config.py +1038 -0
careamics/config/data/patch_filter/__init__.py +15 -0
careamics/config/data/patch_filter/filter_config.py +16 -0
careamics/config/data/patch_filter/mask_filter_config.py +17 -0
careamics/config/data/patch_filter/max_filter_config.py +15 -0
careamics/config/data/patch_filter/meanstd_filter_config.py +18 -0
careamics/config/data/patch_filter/shannon_filter_config.py +15 -0
careamics/config/data/patching_strategies/__init__.py +15 -0
careamics/config/data/patching_strategies/_overlapping_patched_config.py +102 -0
careamics/config/data/patching_strategies/_patched_config.py +56 -0
careamics/config/data/patching_strategies/random_patching_config.py +45 -0
careamics/config/data/patching_strategies/sequential_patching_config.py +25 -0
careamics/config/data/patching_strategies/tiled_patching_config.py +40 -0
careamics/config/data/patching_strategies/whole_patching_config.py +12 -0
careamics/config/data/tile_information.py +65 -0
careamics/config/lightning/__init__.py +15 -0
careamics/config/lightning/callbacks/__init__.py +8 -0
careamics/config/lightning/callbacks/callback_config.py +116 -0
careamics/config/lightning/optimizer_configs.py +186 -0
careamics/config/lightning/training_config.py +70 -0
careamics/config/losses/__init__.py +8 -0
careamics/config/losses/loss_config.py +60 -0
careamics/config/ng_configs/__init__.py +5 -0
careamics/config/ng_configs/n2v_configuration.py +64 -0
careamics/config/ng_configs/ng_configuration.py +256 -0
careamics/config/ng_factories/__init__.py +9 -0
careamics/config/ng_factories/algorithm_factory.py +120 -0
careamics/config/ng_factories/data_factory.py +154 -0
careamics/config/ng_factories/n2v_factory.py +256 -0
careamics/config/ng_factories/training_factory.py +69 -0
careamics/config/noise_model/__init__.py +12 -0
careamics/config/noise_model/likelihood_config.py +60 -0
careamics/config/noise_model/noise_model_config.py +149 -0
careamics/config/support/__init__.py +31 -0
careamics/config/support/supported_activations.py +27 -0
careamics/config/support/supported_algorithms.py +40 -0
careamics/config/support/supported_architectures.py +13 -0
careamics/config/support/supported_data.py +122 -0
careamics/config/support/supported_filters.py +17 -0
careamics/config/support/supported_loggers.py +10 -0
careamics/config/support/supported_losses.py +32 -0
careamics/config/support/supported_optimizers.py +57 -0
careamics/config/support/supported_patching_strategies.py +22 -0
careamics/config/support/supported_pixel_manipulations.py +15 -0
careamics/config/support/supported_struct_axis.py +21 -0
careamics/config/support/supported_transforms.py +12 -0
careamics/config/transformations/__init__.py +22 -0
careamics/config/transformations/n2v_manipulate_config.py +79 -0
careamics/config/transformations/normalize_config.py +59 -0
careamics/config/transformations/transform_config.py +45 -0
careamics/config/transformations/transform_unions.py +29 -0
careamics/config/transformations/xy_flip_config.py +43 -0
careamics/config/transformations/xy_random_rotate90_config.py +35 -0
careamics/config/utils/__init__.py +8 -0
careamics/config/utils/configuration_io.py +85 -0
careamics/config/validators/__init__.py +18 -0
careamics/config/validators/axes_validators.py +90 -0
careamics/config/validators/model_validators.py +84 -0
careamics/config/validators/patch_validators.py +55 -0
careamics/conftest.py +39 -0
careamics/dataset/__init__.py +17 -0
careamics/dataset/dataset_utils/__init__.py +19 -0
