careamics 0.0.5__py3-none-any.whl → 0.0.7__py3-none-any.whl

careamics/utils/plotting.py

@@ -0,0 +1,78 @@
+"""Plotting utilities."""
+
+from typing import Optional
+
+import matplotlib.pyplot as plt
+import numpy as np
+import torch
+from numpy.typing import NDArray
+
+from careamics.models.lvae.noise_models import GaussianMixtureNoiseModel
+
+
+def plot_noise_model_probability_distribution(
+    noise_model: GaussianMixtureNoiseModel,
+    signalBinIndex: int,
+    histogram: NDArray,
+    channel: Optional[str] = None,
+    number_of_bins: int = 100,
+) -> None:
+    """Plot probability distribution P(x|s) for a certain ground truth signal.
+
+    Predictions from both Histogram and GMM-based
+    Noise models are displayed for comparison.
+
+    Parameters
+    ----------
+    noise_model : GaussianMixtureNoiseModel
+        Trained GaussianMixtureNoiseModel.
+    signalBinIndex : int
+        Index of signal bin. Values go from 0 to number of bins (`n_bin`).
+    histogram : NDArray
+        Histogram based noise model.
+    channel : Optional[str], optional
+        Channel name used for plotting. Default is None.
+    number_of_bins : int, optional
+        Number of bins in the resulting histogram. Default is 100.
+    """
+    min_signal = noise_model.min_signal.item()
+    max_signal = noise_model.max_signal.item()
+    bin_size = (max_signal - min_signal) / number_of_bins
+
+    query_signal_normalized = signalBinIndex / number_of_bins
+    query_signal = query_signal_normalized * (max_signal - min_signal) + min_signal
+    query_signal += bin_size / 2
+    query_signal = torch.tensor(query_signal)
+
+    query_observations = torch.arange(min_signal, max_signal, bin_size)
+    query_observations += bin_size / 2
+
+    likelihoods = noise_model.likelihood(
+        observations=query_observations, signals=query_signal
+    ).numpy()
+
+    plt.figure(figsize=(12, 5))
+    if channel:
+        plt.suptitle(f"Noise model for channel {channel}")
+    else:
+        plt.suptitle("Noise model")
+
+    plt.subplot(1, 2, 1)
+    plt.xlabel("Observation Bin")
+    plt.ylabel("Signal Bin")
+    plt.imshow(histogram**0.25, cmap="gray")
+    plt.axhline(y=signalBinIndex + 0.5, linewidth=5, color="blue", alpha=0.5)
+
+    plt.subplot(1, 2, 2)
+    plt.plot(
+        query_observations,
+        likelihoods,
+        label="GMM : " + " signal = " + str(np.round(query_signal, 2)),
+        marker=".",
+        color="red",
+        linewidth=2,
+    )
+    plt.xlabel("Observations (x) for signal s = " + str(query_signal))
+    plt.ylabel("Probability Density")
+    plt.title("Probability Distribution P(x|s) at signal =" + str(query_signal))
+    plt.legend()

careamics/utils/torch_utils.py

@@ -5,7 +5,7 @@ These functions are used to control certain aspects and behaviours of PyTorch.
 """
 
 import inspect
-from typing import Dict, Union
+from typing import Union
 
 import torch
 
@@ -27,12 +27,12 @@ def filter_parameters(
     ----------
     func : type
         Class object.
-    user_params : Dict
+    user_params : dict
         User provided parameters.
 
     Returns
     -------
-    Dict
+    dict
         Parameters matching `func`'s signature.
     """
     # Get the list of all default parameters
@@ -64,13 +64,13 @@ def get_optimizer(name: str) -> torch.optim.Optimizer:
     return getattr(torch.optim, name)
 
 
-def get_optimizers() -> Dict[str, str]:
+def get_optimizers() -> dict[str, str]:
     """
     Return the list of all optimizers available in torch.optim.
 
