careamics 0.0.9__py3-none-any.whl → 0.0.11__py3-none-any.whl

careamics/config/n2v_configuration.py

@@ -1,266 +0,0 @@
-"""N2V configuration."""
-
-from bioimageio.spec.generic.v0_3 import CiteEntry
-from pydantic import 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
-
-N2V = "Noise2Void"
-N2V2 = "N2V2"
-STRUCT_N2V = "StructN2V"
-STRUCT_N2V2 = "StructN2V2"
-
-N2V_REF = CiteEntry(
-    text='Krull, A., Buchholz, T.O. and Jug, F., 2019. "Noise2Void - Learning '
-    'denoising from single noisy images". In Proceedings of the IEEE/CVF '
-    "conference on computer vision and pattern recognition (pp. 2129-2137).",
-    doi="10.1109/cvpr.2019.00223",
-)
-
-N2V2_REF = CiteEntry(
-    text="Höck, E., Buchholz, T.O., Brachmann, A., Jug, F. and Freytag, A., "
-    '2022. "N2V2 - Fixing Noise2Void checkerboard artifacts with modified '
-    'sampling strategies and a tweaked network architecture". In European '
-    "Conference on Computer Vision (pp. 503-518).",
-    doi="10.1007/978-3-031-25069-9_33",
-)
-
-STRUCTN2V_REF = CiteEntry(
-    text="Broaddus, C., Krull, A., Weigert, M., Schmidt, U. and Myers, G., 2020."
-    '"Removing structured noise with self-supervised blind-spot '
-    'networks". In 2020 IEEE 17th International Symposium on Biomedical '
-    "Imaging (ISBI) (pp. 159-163).",
-    doi="10.1109/isbi45749.2020.9098336",
-)
-
-N2V_DESCRIPTION = (
-    "Noise2Void is a UNet-based self-supervised algorithm that "
-    "uses blind-spot training to denoise images. In short, in every "
-    "patches during training, random pixels are selected and their "
-    "value replaced by a neighboring pixel value. The network is then "
-    "trained to predict the original pixel value. The algorithm "
-    "relies on the continuity of the signal (neighboring pixels have "
-    "similar values) and the pixel-wise independence of the noise "
-    "(the noise in a pixel is not correlated with the noise in "
-    "neighboring pixels)."
-)
-
-N2V2_DESCRIPTION = (
-    "N2V2 is a variant of Noise2Void. "
-    + N2V_DESCRIPTION
-    + "\nN2V2 introduces blur-pool layers and removed skip "
-    "connections in the UNet architecture to remove checkboard "
-    "artefacts, a common artefacts ocurring in Noise2Void."
-)
-
-STR_N2V_DESCRIPTION = (
-    "StructN2V is a variant of Noise2Void. "
-    + N2V_DESCRIPTION
-    + "\nStructN2V uses a linear mask (horizontal or vertical) to replace "
-    "the pixel values of neighbors of the masked pixels by a random "
-    "value. Such masking allows removing 1D structured noise from the "
-    "the images, the main failure case of the original N2V."
-)
-
-STR_N2V2_DESCRIPTION = (
-    "StructN2V2 is a a variant of Noise2Void that uses both "
-    "structN2V and N2V2. "
-    + N2V_DESCRIPTION
-    + "\nStructN2V2 uses a linear mask (horizontal or vertical) to replace "
-    "the pixel values of neighbors of the masked pixels by a random "
-    "value. Such masking allows removing 1D structured noise from the "
-    "the images, the main failure case of the original N2V."
-    "\nN2V2 introduces blur-pool layers and removed skip connections in "
-    "the UNet architecture to remove checkboard artefacts, a common "
-    "artefacts ocurring in Noise2Void."
-)
-
-
-class N2VConfiguration(Configuration):
-    """N2V configuration."""
-
-    algorithm_config: N2VAlgorithm
-
-    data_config: N2VDataConfig
-
-    @model_validator(mode="after")
-    def validate_n2v2(self) -> Self:
-        """Validate that the N2V2 strategy and models are set correctly.
-
-        Returns
-        -------
-        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
-            ):
-                raise ValueError(
-                    f"N2V2 can only be used with the "
-                    f"{SupportedPixelManipulation.MEDIAN} pixel manipulation strategy"
-                    f". Change the N2VManipulate transform strategy."
-                )
-        else:
-            if (
-                self.data_config.get_masking_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."
-                )
-        return self
-
-    def set_n2v2(self, use_n2v2: bool) -> None:
-        """
-        Set the configuration to use N2V2 or the vanilla Noise2Void.
-
-        Parameters
-        ----------
-        use_n2v2 : bool
-            Whether to use N2V2.
-        """
-        self.data_config.set_n2v2(use_n2v2)
-        self.algorithm_config.model.n2v2 = use_n2v2
-
-    def get_algorithm_friendly_name(self) -> str:
-        """
-        Get the friendly name of the algorithm.
-
-        Returns
-        -------
-        str
-            Friendly name.
-        """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
-
-        if use_n2v2 and use_structN2V:
-            return STRUCT_N2V2
-        elif use_n2v2:
-            return N2V2
-        elif use_structN2V:
-            return STRUCT_N2V
-        else:
-            return N2V
-
-    def get_algorithm_keywords(self) -> list[str]:
-        """
-        Get algorithm keywords.
-
-        Returns
-        -------
-        list[str]
-            List of keywords.
-        """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
-
-        keywords = [
-            "denoising",
-            "restoration",
-            "UNet",
-            "3D" if "Z" in self.data_config.axes else "2D",
-            "CAREamics",
-            "pytorch",
-            N2V,
-        ]
-
-        if use_n2v2:
-            keywords.append(N2V2)
-        if use_structN2V:
-            keywords.append(STRUCT_N2V)
-
-        return keywords
-
-    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.
-        """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
-
-        references = [
-            N2V_REF.text + " doi: " + N2V_REF.doi,
-            N2V2_REF.text + " doi: " + N2V2_REF.doi,
-            STRUCTN2V_REF.text + " doi: " + STRUCTN2V_REF.doi,
-        ]
-
-        # return the (struct)N2V(2) references
-        if use_n2v2 and use_structN2V:
-            return "\n".join(references)
-        elif use_n2v2:
-            references.pop(-1)
-            return "\n".join(references)
-        elif use_structN2V:
-            references.pop(-2)
-            return "\n".join(references)
-        else:
-            return references[0]
-
-    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.
-        """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
-
-        references = [N2V_REF]
-
-        if use_n2v2:
-            references.append(N2V2_REF)
-
-        if use_structN2V:
-            references.append(STRUCTN2V_REF)
-
-        return references
-
-    def get_algorithm_description(self) -> str:
-        """
-        Return a description of the algorithm.
-
-        This method is used to generate the README of the BioImage Model Zoo export.
-
-        Returns
-        -------
-        str
-            Description of the algorithm.
-        """
-        use_n2v2 = self.algorithm_config.model.n2v2
-        use_structN2V = self.data_config.is_using_struct_n2v()
-
-        if use_n2v2 and use_structN2V:
-            return STR_N2V2_DESCRIPTION
-        elif use_n2v2:
-            return N2V2_DESCRIPTION
-        elif use_structN2V:
-            return STR_N2V_DESCRIPTION
-        else:
-            return N2V_DESCRIPTION