careamics 0.0.9__tar.gz → 0.0.10__tar.gz

{careamics-0.0.9 → careamics-0.0.10}/.pre-commit-config.yaml

@@ -43,7 +43,7 @@ repos:
     rev: v1.8.0
     hooks:
       - id: numpydoc-validation
-        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*|^scripts/.*"
+        exclude: "^src/careamics/dataset_ng/.*|^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*|^scripts/.*"
 
   # # jupyter linting and formatting
   # - repo: https://github.com/nbQA-dev/nbQA

{careamics-0.0.9 → careamics-0.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.9
+Version: 0.0.10
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -17,19 +17,19 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Typing :: Typed
 Requires-Python: >=3.9
 Requires-Dist: bioimageio-core==0.7
-Requires-Dist: matplotlib<=3.10.0
+Requires-Dist: matplotlib<=3.10.1
 Requires-Dist: numpy<2.0.0
 Requires-Dist: pillow<=11.1.0
-Requires-Dist: psutil<=6.1.1
+Requires-Dist: psutil<=7.0.0
 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<=0.25.1
-Requires-Dist: tifffile<=2025.1.10
+Requires-Dist: scikit-image<=0.25.2
+Requires-Dist: tifffile<=2025.3.13
 Requires-Dist: torch<=2.6.0,>=2.0
-Requires-Dist: torchvision<=0.20.1
 Requires-Dist: torchvision<=0.21.0
-Requires-Dist: typer<=0.15.1,>=0.12.3
+Requires-Dist: typer<=0.15.2,>=0.12.3
+Requires-Dist: xarray<2025.3.0
 Requires-Dist: zarr<3.0.0
 Provides-Extra: dev
 Requires-Dist: onnx; extra == 'dev'
@@ -40,7 +40,6 @@ Requires-Dist: sybil; extra == 'dev'
 Provides-Extra: examples
 Requires-Dist: careamics-portfolio; extra == 'examples'
 Requires-Dist: jupyter; extra == 'examples'
-Requires-Dist: matplotlib; extra == 'examples'
 Provides-Extra: tensorboard
 Requires-Dist: protobuf==5.29.1; extra == 'tensorboard'
 Requires-Dist: tensorboard; extra == 'tensorboard'

{careamics-0.0.9 → careamics-0.0.10}/pyproject.toml

@@ -45,18 +45,18 @@ dependencies = [
     'numpy<2.0.0',
     'torch>=2.0,<=2.6.0',
     'torchvision<=0.21.0',
-    'torchvision<=0.20.1',
     'bioimageio.core==0.7',
-    'tifffile<=2025.1.10',
-    'psutil<=6.1.1',
+    'tifffile<=2025.3.13',
+    'psutil<=7.0.0',
     'pydantic>=2.5,<2.11',
     'pytorch_lightning>=2.2,<=2.5.0.post0',
     'pyyaml<=6.0.2,!=6.0.0',
-    'typer>=0.12.3,<=0.15.1',
-    'scikit-image<=0.25.1',
+    'typer>=0.12.3,<=0.15.2',
+    'scikit-image<=0.25.2',
     'zarr<3.0.0',
     'pillow<=11.1.0',
-    'matplotlib<=3.10.0'
+    'matplotlib<=3.10.1',
+    'xarray<2025.3.0'
 ]
 
 [project.optional-dependencies]
@@ -70,7 +70,7 @@ dev = [
 ]
 
 # notebooks
-examples = ["jupyter", "careamics-portfolio", "matplotlib"]
+examples = ["jupyter", "careamics-portfolio"]
 
 # loggers
 wandb = ["wandb"]
@@ -126,6 +126,8 @@ convention = "numpy"
 [tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
 "setup.py" = ["D"]
+# temporarily ignore docstrings in next generation dataset development
+"src/careamics/dataset_ng/*" = ["D"]
 
 [tool.black]
 line-length = 88

{careamics-0.0.9 → careamics-0.0.10}/src/careamics/__init__.py

@@ -11,8 +11,6 @@ __all__ = [
     "CAREamist",
     "Configuration",
     "algorithm_factory",
-    "configuration_factory",
-    "data_factory",
     "load_configuration",
     "save_configuration",
 ]
@@ -21,8 +19,6 @@ from .careamist import CAREamist
 from .config import (
     Configuration,
     algorithm_factory,
-    configuration_factory,
-    data_factory,
     load_configuration,
     save_configuration,
 )

{careamics-0.0.9 → careamics-0.0.10}/src/careamics/careamist.py

@@ -157,7 +157,6 @@ class CAREamist:
                 self.cfg = load_configuration(source)
 
                 # instantiate model
-                # TODO call model factory here
                 if isinstance(self.cfg.algorithm_config, UNetBasedAlgorithm):
                     self.model = FCNModule(
                         algorithm_config=self.cfg.algorithm_config,