     Returns
     -------
-    Dict
+    dict
         Optimizers available in torch.optim.
     """
     optims = {}
@@ -106,13 +106,13 @@ def get_scheduler(
     return getattr(torch.optim.lr_scheduler, name)
 
 
-def get_schedulers() -> Dict[str, str]:
+def get_schedulers() -> dict[str, str]:
     """
     Return the list of all schedulers available in torch.optim.lr_scheduler.
 
     Returns
     -------
-    Dict
+    dict
         Schedulers available in torch.optim.lr_scheduler.
     """
     schedulers = {}

{careamics-0.0.5.dist-info → careamics-0.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.5
+Version: 0.0.7
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -17,17 +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: 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<=0.25.1
+Requires-Dist: tifffile<=2025.1.10
+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: zarr<3.0.0
 Provides-Extra: dev
 Requires-Dist: onnx; extra == 'dev'
@@ -40,7 +42,7 @@ 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-0.0.7.dist-info/RECORD

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careamics/config/architectures/custom_model.py

@@ -1,162 +0,0 @@
-"""Custom architecture Pydantic model."""
-
-from __future__ import annotations
-
-import inspect
-from pprint import pformat
-from typing import Any, Literal
-
-from pydantic import ConfigDict, field_validator, model_validator
-from torch.nn import Module
-from typing_extensions import Self
-
-from .architecture_model import ArchitectureModel
-from .register_model import get_custom_model
-
-
-class CustomModel(ArchitectureModel):
-    """Custom model configuration.
-
-    This Pydantic model allows storing parameters for a custom model. In order for the
-    model to be valid, the specific model needs to be registered using the
-    `register_model` decorator, and its name correctly passed to this model
-    configuration (see Examples).
-
-    Attributes
-    ----------
-    architecture : Literal["custom"]
-        Discriminator for the custom model, must be set to "custom".
-    name : str
-        Name of the custom model.
-    parameters : CustomParametersModel
-        All parameters, required for the initialization of the torch module have to be
-        passed here.
-
-    Raises
-    ------
-    ValueError
-        If the custom model `name` is unknown.
-    ValueError
-        If the custom model is not a torch Module subclass.
-    ValueError
-        If the custom model parameters are not valid.
-
-    Examples
-    --------
-    >>> from torch import nn, ones
-    >>> from careamics.config import CustomModel, register_model
-    >>> # Register a custom model
-    >>> @register_model(name="my_linear")
-    ... class LinearModel(nn.Module):
-    ...    def __init__(self, in_features, out_features, *args, **kwargs):
-    ...        super().__init__()
-    ...        self.in_features = in_features
-    ...        self.out_features = out_features
-    ...        self.weight = nn.Parameter(ones(in_features, out_features))
-    ...        self.bias = nn.Parameter(ones(out_features))
-    ...    def forward(self, input):
-    ...        return (input @ self.weight) + self.bias
-    ...
-    >>> # Create a configuration
-    >>> config_dict = {
-    ...     "architecture": "custom",
-    ...     "name": "my_linear",
-    ...     "in_features": 10,
-    ...     "out_features": 5,
-    ... }
-    >>> config = CustomModel(**config_dict)
-    """
-
-    # pydantic model config
-    model_config = ConfigDict(
-        extra="allow",
-    )
-
-    # discriminator used for choosing the pydantic model in Model
-    architecture: Literal["custom"]
-    """Name of the architecture."""
-
-    name: str
-    """Name of the custom model."""
-
-    @field_validator("name")
-    @classmethod
-    def custom_model_is_known(cls, value: str) -> str:
-        """Check whether the custom model is known.
-
-        Parameters
-        ----------
-        value : str
-            Name of the custom model as registered using the `@register_model`
-            decorator.
-
-        Returns
-        -------
-        str
-            The custom model name.
-        """
-        # delegate error to get_custom_model
-        model = get_custom_model(value)
-
-        # check if it is a torch Module subclass
-        if not issubclass(model, Module):
-            raise ValueError(
-                f'Retrieved class {model} with name "{value}" is not a '
-                f"torch.nn.Module subclass."
-            )
-
-        return value
-
-    @model_validator(mode="after")
-    def check_parameters(self: Self) -> Self:
-        """Validate model by instantiating the model with the parameters.
-
-        Returns
-        -------
-        Self
-            The validated model.
-        """
-        # instantiate model
-        try:
-            get_custom_model(self.name)(**self.model_dump())
-        except Exception as e:
-            raise ValueError(
-                f"while passing parameters to the model {e}. Verify that all "
-                f"mandatory parameters are provided, and that either the {e} accepts "
-                f"*args and **kwargs in its __init__() method, or that no additional"
-                f"parameter is provided. Trace: "
-                f"filename: {inspect.trace()[-1].filename}, function: "
-                f"{inspect.trace()[-1].function}, line: {inspect.trace()[-1].lineno}"
-            ) from None
-
-        return self
-
-    def __str__(self) -> str:
-        """Pretty string representing the configuration.
-
-        Returns
-        -------
-        str
-            Pretty string.
-        """
-        return pformat(self.model_dump())
-
-    def model_dump(self, **kwargs: Any) -> dict[str, Any]:
-        """Dump the model configuration.
-
-        Parameters
-        ----------
-        **kwargs : Any
-            Additional keyword arguments from Pydantic BaseModel model_dump method.
-
-        Returns
-        -------
-        dict[str, Any]
-            Model configuration.
-        """
-        model_dict = super().model_dump()
-
-        # remove the name key
-        model_dict.pop("name")
-
-        return model_dict

