careamics 0.0.5__tar.gz → 0.0.6__tar.gz

{careamics-0.0.5 → careamics-0.0.6}/.github/dependabot.yml

@@ -6,7 +6,5 @@ updates:
     schedule:
       interval: "daily"
       time: "08:00"
-    groups:
-      python-packages:
-        patterns:
-          - "*"
+    ignore:
+      - dependency-name: "numpy"

{careamics-0.0.5 → careamics-0.0.6}/.pre-commit-config.yaml

@@ -9,16 +9,16 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.22
+    rev: v0.23
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.8.6
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
-        args: [--fix, --target-version, py38]
+        args: [--fix, --target-version, py39]
 
   - repo: https://github.com/psf/black
     rev: 24.10.0
@@ -26,14 +26,15 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
       - id: mypy
         files: "^src/"
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/config/likelihood_model.py|^src/careamics/losses/loss_factory.py|^src/careamics/losses/lvae/losses.py"
         args: ["--config-file", "mypy.ini"]
         additional_dependencies:
-          - numpy
+          - numpy<2.0.0
+          - pydantic
           - types-PyYAML
           - types-setuptools
 
@@ -55,6 +56,6 @@ repos:
 
   # strip out jupyter notebooks
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.0
+    rev: 0.8.1
     hooks:
       - id: nbstripout

careamics-0.0.6/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+rse@fht.org.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

{careamics-0.0.5 → careamics-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.5
+Version: 0.0.6
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -18,16 +18,16 @@ Classifier: Typing :: Typed
 Requires-Python: >=3.9
 Requires-Dist: bioimageio-core==0.7
 Requires-Dist: numpy<2.0.0
-Requires-Dist: pillow<=10.3.0
-Requires-Dist: psutil<=6.1
-Requires-Dist: pydantic<2.9,>=2.5
-Requires-Dist: pytorch-lightning<=2.4,>=2.2
+Requires-Dist: pillow<=11.1.0
+Requires-Dist: psutil<=6.1.1
+Requires-Dist: pydantic<2.11,>=2.5
+Requires-Dist: pytorch-lightning<=2.5.0.post0,>=2.2
 Requires-Dist: pyyaml!=6.0.0,<=6.0.2
-Requires-Dist: scikit-image<=0.23.2
-Requires-Dist: tifffile<=2024.8.30
-Requires-Dist: torch<=2.5,>=2.0
-Requires-Dist: torchvision<=0.20
-Requires-Dist: typer==0.12.3
+Requires-Dist: scikit-image<=0.25.0
+Requires-Dist: tifffile<=2025.1.10
+Requires-Dist: torch<=2.5.1,>=2.0
+Requires-Dist: torchvision<=0.20.1
+Requires-Dist: typer<=0.15.1,>=0.12.3
 Requires-Dist: zarr<3.0.0
 Provides-Extra: dev
 Requires-Dist: onnx; extra == 'dev'
@@ -40,7 +40,7 @@ Requires-Dist: careamics-portfolio; extra == 'examples'
 Requires-Dist: jupyter; extra == 'examples'
 Requires-Dist: matplotlib; extra == 'examples'
 Provides-Extra: tensorboard
-Requires-Dist: protobuf==3.20.3; extra == 'tensorboard'
+Requires-Dist: protobuf==5.29.1; extra == 'tensorboard'
 Requires-Dist: tensorboard; extra == 'tensorboard'
 Provides-Extra: wandb
 Requires-Dist: wandb; extra == 'wandb'

{careamics-0.0.5 → careamics-0.0.6}/mypy.ini

@@ -1,5 +1,6 @@
 [mypy]
 ignore_missing_imports = True
+plugins = pydantic.mypy
 
 [mypy-careamics.lvae_training.*]
 follow_imports = skip

{careamics-0.0.5 → careamics-0.0.6}/pyproject.toml

@@ -43,18 +43,18 @@ classifiers = [
 ]
 dependencies = [
     'numpy<2.0.0',
-    'torch>=2.0,<=2.5',
-    'torchvision<=0.20',
+    'torch>=2.0,<=2.5.1',
+    'torchvision<=0.20.1',
     'bioimageio.core==0.7',
-    'tifffile<=2024.8.30',
-    'psutil<=6.1',
-    'pydantic>=2.5,<2.9',
-    'pytorch_lightning>=2.2,<=2.4',
+    'tifffile<=2025.1.10',
+    'psutil<=6.1.1',
+    'pydantic>=2.5,<2.11',
+    'pytorch_lightning>=2.2,<=2.5.0.post0',
     'pyyaml<=6.0.2,!=6.0.0',
-    'typer==0.12.3',
-    'scikit-image<=0.23.2',
+    'typer>=0.12.3,<=0.15.1',
+    'scikit-image<=0.25.0',
     'zarr<3.0.0',
-    'pillow<=10.3.0',
+    'pillow<=11.1.0',
 ]
 