careamics/dataset/dataset_utils/dataset_utils.py +118 -0
careamics/dataset/dataset_utils/file_utils.py +141 -0
careamics/dataset/dataset_utils/iterate_over_files.py +84 -0
careamics/dataset/dataset_utils/running_stats.py +189 -0
careamics/dataset/in_memory_dataset.py +303 -0
careamics/dataset/in_memory_pred_dataset.py +88 -0
careamics/dataset/in_memory_tiled_pred_dataset.py +131 -0
careamics/dataset/iterable_dataset.py +294 -0
careamics/dataset/iterable_pred_dataset.py +121 -0
careamics/dataset/iterable_tiled_pred_dataset.py +141 -0
careamics/dataset/patching/__init__.py +1 -0
careamics/dataset/patching/patching.py +300 -0
careamics/dataset/patching/random_patching.py +110 -0
careamics/dataset/patching/sequential_patching.py +212 -0
careamics/dataset/patching/validate_patch_dimension.py +64 -0
careamics/dataset/tiling/__init__.py +10 -0
careamics/dataset/tiling/collate_tiles.py +33 -0
careamics/dataset/tiling/lvae_tiled_patching.py +375 -0
careamics/dataset/tiling/tiled_patching.py +166 -0
careamics/dataset_ng/README.md +212 -0
careamics/dataset_ng/__init__.py +0 -0
careamics/dataset_ng/dataset.py +365 -0
careamics/dataset_ng/demos/bsd68_demo.ipynb +361 -0
careamics/dataset_ng/demos/bsd68_zarr_demo.ipynb +453 -0
careamics/dataset_ng/demos/care_U2OS_demo.ipynb +330 -0
careamics/dataset_ng/demos/demo_custom_image_stack.ipynb +736 -0
careamics/dataset_ng/demos/demo_datamodule.ipynb +447 -0
careamics/dataset_ng/demos/demo_dataset.ipynb +278 -0
careamics/dataset_ng/demos/demo_patch_extractor.py +51 -0
careamics/dataset_ng/demos/mouse_nuclei_demo.ipynb +293 -0
careamics/dataset_ng/factory.py +180 -0
careamics/dataset_ng/grouped_index_sampler.py +73 -0
careamics/dataset_ng/image_stack/__init__.py +14 -0
careamics/dataset_ng/image_stack/czi_image_stack.py +396 -0
careamics/dataset_ng/image_stack/file_image_stack.py +140 -0
careamics/dataset_ng/image_stack/image_stack_protocol.py +93 -0
careamics/dataset_ng/image_stack/image_utils/__init__.py +6 -0
careamics/dataset_ng/image_stack/image_utils/image_stack_utils.py +125 -0
careamics/dataset_ng/image_stack/in_memory_image_stack.py +93 -0
careamics/dataset_ng/image_stack/zarr_image_stack.py +170 -0
careamics/dataset_ng/image_stack_loader/__init__.py +19 -0
careamics/dataset_ng/image_stack_loader/image_stack_loader_protocol.py +70 -0
careamics/dataset_ng/image_stack_loader/image_stack_loaders.py +273 -0
careamics/dataset_ng/image_stack_loader/zarr_utils.py +130 -0
careamics/dataset_ng/legacy_interoperability.py +175 -0
careamics/dataset_ng/microsplit_input_synth.py +377 -0
careamics/dataset_ng/patch_extractor/__init__.py +7 -0
careamics/dataset_ng/patch_extractor/limit_file_extractor.py +50 -0
careamics/dataset_ng/patch_extractor/patch_construction.py +151 -0
careamics/dataset_ng/patch_extractor/patch_extractor.py +117 -0
careamics/dataset_ng/patch_filter/__init__.py +20 -0
careamics/dataset_ng/patch_filter/coordinate_filter_protocol.py +27 -0
careamics/dataset_ng/patch_filter/filter_factory.py +95 -0
careamics/dataset_ng/patch_filter/mask_filter.py +96 -0
careamics/dataset_ng/patch_filter/max_filter.py +188 -0
careamics/dataset_ng/patch_filter/mean_std_filter.py +218 -0
careamics/dataset_ng/patch_filter/patch_filter_protocol.py +50 -0
careamics/dataset_ng/patch_filter/shannon_filter.py +188 -0
careamics/dataset_ng/patching_strategies/__init__.py +26 -0
careamics/dataset_ng/patching_strategies/patching_strategy_factory.py +50 -0
careamics/dataset_ng/patching_strategies/patching_strategy_protocol.py +161 -0
