careamics 0.0.15__tar.gz → 0.0.16__tar.gz

{careamics-0.0.15 → careamics-0.0.16}/.github/workflows/ci.yml

@@ -27,9 +27,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         # 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, windows-latest] # macos-latest
+        platform: [ubuntu-latest, windows-latest] # macos-latest  
 
     steps:
       - name: 🛑 Cancel Previous Runs

{careamics-0.0.15 → careamics-0.0.16}/.github/workflows/ci_macos.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         # 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: [macos-latest]
 

{careamics-0.0.15 → careamics-0.0.16}/.pre-commit-config.yaml

@@ -14,11 +14,11 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.12.11
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
-        args: [--fix, --target-version, py310]
+        args: [--fix, --target-version, py311]
 
   - repo: https://github.com/psf/black
     rev: 25.1.0
@@ -26,14 +26,14 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.1
+    rev: v1.17.1
     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<2.0.0
+          - numpy
           - pydantic
           - types-PyYAML
           - types-setuptools

{careamics-0.0.15 → careamics-0.0.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.15
+Version: 0.0.16
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -10,28 +10,31 @@ License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
-Requires-Python: >=3.10
-Requires-Dist: bioimageio-core==0.9.0
-Requires-Dist: matplotlib<=3.10.3
-Requires-Dist: numpy<2.0.0
-Requires-Dist: pillow<=11.2.1
-Requires-Dist: psutil<=7.0.0
+Requires-Python: >=3.11
+Requires-Dist: bioimageio-core>=0.9.0
+Requires-Dist: matplotlib<=3.10.6
+Requires-Dist: numpy>=1.21
+Requires-Dist: numpy>=2.1.0; python_version >= '3.13'
+Requires-Dist: pillow<=11.3.0
+Requires-Dist: psutil<=7.1.0
 Requires-Dist: pydantic<=2.12,>=2.11
-Requires-Dist: pytorch-lightning<=2.5.2,>=2.2
-Requires-Dist: pyyaml!=6.0.0,<=6.0.2
+Requires-Dist: pytorch-lightning<=2.5.5,>=2.2
+Requires-Dist: pyyaml!=6.0.0,<=6.0.3
 Requires-Dist: scikit-image<=0.25.2
-Requires-Dist: tifffile<=2025.5.10
-Requires-Dist: torch<=2.7.1,>=2.0
-Requires-Dist: torchvision<=0.22.1
-Requires-Dist: typer<=0.16.0,>=0.12.3
-Requires-Dist: zarr<3.0.0
+Requires-Dist: tifffile<=2025.9.30
+Requires-Dist: torch<=2.8.0,>=2.0
+Requires-Dist: torchvision<=0.23.0
+Requires-Dist: typer<=0.19.2,>=0.12.3
+Requires-Dist: validators<=0.35.0
+Requires-Dist: zarr<4.0.0,>=3.0.0
 Provides-Extra: czi
 Requires-Dist: pylibczirw<6.0.0,>=4.1.2; extra == 'czi'
 Provides-Extra: dev
+Requires-Dist: ml-dtypes>=0.5.0; extra == 'dev'
 Requires-Dist: onnx; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'

{careamics-0.0.15 → careamics-0.0.16}/pyproject.toml

@@ -20,7 +20,7 @@ name = "careamics"
 dynamic = ["version"]
 description = "Toolbox for running N2V and friends."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = { text = "BSD-3-Clause" }
 authors = [
     { name = 'CAREamics team', email = 'rse@fht.org' },
@@ -34,27 +34,29 @@ authors = [
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: BSD License",
     "Typing :: Typed",
 ]
 dependencies = [
-    'numpy<2.0.0',
-    'torch>=2.0,<=2.7.1',
-    'torchvision<=0.22.1',
-    'bioimageio.core==0.9.0',
-    'tifffile<=2025.5.10',
-    'psutil<=7.0.0',
+    "numpy>=1.21",
+    "numpy>=2.1.0; python_version>='3.13'", # prevents ml_dtypes conflict in py313
+    'torch>=2.0,<=2.8.0',
+    'torchvision<=0.23.0',
+    'bioimageio.core>=0.9.0',
+    'tifffile<=2025.9.30',
+    'psutil<=7.1.0',
     'pydantic>=2.11,<=2.12',
-    'pytorch_lightning>=2.2,<=2.5.2',
-    'pyyaml<=6.0.2,!=6.0.0',
-    'typer>=0.12.3,<=0.16.0',
+    'pytorch_lightning>=2.2,<=2.5.5',
+    'pyyaml!=6.0.0,<=6.0.3',
+    'typer>=0.12.3,<=0.19.2',
     'scikit-image<=0.25.2',
-    'zarr<3.0.0',
-    'pillow<=11.2.1',
-    'matplotlib<=3.10.3',
+    'zarr>=3.0.0,<4.0.0',
+    'pillow<=11.3.0',
+    'matplotlib<=3.10.6',
+    'validators<=0.35.0'
 ]
 