 [project.optional-dependencies]
@@ -72,7 +72,7 @@ examples = ["jupyter", "careamics-portfolio", "matplotlib"]
 
 # loggers
 wandb = ["wandb"]
-tensorboard = ["tensorboard", "protobuf==3.20.3"]
+tensorboard = ["tensorboard", "protobuf==5.29.1"]
 
 [project.urls]
 homepage = "https://careamics.github.io/"
@@ -190,6 +190,7 @@ checks = [
     "GL02", # Closing quotes should be placed in the line after the last text 
     # in the docstring
     "GL03", # Double line break found
+    "RT04", # Return value description should start with a capital letter
 ]
 exclude = [ # don't report on objects that match any of these regex
     "test_*",

careamics-0.0.6/src/careamics/__init__.py

@@ -0,0 +1,28 @@
+"""Main CAREamics module."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("careamics")
+except PackageNotFoundError:
+    __version__ = "uninstalled"
+
+__all__ = [
+    "CAREamist",
+    "Configuration",
+    "algorithm_factory",
+    "configuration_factory",
+    "data_factory",
+    "load_configuration",
+    "save_configuration",
+]
+
+from .careamist import CAREamist
+from .config import (
+    Configuration,
+    algorithm_factory,
+    configuration_factory,
+    data_factory,
+    load_configuration,
+    save_configuration,
+)

{careamics-0.0.5 → careamics-0.0.6}/src/careamics/careamist.py

@@ -13,7 +13,7 @@ from pytorch_lightning.callbacks import (
 )
 from pytorch_lightning.loggers import CSVLogger, TensorBoardLogger, WandbLogger
 
-from careamics.config import Configuration, FCNAlgorithmConfig, load_configuration
+from careamics.config import Configuration, UNetBasedAlgorithm, load_configuration
 from careamics.config.support import (
     SupportedAlgorithm,
     SupportedArchitecture,
@@ -137,7 +137,7 @@ class CAREamist:
             self.cfg = source
 
             # instantiate model
-            if isinstance(self.cfg.algorithm_config, FCNAlgorithmConfig):
+            if isinstance(self.cfg.algorithm_config, UNetBasedAlgorithm):
                 self.model = FCNModule(
                     algorithm_config=self.cfg.algorithm_config,
                 )
@@ -157,7 +157,8 @@ class CAREamist:
                 self.cfg = load_configuration(source)
 
                 # instantiate model
-                if isinstance(self.cfg.algorithm_config, FCNAlgorithmConfig):
+                # TODO call model factory here
+                if isinstance(self.cfg.algorithm_config, UNetBasedAlgorithm):
                     self.model = FCNModule(
                         algorithm_config=self.cfg.algorithm_config,
                     )  # type: ignore

{careamics-0.0.5 → careamics-0.0.6}/src/careamics/cli/conf.py

@@ -3,12 +3,11 @@
 import sys
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Optional
+from typing import Annotated, Optional
 
 import click
 import typer
 import yaml
-from typing_extensions import Annotated
 
 from ..config import (
     Configuration,

{careamics-0.0.5 → careamics-0.0.6}/src/careamics/cli/main.py

@@ -7,11 +7,10 @@ its implementation is contained in the conf.py file.
 """
 
 from pathlib import Path
-from typing import Optional
+from typing import Annotated, Optional
 
 import click
 import typer
-from typing_extensions import Annotated
 
 from ..careamist import CAREamist
 from . import conf

{careamics-0.0.5 → careamics-0.0.6}/src/careamics/cli/utils.py

@@ -1,11 +1,11 @@
 """Utility functions for the CAREamics CLI."""
 
