careamics 0.1.0rc4__py3-none-any.whl → 0.1.0rc6__py3-none-any.whl

{careamics-0.1.0rc4.dist-info → careamics-0.1.0rc6.dist-info}/METADATA

@@ -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.dist-info/RECORD

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careamics/config/noise_models.py

@@ -1,162 +0,0 @@
-from __future__ import annotations
-
-from enum import Enum
-from typing import Dict, Union
-
-from pydantic import BaseModel, ConfigDict, Field, field_validator
-
-
-class NoiseModelType(str, Enum):
-    """
-    Available noise models.
-
-    Currently supported noise models:
-
-        - hist: Histogram noise model.
-        - gmm: Gaussian mixture model noise model.F
-    """
-
-    NONE = "none"
-    HIST = "hist"
-    GMM = "gmm"
-
-    # TODO add validator decorator
-    @classmethod
-    def validate_noise_model_type(
-        cls, noise_model: Union[str, NoiseModel], parameters: dict
-    ) -> None:
-        """_summary_.
-
-        Parameters
-        ----------
-        noise_model : Union[str, NoiseModel]
-            _description_
-        parameters : dict
-            _description_
-
-        Returns
-        -------
-        BaseModel
-            _description_
-        """
-        if noise_model == NoiseModelType.HIST.value:
-            HistogramNoiseModel(**parameters)
-            return HistogramNoiseModel().model_dump() if not parameters else parameters
-
-        elif noise_model == NoiseModelType.GMM.value:
-            GaussianMixtureNoiseModel(**parameters)
-            return (
-                GaussianMixtureNoiseModel().model_dump()
-                if not parameters
-                else parameters
-            )
-
-
-class NoiseModel(BaseModel):
-    """_summary_.
-
-    Parameters
-    ----------
-    BaseModel : _type_
-        _description_
-
-    Returns
-    -------
-    _type_
-        _description_
-
-    Raises
-    ------
-    ValueError
-        _description_
-    """
-
-    model_config = ConfigDict(
-        use_enum_values=True,
-        protected_namespaces=(),  # allows to use model_* as a field name
-        validate_assignment=True,
-    )
-
-    model_type: NoiseModelType
-    parameters: Dict = Field(default_factory=dict, validate_default=True)
-
-    @field_validator("parameters")
-    @classmethod
-    def validate_parameters(cls, data, values) -> Dict:
-        """_summary_.
-
-        Parameters
-        ----------
-        parameters : Dict
-            _description_
-
-        Returns
-        -------
-        Dict
-            _description_
-        """
-        if values.data["model_type"] not in [NoiseModelType.GMM, NoiseModelType.HIST]:
-            raise ValueError(
-                f"Incorrect noise model {values.data['model_type']}."
-                f"Please refer to the documentation"  # TODO add link to documentation
-            )
-
-        parameters = NoiseModelType.validate_noise_model_type(
-            values.data["model_type"], data
-        )
-        return parameters
-
-
-class HistogramNoiseModel(BaseModel):
-    """
-    Histogram noise model.
-
-    Attributes
-    ----------
-    min_value : float
-        Minimum value in the input.
-    max_value : float
-        Maximum value in the input.
-    bins : int
-        Number of bins of the histogram.
-    """
-
-    min_value: float = Field(default=350.0, ge=0.0, le=65535.0)
-    max_value: float = Field(default=6500.0, ge=0.0, le=65535.0)
-    bins: int = Field(default=256, ge=1)
-
-
-class GaussianMixtureNoiseModel(BaseModel):
-    """
-    Gaussian mixture model noise model.
-
-    Attributes
-    ----------
-    min_signal : float
-    Minimum signal intensity expected in the image.
-    max_signal : float
-    Maximum signal intensity expected in the image.
-    weight : array
-    A [3*n_gaussian, n_coeff] sized array containing the values of the weights
-    describing the noise model.
-    Each gaussian contributes three parameters (mean, standard deviation and weight),
-    hence the number of rows in `weight` are 3*n_gaussian.
-    If `weight = None`, the weight array is initialized using the `min_signal` and
-    `max_signal` parameters.
-    n_gaussian: int
-    Number of gaussians.
-    n_coeff: int
-    Number of coefficients to describe the functional relationship between gaussian
-    parameters and the signal.
-    2 implies a linear relationship, 3 implies a quadratic relationship and so on.
-    device: device
-    GPU device.
-    min_sigma: int
-    """
-
-    num_components: int = Field(default=3, ge=1)
-    min_value: float = Field(default=350.0, ge=0.0, le=65535.0)
-    max_value: float = Field(default=6500.0, ge=0.0, le=65535.0)
-    n_gaussian: int = Field(default=3, ge=1)
-    n_coeff: int = Field(default=2, ge=1)
-    min_sigma: int = Field(default=50, ge=1)