 [project.optional-dependencies]
@@ -67,8 +69,11 @@ dev = [
     "pre-commit",
     "pytest",
     "pytest-cov",
-    "onnx",
     "sybil",      # doctesting
+
+    # libraries used in some tests
+    "onnx",
+    "ml_dtypes>=0.5.0" # required by onnx, causes issues in gh runners with py313
 ]
 
 # notebooks

{careamics-0.0.15 → careamics-0.0.16}/src/careamics/careamist.py

@@ -208,17 +208,11 @@ class CAREamist:
 
         # instantiate trainer
         self.trainer = Trainer(
-            max_epochs=self.cfg.training_config.num_epochs,
-            precision=self.cfg.training_config.precision,
-            max_steps=self.cfg.training_config.max_steps,
-            check_val_every_n_epoch=self.cfg.training_config.check_val_every_n_epoch,
             enable_progress_bar=enable_progress_bar,
-            accumulate_grad_batches=self.cfg.training_config.accumulate_grad_batches,
-            gradient_clip_val=self.cfg.training_config.gradient_clip_val,
-            gradient_clip_algorithm=self.cfg.training_config.gradient_clip_algorithm,
             callbacks=self.callbacks,
             default_root_dir=self.work_dir,
             logger=experiment_logger,
+            **self.cfg.training_config.lightning_trainer_config or {},
         )
 
         # place holder for the datamodules
@@ -264,7 +258,7 @@ class CAREamist:
                 HyperParametersCallback(self.cfg),
                 ModelCheckpoint(
                     dirpath=self.work_dir / Path("checkpoints"),
-                    filename=self.cfg.experiment_name,
+                    filename=f"{self.cfg.experiment_name}_{{epoch:02d}}_step_{{step}}",
                     **self.cfg.training_config.checkpoint_callback.model_dump(),
                 ),
             ]
@@ -823,12 +817,12 @@ class CAREamist:
 
         # extract file names
         source_path: Union[Path, str, NDArray]
-        source_data_type: Literal["array", "tiff", "custom"]
+        source_data_type: Literal["array", "tiff", "czi", "custom"]
         if isinstance(source, PredictDataModule):
             source_path = source.pred_data
             source_data_type = source.data_type
             extension_filter = source.extension_filter
-        elif isinstance(source, str | Path):
+        elif isinstance(source, (str | Path)):
             source_path = source
             source_data_type = data_type or self.cfg.data_config.data_type
             extension_filter = SupportedData.get_extension_pattern(
@@ -841,7 +835,7 @@ class CAREamist:
             raise ValueError(
                 "Predicting to disk is not supported for input type 'array'."
             )
-        assert isinstance(source_path, str | Path)  # because data_type != "array"
+        assert isinstance(source_path, (Path | str))  # because data_type != "array"
         source_path = Path(source_path)
 
         file_paths = list_files(source_path, source_data_type, extension_filter)
@@ -879,7 +873,7 @@ class CAREamist:
 
     def export_to_bmz(
         self,
-        path_to_archive: Union[Path, str],
+        path_to_archive: Union[Path | str],
         friendly_model_name: str,
         input_array: NDArray,
         authors: list[dict],

