careamics 0.1.0rc4__tar.gz → 0.1.0rc5__tar.gz

careamics-0.1.0rc5/.github/pull_request_template.md

@@ -0,0 +1,39 @@
+### Description
+
+Please provide a brief description of the changes in this PR. Include any relevant context or background information.
+
+- **What**: Clearly and concisely describe what changes you have made.
+- **Why**: Explain the reasoning behind these changes. What problem are you solving? Why is this change necessary?
+- **How**: Describe how you implemented these changes. Provide an overview of the approach and any important implementation details.
+
+### Changes Made
+
+- **Added**: List new features or files added.
+- **Modified**: Describe existing features or files modified.
+- **Removed**: Detail features or files that were removed.
+
+### Related Issues
+
+Link to any related issues or discussions. Use keywords like "Fixes", "Resolves", or "Closes" to link to issues automatically.
+
+- Fixes #
+- Resolves #
+- Closes #
+
+### Breaking changes
+
+Describe any breaking change.
+
+
+### Additional Notes and Examples
+
+Include any additional notes or context that reviewers should be aware of, including snippets of code illustrating your new feature.
+
+---
+
+**Please ensure your PR meets the following requirements:**
+
+- [ ] Code builds and passes tests locally, including doctests
+- [ ] New tests have been added (for bug fixes/features)
+- [ ] Pre-commit passes
+- [ ] PR to the documentation exists (for bug fixes / features)

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/.pre-commit-config.yaml

@@ -9,23 +9,23 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.14
+    rev: v0.16
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+    rev: v0.4.3
     hooks:
       - id: ruff
         args: [--fix, --target-version, py38]
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.4.2
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.10.0
     hooks:
       - id: mypy
         files: "^src/"
@@ -36,13 +36,13 @@ repos:
 
   # check docstrings
   - repo: https://github.com/numpy/numpydoc
-    rev: v1.6.0
+    rev: v1.7.0
     hooks:
       - id: numpydoc-validation
 
   # jupyter linting and formatting
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.8.5
     hooks:
       - id: nbqa-ruff
         args: [--fix]
@@ -51,6 +51,6 @@ repos:
 
   # strip out jupyter notebooks
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.1.0rc4
+Version: 0.1.0rc5
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -16,7 +16,6 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Typing :: Typed
 Requires-Python: >=3.8
-Requires-Dist: albumentations
 Requires-Dist: bioimageio-core>=0.6.0
 Requires-Dist: psutil
 Requires-Dist: pydantic>=2.5
@@ -48,7 +47,7 @@ Description-Content-Type: text/markdown
   </a>
 </p>
 
-# CAREamics Restoration
+# CAREamics
 
 [![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
@@ -56,67 +55,23 @@ Description-Content-Type: text/markdown
 [![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
 
-## Installation
 
-``` bash
-pip install careamics
-```
-For more details on the options please follow the installation [guide](https://careamics.github.io/careamics/).
+CAREamics is a PyTorch library aimed at simplifying the use of Noise2Void and its many
+variants and cousins (CARE, Noise2Noise, N2V2, P(P)N2V, HDN, muSplit etc.).
 
-## Usage
+## Why CAREamics?
 
-CAREamics uses the Engine object to construct the pipeline for both training and prediction. First we import the Engine.
-```python
-from careamics_restoration.engine import Engine
-```
-The Engine could be initialized in 2 ways:
-1. Using the [yaml config](examples/n2v_2D_reference.yml) file
+Noise2Void is a widely used denoising algorithm, and is readily available from the `n2v`
+python package. However, n2v is based on TensorFlow and Keras and we found it 
+increasingly hard to maintain. In addition, more recent methods (PPN2V, DivNoising,
+HDN) are all implemented in PyTorch, but are lacking the extra features that would make
+them usable by the community.
 
-Specify the mandatory parameters in the config file
-```yaml
-experiment_name: Name of the experiment
-working_directory: Path to the working directory, where all the outputs will be stored
+The aim of CAREamics is to provide a PyTorch library reuniting all the latest methods
+in one package, while providing a simple and consistent API. The library relies on 
+PyTorch Lightning as a back-end. In addition, we will provide extensive documentation and 
+tutorials on how to best apply these methods in a scientific context.
 
-algorithm: 
-    loss: type of loss function, e.g. n2v for Noise2Void
-    model: model architecture, e.g. UNet
-    is_3D: True if 3D data, False if 2D data
-
-training:
-  num_epochs: Number of training epochs
-  patch_size: Size of the patches, List of 2 or 3 elements
-  batch_size: Batch size for training
-
-extraction_strategy: Controls how the patches are extracted from the data
-
-data:
-    data_format: File extension, e.g. tif
-    axes: Defines the shape of the input data
-```
-Full description of the configuration parameters is in the [documentation](https://careamics.github.io/careamics/).
-
-
-```python
-engine = Engine(config_path="config.yml")
-
-```
-2. Using the path to the pretrained model
-It's also possible to initialize the Engine using the model checkpoint, saved during the training or downloaded from the [BioImage Model Zoo](https://bioimage.io/#/).
-Checkpoint must contain model_state_dict.
-Read more abount saving and loading models in the [documentation](https://careamics.github.io/careamics/).
-
-Once Engine is initialized, we can start training, providing the relative paths to train and validation data
-
-```python
-engine.train(train_path=train_path, val_path=val_path)
-```
-Training will run for the specified number of epochs and save the model checkpoint in the working directory.
-
-Prediction could be done directly after the training or by loading the pretrained model checkpoint.
-
-```python
-predictions = engine.predict(pred_path=predict_path)
-```
-
-For more examples please take a look at the [notebooks](examples).
+## Installation and use
 
