careamics 0.1.0rc4__tar.gz → 0.1.0rc6__tar.gz

careamics-0.1.0rc6/.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-0.1.0rc6}/.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
         platform: [ubuntu-latest, macos-13, windows-latest]
 

{careamics-0.1.0rc4 → careamics-0.1.0rc6}/.pre-commit-config.yaml

@@ -9,23 +9,23 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.14
+    rev: v0.18
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+    rev: v0.4.7
     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/"
@@ -36,21 +36,21 @@ 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
-    hooks:
-      - id: nbqa-ruff
-        args: [--fix]
-      - id: nbqa-black
-      #- id: nbqa-mypy
+  # # jupyter linting and formatting
+  # - repo: https://github.com/nbQA-dev/nbQA
+  #   rev: 1.8.5
+  #   hooks:
+  #     - id: nbqa-ruff
+  #       args: [--fix]
+  #     - id: nbqa-black
+  #     #- id: nbqa-mypy
 
   # 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-0.1.0rc6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.1.0rc4
+Version: 0.1.0rc6
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -14,9 +14,9 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 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 +48,7 @@ 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 +56,23 @@ 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-0.1.0rc6/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-0.1.0rc6}/examples/2D/n2v/example_BSD68_lightning.ipynb

@@ -18,11 +18,7 @@
     "    CAREamicsPredictDataModule,\n",
     "    CAREamicsTrainDataModule,\n",
     ")\n",
-<<<<<<< Updated upstream
     "from careamics.lightning_prediction import CAREamicsPredictionLoop\n",
-=======
-    "from careamics.lightning_prediction import CAREamicsFiring\n",
->>>>>>> Stashed changes
     "from careamics.utils.metrics import psnr"
    ]
   },
@@ -172,11 +168,7 @@
     "train_data_module = CAREamicsTrainDataModule(\n",
     "    train_data=train_path,\n",
     "    val_data=val_path,\n",
-<<<<<<< Updated upstream
     "    data_type=\"tiff\",  # to use np.ndarray, set data_type to \"array\"\n",
-=======
-    "    data_type=\"tiff\",\n",
->>>>>>> Stashed changes
     "    patch_size=(64, 64),\n",
     "    axes=\"SYX\",\n",
     "    batch_size=128,\n",

{careamics-0.1.0rc4 → careamics-0.1.0rc6}/pyproject.toml

@@ -33,12 +33,12 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: BSD License",
     "Typing :: Typed",
 ]
 dependencies = [
     'torch>=2.0.0',
-    'albumentations',
     'bioimageio.core>=0.6.0',
     'tifffile',
     'psutil',
@@ -74,7 +74,7 @@ repository = "https://github.com/CAREamics/careamics"
 line-length = 88
 target-version = "py38"
 src = ["src"]
-select = [
+lint.select = [
     "E",  # style errors
     "W",  # style warnings
     "F",  # flakes
@@ -87,7 +87,7 @@ select = [
     "A001", # flake8-builtins
     "RUF",  # ruff-specific rules
 ]
-ignore = [
+lint.ignore = [
     "D100", # Missing docstring in public module
     "D107", # Missing docstring in __init__
     "D203", # 1 blank line required before class docstring
@@ -104,13 +104,12 @@ ignore = [
     "UP006", # Replace typing.List by list, mandatory for py3.8
     "UP007", # Replace Union by |, mandatory for py3.9
 ]
-ignore-init-module-imports = true
 show-fixes = true
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
 "setup.py" = ["D"]
 

{careamics-0.1.0rc4 → careamics-0.1.0rc6}/src/careamics/callbacks/hyperparameters_callback.py

@@ -1,3 +1,5 @@
+"""Callback saving CAREamics configuration as hyperparameters in the model."""
+
 from pytorch_lightning import LightningModule, Trainer
 from pytorch_lightning.callbacks import Callback
 
@@ -11,13 +13,18 @@ class HyperParametersCallback(Callback):
     This allows saving the configuration as dictionnary in the checkpoints, and
     loading it subsequently in a CAREamist instance.
 
+    Parameters
+    ----------
+    config : Configuration
+        CAREamics configuration to be saved as hyperparameter in the model.
+
     Attributes
     ----------
     config : Configuration
         CAREamics configuration to be saved as hyperparameter in the model.
     """
 
-    def __init__(self, config: Configuration):
+    def __init__(self, config: Configuration) -> None:
         """
         Constructor.
 
@@ -28,14 +35,14 @@ class HyperParametersCallback(Callback):
         """
         self.config = config
 
-    def on_train_start(self, trainer: Trainer, pl_module: LightningModule):
+    def on_train_start(self, trainer: Trainer, pl_module: LightningModule) -> None:
         """
         Update the hyperparameters of the model with the configuration on train start.
 
         Parameters
         ----------
         trainer : Trainer
-            PyTorch Lightning trainer.
+            PyTorch Lightning trainer, unused.
         pl_module : LightningModule
             PyTorch Lightning module.
         """

{careamics-0.1.0rc4 → careamics-0.1.0rc6}/src/careamics/callbacks/progress_bar_callback.py

@@ -1,3 +1,5 @@
+"""Progressbar callback."""
+
 import sys
 from typing import Dict, Union
 
@@ -10,7 +12,13 @@ class ProgressBarCallback(TQDMProgressBar):
     """Progress bar for training and validation steps."""
 
     def init_train_tqdm(self) -> tqdm:
-        """Override this to customize the tqdm bar for training."""
+        """Override this to customize the tqdm bar for training.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
         bar = tqdm(
             desc="Training",
             position=(2 * self.process_position),
@@ -23,7 +31,13 @@ class ProgressBarCallback(TQDMProgressBar):
         return bar
 
     def init_validation_tqdm(self) -> tqdm:
-        """Override this to customize the tqdm bar for validation."""
+        """Override this to customize the tqdm bar for validation.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
         # The main progress bar doesn't exist in `trainer.validate()`
         has_main_bar = self.train_progress_bar is not None
         bar = tqdm(
@@ -37,7 +51,13 @@ class ProgressBarCallback(TQDMProgressBar):
         return bar
 
     def init_test_tqdm(self) -> tqdm:
-        """Override this to customize the tqdm bar for testing."""
+        """Override this to customize the tqdm bar for testing.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
         bar = tqdm(
             desc="Testing",
             position=(2 * self.process_position),
@@ -52,6 +72,19 @@ class ProgressBarCallback(TQDMProgressBar):
     def get_metrics(
         self, trainer: Trainer, pl_module: LightningModule
     ) -> Dict[str, Union[int, str, float, Dict[str, float]]]:
-        """Override this to customize the metrics displayed in the progress bar."""
+        """Override this to customize the metrics displayed in the progress bar.
+
+        Parameters
+        ----------
+        trainer : Trainer
+            The trainer object.
+        pl_module : LightningModule
+            The LightningModule object, unused.
+
+        Returns
+        -------
+        dict
+            A dictionary with the metrics to display in the progress bar.
+        """
         pbar_metrics = trainer.progress_bar_metrics
         return {**pbar_metrics}