{careamics-0.0.15 → careamics-0.0.16}/src/careamics/cli/conf.py

@@ -116,7 +116,11 @@ def care(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -175,6 +179,7 @@ def care(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,
@@ -203,7 +208,11 @@ def n2n(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -259,6 +268,7 @@ def n2n(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,
@@ -287,7 +297,11 @@ def n2v(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -364,6 +378,7 @@ def n2v(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,

{careamics-0.0.15 → careamics-0.0.16}/src/careamics/config/__init__.py

@@ -12,8 +12,10 @@ __all__ = [
     "Configuration",
     "DataConfig",
     "GaussianMixtureNMConfig",
+    "HDNAlgorithm",
     "InferenceConfig",
     "LVAELossConfig",
+    "MicroSplitAlgorithm",
     "MultiChannelNMConfig",
     "N2NAlgorithm",
     "N2VAlgorithm",
@@ -22,6 +24,8 @@ __all__ = [
     "VAEBasedAlgorithm",
     "algorithm_factory",
     "create_care_configuration",
+    "create_hdn_configuration",
+    "create_microsplit_configuration",
     "create_n2n_configuration",
     "create_n2v_configuration",
     "load_configuration",
@@ -30,6 +34,8 @@ __all__ = [
 
 from .algorithms import (
     CAREAlgorithm,
+    HDNAlgorithm,
+    MicroSplitAlgorithm,
     N2NAlgorithm,
     N2VAlgorithm,
     UNetBasedAlgorithm,
@@ -40,6 +46,8 @@ from .configuration import Configuration
 from .configuration_factories import (
     algorithm_factory,
     create_care_configuration,
+    create_hdn_configuration,
+    create_microsplit_configuration,
     create_n2n_configuration,
     create_n2v_configuration,
 )

{careamics-0.0.15 → careamics-0.0.16}/src/careamics/config/algorithms/__init__.py

@@ -2,6 +2,8 @@
 
 __all__ = [
     "CAREAlgorithm",
+    "HDNAlgorithm",
+    "MicroSplitAlgorithm",
     "N2NAlgorithm",
     "N2VAlgorithm",
     "UNetBasedAlgorithm",
@@ -9,6 +11,8 @@ __all__ = [
 ]
 
 from .care_algorithm_model import CAREAlgorithm
+from .hdn_algorithm_model import HDNAlgorithm
+from .microsplit_algorithm_model import MicroSplitAlgorithm
 from .n2n_algorithm_model import N2NAlgorithm
 from .n2v_algorithm_model import N2VAlgorithm
 from .unet_algorithm_model import UNetBasedAlgorithm

careamics-0.0.16/src/careamics/config/algorithms/hdn_algorithm_model.py

@@ -0,0 +1,103 @@
+"""HDN algorithm configuration."""
+
+from typing import Literal
+
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import ConfigDict
+
+from careamics.config.algorithms.vae_algorithm_model import VAEBasedAlgorithm
+from careamics.config.architectures import LVAEModel
+from careamics.config.loss_model import LVAELossConfig
+
+HDN = "Hierarchical DivNoising"
+
+HDN_DESCRIPTION = (
+    "HDN leverages a hierarchical VAE to perform image "
+    "restoration. It is designed to be interpretable and unsupervised, "
+    "making it suitable for a wide range of microscopy images."
+)
+HDN_REF = CiteEntry(
+    text='Prakash, M., Delbracio, M., Milanfar, P., Jug, F. 2022. "Interpretable '
+    'Unsupervised Diversity Denoising and Artefact Removal." The International '
+    "Conference on Learning Representations (ICLR).",
+    doi="10.1561/2200000056",
+)
+
+
+class HDNAlgorithm(VAEBasedAlgorithm):
+    """HDN algorithm configuration."""
+
+    model_config = ConfigDict(validate_assignment=True)
+
+    algorithm: Literal["hdn"] = "hdn"
+
+    loss: LVAELossConfig
+
+    model: LVAEModel  # TODO add validators
+
+    is_supervised: bool = False
+
+    def get_algorithm_friendly_name(self) -> str:
+        """
+        Get the algorithm friendly name.
+
+        Returns
+        -------
+        str
+            Friendly name of the algorithm.
+        """
+        return HDN
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        return [
+            "restoration",
+            "VAE",
+            "3D" if self.model.is_3D() else "2D",
+            "CAREamics",
+            "pytorch",
+        ]
+
+    def get_algorithm_references(self) -> str:
+        """
+        Get the algorithm references.
+
+        This is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Algorithm references.
+        """
+        return HDN_REF.text + " doi: " + HDN_REF.doi
+
+    def get_algorithm_citations(self) -> list[CiteEntry]:
+        """
+        Return a list of citation entries of the current algorithm.
+
+        This is used to generate the model description for the BioImage Model Zoo.
+
+        Returns
+        -------
+        List[CiteEntry]
+            List of citation entries.
+        """
+        return [HDN_REF]
+
+    def get_algorithm_description(self) -> str:
+        """
+        Get the algorithm description.
+
+        Returns
+        -------
+        str
+            Algorithm description.
+        """
+        return HDN_DESCRIPTION