careamics/config/architectures/register_model.py

@@ -1,103 +0,0 @@
-"""Custom model registration utilities."""
-
-from typing import Callable
-
-from torch.nn import Module
-
-CUSTOM_MODELS = {}  # dictionary of custom models {"name": __class__}
-
-
-def register_model(name: str) -> Callable:
-    """Decorator used to register a torch.nn.Module class with a given `name`.
-
-    Parameters
-    ----------
-    name : str
-        Name of the model.
-
-    Returns
-    -------
-    Callable
-        Function allowing to instantiate the wrapped Module class.
-
-    Raises
-    ------
-    ValueError
-        If a model is already registered with that name.
-
-    Examples
-    --------
-    ```python
-    @register_model(name="linear")
-    class LinearModel(nn.Module):
-        def __init__(self, in_features, out_features):
-            super().__init__()
-
-            self.weight = nn.Parameter(ones(in_features, out_features))
-            self.bias = nn.Parameter(ones(out_features))
-
-        def forward(self, input):
-            return (input @ self.weight) + self.bias
-    ```
-    """
-    if name is None or name == "":
-        raise ValueError("Model name cannot be empty.")
-
-    if name in CUSTOM_MODELS:
-        raise ValueError(
-            f"Model {name} already exists. Choose a different name or run "
-            f"`clear_custom_models()` to empty the registry."
-        )
-
-    def add_custom_model(model: Module) -> Module:
-        """Add a custom model to the registry and return it.
-
-        Parameters
-        ----------
-        model : Module
-            Module class to register.
-
-        Returns
-        -------
-        Module
-            The registered model.
-        """
-        # add model to the registry
-        CUSTOM_MODELS[name] = model
-
-        return model
-
-    return add_custom_model
-
-
-def get_custom_model(name: str) -> Module:
-    """Get the custom model corresponding to `name` from the registry.
-
-    Parameters
-    ----------
-    name : str
-        Name of the model to retrieve.
-
-    Returns
-    -------
-    Module
-        The requested model.
-
-    Raises
-    ------
-    ValueError
-        If the model is not registered.
-    """
-    if name not in CUSTOM_MODELS:
-        raise ValueError(
-            f"Model {name} is unknown. Have you registered it using "
-            f'@register_model("{name}") as decorator?'
-        )
-
-    return CUSTOM_MODELS[name]
-
-
-def clear_custom_models() -> None:
-    """Clear the custom models registry."""
-    # clear dictionary
-    CUSTOM_MODELS.clear()