{careamics-0.0.9 → careamics-0.0.10}/src/careamics/config/__init__.py

@@ -8,29 +8,22 @@ while `*_configuration` is reserved for the main configuration models, including
 
 __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",
 ]
@@ -43,21 +36,16 @@ from .algorithms import (
     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 .data import DataConfig
 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-0.0.9/src/careamics/config/care_configuration.py → careamics-0.0.10/src/careamics/config/algorithms/care_algorithm_model.py

@@ -1,10 +1,17 @@
-"""CARE Pydantic configuration."""
+"""CARE algorithm configuration."""
+
+from typing import Annotated, Literal
 
 from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import AfterValidator
+
+from careamics.config.architectures import UNetModel
+from careamics.config.validators import (
+    model_without_final_activation,
+    model_without_n2v2,
+)
 
-from careamics.config.algorithms.care_algorithm_model import CAREAlgorithm
-from careamics.config.configuration import Configuration
-from careamics.config.data import DataConfig
+from .unet_algorithm_model import UNetBasedAlgorithm
 
 CARE = "CARE"
 
@@ -24,14 +31,29 @@ CARE_REF = CiteEntry(
 )
 
 
-class CAREConfiguration(Configuration):
-    """CARE configuration."""
+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."""
 
-    algorithm_config: CAREAlgorithm
-    """Algorithm configuration."""
+    loss: Literal["mae", "mse"] = "mae"
+    """CARE-compatible loss function."""
 
-    data_config: DataConfig
-    """Data configuration."""
+    model: Annotated[
+        UNetModel,
+        AfterValidator(model_without_n2v2),
+        AfterValidator(model_without_final_activation),
+    ]
+    """UNet without a final activation function and without the `n2v2` modifications."""
 
     def get_algorithm_friendly_name(self) -> str:
         """
@@ -56,7 +78,7 @@ class CAREConfiguration(Configuration):
         return [
             "restoration",
             "UNet",
-            "3D" if "Z" in self.data_config.axes else "2D",
+            "3D" if self.model.is_3D() else "2D",
             "CAREamics",
             "pytorch",
             CARE,

careamics-0.0.9/src/careamics/config/n2n_configuration.py → careamics-0.0.10/src/careamics/config/algorithms/n2n_algorithm_model.py

@@ -1,10 +1,17 @@
-"""N2N configuration."""
+"""N2N Algorithm configuration."""
+
+from typing import Annotated, Literal
 
 from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import AfterValidator
+
+from careamics.config.architectures import UNetModel
+from careamics.config.validators import (
+    model_without_final_activation,
+    model_without_n2v2,
+)
 
-from careamics.config.algorithms import N2NAlgorithm
-from careamics.config.configuration import Configuration
-from careamics.config.data import DataConfig
+from .unet_algorithm_model import UNetBasedAlgorithm
 
 N2N = "Noise2Noise"
 
@@ -25,14 +32,21 @@ N2N_REF = CiteEntry(
 )
 
 
-class N2NConfiguration(Configuration):
-    """Noise2Noise configuration."""
+class N2NAlgorithm(UNetBasedAlgorithm):
+    """Noise2Noise Algorithm configuration."""
+
+    algorithm: Literal["n2n"] = "n2n"
+    """N2N Algorithm name."""
 
-    algorithm_config: N2NAlgorithm
-    """Algorithm configuration."""
+    loss: Literal["mae", "mse"] = "mae"
+    """N2N-compatible loss function."""
 
-    data_config: DataConfig
-    """Data configuration."""
+    model: Annotated[
+        UNetModel,
+        AfterValidator(model_without_n2v2),
+        AfterValidator(model_without_final_activation),
+    ]
+    """UNet without a final activation function and without the `n2v2` modifications."""
 
     def get_algorithm_friendly_name(self) -> str:
         """
@@ -57,7 +71,7 @@ class N2NConfiguration(Configuration):
         return [
             "restoration",
             "UNet",
-            "3D" if "Z" in self.data_config.axes else "2D",
+            "3D" if self.model.is_3D() else "2D",
             "CAREamics",
             "pytorch",
             N2N,

careamics-0.0.9/src/careamics/config/n2v_configuration.py → careamics-0.0.10/src/careamics/config/algorithms/n2v_algorithm_model.py

@@ -1,13 +1,20 @@
-"""N2V configuration."""
+""""N2V Algorithm configuration."""
+
+from typing import Annotated, Literal
 
 from bioimageio.spec.generic.v0_3 import CiteEntry
-from pydantic import model_validator
+from pydantic import AfterValidator, ConfigDict, model_validator
 from typing_extensions import Self
 