careamics/dataset_ng/patching_strategies/random_patching.py +393 -0
careamics/dataset_ng/patching_strategies/sequential_patching.py +99 -0
careamics/dataset_ng/patching_strategies/tiling_strategy.py +207 -0
careamics/dataset_ng/patching_strategies/whole_sample.py +61 -0
careamics/file_io/__init__.py +15 -0
careamics/file_io/read/__init__.py +11 -0
careamics/file_io/read/get_func.py +57 -0
careamics/file_io/read/tiff.py +58 -0
careamics/file_io/write/__init__.py +15 -0
careamics/file_io/write/get_func.py +63 -0
careamics/file_io/write/tiff.py +40 -0
careamics/lightning/__init__.py +32 -0
careamics/lightning/callbacks/__init__.py +13 -0
careamics/lightning/callbacks/data_stats_callback.py +33 -0
careamics/lightning/callbacks/hyperparameters_callback.py +49 -0
careamics/lightning/callbacks/prediction_writer_callback/__init__.py +20 -0
careamics/lightning/callbacks/prediction_writer_callback/file_path_utils.py +56 -0
careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py +234 -0
careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py +399 -0
careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py +215 -0
careamics/lightning/callbacks/progress_bar_callback.py +90 -0
careamics/lightning/dataset_ng/__init__.py +1 -0
careamics/lightning/dataset_ng/callbacks/__init__.py +1 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/__init__.py +29 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/cached_tiles_strategy.py +164 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/file_path_utils.py +33 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/prediction_writer_callback.py +219 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/write_image_strategy.py +91 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/write_strategy.py +27 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/write_strategy_factory.py +214 -0
careamics/lightning/dataset_ng/callbacks/prediction_writer/write_tiles_zarr_strategy.py +375 -0
careamics/lightning/dataset_ng/data_module.py +529 -0
careamics/lightning/dataset_ng/data_module_utils.py +395 -0
careamics/lightning/dataset_ng/lightning_modules/__init__.py +9 -0
careamics/lightning/dataset_ng/lightning_modules/care_module.py +97 -0
careamics/lightning/dataset_ng/lightning_modules/n2v_module.py +106 -0
careamics/lightning/dataset_ng/lightning_modules/unet_module.py +221 -0
careamics/lightning/dataset_ng/prediction/__init__.py +16 -0
careamics/lightning/dataset_ng/prediction/convert_prediction.py +198 -0
careamics/lightning/dataset_ng/prediction/stitch_prediction.py +171 -0
careamics/lightning/lightning_module.py +914 -0
careamics/lightning/microsplit_data_module.py +632 -0
careamics/lightning/predict_data_module.py +341 -0
careamics/lightning/train_data_module.py +666 -0
careamics/losses/__init__.py +21 -0
careamics/losses/fcn/__init__.py +1 -0
careamics/losses/fcn/losses.py +125 -0
careamics/losses/loss_factory.py +80 -0
careamics/losses/lvae/__init__.py +1 -0
careamics/losses/lvae/loss_utils.py +83 -0
careamics/losses/lvae/losses.py +589 -0
careamics/lvae_training/__init__.py +0 -0
careamics/lvae_training/calibration.py +191 -0
careamics/lvae_training/dataset/__init__.py +20 -0
careamics/lvae_training/dataset/config.py +135 -0
careamics/lvae_training/dataset/lc_dataset.py +274 -0
careamics/lvae_training/dataset/ms_dataset_ref.py +1067 -0
careamics/lvae_training/dataset/multich_dataset.py +1121 -0
careamics/lvae_training/dataset/multicrop_dset.py +196 -0