+Check out the [documentation](https://careamics.github.io/) for installation instructions and guides!

careamics-0.1.0rc5/README.md

@@ -0,0 +1,34 @@
+<p align="center">
+  <a href="https://careamics.github.io/">
+    <img src="https://raw.githubusercontent.com/CAREamics/.github/main/profile/images/banner_careamics.png">
+  </a>
+</p>
+
+# CAREamics
+
+[![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
+[![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
+[![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
+
+
+CAREamics is a PyTorch library aimed at simplifying the use of Noise2Void and its many
+variants and cousins (CARE, Noise2Noise, N2V2, P(P)N2V, HDN, muSplit etc.).
+
+## Why CAREamics?
+
+Noise2Void is a widely used denoising algorithm, and is readily available from the `n2v`
+python package. However, n2v is based on TensorFlow and Keras and we found it 
+increasingly hard to maintain. In addition, more recent methods (PPN2V, DivNoising,
+HDN) are all implemented in PyTorch, but are lacking the extra features that would make
+them usable by the community.
+
+The aim of CAREamics is to provide a PyTorch library reuniting all the latest methods
+in one package, while providing a simple and consistent API. The library relies on 
+PyTorch Lightning as a back-end. In addition, we will provide extensive documentation and 
+tutorials on how to best apply these methods in a scientific context.
+
+## Installation and use
+
+Check out the [documentation](https://careamics.github.io/) for installation instructions and guides!

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/pyproject.toml

@@ -38,7 +38,6 @@ classifiers = [
 ]
 dependencies = [
     'torch>=2.0.0',
-    'albumentations',
     'bioimageio.core>=0.6.0',
     'tifffile',
     'psutil',

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/src/careamics/careamist.py

@@ -73,8 +73,7 @@ class CAREamist:
         source: Union[Path, str],
         work_dir: Optional[str] = None,
         experiment_name: str = "CAREamics",
-    ) -> None:
-        ...
+    ) -> None: ...
 
     @overload
     def __init__(  # numpydoc ignore=GL08
@@ -82,8 +81,7 @@ class CAREamist:
         source: Configuration,
         work_dir: Optional[str] = None,
         experiment_name: str = "CAREamics",
-    ) -> None:
-        ...
+    ) -> None: ...
 
     def __init__(
         self,
@@ -478,8 +476,7 @@ class CAREamist:
         source: CAREamicsPredictData,
         *,
         checkpoint: Optional[Literal["best", "last"]] = None,
-    ) -> Union[list, np.ndarray]:
-        ...
+    ) -> Union[list, np.ndarray]: ...
 
     @overload
     def predict(  # numpydoc ignore=GL08
@@ -497,8 +494,7 @@ class CAREamist:
         read_source_func: Optional[Callable] = None,
         extension_filter: str = "",
         checkpoint: Optional[Literal["best", "last"]] = None,
-    ) -> Union[list, np.ndarray]:
-        ...
+    ) -> Union[list, np.ndarray]: ...
 
     @overload
     def predict(  # numpydoc ignore=GL08
@@ -514,8 +510,7 @@ class CAREamist:
         tta_transforms: bool = True,
         dataloader_params: Optional[Dict] = None,
         checkpoint: Optional[Literal["best", "last"]] = None,
-    ) -> Union[list, np.ndarray]:
-        ...
+    ) -> Union[list, np.ndarray]: ...
 
     def predict(
         self,
@@ -548,6 +543,12 @@ class CAREamist:
         Test-time augmentation (TTA) can be switched off using the `tta_transforms`
         parameter.
 
+        Note that if you are using a UNet model and tiling, the tile size must be
+        divisible in every dimension by 2**d, where d is the depth of the model. This
+        avoids artefacts arising from the broken shift invariance induced by the
+        pooling layers of the UNet. If your image has less dimensions, as it may
+        happen in the Z dimension, consider padding your image.
+
         Parameters
         ----------
         source : Union[CAREamicsClay, Path, str, np.ndarray]
@@ -602,7 +603,7 @@ class CAREamist:
                 )
             # create predict config, reuse training config if parameters missing
             prediction_config = create_inference_configuration(
-                training_configuration=self.cfg,
+                configuration=self.cfg,
                 tile_size=tile_size,
                 tile_overlap=tile_overlap,
                 data_type=data_type,

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/src/careamics/config/__init__.py

@@ -1,6 +1,5 @@
 """Configuration module."""
 
-
 __all__ = [
     "AlgorithmConfig",
     "DataConfig",

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/src/careamics/config/architectures/unet_model.py

@@ -39,6 +39,7 @@ class UNetModel(ArchitectureModel):
         "None", "Sigmoid", "Softmax", "Tanh", "ReLU", "LeakyReLU"
     ] = Field(default="None", validate_default=True)
     n2v2: bool = Field(default=False, validate_default=True)
+    independent_channels: bool = Field(default=True, validate_default=True)
 
     @field_validator("num_channels_init")
     @classmethod

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/src/careamics/config/callback_model.py

@@ -1,4 +1,5 @@
 """Checkpoint saving configuration."""
+
 from __future__ import annotations
 
 from datetime import timedelta

{careamics-0.1.0rc4 → careamics-0.1.0rc5}/src/careamics/config/configuration_example.py

@@ -57,11 +57,9 @@ def full_configuration_example() -> Configuration:
             },
             {
                 "name": SupportedTransform.NDFLIP.value,
-                "is_3D": False,
             },
             {
                 "name": SupportedTransform.XY_RANDOM_ROTATE90.value,
-                "is_3D": False,
             },
             {
                 "name": SupportedTransform.N2V_MANIPULATE.value,