-from careamics.config.algorithms import N2VAlgorithm
-from careamics.config.configuration import Configuration
-from careamics.config.data.n2v_data_model import N2VDataConfig
-from careamics.config.support import SupportedPixelManipulation
+from careamics.config.architectures import UNetModel
+from careamics.config.support import SupportedPixelManipulation, SupportedStructAxis
+from careamics.config.transformations import N2VManipulateModel
+from careamics.config.validators import (
+    model_matching_in_out_channels,
+    model_without_final_activation,
+)
+
+from .unet_algorithm_model import UNetBasedAlgorithm
 
 N2V = "Noise2Void"
 N2V2 = "N2V2"
@@ -80,12 +87,24 @@ STR_N2V2_DESCRIPTION = (
 )
 
 
-class N2VConfiguration(Configuration):
-    """N2V configuration."""
+class N2VAlgorithm(UNetBasedAlgorithm):
+    """N2V Algorithm configuration."""
+
+    model_config = ConfigDict(validate_assignment=True)
 
-    algorithm_config: N2VAlgorithm
+    algorithm: Literal["n2v"] = "n2v"
+    """N2V Algorithm name."""
 
-    data_config: N2VDataConfig
+    loss: Literal["n2v"] = "n2v"
+    """N2V loss function."""
+
+    n2v_config: N2VManipulateModel = N2VManipulateModel()
+
+    model: Annotated[
+        UNetModel,
+        AfterValidator(model_matching_in_out_channels),
+        AfterValidator(model_without_final_activation),
+    ]
 
     @model_validator(mode="after")
     def validate_n2v2(self) -> Self:
@@ -96,31 +115,26 @@ class N2VConfiguration(Configuration):
         Self
             The validateed configuration.
 
-
         Raises
         ------
         ValueError
             If N2V2 is used with the wrong pixel manipulation strategy.
         """
-        if self.algorithm_config.model.n2v2:
-            if (
-                self.data_config.get_masking_strategy()
-                != SupportedPixelManipulation.MEDIAN.value
-            ):
+        if self.model.n2v2:
+            if self.n2v_config.strategy != SupportedPixelManipulation.MEDIAN.value:
                 raise ValueError(
                     f"N2V2 can only be used with the "
-                    f"{SupportedPixelManipulation.MEDIAN} pixel manipulation strategy"
-                    f". Change the N2VManipulate transform strategy."
+                    f"{SupportedPixelManipulation.MEDIAN} pixel manipulation strategy. "
+                    f"Change the `strategy` parameters in `n2v_config` to "
+                    f"{SupportedPixelManipulation.MEDIAN}."
                 )
         else:
-            if (
-                self.data_config.get_masking_strategy()
-                != SupportedPixelManipulation.UNIFORM.value
-            ):
+            if self.n2v_config.strategy != SupportedPixelManipulation.UNIFORM.value:
                 raise ValueError(
                     f"N2V can only be used with the "
-                    f"{SupportedPixelManipulation.UNIFORM} pixel manipulation strategy"
-                    f". Change the N2VManipulate transform strategy."
+                    f"{SupportedPixelManipulation.UNIFORM} pixel manipulation strategy."
+                    f" Change the `strategy` parameters in `n2v_config` to "
+                    f"{SupportedPixelManipulation.UNIFORM}."
                 )
         return self
 
@@ -128,13 +142,30 @@ class N2VConfiguration(Configuration):
         """
         Set the configuration to use N2V2 or the vanilla Noise2Void.
 
+        This method ensures that N2V2 is set correctly and remain coherent, as opposed
+        to setting the different parameters individually.
+
         Parameters
         ----------
         use_n2v2 : bool
             Whether to use N2V2.
         """
-        self.data_config.set_n2v2(use_n2v2)
-        self.algorithm_config.model.n2v2 = use_n2v2
+        if use_n2v2:
+            self.n2v_config.strategy = SupportedPixelManipulation.MEDIAN.value
+            self.model.n2v2 = True
+        else:
+            self.n2v_config.strategy = SupportedPixelManipulation.UNIFORM.value
+            self.model.n2v2 = False
+
+    def is_struct_n2v(self) -> bool:
+        """Check if the configuration is using structN2V.
+
+        Returns
+        -------
+        bool
+            Whether the configuration is using structN2V.
+        """
+        return self.n2v_config.struct_mask_axis != SupportedStructAxis.NONE.value
 
     def get_algorithm_friendly_name(self) -> str:
         """
@@ -145,8 +176,8 @@ class N2VConfiguration(Configuration):
         str
             Friendly name.
         """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
+        use_n2v2 = self.model.n2v2
+        use_structN2V = self.is_struct_n2v()
 