careamics/config/support/supported_extraction_strategies.py

@@ -1,24 +0,0 @@
-"""
-Extraction strategy module.
-
-This module defines the various extraction strategies available in CAREamics.
-"""
-from careamics.utils import BaseEnum
-
-
-class SupportedExtractionStrategy(str, BaseEnum):
-    """
-    Available extraction strategies.
-
-    Currently supported:
-        - random: random extraction.
-        # TODO
-        - sequential: grid extraction, can miss edge values.
-        - tiled: tiled extraction, covers the whole image.
-    """
-
-    RANDOM = "random"
-    RANDOM_ZARR = "random_zarr"
-    SEQUENTIAL = "sequential"
-    TILED = "tiled"
-    NONE = "none"

careamics/config/transformations/nd_flip_model.py

@@ -1,32 +0,0 @@
-"""Pydantic model for the NDFlip transform."""
-from typing import Literal
-
-from pydantic import ConfigDict, Field
-
-from .transform_model import TransformModel
-
-
-class NDFlipModel(TransformModel):
-    """
-    Pydantic model used to represent NDFlip transformation.
-
-    Attributes
-    ----------
-    name : Literal["NDFlip"]
-        Name of the transformation.
-    p : float
-        Probability of applying the transformation, by default 0.5.
-    is_3D : bool
-        Whether the transformation should be applied in 3D, by default False.
-    flip_z : bool
-        Whether to flip the z axis, by default True.
-    """
-
-    model_config = ConfigDict(
-        validate_assignment=True,
-    )
-
-    name: Literal["NDFlip"] = "NDFlip"
-    p: float = Field(default=0.5, ge=0.0, le=1.0)
-    is_3D: bool = Field(default=False)
-    flip_z: bool = Field(default=True)

careamics/dataset/patching/patch_transform.py

@@ -1,44 +0,0 @@
-from typing import List, Union
-
-import albumentations as Aug
-
-from careamics.config.data_model import TRANSFORMS_UNION
-from careamics.transforms import get_all_transforms
-
-
-# TODO add some explanations on how the additional_targets is used
-def get_patch_transform(
-    patch_transforms: Union[List[TRANSFORMS_UNION], Aug.Compose],
-    with_target: bool,
-    normalize_mask: bool = True,
-) -> Aug.Compose:
-    """Return a pixel manipulation function."""
-    # if we passed a Compose, we just return it
-    if isinstance(patch_transforms, Aug.Compose):
-        return patch_transforms
-
-    # empty list of transforms is a NoOp
-    elif len(patch_transforms) == 0:
-        return Aug.Compose(
-            [Aug.NoOp()],
-            additional_targets={},  # TODO this part need be checked (wrt segmentation)
-        )
-
-    # else we have a list of transforms
-    else:
-        # retrieve all transforms
-        all_transforms = get_all_transforms()
-
-        # instantiate all transforms
-        transforms = [
-            all_transforms[transform.name](**transform.model_dump())
-            for transform in patch_transforms
-        ]
-
-        return Aug.Compose(
-            transforms,
-            # apply image aug to "target"
-            additional_targets={"target": "image"}
-            if (with_target and normalize_mask)  # TODO check this
-            else {},
-        )

careamics/losses/noise_model_factory.py

@@ -1,40 +0,0 @@
-from typing import Type, Union
-
-from ..config.noise_models import NoiseModel, NoiseModelType
-from .noise_models import GaussianMixtureNoiseModel, HistogramNoiseModel
-
-
-def noise_model_factory(
-    noise_config: NoiseModel,
-) -> Type[Union[HistogramNoiseModel, GaussianMixtureNoiseModel, None]]:
-    """Create loss model based on Configuration.
-
-    Parameters
-    ----------
-    config : Configuration
-        Configuration.
-
-    Returns
-    -------
-    Noise model
-
-    Raises
-    ------
-    NotImplementedError
-        If the noise model is unknown.
-    """
-    noise_model_type = noise_config.model_type if noise_config else None
-
-    if noise_model_type == NoiseModelType.HIST:
-        return HistogramNoiseModel
-
-    elif noise_model_type == NoiseModelType.GMM:
-        return GaussianMixtureNoiseModel
-
-    elif noise_model_type is None:
-        return None
-
-    else:
-        raise NotImplementedError(
-            f"Noise model {noise_model_type} is not yet supported."
-        )