-from typing import Optional, Tuple
+from typing import Optional
 
 
 def handle_2D_3D_callback(
-    value: Optional[Tuple[int, int, int]]
-) -> Optional[Tuple[int, ...]]:
+    value: Optional[tuple[int, int, int]]
+) -> Optional[tuple[int, ...]]:
     """
     Callback for options that require 2D or 3D inputs.
 

careamics-0.0.6/src/careamics/config/__init__.py

@@ -0,0 +1,63 @@
+"""CAREamics Pydantic configuration models.
+
+To maintain clarity at the module level, we follow the following naming conventions:
+`*_model` is specific for sub-configurations (e.g. architecture, data, algorithm),
+while `*_configuration` is reserved for the main configuration models, including the
+`Configuration` base class and its algorithm-specific child classes.
+"""
+
+__all__ = [
+    "CAREAlgorithm",
+    "CAREConfiguration",
+    "CheckpointModel",
+    "Configuration",
+    "DataConfig",
+    "GaussianMixtureNMConfig",
+    "GeneralDataConfig",
+    "InferenceConfig",
+    "LVAELossConfig",
+    "MultiChannelNMConfig",
+    "N2NAlgorithm",
+    "N2NConfiguration",
+    "N2VAlgorithm",
+    "N2VConfiguration",
+    "N2VDataConfig",
+    "TrainingConfig",
+    "UNetBasedAlgorithm",
+    "VAEBasedAlgorithm",
+    "algorithm_factory",
+    "configuration_factory",
+    "create_care_configuration",
+    "create_n2n_configuration",
+    "create_n2v_configuration",
+    "data_factory",
+    "load_configuration",
+    "save_configuration",
+]
+
+from .algorithms import (
+    CAREAlgorithm,
+    N2NAlgorithm,
+    N2VAlgorithm,
+    UNetBasedAlgorithm,
+    VAEBasedAlgorithm,
+)
+from .callback_model import CheckpointModel
+from .care_configuration import CAREConfiguration
+from .configuration import Configuration
+from .configuration_factories import (
+    algorithm_factory,
+    configuration_factory,
+    create_care_configuration,
+    create_n2n_configuration,
+    create_n2v_configuration,
+    data_factory,
+)
+from .configuration_io import load_configuration, save_configuration
+from .data import DataConfig, GeneralDataConfig, N2VDataConfig
+from .inference_model import InferenceConfig
+from .loss_model import LVAELossConfig
+from .n2n_configuration import N2NConfiguration
+from .n2v_configuration import N2VConfiguration
+from .nm_model import GaussianMixtureNMConfig, MultiChannelNMConfig
+from .training_model import TrainingConfig

careamics-0.0.6/src/careamics/config/algorithms/__init__.py

@@ -0,0 +1,15 @@
+"""Algorithm configurations."""
+
+__all__ = [
+    "CAREAlgorithm",
+    "N2NAlgorithm",
+    "N2VAlgorithm",
+    "UNetBasedAlgorithm",
+    "VAEBasedAlgorithm",
+]
+
+from .care_algorithm_model import CAREAlgorithm
+from .n2n_algorithm_model import N2NAlgorithm
+from .n2v_algorithm_model import N2VAlgorithm
+from .unet_algorithm_model import UNetBasedAlgorithm
+from .vae_algorithm_model import VAEBasedAlgorithm

careamics-0.0.6/src/careamics/config/algorithms/care_algorithm_model.py

@@ -0,0 +1,50 @@
+"""CARE algorithm configuration."""
+
+from typing import Literal
+
+from pydantic import field_validator
+
+from careamics.config.architectures import UNetModel
+
+from .unet_algorithm_model import UNetBasedAlgorithm
+
+
+class CAREAlgorithm(UNetBasedAlgorithm):
+    """CARE algorithm configuration.
+
+    Attributes
+    ----------
+    algorithm : "care"
+        CARE Algorithm name.
+    loss : {"mae", "mse"}
+        CARE-compatible loss function.
+    """
+
+    algorithm: Literal["care"] = "care"
+    """CARE Algorithm name."""
+
+    loss: Literal["mae", "mse"] = "mae"
+    """CARE-compatible loss function."""
+
+    @classmethod
+    @field_validator("model")
+    def model_without_n2v2(cls, value: UNetModel) -> UNetModel:
+        """Validate that the model does not have the n2v2 attribute.
+
+        Parameters
+        ----------
+        value : UNetModel
+            Model to validate.
+
+        Returns
+        -------
+        UNetModel
+            The validated model.
+        """
+        if value.n2v2:
+            raise ValueError(
+                "The N2N algorithm does not support the `n2v2` attribute. "
+                "Set it to `False`."
+            )
+
+        return value