careamics/lvae_training/dataset/multifile_dataset.py +335 -0
careamics/lvae_training/dataset/types.py +32 -0
careamics/lvae_training/dataset/utils/__init__.py +0 -0
careamics/lvae_training/dataset/utils/data_utils.py +114 -0
careamics/lvae_training/dataset/utils/empty_patch_fetcher.py +65 -0
careamics/lvae_training/dataset/utils/index_manager.py +491 -0
careamics/lvae_training/dataset/utils/index_switcher.py +165 -0
careamics/lvae_training/eval_utils.py +987 -0
careamics/lvae_training/get_config.py +84 -0
careamics/lvae_training/lightning_module.py +701 -0
careamics/lvae_training/metrics.py +214 -0
careamics/lvae_training/train_lvae.py +342 -0
careamics/lvae_training/train_utils.py +121 -0
careamics/model_io/__init__.py +7 -0
careamics/model_io/bioimage/__init__.py +11 -0
careamics/model_io/bioimage/_readme_factory.py +113 -0
careamics/model_io/bioimage/bioimage_utils.py +56 -0
careamics/model_io/bioimage/cover_factory.py +171 -0
careamics/model_io/bioimage/model_description.py +341 -0
careamics/model_io/bmz_io.py +251 -0
careamics/model_io/model_io_utils.py +95 -0
careamics/models/__init__.py +5 -0
careamics/models/activation.py +40 -0
careamics/models/layers.py +495 -0
careamics/models/lvae/__init__.py +3 -0
careamics/models/lvae/layers.py +1371 -0
careamics/models/lvae/likelihoods.py +394 -0
careamics/models/lvae/lvae.py +848 -0
careamics/models/lvae/noise_models.py +738 -0
careamics/models/lvae/stochastic.py +394 -0
careamics/models/lvae/utils.py +404 -0
careamics/models/model_factory.py +54 -0
careamics/models/unet.py +449 -0
careamics/nm_training_placeholder.py +203 -0
careamics/prediction_utils/__init__.py +21 -0
careamics/prediction_utils/lvae_prediction.py +158 -0
careamics/prediction_utils/lvae_tiling_manager.py +362 -0
careamics/prediction_utils/prediction_outputs.py +238 -0
careamics/prediction_utils/stitch_prediction.py +193 -0
careamics/py.typed +5 -0
careamics/transforms/__init__.py +22 -0
careamics/transforms/compose.py +173 -0
careamics/transforms/n2v_manipulate.py +150 -0
careamics/transforms/n2v_manipulate_torch.py +149 -0
careamics/transforms/normalize.py +374 -0
careamics/transforms/pixel_manipulation.py +406 -0
careamics/transforms/pixel_manipulation_torch.py +388 -0
careamics/transforms/struct_mask_parameters.py +20 -0
careamics/transforms/transform.py +24 -0
careamics/transforms/tta.py +88 -0
careamics/transforms/xy_flip.py +131 -0
careamics/transforms/xy_random_rotate90.py +108 -0
careamics/utils/__init__.py +19 -0
careamics/utils/autocorrelation.py +40 -0
careamics/utils/base_enum.py +60 -0
careamics/utils/context.py +67 -0
careamics/utils/deprecation.py +63 -0
careamics/utils/lightning_utils.py +71 -0
careamics/utils/logging.py +323 -0
careamics/utils/metrics.py +394 -0
careamics/utils/path_utils.py +26 -0
careamics/utils/plotting.py +76 -0
careamics/utils/ram.py +15 -0
careamics/utils/receptive_field.py +108 -0
careamics/utils/serializers.py +62 -0
careamics/utils/torch_utils.py +150 -0
careamics/utils/version.py +38 -0
careamics-0.0.19.dist-info/METADATA +80 -0
careamics-0.0.19.dist-info/RECORD +279 -0
careamics-0.0.19.dist-info/WHEEL +4 -0
careamics-0.0.19.dist-info/entry_points.txt +2 -0
careamics-0.0.19.dist-info/licenses/LICENSE +28 -0

careamics-0.0.19.dist-info/RECORD ADDED Viewed

@@ -0,0 +1,279 @@
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+BSD 3-Clause License
+Copyright (c) 2023, CAREamics contributors
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.