         if use_n2v2 and use_structN2V:
             return STRUCT_N2V2
@@ -166,14 +197,14 @@ class N2VConfiguration(Configuration):
         list[str]
             List of keywords.
         """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
+        use_n2v2 = self.model.n2v2
+        use_structN2V = self.is_struct_n2v()
 
         keywords = [
             "denoising",
             "restoration",
             "UNet",
-            "3D" if "Z" in self.data_config.axes else "2D",
+            "3D" if self.model.is_3D() else "2D",
             "CAREamics",
             "pytorch",
             N2V,
@@ -197,8 +228,8 @@ class N2VConfiguration(Configuration):
         str
             Algorithm references.
         """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
+        use_n2v2 = self.model.n2v2
+        use_structN2V = self.is_struct_n2v()
 
         references = [
             N2V_REF.text + " doi: " + N2V_REF.doi,
@@ -229,8 +260,8 @@ class N2VConfiguration(Configuration):
         List[CiteEntry]
             List of citation entries.
         """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
+        use_n2v2 = self.model.n2v2
+        use_structN2V = self.is_struct_n2v()
 
         references = [N2V_REF]
 
@@ -253,8 +284,8 @@ class N2VConfiguration(Configuration):
         str
             Description of the algorithm.
         """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
+        use_n2v2 = self.model.n2v2
+        use_structN2V = self.is_struct_n2v()
 
         if use_n2v2 and use_structN2V:
             return STR_N2V2_DESCRIPTION

{careamics-0.0.9 → careamics-0.0.10}/src/careamics/config/configuration.py

@@ -10,10 +10,20 @@ from bioimageio.spec.generic.v0_3 import CiteEntry
 from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
 from typing_extensions import Self
 
-from careamics.config.algorithms import UNetBasedAlgorithm, VAEBasedAlgorithm
-from careamics.config.data import GeneralDataConfig
+from careamics.config.algorithms import (
+    CAREAlgorithm,
+    N2NAlgorithm,
+    N2VAlgorithm,
+)
+from careamics.config.data import DataConfig
 from careamics.config.training_model import TrainingConfig
 
+ALGORITHMS = Union[
+    CAREAlgorithm,
+    N2NAlgorithm,
+    N2VAlgorithm,
+]
+
 
 class Configuration(BaseModel):
     """
@@ -87,7 +97,7 @@ class Configuration(BaseModel):
     Examples
     --------
     Minimum example:
-    >>> from careamics import configuration_factory
+    >>> from careamics import Configuration
     >>> config_dict = {
     ...         "experiment_name": "N2V_experiment",
     ...         "algorithm_config": {
@@ -106,7 +116,7 @@ class Configuration(BaseModel):
     ...             "axes": "SYX",
     ...         },
     ...     }
-    >>> config = configuration_factory(config_dict)
+    >>> config = Configuration(**config_dict)
     """
 
     model_config = ConfigDict(
@@ -123,13 +133,11 @@ class Configuration(BaseModel):
     """Name of the experiment, used to name logs and checkpoints."""
 
     # Sub-configurations
-    algorithm_config: Union[UNetBasedAlgorithm, VAEBasedAlgorithm] = Field(
-        discriminator="algorithm"
-    )
+    algorithm_config: ALGORITHMS = Field(discriminator="algorithm")
     """Algorithm configuration, holding all parameters required to configure the
     model."""
 
-    data_config: GeneralDataConfig
+    data_config: DataConfig
     """Data configuration, holding all parameters required to configure the training
     data loader."""
 
@@ -233,7 +241,7 @@ class Configuration(BaseModel):
         str
             Algorithm name.
         """
-        raise ValueError("Unknown algorithm.")
+        return self.algorithm_config.get_algorithm_friendly_name()
 
     def get_algorithm_description(self) -> str:
         """
@@ -246,7 +254,7 @@ class Configuration(BaseModel):
         str
             Description of the algorithm.
         """
-        raise ValueError("No algorithm description available.")
+        return self.algorithm_config.get_algorithm_description()
 
     def get_algorithm_citations(self) -> list[CiteEntry]:
         """
@@ -259,7 +267,7 @@ class Configuration(BaseModel):
         List[CiteEntry]
             List of citation entries.
         """
-        raise ValueError("No algorithm citations available.")
+        return self.algorithm_config.get_algorithm_citations()
 
     def get_algorithm_references(self) -> str:
         """
@@ -272,7 +280,7 @@ class Configuration(BaseModel):
         str
             Algorithm references.
         """
-        raise ValueError("No algorithm references available.")
+        return self.algorithm_config.get_algorithm_references()
 
     def get_algorithm_keywords(self) -> list[str]:
         """
@@ -283,7 +291,7 @@ class Configuration(BaseModel):
         list[str]
             List of keywords.
         """
-        return ["CAREamics"]
+        return self.algorithm_config.get_algorithm_keywords()
 
     def model_dump(
         self,