careamics-0.0.16/src/careamics/config/algorithms/microsplit_algorithm_model.py

@@ -0,0 +1,103 @@
+"""MicroSplit algorithm configuration."""
+
+from typing import Literal
+
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import ConfigDict
+
+from careamics.config.algorithms.vae_algorithm_model import VAEBasedAlgorithm
+from careamics.config.architectures import LVAEModel
+from careamics.config.loss_model import LVAELossConfig
+
+MICROSPLIT = "MicroSplit"
+
+MICROSPLIT_DESCRIPTION = """MicroSplit is a self-supervised deep learning method for
+microscopy image splitting that combines the strengths of both denoising and
+representation learning approaches."""
+
+MICROSPLIT_REF = CiteEntry(
+    text='Prakash, M., Delbracio, M., Milanfar, P., Jug, F. 2022. "Interpretable '
+    'Unsupervised Diversity Denoising and Artefact Removal." The International '
+    "Conference on Learning Representations (ICLR).",
+    doi="10.1561/2200000056",
+)
+
+
+class MicroSplitAlgorithm(VAEBasedAlgorithm):
+    """MicroSplit algorithm configuration."""
+
+    model_config = ConfigDict(validate_assignment=True)
+
+    algorithm: Literal["microsplit"] = "microsplit"
+
+    loss: LVAELossConfig
+
+    model: LVAEModel  # TODO add validators
+
+    is_supervised: bool = True
+
+    def get_algorithm_friendly_name(self) -> str:
+        """
+        Get the algorithm friendly name.
+
+        Returns
+        -------
+        str
+            Friendly name of the algorithm.
+        """
+        return MICROSPLIT
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        return [
+            "restoration",
+            "VAE",
+            "self-supervised",
+            "3D" if self.model.is_3D() else "2D",
+            "CAREamics",
+            "pytorch",
+        ]
+
+    def get_algorithm_references(self) -> str:
+        """
+        Get the algorithm references.
+
+        This is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Algorithm references.
+        """
+        return MICROSPLIT_REF.text + " doi: " + MICROSPLIT_REF.doi
+
+    def get_algorithm_citations(self) -> list[CiteEntry]:
+        """
+        Return a list of citation entries of the current algorithm.
+
+        This is used to generate the model description for the BioImage Model Zoo.
+
+        Returns
+        -------
+        List[CiteEntry]
+            List of citation entries.
+        """
+        return [MICROSPLIT_REF]
+
+    def get_algorithm_description(self) -> str:
+        """
+        Get the algorithm description.
+
+        Returns
+        -------
+        str
+            Algorithm description.
+        """
+        return MICROSPLIT_DESCRIPTION

{careamics-0.0.15 → careamics-0.0.16}/src/careamics/config/algorithms/n2v_algorithm_model.py

@@ -1,10 +1,9 @@
 """N2V Algorithm configuration."""
 
-from typing import Annotated, Literal
+from typing import Annotated, Literal, Self
 
 from bioimageio.spec.generic.v0_3 import CiteEntry
 from pydantic import AfterValidator, ConfigDict, model_validator
-from typing_extensions import Self
 
 from careamics.config.architectures import UNetModel
 from careamics.config.support import SupportedPixelManipulation, SupportedStructAxis