careamics-0.0.6/src/careamics/config/algorithms/n2n_algorithm_model.py

@@ -0,0 +1,42 @@
+"""N2N Algorithm configuration."""
+
+from typing import Literal
+
+from pydantic import field_validator
+
+from careamics.config.architectures import UNetModel
+
+from .unet_algorithm_model import UNetBasedAlgorithm
+
+
+class N2NAlgorithm(UNetBasedAlgorithm):
+    """N2N Algorithm configuration."""
+
+    algorithm: Literal["n2n"] = "n2n"
+    """N2N Algorithm name."""
+
+    loss: Literal["mae", "mse"] = "mae"
+    """N2N-compatible loss function."""
+
+    @classmethod
+    @field_validator("model")
+    def model_without_n2v2(cls, value: UNetModel) -> UNetModel:
+        """Validate that the model does not have the n2v2 attribute.
+
+        Parameters
+        ----------
+        value : UNetModel
+            Model to validate.
+
+        Returns
+        -------
+        UNetModel
+            The validated model.
+        """
+        if value.n2v2:
+            raise ValueError(
+                "The N2N algorithm does not support the `n2v2` attribute. "
+                "Set it to `False`."
+            )
+
+        return value

careamics-0.0.6/src/careamics/config/algorithms/n2v_algorithm_model.py

@@ -0,0 +1,35 @@
+""""N2V Algorithm configuration."""
+
+from typing import Literal
+
+from pydantic import model_validator
+from typing_extensions import Self
+
+from .unet_algorithm_model import UNetBasedAlgorithm
+
+
+class N2VAlgorithm(UNetBasedAlgorithm):
+    """N2V Algorithm configuration."""
+
+    algorithm: Literal["n2v"] = "n2v"
+    """N2V Algorithm name."""
+
+    loss: Literal["n2v"] = "n2v"
+    """N2V loss function."""
+
+    @model_validator(mode="after")
+    def algorithm_cross_validation(self: Self) -> Self:
+        """Validate the algorithm model for N2V.
+
+        Returns
+        -------
+        Self
+            The validated model.
+        """
+        if self.model.in_channels != self.model.num_classes:
+            raise ValueError(
+                "N2V requires the same number of input and output channels. Make "
+                "sure that `in_channels` and `num_classes` are the same."
+            )
+
+        return self

careamics-0.0.6/src/careamics/config/algorithms/unet_algorithm_model.py

@@ -0,0 +1,88 @@
+"""UNet-based algorithm Pydantic model."""
+
+from pprint import pformat
+from typing import Literal
+
+from pydantic import BaseModel, ConfigDict
+
+from careamics.config.architectures import UNetModel
+from careamics.config.optimizer_models import LrSchedulerModel, OptimizerModel
+
+
+class UNetBasedAlgorithm(BaseModel):
+    """General UNet-based algorithm configuration.
+
+    This Pydantic model validates the parameters governing the components of the
+    training algorithm: which algorithm, loss function, model architecture, optimizer,
+    and learning rate scheduler to use.
+
+    Currently, we only support N2V, CARE, and N2N algorithms. In order to train these
+    algorithms, use the corresponding configuration child classes (e.g.
+    `N2VAlgorithm`) to ensure coherent parameters (e.g. specific losses).
+
+
+    Attributes
+    ----------
+    algorithm : {"n2v", "care", "n2n"}
+        Algorithm to use.
+    loss : {"n2v", "mae", "mse"}
+        Loss function to use.
+    model : UNetModel
+        Model architecture to use.
+    optimizer : OptimizerModel, optional
+        Optimizer to use.
+    lr_scheduler : LrSchedulerModel, optional
+        Learning rate scheduler to use.
+
+    Raises
+    ------
+    ValueError
+        Algorithm parameter type validation errors.
+    ValueError
+        If the algorithm, loss and model are not compatible.
+    """
+
+    # Pydantic class configuration
+    model_config = ConfigDict(
+        protected_namespaces=(),  # allows to use model_* as a field name
+        validate_assignment=True,
+        extra="allow",
+    )
+
+    # Mandatory fields
+    algorithm: Literal["n2v", "care", "n2n"]
+    """Algorithm name, as defined in SupportedAlgorithm."""
+
+    loss: Literal["n2v", "mae", "mse"]
+    """Loss function to use, as defined in SupportedLoss."""
+
+    model: UNetModel
+    """UNet model configuration."""
+
+    # Optional fields
+    optimizer: OptimizerModel = OptimizerModel()
+    """Optimizer to use, defined in SupportedOptimizer."""
+
+    lr_scheduler: LrSchedulerModel = LrSchedulerModel()
+    """Learning rate scheduler to use, defined in SupportedLrScheduler."""
+
+    def __str__(self) -> str:
+        """Pretty string representing the configuration.
+
+        Returns
+        -------
+        str
+            Pretty string.
+        """
+        return pformat(self.model_dump())
+
+    @classmethod
+    def get_compatible_algorithms(cls) -> list[str]:
+        """Get the list of compatible algorithms.
+
+        Returns
+        -------
+        list of str
+            List of compatible algorithms.
+        """
+        return ["n2v", "care", "n2n"]